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Sample records for anharmonic force field

  1. Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Robert W. [Department of Biomedical Informatics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20815 (United States)], E-mail: bob@bob.usuhs.mil; Schluecker, Sebastian [Institute of Physical Chemistry, University of Wuerzburg, Wuerzburg (Germany); Hudson, Bruce S. [Department of Chemistry, Syracuse University, Syracuse, NY (United States)

    2008-01-22

    A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.

  2. Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

    International Nuclear Information System (INIS)

    Williams, Robert W.; Schluecker, Sebastian; Hudson, Bruce S.

    2008-01-01

    A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes

  3. Anharmonic 1D actuator model including electrostatic and Casimir forces with fractional damping perturbed by an external force

    Science.gov (United States)

    Mansoori Kermani, Maryam; Dehestani, Maryam

    2018-06-01

    We modeled a one-dimensional actuator including the Casimir and electrostatic forces perturbed by an external force with fractional damping. The movable electrode was assumed to oscillate by an anharmonic elastic force originated from Murrell-Mottram or Lippincott potential. The nonlinear equations have been solved via the Adomian decomposition method. The behavior of the displacement of the electrode from equilibrium position, its velocity and acceleration were described versus time. Also, the changes of the displacement have been investigated according to the frequency of the external force and the voltage of the electrostatic force. The convergence of the Adomian method and the effect of the orders of expansion on the displacement versus time, frequency, and voltage were discussed. The pull-in parameter was obtained and compared with the other models in the literature. This parameter was described versus the equilibrium position and anharmonicity constant.

  4. Anharmonic 1D actuator model including electrostatic and Casimir forces with fractional damping perturbed by an external force

    Science.gov (United States)

    Mansoori Kermani, Maryam; Dehestani, Maryam

    2018-03-01

    We modeled a one-dimensional actuator including the Casimir and electrostatic forces perturbed by an external force with fractional damping. The movable electrode was assumed to oscillate by an anharmonic elastic force originated from Murrell-Mottram or Lippincott potential. The nonlinear equations have been solved via the Adomian decomposition method. The behavior of the displacement of the electrode from equilibrium position, its velocity and acceleration were described versus time. Also, the changes of the displacement have been investigated according to the frequency of the external force and the voltage of the electrostatic force. The convergence of the Adomian method and the effect of the orders of expansion on the displacement versus time, frequency, and voltage were discussed. The pull-in parameter was obtained and compared with the other models in the literature. This parameter was described versus the equilibrium position and anharmonicity constant.

  5. Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

    Science.gov (United States)

    Pietropolli Charmet, Andrea; Cornaton, Yann

    2018-05-01

    This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

  6. Dirac bound states of anharmonic oscillator in external fields

    International Nuclear Information System (INIS)

    Hamzavi, Majid; Ikhdair, Sameer M.; Falaye, Babatunde J.

    2014-01-01

    We explore the effect of the external magnetic and Aharonov–Bohm (AB) flux fields on the energy levels of Dirac particle subjects to mixed scalar and vector anharmonic oscillator field in the two-dimensional (2D) space. We calculate the exact energy eigenvalues and the corresponding un-normalized two-spinor-components wave functions in terms of the chemical potential parameter, magnetic field strength, AB flux field and magnetic quantum number by using the Nikiforov–Uvarov (NU) method. -- Highlights: • Effect of the external fields on the energy levels of Dirac particle with the anharmonic oscillator is investigated. • The solutions are discussed in view of spin and pseudospin symmetries limits. • The energy levels and wave function are presented by the Nikiforov–Uvarov method

  7. Effects of hypersonic field and anharmonic interactions on channelling radiation

    International Nuclear Information System (INIS)

    George, Juby; Pathak, Anand P; Goteti, L N S Prakash; Nagamani, G

    2007-01-01

    The effects of a hypersonic field on positron channelling radiation are considered. Anharmonic effects of the transverse potential induced by these longitudinal fields are incorporated and the wavefunction of the planar channelled positron is found by the solution of Dirac equation under the resonant influence of hypersound. An expression for the resonant frequency is estimated. The transition probabilities and the intensity of the channelling radiation are also calculated. It is found that the anharmonic effects change the spectral distributions considerably

  8. Frequency and zero-point vibrational energy scale factors for double-hybrid density functionals (and other selected methods): can anharmonic force fields be avoided?

    Science.gov (United States)

    Kesharwani, Manoj K; Brauer, Brina; Martin, Jan M L

    2015-03-05

    We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.

  9. Dynamic of cold-atom tips in anharmonic potentials

    Science.gov (United States)

    Menold, Tobias; Federsel, Peter; Rogulj, Carola; Hölscher, Hendrik; Fortágh, József

    2016-01-01

    Background: Understanding the dynamics of ultracold quantum gases in an anharmonic potential is essential for applications in the new field of cold-atom scanning probe microscopy. Therein, cold atomic ensembles are used as sensitive probe tips to investigate nanostructured surfaces and surface-near potentials, which typically cause anharmonic tip motion. Results: Besides a theoretical description of this anharmonic tip motion, we introduce a novel method for detecting the cold-atom tip dynamics in situ and real time. In agreement with theory, the first measurements show that particle interactions and anharmonic motion have a significant impact on the tip dynamics. Conclusion: Our findings will be crucial for the realization of high-sensitivity force spectroscopy with cold-atom tips and could possibly allow for the development of advanced spectroscopic techniques such as Q-control. PMID:28144505

  10. Ab initio calculations of anharmonic vibrational circular dichroism intensities of trans-2,3-dideuteriooxirane

    DEFF Research Database (Denmark)

    Bak, KL; Bludsky, O.; Jorgensen, P

    1995-01-01

    A priori theory is derived for anharmonic calculations of vibrational circular dichroism (VCD). The anharmonic VCD expression is gauge origin independent and reduce to the magnetic field perturbation theory expression in the double-harmonic approximation. The theory has been implemented using...... for the atomic axial tensors and using second-order Moller-Plesset theory for the atomic polar tensors and the force fields, The changes of the vibrational rotatory strengths from anharmonicities are small, and do not explain the previously observed large discrepancies between the double-harmonic results...

  11. First-principles study of anharmonic phonon effects in tetrahedral semiconductors via an external electric field

    Energy Technology Data Exchange (ETDEWEB)

    Dabiri, Zohreh, E-mail: z.dabiri@stu.yazd.ac.ir [Physics Department, Yazd University, P.O. Box 89195-741, Yazd (Iran, Islamic Republic of); Kazempour, Ali [Department of Physics, Payame Noor University, P.O. BOX 119395-3697, Tehran (Iran, Islamic Republic of); Nano Structured Coatings Institute of Yazd Payame Noor University, P.O. Code 89431-74559, Yazd (Iran, Islamic Republic of); Sadeghzadeh, Mohammad Ali [Physics Department, Yazd University, P.O. Box 89195-741, Yazd (Iran, Islamic Republic of)

    2016-11-15

    The strength of phonon anharmonicity is investigated in the framework of the Density Functional Perturbation Theory via an applied constant electric field. In contrast to routine approaches, we have employed the electric field as an effective probe to quest after the quasi-harmonic and anharmonic effects. Two typical tetrahedral semiconductors (diamond and silicon) have been selected to test the efficiency of this approach. In this scheme the applied field is responsible for establishing the perturbation and also inducing the anharmonicity in systems. The induced polarization is a result of changing the electronic density while ions are located at their ground state coordinates or at a specified strain. Employing this method, physical quantities of the semiconductors are calculated in presence of the electron–phonon interaction directly and, phonon–phonon interaction, indirectly. The present approach, which is in good agreement with previous theoretical and experimental studies, can be introduced as a benchmark to simply investigate the anharmonicity and pertinent consequences in materials.

  12. Kinks in systems with cubic and quartic anharmonicity

    International Nuclear Information System (INIS)

    Kashcheev, V.N.

    1988-01-01

    For a classical system of interacting particles with on-site cubic or quartic anharmonicity explicit analytic solutions of the d'Alembert equation are obtained in the form of kinks in the presence of dissipation (viscous or Rayleigh) and a constant force. These kinks will be asymptotically stable in the case of quartic anharmonicity and unstable in the case cubic anharmonicity

  13. Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions.

    Science.gov (United States)

    Danecek, Petr; Kapitán, Josef; Baumruk, Vladimír; Bednárová, Lucie; Kopecký, Vladimír; Bour, Petr

    2007-06-14

    The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800 cm(-1)) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third

  14. Hydrogen atom in a uniform electromagnetic field as an anharmonic oscillator

    International Nuclear Information System (INIS)

    Kibler, M.; Negadi, T.

    1984-01-01

    This work establishes, by means of the Kustaanheimo-Stiefel transformation, a connection between two branches of theoretical physics which are, in present times, the object of numerous studies: the quantum mechanics of anharmonic oscillators and of the hydrogen atom in a (strong) homogeneous and constant electromagnetic field

  15. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    International Nuclear Information System (INIS)

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations [i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface] is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules

  16. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

  17. First-Principles Lattice Dynamics Method for Strongly Anharmonic Crystals

    Science.gov (United States)

    Tadano, Terumasa; Tsuneyuki, Shinji

    2018-04-01

    We review our recent development of a first-principles lattice dynamics method that can treat anharmonic effects nonperturbatively. The method is based on the self-consistent phonon theory, and temperature-dependent phonon frequencies can be calculated efficiently by incorporating recent numerical techniques to estimate anharmonic force constants. The validity of our approach is demonstrated through applications to cubic strontium titanate, where overall good agreement with experimental data is obtained for phonon frequencies and lattice thermal conductivity. We also show the feasibility of highly accurate calculations based on a hybrid exchange-correlation functional within the present framework. Our method provides a new way of studying lattice dynamics in severely anharmonic materials where the standard harmonic approximation and the perturbative approach break down.

  18. Nonadiabatic anharmonic electron transfer

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, P. P. [Molecular Physics Research, 6547 Kristina Ursula Court, Falls Church, Virginia 22044 (United States)

    2013-03-28

    The effect of an inner sphere, local mode vibration on an electron transfer is modeled using the nonadiabatic transition probability (rate) expression together with both the anharmonic Morse and the harmonic oscillator potential. For an anharmonic inner sphere mode, a variational analysis uses harmonic oscillator basis functions to overcome the difficulties evaluating Morse-model Franck-Condon overlap factors. Individual matrix elements are computed with the use of new, fast, robust, and flexible recurrence relations. The analysis therefore readily addresses changes in frequency and/or displacement of oscillator minimums in the different electron transfer states. Direct summation of the individual Boltzmann weighted Franck-Condon contributions avoids the limitations inherent in the use of the familiar high-temperature, Gaussian form of the rate constant. The effect of harmonic versus anharmonic inner sphere modes on the electron transfer is readily seen, especially in the exoergic, inverted region. The behavior of the transition probability can also be displayed as a surface for all temperatures and values of the driving force/exoergicity {Delta}=-{Delta}G. The temperature insensitivity of the transfer rate is clearly seen when the exoergicity equals the collective reorganization energy ({Delta}={Lambda}{sub s}) along a maximum ln (w) vs. {Delta} ridge of the surface. The surface also reveals additional regions for {Delta} where ln (w) appears to be insensitive to temperature, or effectively activationless, for some kinds of inner sphere contributions.

  19. Squeezing and other non-classical features in k-photon anharmonic oscillator in binomial and negative binomial states of the field

    International Nuclear Information System (INIS)

    Joshi, A.; Lawande, S.V.

    1990-01-01

    A systematic study of squeezing obtained from k-photon anharmonic oscillator (with interaction hamiltonian of the form (a † ) k , k ≥ 2) interacting with light whose statistics can be varied from sub-Poissonian to poissonian via binomial state of field and super-Poissonian to poissonian via negative binomial state of field is presented. The authors predict that for all values of k there is a tendency increase in squeezing with increased sub-Poissonian character of the field while the reverse is true with super-Poissonian field. They also present non-classical behavior of the first order coherence function explicitly for k = 2 case (i.e., for two-photon anharmonic oscillator model used for a Kerr-like medium) with variation in the statistics of the input light

  20. Terahertz generation via laser coupling to anharmonic carbon nanotube array

    Science.gov (United States)

    Sharma, Soni; Vijay, A.

    2018-02-01

    A scheme of terahertz radiation generation employing a matrix of anharmonic carbon nanotubes (CNTs) embedded in silica is proposed. The matrix is irradiated by two collinear laser beams that induce large excursions on CNT electrons and exert a nonlinear force at the beat frequency ω = ω1-ω2. The force derives a nonlinear current producing THz radiation. The THz field is resonantly enhanced at the plasmon resource, ω = ω p ( 1 + β ) / √{ 2 } , where ωp is the plasma frequency and β is a characteristic parameter. Collisions are a limiting factor, suppressing the plasmon resonance. For typical values of plasma parameters, we obtain power conversion efficiency of the order of 10-6.

  1. Anharmonic vibrational spectroscopic investigation of malonaldehyde

    International Nuclear Information System (INIS)

    Alparone, A.; Millefiori, S.

    2003-01-01

    Anharmonic IR spectra of H-bonded and non-H-bonded conformers of malonaldehyde (MA) and its isotopomers MA-D 6 D 8 and MA-D 7 D 9 have been computed by the Vibrational-Self-Consistent-Field (VSCF) and the correlation-corrected-VSCF (CC-VSCF) techniques using ab initio MP2/6-31G*(+p) potential energies. The agreement between the experimental and calculated frequencies is significantly improved to within 2-3%. Anharmonic contributions are substantial especially for νOH of the H-bonded form, by reducing the harmonic value by more than 500 cm -1 . The effect is less important in the non-H-bonded form. The νOH stretching mode is strongly coupled with the ν 3 mode (essentially νCH 7 ) and with the in-plane and out-of-plane OH bending deformations. H-bond formation and deuteration batochromically shift νOH by an amount which is influenced by the anharmonic terms, the major contribution arising from coupling between modes. The comparison with the νOH mode of some other H-bonded systems suggests that anharmonic correction follows H-bonding strength

  2. Anharmonic oscillator and Bogoliubov transformation

    International Nuclear Information System (INIS)

    Pattnayak, G.C.; Torasia, S.; Rath, B.

    1990-01-01

    The anharmonic oscillator occupies a cornerstone in many problems in physics. It was observed that none of the authors have tested Bogoliubov transformation to study anharmonic oscillator. The groundstate energy of the anharmonic oscillator is studied using Bogoliubov transformation and the results presented. (author)

  3. Carrier relaxation in (In,Ga)As quantum dots with magnetic field-induced anharmonic level structure

    Energy Technology Data Exchange (ETDEWEB)

    Kurtze, H.; Bayer, M. [Experimentelle Physik 2, TU Dortmund, D-44221 Dortmund (Germany)

    2016-07-04

    Sophisticated models have been worked out to explain the fast relaxation of carriers into quantum dot ground states after non-resonant excitation, overcoming the originally proposed phonon bottleneck. We apply a magnetic field along the quantum dot heterostructure growth direction to transform the confined level structure, which can be approximated by a Fock–Darwin spectrum, from a nearly equidistant level spacing at zero field to strong anharmonicity in finite fields. This changeover leaves the ground state carrier population rise time unchanged suggesting that fast relaxation is maintained upon considerable changes of the level spacing. This corroborates recent models explaining the relaxation by polaron formation in combination with quantum kinetic effects.

  4. Influence of anharmonic effects on the structural-mechanical and thermophysical properties of filled polymer systems

    International Nuclear Information System (INIS)

    Bordyuk, N.A.; Nikitchuk, V.I.; Voloshin, O.M.

    1995-01-01

    The force constants of anharmonicity, the total energy, and the force of interaction between structural elements of PVC systems are determined from the values of the quasielastic constants of filled polymer systems

  5. Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations.

    Science.gov (United States)

    Ruggiero, Michael T; Zeitler, J Axel

    2016-11-17

    Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

  6. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Orientational anharmonicity of interatomic interaction in cubic monocrystals

    International Nuclear Information System (INIS)

    Belomestnykh, Vladimir N.; Tesleva, Elena P.

    2010-01-01

    Anharmonicity of interatomic interaction from a position of physical acoustics under the standard conditions is investigated. It is shown that the measure of anharmonicity of interatomic interaction (Grilneisen parameter) is explicitly expressed through velocities of sound. Calculation results of orientation anharmonicity are shown on the example of 116 cubic monocrystals with different lattice structural type and type of chemical bond. Two types of anharmonicity interatomic interaction anisotropy are determined. Keywords: acoustics, orientational anharmonicity, Gruneisen parameter, velocity of sound

  8. The construction of partner potential from the general potential anharmonic in D-dimensional Schrodinger system

    Science.gov (United States)

    Suparmi; Cari, C.; Wea, K. N.; Wahyulianti

    2018-03-01

    The Schrodinger equation is the fundamental equation in quantum physics. The characteristic of the particle in physics potential field can be explained by using the Schrodinger equation. In this study, the solution of 4 dimensional Schrodinger equation for the anharmonic potential and the anharmonic partner potential have done. The method that used to solve the Schrodinger equation was the ansatz wave method, while to construction the partner potential was the supersymmetric method. The construction of partner potential used to explain the experiment result that cannot be explained by the original potential. The eigenvalue for anharmonic potential and the anharmonic partner potential have the same characteristic. Every increase of quantum orbital number the eigenvalue getting smaller. This result corresponds to Bohrn’s atomic theory that the eigenvalue is inversely proportional to the atomic shell. But the eigenvalue for the anharmonic partner potential higher than the eigenvalue for the anharmonic original potential.

  9. Bizarre behavior of heat capacity in crystals due to interplay between two types of anharmonicities.

    Science.gov (United States)

    Yurchenko, Stanislav O; Komarov, Kirill A; Kryuchkov, Nikita P; Zaytsev, Kirill I; Brazhkin, Vadim V

    2018-04-07

    The heat capacity of classical crystals is determined by the Dulong-Petit value C V ≃ D (where D is the spatial dimension) for softly interacting particles and has the gas-like value C V ≃ D/2 in the hard-sphere limit, while deviations are governed by the effects of anharmonicity. Soft- and hard-sphere interactions, which are associated with the enthalpy and entropy of crystals, are specifically anharmonic owing to violation of a linear relation between particle displacements and corresponding restoring forces. Here, we show that the interplay between these two types of anharmonicities unexpectedly induces two possible types of heat capacity anomalies. We studied thermodynamics, pair correlations, and collective excitations in 2D and 3D crystals of particles with a limited range of soft repulsions to prove the effect of interplay between the enthalpy and entropy types of anharmonicities. The observed anomalies are triggered by the density of the crystal, changing the interaction regime in the zero-temperature limit, and can provide about 10% excess of the heat capacity above the Dulong-Petit value. Our results facilitate understanding effects of complex anharmonicity in molecular and complex crystals and demonstrate the possibility of new effects due to the interplay between different types of anharmonicities.

  10. Stochastic many-body perturbation theory for anharmonic molecular vibrations

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, Matthew R. [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); Hirata, So, E-mail: sohirata@illinois.edu [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)

    2014-08-28

    A new quantum Monte Carlo (QMC) method for anharmonic vibrational zero-point energies and transition frequencies is developed, which combines the diagrammatic vibrational many-body perturbation theory based on the Dyson equation with Monte Carlo integration. The infinite sums of the diagrammatic and thus size-consistent first- and second-order anharmonic corrections to the energy and self-energy are expressed as sums of a few m- or 2m-dimensional integrals of wave functions and a potential energy surface (PES) (m is the vibrational degrees of freedom). Each of these integrals is computed as the integrand (including the value of the PES) divided by the value of a judiciously chosen weight function evaluated on demand at geometries distributed randomly but according to the weight function via the Metropolis algorithm. In this way, the method completely avoids cumbersome evaluation and storage of high-order force constants necessary in the original formulation of the vibrational perturbation theory; it furthermore allows even higher-order force constants essentially up to an infinite order to be taken into account in a scalable, memory-efficient algorithm. The diagrammatic contributions to the frequency-dependent self-energies that are stochastically evaluated at discrete frequencies can be reliably interpolated, allowing the self-consistent solutions to the Dyson equation to be obtained. This method, therefore, can compute directly and stochastically the transition frequencies of fundamentals and overtones as well as their relative intensities as pole strengths, without fixed-node errors that plague some QMC. It is shown that, for an identical PES, the new method reproduces the correct deterministic values of the energies and frequencies within a few cm{sup −1} and pole strengths within a few thousandths. With the values of a PES evaluated on the fly at random geometries, the new method captures a noticeably greater proportion of anharmonic effects.

  11. Anharmonicity in nuclear wobbling motion

    International Nuclear Information System (INIS)

    Oi, M.

    2007-01-01

    An unexpected strong anharmonicity was observed in the wobbling spectrum in 163 Lu. In an attempt to understand what causes the deviation from the original wobbling model by Bohr and Mottelson, an analysis is presented using several different approaches, such as exact diagonalization, a semiclassical model to deal with anharmonic wobbling motion, and a microscopic method based on the self-consistent cranking calculation

  12. Nonlinear (Anharmonic Casimir Oscillator

    Directory of Open Access Journals (Sweden)

    Habibollah Razmi

    2011-01-01

    Full Text Available We want to study the dynamics of a simple linear harmonic micro spring which is under the influence of the quantum Casimir force/pressure and thus behaves as a (an nonlinear (anharmonic Casimir oscillator. Generally, the equation of motion of this nonlinear micromechanical Casimir oscillator has no exact solvable (analytical solution and the turning point(s of the system has (have no fixed position(s; however, for particular values of the stiffness of the micro spring and at appropriately well-chosen distance scales and conditions, there is (are approximately sinusoidal solution(s for the problem (the variable turning points are collected in a very small interval of positions. This, as a simple and elementary plan, may be useful in controlling the Casimir stiction problem in micromechanical devices.

  13. Microscopic approach to nuclear anharmonicities

    International Nuclear Information System (INIS)

    Matsuo, Masayuki; Shimizu, Yoshifumi; Matsuyanagi, Kenichi

    1985-01-01

    Present status of microscopic study of nuclear anharmonicity phenomena is reviewed from the viewpoint of the time-dependent Hartree-Bogoliubov approach. Both classical- and quantum-mechanical aspects of this approach are discussed. The Bohr-Mottelson-type collective Hamiltonian for anharmonic gamma vibrations is microscopically derived by means of the self-consistent-collective-coordinate method, and applied to the problem of two-phonon states of 168 Er. (orig.)

  14. Anharmonicities of coupled β and γ vibrations discussed in a simple model

    International Nuclear Information System (INIS)

    Piepenbring, R.; Silvestre-Brac, B.; Szymanski, Z.

    1984-01-01

    The multiphonon method based on β and γ phonons is tested in a simple model allowing an exact solution for a many body fermion system where pairing and quadrupole forces are acting. The properties exhibiting the anharmonicities of the lowest-lying vibrational states of positive parity are nicely reproduced by this method. (orig.)

  15. Anharmonicities of coupled β and γ vibrations discussed in a simple model

    International Nuclear Information System (INIS)

    Piepenbring, R.; Silvestre-Brac, B.; Szymanski, Z.

    1983-11-01

    The multiphonon method based on β and γ phonons is tested in a simple model allowing an exact solution for a many body fermion system where pairing and quadrupole forces are acting. The properties exhibiting the anharmonicities of the lowest-lying vibrational states of positive parity are nicely reproduced by this method

  16. Detecting anharmonicity at a glance

    International Nuclear Information System (INIS)

    Giliberti, M; Stellato, M; Barbieri, S; Cavinato, M; Rigon, E; Tamborini, M

    2014-01-01

    Harmonic motion is generally presented in such a way that most of the students believe that the small oscillations of a body are all harmonic. Since the situation is not actually so simple, and since the comprehension of harmonic motion is essential in many physical contexts, we present here some suggestions, addressed to undergraduate students and pre-service teachers, that allow one to find out at a glance the anharmonicity of a motion. Starting from a didactically motivated definition of harmonic motion, and stressing the importance of the interplay between mathematics and experiments, we give a four-point criterion for anharmonicity together with some emblematic examples. The role of linear damping is also analysed in relation to the gradual changing of harmonicity into anharmonicity when the ratio between the damping coefficient and the zero-friction angular frequency increases. (paper)

  17. Heat transport in an anharmonic crystal

    Science.gov (United States)

    Acharya, Shiladitya; Mukherjee, Krishnendu

    2018-04-01

    We study transport of heat in an ordered, anharmonic crystal in the form of slab geometry in three dimensions. Apart from attaching baths of Langevin type to two extreme surfaces, we also attach baths of same type to the intermediate surfaces of the slab. Since the crystal is uninsulated, it exchanges energy with the intermediate heat baths. We find that both Fourier’s law of heat conduction and the Newton’s law of cooling hold to leading order in anharmonic coupling. The leading behavior of the temperature profile is exponentially falling from high to low temperature surface of the slab. As the anharmonicity increases, profiles fall more below the harmonic one in the log plot. In the thermodynamic limit thermal conductivity remains independent of the environment temperature and its leading order anharmonic contribution is linearly proportional to the temperature change between the two extreme surfaces of the slab. A fast crossover from one-dimensional (1D) to three-dimensional (3D) behavior of the thermal conductivity is observed in the system.

  18. Tunneling Kinetics and Nonadiabatic Proton-Coupled Electron Transfer in Proteins: The Effect of Electric Fields and Anharmonic Donor-Acceptor Interactions.

    Science.gov (United States)

    Salna, Bridget; Benabbas, Abdelkrim; Russo, Douglas; Champion, Paul M

    2017-07-20

    A proper description of proton donor-acceptor (D-A) distance fluctuations is crucial for understanding tunneling in proton-coupled electron transport (PCET). The typical harmonic approximation for the D-A potential results in a Gaussian probability distribution, which does not appropriately reflect the electronic repulsion forces that increase the energetic cost of sampling shorter D-A distances. Because these shorter distances are the primary channel for thermally activated tunneling, the analysis of tunneling kinetics depends sensitively on the inherently anharmonic nature of the D-A interaction. Thus, we have used quantum chemical calculations to account for the D-A interaction and developed an improved model for the analysis of experimental tunneling kinetics. Strong internal electric fields are also considered and found to contribute significantly to the compressive forces when the D-A distance distribution is positioned below the van der Waals contact distance. This model is applied to recent experiments on the wild type (WT) and a double mutant (DM) of soybean lipoxygenase-1 (SLO). The compressive force necessary to prepare the tunneling-active distribution in WT SLO is found to fall in the ∼ nN range, which greatly exceeds the measured values of molecular motor and protein unfolding forces. This indicates that ∼60-100 MV/cm electric fields, aligned along the D-A bond axis, must be generated by an enzyme conformational interconversion that facilitates the PCET tunneling reaction. Based on the absolute value of the measured tunneling rate, and using previously calculated values of the electronic matrix element, the population of this tunneling-active conformation is found to lie in the range 10 -5 -10 -7 , indicating this is a rare structural fluctuation that falls well below the detection threshold of recent ENDOR experiments. Additional analysis of the DM tunneling kinetics leads to a proposal that a disordered (high entropy) conformation could be

  19. Perturbative treatment of anharmonic vibrational effects on bond distances: an extended Langevin dynamics method.

    Science.gov (United States)

    Shen, Tonghao; Su, Neil Qiang; Wu, Anan; Xu, Xin

    2014-03-05

    In this work, we first review the perturbative treatment of an oscillator with cubic anharmonicity. It is shown that there is a quantum-classical correspondence in terms of mean displacement, mean-squared displacement, and the corresponding variance in the first-order perturbation theory, provided that the amplitude of the classical oscillator is fixed at the zeroth-order energy of quantum mechanics EQM (0). This correspondence condition is realized by proposing the extended Langevin dynamics (XLD), where the key is to construct a proper driving force. It is assumed that the driving force adopts a simple harmonic form with its amplitude chosen according to EQM (0), while the driving frequency chosen as the harmonic frequency. The latter can be improved by using the natural frequency of the system in response to the potential if its anharmonicity is strong. By comparing to the accurate numeric results from discrete variable representation calculations for a set of diatomic species, it is shown that the present method is able to capture the large part of anharmonicity, being competitive with the wave function-based vibrational second-order perturbation theory, for the whole frequency range from ∼4400 cm(-1) (H2 ) to ∼160 cm(-1) (Na2 ). XLD shows a substantial improvement over the classical molecular dynamics which ceases to work for hard mode when zero-point energy effects are significant. Copyright © 2013 Wiley Periodicals, Inc.

  20. Low-temperature anharmonicity in cesium chloride (CsCl)

    Energy Technology Data Exchange (ETDEWEB)

    Sist, Mattia; Faerch Fischer, Karl Frederik; Brummerstedt Iversen, Bo [Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University (Denmark); Kasai, Hidetaka [Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University (Denmark); Faculty of Pure and Applied Sciences, TIMS and CiRfSE, University of Tsukuba (Japan)

    2017-03-20

    Anharmonic lattice vibrations govern heat transfer in materials, and anharmonicity is commonly assumed to be dominant at high temperature. The textbook cubic ionic defect-free crystal CsCl is shown to have an unexplained low thermal conductivity at room temperature (ca. 1 W/(m K)), which increases to around 13 W/(m K) at 25 K. Through high-resolution X-ray diffraction it is unexpectedly shown that the Cs atomic displacement parameter becomes anharmonic at 20 K. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. Finite-element time evolution operator for the anharmonic oscillator

    Science.gov (United States)

    Milton, Kimball A.

    1995-01-01

    The finite-element approach to lattice field theory is both highly accurate (relative errors approximately 1/N(exp 2), where N is the number of lattice points) and exactly unitary (in the sense that canonical commutation relations are exactly preserved at the lattice sites). In this talk I construct matrix elements for dynamical variables and for the time evolution operator for the anharmonic oscillator, for which the continuum Hamiltonian is H = p(exp 2)/2 + lambda q(exp 4)/4. Construction of such matrix elements does not require solving the implicit equations of motion. Low order approximations turn out to be extremely accurate. For example, the matrix element of the time evolution operator in the harmonic oscillator ground state gives a results for the anharmonic oscillator ground state energy accurate to better than 1 percent, while a two-state approximation reduces the error to less than 0.1 percent.

  2. A New Quasi-Exactly Solvable Problem and Its Connection with an Anharmonic Oscillator

    International Nuclear Information System (INIS)

    Yang Dabao; Zhang Fulin; Chen Jingling

    2010-01-01

    The two-dimensional hydrogen with a linear potential in a magnetic field is solved by two different methods. Furthermore the connection between the model and an anharmonic oscillator is investigated by methods of KS transformation. (general)

  3. Confinement-induced resonances in anharmonic waveguides

    Energy Technology Data Exchange (ETDEWEB)

    Peng Shiguo [Department of Physics, Tsinghua University, Beijing 100084 (China); Centre for Atom Optics and Ultrafast Spectroscopy, Swinburne University of Technology, Melbourne 3122 (Australia); Hu Hui; Liu Xiaji; Drummond, Peter D. [Centre for Atom Optics and Ultrafast Spectroscopy, Swinburne University of Technology, Melbourne 3122 (Australia)

    2011-10-15

    We develop the theory of anharmonic confinement-induced resonances (ACIRs). These are caused by anharmonic excitation of the transverse motion of the center of mass (c.m.) of two bound atoms in a waveguide. As the transverse confinement becomes anisotropic, we find that the c.m. resonant solutions split for a quasi-one-dimensional (1D) system, in agreement with recent experiments. This is not found in harmonic confinement theories. A new resonance appears for repulsive couplings (a{sub 3D}>0) for a quasi-two-dimensional (2D) system, which is also not seen with harmonic confinement. After inclusion of anharmonic energy corrections within perturbation theory, we find that these ACIRs agree extremely well with anomalous 1D and 2D confinement-induced resonance positions observed in recent experiments. Multiple even- and odd-order transverse ACIRs are identified in experimental data, including up to N=4 transverse c.m. quantum numbers.

  4. The effects of static quartic anharmonicity on the quantum dynamics of a linear oscillator with time-dependent harmonic frequency: Perturbative analysis and numerical calculations

    International Nuclear Information System (INIS)

    Sarkar, P.; Bhattacharyya, S.P.

    1995-01-01

    The effects of quartic anharmonicity on the quantum dynamics of a linear oscillator with time-dependent force constant (K) or harmonic frequency (ω) are studied both perturbatively and numerically by the time-dependent Fourier grid Hamiltonian method. In the absence of anharmonicity, the ground-state population decreases and the population of an accessible excited state (k = 2.4, 6 ... ) increases with time. However, when anharmonicity is introduced, both the ground- and excited-state populations show typical oscillations. For weak coupling, the population of an accessible excited state at a certain instant of time (short) turns out to be a parabolic function of the anharmonic coupling constant (λ), when all other parameters of the system are kept fixed. This parabolic nature of the excited-state population vs. the λ profile is independent of the specific form of the time dependence of the force constant, K t . However, it depends upon the rate at which K t relaxes. For small anharmonic coupling strength and short time scales, the numerical results corroborate expectations based on the first-order time-dependent perturbative analysis, using a suitably repartitioned Hamiltonian that makes H 0 time-independent. Some of the possible experimental implications of our observations are analyzed, especially in relation to intensity oscillations observed in some charge-transfer spectra in systems in which the dephasing rates are comparable with the time scale of the electron transfer. 21 refs., 7 figs., 1 tab

  5. Nuclear catalysis mediated by localized anharmonic vibrations

    OpenAIRE

    Dubinko, Vladimir

    2015-01-01

    In many-body nonlinear systems with sufficient anharmonicity, a special kind of lattice vibrations, namely, Localized Anharmonic Vibrations (LAVs) can be excited either thermally or by external triggering, in which the amplitude of atomic oscillations greatly exceeds that of harmonic oscillations (phonons) that determine the system temperature. Coherency and persistence of LAVs may have drastic effect on quantum tunneling due to correlation effects discovered by Schrodinger and Robertson in 1...

  6. Geometric Energy Derivatives at the Complete Basis Set Limit: Application to the Equilibrium Structure and Molecular Force Field of Formaldehyde.

    Science.gov (United States)

    Morgan, W James; Matthews, Devin A; Ringholm, Magnus; Agarwal, Jay; Gong, Justin Z; Ruud, Kenneth; Allen, Wesley D; Stanton, John F; Schaefer, Henry F

    2018-03-13

    Geometric energy derivatives which rely on core-corrected focal-point energies extrapolated to the complete basis set (CBS) limit of coupled cluster theory with iterative and noniterative quadruple excitations, CCSDTQ and CCSDT(Q), are used as elements of molecular gradients and, in the case of CCSDT(Q), expansion coefficients of an anharmonic force field. These gradients are used to determine the CCSDTQ/CBS and CCSDT(Q)/CBS equilibrium structure of the S 0 ground state of H 2 CO where excellent agreement is observed with previous work and experimentally derived results. A fourth-order expansion about this CCSDT(Q)/CBS reference geometry using the same level of theory produces an exceptional level of agreement to spectroscopically observed vibrational band origins with a MAE of 0.57 cm -1 . Second-order vibrational perturbation theory (VPT2) and variational discrete variable representation (DVR) results are contrasted and discussed. Vibration-rotation, anharmonicity, and centrifugal distortion constants from the VPT2 analysis are reported and compared to previous work. Additionally, an initial application of a sum-over-states fourth-order vibrational perturbation theory (VPT4) formalism is employed herein, utilizing quintic and sextic derivatives obtained with a recursive algorithmic approach for response theory.

  7. A study of anharmonic al and nonlinear behaviours of vibrations of atomic nuclei

    International Nuclear Information System (INIS)

    Volpe, M.C.

    1997-01-01

    Double Giant Resonances, vibrational states in which a Giant Resonance is excited on top of another Giant Resonance, have been in the last years the object of many theories and studies. Whereas the measured energies and widths of these states agree with a theoretical predictions, the measured excitation cross sections on the other hand are almost always larger than the calculated ones. The standard theoretical approaches are based both on a harmonic approximation for the collective motion on the nucleus and on its linear response to an external field. In this work the influence of anharmonicities and non-linearities in the external field on the excitation of Double Giant Resonances are studied. First, an oscillator model and an extension of the Lipkin-Meshkow-Glick model are used to study the effects of anharmonicities and non-linearities on the excitation probabilities. The results show that these terms can influence the excitation probability of the second excited state in a significant way. Secondly, these exactly soluble schematic models are used to study some of the approximations made in microscopic calculations based on boson expansion methods and also some aspects on the time-dependent mean field approach. Finally, a microscopic calculation of the Coulomb excitation cross sections of Double Giant Resonances is presented for several nuclei. It is found that, for 208 Pb, the inclusion of anharmonicities and non-linearities and the consideration of many states that play a role in the excitation process give a satisfactory agreement between calculated and observed cross sections. (author)

  8. Theory of a quantum anharmonic oscillator

    International Nuclear Information System (INIS)

    Carusotto, S.

    1988-01-01

    The time evolution of a quantum single-quartic anharmonic oscillator is considered. The study is carried on in operational form by use of the raising and lowering operators of the oscillator. The equation of motion is solved by application of a new integration method based on iteration techniques, and the rigorous solutions that describe the time development of the displacement and momentum operators of the oscillator are obtained. These operators are presented as a Laplace transform and a subsequent inverse Laplace transform of suitable functionals. Finally, the results are employed to describe the time evolution of a quasiclassical anharmonic oscillator

  9. An assessment of mean-field mixed semiclassical approaches: Equilibrium populations and algorithm stability

    International Nuclear Information System (INIS)

    Bellonzi, Nicole; Jain, Amber; Subotnik, Joseph E.

    2016-01-01

    We study several recent mean-field semiclassical dynamics methods, focusing on the ability to recover detailed balance for long time (equilibrium) populations. We focus especially on Miller and Cotton’s [J. Phys. Chem. A 117, 7190 (2013)] suggestion to include both zero point electronic energy and windowing on top of Ehrenfest dynamics. We investigate three regimes: harmonic surfaces with weak electronic coupling, harmonic surfaces with strong electronic coupling, and anharmonic surfaces with weak electronic coupling. In most cases, recent additions to Ehrenfest dynamics are a strong improvement upon mean-field theory. However, for methods that include zero point electronic energy, we show that anharmonic potential energy surfaces often lead to numerical instabilities, as caused by negative populations and forces. We also show that, though the effect of negative forces can appear hidden in harmonic systems, the resulting equilibrium limits do remain dependent on any windowing and zero point energy parameters.

  10. Anharmonic effects in the quantum cluster equilibrium method

    Science.gov (United States)

    von Domaros, Michael; Perlt, Eva

    2017-03-01

    The well-established quantum cluster equilibrium (QCE) model provides a statistical thermodynamic framework to apply high-level ab initio calculations of finite cluster structures to macroscopic liquid phases using the partition function. So far, the harmonic approximation has been applied throughout the calculations. In this article, we apply an important correction in the evaluation of the one-particle partition function and account for anharmonicity. Therefore, we implemented an analytical approximation to the Morse partition function and the derivatives of its logarithm with respect to temperature, which are required for the evaluation of thermodynamic quantities. This anharmonic QCE approach has been applied to liquid hydrogen chloride and cluster distributions, and the molar volume, the volumetric thermal expansion coefficient, and the isobaric heat capacity have been calculated. An improved description for all properties is observed if anharmonic effects are considered.

  11. Forces in electromagnetic field and gravitational field

    OpenAIRE

    Weng, Zihua

    2008-01-01

    The force can be defined from the linear momentum in the gravitational field and electromagnetic field. But this definition can not cover the gradient of energy. In the paper, the force will be defined from the energy and torque in a new way, which involves the gravitational force, electromagnetic force, inertial force, gradient of energy, and some other new force terms etc. One of these new force terms can be used to explain why the solar wind varies velocity along the magnetic force line in...

  12. Analytic cubic and quartic force fields using density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Ringholm, Magnus; Gao, Bin; Thorvaldsen, Andreas J.; Ruud, Kenneth [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Jonsson, Dan [Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); High Performance Computing Group, University of Tromsø—The Arctic University of Norway, 9037 Tromsø (Norway); Bast, Radovan [Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-10691 Stockholm, Sweden and PDC Center for High Performance Computing, Royal Institute of Technology, S-10044 Stockholm (Sweden); Ekström, Ulf; Helgaker, Trygve [Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo (Norway)

    2014-01-21

    We present the first analytic implementation of cubic and quartic force constants at the level of Kohn–Sham density-functional theory. The implementation is based on an open-ended formalism for the evaluation of energy derivatives in an atomic-orbital basis. The implementation relies on the availability of open-ended codes for evaluation of one- and two-electron integrals differentiated with respect to nuclear displacements as well as automatic differentiation of the exchange–correlation kernels. We use generalized second-order vibrational perturbation theory to calculate the fundamental frequencies of methane, ethane, benzene, and aniline, comparing B3LYP, BLYP, and Hartree–Fock results. The Hartree–Fock anharmonic corrections agree well with the B3LYP corrections when calculated at the B3LYP geometry and from B3LYP normal coordinates, suggesting that the inclusion of electron correlation is not essential for the reliable calculation of cubic and quartic force constants.

  13. Large time asymptotics of solutions to the anharmonic oscillator model from nonlinear optics

    OpenAIRE

    Jochmann, Frank

    2005-01-01

    The anharmonic oscillator model describing the propagation of electromagnetic waves in an exterior domain containing a nonlinear dielectric medium is investigated. The system under consideration consists of a generally nonlinear second order differential equation for the dielectrical polarization coupled with Maxwell's equations for the electromagnetic field. Local decay of the electromagnetic field for t to infinity in the charge free case is shown for a large class of potentials. (This pape...

  14. An efficient and accurate framework for calculating lattice thermal conductivity of solids: AFLOW—AAPL Automatic Anharmonic Phonon Library

    Science.gov (United States)

    Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Carrete, Jesús; Toher, Cormac; de Jong, Maarten; Asta, Mark; Fornari, Marco; Nardelli, Marco Buongiorno; Curtarolo, Stefano

    2017-10-01

    One of the most accurate approaches for calculating lattice thermal conductivity, , is solving the Boltzmann transport equation starting from third-order anharmonic force constants. In addition to the underlying approximations of ab-initio parameterization, two main challenges are associated with this path: high computational costs and lack of automation in the frameworks using this methodology, which affect the discovery rate of novel materials with ad-hoc properties. Here, the Automatic Anharmonic Phonon Library (AAPL) is presented. It efficiently computes interatomic force constants by making effective use of crystal symmetry analysis, it solves the Boltzmann transport equation to obtain , and allows a fully integrated operation with minimum user intervention, a rational addition to the current high-throughput accelerated materials development framework AFLOW. An "experiment vs. theory" study of the approach is shown, comparing accuracy and speed with respect to other available packages, and for materials characterized by strong electron localization and correlation. Combining AAPL with the pseudo-hybrid functional ACBN0 is possible to improve accuracy without increasing computational requirements.

  15. Quantum versus semiclassical description of selftrapping: anharmonic effects

    International Nuclear Information System (INIS)

    Raghavan, S.; Bishop, A.R.; Kenkre, V.M.

    1998-09-01

    Selftrapping has been traditionally studied on the assumption that quasiparticles interact with harmonic phonons and that this interaction is linear in the displacement of the phonon. To complement recent semiclassical studies of anharmonicity and nonlinearity in this context, we present below a fully quantum mechanical analysis of a two-site system, where the oscillator is described by a tunably anharmonic potential, with a square well with infinite walls and the harmonic potential as its extreme limits, and wherein the interaction is nonlinear in the oscillator displacement. We find that even highly anharmonic polarons behave similar to their harmonic counterparts in that selftrapping is preserved for long times in the limit of strong coupling, and that the polaronic tunneling time scale depends exponentially on the polaron binding energy. Further, in agreement with earlier results related to harmonic polarons, the semiclassical approximation agrees with the full quantum result in the massive oscillator limit of small oscillator frequency and strong quasiparticle-oscillator coupling. (author)

  16. Novel interpolative perturbation theory for quantum anharmonic oscillators in one and three dimensions and the ground state of a lattice model of the phi4 field theory

    International Nuclear Information System (INIS)

    Ginsburg, C.A.

    1977-01-01

    A new method for approximating the eigenfunctions and eigenvalues of anharmonic oscillators. An attempt was made to develop an analytic method which provides simple formulae for all values of the parameters as the W.K.B. approximation and perturbation theory do for certain limiting case, and which has the convergence properties associated with the computer methods. The procedure is based upon combining knowledge of the asymptotic behavior of the wave function for large and small values of the coordinate(s) to obtain approximations valid for all values of coordinate(s) and all strengths of the anharmonicity. A systematic procedure for improving these approximations is developed. Finally the groundstate of a lattice model of the phi 4 field theory which consists of an infinite number of coupled anharmonic oscillators. A first order calculation yields a covariant expression for the groundstate eigenvalue with the physical mass, m, given by a characteristic polynomial which involves the bare mass, μ, the lattice spacing, l, and the coupling constant, lambda. For l > 0, μ can be adjusted (a mass renormalization) 0 < m < infinity. As l → 0 lambda (l) (a charge renormalization) is adjusted so that lambda/sup 1/3//l → eta, a constant, as l → 0. Then eta can be chosen so that m can take any experimental value

  17. Intrinsic anharmonic effects on the phonon frequencies and effective spin-spin interactions in a quantum simulator made from trapped ions in a linear Paul trap

    Science.gov (United States)

    McAneny, M.; Freericks, J. K.

    2014-11-01

    The Coulomb repulsion between ions in a linear Paul trap gives rise to anharmonic terms in the potential energy when expanded about the equilibrium positions. We examine the effect of these anharmonic terms on the accuracy of a quantum simulator made from trapped ions. To be concrete, we consider a linear chain of Yb171+ ions stabilized close to the zigzag transition. We find that for typical experimental temperatures, frequencies change by no more than a factor of 0.01 % due to the anharmonic couplings. Furthermore, shifts in the effective spin-spin interactions (driven by a spin-dependent optical dipole force) are also, in general, less than 0.01 % for detunings to the blue of the transverse center-of-mass frequency. However, detuning the spin interactions near other frequencies can lead to non-negligible anharmonic contributions to the effective spin-spin interactions. We also examine an odd behavior exhibited by the harmonic spin-spin interactions for a range of intermediate detunings, where nearest-neighbor spins with a larger spatial separation on the ion chain interact more strongly than nearest neighbors with a smaller spatial separation.

  18. Quantum anharmonic oscillator: The airy function approach

    Energy Technology Data Exchange (ETDEWEB)

    Maiz, F., E-mail: fethimaiz@gmail.com [King Khalid University, Faculty of Science, Physics Department, PO Box 9004, Abha 61413, Asseer (Saudi Arabia); University of Cartage, Nabeul Engineering Preparatory Institute, Merazka, 8000 Nabeul (Tunisia); AlFaify, S. [King Khalid University, Faculty of Science, Physics Department, PO Box 9004, Abha 61413, Asseer (Saudi Arabia)

    2014-05-15

    New and simple numerical method is being reported to solve anharmonic oscillator problems. The method is setup to approach the real potential V(x) of the anharmonic oscillator system as a piecewise linear potential u(x) and to solve the Schrödinger equation of the system using the Airy function. Then, solutions continuity conditions lead to the energy quantification condition, and consequently, the energy eigenvalues. For testing purpose, the method was applied on the sextic and octic oscillators systems. The proposed method is found to be realistic, computationally simple, and having high degrees of accuracy. In addition, it can be applied to any form of potential. The results obtained by the proposed method were seen closely agreeing with results reached by other complicated methods.

  19. Semi-quartic force fields retrieved from multi-mode expansions: Accuracy, scaling behavior, and approximations

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Raghunathan [Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel (Switzerland); Rauhut, Guntram, E-mail: rauhut@theochem.uni-stuttgart.de [Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany)

    2015-04-21

    Semi-quartic force fields (QFF) rely on a Taylor-expansion of the multi-dimensional Born-Oppenheimer potential energy surface (PES) and are frequently used within the calculation of anharmonic vibrational frequencies based on 2nd order vibrational perturbation theory (VPT2). As such they are usually determined by differentiation of the electronic energy with respect to the nuclear coordinates. Alternatively, potential energy surfaces can be expanded in terms of multi-mode expansions, which typically do not require any derivative techniques. The computational effort to retrieve QFF from size-reduced multi-mode expansions has been studied and has been compared with standard Taylor-expansions. As multi-mode expansions allow for the convenient introduction of subtle approximations, these will be discussed in some detail. In addition, a preliminary study about the applicability of a generalized Duschinsky transformation to QFFs is provided. This transformation allows for the efficient evaluation of VPT2 frequencies of isotopologues from the PES of the parent compound and thus avoids the recalculation of PESs in different axes systems.

  20. Ground state energy values and moments of the anharmonic oscillator

    International Nuclear Information System (INIS)

    Seetharaman, M.; Raghavan, Sekhar; Subba Rao, G.

    1981-01-01

    It is shown that a very satisfactory estimate of the energy values (for all values of the anharmonicity) and moments of the ground state of the quartic anharmonic oscillator can be obtained in the variational method, by considering trial wavefunctions which have the correct asymptotic properties. The results derived with a single variational parameter are a considerable improvement over the recent results of C.A. Ginsburg and E.W. Montroll (1978). (author)

  1. HIGH-RESOLUTION IR ABSORPTION SPECTROSCOPY OF POLYCYCLIC AROMATIC HYDROCARBONS: THE REALM OF ANHARMONICITY

    Energy Technology Data Exchange (ETDEWEB)

    Maltseva, Elena; Buma, Wybren Jan [University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Petrignani, Annemieke; Candian, Alessandra; Mackie, Cameron J.; Tielens, Alexander G. G. M. [Leiden Observatory, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Huang, Xinchuan; Lee, Timothy J. [SETI Institute, 189 Bernardo Avenue, Suite 100, Mountain View, CA 94043 (United States); Oomens, Jos, E-mail: w.j.buma@uva.nl, E-mail: petrignani@strw.leidenuniv.nl [Radboud University, Toernooiveld 7, 6525 ED Nijmegen (Netherlands)

    2015-11-20

    We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3-μm CH stretching region of polycyclic aromatic hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold (∼4 K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main bands that fall within 0.5% of the experimental frequencies. The implications for the aromatic infrared bands, specifically the 3-μm band, are discussed.

  2. High-Resolution IR Absorption Spectroscopy of Polycyclic Aromatic Hydrocarbons: The Realm of Anharmonicity

    Science.gov (United States)

    Maltseva, Elena; Petrignani, Annemieke; Candian, Alessandra; Mackie, Cameron J.; Huang, Xinchuan; Lee, Timothy J.; Tielens, Alexander G. G. M.; Oomens, Jos; Buma, Wybren Jan

    2016-01-01

    We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3 micrometers CH stretching region of Polycyclic Aromatic Hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold ((is) approximately 4K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions enhanced with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main modes that fall within 0.5% of the experimental frequencies. The implications for the Aromatic Infrared Bands, specifically the 3-m band are discussed.

  3. Anharmonic effective pair potentials of gold under high pressure and high temperature

    CERN Document Server

    Okube, M; Ohtaka, O; Fukui, H; Katayama, Y; Utsumi, W

    2002-01-01

    In order to examine the effect of pressure on the anharmonicity of Au, extended x-ray absorption fine-structure spectra near the Au L sub 3 edge were measured in the temperature range from 300 to 1100 K under pressures up to 14 GPa using large-volume high-pressure devices and synchrotron radiation. The anharmonic effective pair potentials of Au, V (u) = au sup 2 + bu sup 3 , at 0.1 MPa, 6 and 14 GPa have been calculated. The pressure dependence of the thermal expansion coefficients has also been evaluated. The reliability of the anharmonic correction proposed on the basis of the Anderson scale has been discussed.

  4. Quantum versus semiclassical description of self-trapping: Anharmonic effects

    International Nuclear Information System (INIS)

    Raghavan, S.; Bishop, A.R.; Kenkre, V.M.

    1999-01-01

    Self-trapping has been traditionally studied on the assumption that quasiparticles interact with harmonic phonons and that this interaction is linear in the displacement of the phonon. To complement recent semiclassical studies of anharmonicity and nonlinearity in this context, we present below a fully quantum-mechanical analysis of a two-site system, where the oscillator is described by a tunably anharmonic potential, with a square well with infinite walls and the harmonic potential as its extreme limits, and wherein the interaction is nonlinear in the oscillator displacement. We find that even highly anharmonic polarons behave similar to their harmonic counterparts in that self-trapping is preserved for long times in the limit of strong coupling, and that the polaronic tunneling time scale depends exponentially on the polaron binding energy. Further, in agreement, with earlier results related to harmonic polarons, the semiclassical approximation agrees with the full quantum result in the massive oscillator limit of small oscillator frequency and strong quasiparticle-oscillator coupling. copyright 1999 The American Physical Society

  5. The Martini Coarse-Grained Force Field

    NARCIS (Netherlands)

    Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

    2013-01-01

    The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

  6. Kinematic anharmonicity of internal rotation of molecules

    International Nuclear Information System (INIS)

    Bataev, V.A.; Pupyshev, V.I.; Godunov, I.A.

    2017-01-01

    The methods of analysis the strongly coupled vibrations are proposed for a number of molecules of aromatic and heterocyclic carbonyl (and some others) compounds. The qualitative principles are formulated for molecular systems with a significant kinematic anharmonicity.

  7. The anharmonic phonon decay rate in group-III nitrides

    International Nuclear Information System (INIS)

    Srivastava, G P

    2009-01-01

    Measured lifetimes of hot phonons in group-III nitrides have been explained theoretically by considering three-phonon anharmonic interaction processes. The basic ingredients of the theory include full phonon dispersion relations obtained from the application of an adiabatic bond charge model and crystal anharmonic potential within the isotropic elastic continuum model. The role of various decay routes, such as Klemens, Ridley, Vallee-Bogani and Barman-Srivastava channels, in determining the lifetimes of the Raman active zone-centre longitudinal optical (LO) modes in BN (zincblende structure) and A 1 (LO) modes in AlN, GaN and InN (wurtzite structure) has been quantified.

  8. Fragility, anharmonicity and anelasticity of silver borate glasses

    International Nuclear Information System (INIS)

    Carini, Giovanni; Carini, Giuseppe; D'Angelo, Giovanna; Tripodo, Gaspare; Bartolotta, Antonio; Marco, Gaetano Di

    2006-01-01

    The fragility and the anharmonicity of (Ag 2 O) x (B 2 O 3 ) 1-x borate glasses have been quantified by measuring the change in the specific heat capacity at the glass transition temperature T g and the room-temperature thermodynamic Grueneisen parameter. Increasing the silver oxide content above X = 0.10 leads to an increase of both the parameters, showing that a growing fragility of a glass-forming liquid is predictive of an increasing overall anharmonicity of its glassy state. The attenuation and velocity of ultrasonic waves of frequencies in the range of 10-70 MHz have also been measured in silver borate glasses as a function of temperature between 1.5 and 300 K. The experimental data reveal anelastic behaviours which are governed by (i) quantum-mechanical tunnelling below 20 K (ii) thermally activated relaxations between 20 and 200 K and (iii) vibrational anharmonicity at even higher temperatures. Evaluation of tunnelling (C) and relaxation (C * ) strengths shows that C is independent of the structural changes affecting the borate network with increasing metal oxide content and is at least one order of magnitude smaller than C * . The latter observation implies that only a small fraction of the locally mobile defects are subjected to tunnelling motions

  9. Anharmonicity of lattice vibrations induced by charged nickel additions in A sup 2 B sup 6 semiconductors

    CERN Document Server

    Sokolov, V I; Shirokov, E A; Kislov, A N

    2002-01-01

    Paper presents the results of investigations into lattice vibrations induced by nickel impurities charged negatively as to the lattice in ZnSe:Ni, ZnO:Ni, ZnS:Ni, CdS:Ni semiconductors. To investigate into vibrations one applies a sensitive technique of field exciton-oscillation spectroscopy. One observes experimentally oscillating reiterations of the impurity exciton head line including the intensive peaks of combined repetitions up to the 8-th order. The experimental results are discussed on the basis of the model estimations of oscillations of a lattice with a charged impurity centre, as well as, on the ground of calculations for oscillations of monoatomic chain with high anharmonicity. Charged impurity centres are shown to induce new oscillations of lattice - impurity anharmonic modes

  10. Comparison of Degrees of Potential-Energy-Surface Anharmonicity for Complexes and Clusters with Hydrogen Bonds

    Science.gov (United States)

    Kozlovskaya, E. N.; Doroshenko, I. Yu.; Pogorelov, V. E.; Vaskivskyi, Ye. V.; Pitsevich, G. A.

    2018-01-01

    Previously calculated multidimensional potential-energy surfaces of the MeOH monomer and dimer, water dimer, malonaldehyde, formic acid dimer, free pyridine-N-oxide/trichloroacetic acid complex, and protonated water dimer were analyzed. The corresponding harmonic potential-energy surfaces near the global minima were constructed for series of clusters and complexes with hydrogen bonds of different strengths based on the behavior of the calculated multidimensional potential-energy surfaces. This enabled the introduction of an obvious anharmonicity parameter for the calculated potential-energy surfaces. The anharmonicity parameter was analyzed as functions of the size of the analyzed area near the energy minimum, the number of points over which energies were compared, and the dimensionality of the solved vibrational problem. Anharmonicity parameters for potential-energy surfaces in complexes with strong, medium, and weak H-bonds were calculated under identical conditions. The obtained anharmonicity parameters were compared with the corresponding diagonal anharmonicity constants for stretching vibrations of the bridging protons and the lengths of the hydrogen bridges.

  11. Superconductivity mediated by anharmonic phonons: application to β-pyrochlore oxides

    Science.gov (United States)

    Hattori, Kazumasa; Tsunetsugu, Hirokazu

    2010-03-01

    We investigate three dimensional anharmonic phonons under tetrahedral symmetry and superconductivity mediated by these phonons. Three dimensional anharmonic phonon spectra are calculated directly by solving Schr"odinger equation and the superconducting transition temperature is determined by using the theory of strong coupling superconductivity assuming an isotropic gap function. With increasing the third order anharmonicity b of the tetrahedral potential, we find a crossover in the energy spectrum to a quantum tunneling regime. We obtain strongly enhanced transition temperatures around the crossover point. The first order transition observed in KOs2O6 is discussed in terms of the first excited state energy δ, and the coupling constant λ in the strong coupling theory of superconductivity. Our results suggest that the decrease of λ and increase of δ below the first order transition temperature. We point out that the change in the oscillation amplitude and characterizes this isomorphic transition. The chemical trends of the superconducting transition temperature, λ, and δ in the β-pyrochlore compounds are also discussed.

  12. Comparative study of quantum anharmonic potentials

    International Nuclear Information System (INIS)

    Amore, Paolo; Aranda, Alfredo; De Pace, Arturo; Lopez, Jorge A.

    2004-01-01

    We perform a study of various anharmonic potentials using a recently developed method. We calculate both the wave functions and the energy eigenvalues for the ground and first excited states of the quartic, sextic and octic potentials with high precision, comparing the results with other techniques available in the literature

  13. Exact solutions and ladder operators for a new anharmonic oscillator

    International Nuclear Information System (INIS)

    Dong Shihai; Sun Guohua; Lozada-Cassou, M.

    2005-01-01

    In this Letter, we propose a new anharmonic oscillator and present the exact solutions of the Schrodinger equation with this oscillator. The ladder operators are established directly from the normalized radial wave functions and used to evaluate the closed expressions of matrix elements for some related functions. Some comments are made on the general calculation formula and recurrence relation for off-diagonal matrix elements. Finally, we show that this anharmonic oscillator possesses a hidden symmetry between E(r) and E(ir) by substituting r->ir

  14. Consistent force fields for saccharides

    DEFF Research Database (Denmark)

    Rasmussen, Kjeld

    1999-01-01

    Consistent force fields for carbohydrates were hitherto developed by extensive optimization ofpotential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x......-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originatedin Israel and was further developed in Denmark. The actual methods and strategies employed havebeen described previously. Extensive testing of the force field...

  15. Deriving force field parameters for coordination complexes

    DEFF Research Database (Denmark)

    Norrby, Per-Ola; Brandt, Peter

    2001-01-01

    The process of deriving molecular mechanics force fields for coordination complexes is outlined. Force field basics are introduced with an emphasis on special requirements for metal complexes. The review is then focused on how to set up the initial model, define the target, refine the parameters......, and validate the final force field, Alternatives to force field derivation are discussed briefly....

  16. Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes.

    Science.gov (United States)

    Šebek, Jiří; Pele, Liat; Potma, Eric O; Gerber, R Benny

    2011-07-28

    First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems. This journal is © the Owner Societies 2011

  17. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

  18. Scattering of Neutrons by an Anharmonic Crystal

    Energy Technology Data Exchange (ETDEWEB)

    Hoegberg, T; Bohlin, L; Ebbsjoe, I

    1967-04-15

    Numerical calculations have been performed for the anharmonic effects in neutron scattering. The phonon frequency widths and shifts have been calculated as a function of neutron frequency at different wave numbers and temperatures for a potential with central symmetry and for a face-centered cubic lattice.

  19. Anharmonic vibrational properties in periodic systems: energy, electron-phonon coupling, and stress

    OpenAIRE

    Monserrat, Bartomeu; Drummond, N. D.; Needs, R. J.

    2013-01-01

    A unified approach is used to study vibrational properties of periodic systems with first-principles methods and including anharmonic effects. Our approach provides a theoretical basis for the determination of phonon-dependent quantities at finite temperatures. The low-energy portion of the Born-Oppenheimer energy surface is mapped and used to calculate the total vibrational energy including anharmonic effects, electron-phonon coupling, and the vibrational contribution to the stress tensor. W...

  20. E x circle epsilon Jahn-Teller anharmonic coupling for an octahedral system

    CERN Document Server

    Avram, N M; Kibler, M R

    2001-01-01

    The coupling between doubly degenerate electronic states and doubly degenerate vibrations is analyzed for an octahedral system on the basis of the introduction of an anharmonic Morse potential for the vibronic part. The vibrations are described by anharmonic coherent states and their linear coupling with the electronic states is considered. The matrix elements of the vibronic interaction are built and the energy levels corresponding to the interaction Hamiltonian are derived.

  1. Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

    Science.gov (United States)

    Latouche, Camille; Bloino, Julien; Barone, Vincenzo

    2014-06-01

    Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

  2. Near field plasmon and force microscopy

    NARCIS (Netherlands)

    de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

    1995-01-01

    A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the

  3. Crystal anharmonicity in Li(H,D) and Na(H,D) systems

    International Nuclear Information System (INIS)

    Islam, A.K.M.A.; Haque, E.; Azad, A.S.

    1993-05-01

    The reliability of our recently developed potential model is tested by extending the study to various anharmonic properties, e.g., third order elastic constants, fourth order elastic constants, Grueneisen parameters, and the pressure derivatives of second order elastic constants of hydrides and deuterides of lithium and sodium. A comparison of the calculated properties with the available experimental results and other theoretical estimates shows the validity and reliability of the derived potential in the study of crystal anharmonicities also. (author). 43 refs, 2 figs, 4 tabs

  4. Neutron scattering by anharmonic crystals and the effect of sublattice displacements

    International Nuclear Information System (INIS)

    Viswanathan, K.S.; Phillip, Jacob

    1979-01-01

    A theory has been described for the scattering of neutrons by anharmonic crystals, for which terms of the type Vsup(3) (k 1 j 1 ;-k 1 j 1 ;aj) which contribute to the sublattice displacements are not neglected. It is shown that the sublattice displacements will modify the phase factor arising from the scattering by any atom in the unit cell, and the Debye-Waller factor also gets altered both by the sublattice displacements as well as by higher order terms arising from anharmonicity. (author)

  5. Ehrenfest force in inhomogeneous magnetic field

    International Nuclear Information System (INIS)

    Sisakyan, A.N.; Shevchenko, O.Yu.; Samojlov, V.N.

    2000-01-01

    The Ehrenfest force in an inhomogeneous magnetic field is calculated. It is shown that there exist such (very rare) topologically nontrivial physical situations when the Gauss theorem in its classic formulation fails and, as a consequence, apart from the usual Lorentz force an additional, purely imaginary force acts on the charged particle. This force arises only in inhomogeneous magnetic fields of special configurations, has a purely quantum origin, and disappears in the classical limit

  6. Anharmonic phonons and the isotope effect in superconductivity

    International Nuclear Information System (INIS)

    Crespi, V.H.; Cohen, M.L.; Penn, D.R.

    1991-01-01

    Anharmonic interionic potentials are examined in an Einstein model to study the unusual isotope-effect exponents for the high-T c oxides. The mass dependences of the electron-phonon coupling constant λ and the average phonon frequency √ left-angle ω 2 right-angle are computed from weighted sums over the oscillator levels. The isotope-effect exponent is depressed below 1/2 by either a double-well potential or a potential with positive quadratic and quartic parts. Numerical solutions of Schroedinger's equation for double-well potentials produce λ's in the range 1.5--4 for a material with a vanishing isotope-effect parameter α. However, low phonon frequencies limit T c to roughly 15 K. A negative quartic perturbation to a harmonic well can increase α above 1/2. In the extreme-strong-coupling limit, α is 1/2, regardless of anharmonicity

  7. Proof of Nishida's Conjecture on Anharmonic Lattices

    Science.gov (United States)

    Rink, Bob

    2006-02-01

    We prove Nishida's 1971 conjecture stating that almost all low-energetic motions of the anharmonic Fermi-Pasta-Ulam lattice with fixed endpoints are quasi-periodic. The proof is based on the formal computations of Nishida, the KAM theorem, discrete symmetry considerations and an algebraic trick that considerably simplifies earlier results.

  8. Spherical anharmonic oscillator in self-similar approximation

    International Nuclear Information System (INIS)

    Yukalova, E.P.; Yukalov, V.I.

    1992-01-01

    The method of self-similar approximation is applied here for calculating the eigenvalues of the three-dimensional spherical anharmonic oscillator. The advantage of this method is in its simplicity and high accuracy. The comparison with other known analytical methods proves that this method is more simple and accurate. 25 refs

  9. Anharmonic phonons and magnons in BiFeO3

    Energy Technology Data Exchange (ETDEWEB)

    Delaire, Olivier A [ORNL; Ma, Jie [ORNL; Stone, Matthew B [ORNL; Huq, Ashfia [ORNL; Gout, Delphine J [ORNL; Brown, Craig [National Institute of Standards and Technology (NIST); Wang, Kefeng [Nanjing National Laboratory of Microstructures, Nanjing University, Nanjing; Ren, Zhifeng [Boston College, Chestnut Hill

    2012-01-01

    The phonon density of states (DOS) and magnetic excitation spectrum of polycrystalline BiFeO3 were measured for temperatures 200 < T < 750K , using inelastic neutron scattering (INS). Our results indicate that the magnetic spectrum of BiFeO3 closely resembles that of similar Fe perovskites, such as LaFeO3, despite the cycloid modulation in BiFeO3. We do not find any evidence for a spin gap. A strong T-dependence of the phonon DOS was found, with a marked broadening of the whole spectrum, providing evidence of strong anharmonicity. This anharmonicity is corroborated by large amplitude motions of Bi and O ions observed with neutron diffraction. These results highlight the importance of spin-phonon coupling in this material.

  10. Vibrational spectroscopy of the G...C base pair: Experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings

    Czech Academy of Sciences Publication Activity Database

    Brauer, B.; Gerber, R. B.; Kabeláč, Martin; Hobza, Pavel; Bakker, J. M.; Abo-Riziq, A.; Vries de, M. S.

    2005-01-01

    Roč. 109, - (2005), s. 6974-6984 ISSN 1089-5639 Grant - others:NSF(US) CHE-0244341 Institutional research plan: CEZ:AV0Z40550506 Keywords : nucleic acids bases * vibrational spectrum * frequencies anharmonicity Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.898, year: 2005

  11. Anharmonic thermal vibrations of be metal found in the MEM nuclear density map

    International Nuclear Information System (INIS)

    Takata, Masaki; Sakata, Makoto; Larsen, F.K.; Kumazawa, Shintaro; Iversen, B.B.

    1993-01-01

    A direct observation of the thermal vibrations of Be metal was performed by the Maximum Entropy Method (MEM) using neutron single crystal data. In the previous study, the existence of the small but significant cubic anharmonicity of Be has been found by the conventional least squares refinement of the observed structure factors [Larsen, Lehmann and Merisalo (1980) Acta Cryst. A36, 159-163]. In the present study, the same data were used for the MEM analysis which are comprised of 48 reflections up to sinθ/λ = 1.41A -1 in order to obtain the high resolution nuclear density of Be without using any thermal vibrational model. It was directly visible in the MEM map that not only the cubic terms but also quartic anharmonicities exist in the thermal vibrations of Be nuclei. In order to evaluate thermal parameters of Be including anharmonic terms quantitatively, the least squares refinement of the effective one-particle potential (OPP) parameters up to quartic term was carried out by using the MEM nuclear densities around atomic sites as the data set to be fitted. It was found that the present treatment has a great advantage to decide the most appropriate model of OPP by visually comparing the model with MEM density map. As a result of the least squares refinement, the anharmonic thermal parameters are obtained as α 33 = -0.340(5)[eV/A 3 ], α 40 = 0, β 20 = 9.89(1)[eV/A 4 ] and γ 00 = 0. No other anharmonic term was significant. (author)

  12. Time evolution of gibbs states for an anharmonic lattice

    Energy Technology Data Exchange (ETDEWEB)

    Marchioro, C; Pellegrinotti, A; Suhov, Y [Camerino Univ. (Italy). Istituto di Matematica; Pulvirenti, M [L' Aquila Univ. (Italy). Istituto di Matematica; Rome Univ. (Italy). Istituto di Matematica)

    1979-01-01

    In this paper we study the time evolution of a regular class of states of an infinite classical system of anharmonic oscillators. The conditional probabilities are investigated and an explicit form for these is given.

  13. Instantons and Borel resummability for the perturbed supersymmetric anharmonic oscillator

    International Nuclear Information System (INIS)

    Verbaarschot, J.J.M.; West, P.

    1991-01-01

    In this paper we give an analytical derivation of the large-order behavior of the perturbation series for both the ground state and the excited states of the supersymmetric anharmonic oscillator and of the anharmonic oscillator obtained from the supersymmetric case by varying the strength of the fermion coupling. The results which are obtained with the help of instanton calculus coincide with those obtained numerically in previous work. The large-order perturbation series of the ground state vanishes in the supersymmetric case, whereas away from the supersymmetric point the perturbation series diverges factorially. The perturbation series of the excited states diverges factorially both at the supersymmetric point and away from this point

  14. Anharmonicity, mechanical instability, and thermodynamic properties of the Cr-Re σ-phase

    Energy Technology Data Exchange (ETDEWEB)

    Palumbo, Mauro, E-mail: mauro.palumbo@rub.de; Fries, Suzana G. [ICAMS, Ruhr University Bochum, Universität Str. 150, D-44801 Bochum (Germany); Pasturel, Alain [SIMAP, UMR CNRS-INPG-UJF 5266, BP 75, F-38402 Saint Martin d’Hères (France); Alfè, Dario [Department of Earth Sciences, Department of Physics and Astronomy, London Centre for Nanotechnology and Thomas Young Centre-UCL, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2014-04-14

    Using density-functional theory in combination with the direct force method and molecular dynamics we investigate the vibrational properties of a binary Cr-Re σ-phase. In the harmonic approximation, we have computed phonon dispersion curves and density of states, evidencing structural and chemical effects. We found that the σ-phase is mechanically unstable in some configurations, for example, when all crystallographic sites are occupied by Re atoms. By using a molecular-dynamics-based method, we have analysed the anharmonicity in the system and found negligible effects (∼0.5 kJ/mol) on the Helmholtz energy of the binary Cr-Re σ-phase up to 2000 K (∼0.8T{sub m}). Finally, we show that the vibrational contribution has significant consequences on the disordering of the σ-phase at high temperature.

  15. Transition States from Empirical Force Fields

    DEFF Research Database (Denmark)

    Jensen, Frank; Norrby, Per-Ola

    2003-01-01

    This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...

  16. Anharmonic Rovibrational Partition Functions for Fluxional Species at High Temperatures via Monte Carlo Phase Space Integrals

    Energy Technology Data Exchange (ETDEWEB)

    Jasper, Ahren W. [Chemical Sciences and Engineering; Gruey, Zackery B. [Chemical Sciences and Engineering; Harding, Lawrence B. [Chemical Sciences and Engineering; Georgievskii, Yuri [Chemical Sciences and Engineering; Klippenstein, Stephen J. [Chemical Sciences and Engineering; Wagner, Albert F. [Chemical Sciences and Engineering

    2018-02-03

    Monte Carlo phase space integration (MCPSI) is used to compute full dimensional and fully anharmonic, but classical, rovibrational partition functions for 22 small- and medium-sized molecules and radicals. Several of the species considered here feature multiple minima and low-frequency nonlocal motions, and efficiently sampling these systems is facilitated using curvilinear (stretch, bend, and torsion) coordinates. The curvilinear coordinate MCPSI method is demonstrated to be applicable to the treatment of fluxional species with complex rovibrational structures and as many as 21 fully coupled rovibrational degrees of freedom. Trends in the computed anharmonicity corrections are discussed. For many systems, rovibrational anharmonicities at elevated temperatures are shown to vary consistently with the number of degrees of freedom and with temperature once rovibrational coupling and torsional anharmonicity are accounted for. Larger corrections are found for systems with complex vibrational structures, such as systems with multiple large-amplitude modes and/or multiple minima.

  17. Phonon anharmonicity and Gruneisen parameters of alpha-plutonium

    International Nuclear Information System (INIS)

    Filanovich, A.N.; Povzner, A.A.

    2015-01-01

    A self-consistent thermodynamic model of alpha-phase of plutonium is constructed. The calculations of thermal and elastic properties of α-Pu, carried out within this model, demonstrate that anomalously strong temperature dependence of the bulk modulus and unusually high value of the coefficient of thermal expansion of α-Pu are caused by its strong lattice anharmonicity. The isothermal and isobaric Gruneisen parameters of α-Pu and δ-Pu Pu_0_._9_6Ga_0_._0_4 are calculated. It is shown that wide spread of the values of Gruneisen parameter of α-Pu, obtained previously from different experimental data, is explained by the dependence of Gruneisen parameter of α-Pu on temperature. - Highlights: • A self-consistent thermodynamic model of alpha-plutonium is developed. • Thermal and elastic properties of alpha-plutonium are calculated. • The reason of spread in the values of Gruneisen parameter of alpha-Pu is established. • Different types of phonon anharmonicity in alpha-Pu and delta-Pu are revealed.

  18. Time evolution of gibbs states for an anharmonic lattice

    International Nuclear Information System (INIS)

    Marchioro, C.; Pellegrinotti, A.; Suhov, Y.; Pulvirenti, M.; Rome Univ.

    1979-01-01

    In this paper we study the time evolution of a regular class of states of an infinite classical system of anharmonic oscillators. The conditional probabilities are investigated and an explicit form for these is given. (orig.) [de

  19. Variational random phase approximation for the anharmonic oscillator

    International Nuclear Information System (INIS)

    Dukelsky, J.; Schuck, P.

    1990-04-01

    The recently derived Variational Random Phase Approximation is examined using the anharmonic oscillator model. Special attention is paid to the ground state RPA wave function and the convergence of the proposed truncation scheme to obtain the diagonal density matrix. Comparison with the standard Coupled Cluster method is made

  20. First-principles theory of anharmonicity and the inverse isotope effect in superconducting palladium-hydride compounds.

    Science.gov (United States)

    Errea, Ion; Calandra, Matteo; Mauri, Francesco

    2013-10-25

    Palladium hydrides display the largest isotope effect anomaly known in the literature. Replacement of hydrogen with the heavier isotopes leads to higher superconducting temperatures, a behavior inconsistent with harmonic theory. Solving the self-consistent harmonic approximation by a stochastic approach, we obtain the anharmonic free energy, the thermal expansion, and the superconducting properties fully ab initio. We find that the phonon spectra are strongly renormalized by anharmonicity far beyond the perturbative regime. Superconductivity is phonon mediated, but the harmonic approximation largely overestimates the superconducting critical temperatures. We explain the inverse isotope effect, obtaining a -0.38 value for the isotope coefficient in good agreement with experiments, hydrogen anharmonicity being mainly responsible for the isotope anomaly.

  1. Anharmonic behavior and structural phase transition in Yb2O3

    Directory of Open Access Journals (Sweden)

    Sugandha Dogra Pandey

    2013-12-01

    Full Text Available The investigation of structural phase transition and anharmonic behavior of Yb2O3 has been carried out by high-pressure and temperature dependent Raman scattering studies respectively. In situ Raman studies under high pressure were carried out in a diamond anvil cell at room temperature which indicate a structural transition from cubic to hexagonal phase at and above 20.6 GPa. In the decompression cycle, Yb2O3 retained its high pressure phase. We have observed a Stark line in the Raman spectra at 337.5 cm−1 which arises from the electronic transition between 2F5/2 and 2F7/2 multiplates of Yb3+ (4f13 levels. These were followed by temperature dependent Raman studies in the range of 80–440 K, which show an unusual mode hardening with increasing temperature. The hardening of the most dominant mode (Tg + Ag was analyzed in light of the theory of anharmonic phonon-phonon interaction and thermal expansion of the lattice. Using the mode Grüneisen parameter obtained from high pressure Raman measurements; we have calculated total anharmonicity of the Tg + Ag mode from the temperature dependent Raman data.

  2. Force-free field model of ball lightning

    International Nuclear Information System (INIS)

    Tsui, K.H.

    2001-01-01

    Due to the nature that the force-free magnetic field, whose current carried by the conducting plasma is everywhere parallel to the magnetic field it generates, is the minimum energy configuration under the constraint of magnetic helicity conservation, ball lightning is considered as a self-organized phenomenon with a plasma fireball immersed in a spherical force-free magnetic field. Since this field does not exert force on the plasma, the plasma pressure, by itself, is in equilibrium with the surrounding environment, and the force-free magnetic field can take on any value without affecting the plasma. Due to this second feature, singular solutions of the magnetic field that are otherwise excluded are allowed, which enable a large amount of energy to be stored to sustain the ball lightning. The singularity is truncated only by the physical limit of current density that a plasma can carry. Scaling the customary soccer-size fireball to larger dimensions could account for day and night sightings of luminous objects in the sky

  3. Infrared and Raman Spectra of and Isotopomers: A DFT-PT2 Anharmonic Study

    Directory of Open Access Journals (Sweden)

    Andrea Alparone

    2013-01-01

    Full Text Available IR and Raman spectra of selenophene and of its perdeuterated isotopomer have been obtained in gas phase through density-functional theory (DFT computations. Vibrational wavenumbers have been calculated using harmonic and anharmonic second-order perturbation theory (PT2 procedures with the B3LYP method and the 6-311 basis set. Anharmonic overtones have been determined by means of the PT2 method. The introduction of anharmonic terms decreases the harmonic wavenumbers, giving a significantly better agreement with the experimental data. The most significant anharmonic effects occur for the C–H and C–D stretching modes, the observed H/D isotopic wavenumber redshifts being satisfactorily reproduced by the PT2 computations within 6–20 cm−1 (1–3%. In the spectral region between 500 cm−1 and 1500 cm−1, the IR spectra are dominated by the out-of-plane C–H (C–D bending transition, whereas the Raman spectra are mainly characterized by a strong peak mainly attributed to the C=C + C–C bonds stretching vibration with the contribution of the in-plane C–H (C–D bending deformation. The current results confirm that the PT2 approach combined with the B3LYP/6-311 level of calculation is a satisfactory choice for predicting vibrational spectra of cyclic molecules.

  4. Near field plasmon and force microscopy

    OpenAIRE

    de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

    1995-01-01

    A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the probe size to about 20 nm. At variance to previous work, utilizing a scanning tunneling microscope (STM) with a metallic tip, a dielectric silicon-nitride tip is used in contact mode. This arrangement ...

  5. Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

    Science.gov (United States)

    Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

    2016-07-28

    The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

  6. Remarks on the choice of trial hamiltonians for the quantum statistical treatment of anharmonic systems

    International Nuclear Information System (INIS)

    Tsallis, C.; Valle, J.W.F.

    1979-01-01

    The use of the Variational Method to discuss Quantum Statistical Mechanics of anharmonic systems requires, in order to be able to obtain the correct classical limit, the allowance for renormalization of every operator whose definition depends on the harmonic coefficients. The point is exhibited for a single anharmonic oscillator. In this particular case there is no need for mass renormalization. (Author) [pt

  7. Implementation of ternary Shor’s algorithm based on vibrational states of an ion in anharmonic potential

    Science.gov (United States)

    Liu, Wei; Chen, Shu-Ming; Zhang, Jian; Wu, Chun-Wang; Wu, Wei; Chen, Ping-Xing

    2015-03-01

    It is widely believed that Shor’s factoring algorithm provides a driving force to boost the quantum computing research. However, a serious obstacle to its binary implementation is the large number of quantum gates. Non-binary quantum computing is an efficient way to reduce the required number of elemental gates. Here, we propose optimization schemes for Shor’s algorithm implementation and take a ternary version for factorizing 21 as an example. The optimized factorization is achieved by a two-qutrit quantum circuit, which consists of only two single qutrit gates and one ternary controlled-NOT gate. This two-qutrit quantum circuit is then encoded into the nine lower vibrational states of an ion trapped in a weakly anharmonic potential. Optimal control theory (OCT) is employed to derive the manipulation electric field for transferring the encoded states. The ternary Shor’s algorithm can be implemented in one single step. Numerical simulation results show that the accuracy of the state transformations is about 0.9919. Project supported by the National Natural Science Foundation of China (Grant No. 61205108) and the High Performance Computing (HPC) Foundation of National University of Defense Technology, China.

  8. Investigation of the vibration spectrum of SbSI crystals in harmonic and in anharmonic approximations

    International Nuclear Information System (INIS)

    Audzijonis, A.; Zigas, L.; Vinokurova, I.V.; Farberovic, O.V.; Zaltauskas, R.; Cijauskas, E.; Pauliukas, A.; Kvedaravicius, A.

    2006-01-01

    The force constants of SbSI crystal have been calculated by the pseudo-potential method. The frequencies and normal coordinates of SbSI vibration modes along the c (z) direction have been determined in harmonic approximation. The potential energies of SbSI normal modes dependence on normal coordinates along the c (z) direction V(z) have been determined in anharmonic approximation, taking into account the interaction between the phonons. It has been found, that in the range of 30-120 cm -1 , the vibrational spectrum is determined by a V(z) double-well normal mode, but in the range of 120-350 cm -1 , it is determined by a V(z) single-well normal mode

  9. Accurate Anharmonic Zero-Point Energies for Some Combustion-Related Species from Diffusion Monte Carlo.

    Science.gov (United States)

    Harding, Lawrence B; Georgievskii, Yuri; Klippenstein, Stephen J

    2017-06-08

    Full-dimensional analytic potential energy surfaces based on CCSD(T)/cc-pVTZ calculations have been determined for 48 small combustion-related molecules. The analytic surfaces have been used in Diffusion Monte Carlo calculations of the anharmonic zero-point energies. The resulting anharmonicity corrections are compared to vibrational perturbation theory results based both on the same level of electronic structure theory and on lower-level electronic structure methods (B3LYP and MP2).

  10. Harmonic and Anharmonic Behaviour of a Simple Oscillator

    Science.gov (United States)

    O'Shea, Michael J.

    2009-01-01

    We consider a simple oscillator that exhibits harmonic and anharmonic regimes and analyse its behaviour over the complete range of possible amplitudes. The oscillator consists of a mass "m" fixed at the midpoint of a horizontal rope. For zero initial rope tension and small amplitude the period of oscillation, tau, varies as tau is approximately…

  11. Two-step approach to the dynamics of coupled anharmonic oscillators

    International Nuclear Information System (INIS)

    Chung, N. N.; Chew, L. Y.

    2009-01-01

    We have further extended the two-step approach developed by Chung and Chew [N. N. Chung and L. Y. Chew, Phys. Rev. A 76, 032113 (2007)] to the solution of the quantum dynamics of general systems of N-coupled anharmonic oscillators. The idea is to employ an optimized basis set to represent the dynamical quantum states of these oscillator systems. The set is generated via the action of the optimized Bogoliubov transformed bosonic operators on the optimal squeezed vacuum product state. The procedure requires (i) applying the two-step approach to the eigendecomposition of the time evolution operator and (ii) transforming the representation of the initial state from the original to the optimal bases. We have applied the formalism to examine the dynamics of squeezing and entanglement of several anharmonic oscillator systems.

  12. Anharmonic solution of Schrödinger time-independent equation

    Indian Academy of Sciences (India)

    243–261. Anharmonic solution of Schrödinger time-independent equation. MOHAMMED ASHRAFUL ISLAM1,2,∗ and JAMAL NAZRUL ISLAM1. 1Research Centre for Mathematical and Physical Sciences, University of Chittagong, Chittagong,. Bangladesh. 2Department of Mathematics, University of Chittagong, Chittagong, ...

  13. The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

    Science.gov (United States)

    Leib, Raz; Karniel, Amir; Nisky, Ilana

    2015-05-01

    During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.

  14. Anharmonic phonons and second-order phase-transitions by the stochastic self-consistent harmonic approximation

    Science.gov (United States)

    Mauri, Francesco

    Anharmonic effects can generally be treated within perturbation theory. Such an approach breaks down when the harmonic solution is dynamically unstable or when the anharmonic corrections of the phonon energies are larger than the harmonic frequencies themselves. This situation occurs near lattice-related second-order phase-transitions such as charge-density-wave (CDW) or ferroelectric instabilities or in H-containing materials, where the large zero-point motion of the protons results in a violation of the harmonic approximation. Interestingly, even in these cases, phonons can be observed, measured, and used to model transport properties. In order to treat such cases, we developed a stochastic implementation of the self-consistent harmonic approximation valid to treat anharmonicity in the nonperturbative regime and to obtain, from first-principles, the structural, thermodynamic and vibrational properties of strongly anharmonic systems. I will present applications to the ferroelectric transitions in SnTe, to the CWD transitions in NbS2 and NbSe2 (in bulk and monolayer) and to the hydrogen-bond symmetrization transition in the superconducting hydrogen sulfide system, that exhibits the highest Tc reported for any superconductor so far. In all cases we are able to predict the transition temperature (pressure) and the evolution of phonons with temperature (pressure). This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement No. 696656 GrapheneCore1.

  15. Internal molecular dynamics of LaI3. I. Potential energy function of vibrational modes in harmonic and anharmonic approximations

    International Nuclear Information System (INIS)

    Giricheva, N.I.; Girichev, G.V.; Smorodin, S.V.

    2007-01-01

    Scanning of potential energy surface in the LaI 3 molecule along normal coordinates are realized using the B3LYP/SDD,SDD method. The most anharmonicity is shown to have a potential function of non-planar oscillation ν 2 (A 2 ''). Effect of anharmonicity on the value of mean-square oscillation amplitudes and oscillation spectrum of the molecule is established. It is noted that the account of anharmonicity of potential functions leads to decreasing mean-square oscillation amplitudes [ru

  16. Harmonic force field for nitro compounds.

    Science.gov (United States)

    Bellido, Edson P; Seminario, Jorge M

    2012-06-01

    Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).

  17. Anharmonic rovibrational calculations of singlet cyclic C{sub 4} using a new ab initio potential and a quartic force field

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xiaohong; Bowman, Joel M., E-mail: jmbowma@emory.edu [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States); Huang, Xinchuan [SETI Institute, 189 Bernardo Ave, Suite 100, Mountain View, California 94043 (United States); Lee, Timothy J., E-mail: Timothy.J.Lee@nasa.gov [MS 245-1, NASA Ames Research Center, Mofffett Field, California 94035 (United States)

    2013-12-14

    We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C{sub 4}. Vibrational fundamentals, combinations, and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configuration-interaction (VCI) approach. Agreement is within 10 cm{sup −1} between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2-QFF and MM-QFF results is also good for the C{sub 4} combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of {sup 12}C{sub 4} and two C{sub 2v}-symmetry, single {sup 13}C-substituted isotopologues are presented, which may help identification of cyclic C{sub 4} in future experimental analyses or astronomical observations.

  18. A study of anharmonic al and nonlinear behaviours of vibrations of atomic nuclei; Etude des comportements anharmonioques et non lineaires des vibrations des noyaux atomiques

    Energy Technology Data Exchange (ETDEWEB)

    Volpe, M.C. [Caen Univ., 14 (France)

    1997-12-31

    Double Giant Resonances, vibrational states in which a Giant Resonance is excited on top of another Giant Resonance, have been in the last years the object of many theories and studies. Whereas the measured energies and widths of these states agree with a theoretical predictions, the measured excitation cross sections on the other hand are almost always larger than the calculated ones. The standard theoretical approaches are based both on a harmonic approximation for the collective motion on the nucleus and on its linear response to an external field. In this work the influence of anharmonicities and non-linearities in the external field on the excitation of Double Giant Resonances are studied. First, an oscillator model and an extension of the Lipkin-Meshkow-Glick model are used to study the effects of anharmonicities and non-linearities on the excitation probabilities. The results show that these terms can influence the excitation probability of the second excited state in a significant way. Secondly, these exactly soluble schematic models are used to study some of the approximations made in microscopic calculations based on boson expansion methods and also some aspects on the time-dependent mean field approach. Finally, a microscopic calculation of the Coulomb excitation cross sections of Double Giant Resonances is presented for several nuclei. It is found that, for {sup 208} Pb, the inclusion of anharmonicities and non-linearities and the consideration of many states that play a role in the excitation process give a satisfactory agreement between calculated and observed cross sections. (author). 113 refs.

  19. Phonon density of states and anharmonicity of UO2

    Science.gov (United States)

    Pang, Judy W. L.; Chernatynskiy, Aleksandr; Larson, Bennett C.; Buyers, William J. L.; Abernathy, Douglas L.; McClellan, Kenneth J.; Phillpot, Simon R.

    2014-03-01

    Phonon density of states (PDOS) measurements have been performed on polycrystalline UO2 at 295 and 1200 K using time-of-flight inelastic neutron scattering to investigate the impact of anharmonicity on the vibrational spectra and to benchmark ab initio PDOS simulations performed on this strongly correlated Mott insulator. Time-of-flight PDOS measurements include anharmonic linewidth broadening, inherently, and the factor of ˜7 enhancement of the oxygen spectrum relative to the uranium component by the increased neutron sensitivity to the oxygen-dominated optical phonon modes. The first-principles simulations of quasiharmonic PDOS spectra were neutron weighted and anharmonicity was introduced in an approximate way by convolution with wave-vector-weighted averages over our previously measured phonon linewidths for UO2, which are provided in numerical form. Comparisons between the PDOS measurements and the simulations show reasonable agreement overall, but they also reveal important areas of disagreement for both high and low temperatures. The discrepancies stem largely from a ˜10 meV compression in the overall bandwidth (energy range) of the oxygen-dominated optical phonons in the simulations. A similar linewidth-convoluted comparison performed with the PDOS spectrum of Dolling et al. obtained by shell-model fitting to their historical phonon dispersion measurements shows excellent agreement with the time-of-flight PDOS measurements reported here. In contrast, we show by comparisons of spectra in linewidth-convoluted form that recent first-principles simulations for UO2 fail to account for the PDOS spectrum determined from the measurements of Dolling et al. These results demonstrate PDOS measurements to be stringent tests for ab inito simulations of phonon physics in UO2 and they indicate further the need for advances in theory to address the lattice dynamics of UO2.

  20. Induced forces in the gravitational field

    International Nuclear Information System (INIS)

    Voracek, P.

    1979-01-01

    In this paper the expression for the magnitude of the so-called induced force, acting on a mass particle, is deduced. The origin of this force is causally connected to the increase of the rest mass of the particle in the gravitational field. (orig.)

  1. Controlling Casimir force via coherent driving field

    Science.gov (United States)

    Ahmad, Rashid; Abbas, Muqaddar; Ahmad, Iftikhar; Qamar, Sajid

    2016-04-01

    A four level atom-field configuration is used to investigate the coherent control of Casimir force between two identical plates made up of chiral atomic media and separated by vacuum of width d. The electromagnetic chirality-induced negative refraction is obtained via atomic coherence. The behavior of Casimir force is investigated using Casimir-Lifshitz formula. It is noticed that Casimir force can be switched from repulsive to attractive and vice versa via coherent control of the driving field. This switching feature provides new possibilities of using the repulsive Casimir force in the development of new emerging technologies, such as, micro-electro-mechanical and nano-electro-mechanical systems, i.e., MEMS and NEMS, respectively.

  2. Hierarchical atom type definitions and extensible all-atom force fields.

    Science.gov (United States)

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  3. Evaluating amber force fields using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

    NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

  4. Anharmonic phonon-phonon scattering modeling of three-dimensional atomistic transport: An efficient quantum treatment

    Science.gov (United States)

    Lee, Y.; Bescond, M.; Logoteta, D.; Cavassilas, N.; Lannoo, M.; Luisier, M.

    2018-05-01

    We propose an efficient method to quantum mechanically treat anharmonic interactions in the atomistic nonequilibrium Green's function simulation of phonon transport. We demonstrate that the so-called lowest-order approximation, implemented through a rescaling technique and analytically continued by means of the Padé approximants, can be used to accurately model third-order anharmonic effects. Although the paper focuses on a specific self-energy, the method is applicable to a very wide class of physical interactions. We apply this approach to the simulation of anharmonic phonon transport in realistic Si and Ge nanowires with uniform or discontinuous cross sections. The effect of increasing the temperature above 300 K is also investigated. In all the considered cases, we are able to obtain a good agreement with the routinely adopted self-consistent Born approximation, at a remarkably lower computational cost. In the more complicated case of high temperatures (≫300 K), we find that the first-order Richardson extrapolation applied to the sequence of the Padé approximants N -1 /N results in a significant acceleration of the convergence.

  5. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

    Science.gov (United States)

    Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael F

    2012-02-14

    Molecular dynamics simulations of cellulose have recently become more prevalent due to increased interest in renewable energy applications, and many atomistic and coarse-grained force fields exist that can be applied to cellulose. However, to date no systematic comparison between carbohydrate force fields has been conducted for this important system. To that end, we present a molecular dynamics simulation study of hydrated, 36-chain cellulose Iβ microfibrils at room temperature with three carbohydrate force fields (CHARMM35, GLYCAM06, and Gromos 45a4) up to the near-microsecond time scale. Our results indicate that each of these simulated microfibrils diverge from the cellulose Iβ crystal structure to varying degrees under the conditions tested. The CHARMM35 and GLYCAM06 force fields eventually result in structures similar to those observed at 500 K with the same force fields, which are consistent with the experimentally observed high-temperature behavior of cellulose I. The third force field, Gromos 45a4, produces behavior significantly different from experiment, from the other two force fields, and from previously reported simulations with this force field using shorter simulation times and constrained periodic boundary conditions. For the GLYCAM06 force field, initial hydrogen-bond conformations and choice of electrostatic scaling factors significantly affect the rate of structural divergence. Our results suggest dramatically different time scales for convergence of properties of interest, which is important in the design of computational studies and comparisons to experimental data. This study highlights that further experimental and theoretical work is required to understand the structure of small diameter cellulose microfibrils typical of plant cellulose.

  6. Investigating vibrational anharmonic couplings in cyanide-bridged transition metal mixed valence complexes using two-dimensional infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Slenkamp, Karla M.; Lynch, Michael S.; Van Kuiken, Benjamin E.; Brookes, Jennifer F.; Bannan, Caitlin C.; Daifuku, Stephanie L.; Khalil, Munira, E-mail: mkhalil@chem.washington.edu [Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195 (United States)

    2014-02-28

    Using polarization-selective two-dimensional infrared (2D IR) spectroscopy, we measure anharmonic couplings and angles between the transition dipole moments of the four cyanide stretching (ν{sub CN}) vibrations found in [(NH{sub 3}){sub 5}Ru{sup III}NCFe{sup II}(CN){sub 5}]{sup −} (FeRu) dissolved in D{sub 2}O and formamide and [(NC){sub 5}Fe{sup II}CNPt{sup IV}(NH{sub 3}){sub 4}NCFe{sup II}(CN){sub 5}]{sup 4−} (FePtFe) dissolved in D{sub 2}O. These cyanide-bridged transition metal complexes serve as model systems for studying the role of high frequency vibrational modes in ultrafast photoinduced charge transfer reactions. Here, we focus on the spectroscopy of the ν{sub CN} modes in the electronic ground state. The FTIR spectra of the ν{sub CN} modes of the bimetallic and trimetallic systems are strikingly different in terms of frequencies, amplitudes, and lineshapes. The experimental 2D IR spectra of FeRu and FePtFe and their fits reveal a set of weakly coupled anharmonic ν{sub CN} modes. The vibrational mode anharmonicities of the individual ν{sub CN} modes range from 14 to 28 cm{sup −1}. The mixed-mode anharmonicities range from 2 to 14 cm{sup −1}. In general, the bridging ν{sub CN} mode is most weakly coupled to the radial ν{sub CN} mode, which involves the terminal CN ligands. Measurement of the relative transition dipole moments of the four ν{sub CN} modes reveal that the FeRu molecule is almost linear in solution when dissolved in formamide, but it assumes a bent geometry when dissolved in D{sub 2}O. The ν{sub CN} modes are modelled as bilinearly coupled anharmonic oscillators with an average coupling constant of 6 cm{sup −1}. This study elucidates the role of the solvent in modulating the molecular geometry and the anharmonic vibrational couplings between the ν{sub CN} modes in cyanide-bridged transition metal mixed valence complexes.

  7. The curious case of cuprous chloride: Giant thermal resistance and anharmonic quasiparticle spectra driven by dispersion nesting

    Science.gov (United States)

    Mukhopadhyay, Saikat; Bansal, Dipanshu; Delaire, Olivier; Perrodin, Didier; Bourret-Courchesne, Edith; Singh, David J.; Lindsay, Lucas

    2017-09-01

    Strongly anharmonic phonon properties of CuCl are investigated with inelastic neutron-scattering measurements and first-principles simulations. An unusual quasiparticle spectral peak emerges in the phonon density of states with increasing temperature, in both simulations and measurements, emanating from exceptionally strong coupling between conventional phonon modes. Associated with this strong anharmonicity, the lattice thermal conductivity of CuCl is extremely low and exhibits anomalous, nonmonotonic pressure dependence. We show how this behavior arises from the structure of the phonon dispersions augmenting the phase space available for anharmonic three-phonon scattering processes, and contrast this mechanism with common arguments based on negative Grüneisen parameters. These results demonstrate the importance of considering intrinsic phonon-dispersion structure toward understanding scattering processes and designing new ultralow thermal conductivity materials.

  8. Raman scattering study of the anharmonic effects in CeO2-y nanocrystals

    Science.gov (United States)

    Popović, Z. V.; Dohčević-Mitrović, Z.; Cros, A.; Cantarero, A.

    2007-12-01

    We have studied the temperature dependence of the F2g Raman mode phonon frequency and broadening in CeO2-y nanocrystals. The phonon softening and phonon linewidth are calculated using a model which takes into account the three-and four-phonon anharmonic processes. A detailed comparison of the experimental data with theoretical calculations revealed the predominance of four-phonon anharmonic processes in the temperature dependence of the phonon energy and broadening of the nanocrystals. On the other hand, three-phonon processes dominate the temperature behavior of phonons in polycrystalline samples. The anti-Stokes/Stokes peak intensity ratio was also investigated and found to be smaller for nanosized CeO2 powders than in the bulk counterpart.

  9. Raman scattering study of the anharmonic effects in CeO2-y nanocrystals

    International Nuclear Information System (INIS)

    Popovic, Z V; Dohcevic-Mitrovic, Z; Cros, A; Cantarero, A

    2007-01-01

    We have studied the temperature dependence of the F 2g Raman mode phonon frequency and broadening in CeO 2-y nanocrystals. The phonon softening and phonon linewidth are calculated using a model which takes into account the three-and four-phonon anharmonic processes. A detailed comparison of the experimental data with theoretical calculations revealed the predominance of four-phonon anharmonic processes in the temperature dependence of the phonon energy and broadening of the nanocrystals. On the other hand, three-phonon processes dominate the temperature behavior of phonons in polycrystalline samples. The anti-Stokes/Stokes peak intensity ratio was also investigated and found to be smaller for nanosized CeO 2 powders than in the bulk counterpart

  10. Force fields for silicas and aluminophosphates based on ab initio calculations

    NARCIS (Netherlands)

    Beest, van B.W.H.; Kramer, G.J.; Santen, van R.A.

    1990-01-01

    Authors address the problem of finding interat. force fields for silicas from ab initio calcns. on small clusters. The force field cannot be detd. from cluster data alone; incorporation of bulk-system information into the force field remains essential. Bearing this in mind, authors derive a force

  11. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Science.gov (United States)

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  12. Preface: Special Topic: From Quantum Mechanics to Force Fields

    Science.gov (United States)

    Piquemal, Jean-Philip; Jordan, Kenneth D.

    2017-10-01

    This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

  13. Approximate photochemical dynamics of azobenzene with reactive force fields

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-01

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work).

  14. Force-field compensation in a manual tracking task.

    Directory of Open Access Journals (Sweden)

    Valentina Squeri

    2010-06-01

    Full Text Available This study addresses force/movement control in a dynamic "hybrid" task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%, which is a function of the implicit accuracy of the tracking task.

  15. Ponderomotive Forces in Cosmos

    Science.gov (United States)

    Lundin, R.; Guglielmi, A.

    2006-12-01

    This review is devoted to ponderomotive forces and their importance for the acceleration of charged particles by electromagnetic waves in space plasmas. Ponderomotive forces constitute time-averaged nonlinear forces acting on a media in the presence of oscillating electromagnetic fields. Ponderomotive forces represent a useful analytical tool to describe plasma acceleration. Oscillating electromagnetic fields are also related with dissipative processes, such as heating of particles. Dissipative processes are, however, left outside these discussions. The focus will be entirely on the (conservative) ponderomotive forces acting in space plasmas. The review consists of seven sections. In Section 1, we explain the rational for using the auxiliary ponderomotive forces instead of the fundamental Lorentz force for the study of particle motions in oscillating fields. In Section 2, we present the Abraham, Miller, Lundin-Hultqvist and Barlow ponderomotive forces, and the Bolotovsky-Serov ponderomotive drift. The hydrodynamic, quasi-hydrodynamic, and ‘`test-particle’' approaches are used for the study of ponderomotive wave-particle interaction. The problems of self-consistency and regularization are discussed in Section 3. The model of static balance of forces (Section 4) exemplifies the interplay between thermal, gravitational and ponderomotive forces, but it also introduces a set of useful definitions, dimensionless parameters, etc. We analyze the Alfvén and ion cyclotron waves in static limit with emphasis on the specific distinction between traveling and standing waves. Particular attention has been given to the impact of traveling Alfvén waves on the steady state anabatic wind that blows over the polar regions (Section~5). We demonstrate the existence of a wave-induced cold anabatic wind. We also show that, at a critical point, the ponderomotive acceleration of the wind is a factor of 3 greater than the thermal acceleration. Section 6 demonstrates various

  16. Fluctuations and Anharmonicity in Lead Iodide Perovskites from Molecular Dynamics Supercell Simulationss

    KAUST Repository

    Carignano, Marcelo André s; Aravindh, S. Assa; Roqan, Iman S.; Even, Jacky; Katan, Claudine

    2017-01-01

    cations as the temperature is decreased from 450 K. The reverse transformation from tetragonal to cubic is also monitored through the large distribution of the octahedral tilting angles accompanied by an increase in the anharmonicity of the iodine atoms

  17. Mellin-Barnes regularization, Borel summation and the Bender-Wu asymptotics for the anharmonic oscillator

    International Nuclear Information System (INIS)

    Kowalenko, V.; Rawlinson, A.A.

    1998-01-01

    We introduce the numerical technique of Mellin-Barnes regularization, which can be used to evaluate both convergent and divergent series. The technique is shown to be numerically equivalent to the corresponding results obtained by Borel summation. Both techniques are then applied to the Bender-Wu formula, which represents an asymptotic expansion for the energy levels of the anharmonic oscillator. We find that this formula is unable to give accurate values for the ground state energy, particularly when the coupling is greater than 0.1. As a consequence, the inability of the Bender-Wu formula to yield exact values for the energy level of the anharmonic oscillator cannot be attributed to its asymptotic nature. (authors)

  18. Software Process Improvement Using Force Field Analysis ...

    African Journals Online (AJOL)

    An improvement plan is then drawn and implemented. This paper studied the state of Nigerian software development organizations based on selected attributes. Force field analysis is used to partition the factors obtained into driving and restraining forces. An attempt was made to improve the software development process ...

  19. Generalized theory of spin fluctuations in itinerant electron magnets: Crucial role of spin anharmonicity

    International Nuclear Information System (INIS)

    Solontsov, A.

    2015-01-01

    The paper critically overviews the recent developments of the theory of spatially dispersive spin fluctuations (SF) in itinerant electron magnetism with particular emphasis on spin-fluctuation coupling or spin anharmonicity. It is argued that the conventional self-consistent renormalized (SCR) theory of spin fluctuations is usually used aside of the range of its applicability actually defined by the constraint of weak spin anharmonicity based on the random phase approximation (RPA) arguments. An essential step in understanding SF in itinerant magnets beyond RPA-like arguments was made recently within the soft-mode theory of SF accounting for strong spin anharmonicity caused by zero-point SF. In the present paper we generalize it to apply for a wider range of temperatures and regimes of SF and show it to lead to qualitatively new results caused by zero-point effects. - Highlights: • We review the spin-fluctuation theory of itinerant electron magnets with account of zero-point effects. • We generalize the existing theory to account for different regimes of spin fluctuations. • We show that zero-point spin fluctuations play a crucial role in both low- and high-temperature properties of metallic magnets. • We argue that a new scheme of calculation of ground state properties of magnets is needed including zero-point effects

  20. Force-free magnetic fields - The magneto-frictional method

    Science.gov (United States)

    Yang, W. H.; Sturrock, P. A.; Antiochos, S. K.

    1986-01-01

    The problem under discussion is that of calculating magnetic field configurations in which the Lorentz force j x B is everywhere zero, subject to specified boundary conditions. We choose to represent the magnetic field in terms of Clebsch variables in the form B = grad alpha x grad beta. These variables are constant on any field line so that each field line is labeled by the corresponding values of alpha and beta. When the field is described in this way, the most appropriate choice of boundary conditions is to specify the values of alpha and beta on the bounding surface. We show that such field configurations may be calculated by a magneto-frictional method. We imagine that the field lines move through a stationary medium, and that each element of magnetic field is subject to a frictional force parallel to and opposing the velocity of the field line. This concept leads to an iteration procedure for modifying the variables alpha and beta, that tends asymptotically towards the force-free state. We apply the method first to a simple problem in two rectangular dimensions, and then to a problem of cylindrical symmetry that was previously discussed by Barnes and Sturrock (1972). In one important respect, our new results differ from the earlier results of Barnes and Sturrock, and we conclude that the earlier article was in error.

  1. Internal oscillation frequencies and anharmonic effects for the double sine-Gordon kink

    DEFF Research Database (Denmark)

    Salerno, M.; Samuelsen, Mogens Rugholm

    1989-01-01

    A simple derivation of the small oscillation frequency around 4π-kink solutions of the double sine-Gordon equation is presented. Small corrections to these frequencies due to anharmonic effects are also numerically and analytically investigated. The analysis is based on energetic considerations...

  2. High-pressure phase diagram of hydrogen and deuterium sulfides from first principles: Structural and vibrational properties including quantum and anharmonic effects

    Science.gov (United States)

    Bianco, Raffaello; Errea, Ion; Calandra, Matteo; Mauri, Francesco

    2018-06-01

    We study the structural and vibrational properties of the high-temperature superconducting sulfur trihydride and trideuteride in the high-pressure I m 3 ¯m and R 3 m phases by first-principles density-functional-theory calculations. On lowering pressure, the rhombohedral transition I m 3 ¯m →R 3 m is expected, with hydrogen-bond desymmetrization and occurrence of trigonal lattice distortion. With both Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional, in hydrostatic conditions we find that, contrary to what is suggested in some recent experiments, if the rhombohedral distortion exists it affects mainly the hydrogen bonds, whereas the resulting cell distortion is minimal. We estimate that the occurrence of a stress anisotropy of approximately 10 % could explain this discrepancy. Assuming hydrostatic conditions, we calculate the critical pressure at which the rhombohedral transition occurs. Quantum and anharmonic effects, which are relevant in this system, are included at nonperturbative level with the stochastic self-consistent harmonic approximation. Within this approach, we determine the transition pressure by calculating the free-energy Hessian, a method that allows to estimate the critical pressure with much higher precision (and much lower computational cost) compared with the free-energy "finite-difference" approach previously used. Using PBE and BLYP, we find that quantum anharmonic effects are responsible for a strong reduction of the critical pressure with respect to the one obtained with the classical harmonic approach. Interestingly, for the two functionals, even if the transition pressures at classical harmonic level differ by 83 GPa, the transition pressures including quantum anharmonic effects differ only by 23 GPa. Moreover, we observe a prominent isotope effect, as we estimate higher transition pressure for D3S than for H3S . Finally, within the stochastic self-consistent harmonic approximation, with PBE

  3. Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections

    International Nuclear Information System (INIS)

    Choe, G.S.; Cheng, C.Z.

    2002-01-01

    In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

  4. Nanomaterials for in vivo imaging of mechanical forces and electrical fields

    Science.gov (United States)

    Mehlenbacher, Randy D.; Kolbl, Rea; Lay, Alice; Dionne, Jennifer A.

    2018-02-01

    Cellular signalling is governed in large part by mechanical forces and electromagnetic fields. Mechanical forces play a critical role in cell differentiation, tissue organization and diseases such as cancer and heart disease; electrical fields are essential for intercellular communication, muscle contraction, neural signalling and sensory perception. Therefore, quantifying a biological system's forces and fields is crucial for understanding physiology and disease pathology and for developing medical tools for repair and recovery. This Review highlights advances in sensing mechanical forces and electrical fields in vivo, focusing on optical probes. The emergence of biocompatible optical probes, such as genetically encoded voltage indicators, molecular rotors, fluorescent dyes, semiconducting nanoparticles, plasmonic nanoparticles and lanthanide-doped upconverting nanoparticles, offers exciting opportunities to push the limits of spatial and temporal resolution, stability, multi-modality and stimuli sensitivity in bioimaging. We further discuss the materials design principles behind these probes and compare them across various metrics to facilitate sensor selection. Finally, we examine which advances are necessary to fully unravel the role of mechanical forces and electrical fields in vivo, such as the ability to probe the vectorial nature of forces, the development of combined force and field sensors, and the design of efficient optical actuators.

  5. Martini Force Field Parameters for Glycolipids

    NARCIS (Netherlands)

    Lopez, Cesar A.; Sovova, Zofie; van Eerden, Floris J.; de Vries, Alex H.; Marrink, Siewert J.

    We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its

  6. The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.

    Science.gov (United States)

    Bende, Attila; Muntean, Cristina M

    2014-03-01

    The theoretical IR and Raman spectra of the guanine-cytosine DNA base pairs in Watson-Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H⁺ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

  7. Raman scattering study of the anharmonic effects in CeO{sub 2-y} nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Popovic, Z V [Center for Solid State Physics and New Materials, Institute of Physics, Pregrevica 118, 11080 Belgrade (Serbia); Dohcevic-Mitrovic, Z [Center for Solid State Physics and New Materials, Institute of Physics, Pregrevica 118, 11080 Belgrade (Serbia); Cros, A [Materials Science Institute, University of Valencia, P O Box 22085, E-46071, Valencia (Spain); Cantarero, A [Materials Science Institute, University of Valencia, P O Box 22085, E-46071, Valencia (Spain)

    2007-12-12

    We have studied the temperature dependence of the F{sub 2g} Raman mode phonon frequency and broadening in CeO{sub 2-y} nanocrystals. The phonon softening and phonon linewidth are calculated using a model which takes into account the three-and four-phonon anharmonic processes. A detailed comparison of the experimental data with theoretical calculations revealed the predominance of four-phonon anharmonic processes in the temperature dependence of the phonon energy and broadening of the nanocrystals. On the other hand, three-phonon processes dominate the temperature behavior of phonons in polycrystalline samples. The anti-Stokes/Stokes peak intensity ratio was also investigated and found to be smaller for nanosized CeO{sub 2} powders than in the bulk counterpart.

  8. Generalized force in classical field theory. [Euler-Lagrange equations

    Energy Technology Data Exchange (ETDEWEB)

    Krause, J [Universidad Central de Venezuela, Caracas

    1976-02-01

    The source strengths of the Euler-Lagrange equations, for a system of interacting fields, are heuristically interpreted as generalized forces. The canonical form of the energy-momentum tensor thus consistently appears, without recourse to space-time symmetry arguments. A concept of 'conservative' generalized force in classical field theory is also briefly discussed.

  9. Anharmonic potential in the oscillator representation

    International Nuclear Information System (INIS)

    Dineykhan, M.; Efimov, G.V.

    1994-01-01

    In the non relativistic and relativized Schroedinger equation the Wick ordering method called the oscillator representation is proposed to calculate the energy spectrum for a wide class of potentials allowing the existence of a bound state. The oscillator representation method gives a unique regular way to describe and calculate the energy levels of ground as well as orbital and radial excitation states for a wide class of potentials. The results of the zeroth approximation oscillator representation are in good agreement with the exact values for the anharmonic potentials. The oscillator representation method was applied to the relativized Schroedinger equation too. The perturbation series converges fairly fast, i.e., the highest perturbation corrections over the interaction Hamiltonian are small enough. 29 refs.; 4 tabs. (author)

  10. Force-Field Prediction of Materials Properties in Metal-Organic Frameworks

    Science.gov (United States)

    2016-01-01

    In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can be observed when looking at properties sensitive to framework vibrational modes. This observation is more pronounced upon the introduction of framework charges. PMID:28008758

  11. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  12. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

    The polarized absorption spectra of the sucrose crystal in the 5300 - 7300 cm -1 region have been measured. The assignments of all the eight OH stretching overtones are proposed and their mechanical anharmonicities are estimated. The discrepancies from the oriented gas model (OGM) in the observed relative band intensities, especially of the -CH vibrations, are assumed to be connected with vibronic couplings enhanced by the helical arrangement of molecules joined by hydrogen bondings. It seems that this kind of interactions might be important for the second harmonic generation (SHG) by the sucrose crystal.

  13. Jacobian elliptic wave solutions in an anharmonic molecular crystal model

    International Nuclear Information System (INIS)

    Teh, C.G.R.; Lee, B.S.; Koo, W.K.

    1997-07-01

    Explicit Jacobian elliptic wave solutions are found in the anharmonic molecular crystal model for both the continuum limit and discrete modes. This class of wave solutions include the famous pulse-like and kink-like solitary modes. We would also like to report on the existence of some highly discrete staggered solitary wave modes not found in the continuum limit. (author). 9 refs, 1 fig

  14. Energy eigenvalues and squeezing properties of general systems of coupled quantum anharmonic oscillators

    International Nuclear Information System (INIS)

    Chung, N. N.; Chew, L. Y.

    2007-01-01

    We have generalized the two-step approach to the solution of systems of N coupled quantum anharmonic oscillators. By using the squeezed vacuum state of each individual oscillator, we construct the tensor product state, and obtain the optimal squeezed vacuum product state through energy minimization. We then employ this optimal state and its associated bosonic operators to define a basis set to construct the Heisenberg matrix. The diagonalization of the matrix enables us to obtain the energy eigenvalues of the coupled oscillators. In particular, we have applied our formalism to determine the eigenenergies of systems of two coupled quantum anharmonic oscillators perturbed by a general polynomial potential, as well as three and four coupled systems. Furthermore, by performing a first-order perturbation analysis about the optimal squeezed vacuum product state, we have also examined into the squeezing properties of two coupled oscillator systems

  15. Dynamics of solar magnetic fields. VI. Force-free magnetic fields and motions of magnetic foot-points

    International Nuclear Information System (INIS)

    Low, B.C.; Nakagawa, Y.

    1975-01-01

    A mathematical model is developed to consider the evolution of force-free magnetic fields in relation to the displacements of their foot-points. For a magnetic field depending on only two Cartesian coordinates and time, the problem reduces to solving a nonlinear elliptic partial differential equation. As illustration of the physical process, two specific examples of evolving force-free magnetic fields are examined in detail, one evolving with rising and the other with descending field lines. It is shown that these two contrasting behaviors of the field lines correspond to sheared motions of their foot-points of quite different characters. The physical implications of these two examples of evolving force-free magnetic fields are discussed. (auth)

  16. Equivalence of classical spins and Hartree-Fock-Bogoliubov approximation of the Fermionic Anharmonic Oscillator

    International Nuclear Information System (INIS)

    Thomaz, M.T.; Toledo Piza, A.F.R. de

    1994-01-01

    We show that the Hartree-Fock-Bogoliubov (alias Gaussian) approximation of the initial condition problem of the Fermionic Anharmonic Oscillator i equivalent to a bosonic Hamiltonian system of two classical spin. (author)

  17. Perspective: Ab initio force field methods derived from quantum mechanics

    Science.gov (United States)

    Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

    2018-03-01

    It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

  18. Rotational states of Bose gases with attractive interactions in anharmonic traps

    International Nuclear Information System (INIS)

    Lundh, Emil; Collin, Anssi; Suominen, Kalle-Antti

    2004-01-01

    A rotated and harmonically trapped Bose gas with attractive interactions is expected to either remain stationary or escape from the trap. Here we report that, on the contrary, in an anharmonic trapping potential the Bose gas with attractive interactions responds to external rotation very differently, namely, through center-of-mass motion or by formation of vortices

  19. Effect of anharmonicity and Debye-Waller factor on the superconductivity of PdHsub(x) and PdDsub(x)

    International Nuclear Information System (INIS)

    Griessen, R.; Groot, D.G. de

    1983-01-01

    On the basis of existing superconducting tunnelling, neutron scattering, electrical resistivity and Raman scattering data and new thermal expansion, elastic moduli and point-contact spectroscopy data it is concluded that the anharmonicity of the proton (deuteron)-palladium potential is such that Msub(H)#betta#sub(H) 2 /(Msub(D)#betta#sub(D) 2 ) = 1.12 +- 0.05 Msub(H(D)) is the mass and #betta#sub(H(D)) the frequency of the vibration of hydrogen (deuterium). This anharmonicity is approximately 2 times too weak to reproduce the observed inverse isotope effect in the superconducting transition temperature of concentrated PdHsub(x) and PdDsub(x) alloys. Within a pseudopotential formalism it is shown that the Debye-Waller factor arising from the large zero-point amplitude of the interstitial hydrogen (deuterium) leads to a contribution to the inverse isotope effect in Tsub(c) which is as large as that of anharmonicity alone. (Auth.)

  20. Anharmonic correlated Debye model high-order expanded interatomic effective potential and Debye-Waller factors of bcc crystals

    Energy Technology Data Exchange (ETDEWEB)

    Van Hung, Nguyen, E-mail: hungnv@vnu.edu.vn [Department of Physics, Hanoi University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi (Viet Nam); Hue, Trinh Thi [Department of Physics, Hanoi University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi (Viet Nam); Khoa, Ha Dang [School of Engineering Physics, Hanoi University of Science and Technology, 1 Dai Co Viet, Hanoi (Viet Nam); Vuong, Dinh Quoc [Quang Ninh Education & Training Department, Nguyen Van Cu, Ha Long, Quang Ninh (Viet Nam)

    2016-12-15

    High-order expanded interatomic effective potential and Debye-Waller factors (DWFs) for local vibrational amplitudes in X-ray absorption fine structure (XAFS) of bcc crystals have been studied based on the anharmonic correlated Debye model. DWFs are presented in terms of cumulant expansion up to the fourth order and the many-body effects are taken into account in the present one-dimensional model based on the first shell near neighbor contribution approach used in the derivations of the anharmonic effective potential and XAFS cumulants where Morse potential is assumed to describe the single-pair atomic interaction. Analytical expressions for the dispersion relation, correlated Debye frequency and temperature and four first temperature-dependent XAFS cumulants have been derived based on the many-body perturbation approach. Thermodynamic properties and anharmonic effects in XAFS of bcc crystals described by the obtained cumulants have been in detail discussed. The advantage and efficiency of the present theory are illustrated by good agreement of the numerical results for Mo, Fe and W with experiment.

  1. A new united atom force field for adsorption of alkenes in zeolites

    NARCIS (Netherlands)

    Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.

    2008-01-01

    A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we

  2. Solitons in a random force field

    International Nuclear Information System (INIS)

    Bass, F.G.; Konotop, V.V.; Sinitsyn, Y.A.

    1985-01-01

    We study the dynamics of a soliton of the sine-Gordon equation in a random force field in the adiabatic approximation. We obtain an Einstein-Fokker equation and find the distribution function for the soliton parameters which we use to evaluate its statistical characteristics. We derive an equation for the averaged functions of the soliton parameters. We determine the limits of applicability of the delta-correlated in time random field approximation

  3. Relativistic derivation of the ponderomotive force produced by two intense laser fields

    International Nuclear Information System (INIS)

    Stroscio, M.A.

    1985-01-01

    The ponderomotive force plays a fundamental role in the absorption of laser light on self-consistent plasma density profiles, in multiple-photon ionization, and in intense field electrodynamics. The relativistic corrections to the ponderomotive force of a transversely polarized electromagnetic wave lead to an approximately 20-percent reduction in the single particle ponderomotive force produced by a 10-γm 10 16 -W/cm 2 laser field. Recent experimental investigations are based on using two intense laser fields to produce desired lasermatter interactions. This paper presents the first derivation of the nonlinear relativistic ponderomotive force produced by two intense laser fields. The results demonstrate that relativistic ponderomotive forces are not additive

  4. Improved Parameters for the Martini Coarse-Grained Protein Force Field

    NARCIS (Netherlands)

    de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

    The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too

  5. Thermodynamic properties for applications in chemical industry via classical force fields.

    Science.gov (United States)

    Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran

    2012-01-01

    Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.

  6. Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections; TOPICAL

    International Nuclear Information System (INIS)

    G.S. Choe; C.Z. Cheng

    2002-01-01

    In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

  7. Steady-state mechanical squeezing and ground-state cooling of a Duffing anharmonic oscillator in an optomechanical cavity assisted by a nonlinear medium

    Science.gov (United States)

    Momeni, F.; Naderi, M. H.

    2018-05-01

    In this paper, we study theoretically a hybrid optomechanical system consisting of a degenerate optical parametric amplifier inside a driven optical cavity with a moving end mirror which is modeled as a stiffening Duffing-like anharmonic quantum mechanical oscillator. By providing analytical expressions for the critical values of the system parameters corresponding to the emergence of the multistability behavior in the steady-state response of the system, we show that the stiffening mechanical Duffing anharmonicity reduces the width of the multistability region while the optical parametric nonlinearity can be exploited to drive the system toward the multistability region. We also show that for appropriate values of the mechanical anharmonicity strength the steady-state mechanical squeezing and the ground-state cooling of the mechanical resonator can be achieved. Moreover, we find that the presence of the nonlinear gain medium can lead to the improvement of the mechanical anharmonicity-induced cooling of the mechanical motion, as well as to the mechanical squeezing beyond the standard quantum limit of 3 dB.

  8. Novel concepts in near-field optics: from magnetic near-field to optical forces

    Science.gov (United States)

    Yang, Honghua

    Driven by the progress in nanotechnology, imaging and spectroscopy tools with nanometer spatial resolution are needed for in situ material characterizations. Near-field optics provides a unique way to selectively excite and detect elementary electronic and vibrational interactions at the nanometer scale, through interactions of light with matter in the near-field region. This dissertation discusses the development and applications of near-field optical imaging techniques, including plasmonic material characterization, optical spectral nano-imaging and magnetic field detection using scattering-type scanning near-field optical microscopy (s-SNOM), and exploring new modalities of optical spectroscopy based on optical gradient force detection. Firstly, the optical dielectric functions of one of the most common plasmonic materials---silver is measured with ellipsometry, and analyzed with the Drude model over a broad spectral range from visible to mid-infrared. This work was motivated by the conflicting results of previous measurements, and the need for accurate values for a wide range of applications of silver in plasmonics, optical antennas, and metamaterials. This measurement provides a reference for dielectric functions of silver used in metamaterials, plasmonics, and nanophotonics. Secondly, I implemented an infrared s-SNOM instrument for spectroscopic nano-imaging at both room temperature and low temperature. As one of the first cryogenic s-SNOM instruments, the novel design concept and key specifications are discussed. Initial low-temperature and high-temperature performances of the instrument are examined by imaging of optical conductivity of vanadium oxides (VO2 and V2O 3) across their phase transitions. The spectroscopic imaging capability is demonstrated on chemical vibrational resonances of Poly(methyl methacrylate) (PMMA) and other samples. The third part of this dissertation explores imaging of optical magnetic fields. As a proof-of-principle, the magnetic

  9. Ponderomotive force, magnetic fields and hydrodynamics of laser produced plasmas

    International Nuclear Information System (INIS)

    Bobin, J.-L.; Wee Woo; Degroot, J.-S.

    1977-01-01

    Nonlinear effects deeply change the structure of a laser driven plasma flow. For high intensities, the radiation pressure should be taken into account. It acts through a ponderomotive force proportional to the electron density and to the gradient of the mean electric field energy density of the incident wave. Static magnetic fields originate from a term in the ponderomotive force which includes radiation absorption and whose curl is non zero. The basic properties of the structure are determined analytically in the absence of thermal conductivity and magnetic fields: steep density gradient close to the cut-off density, shelf at lower densities. The conditions of a steady state regime are set up. The isothermal case is specially investigated. It is shown that the cavities which are created in a motionless plasma may disappear due to the onset of a flow. Regions in which electromagnetic forces arising from the static field compensate the ponderomotive force are determined. The subsequent effects on the flow itself are studied [fr

  10. Energy buildup in sheared force-free magnetic fields

    Science.gov (United States)

    Wolfson, Richard; Low, Boon C.

    1992-01-01

    Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.

  11. Computer Program for Inelastic Neutron Scattering by an Anharmonic Crystal

    International Nuclear Information System (INIS)

    Bohlin, L.; Ebbsjoe, I.; Hoegberg, T.

    1969-02-01

    A description is given of the program SAW (Shift and Width), which calculates the energy-dependent shift and width of the intensity peaks obtained for thermal neutrons scattered inelastically by an anharmonic crystal. The program has been coded in FORTRAN IV and may be applied to every solid with a monatomic face-centered cubic lattice where the intermolecular interactions can be described by a centro-symmetrical potential. Interactions beyond third neighbours are neglected

  12. Computer Program for Inelastic Neutron Scattering by an Anharmonic Crystal

    Energy Technology Data Exchange (ETDEWEB)

    Bohlin, L; Ebbsjoe, I; Hoegberg, T

    1969-02-15

    A description is given of the program SAW (Shift and Width), which calculates the energy-dependent shift and width of the intensity peaks obtained for thermal neutrons scattered inelastically by an anharmonic crystal. The program has been coded in FORTRAN IV and may be applied to every solid with a monatomic face-centered cubic lattice where the intermolecular interactions can be described by a centro-symmetrical potential. Interactions beyond third neighbours are neglected.

  13. Optical Near-field Interactions and Forces for Optoelectronic Devices

    Science.gov (United States)

    Kohoutek, John Michael

    Throughout history, as a particle view of the universe began to take shape, scientists began to realize that these particles were attracted to each other and hence came up with theories, both analytical and empirical in nature, to explain their interaction. The interaction pair potential (empirical) and electromagnetics (analytical) theories, both help to explain not only the interaction between the basic constituents of matter, such as atoms and molecules, but also between macroscopic objects, such as two surfaces in close proximity. The electrostatic force, optical force, and Casimir force can be categorized as such forces. A surface plasmon (SP) is a collective motion of electrons generated by light at the interface between two mediums of opposite signs of dielectric susceptibility (e.g. metal and dielectric). Recently, surface plasmon resonance (SPR) has been exploited in many areas through the use of tiny antennas that work on similar principles as radio frequency (RF) antennas in optoelectronic devices. These antennas can produce a very high gradient in the electric field thereby leading to an optical force, similar in concept to the surface forces discussed above. The Atomic Force Microscope (AFM) was introduced in the 1980s at IBM. Here we report on its uses in measuring these aforementioned forces and fields, as well as actively modulating and manipulating multiple optoelectronic devices. We have shown that it is possible to change the far field radiation pattern of an optical antenna-integrated device through modification of the near-field of the device. This modification is possible through change of the local refractive index or reflectivity of the "hot spot" of the device, either mechanically or optically. Finally, we have shown how a mechanically active device can be used to detect light with high gain and low noise at room temperature. It is the aim of several of these integrated and future devices to be used for applications in molecular sensing

  14. Machine learning of accurate energy-conserving molecular force fields

    Science.gov (United States)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

  15. Various aspects of magnetic field influence on forced convection

    Directory of Open Access Journals (Sweden)

    Pleskacz Lukasz

    2016-01-01

    Full Text Available Flows in the channels of various geometry can be found everywhere in industrial or daily life applications. They are used to deliver media to certain locations or they are the place where heat may be exchanged. For Authors both points of view are interesting. The enhancement methods for heat transfer during the forced convection are demanded due to a technological development and tendency to miniaturization. At the same time it is also worth to find mechanisms that would help to avoid negative effects like pressure losses or sedimentation in the channel flows. This paper shows and discuss various aspects of magnetic field influence on forced convection. A mathematical model consisted of the mass, momentum and energy conservation equations. In the momentum conservation equation magnetic force term was included. In order to calculate this magnetic force Biot-Savart’s law was utilized. Numerical analysis was performed with the usage of commonly applied software. However, userdefined functions were implemented. The results revealed that both temperature and velocity fields were influenced by the strong magnetic field.

  16. Valence force fields and the lattice dynamics of beryllium oxide

    International Nuclear Information System (INIS)

    Ramani, R.; Mani, K.K.; Singh, R.P.

    1976-01-01

    The lattice dynamics of beryllium oxide have been studied using a rigid-ion model, with short-range forces represented by a valence force field. Various existing calculations on group-IV elements using such a field have been examined as a prelude to transference of force constants from diamond to beryllium oxide. The effects of ionicity on the force constants have been included in the form of scale factors. It is shown that no satisfactory fit to the long-wavelength data on BeO can be found with transferred force constants. However, adequate least-squares fits can be found both with four- and six-parameter valence force fields, the discrepancy with experiment being large only for one optical mode at the Brillouin-zone center. Dispersion curves along Δ and Σ are presented and are in fair agreement with experiment, deviations arising essentially from the quality of the fit to the long-wavelength data. The bond-bending interactions are found to play a significant role and arguments have been presented to show that the inclusion of further angle-angle interactions would yield a very satisfactory picture of the dynamics

  17. Nonequilibrium forces between neutral atoms mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2010-01-01

    We study forces between two neutral atoms, modeled as three-dimensional harmonic oscillators, arising from mutual influences mediated by an electromagnetic field but not from their direct interactions. We allow as dynamical variables the center-of-mass motion of the atom, its internal degrees of freedom, and the quantum field treated relativistically. We adopt the method of nonequilibrium quantum field theory which can provide a first-principles, systematic, and unified description including the intrinsic and induced dipole fluctuations. The inclusion of self-consistent back-actions makes possible a fully dynamical description of these forces valid for general atom motion. In thermal equilibrium we recover the known forces--London, van der Waals, and Casimir-Polder--between neutral atoms in the long-time limit. We also reproduce a recently reported force between atoms when the system is out of thermal equilibrium at late times. More noteworthy is the discovery of the existence of a type of (or identification of the source of some known) interatomic force which we call the ''entanglement force,'' originating from the quantum correlations of the internal degrees of freedom of entangled atoms.

  18. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

    Science.gov (United States)

    Best, Robert B; Hummer, Gerhard

    2009-07-02

    Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

  19. Physical Limitations of Empirical Field Models: Force Balance and Plasma Pressure

    International Nuclear Information System (INIS)

    Sorin Zaharia; Cheng, C.Z.

    2002-01-01

    In this paper, we study whether the magnetic field of the T96 empirical model can be in force balance with an isotropic plasma pressure distribution. Using the field of T96, we obtain values for the pressure P by solving a Poisson-type equation (gradient) 2 P = (gradient) · (J x B) in the equatorial plane, and 1-D profiles on the Sun-Earth axis by integrating (gradient)P = J x B. We work in a flux coordinate system in which the magnetic field is expressed in terms of Euler potentials. Our results lead to the conclusion that the T96 model field cannot be in equilibrium with an isotropic pressure. We also analyze in detail the computation of Birkeland currents using the Vasyliunas relation and the T96 field, which yields unphysical results, again indicating the lack of force balance in the empirical model. The underlying reason for the force imbalance is likely the fact that the derivatives of the least-square fitted model B are not accurate predictions of the actual magnetospheric field derivatives. Finally, we discuss a possible solution to the problem of lack of force balance in empirical field models

  20. Scattering of acoustic waves from a surface in the presence of an anharmonic interface

    DEFF Research Database (Denmark)

    Kulak, A.; Lodziana, Zbigniew; Srokowski, T.

    2002-01-01

    Energy transfer coefficient (analogue of LDOS) and aperiodicity index are defined to characterise the nonlinear response and the surface resonances in a thin layer separated from the underlying bulk crystal by an anharmonic interface. Regions of periodic, aperiodic and intermittent motion of the ...

  1. Two new types of solvability of the one-dimensional anharmonic oscillators

    International Nuclear Information System (INIS)

    Znojil, M.

    1989-01-01

    In the Schroedinger picture, we propose a new modification of the so-called Hill-determinant technique. It is shown to guarantee a proper matching of the two underlying power series Ψ(x) at x=0. In the Heisenberg picture, an evolution of the same one-dimensional polynomially anharmonic oscillator is considered. A modified Peano-Baker method is applied and shown to define the explicit solutions by recurrences. 11 refs

  2. Rapid parameterization of small molecules using the Force Field Toolkit.

    Science.gov (United States)

    Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C

    2013-12-15

    The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

  3. Effects of cosmic-string framework on the thermodynamical properties of anharmonic oscillator using the ordinary statistics and the q-deformed superstatistics approaches

    Energy Technology Data Exchange (ETDEWEB)

    Sobhani, Hadi; Hassanabadi, Hassan [Shahrood University of Technology, Faculty of Physics, Shahrood (Iran, Islamic Republic of); Chung, Won Sang [Gyeongsang National University, Department of Physics and Research Institute of Natural Science, College of Natural Science, Jinju (Korea, Republic of)

    2018-02-15

    In this article, we determine the thermodynamical properties of the anharmonic canonical ensemble within the cosmic-string framework. We use the ordinary statistics and the q-deformed superstatistics for this study. The q-deformed superstatistics is derived by modifying the probability density in the original superstatistics. The Schroedinger equation is rewritten in the cosmic-string framework. Next, the anharmonic oscillator is investigated in detail. The wave function and the energy spectrum of the considered system are derived using the bi-confluent Heun functions. In the next step, we first determine the thermodynamical properties for the canonical ensemble of the anharmonic oscillator in the cosmic-string framework using the ordinary statistics approach. Also, these quantities have been obtained in the q-deformed superstatistics. For vanishing deformation parameter, the ordinary results are obtained. (orig.)

  4. Quantum theory of anharmonic oscillators

    International Nuclear Information System (INIS)

    Yamazaki, K.; Kyoto Univ.

    1983-01-01

    This in investigation of an anharmonic oscillator characterized by the potential ωsub(o) 2 /2 g 2 + lambda'q 4 . By using the equations of motion and the relations obtained by evaluating where O is an arbitrary operator, H is our total Hamiltonian and |i> and |j> are exact eigenstates of H, we derive an exact recurrence formula. This formula allows us to express tau-functions with a higher power of the variables through tau-functions with a lower power of the variables and energy eigenvalues. In this way we derive several exact relations, which are, in a sense, generalizations of the virial theorem and sum rules. These exact relations are the central equations of this paper. On the basis of these exact relations we propose our 'nearest neighbour level' (N.N.L.) approximation, which seems to provide a good approximation scheme. We can also use our exact relations to test the validity of various approximation methods, and as an example, we discuss the 'New-Tamm-Dancoff' (N.T.D)-type of approximation in detail. (Author)

  5. Fluctuations and Anharmonicity in Lead Iodide Perovskites from Molecular Dynamics Supercell Simulationss

    KAUST Repository

    Carignano, Marcelo Andrés

    2017-09-05

    We present a systematic study based on first principles molecular dynamics simulations of lead iodide perovskites with three different cations, including methylammonium (MA), formamidinium (FA) and cesium. Using the high temperature perovskite structure as a reference, we investigate the instabilities that develop as the material is cooled down to 370 K. All three perovskites display anharmonicity in the motion of the iodine atoms, with the stronger effect observed for the MAPbI$_3$ and CsPbI$_3$. At high temperature, this behavior can be traced back to the reduced effective size of the Cs$^+$ and MA$^+$ cations. MAPbI$_3$ undergoes a spontaneous phase transition within our simulation model driven by the dipolar interaction between neighboring MA cations as the temperature is decreased from 450 K. The reverse transformation from tetragonal to cubic is also monitored through the large distribution of the octahedral tilting angles accompanied by an increase in the anharmonicity of the iodine atoms motion. Both MA and FA hybrid perovskites show a strong coupling between the molecular orientations and the local lattice deformations, suggesting mixed order-disorder/displacive characters of the high temperature phase transitions.

  6. Study of thermophysical and anharmonic properties of fluorite compounds

    International Nuclear Information System (INIS)

    Singh, R.K.; Pandey, N.K.

    1983-01-01

    An extensive study is made of thermophysical and anharmonic properties of fluorite compounds using an interionic potential, which consists of a long-range Coulomb and three-body interactions and the short-range overlap repulsion and van der Waals attraction. The agreement achieved between experimental and theoretical results on third-order elastic constants and pressure derivatives of second order elastic constants are generally better than those obtained by others. This potential succeeds in predicting various thermophysical properties, like compressibility and its pressure and temperature derivatives, thermal expansion and Grueneisen parameters of seven crystals of fluorite structure. (author)

  7. Magnetoelectric force microscopy based on magnetic force microscopy with modulated electric field.

    Science.gov (United States)

    Geng, Yanan; Wu, Weida

    2014-05-01

    We present the realization of a mesoscopic imaging technique, namely, the Magnetoelectric Force Microscopy (MeFM), for visualization of local magnetoelectric effect. The basic principle of MeFM is the lock-in detection of local magnetoelectric response, i.e., the electric field-induced magnetization, using magnetic force microscopy. We demonstrate MeFM capability by visualizing magnetoelectric domains on single crystals of multiferroic hexagonal manganites. Results of several control experiments exclude artifacts or extrinsic origins of the MeFM signal. The parameters are tuned to optimize the signal to noise ratio.

  8. Mapping the force field of a hydrogen-bonded assembly

    Science.gov (United States)

    Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2014-05-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  9. Pressure measurements of TO-phonon anharmonicity in isotopic ZnS

    Energy Technology Data Exchange (ETDEWEB)

    Tallman, R.E.; Weinstein, B.A. [SUNY at Buffalo, Department of Physics, Buffalo, NY 14260 (United States); Ritter, T.M. [Dept. of Chemistry and Physics, UNC Pembroke, NC 28372 (United States); Cantarero, A. [Dept. of Physics and Institute of Materials Science, University of Valencia (Spain); Serrano, J.; Lauck, R.; Cardona, M. [Max-Planck-Institut fuer Festkoerperforschung, 70569 Stuttgart (Germany)

    2004-03-01

    We have measured the dependence on pressure of the line-widths of the TO and LO Raman phonons of {beta}-ZnS. In order to enhance the phenomena observed, and to eliminate possible effects of isotopic disorder, we have measured a nearly isotopically pure crystal, {sup 68}Zn{sup 32}S. The strongly structured pressure effects observed are interpreted on the basis of anharmonic decay and the corresponding two-phonon density of states. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  10. A test on reactive force fields for the study of silica dimerization reactions

    Energy Technology Data Exchange (ETDEWEB)

    Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117, 7491 Trondheim (Norway)

    2015-11-14

    We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.

  11. Nuclear Forces from Effective Field Theory

    International Nuclear Information System (INIS)

    Krebs, H.

    2011-01-01

    Chiral effective field theory allows for a systematic and model-independent derivation of the forces between nucleons in harmony with the symmetries of the quantum chromodynamics. After a brief review on the current status in the development of the chiral nuclear forces I will focus on the role of the Δ-resonance contributions in the nuclear dynamics.We find improvement in the convergence of the chiral expansion of the nuclear forces if we explicitly take into account the Δ-resonance degrees of freedom. The overall results for two-nucleon forces with and without explicit Δ-resonance degrees of freedom are remarkably similar. We discussed the long- and shorter-range N 3 LO contributions to chiral three-nucleon forces. No additional free parameters appear at this order. There are five different topology classes which contribute to the forces. Three of them describe long-range contributions which constitute the first systematic corrections to the leading 2π exchange that appear at N 2 LO. Another two contributions are of a shorter range and include, additionally to an exchange of pions, also one short-range contact interaction and all corresponding 1/m corrections. The requirement of renormalizability leads to unique expressions for N 3 LO contributions to the three-nucleon force (except for 1/m-corrections). We presented the complete N 2 LO analysis of the nuclear forces with explicit Δ-isobar degrees of freedom. Although the overall results in the isospin-conserving case are very similar in the Δ-less and Δ-full theories, we found a much better convergence in all peripheral partial waves once Δ-resonance is explicitly taken into account. The leading CSB contributions to nuclear forces are proportional to nucleon- and Δ-mass splittings. There appear strong cancellations between the two contributions which at leading order yield weaker V III potentials. This effect is, however, entirely compensated at subleading order such that the results in the theories

  12. Comparison of three empirical force fields for phonon calculations in CdSe quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Kelley, Anne Myers [Chemistry and Chemical Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States)

    2016-06-07

    Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ~2.8 and ~5.2 nm (~410 and ~2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies for the strongly Raman-active “longitudinal optical” phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.

  13. Rapid changes in corticospinal excitability during force field adaptation of human walking

    DEFF Research Database (Denmark)

    Barthélemy, Dorothy; Alain, S; Grey, Michael James

    2012-01-01

    measured changes in motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) in the tibialis anterior (TA) muscle before, during, and after subjects adapted to a force field applied to the ankle joint during treadmill walking. When the force field assisted dorsiflexion during...... the swing phase of the step cycle, subjects adapted by decreasing TA EMG activity. In contrast, when the force field resisted dorsiflexion, they increased TA EMG activity. After the force field was removed, normal EMG activity gradually returned over the next 5 min of walking. TA MEPs elicited in the early...... be explained by changes in background TA EMG activity. These effects seemed specific to walking, as similar changes in TA MEP were not seen when seated subjects were tested during static dorsiflexion. These observations suggest that the corticospinal tract contributes to the adaptation of walking...

  14. Topological and statistical properties of nonlinear force-free fields

    Science.gov (United States)

    Mangalam, A.; Prasad, A.

    2018-01-01

    We use our semi-analytic solution of the nonlinear force-free field equation to construct three-dimensional magnetic fields that are applicable to the solar corona and study their statistical properties for estimating the degree of braiding exhibited by these fields. We present a new formula for calculating the winding number and compare it with the formula for the crossing number. The comparison is shown for a toy model of two helices and for realistic cases of nonlinear force-free fields; conceptually the formulae are nearly the same but the resulting distributions calculated for a given topology can be different. We also calculate linkages, which are useful topological quantities that are independent measures of the contribution of magnetic braiding to the total free energy and relative helicity of the field. Finally, we derive new analytical bounds for the free energy and relative helicity for the field configurations in terms of the linking number. These bounds will be of utility in estimating the braided energy available for nano-flares or for eruptions.

  15. Charm production and the confining force field

    International Nuclear Information System (INIS)

    Andersson, B.; Bengtsson, H.-U.; Gustafson, G.

    1983-03-01

    We show that charm production at SPS energies can be understood simply from O(α 2 sub (s)) QCD processes when combined with fragmentation of the colour fields stretched by the final state partons. The tension of the confining force field responsible for particle production is found to pull the charmed particles away from the reaction centre, giving rise to a harder x sub (F)-spectrum than would be expected from the bare QCD matrix elements. (Authors)

  16. Polaronic Nonmetal-Correlated Metal Crossover System β'-CuxV2O5 with Anharmonic Copper Oscillation and Thermoelectric Conversion Performance

    Science.gov (United States)

    Onoda, Masashige; Sato, Takuma

    2017-12-01

    The crystal structures and electronic properties of β'CuxV2O5 are explored through measurements of X-ray four-circle diffraction, electrical resistivity, thermoelectric power, thermal conductivity, magnetization, and electron paramagnetic resonance. For various compositions with 0.243 ≤ x ≤ 0.587, the crystal structures are redetermined through the anharmonic approach of the copper displacement factors, where the anharmonicity is reduced with increasing Cu concentration. The electron transport for x ≤ 0.45 is nonmetallic due to polaron hopping and the random potential of Cu ions, while for x = 0.60, a correlated Fermi-liquid state appears with a Wilson ratio of 1.3 and a Kadowaki-Woods ratio close to the universal value for heavy-fermion systems. At around x = 0.50, the polaronic bandwidth may broaden so that the Hubbard subbands caused by the electron correlation will overlap. The nonmetallic composition in the proximity of the nonmetal-metal crossover shows a dimensionless thermoelectric power factor of 10-2 at 300 K, partly due to the anharmonic copper oscillation.

  17. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

    Science.gov (United States)

    Riniker, Sereina

    2018-03-26

    In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

  18. A new force field including charge directionality for TMAO in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes; Bonn, Mischa [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Sulpizi, Marialore, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de [Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz (Germany)

    2016-08-14

    We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

  19. A new force field including charge directionality for TMAO in aqueous solution

    International Nuclear Information System (INIS)

    Usui, Kota; Nagata, Yuki; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore

    2016-01-01

    We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O TMAO ) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O TMAO to mimic the O TMAO lone pairs and we migrate the negative charge on the O TMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

  20. The influence of anharmonic core vibrations in the X-ray bond charge analysis of A/sup N/B/sup 8-N/ compounds

    International Nuclear Information System (INIS)

    Pietsch, U.

    1982-01-01

    X-ray structure amplitudes of elemental and A 3 B 5 semiconductors can be described by means of spherical atomic form factors and an additional scattered particle at the position of the centre of the covalent bond between next neighbours named bond charge. For this analysis anharmonic core vibrations were neglegted. In this note the influence is estimated of anharmonic core vibrations on the total structure amplitudes of some zinc-blende compounds (GaAs, ZnSe, CuBr, InSb, and CuCl)

  1. Dusty plasmas in a constant electric field: Role of the electron drag force

    International Nuclear Information System (INIS)

    Khrapak, S.A.; Morfill, G.E.

    2004-01-01

    We investigate the forces experienced by a microparticle immersed in a weakly ionized plasma with constant electric field. These are electric force and the forces associated with the momentum transfer from electrons and ions drifting in the field (electron and ion drag forces). It is shown that the effect of the electron drag, which is often neglected, can be substantial in a certain parameter range. Numerical calculation of the forces for a reasonable set of plasma parameters is performed to illustrate the importance of this effect

  2. Van der Waals Forces and Photon-Less Effective Field Theory

    International Nuclear Information System (INIS)

    Arriola, E.R.

    2011-01-01

    In the ultra-cold regime Van der Waals forces between neutral atoms can be represented by short range effective interactions. We show that universal low energy scaling features of the underlying vdW long range force stemming from two photon exchange impose restrictions on an Effective Field Theory without explicit photons. The role of naively redundant operators, relevant to the definition of three body forces, is also analyzed. (author)

  3. Vibrational spectra and thermal rectification in three-dimensional anharmonic lattices

    International Nuclear Information System (INIS)

    Lan Jinghua; Li Baowen

    2007-01-01

    We study thermal rectification in a three-dimensional model consisting of two segments of anharmonic lattices. One segment consists of layers of harmonic oscillator arrays coupled to a substrate potential, which is a three-dimensional Frenkel-Kontorova model, and the other segment is a three-dimensional Fermi-Pasta-Ulam model. We study the vibrational bands of the two lattices analytically and numerically, and find that, by choosing the system parameters properly, the rectification can be as high as a few thousands, which is high enough to be observed in experiment. Possible experiments in nanostructures are discussed

  4. Explicit polarization: a quantum mechanical framework for developing next generation force fields.

    Science.gov (United States)

    Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

    2014-09-16

    Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples

  5. TET Offensive II Field Force Vietnam After Action Report 31 January - 18 February 1968

    Science.gov (United States)

    1968-03-01

    and the 5th VC Division. V During this same period of time there were no majur shifts in ARVN forces . However III Corps shifted three...8217-".•: ’ ’SSIFJED U.S. ARMY. VIETNAM. II FIELD FORCE . TET OFFENSIVE II FIELD FORCE VIETNAM AFTER ACTION REPORT, 31 JANUARY-18 FEB- RUARY 1968...H FIELD FORCE VIETNAM AFTER ACTION REPORT 31 January-18 February 1968 RECORD K0- ! FlSjl fi-.-A-,>-•: it tT*\\ : *si h s» -wP Mr-, £< St

  6. Finger-Shaped GelForce: Sensor for Measuring Surface Traction Fields for Robotic Hand.

    Science.gov (United States)

    Sato, K; Kamiyama, K; Kawakami, N; Tachi, S

    2010-01-01

    It is believed that the use of haptic sensors to measure the magnitude, direction, and distribution of a force will enable a robotic hand to perform dexterous operations. Therefore, we develop a new type of finger-shaped haptic sensor using GelForce technology. GelForce is a vision-based sensor that can be used to measure the distribution of force vectors, or surface traction fields. The simple structure of the GelForce enables us to develop a compact finger-shaped GelForce for the robotic hand. GelForce that is developed on the basis of an elastic theory can be used to calculate surface traction fields using a conversion equation. However, this conversion equation cannot be analytically solved when the elastic body of the sensor has a complicated shape such as the shape of a finger. Therefore, we propose an observational method and construct a prototype of the finger-shaped GelForce. By using this prototype, we evaluate the basic performance of the finger-shaped GelForce. Then, we conduct a field test by performing grasping operations using a robotic hand. The results of this test show that using the observational method, the finger-shaped GelForce can be successfully used in a robotic hand.

  7. Improved models of dense anharmonic lattices

    Energy Technology Data Exchange (ETDEWEB)

    Rosenau, P., E-mail: rosenau@post.tau.ac.il; Zilburg, A.

    2017-01-15

    We present two improved quasi-continuous models of dense, strictly anharmonic chains. The direct expansion which includes the leading effect due to lattice dispersion, results in a Boussinesq-type PDE with a compacton as its basic solitary mode. Without increasing its complexity we improve the model by including additional terms in the expanded interparticle potential with the resulting compacton having a milder singularity at its edges. A particular care is applied to the Hertz potential due to its non-analyticity. Since, however, the PDEs of both the basic and the improved model are ill posed, they are unsuitable for a study of chains dynamics. Using the bond length as a state variable we manipulate its dispersion and derive a well posed fourth order PDE. - Highlights: • An improved PDE model of a Newtonian lattice renders compacton solutions. • Compactons are classical solutions of the improved model and hence amenable to standard analysis. • An alternative well posed model enables to study head on interactions of lattices' solitary waves. • Well posed modeling of Hertz potential.

  8. Radiation reaction force and unification of electromagnetic and gravitational fields

    International Nuclear Information System (INIS)

    Lo, C.Y.; Goldstein, G.R.; Napier, A.

    1981-04-01

    A unified theory of electromagnetic and gravitational fields should modify classical electrodynamics such that the radiation reaction force is accounted for. The analysis leads to a five-dimensional unified theory of five variables. The theory is supported by showing that, for the case of a charged particle moving in a constant magnetic field, the radiation reaction force is indeed included. Moreover, this example shows explicitly that physical changes are associated with the fifth variable. Thus, the notion of a physical five-dimensional space should be seriously taken into consideration

  9. Systematic Parameterization of Lignin for the CHARMM Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg; Crowley, Michael

    2017-07-06

    Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between

  10. A quantum anharmonic oscillator model for the stock market

    Science.gov (United States)

    Gao, Tingting; Chen, Yu

    2017-02-01

    A financially interpretable quantum model is proposed to study the probability distributions of the stock price return. The dynamics of a quantum particle is considered an analog of the motion of stock price. Then the probability distributions of price return can be computed from the wave functions that evolve according to Schrodinger equation. Instead of a harmonic oscillator in previous studies, a quantum anharmonic oscillator is applied to the stock in liquid market. The leptokurtic distributions of price return can be reproduced by our quantum model with the introduction of mixed-state and multi-potential. The trend following dominant market, in which the price return follows a bimodal distribution, is discussed as a specific case of the illiquid market.

  11. Anharmonic, dimensionality and size effects in phonon transport

    Science.gov (United States)

    Thomas, Iorwerth O.; Srivastava, G. P.

    2017-12-01

    We have developed and employed a numerically efficient semi- ab initio theory, based on density-functional and relaxation-time schemes, to examine anharmonic, dimensionality and size effects in phonon transport in three- and two-dimensional solids of different crystal symmetries. Our method uses third- and fourth-order terms in crystal Hamiltonian expressed in terms of a temperature-dependent Grüneisen’s constant. All input to numerical calculations are generated from phonon calculations based on the density-functional perturbation theory. It is found that four-phonon processes make important and measurable contribution to lattice thermal resistivity above the Debye temperature. From our numerical results for bulk Si, bulk Ge, bulk MoS2 and monolayer MoS2 we find that the sample length dependence of phonon conductivity is significantly stronger in low-dimensional solids.

  12. Non-Gaussian wave packet dynamics in anharmonic potential: Cumulant expansion treatment

    International Nuclear Information System (INIS)

    Toutounji, Mohamad

    2015-01-01

    This manuscript utilizes cumulant expansion as an alternative algebraic approach to evaluating integrals and solving a system of nonlinear differential equations for probing anharmonic dynamics in condensed phase systems using Morse oscillator. These integrals and differential equations become harder to solve as the anharmonicity of the system goes beyond that of Morse oscillator description. This algebraic approach becomes critically important in case of Morse oscillator as it tends to exhibit divergent dynamics and numerical uncertainties at low temperatures. The autocorrelation function is calculated algebraically and compared to the exact one for they match perfectly. It is also compared to the approximate autocorrelation function using the differential equations technique reported in Toutounji (2014) for weak and strong electron–phonon coupling cases. It is found that the present cumulant method is more efficient, and easier to use, than the exact expression. Deviation between the approximate autocorrelation function and the exact autocorrelation function starts to arise as the electron–phonon coupling strength increases. The autocorrelation function obtained using cumulants identically matches the exact autocorrelation function, thereby surpassing the approach presented in Toutounji (2014). The advantage of the present methodology is its applicability to various types of electron–phonon coupling cases. Additionally, the herein approach only uses algebraic techniques, thereby avoiding both the divergence integral and solving a set of linear first- and second-order partial differential equations as was done in previous work. Model calculations are presented to demonstrate the accuracy of the herein work

  13. Secondary Structure of Rat and Human Amylin across Force Fields.

    Directory of Open Access Journals (Sweden)

    Kyle Quynn Hoffmann

    Full Text Available The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient

  14. The influence of catch trials on the consolidation of motor memory in force field adaptation tasks

    Directory of Open Access Journals (Sweden)

    Anne eFocke

    2013-07-01

    Full Text Available In computational neuroscience it is generally accepted that human motor memory contains neural representations of the physics of the musculoskeletal system and the objects in the environment. These representations are called internal models. Force field studies, in which subjects have to adapt to dynamic perturbations induced by a robotic manipulandum, are an established tool to analyze the characteristics of such internal models. The aim of the current study was to investigate whether catch trials during force field learning could influence the consolidation of motor memory in more complex tasks. Thereby, the force field was more than double the force field of previous studies (35 Ns/m. Moreover, the arm of the subjects was not supported. A total of forty-six subjects participated in this study and performed center-out movements at a robotic manipulandum in two different force fields. Two control groups learned force field A on day 1 and were retested in the same force field on day 3 (AA. Two test groups additionally learned an interfering force field B (=-A on day 2 (ABA. The difference between the two test and control groups, respectively, was the absence (0% or presence (19% of catch trials, in which the force field was turned off suddenly. The results showed consolidation of force field A on day 3 for both control groups. Test groups showed no consolidation of force field A (19% catch trials and even poorer performance on day 3 (0% catch trials. In conclusion, it can be stated that catch trials seem to have a positive effect on the performance on day 3 but do not trigger a consolidation process as shown in previous studies that used a lower force field viscosity with supported arm. These findings indicate that the results of previous studies in which less complex tasks were analyzed, cannot be fully transferred to more complex tasks. Moreover, the effects of catch trials in these situations are insufficiently understood and further research

  15. Accurate van der Waals force field for gas adsorption in porous materials.

    Science.gov (United States)

    Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

    2017-09-05

    An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    International Nuclear Information System (INIS)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%

  17. Modulated anharmonic ADPs are intrinsic to aperiodic crystals: a case study on incommensurate Rb2ZnCl4

    International Nuclear Information System (INIS)

    Li, Liang; Wölfel, Alexander; Schönleber, Andreas; Mondal, Swastik; Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J.; Smaalen, Sander van

    2011-01-01

    The superspace maximum entropy method (MEM) density in combination with structure refinements has been used to uncover the modulation in incommensurate Rb 2 ZnCl 4 close to the lock-in transition. Modulated atomic displacement parameters (ADPs) and modulated anharmonic ADPs are found to form an intrinsic part of the modulation. Refined values for the displacement modulation function depend on the presence or absence of modulated ADPs in the model. A combination of structure refinements, analysis of the superspace MEM density and interpretation of difference-Fourier maps has been used to characterize the incommensurate modulation of rubidium tetrachlorozincate, Rb 2 ZnCl 4 , at a temperature of T = 196 K, close to the lock-in transition at T lock-in = 192 K. The modulation is found to consist of a combination of displacement modulation functions, modulated atomic displacement parameters (ADPs) and modulated third-order anharmonic ADPs. Up to fifth-order Fourier coefficients could be refined against diffraction data containing up to fifth-order satellite reflections. The center-of-charge of the atomic basins of the MEM density and the displacive modulation functions of the structure model provide equivalent descriptions of the displacive modulation. Modulations of the ADPs and anharmonic ADPs are visible in the MEM density, but extracting quantitative information about these modulations appears to be difficult. In the structure refinements the modulation parameters of the ADPs form a dependent set, and ad hoc restrictions had to be introduced in the refinements. It is suggested that modulated harmonic ADPs and modulated third-order anharmonic ADPs form an intrinsic part, however small, of incommensurately modulated structures in general. Refinements of alternate models with and without parameters for modulated ADPs lead to significant differences between the parameters of the displacement modulation in these two types of models, thus showing the modulation of ADPs to

  18. Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-01-01

    In this paper we give a first principles microphysics derivation of the nonequilibrium forces between an atom, treated as a three-dimensional harmonic oscillator, and a bulk dielectric medium modeled as a continuous lattice of oscillators coupled to a reservoir. We assume no direct interaction between the atom and the medium but there exist mutual influences transmitted via a common electromagnetic field. By employing concepts and techniques of open quantum systems we introduce coarse-graining to the physical variables--the medium, the quantum field, and the atom's internal degrees of freedom, in that order--to extract their averaged effects from the lowest tier progressively to the top tier. The first tier of coarse-graining provides the averaged effect of the medium upon the field, quantified by a complex permittivity (in the frequency domain) describing the response of the dielectric to the field in addition to its back action on the field through a stochastic forcing term. The last tier of coarse-graining over the atom's internal degrees of freedom results in an equation of motion for the atom's center of mass from which we can derive the force on the atom. Our nonequilibrium formulation provides a fully dynamical description of the atom's motion including back-action effects from all other relevant variables concerned. In the long-time limit we recover the known results for the atom-dielectric force when the combined system is in equilibrium or in a nonequilibrium stationary state.

  19. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... of the TS geometry on the flexibility of the system has been probed by fixing layers of atoms around the active site and using increasingly larger nonbonded cutoffs. The variability over the 20 structures is found to decrease as the system is made more flexible. Relative energies have been calculated...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...

  20. Development of a reactive force field for iron-oxyhydroxide systems.

    Science.gov (United States)

    Aryanpour, Masoud; van Duin, Adri C T; Kubicki, James D

    2010-06-03

    We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for alpha-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed.

  1. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and...

  2. Thermal behaviour of the Debye-Waller factor and the specific heat of anharmonic crystals

    International Nuclear Information System (INIS)

    Lima, R.A.T. de; Tsallis, C.

    1979-08-01

    The influence of the cubic and quartic crystalline anharmonicity on the classical and quantum thermal behaviour of the specific heat, Debye temperaturetheta, Debye-Waller factor W, crystalline expansion and phonon spectrum is studied, within the framework of the Variational Method in Statistical Mechanics. The sistems, mainly focalized are the single oscillator, the mono-atomic linear chain and simple cubic crystal. The trial Hamiltonian is an harmonic one, therefore the various anharmonic influences are mainly absorbed into the renormalization of theta(T). Several differences between the classical and quantum results are exhibited. Satisfactory qualitative agreement with experience was obtained in the low-temperature regime, in particular in what concerns the existence of a minimum in theta(T) which has been observed in Cu, Al, Ag, Au and Pb. For the intermediate-temperature regime the customary linear behaviour of W(T) (hence theta(T) almost constant) is reobtained. Finally in the high-temperature regime, the present treatment leads to a √T - dependence for the W-factor, which implies in the wrong curvature with respect to experimental data. A possible explanation of this disagreement might be related to the melting phenomenon, which is not covered by the present theory. (Author) [pt

  3. Martini Coarse-Grained Force Field : Extension to DNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

    We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the

  4. Martini Coarse-Grained Force Field : Extension to Carbohydrates

    NARCIS (Netherlands)

    Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

    2009-01-01

    We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

  5. Isotopic effects on phonon anharmonicity in layered van der Waals crystals: Isotopically pure hexagonal boron nitride

    Science.gov (United States)

    Cuscó, Ramon; Artús, Luis; Edgar, James H.; Liu, Song; Cassabois, Guillaume; Gil, Bernard

    2018-04-01

    Hexagonal boron nitride (h -BN) is a layered crystal that is attracting a great deal of attention as a promising material for nanophotonic applications. The strong optical anisotropy of this crystal is key to exploit polaritonic modes for manipulating light-matter interactions in 2D materials. h -BN has also great potential for solid-state neutron detection and neutron imaging devices, given the exceptionally high thermal neutron capture cross section of the boron-10 isotope. A good knowledge of phonons in layered crystals is essential for harnessing long-lived phonon-polariton modes for nanophotonic applications and may prove valuable for developing solid-state 10BN neutron detectors with improved device architectures and higher detection efficiencies. Although phonons in graphene and isoelectronic materials with a similar hexagonal layer structure have been studied, the effect of isotopic substitution on the phonons of such lamellar compounds has not been addressed yet. Here we present a Raman scattering study of the in-plane high-energy Raman active mode on isotopically enriched single-crystal h -BN. Phonon frequency and lifetime are measured in the 80-600-K temperature range for 10B-enriched, 11B-enriched, and natural composition high quality crystals. Their temperature dependence is explained in the light of perturbation theory calculations of the phonon self-energy. The effects of crystal anisotropy, isotopic disorder, and anharmonic phonon-decay channels are investigated in detail. The isotopic-induced changes in the phonon density of states are shown to enhance three-phonon anharmonic decay channels in 10B-enriched crystals, opening the possibility of isotope tuning of the anharmonic phonon decay processes.

  6. Artificial force fields for multi-agent simulations of maritime traffic and risk estimation

    NARCIS (Netherlands)

    Xiao, F.; Ligteringen, H.; Van Gulijk, C.; Ale, B.J.M.

    2012-01-01

    A probabilistic risk model is designed to estimate probabilities of collisions for shipping accidents in busy waterways. We propose a method based on multi-agent simulation that uses an artificial force field to model ship maneuvers. The artificial force field is calibrated by AIS data (Automatic

  7. Approximation methods for the partition functions of anharmonic systems

    International Nuclear Information System (INIS)

    Lew, P.; Ishida, T.

    1979-07-01

    The analytical approximations for the classical, quantum mechanical and reduced partition functions of the diatomic molecule oscillating internally under the influence of the Morse potential have been derived and their convergences have been tested numerically. This successful analytical method is used in the treatment of anharmonic systems. Using Schwinger perturbation method in the framework of second quantization formulism, the reduced partition function of polyatomic systems can be put into an expression which consists separately of contributions from the harmonic terms, Morse potential correction terms and interaction terms due to the off-diagonal potential coefficients. The calculated results of the reduced partition function from the approximation method on the 2-D and 3-D model systems agree well with the numerical exact calculations

  8. Spectra-structure correlations in NIR region: Spectroscopic and anharmonic DFT study of n-hexanol, cyclohexanol and phenol

    Science.gov (United States)

    Beć, Krzysztof B.; Grabska, Justyna; Czarnecki, Mirosław A.

    2018-05-01

    We investigated near-infrared (7500-4000 cm-1) spectra of n-hexanol, cyclohexanol and phenol in CCl4 (0.2 M) by using anharmonic quantum calculations. These molecules represent three major kinds of alcohols; linear and cyclic aliphatic, and aromatic ones. Vibrational second-order perturbation theory (VPT2) was employed to calculate the first overtones and binary combination modes and to reproduce the experimental NIR spectra. The level of conformational flexibility of these three alcohols varies from one stable conformer of phenol through four conformers of cyclohexanol to few hundreds conformers in the case of n-hexanol. To take into account the most relevant conformational population of n-hexanol, a systematic conformational search was performed. Accurate reproduction of the experimental NIR spectra was achieved and detailed spectra-structure correlations were obtained for these three alcohols. VPT2 approach provides less reliable description of highly anharmonic modes, i.e. OH stretching. In the present work this limitation was manifested in erroneous results yielded by VPT2 for 2νOH mode of cyclohexanol. To study the anharmonicity of this mode we solved the corresponding time-independent Schrödinger equation based on a dense-grid probing of the relevant vibrational potential. These results allowed for significant improvement of the agreement between the calculated and experimental 2νOH band of cyclohexanol. Various important biomolecules include similar structural units to the systems investigated here. A detailed knowledge on spectral properties of these three types of alcohols is therefore essential for advancing our understanding of NIR spectroscopy of biomolecules.

  9. Remark on the solution of the Schroedinger equation for anharmonic oscillators via the Feynman path integral

    International Nuclear Information System (INIS)

    Rezende, J.

    1983-01-01

    We give a simple proof of Feynman's formula for the Green's function of the n-dimensional harmonic oscillator valid for every time t with Im t<=0. As a consequence the Schroedinger equation for the anharmonic oscillator is integrated and expressed by the Feynman path integral on Hilbert space. (orig.)

  10. Building machine learning force fields for nanoclusters

    Science.gov (United States)

    Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro

    2018-06-01

    We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.

  11. A levitation force and magnetic field distribution measurement system in three dimensions

    International Nuclear Information System (INIS)

    Yang, W.M.; Chao, X.X.; Shu, Z.B.; Zhu, S.H.; Wu, X.L.; Bian, X.B.; Liu, P.

    2006-01-01

    A levitation force and magnetic field distribution measurement system in three dimension has been designed and constructed, which can be used for the levitation force measurement between a superconductor and a magnet, or magnet to magnet in three dimensions; and for the measurement of magnetic field distribution in three dimensions according to your need in space. It can also give out the dynamical changing result of magnetic field density with time during levitation force measurement. If we change the sensor of the detector of the measurement system, it also can be used for other kinds of measurement of physical properties. It is a good device for the measurement of magnetic properties of materials. In addition the device can also be used to work at carving in three dimensions

  12. Self-consistent mean field forces in turbulent plasmas: Current and momentum relaxation

    International Nuclear Information System (INIS)

    Hegna, C.C.

    1997-08-01

    The properties of turbulent plasmas are described using the two-fluid equations. Under some modest assumptions, global constraints for the turbulent mean field forces that act on the ion and electron fluids are derived. These constraints imply a functional form for the parallel mean field forces in the Ohm's law and the momentum balance equation. These forms suggest that the fluctuations attempt to relax the plasma to a state where both the current and the bulk plasma momentum are aligned along the mean magnetic field with proportionality constants that are global constants. Observations of flow profile evolution during discrete dynamo activity in reversed field pinch experiments are interpreted

  13. Sultan - forced flow, high field test facility

    International Nuclear Information System (INIS)

    Horvath, I.; Vecsey, G.; Weymuth, P.; Zellweger, J.

    1981-01-01

    Three European laboratories: CNEN (Frascati, I) ECN (Petten, NL) and SIN (Villigen, CH) decided to coordinate their development efforts and to install a common high field forced flow test facility at Villigen Switzerland. The test facility SULTAN (Supraleiter Testanlage) is presently under construction. As a first step, an 8T/1m bore solenoid with cryogenic periphery will be ready in 1981. The cryogenic system, data acquisition system and power supplies which are contributed by SIN are described. Experimental feasibilities, including cooling, and instrumentation are reviewed. Progress of components and facility construction is described. Planned extension of the background field up to 12T by insert coils is outlined. 5 refs

  14. The Alexandria library, a quantum-chemical database of molecular properties for force field development.

    Science.gov (United States)

    Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

    2018-04-10

    Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

  15. The Alexandria library, a quantum-chemical database of molecular properties for force field development

    Science.gov (United States)

    Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

    2018-04-01

    Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

  16. Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions

    Czech Academy of Sciences Publication Activity Database

    Daněček, Petr; Kapitán, Josef; Baumruk, V.; Bednárová, Lucie; Kopecký, V.; Bouř, Petr

    2007-01-01

    Roč. 126, č. 22 (2007), s. 224513-1 ISSN 0021-9606 R&D Projects: GA ČR GA203/06/0420; GA ČR GA202/07/0732; GA AV ČR IAA400550702 Institutional research plan: CEZ:AV0Z40550506 Keywords : IR * Raman * ROA spectra * Anharmonic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.044, year: 2007

  17. Reactive Force Field for Liquid Hydrazoic Acid with Applications to Detonation Chemistry

    Science.gov (United States)

    Furman, David; Dubnikova, Faina; van Duin, Adri; Zeiri, Yehuda; Kosloff, Ronnie

    The development of a reactive force field (ReaxFF formalism) for Hydrazoic acid (HN3), a highly sensitive liquid energetic material, is reported. The force field accurately reproduces results of density functional theory (DFT) calculations. The quality and performance of the force field are examined by detailed comparison with DFT calculations related to uni, bi and trimolecular thermal decomposition routes. Reactive molecular dynamics (RMD) simulations are performed to reveal the initial chemical events governing the detonation chemistry of liquid HN3. The outcome of these simulations compares very well with recent results of tight-binding DFT molecular dynamics and thermodynamic calculations. Based on our RMD simulations, predictions were made for the activation energies and volumes in a broad range of temperatures and initial material compressions. Work Supported by The Center of Excellence for Explosives Detection, Mitigation and Response, Department of Homeland Security.

  18. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    Energy Technology Data Exchange (ETDEWEB)

    Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de [Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg (Germany); Kibies, Patrick; Frach, Roland; Kast, Stefan M., E-mail: stefan.kast@tu-dortmund.de [Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund (Germany); Imoto, Sho, E-mail: sho.imoto@theochem.rub.de; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany); Suladze, Saba; Winter, Roland [Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund (Germany)

    2016-04-14

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  19. Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

    Science.gov (United States)

    Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

    2016-04-14

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  20. Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    International Nuclear Information System (INIS)

    Hölzl, Christoph; Horinek, Dominik; Kibies, Patrick; Frach, Roland; Kast, Stefan M.; Imoto, Sho; Marx, Dominik; Suladze, Saba; Winter, Roland

    2016-01-01

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  1. Quantum mechanical force field for water with explicit electronic polarization.

    Science.gov (United States)

    Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

    2013-08-07

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

  2. The growth of the concept of forces and fields

    International Nuclear Information System (INIS)

    Mukherji, Visvapriya

    1979-01-01

    The history and development of the concept of forces and fields in nature as was existing since two millenia ago to the ones that are being proposed and modified in the present day schools of field theorists have been traced. The concepts of Aristotle, Galileo, Democritus, Roemer, Newton, etc. which are considered classical in nature are outlined. The modern idea of field theories which owes its origin to the hypothesis propounded by Euler and the later developments by Laplace, Kelvin and Maxwell are described. Finally, Einstein's theory of relativity which projected a very novel interpretation of the gravitational field has also been explained in brief. Some of the hitherto unanswered questions in the field are also posed. (K.B.)

  3. Calculation of the radiation force on a cylinder in a standing wave acoustic field

    Energy Technology Data Exchange (ETDEWEB)

    Haydock, David [Unilever R and D Colworth, Sharnbrook, Bedford MK44 1LQ (United Kingdom); Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2005-04-15

    We present a new calculation of the radiation force on a cylinder in a standing wave acoustic field. We use the formula to calculate the force on a cylinder which is free to move in the field and one which is fixed in space.

  4. Calculation of the radiation force on a cylinder in a standing wave acoustic field

    International Nuclear Information System (INIS)

    Haydock, David

    2005-01-01

    We present a new calculation of the radiation force on a cylinder in a standing wave acoustic field. We use the formula to calculate the force on a cylinder which is free to move in the field and one which is fixed in space

  5. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    Science.gov (United States)

    Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

    2014-12-01

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

  6. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Zhaochuan; Vlugt, Thijs J. H., E-mail: t.j.h.vlugt@tudelft.nl [Process and Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft,The Netherlands (Netherlands); Koster, Rik S.; Fang, Changming; Huis, Marijn A. van [Debye Institute for Nanomaterials Science and Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); Wang, Shuaiwei [Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan 450006 (China); Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W. [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands)

    2014-12-28

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., “Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth,” Nano Lett. 14, 3661–3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

  7. Effects of Force Field Selection on the Computational Ranking of MOFs for CO2 Separations.

    Science.gov (United States)

    Dokur, Derya; Keskin, Seda

    2018-02-14

    Metal-organic frameworks (MOFs) have been considered as highly promising materials for adsorption-based CO 2 separations. The number of synthesized MOFs has been increasing very rapidly. High-throughput molecular simulations are very useful to screen large numbers of MOFs in order to identify the most promising adsorbents prior to extensive experimental studies. Results of molecular simulations depend on the force field used to define the interactions between gas molecules and MOFs. Choosing the appropriate force field for MOFs is essential to make reliable predictions about the materials' performance. In this work, we performed two sets of molecular simulations using the two widely used generic force fields, Dreiding and UFF, and obtained adsorption data of CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 mixtures in 100 different MOF structures. Using this adsorption data, several adsorbent evaluation metrics including selectivity, working capacity, sorbent selection parameter, and percent regenerability were computed for each MOF. MOFs were then ranked based on these evaluation metrics, and top performing materials were identified. We then examined the sensitivity of the MOF rankings to the force field type. Our results showed that although there are significant quantitative differences between some adsorbent evaluation metrics computed using different force fields, rankings of the top MOF adsorbents for CO 2 separations are generally similar: 8, 8, and 9 out of the top 10 most selective MOFs were found to be identical in the ranking for CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 separations using Dreiding and UFF. We finally suggested a force field factor depending on the energy parameters of atoms present in the MOFs to quantify the robustness of the simulation results to the force field selection. This easily computable factor will be highly useful to determine whether the results are sensitive to the force field type or not prior to performing computationally demanding

  8. A nonlinear eigenvalue problem for self-similar spherical force-free magnetic fields

    Energy Technology Data Exchange (ETDEWEB)

    Lerche, I. [Institut für Geowissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther Universität, D-06099 Halle (Germany); Low, B. C. [High Altitude Observatory, National Center for Atmospheric Research, Boulder, Colorado 80307 (United States)

    2014-10-15

    An axisymmetric force-free magnetic field B(r, θ) in spherical coordinates is defined by a function r sin θB{sub φ}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r sin θB{sub φ}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(θ))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(θ) as its eigenfunction [B. C. Low and Y. Q Lou, Astrophys. J. 352, 343 (1990)]. A complete analysis is presented of the eigenvalue spectrum for a given n, providing a unified understanding of the eigenfunctions and the physical relationship between the field's degree of multi-polarity and rate of radial decay via the parameter n. These force-free fields, self-similar on spheres of constant r, have basic astrophysical applications. As explicit solutions they have, over the years, served as standard benchmarks for testing 3D numerical codes developed to compute general force-free fields in the solar corona. The study presented includes a set of illustrative multipolar field solutions to address the magnetohydrodynamics (MHD) issues underlying the observation that the solar corona has a statistical preference for negative and positive magnetic helicities in its northern and southern hemispheres, respectively; a hemispherical effect, unchanging as the Sun's global field reverses polarity in successive eleven-year cycles. Generalizing these force-free fields to the separable form B=(H(θ,φ))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for φ-dependence greatly complicates the governing equations that have remained intractable. The axisymmetric results obtained are discussed in relation to this generalization and the Parker Magnetostatic Theorem. The axisymmetric solutions are mathematically related to a family of 3D time-dependent ideal MHD solutions for a polytropic fluid of index γ = 4

  9. Force fields of charged particles in micro-nanofluidic preconcentration systems

    Science.gov (United States)

    Gong, Lingyan; Ouyang, Wei; Li, Zirui; Han, Jongyoon

    2017-12-01

    Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system. This letter studies the particle trapping phenomena that are not explainable in the 1D model through the calculation of the two-dimensional (2D) force fields. The trapping of charged particles is shown to significantly distort the electric field and fluid flow pattern, which in turn leads to the different trapping behaviors of particles of different sizes. The mechanisms behind the protrusions and instability of the focused band, which are important factors determining overall preconcentration efficiency, are revealed through analyzing the rotating fluxes of particles in the vicinity of the ion-selective membrane. The differences in the enrichment factors of differently sized particles are understood through the interplay between the electric force and convective fluid flow. These results provide insights into the electrokinetic concentration effect, which could facilitate the design and optimization of ICP-based preconcentration systems.

  10. Self-consistent Optomechanical Dynamics and Radiation Forces in Thermal Light Fields

    International Nuclear Information System (INIS)

    Sonnleitner, M.

    2014-01-01

    We discuss two different aspects of the mechanical interaction between neutral matter and electromagnetic radiation.The first part addresses the complex dynamics of an elastic dielectric deformed by optical forces. To do so we use a one-dimensional model describing the medium by an array of beam splitters such that the interaction with the incident waves can be described with a transfer-matrix approach. Since the force on each individual beam splitter is known we thus obtain the correct volumetric force density inside the medium. Sending a light field through an initially homogeneous dielectric then results in density modulations which in turn alter the optical properties of this medium.The second part is concerned with mechanical light-effects on atoms in thermal radiation fields. At hand of a generic setup of an atom interacting with a hot sphere emitting blackbody radiation we show that the emerging gradient force may surpass gravity by several orders of magnitude. The strength of the repulsive scattering force strongly depends on the spectrum of the involved atoms and can be neglected in some setups. A special emphasis lies on possible implications on astrophysical scenarios where the interactions between heated dust and atoms, molecules or nanoparticles are of crucial interest. (author) [de

  11. Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

    Science.gov (United States)

    Saito, Minoru; Okazaki, Isao

    2009-12-01

    The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

  12. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

    Science.gov (United States)

    Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.

    2015-01-01

    Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208

  13. Life on the edge: squirrel-cage fringe fields and their effects in the MBE-4 combiner experiment

    International Nuclear Information System (INIS)

    Fawley, W.M.

    1996-02-01

    The MBE-4 combiner experiment employs an electrostatic combined-function focusing/bending element, the so-called ''squirrel-cage'' just before the actual merging region. There has been concern that non-linear fields, primarily in the fringe regions at the beginning and end of the cage, may be strong enough to lead to significant emittance degradation. This note present the results of numerical calculations which determined the anharmonic, non-linear components of the 3D fields in the cage and the resultant, orbit-integrated effects upon the MBE-4 beamlets. We find that while the anharmonic effects are small compared to the dipole deflection, the resultant transverse emittance growth is significant when compared to the expected value of the initial emittance of the individual beamlets

  14. Electric field and dielectrophoretic force on a dielectric particle chain in a parallel-plate electrode system

    International Nuclear Information System (INIS)

    Techaumnat, B; Eua-arporn, B; Takuma, T

    2004-01-01

    This paper presents results of calculations of the electric field and dielectrophoretic force on a dielectric particle chain suspended in a host liquid lying between parallel-plate electrodes. The method of calculation is based on the method of multipole images using the multipole re-expansion technique. We have investigated the effect of the particle permittivity, the tilt angle (between the chain and the applied field) and the chain arrangement on the electric field and force. The results show that the electric field intensification rises in accordance with the increase in the ratio of the particle-to-liquid permittivity, Γ ε . The electric field at the contact point between the particles decreases with increasing tilt angle, while the maximal field at the contact point between the particles and the plate electrodes is almost unchanged. The maximal field can be approximated by a simple formula, which is a quadratic function of Γ ε . The dielectrophoretic force depends significantly on the distance from other particles or an electrode. However, for the tilt angles in this paper, the horizontal force on the upper particle of the chain always has the direction opposite to the shear direction. The maximal horizontal force of a chain varies proportional to (Γ ε - 1) 1.7 if the particles in the chain are still in contact with each other. The approximated force, based on the force on an isolated chain, has been compared with our calculation results. The comparison shows that no approximation model agrees well with our results throughout the range of permittivity ratios

  15. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  16. ATK-ForceField: a new generation molecular dynamics software package

    Science.gov (United States)

    Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

    2017-12-01

    ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

  17. X ray absorption fine structure of systems in the anharmonic limit

    Science.gov (United States)

    Mustredeleon, J.; Conradson, S. D.; Batistic, I.; Bishop, A. R.; Raistrick, I.; Jackson, W. E.; Brown, G. E.

    A new approach to the analysis of x-ray absorption fine structure (XAFS) data is presented. It is based on the use of radial distribution functions directly calculated from a single-particle ion Hamiltonian containing model potentials. The starting point of this approach is the statistical average of the XAFS for an atomic pair. This average can be computed using a radial distribution function (RDF), which can be expressed in terms of the eigenvalues and wavefunctions associated with the model potential. The pair potential describing the ionic motion is then expressed in terms of parameters that are determined by fitting this statistical average to the experimental XAFS spectrum. This approach allows the use of XAFS as a tool for mapping near-neighbor interatomic potentials, and allows the treatment of systems which exhibit strongly anharmonic potentials which can be treated by perturbative methods. Using this method we have analyzed the high temperature behavior of the oxygen contributions to the Fe K-edge XAFS in the ferrosilicate minerals andradite (Ca3Fe2Si3O12) and magnesiowustite (Mg(0.9)Fe(0.1)O). Using a temperature dependent anharmonic correction derived from these model compounds, we have found evidence for a local structural change in the Fe-O coordination environment upon melting of the geologically important mineral fayalite (Fe2SiO4). We have also employed this method to the study of the axial oxygen contributions to the polarized Cu K-edge XAFS on oriented samples of YBa2Cu3O7 and related compounds. From this study we find evidence for an axial oxygen-centered lattice distortion accompanying the superconducting phase transition and a correlation between this distortion and Tc. The relation of the observed lattice distortion to mechanisms of superconductivity is discussed.

  18. X-ray absorption fine structure of systems in the anharmonic limit

    International Nuclear Information System (INIS)

    Mustre de Leon, J.; Conradson, S.D.; Batistic, I.; Bishop, A.R.; Raistrick, I.; Jackson, W.E.; Brown, G.E.

    1991-01-01

    A new approach to the analysis of x-ray absorption fine structure (XAFS) data is presented. It is based on the use of radial distribution functions directly calculated from a single-particle ion hamiltonian containing model potentials. The starting point of this approach is the statistical average of the XAFS for an atomic pair. This average can be computed using a radial distribution function (RDF), which can be expressed in terms of the eigenvalues and wavefunctions associated with the model potential. The pair potential describing the ionic motion is then expressed in terms of parameters that are determined by fitting this statistical average to the experimental XAFS spectrum. This approach allow the use of XAFS as a tool for mapping near-neighbor interatomic potentials, and allows the treatment of systems which exhibit strongly anharmonic potentials which can be treated by perturbative methods. Using this method we have analyzed the high temperature behavior of the oxygen contributions to the Fe K-edge XAFS in the ferrosilicate minerals andradite (Ca 3 Fe 2 Si 3 O 12 ) and magnesiowustite (Mg 0.9 Fe 0.1 O). Using a temperature dependent anharmonic correction derived from these model compounds, we have found evidence for a local structural change in the Fe-O coordination environment upon melting of the geologically important mineral fayalite (Fe 2 SiO 4 ). We have also employed this method to the study of the axial oxygen contributions to the polarized Cu K-edge XAFS on oriented samples of YBa 2 Cu 3 O 7 and related compounds. From this study we find evidence for an axial oxygen-centered lattice distortion accompanying the superconducting phase transition and a correlation between this distortion and T c . The relation of the observed lattice distortion to mechanisms of superconductivity is discussed. 33 refs., 6 figs

  19. On the absorbing force of magnetic fields acting on magnetic particle under magnetic particle examination

    International Nuclear Information System (INIS)

    Maeda, N.

    1988-01-01

    During the magnetic particle examination, magnetic particles near defects are deposited by an absorbing force of magnetic fields acting on the magnetic particles. Therefore, a quantitative determination of this absorbing force is a theoretical and experimental basis for solving various problems associated with magnetic particle examinations. The absorbing force is formulated based on a magnetic dipole model, and a measuring method of the absorbing force using magnetic fields formed around linear current is proposed. Measurements according to this method produced appropriate results, verifying the validation of the concept and the measuring method

  20. Relationship of scattering phase shifts to special radiation force conditions for spheres in axisymmetric wave-fields.

    Science.gov (United States)

    Marston, Philip L; Zhang, Likun

    2017-05-01

    When investigating the radiation forces on spheres in complicated wave-fields, the interpretation of analytical results can be simplified by retaining the s-function notation and associated phase shifts imported into acoustics from quantum scattering theory. For situations in which dissipation is negligible, as taken to be the case in the present investigation, there is an additional simplification in that partial-wave phase shifts become real numbers that vanish when the partial-wave index becomes large and when the wave-number-sphere-radius product vanishes. By restricting attention to monopole and dipole phase shifts, transitions in the axial radiation force for axisymmetric wave-fields are found to be related to wave-field parameters for traveling and standing Bessel wave-fields by considering the ratio of the phase shifts. For traveling waves, the special force conditions concern negative forces while for standing waves, the special force conditions concern vanishing radiation forces. An intermediate step involves considering the functional dependence on phase shifts. An appendix gives an approximation for zero-force plane standing wave conditions. Connections with early investigations of acoustic levitation are mentioned and some complications associated with viscosity are briefly noted.

  1. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

    Science.gov (United States)

    Vanommeslaeghe, K; MacKerell, A D

    2012-12-21

    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .

  2. Vector field statistical analysis of kinematic and force trajectories.

    Science.gov (United States)

    Pataky, Todd C; Robinson, Mark A; Vanrenterghem, Jos

    2013-09-27

    When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of 'non-directed' hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called 'statistical parametric mapping' (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems. © 2013 Published by Elsevier Ltd. All rights reserved.

  3. Mean-field Ohm's law and coaxial helicity injection in force-free plasmas

    International Nuclear Information System (INIS)

    Weening, R. H.

    2011-01-01

    A theoretical analysis of steady-state coaxial helicity injection (CHI) in force-free plasmas is presented using a parallel mean-field Ohm's law that includes resistivity η and hyper-resistivity Λ terms. Using Boozer coordinates, a partial differential equation is derived for the time evolution of the mean-field poloidal magnetic flux, or magnetic Hamiltonian function, from the parallel mean-field Ohm's law. A general expression is obtained from the mean-field theory for the efficiency of CHI current drive in force-free plasmas. Inductances of internal energy, magnetic helicity, and poloidal magnetic flux are used to characterize axisymmetric plasma equilibria that have a model current profile. Using the model current profile, a method is suggested to determine the level of magnetohydrodynamic activity at the magnetic axis and the consequent deviation from the completely relaxed Taylor state. The mean-field Ohm's law model suggests that steady-state CHI can be viewed most simply as a boundary layer problem.

  4. New approaches and solutions of the nonlinear force-free field

    International Nuclear Information System (INIS)

    Xie Baisong; Yin Xintao; Luo Xia

    2006-01-01

    New approaches to nonlinear force-free field equations are presented and new exact solutions are found analytically. Examples are given and some implications of the results to astrophysical solar plasmas as well as tokamak plasmas are discussed

  5. Quantum effects in amplitude death of coupled anharmonic self-oscillators

    Science.gov (United States)

    Amitai, Ehud; Koppenhöfer, Martin; Lörch, Niels; Bruder, Christoph

    2018-05-01

    Coupling two or more self-oscillating systems may stabilize their zero-amplitude rest state, therefore quenching their oscillation. This phenomenon is termed "amplitude death." Well known and studied in classical self-oscillators, amplitude death was only recently investigated in quantum self-oscillators [Ishibashi and Kanamoto, Phys. Rev. E 96, 052210 (2017), 10.1103/PhysRevE.96.052210]. Quantitative differences between the classical and quantum descriptions were found. Here, we demonstrate that for quantum self-oscillators with anharmonicity in their energy spectrum, multiple resonances in the mean phonon number can be observed. This is a result of the discrete energy spectrum of these oscillators, and is not present in the corresponding classical model. Experiments can be realized with current technology and would demonstrate these genuine quantum effects in the amplitude death phenomenon.

  6. Quantifying the Attractive Force Exerted on the Pinned Calcium Spiral Waves by Using the Adventive Field

    International Nuclear Information System (INIS)

    Qiu Kang; Tang Jun; Luo Jin-Ming; Ma Jun

    2013-01-01

    The cytosolic calcium system is inhomogenous because of the discrete and random distribution of ion channels on the ER membrane. It is well known that the spiral tip can be pinned by the heterogenous area, and the field can detach the spiral from the heterogeneity. We use the adventive field to counteract the attractive force exerting on the calcium spiral wave by the heterogeneity, then the strength of the adventive field is used to quantify the attractive force indirectly. Two factors determining the attractive force are studied. It is found that: (1) the attractive force sharply increases with size of the heterogeneity for small-size heterogeneity, whereas the force increases to a saturated value for large-size heterogeneity; (2) for large-size heterogeneity, the force almost remains constant unless the level of the heterogeneity vanishes, the force decreases to zero linearly and sharply, and for small-size heterogeneity, the force decreases successively with the level of the heterogeneity. Furthermore, it is found that the forces exist only when the spiral tip is very close to the heterogenous area. Our study may shed some light on the control or suppression of the calcium spiral wave

  7. Coupled energy-drift and force-balance equations for high-field hot-carrier transport

    International Nuclear Information System (INIS)

    Huang, Danhong; Alsing, P.M.; Apostolova, T.; Cardimona, D.A.

    2005-01-01

    Coupled energy-drift and force-balance equations that contain a frictional force for the center-of-mass motion of electrons are derived for hot-electron transport under a strong dc electric field. The frictional force is found to be related to the net rate of phonon emission, which takes away the momentum of a phonon from an electron during each phonon-emission event. The net rate of phonon emission is determined by the Boltzmann scattering equation, which depends on the distribution of electrons interacting with phonons. The work done by the frictional force is included into the energy-drift equation for the electron-relative scattering motion and is found to increase the thermal energy of the electrons. The importance of the hot-electron effect in the energy-drift term under a strong dc field is demonstrated in reducing the field-dependent drift velocity and mobility. The Doppler shift in the energy conservation of scattering electrons interacting with impurities and phonons is found to lead to an anisotropic distribution of electrons in the momentum space along the field direction. The importance of this anisotropic distribution is demonstrated through a comparison with the isotropic energy-balance equation, from which we find that defining a state-independent electron temperature becomes impossible. To the leading order, the energy-drift equation is linearized with a distribution function by expanding it into a Fokker-Planck-type equation, along with the expansions of both the force-balance equation and the Boltzmann scattering equation for hot phonons

  8. A bidirectional brain-machine interface algorithm that approximates arbitrary force-fields.

    Directory of Open Access Journals (Sweden)

    Alessandro Vato

    Full Text Available We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop.

  9. A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

    Science.gov (United States)

    Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

    2017-12-01

    We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

  10. Random-phase approximation and its extension for the O(2) anharmonic oscillator

    International Nuclear Information System (INIS)

    Aouissat, Z.; Martin, C.

    2004-01-01

    We apply the random-phase approximation (RPA) and its extension called renormalized RPA to the quantum anharmonic oscillator with an O(2) symmetry. We first obtain the equation for the RPA frequencies in the standard and in the renormalized RPAs using the equation-of-motion method. In the case where the ground state has a broken symmetry, we check the existence of a zero frequency in the standard and in the renormalized RPAs. Then we use a time-dependent approach where the standard-RPA frequencies are obtained as small oscillations around the static solution in the time-dependent Hartree-Bogolyubov equation. We draw the parallel between the two approaches. (orig.)

  11. Random-phase approximation and its extension for the O(2) anharmonic oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Aouissat, Z. [Institut fuer Kernphysik, Technische Hochschule Darmstadt, Schlossgarten 9, D-64289, Darmstadt (Germany); Martin, C. [Groupe de Physique Theorique, Institut de Physique Nucleaire, F-91406, Orsay Cedex (France)

    2004-02-01

    We apply the random-phase approximation (RPA) and its extension called renormalized RPA to the quantum anharmonic oscillator with an O(2) symmetry. We first obtain the equation for the RPA frequencies in the standard and in the renormalized RPAs using the equation-of-motion method. In the case where the ground state has a broken symmetry, we check the existence of a zero frequency in the standard and in the renormalized RPAs. Then we use a time-dependent approach where the standard-RPA frequencies are obtained as small oscillations around the static solution in the time-dependent Hartree-Bogolyubov equation. We draw the parallel between the two approaches. (orig.)

  12. Effects of lorentz force on flow fields of free burning arc and wall stabilized non-transferred arc

    International Nuclear Information System (INIS)

    Peng Yi; Huang Heji; Pan Wenxia

    2013-01-01

    The flow fields of two typical DC plasma arcs, namely the transferred free burning arc and the non-transferred arc were simulated by solving hydrodynamic equations and electromagnetic equations. The effects of the Lorentz force on the characteristics of the flow fields of these two typical DC plasma arcs were estimated. Results show that in the case of the free burning arc, the Lorentz force due to the current self-induced magnetic field has significant impact on the flow fields, as the self-induced magnetic compression is the main arc constraint mechanism. However, in the case of the non-transferred arc generated in a torch with long and narrow inter-electrode inserts and an abruptly expanded anode, the Lorentz force has limited impact on the flow fields of the plasma especially at the downstream of the inter-electrode inserts, compared with the strong wall constraints and relatively high aerodynamic force. This is because the ratio of the electromagnetic force to the aerodynamic force is only about 0.01 in this region. When the main consideration is outlet parameters of the wall stabilized non-transferred DC arc plasma generator, in order to improve the efficiency of the numerical simulation program, the Lorentz force could be neglected in the non-transferred arc in some cases. (authors)

  13. Regularization of fields for self-force problems in curved spacetime: Foundations and a time-domain application

    International Nuclear Information System (INIS)

    Vega, Ian; Detweiler, Steven

    2008-01-01

    We propose an approach for the calculation of self-forces, energy fluxes and waveforms arising from moving point charges in curved spacetimes. As opposed to mode-sum schemes that regularize the self-force derived from the singular retarded field, this approach regularizes the retarded field itself. The singular part of the retarded field is first analytically identified and removed, yielding a finite, differentiable remainder from which the self-force is easily calculated. This regular remainder solves a wave equation which enjoys the benefit of having a nonsingular source. Solving this wave equation for the remainder completely avoids the calculation of the singular retarded field along with the attendant difficulties associated with numerically modeling a delta-function source. From this differentiable remainder one may compute the self-force, the energy flux, and also a waveform which reflects the effects of the self-force. As a test of principle, we implement this method using a 4th-order (1+1) code, and calculate the self-force for the simple case of a scalar charge moving in a circular orbit around a Schwarzschild black hole. We achieve agreement with frequency-domain results to ∼0.1% or better.

  14. Strong anharmonicity in the phonon spectra of PbTe and SnTe from first principles

    Science.gov (United States)

    Ribeiro, Guilherme A. S.; Paulatto, Lorenzo; Bianco, Raffaello; Errea, Ion; Mauri, Francesco; Calandra, Matteo

    2018-01-01

    At room temperature, PbTe and SnTe are efficient thermoelectrics with a cubic structure. At low temperature, SnTe undergoes a ferroelectric transition with a critical temperature strongly dependent on the hole concentration, while PbTe is an incipient ferroelectric. By using the stochastic self-consistent harmonic approximation, we investigate the anharmonic phonon spectra and the occurrence of a ferroelectric transition in both systems. We find that vibrational spectra strongly depend on the approximation used for the exchange-correlation kernel in density-functional theory. If gradient corrections and the theoretical volume are employed, then the calculation of the phonon frequencies as obtained from the diagonalization of the free-energy Hessian leads to phonon spectra in good agreement with experimental data for both systems. In PbTe we evaluate the linear thermal expansion coefficient γ =2.3 ×10-5K-1 , finding it to be in good agreement with experimental value of γ =2.04 ×10-5K-1 . Furthermore, we study the phonon spectrum and we do reproduce the transverse optical mode phonon satellite detected in inelastic neutron scattering and the crossing between the transverse optical and the longitudinal acoustic modes along the Γ X direction. The phonon satellite becomes broader at high temperatures but its energy is essentially temperature independent, in agreement with experiments. We decompose the self-consistent harmonic free energy in second-, third-, and fourth-order anharmonic terms. We find that the third- and fourth-order terms are small. However, treating the third-order term perturbatively on top of the second-order self-consistent harmonic free energy overestimates the energy of the satellite associated with the transverse optical mode. On the contrary, a perturbative treatment on top of the harmonic Hamiltonian breaks down and leads to imaginary phonon frequencies already at 300 K. In the case of SnTe, we describe the occurrence of a ferroelectric

  15. Magnetohydrodynamic Modeling of Solar Coronal Dynamics with an Initial Non-force-free Magnetic Field

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur-313001 (India)

    2017-05-01

    The magnetic fields in the solar corona are generally neither force-free nor axisymmetric and have complex dynamics that are difficult to characterize. Here we simulate the topological evolution of solar coronal magnetic field lines (MFLs) using a magnetohydrodynamic model. The simulation is initialized with a non-axisymmetric non-force-free magnetic field that best correlates with the observed vector magnetograms of solar active regions (ARs). To focus on these ideas, simulations are performed for the flaring AR 11283 noted for its complexity and well-documented dynamics. The simulated dynamics develops as the initial Lorentz force pushes the plasma and facilitates successive magnetic reconnections at the two X-type null lines present in the initial field. Importantly, the simulation allows for the spontaneous development of mass flow, unique among contemporary works, that preferentially reconnects field lines at one of the X-type null lines. Consequently, a flux rope consisting of low-lying twisted MFLs, which approximately traces the major polarity inversion line, undergoes an asymmetric monotonic rise. The rise is attributed to a reduction in the magnetic tension force at the region overlying the rope, resulting from the reconnection. A monotonic rise of the rope is in conformity with the standard scenario of flares. Importantly, the simulated dynamics leads to bifurcations of the flux rope, which, being akin to the observed filament bifurcation in AR 11283, establishes the appropriateness of the initial field in describing ARs.

  16. Microscopic derivation of the force on a dielectric fluid in an electromagnetic field

    International Nuclear Information System (INIS)

    Lai, H.M.; Suen, W.M.; Young, K.

    1982-01-01

    The force acting on a Clausius-Mossotti fluid in an electromagnetic field is evaluated microscopically. Owing to the modification of the two-particle density by the electric field, an additional mechanical force Δf/sup( M/) is found. When this is added to the electrical force f/sup( E/), the total force in the static case becomes identical to that deduced macroscopically by Helmholtz. The analysis is extended to various time-dependent cases, and it is pointed out that Δf/sup( M/) essentially assumes its static value on time scales longer than T/sub c/, the relaxation time of the two-particle density, but is otherwise negligibly small. Thus Peierls's theory of the momentum of light is valid only for pulses much shorter than T/sub c/; the necessary correction due to Δf/sup( M/) in other cases is given and discussed

  17. Scalar meson field and many-body forces. Chapter 23

    International Nuclear Information System (INIS)

    Nyman, E.M.

    1979-01-01

    In applications of field theory to the theory of the nuclear forces, one has frequently assumed that there is a scalar meson. It will then be responsible for most of the medium-range attraction between the nucleons. According to current ideas, however, it is possible to account for the medium-range attraction without an elementary sigma meson. This approach requires a careful treatment of the exchange of interacting pairs of π mesons, such as to include those ππ interactions which are responsible for the formation and decay of the sigma meson. Recently, the scalar field in the nuclear many-body problem has begun to receive more attention. There are two reasons for this change of philosophy. One reason is the discovery of neutron stars. In neutron stars, the nucleon number density can be much higher than in nuclei. One therefore wants to derive the equation of state from a relativistic many-body theory. This forces one to deal explicitly with a set of mesons, such that in the non-relativistic limit one recovers the one-boson-exchange potential. (Auth.)

  18. High pressure behavior of complex phosphate K2Ce[PO4]2: Grüneisen parameter and anharmonicity properties

    Science.gov (United States)

    Mishra, Karuna Kara; Bevara, Samatha; Ravindran, T. R.; Patwe, S. J.; Gupta, Mayanak K.; Mittal, Ranjan; Krishnan, R. Venkata; Achary, S. N.; Tyagi, A. K.

    2018-02-01

    Herein we reported structural stability, vibrational and thermal properties of K2Ce[PO4]2, a relatively underexplored complex phosphate of tetravalent Ce4+ from in situ high-pressure Raman spectroscopic investigations up to 28 GPa using a diamond anvil cell. The studies identified the soft phonons that lead to a reversible phase transformation above 8 GPa, and a phase coexistence of ambient (PI) and high pressure (PII) phases in a wider pressure region 6-11 GPa. From a visual representation of the computed eigen vector displacements, the Ag soft mode at 82 cm-1 is assigned as a lattice mode of K+ cation. Pressure-induced positional disorder is apparent from the substantial broadening of internal modes and the disappearance of low frequency lattice and external modes in phase PII above 18 GPa. Isothermal mode Grüneisen parameters γi of the various phonon modes are calculated and compared for several modes. Using these values, thermal properties such as average Grüneisen parameter, and thermal expansion coefficient are estimated as 0.47, and 2.5 × 10-6 K-1, respectively. The specific heat value was estimated from all optical modes obtained from DFT calculations as 314 J-mol-1 K-1. Our earlier reported temperature dependence of phonon frequencies is used to decouple the "true anharmonic" (explicit contribution at constant volume) and "quasi harmonic" (implicit contribution brought out by volume change) contributions from the total anharmonicity. In addition to the 81 cm-1 Ag lattice mode, several other lattice and external modes of PO43- ions are found to be strongly anharmonic.

  19. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

    NARCIS (Netherlands)

    Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

    2007-01-01

    The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ

  20. Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

    Science.gov (United States)

    Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

    2015-01-01

    Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

  1. Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol

    NARCIS (Netherlands)

    Winger, Moritz; de Vries, Alex H.; van Gunsteren, Wilfred F.

    2009-01-01

    A molecular dynamics (MD) study of ,-dimethoxypolyethylene glycol has been carried out under various conditions with respect to solvent composition, ionic strength, chain length, force field and temperature. A previous MD study on a 15-mer of polyethyleneglycol (PEG) suggested a helical equilibrium

  2. Efficient nonparametric n -body force fields from machine learning

    Science.gov (United States)

    Glielmo, Aldo; Zeni, Claudio; De Vita, Alessandro

    2018-05-01

    We provide a definition and explicit expressions for n -body Gaussian process (GP) kernels, which can learn any interatomic interaction occurring in a physical system, up to n -body contributions, for any value of n . The series is complete, as it can be shown that the "universal approximator" squared exponential kernel can be written as a sum of n -body kernels. These recipes enable the choice of optimally efficient force models for each target system, as confirmed by extensive testing on various materials. We furthermore describe how the n -body kernels can be "mapped" on equivalent representations that provide database-size-independent predictions and are thus crucially more efficient. We explicitly carry out this mapping procedure for the first nontrivial (three-body) kernel of the series, and we show that this reproduces the GP-predicted forces with meV /Å accuracy while being orders of magnitude faster. These results pave the way to using novel force models (here named "M-FFs") that are computationally as fast as their corresponding standard parametrized n -body force fields, while retaining the nonparametric character, the ease of training and validation, and the accuracy of the best recently proposed machine-learning potentials.

  3. Force field inside the void in complex plasmas under microgravity conditions

    International Nuclear Information System (INIS)

    Kretschmer, M.; Khrapak, S.A.; Zhdanov, S.K.; Thomas, H.M.; Morfill, G.E.; Fortov, V.E.; Lipaev, A.M.; Molotkov, V.I.; Ivanov, A.I.; Turin, M.V.

    2005-01-01

    Observations of complex plasmas under microgravity conditions onboard the International Space Station performed with the Plasma-Kristall experiment-Nefedov facility are reported. A weak instability of the boundary between the central void (region free of microparticles) and the microparticle cloud is observed at low gas pressures. The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called the 'trampoline effect'). The trajectories of injected particles are analyzed providing information on the force field inside the void. The experimental results are compared with theory which assumes that the most important forces inside the void are the electric and the ion drag forces. Good agreement is found clearly indicating that under conditions investigated the void formation is caused by the ion drag force

  4. Nonlinear gravitational self-force: Field outside a small body

    Science.gov (United States)

    Pound, Adam

    2012-10-01

    A small extended body moving through an external spacetime gαβ creates a metric perturbation hαβ, which forces the body away from geodesic motion in gαβ. The foundations of this effect, called the gravitational self-force, are now well established, but concrete results have mostly been limited to linear order. Accurately modeling the dynamics of compact binaries requires proceeding to nonlinear orders. To that end, I show how to obtain the metric perturbation outside the body at all orders in a class of generalized wave gauges. In a small buffer region surrounding the body, the form of the perturbation can be found analytically as an expansion for small distances r from a representative worldline. Given only a specification of the body’s multipole moments, the field obtained in the buffer region suffices to find the metric everywhere outside the body via a numerical puncture scheme. Following this procedure at first and second order, I calculate the field in the buffer region around an arbitrarily structured compact body at sufficiently high order in r to numerically implement a second-order puncture scheme, including effects of the body’s spin. I also define nth-order (local) generalizations of the Detweiler-Whiting singular and regular fields and show that in a certain sense, the body can be viewed as a skeleton of multipole moments.

  5. Simulation of the elementary evolution operator with the motional states of an ion in an anharmonic trap

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ludovic; Vaeck, Nathalie [Laboratoire de Chimie Quantique et Photophysique, CP 160/09 Université Libre de Bruxelles, B-1050 Brussels (Belgium); Justum, Yves [Laboratoire de Chimie Physique, UMR 8000 and CNRS, Université Paris-Sud, F-91405 Orsay (France); Desouter-Lecomte, M. [Laboratoire de Chimie Physique, UMR 8000 and CNRS, Université Paris-Sud, F-91405 Orsay (France); Département de Chimie, Université de Liège, Bât B6c, Sart Tilman B-4000, Liège (Belgium)

    2015-04-07

    Following a recent proposal of L. Wang and D. Babikov [J. Chem. Phys. 137, 064301 (2012)], we theoretically illustrate the possibility of using the motional states of a Cd{sup +} ion trapped in a slightly anharmonic potential to simulate the single-particle time-dependent Schrödinger equation. The simulated wave packet is discretized on a spatial grid and the grid points are mapped on the ion motional states which define the qubit network. The localization probability at each grid point is obtained from the population in the corresponding motional state. The quantum gate is the elementary evolution operator corresponding to the time-dependent Schrödinger equation of the simulated system. The corresponding matrix can be estimated by any numerical algorithm. The radio-frequency field which is able to drive this unitary transformation among the qubit states of the ion is obtained by multi-target optimal control theory. The ion is assumed to be cooled in the ground motional state, and the preliminary step consists in initializing the qubits with the amplitudes of the initial simulated wave packet. The time evolution of the localization probability at the grids points is then obtained by successive applications of the gate and reading out the motional state population. The gate field is always identical for a given simulated potential, only the field preparing the initial wave packet has to be optimized for different simulations. We check the stability of the simulation against decoherence due to fluctuating electric fields in the trap electrodes by applying dissipative Lindblad dynamics.

  6. Leveraging intellectual capital through Lewin's Force Field Analysis: The case of software development companies

    Directory of Open Access Journals (Sweden)

    Alexandru Capatina

    2017-09-01

    Full Text Available This article presents an original conceptual framework for the strategic management of intellectual capital assets in software development companies. The framework is based on Lewin's Force Field Analysis. The framework makes it possible to assess software company managers’ opinions regarding the way driving and restraining forces affect the pillars of intellectual capital. The capacity to adapt to change is vital for companies in knowledge-intensive industries. Accordingly, this study examined a sample of 74 Romanian software development companies. The aim was to help companies benefit from managing the driving and restraining forces acting upon the pillars of intellectual capital (human, structural, and relational. The effects of the driving forces, quantified by PathMaker software's Force Field Tool, were observed to be greater than the restraining forces for each pillar of intellectual capital. This paper contributes by showing the explanatory power of this framework. The framework thus offers a tool that helps managers drive change in their organizations through effective intellectual capital management. Furthermore, this article describes how to encourage the implementation of changes that create value for software development companies.

  7. The Quantum Space Phase Transitions for Particles and Force Fields

    Directory of Open Access Journals (Sweden)

    Chung D.-Y.

    2006-07-01

    Full Text Available We introduce a phenomenological formalism in which the space structure is treated in terms of attachment space and detachment space. Attachment space attaches to an object, while detachment space detaches from the object. The combination of these spaces results in three quantum space phases: binary partition space, miscible space and binary lattice space. Binary lattice space consists of repetitive units of alternative attachment space and detachment space. In miscible space, attachment space is miscible to detachment space, and there is no separation between attachment space and detachment spaces. In binary partition space, detachment space and attachment space are in two separat continuous regions. The transition from wavefunction to the collapse of wavefuction under interference becomes the quantum space phase transition from binary lattice space to miscible space. At extremely conditions, the gauge boson force field undergoes a quantum space phase transition to a "hedge boson force field", consisting of a "vacuum" core surrounded by a hedge boson shell, like a bubble with boundary.

  8. Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

    Science.gov (United States)

    Radosinski, Lukasz; Labus, Karolina

    2017-10-05

    Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.

  9. Properties of one-dimensional anharmonic lattice solitons

    Science.gov (United States)

    Szeftel, Jacob; Laurent-Gengoux, Pascal; Ilisca, Ernest; Hebbache, Mohamed

    2000-12-01

    The existence of bell- and kink-shaped solitons moving at constant velocity while keeping a permanent profile is studied in infinite periodic monoatomic chains of arbitrary anharmonicity by taking advantage of the equation of motion being integrable with respect to solitons. A second-order, non-linear differential equation involving advanced and retarded terms must be solved, which is done by implementing a scheme based on the finite element and Newton's methods. If the potential has a harmonic limit, the asymptotic time-decay behaves exponentially and there is a dispersion relation between propagation velocity and decay time. Inversely if the potential has no harmonic limit, the asymptotic regime shows up either as a power-law or faster than exponential. Excellent agreement is achieved with Toda's model. Illustrative examples are also given for the Fermi-Pasta-Ulam and sine-Gordon potentials. Owing to integrability an effective one-body potential is worked out in each case. Lattice and continuum solitons differ markedly from one another as regards the amplitude versus propagation velocity relationship and the asymptotic time behavior. The relevance of the linear stability analysis when applied to solitons propagating in an infinite crystal is questioned. The reasons preventing solitons from arising in a diatomic lattice are discussed.

  10. Gravitomagnetic field of the universe and Coriolis force on the rotating Earth

    International Nuclear Information System (INIS)

    Veto, B

    2011-01-01

    The Machian effect of distant masses of the universe in the frame of reference of the rotating Earth is demonstrated using the gravitomagnetic approach of general relativity. This effect appears in the form of a gravitomagnetic Lorentz force acting on moving bodies on the Earth. The gravitomagnetic field of the universe-deduced from a simple model-exerts a gravitomagnetic Lorentz force on moving bodies, a force parallel to and with comparable strength to the Coriolis force observed on the rotating Earth. It seems after simple considerations that the Coriolis force happens to be the gravitomagnetic Lorentz force exerted by the mass of a black hole universe. The description of the phenomenon is simpler using the gravitomagnetic approach than the standard formulation of general relativity, so the method relying on gravitomagnetism is advisable in lectures intended for master's degree level physics students and advanced undergraduates.

  11. The MARTINI force field : Coarse grained model for biomolecular simulations

    NARCIS (Netherlands)

    Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.

    2007-01-01

    We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To

  12. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  13. Magnetic field sensor based on the Ampere's force using dual-polarization DBR fiber laser

    Science.gov (United States)

    Yao, Shuang; Zhang, Yang; Guan, Baiou

    2015-08-01

    A novel magnetic field sensor using distributed Bragg reflector (DBR) fiber laser by Ampere's force effect is proposed and experimentally demonstrated. The key sensing element, that is the dual-polarization DBR fiber laser, is fixed on the middle part of two copper plates which carry the current. Ampere's force is applied onto the coppers due to an external magnetic field generated by a DC solenoid. Thus, the lateral force from the coppers is converted to a corresponding beat frequency signal shift produced by the DBR laser. The electric current sensing is also realized by the same configuration and same principle simultaneously in an intuitive manner. Good agreement between the theory calculation and the experimental results is obtained, which shows a good linearity. This sensor's sensitivity to the magnetic field and to the electric current finally reaches ~258.92 kHz/mT and ~1.08727 MHz/A, respectively.

  14. A molecular mechanics (MM3(96)) force field for metal-amide complexes

    International Nuclear Information System (INIS)

    Hay, B.P.; Clement, O.; Sandrone, G.; Dixon, D.A.

    1998-01-01

    A molecular mechanics (MM3(96)) force field is reported for modeling metal complexes of amides in which the amide is coordinated through oxygen. This model uses a points-on-a-sphere approach which involves the parameterization of the Msingle bondO stretch, the Msingle bondO double-bond C bend, and the Msingle bondO double-bond Csingle bondX (X = C, H, N) torsion interactions. Relationships between force field parameters and metal ion properties (charge, ionic radius, and electronegativity) are presented that allow the application of this model to a wide range of metal ions. The model satisfactorily reproduces the structures of over fifty amide complexes with the alkaline earths, transition metals, lanthanides, and actinides

  15. Polyad quantum numbers and multiple resonances in anharmonic vibrational studies of polyatomic molecules.

    Science.gov (United States)

    Krasnoshchekov, Sergey V; Stepanov, Nikolay F

    2013-11-14

    In the theory of anharmonic vibrations of a polyatomic molecule, mixing the zero-order vibrational states due to cubic, quartic and higher-order terms in the potential energy expansion leads to the appearance of more-or-less isolated blocks of states (also called polyads), connected through multiple resonances. Such polyads of states can be characterized by a common secondary integer quantum number. This polyad quantum number is defined as a linear combination of the zero-order vibrational quantum numbers, attributed to normal modes, multiplied by non-negative integer polyad coefficients, which are subject to definition for any particular molecule. According to Kellman's method [J. Chem. Phys. 93, 6630 (1990)], the corresponding formalism can be conveniently described using vector algebra. In the present work, a systematic consideration of polyad quantum numbers is given in the framework of the canonical Van Vleck perturbation theory (CVPT) and its numerical-analytic operator implementation for reducing the Hamiltonian to the quasi-diagonal form, earlier developed by the authors. It is shown that CVPT provides a convenient method for the systematic identification of essential resonances and the definition of a polyad quantum number. The method presented is generally suitable for molecules of significant size and complexity, as illustrated by several examples of molecules up to six atoms. The polyad quantum number technique is very useful for assembling comprehensive basis sets for the matrix representation of the Hamiltonian after removal of all non-resonance terms by CVPT. In addition, the classification of anharmonic energy levels according to their polyad quantum numbers provides an additional means for the interpretation of observed vibrational spectra.

  16. Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

    Directory of Open Access Journals (Sweden)

    Jiang Hualiang

    2010-11-01

    Full Text Available Abstract Background Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA, we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM and multiple empirical criteria based method (MECBM hybrided with different force fields. Results Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%. On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational

  17. Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.

    Science.gov (United States)

    Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D

    2002-03-01

    Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.

  18. A NEW CODE FOR NONLINEAR FORCE-FREE FIELD EXTRAPOLATION OF THE GLOBAL CORONA

    International Nuclear Information System (INIS)

    Jiang Chaowei; Feng Xueshang; Xiang Changqing

    2012-01-01

    Reliable measurements of the solar magnetic field are still restricted to the photosphere, and our present knowledge of the three-dimensional coronal magnetic field is largely based on extrapolations from photospheric magnetograms using physical models, e.g., the nonlinear force-free field (NLFFF) model that is usually adopted. Most of the currently available NLFFF codes have been developed with computational volume such as a Cartesian box or a spherical wedge, while a global full-sphere extrapolation is still under development. A high-performance global extrapolation code is in particular urgently needed considering that the Solar Dynamics Observatory can provide a full-disk magnetogram with resolution up to 4096 × 4096. In this work, we present a new parallelized code for global NLFFF extrapolation with the photosphere magnetogram as input. The method is based on the magnetohydrodynamics relaxation approach, the CESE-MHD numerical scheme, and a Yin-Yang spherical grid that is used to overcome the polar problems of the standard spherical grid. The code is validated by two full-sphere force-free solutions from Low and Lou's semi-analytic force-free field model. The code shows high accuracy and fast convergence, and can be ready for future practical application if combined with an adaptive mesh refinement technique.

  19. A Kirkwood-Buff derived force field for alkaline earth halide salts

    Science.gov (United States)

    Naleem, Nawavi; Bentenitis, Nikolaos; Smith, Paul E.

    2018-06-01

    The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX2), where M = Mg2+, Ca2+, Sr2+, Ba2+ and X = Cl-, Br-, I-, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

  20. A Non-Linear Force-Free Field Model for the Evolving Magnetic Structure of Solar Filaments

    Science.gov (United States)

    Mackay, Duncan H.; van Ballegooijen, A. A.

    2009-12-01

    In this paper the effect of a small magnetic element approaching the main body of a solar filament is considered through non-linear force-free field modeling. The filament is represented by a series of magnetic dips. Once the dips are calculated, a simple hydrostatic atmosphere model is applied to determine which structures have sufficient column mass depth to be visible in Hα. Two orientations of the bipole are considered, either parallel or anti-parallel to the overlying arcade. The magnetic polarity that lies closest to the filament is then advected towards the filament. Initially for both the dominant and minority polarity advected elements, right/left bearing barbs are produced for dextral/sinsitral filaments. The production of barbs due to dominant polarity elements is a new feature. In later stages the filament breaks into two dipped sections and takes a highly irregular, non-symmetrical form with multiple pillars. The two sections are connected by field lines with double dips even though the twist of the field is less than one turn. Reconnection is not found to play a key role in the break up of the filament. The non-linear force-free fields produce very different results to extrapolated linear-force free fields. For the cases considered here the linear force-free field does not produce the break up of the filament nor the production of barbs as a result of dominant polarity elements.

  1. Examination of forced unsteady separated flow fields on a rotating wind turbine blade

    Energy Technology Data Exchange (ETDEWEB)

    Huyer, S [Univ. of Colorado, Boulder, CO (US)

    1993-04-01

    The wind turbine industry faces many problems regarding the construction of efficient and predictable wind turbine machines. Steady state, two-dimensional wind tunnel data are generally used to predict aerodynamic loads on wind turbine blades. Preliminary experimental evidence indicates that some of the underlying fluid dynamic phenomena could be attributed to dynamic stall, or more specifically to generation of forced unsteady separated flow fields. A collaborative research effort between the University of Colorado and the National Renewable Energy Laboratory was conducted to systematically categorize the local and global effects of three- dimensional forced unsteady flow fields.

  2. Two-qubit gate operations in superconducting circuits with strong coupling and weak anharmonicity

    International Nuclear Information System (INIS)

    Lü Xinyou; Ashhab, S; Cui Wei; Wu Rebing; Nori, Franco

    2012-01-01

    We theoretically study the implementation of two-qubit gates in a system of two coupled superconducting qubits. In particular, we analyze two-qubit gate operations under the condition that the coupling strength is comparable with or even larger than the anharmonicity of the qubits. By numerically solving the time-dependent Schrödinger equation under the assumption of negligible decoherence, we obtain the dependence of the two-qubit gate fidelity on the system parameters in the case of both direct and indirect qubit-qubit coupling. Our numerical results can be used to identify the ‘safe’ parameter regime for experimentally implementing two-qubit gates with high fidelity in these systems. (paper)

  3. A Basic Experiment on Two-Dimensional Force of HTSC-Bulk in DC Magnetic-Field

    OpenAIRE

    吉田, 欣二郎; 松田, 茂雄; 松本, 洋和

    2000-01-01

    High temperature superconducting (HTSC) bulk can levitate stably on a track which consists of permanent magnets of the same polarity. This is because HTSC-bulk has a pinning force which keeps from vertical displacement due to the weight. We have proposed a new LSM theory which is based on an idea of considering the pinning force as synchronizing force in using armature travelling-magnetic-field instead of permanent magnets. However, the lift force enough to levitate the vehicle on the ground ...

  4. Asymptotic forms for the energy of force-free magnetic field ion figurations of translational symmetry

    Science.gov (United States)

    Sturrock, P. A.; Antiochos, S. K.; Klinchuk, J. A.; Roumeliotis, G.

    1994-01-01

    It is known from computer calculations that if a force-free magnetic field configuration is stressed progressively by footpoint displacements, the configuration expands and approaches the open configuration with the same surface flux distribution and the energy of the field increases progressively. For configurations of translationalsymmetry, it has been found empirically that the energy tends asymptotically to a certain functional form. It is here shown that analysis of a simple model of the asymptotic form of force-free fields of translational symmetry leads to and therefore justifies this functional form. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.

  5. Anharmonicity Rise the Thermal Conductivity in Amorphous Silicon

    Science.gov (United States)

    Lv, Wei; Henry, Asegun

    We recently proposed a new method called Direct Green-Kubo Modal Analysis (GKMA) method, which has been shown to calculate the thermal conductivity (TC) of several amorphous materials accurately. A-F method has been widely used for amorphous materials. However, researchers have found out that it failed on several different materials. The missing component of A-F method is the harmonic approximation and considering only the interactions of modes with similar frequencies, which neglect interactions of modes with large frequency difference. On the contrary, GKMA method, which is based on molecular dynamics, intrinsically includes all types of phonon interactions. In GKMA method, each mode's TC comes from both mode self-correlations (autocorrelations) and mode-mode correlations (crosscorrelations). We have demonstrated that the GKMA predicted TC of a-Si from Tersoff potential is in excellent agreement with one of experimental results. In this work, we will present the GKMA applications on a-Si using multiple potentials and gives us more insight of the effect of anharmonicity on the TC of amorphous silicon. This research was supported Intel grant AGMT DTD 1-15-13 and computational resources by NSF supported XSEDE resources under allocations DMR130105 and TG- PHY130049.

  6. Anharmonic longitudinal motion of bases and dynamics of nonlinear excitation in DNA.

    Science.gov (United States)

    Di Garbo, Angelo

    2016-01-01

    The dynamics of the transcription bubble in DNA is studied by using a nonlinear model in which torsional and longitudinal conformations of the biomolecule are coupled. In the absence of forcing and dissipation the torsional dynamics is described by a perturbed kink of the Sine-Gordon DNA model, while the longitudinal conformational energy propagate as phonons. It was found that for random initial conditions of the longitudinal conformational field the presence of the kink promotes the creation of phonons propagating along the chain axis. Moreover, the presence of forcing, describing the active role of RNA polymerase, determines in agreement to the experimental data a modulation of the velocity of the transcription bubble. Lastly, it was shown that the presence of dissipation impacts the dynamic of the phonon by reducing the amplitude of the corresponding conformational field. On the contrary, dissipation and forcing modulate the velocity of the transcription bubble alone.

  7. Vibrational multiconfiguration self-consistent field theory: implementation and test calculations.

    Science.gov (United States)

    Heislbetz, Sandra; Rauhut, Guntram

    2010-03-28

    A state-specific vibrational multiconfiguration self-consistent field (VMCSCF) approach based on a multimode expansion of the potential energy surface is presented for the accurate calculation of anharmonic vibrational spectra. As a special case of this general approach vibrational complete active space self-consistent field calculations will be discussed. The latter method shows better convergence than the general VMCSCF approach and must be considered the preferred choice within the multiconfigurational framework. Benchmark calculations are provided for a small set of test molecules.

  8. Analytic equation of state for FCC C60 solid based on analytic mean-field potential approach

    International Nuclear Information System (INIS)

    Sun Jiuxun

    2006-01-01

    The analytic mean-field approach (AMFP) was applied to the FCC C60 solid. For the intermolecular forces the Girifalco potential has been utilized. The analytic expressions for the Helmholtz free energy, internal energy and equation of state have been derived. The numerical results of thermodynamic quantities are compared with the molecular dynamic (MD) simulations and the unsymmetrized self-consistent field approach (CUSF) in the literature. It is shown that our AMFP results are in good agreement with the MD data both at low and high temperatures. The results of CUSF are in accordance with the AMFP at low temperature, but at high temperature the difference becomes prominent. Especially the AMFP predicted that the FCC C60 solid is stable upto 2202 K, the spinodal temperature, in good agreement with 2320 K from the MD simulation. However, the CUST just gives 1916 K, a temperature evidently lower than the MD data. The AMFP qualifies as a useful approach that can reasonably consider the anharmonic effects at high temperature

  9. Systematic Studies on Anharmonicity of Rattling Phonons in Type I Clathrates by Low Temperature Heat Capacity Measurements

    Science.gov (United States)

    Tanigaki, Katsumi; Wu, Jiazhen; Tanabe, Yoichi; Heguri, Satoshi; Shiimotani, Hidekazu; Tohoku University Collaboration

    2014-03-01

    Clathrates are featured by cage-like polyhedral hosts mainly composed of the IVth group elements of Si, Ge, or Sn and alkali metal or alkaline-earth metal elements can be accommodated inside as a guest atom. One of the most intriguing issues in clathrates is their outstanding high thermoelectric performances thanks to the low thermal conductivity. Being irrespective of good electric conductivity σ, the guest atom motions provide a low-energy lying less-dispersive phonons and can greatly suppress thermal conductivity κ. This makes clathrates close to the concept of ``phonon glass electron crystal: PGEC'' and useful in thermoelectric materials from the viewpoint of the figure of merit. In the present study, we show that the local phonon anharmonicity indicated by the tunneling-term of the endohedral atoms (αT) and the itinerant-electron term (γeT), both of which show T-linear dependences in specific heat Cp, can successfully be separated by employing single crystals with various carrier concentrations in a wide range of temperture experimennts. The factors affecting on the phonon anharmonicity as well as the strength of electron-phonon interactions will be discussed based on our recent experiments. The research was financially supported by Ministry of Education, Science, Sports and Culture, Grant in Aid for Science, and Technology of Japan.

  10. Transformation of potential energy surfaces for estimating isotopic shifts in anharmonic vibrational frequency calculations

    Energy Technology Data Exchange (ETDEWEB)

    Meier, Patrick; Oschetzki, Dominik; Rauhut, Guntram, E-mail: rauhut@theochem.uni-stuttgart.de [Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany); Berger, Robert [Clemens-Schöpf Institut für Organische Chemie and Biochemie, Technische Universität Darmstadt, Petersenstrasse 22, 64287 Darmstadt (Germany)

    2014-05-14

    A transformation of potential energy surfaces (PES) being represented by multi-mode expansions is introduced, which allows for the calculation of anharmonic vibrational spectra of any isotopologue from a single PES. This simplifies the analysis of infrared spectra due to significant CPU-time savings. An investigation of remaining deviations due to truncations and the so-called multi-level approximation is provided. The importance of vibrational-rotational couplings for small molecules is discussed in detail. In addition, an analysis is proposed, which provides information about the quality of the transformation prior to its execution. Benchmark calculations are provided for a set of small molecules.

  11. Developmant of a Reparametrized Semi-Empirical Force Field to Compute the Rovibrational Structure of Large PAHs

    Science.gov (United States)

    Fortenberry, Ryan

    The Spitzer Space Telescope observation of spectra most likely attributable to diverse and abundant populations of polycyclic aromatic hydrocarbons (PAHs) in space has led to tremendous interest in these molecules as tracers of the physical conditions in different astrophysical regions. A major challenge in using PAHs as molecular tracers is the complexity of the spectral features in the 3-20 μm region. The large number and vibrational similarity of the putative PAHs responsible for these spectra necessitate determination for the most accurate basis spectra possible for comparison. It is essential that these spectra be established in order for the regions explored with the newest generation of observatories such as SOFIA and JWST to be understood. Current strategies to develop these spectra for individual PAHs involve either matrixisolation IR measurements or quantum chemical calculations of harmonic vibrational frequencies. These strategies have been employed to develop the successful PAH IR spectral database as a repository of basis functions used to fit astronomically observed spectra, but they are limited in important ways. Both techniques provide an adequate description of the molecules in their electronic, vibrational, and rotational ground state, but these conditions do not represent energetically hot regions for PAHs near strong radiation fields of stars and are not direct representations of the gas phase. Some non-negligible matrix effects are known in condensed-phase studies, and the inclusion of anharmonicity in quantum chemical calculations is essential to generate physically-relevant results especially for hot bands. While scaling factors in either case can be useful, they are agnostic to the system studied and are not robustly predictive. One strategy that has emerged to calculate the molecular vibrational structure uses vibrational perturbation theory along with a quartic force field (QFF) to account for higher-order derivatives of the potential

  12. Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

    Science.gov (United States)

    Lay, Wesley K; Miller, Mark S; Elcock, Adrian H

    2016-04-12

    GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.

  13. Probing the Importance of Charge Flux in Force Field Modeling.

    Science.gov (United States)

    Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

    2017-08-08

    We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

  14. How well do force fields capture the strength of salt bridges in proteins?

    Directory of Open Access Journals (Sweden)

    Mustapha Carab Ahmed

    2018-06-01

    Full Text Available Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1 to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

  15. Equidistance of the complex two-dimensional anharmonic oscillator spectrum: the exact solution

    International Nuclear Information System (INIS)

    Cannata, F; Ioffe, M V; Nishnianidze, D N

    2012-01-01

    We study a class of quantum two-dimensional models with complex potentials of a specific form. They can be considered as the generalization of a recently studied model with quadratic interaction not amenable to the conventional separation of variables. In the present case, the property of shape invariance provides the equidistant form of the spectrum and the algorithm to construct eigenfunctions analytically. It is shown that the Hamiltonian is non-diagonalizable, and the resolution of identity must also include the corresponding associated functions. In the specific case of anharmonic second plus fourth-order interaction, expressions for the wavefunctions and associated functions are constructed explicitly for the lowest levels, and the recursive algorithm to produce higher level wavefunctions is given. (paper)

  16. Vector electric field measurement via position-modulated Kelvin probe force microscopy

    Science.gov (United States)

    Dwyer, Ryan P.; Smieska, Louisa M.; Tirmzi, Ali Moeed; Marohn, John A.

    2017-10-01

    High-quality spatially resolved measurements of electric fields are critical to understanding charge injection, charge transport, and charge trapping in semiconducting materials. Here, we report a variation of frequency-modulated Kelvin probe force microscopy that enables spatially resolved measurements of the electric field. We measure electric field components along multiple directions simultaneously by employing position modulation and lock-in detection in addition to numeric differentiation of the surface potential. We demonstrate the technique by recording linescans of the in-plane electric field vector in the vicinity of a patch of trapped charge in a 2,7-diphenyl[1]benzothieno[3,2-b][1]benzothiophene (DPh-BTBT) organic field-effect transistor. This technique is simple to implement and should be especially useful for studying electric fields in spatially inhomogeneous samples like organic transistors and photovoltaic blends.

  17. ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

    Science.gov (United States)

    Stolworthy, L D; Shirts, R B

    1997-03-01

    We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

  18. Simplified TiO2 force fields for studies of its interaction with biomolecules

    Science.gov (United States)

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-01

    Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

  19. Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields.

    Science.gov (United States)

    Furman, David; Carmeli, Benny; Zeiri, Yehuda; Kosloff, Ronnie

    2018-05-04

    Particle swarm optimization is a powerful metaheuristic population-based global optimization algorithm. However, when applied to non-separable objective functions its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant particle swarm optimization algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates a superior performance across several nonlinear, multimodal benchmark functions compared to the rotation-invariant Particle Swam Optimization (PSO) algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in ReaxFF-lg reactive force field is carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents a better performance compared to a Genetic Algorithm optimization method in the optimization of a ReaxFF-lg correction model parameters. The computational framework is implemented in a standalone C++ code that allows a straightforward development of ReaxFF reactive force fields.

  20. Nanophotonic force microscopy: characterizing particle-surface interactions using near-field photonics.

    Science.gov (United States)

    Schein, Perry; Kang, Pilgyu; O'Dell, Dakota; Erickson, David

    2015-02-11

    Direct measurements of particle-surface interactions are important for characterizing the stability and behavior of colloidal and nanoparticle suspensions. Current techniques are limited in their ability to measure pico-Newton scale interaction forces on submicrometer particles due to signal detection limits and thermal noise. Here we present a new technique for making measurements in this regime, which we refer to as nanophotonic force microscopy. Using a photonic crystal resonator, we generate a strongly localized region of exponentially decaying, near-field light that allows us to confine small particles close to a surface. From the statistical distribution of the light intensity scattered by the particle we are able to map out the potential well of the trap and directly quantify the repulsive force between the nanoparticle and the surface. As shown in this Letter, our technique is not limited by thermal noise, and therefore, we are able to resolve interaction forces smaller than 1 pN on dielectric particles as small as 100 nm in diameter.

  1. Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

    DEFF Research Database (Denmark)

    Voroshylova, I. V.; Chaban, V. V.

    2014-01-01

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

  2. Dipole and quadrupole forces exerted on atoms in laser fields: The nonperturbative approach

    International Nuclear Information System (INIS)

    Sindelka, Milan; Moiseyev, Nimrod; Cederbaum, Lorenz S.

    2006-01-01

    Manipulation of cold atoms by lasers has so far been studied solely within the framework of the conventional dipole approximation, and the atom-light interaction has been treated using low order perturbation theory. Laser control of atomic motions has been ascribed exclusively to the corresponding light-induced dipole forces. In this work, we present a general theory to derive the potential experienced by an atom in a monochromatic laser field in a context analogous to the Born-Oppenheimer approximation for molecules in the field-free case. The formulation goes beyond the dipole approximation and gives rise to the field-atom coupling potential terms which so far have not been taken into consideration in theoretical or experimental studies. Contrary to conventional approaches, our method is based upon the many electron Floquet theory and remains valid also for high intensity laser fields (i.e., for a strongly nonperturbative atom-light interaction). As an illustration of the developed theory, we investigate the trapping of cold atoms in optical lattices. We find that for some atoms for specific laser parameters, despite the absence of the dipole force, the laser trapping is still possible due to the electric quadrupole forces. Namely, we show that by using realistic laser parameters one can form a quadrupole optical lattice which is sufficiently strong to trap Ca and Na atoms

  3. Forces on a current-carrying wire in a magnetic field: the macro-micro connection

    DEFF Research Database (Denmark)

    Avelar Sotomaior Karam, Ricardo; Kneubil, Fabiana; Robilotta, Manoel

    2017-01-01

    The classic problem of determining the force on a current-carrying wire in a magnetic field is critically analysed. A common explanation found in many introductory textbooks is to represent the force on the wire as the sum of the forces on charge carriers. In this approach neither the nature...... of the forces involved nor their application points are fully discussed. In this paper we provide an alternative microscopic explanation that is suitable for introductory electromagnetism courses at university level. By considering the wire as a superposition of a positive and a negative cylindrical charge...

  4. Thermal expansion, anharmonicity and temperature-dependent Raman spectra of single- and few-layer MoSe₂ and WSe₂.

    Science.gov (United States)

    Late, Dattatray J; Shirodkar, Sharmila N; Waghmare, Umesh V; Dravid, Vinayak P; Rao, C N R

    2014-06-06

    We report the temperature-dependent Raman spectra of single- and few-layer MoSe2 and WSe2 in the range 77-700 K. We observed linear variation in the peak positions and widths of the bands arising from contributions of anharmonicity and thermal expansion. After characterization using atomic force microscopy and high-resolution transmission electron microscopy, the temperature coefficients of the Raman modes were determined. Interestingly, the temperature coefficient of the A(2)(2u) mode is larger than that of the A(1g) mode, the latter being much smaller than the corresponding temperature coefficients of the same mode in single-layer MoS2 and of the G band of graphene. The temperature coefficients of the two modes in single-layer MoSe2 are larger than those of the same modes in single-layer WSe2. We have estimated thermal expansion coefficients and temperature dependence of the vibrational frequencies of MoS2 and MoSe2 within a quasi-harmonic approximation, with inputs from first-principles calculations based on density functional theory. We show that the contrasting temperature dependence of the Raman-active mode A(1g) in MoS2 and MoSe2 arises essentially from the difference in their strain-phonon coupling. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Anharmonic vibrational modes of chemisorbed H on the Rh(001) surface

    International Nuclear Information System (INIS)

    Hamann, D.R.; Feibelman, P.J.

    1988-01-01

    The potential for H atoms in the vicinity of the fourfold hollow chemisorption site on the Rh(001) surface at monolayer coverage is calculated using local-density-functional theory, and the linear-augmented-plane-wave method. The potential is found to contain important anharmonic components, one that couples parallel and perpendicular motion, and another producing azimuthal anisotropy. Variational solutions are found for the ground and low-lying excited states of H and D in this potential. The fundamental asymmetric- and symmetric-stretch H vibrational excitations are found to have energies of 67 and 92 meV. The latter agrees with recent experimental results, and higher-lying experimental modes are interpreted as mixed excitations. Comparisons are made with spring-constant models, calculated potentials for H on Ni and Pd(001), and theories of Bloch states for H on Ni

  6. Cylindrical Penning traps with dynamic orthogonalized anharmonicity compensation for precision experiments

    International Nuclear Information System (INIS)

    Fei Xiang; Snow, W.M.

    1999-01-01

    Harmonic potentials can be produced in cylindrical ion traps by means of dynamic orthogonalized anharmonicity compensation with use of two (or multiple) sets of compensation electrodes. One special example is for traps with multiple identical electrodes which are not only easy to construct and allow access to the center region of the trap for particle loading and releasing, laser beams, and microwaves, but also flexible in forming harmonic potential wells in many locations. The nested trap configuration and the side-by-side trap configuration are readily available in this special scheme. Analytical solutions for cylindrical traps with multiple sets of compensation potentials are presented. This work will be useful for studies involving Penning trap diagnostics, atomic and molecular interactions (including the production of antihydrogen atoms), accurate mass measurements of exotic particles, and precision measurements of the spin precession frequencies of trapped particles

  7. Cylindrical Penning traps with dynamic orthogonalized anharmonicity compensation for precision experiments

    CERN Document Server

    Fei Xiang

    1999-01-01

    Harmonic potentials can be produced in cylindrical ion traps by means of dynamic orthogonalized anharmonicity compensation with use of two (or multiple) sets of compensation electrodes. One special example is for traps with multiple identical electrodes which are not only easy to construct and allow access to the center region of the trap for particle loading and releasing, laser beams, and microwaves, but also flexible in forming harmonic potential wells in many locations. The nested trap configuration and the side-by-side trap configuration are readily available in this special scheme. Analytical solutions for cylindrical traps with multiple sets of compensation potentials are presented. This work will be useful for studies involving Penning trap diagnostics, atomic and molecular interactions (including the production of antihydrogen atoms), accurate mass measurements of exotic particles, and precision measurements of the spin precession frequencies of trapped particles.

  8. The Röntgen interaction and forces on dipoles in time-modulated optical fields

    Science.gov (United States)

    Sonnleitner, Matthias; Barnett, Stephen M.

    2017-12-01

    The Röntgen term is an often neglected contribution to the interaction between an atom and an electromagnetic field in the electric dipole approximation. In this work we discuss how this interaction term leads to a difference between the kinetic and canonical momentum of an atom which, in turn, leads to surprising radiation forces acting on the atom. We use a number of examples to explore the main features of this interaction, namely forces acting against the expected dipole force or accelerations perpendicular to the beam propagation axis.

  9. Continuous micro-feeding of fine cohesive powders actuated by pulse inertia force and acoustic radiation force in ultrasonic standing wave field.

    Science.gov (United States)

    Wang, Hongcheng; Wu, Liqun; Zhang, Ting; Chen, Rangrang; Zhang, Linan

    2018-07-10

    Stable continuous micro-feeding of fine cohesive powders has recently gained importance in many fields. However, it remains a great challenge in practice because of the powder aggregate caused by interparticle cohesive forces in small capillaries. This paper describes a novel method of feeding fine cohesive powder actuated by a pulse inertia force and acoustic radiation force simultaneously in an ultrasonic standing wave field using a tapered glass nozzle. Nozzles with different outlet diameters are fabricated using glass via a heating process. A pulse inertia force is excited to drive powder movement to the outlet section of the nozzle in a consolidated columnar rod mode. An acoustic radiation force is generated to suspend the particles and make the rod break into large quantities of small agglomerates which impact each other randomly. So the aggregation phenomenon in the fluidization of cohesive powders can be eliminated. The suspended powder is discharged continuously from the nozzle orifice owing to the self-gravities and collisions between the inner particles. The micro-feeding rates can be controlled accurately and the minimum values for RespitoseSV003 and Granulac230 are 0.4 mg/s and 0.5 mg/s respectively. The relative standard deviations of all data points are below 0.12, which is considerably smaller than those of existing vibration feeders with small capillaries. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Anharmonic Oxygen Displacements in La2-x (Sr, Ba)xCuO4 Planes and in YBa2Cu3O7 Chains

    International Nuclear Information System (INIS)

    Pickett, W. E.

    1995-01-01

    An earlier calculation of the energy surface for X-point tilts if the CuO6 octahedra in La 2-x (Sr, Ba) x CuO 4 revealed an eight well potential surface. This surface indicated an extremely anharmonic situation and seemed to provide an explanation of a number of observed phenomena in this system, especially the coincidence of a drop in Tc with the occurrence of the low temperature tetragonal phase. We review experimental developments since that time, which indicate new complications. We also reconsider the zone boundary chain-buckling mode of the chain oxygen atoms in YBa 2 Cu 3 O 7 , for which our earlier calculation indicated a very flat (slightly double well) energy surface that would provide very little restoring force to this motion. We have studied the coupling of the chain buckling motion to the carriers by evaluating the shifts of bands near the Fermi energy. These deformation potentials themselves are not large (∼ 0.1-0.2 eV/A) and non-linear coupling is minor out to displacements of 0.25 A. (author)

  11. Effect of magnetic field and radiative condensation on the Jeans instability of dusty plasma with polarization force

    International Nuclear Information System (INIS)

    Prajapati, R.P.

    2013-01-01

    The Jeans instability of self-gravitating dusty plasma with polarization force is investigated considering the effects of magnetic field, dust temperature and radiative condensation. The condition of Jeans instability and expression of critical Jeans wave number are obtained which depend upon polarization force and dust temperature but these are unaffected by the presence of magnetic field. The radiative heat-loss functions also modify the Jeans condition of instability and expression of critical Jeans wave number. It is observed that the polarization force and ratio of radiative heat-loss functions have destabilizing while magnetic field and dust temperature have stabilizing influence on the growth rate of Jeans instability.

  12. Field measurement of basal forces generated by erosive debris flows

    Science.gov (United States)

    McCoy, S.W.; Tucker, G.E.; Kean, J.W.; Coe, J.A.

    2013-01-01

    It has been proposed that debris flows cut bedrock valleys in steeplands worldwide, but field measurements needed to constrain mechanistic models of this process remain sparse due to the difficulty of instrumenting natural flows. Here we present and analyze measurements made using an automated sensor network, erosion bolts, and a 15.24 cm by 15.24 cm force plate installed in the bedrock channel floor of a steep catchment. These measurements allow us to quantify the distribution of basal forces from natural debris‒flow events that incised bedrock. Over the 4 year monitoring period, 11 debris‒flow events scoured the bedrock channel floor. No clear water flows were observed. Measurements of erosion bolts at the beginning and end of the study indicated that the bedrock channel floor was lowered by 36 to 64 mm. The basal force during these erosive debris‒flow events had a large‒magnitude (up to 21 kN, which was approximately 50 times larger than the concurrent time‒averaged mean force), high‒frequency (greater than 1 Hz) fluctuating component. We interpret these fluctuations as flow particles impacting the bed. The resulting variability in force magnitude increased linearly with the time‒averaged mean basal force. Probability density functions of basal normal forces were consistent with a generalized Pareto distribution, rather than the exponential distribution that is commonly found in experimental and simulated monodispersed granular flows and which has a lower probability of large forces. When the bed sediment thickness covering the force plate was greater than ~ 20 times the median bed sediment grain size, no significant fluctuations about the time‒averaged mean force were measured, indicating that a thin layer of sediment (~ 5 cm in the monitored cases) can effectively shield the subjacent bed from erosive impacts. Coarse‒grained granular surges and water‒rich, intersurge flow had very similar basal force distributions despite

  13. Analysis of PM Magnetization Field Effects on the Unbalanced Magnetic Forces due to Rotor Eccentricity in BLDC Motors

    Directory of Open Access Journals (Sweden)

    S. Mahdiuon-Rad

    2013-08-01

    Full Text Available This paper investigates both static and dynamic eccentricities in single phase brushless DC (BLDC motors and analyzes the effect of the PM magnetization field on unbalanced magnetic forces acting on the rotor. Three common types of PM magnetization field patterns including radial, parallel and sinusoidal magnetizations are considered. In both static and dynamic eccentricities, harmonic components of the unbalanced magnetic forces on the rotor are extracted and analyzed. Based on simulation results, the magnetization fields that produce the lowest and highest unbalanced magnetic forces are determined in rotor eccentricity conditions.

  14. On radiation forces acting on a transparent nanoparticle in the field of a focused laser beam

    Energy Technology Data Exchange (ETDEWEB)

    Afanas' ev, A A; Rubinov, A N [B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, Minsk (Belarus); Gaida, L S; Guzatov, D V; Svistun, A Ch [Yanka Kupala State University of Grodno, Grodno (Belarus)

    2015-10-31

    Radiation forces acting on a transparent spherical nanoparticle in the field of a focused Gaussian laser beam are studied theoretically in the Rayleigh scattering regime. Expressions are derived for the scattering force and Cartesian components of the gradient force. The resultant force acting on a nanoparticle located in the centre of a laser beam is found. The parameters of the focused beam and optical properties of the nanoparticle for which the longitudinal component of the gradient force exceeds the scattering force are determined. Characteristics of the transverse gradient force are discussed. (nanophotonics)

  15. Streamwise-body-force-model for rapid simulation combining internal and external flow fields

    Directory of Open Access Journals (Sweden)

    Cui Rong

    2016-10-01

    Full Text Available A streamwise-body-force-model (SBFM is developed and applied in the overall flow simulation for the distributed propulsion system, combining internal and external flow fields. In view of axial stage effects, fan or compressor effects could be simplified as body forces along the streamline. These body forces which are functions of local parameters could be added as source terms in Navier-Stokes equations to replace solid boundary conditions of blades and hubs. The validation of SBFM with uniform inlet and distortion inlet of compressors shows that pressure performance characteristics agree well with experimental data. A three-dimensional simulation of the integration configuration, via a blended wing body aircraft with a distributed propulsion system using the SBFM, has been completed. Lift coefficient and drag coefficient agree well with wind tunnel test results. Results show that to reach the goal of rapid integrated simulation combining internal and external flow fields, the computational fluid dynamics method based on SBFM is reasonable.

  16. Airy function approach and Numerov method to study the anharmonic oscillator potentials V(x = Ax2α + Bx2

    Directory of Open Access Journals (Sweden)

    N. Al Sdran

    2016-06-01

    Full Text Available The numerical solutions of the time independent Schrödinger equation of different one-dimensional potentials forms are sometime achieved by the asymptotic iteration method. Its importance appears, for example, on its efficiency to describe vibrational system in quantum mechanics. In this paper, the Airy function approach and the Numerov method have been used and presented to study the oscillator anharmonic potential V(x = Ax2α + Bx2, (A>0, B<0, with (α = 2 for quadratic, (α =3 for sextic and (α =4 for octic anharmonic oscillators. The Airy function approach is based on the replacement of the real potential V(x by a piecewise-linear potential v(x, while, the Numerov method is based on the discretization of the wave function on the x-axis. The first energies levels have been calculated and the wave functions for the sextic system have been evaluated. These specific values are unlimited by the magnitude of A, B and α. It’s found that the obtained results are in good agreement with the previous results obtained by the asymptotic iteration method for α =3.

  17. Lienard-Wiechert field as covariant dynamics of electric lines of force

    International Nuclear Information System (INIS)

    Arutyunyan, S.G.

    1989-01-01

    The Lienard-Wiechert field of an arbitrarily moving charge is presented as a system of Lorentz-covariant moving electric lines of force. It is shown that the 4-vector describing these lines is written as a sum of the 4-vector of the charge and the isotropic 4-vector directed to the observation point. The motion of this 4-vector is described by the equation coinciding with the equation of motion for magnetic moment in external fields provided that the intrinsic magnetic moment is zero. By the system of lines that corresponds to the complete equation of magnetic moment in external fields the electromagnetic field is restored. It turned out that the spatial magnetic current proportional to the isotropic 4-vector directed to the observation point corresponds to this field. 8 refs

  18. MODELING MAGNETIC FIELD STRUCTURE OF A SOLAR ACTIVE REGION CORONA USING NONLINEAR FORCE-FREE FIELDS IN SPHERICAL GEOMETRY

    International Nuclear Information System (INIS)

    Guo, Y.; Ding, M. D.; Liu, Y.; Sun, X. D.; DeRosa, M. L.; Wiegelmann, T.

    2012-01-01

    We test a nonlinear force-free field (NLFFF) optimization code in spherical geometry using an analytical solution from Low and Lou. Several tests are run, ranging from idealized cases where exact vector field data are provided on all boundaries, to cases where noisy vector data are provided on only the lower boundary (approximating the solar problem). Analytical tests also show that the NLFFF code in the spherical geometry performs better than that in the Cartesian one when the field of view of the bottom boundary is large, say, 20° × 20°. Additionally, we apply the NLFFF model to an active region observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory (SDO) both before and after an M8.7 flare. For each observation time, we initialize the models using potential field source surface (PFSS) extrapolations based on either a synoptic chart or a flux-dispersal model, and compare the resulting NLFFF models. The results show that NLFFF extrapolations using the flux-dispersal model as the boundary condition have slightly lower, therefore better, force-free, and divergence-free metrics, and contain larger free magnetic energy. By comparing the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the Atmospheric Imaging Assembly on board SDO, we find that the NLFFF performs better than the PFSS not only for the core field of the flare productive region, but also for large EUV loops higher than 50 Mm.

  19. Adaptation of multi-joint balance coordination to whole body force fields

    NARCIS (Netherlands)

    Engelhart, Denise; Schouten, Alfred Christiaan; Pasma, Jantsje; Aarts, Ronald G.K.M.; Pasma, J.; Meskers, Carel; Maier, Andrea; van der Kooij, Herman

    2014-01-01

    Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how

  20. The effect of realistic forces in finite epitaxial islands: Equilibrium structure, stability limits and substrate-induced dissociation of migrating clusters

    Science.gov (United States)

    Milchev, Andrey; Markov, Ivan

    1985-06-01

    The behaviour of finite epitaxial islands in the periodic field of the substrate is theoretically investigated. The harmonic interactions, traditionally adopted in the model of Frank and Van der Merwe, are replaced by Toda and Morse potentials and sets of difference recursion equations, governing the equilibrium properties of the system, are derived and solved numerically. It is shown that allowing for anharmonicity in the interactions in the deposit reveals several qualiatively new effects, such as: (1) The existence of substrate-induced rupture of anharmonic clusters which migrate on the substrate. It is predicted that such dissociation should be enhanced, if (a) the energy barrier for surface diffusion is increased, (b) the natural incompatibility between substrate and deposit is decreased, and (c) the size of the clusters grows. (2) A split in the misfit stability limits for pseudomorphism and for spontaneous generation of misfit dislocations with respect to the sign of the misfit. The limits corresponding to negative misfit rapidly increase while the positive misfit limits decrease (in absolute terms) with growing degree of anharmonicity. (3) A marked asymmetry in the magnitude of various properties of the clusters, such as adhesion to the substrate, activation energy for surface diffusion, mean strain, dislocation lengths, etc., with respect to the sign of the mismatch between surface and deposit.

  1. Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

    International Nuclear Information System (INIS)

    Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

    2011-01-01

    In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

  2. Frequency and Temperature Dependence of Anharmonic Phonon Relaxation Rate in Carbon Nanotubes

    International Nuclear Information System (INIS)

    Hepplestone, S P; Srivastava, G P

    2007-01-01

    The relaxation rate of phonon modes in the (10, 10) single wall carbon nanotube undergoing three-phonon interactions at various temperatures has been studied using both qualitative and quantitative approaches based upon Fermi's Golden Rule and a quasi-elastic continuum model for the anharmonic potential. For the quantitative calculations, dispersion relations for the phonon modes were obtained from analytic expressions developed by Zhang et al. The qualitative expressions were derived using simple linear phonon dispersions relations. We show that in the high temperature regime the relaxation rate varies linearly with temperature and with the square of the frequency. In the low temperature regime we show that the relaxation rate varies exponentially with the inverse of temperature. These results have some very interesting implifications for effects for mean free path and thermal conductivity calculations

  3. Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

    Science.gov (United States)

    2014-01-01

    We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

  4. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    International Nuclear Information System (INIS)

    Liu Minxian; Wang Yan

    2012-01-01

    The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

  5. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Liu Minxian, E-mail: liukey_sjtu@263.net [School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Wang Yan [Luoyang Institute of Science and Technology, Luoyang, Henan 471023 (China)

    2012-01-15

    The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

  6. Probing Field Distributions on Waveguide Structures with an Atomic Force/Photon Scanning Tunneling Microscope

    NARCIS (Netherlands)

    Borgonjen, E.G.; Borgonjen, E.G.; Moers, M.H.P.; Moers, M.H.P.; Ruiter, A.G.T.; van Hulst, N.F.

    1995-01-01

    A 'stand-alone' Photon Scanning Tunneling Microscope combined with an Atomic force Microscope, using a micro-fabricated silicon-nitride probe, is applied to the imaging of field distribution in integrated optical ridge waveguides. The electric field on the waveguide is locally probed by coupling to

  7. Anharmonic properties of Raman modes in double wall carbon nano tubes

    Energy Technology Data Exchange (ETDEWEB)

    Marquina, J. [Universidad de los Andes, Facultad de Ciencias, Centro de Estudios Avanzados en Optica, 5101 Merida (Venezuela, Bolivarian Republic of); Power, Ch.; Gonzalez, J. [Universidad de los Andes, Facultad de Ciencias, Centro de Estudios en Semiconductores, 5101 Merida (Venezuela, Bolivarian Republic of); Broto, J. M. [Universite de Toulouse, Laboratoire National des Champs Magnetiques Intenses, CNRS UPR 3228, 31400 Toulouse (France); Flahaut, E., E-mail: castella@ula.v [Universite Paul Sabatier, Laboratoire de Chimie des Materiaux Inorganiques, UMR CNRS 5085, 31062 Toulouse (France)

    2011-07-01

    The temperature dependence of the radial breathing modes (RB Ms) and the zone-center tangential optical phonons (G-bands) of double-walled carbon nano tubes has been investigated between 300 and 700 K using Raman scattering. As expected, with increasing temperature, the frequencies of the Raman peaks, including the RB Ms and G-bands downshift simultaneously. We show here that the temperature dependence of the RB Ms can be fitted by a simple linear dependence and different RB Ms have different frequency shifts. We observe a noticeable nonlinearity in the temperature dependence of the G-band associated with the outer semiconducting tube G+ext (s). The deviation from the linear trend is due to the contribution of the third-order anharmonic term in the lattice potential energy with a pure temperature effect. An estimated value of 1.5 for the Grueneisen parameter of the G+ext (s) band was found. (Author)

  8. Unsteady hydrodynamic forces acting on a robotic hand and its flow field.

    Science.gov (United States)

    Takagi, Hideki; Nakashima, Motomu; Ozaki, Takashi; Matsuuchi, Kazuo

    2013-07-26

    This study aims to clarify the mechanism of generating unsteady hydrodynamic forces acting on a hand during swimming in order to directly measure the forces, pressure distribution, and flow field around the hand by using a robotic arm and particle image velocimetry (PIV). The robotic arm consisted of the trunk, shoulder, upper arm, forearm, and hand, and it was independently computer controllable in five degrees of freedom. The elbow-joint angle of the robotic arm was fixed at 90°, and the arm was moved in semicircles around the shoulder joint in a plane perpendicular to the water surface. Two-component PIV was used for flow visualization around the hand. The data of the forces and pressure acting on the hand were sampled at 200Hz and stored on a PC. When the maximum resultant force acting on the hand was observed, a pair of counter-rotating vortices appeared on the dorsal surface of the hand. A vortex attached to the hand increased the flow velocity, which led to decreased surface pressure, increasing the hydrodynamic forces. This phenomenon is known as the unsteady mechanism of force generation. We found that the drag force was 72% greater and the lift force was 4.8 times greater than the values estimated under steady flow conditions. Therefore, it is presumable that swimmers receive the benefits of this unsteady hydrodynamic force. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Application of Enlisted Force Retention Levels and Career Field Stability

    Science.gov (United States)

    2017-03-23

    APPLICATION OF ENLISTED FORCE RETENTION LEVELS AND CAREER FIELD STABILITY THESIS Presented to the Faculty Department of Operational Sciences ...Fulfillment of the Requirements for the Degree of Master of Science in Operations Research Jamie T. Zimmermann, MS, BS Captain, USAF March 2017...Appendix B. The function proc lifetest is a nonparametric estimate of the survivor function using either the Kaplan-Meier method or the actuarial

  10. Cooper-pair formation by anharmonic rattling modes in the β-pyrochlore superconductor KOs2O6

    Science.gov (United States)

    Chang, Jun; Eremin, Ilya; Thalmeier, Peter

    2009-05-01

    We study the influence of anharmonic rattling phonons in the β-pyrochlore superconductor KOs2O6 using the strong-coupling Eliashberg approach. In particular, by analyzing the specific heat data, we find that the rattling phonon frequency changes discontinuously at the critical temperature of the first-order phase transition. Solving the strong-coupling Eliashberg equations with effective temperature-dependent α2F(ω), we investigate the consequence of this first-order phase transition for the anomalous temperature dependence of the superconducting gap. We discuss our results in the context of the recent experimental data.

  11. AB-INITIO CALCULATIONS OF ANHARMONIC VIBRATIONAL TRANSITION INTENSITIES OF TRANS-2,3-DIDEUTERIOOXIRANE

    DEFF Research Database (Denmark)

    Bludsky, O.; Bak, Keld L.; JORGENSEN, P

    1995-01-01

    The quartic force field and the cubic dipole moment surface are calculated for trans-2,3-dideuteriooxirane at the self-consistent field and the second order Moller-Plesset levels of theory using a triple zeta plus two polarization functions basis set. Contact transformation theory is used to dete...

  12. Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

    KAUST Repository

    Lacoste, Deanna

    2016-06-23

    The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

  13. Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

    KAUST Repository

    Lacoste, Deanna; Xiong, Yuan; Moeck, Jonas P.; Chung, Suk-Ho; Roberts, William L.; Cha, Min

    2016-01-01

    The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

  14. Fano resonance of the ultrasensitve optical force excited by Gaussian evanescent field

    International Nuclear Information System (INIS)

    Yang, Yang; Li, Jiafang; Li, Zhi-Yuan

    2015-01-01

    In this paper, we study the angle-dependent Fano-like optical force spectra of plasmonic Ag nanoparticles, which exhibit extraordinary transformation from Lorentzian resonance to Fano resonance when excited by a Gaussian evanescent wave. We systematically analyze the behavior of this asymmetric scattering induced optical force under different conditions and find that this Fano interference-induced force is ultrasensitive to the excitation wavelength, incident angle and particle size, as well as the core–shell configuration, which could be useful for wavelength- and angle-dependent size-selective optical manipulation. The origin of this Fano resonance is further identified as the interference between the two adjacent-order multipolar plasmonic modes excited in the Ag particle under the excitation of an inhomogeneously distributed evanescent field. (paper)

  15. Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

    Energy Technology Data Exchange (ETDEWEB)

    Tamma, Venkata Ananth [CaSTL Center, Department of Chemistry, University of California, Irvine, California 92697 (United States); Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu [Department of Electrical Engineering and Computer Science, 142 Engineering Tower, University of California, Irvine, California 92697 (United States); Nowak, Derek [Molecular Vista, Inc., 6840 Via Del Oro, San Jose, California 95119 (United States)

    2016-06-06

    We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol and l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.

  16. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

    OpenAIRE

    Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

    2005-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

  17. Implications of confining force field structures in hard hadronic processes

    International Nuclear Information System (INIS)

    Bengtsson, H.-U.

    1983-04-01

    This thesis is centered on the study of confining force field structures in hard scattering processes. Perturbative QCD provides the means of calculating any process on the parton level, but to be able accurately to describe the actual outcome of an event, one still needs a phenomenological model for how quarks and gluons transform into observable hadrons. One such model is based on the assumption that the particles are produced by the confining fields stretched between the partons. The actual particle distributions will then depend on the topology of the confining fields. We have developed a Monte Carlo program to simulate complete events in hard scattering, and we use this to study the properties of the confining field in different trigger situations. We further look at the amount of hard processes that can be expected in experiments that trigger on transverse energy sum (calorimeter experiments). Finally, we investigate charm production within our model. (author)

  18. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

    Science.gov (United States)

    Lemkul, Justin A; MacKerell, Alexander D

    2017-05-09

    Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

  19. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance.

    Science.gov (United States)

    Noel, Martin; Fortin, Karine; Bouyer, Laurent J

    2009-06-03

    Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during

  20. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

    Directory of Open Access Journals (Sweden)

    Bouyer Laurent J

    2009-06-01

    Full Text Available Abstract Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min, during (5 min and after (5 min exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion. To evaluate modifications in feedforward control, strides with no force field ('catch strides' were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%, subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99. Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%, plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive

  1. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

    Science.gov (United States)

    Noel, Martin; Fortin, Karine; Bouyer, Laurent J

    2009-01-01

    Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle

  2. Force field refinement from NMR scalar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Huang Jing [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland); Meuwly, Markus, E-mail: m.meuwly@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

    2012-03-02

    Graphical abstract: We show that two classes of H-bonds are sufficient to quantitatively describe scalar NMR coupling constants in small proteins. Highlights: Black-Right-Pointing-Pointer We present force field refinements based on explicit MD simulations using scalar couplings across hydrogen bonds. Black-Right-Pointing-Pointer This leads to {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.03 Hz at best compared to experiment. Black-Right-Pointing-Pointer A classification of H-bonds according to secondary structure is not sufficiently robust. Black-Right-Pointing-Pointer Grouping H-bonds into two classes and reparametrization yields an RMSD of 0.07 Hz. Black-Right-Pointing-Pointer This is an improvement of 50. - Abstract: NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.

  3. Improvement of a force field to model the edges of clay particles

    International Nuclear Information System (INIS)

    Pouvreau, Maxime

    2016-01-01

    The CLAYFF force field is widely used to model the interfaces of clay minerals - and related layered materials - with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nano sized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O-H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O-H and Mg-O-H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH) 3 and brucite Mg(OH) 2 , whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O-H term was parametrized from an edge model of kaolinite Al 2 Si 2 O 5 (OH) 4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O-H term were performed. The modified force field clearly improves the description of hydroxylated surfaces: the orientation and the vibrational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality [fr

  4. New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking.

    Science.gov (United States)

    Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B

    2017-11-01

    Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Influence of AC external magnetic field on guidance force relaxation between HTS bulk and NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Longcai [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)], E-mail: zhlcai2000@163.com; Wang Suyu; Wang Jiasu; Zheng Jun [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)

    2007-12-01

    Superconducting maglev vehicle is one of the most promising applications of HTS bulks. In such a system, the HTS bulks are always exposed to time-varying external magnetic field, which is generated by the inhomogeneous surface magnetic field of the NdFeB guideway. So it is required to study whether the guidance force of the bulks is influenced by the inhomogeneity. In this paper, we studied the characteristics of the guidance force relaxation between the HTS bulk and the NdFeB guideway by an experiment in which AC external magnetic field generated by an electromagnet was used to simulate the time-varying external magnetic field caused by the inhomogeneity of the guideway. From the experiment results, it was found that the guidance force was decreased with the application of the AC external magnetic field, and the decay increased with the amplitude and was almost independent of the frequency.

  6. Numerical solutions of anharmonic vibration of BaO and SrO molecules

    Energy Technology Data Exchange (ETDEWEB)

    Pramudito, Sidikrubadi; Sanjaya, Nugraha Wanda [Theoretical Physics Division, Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB Dramaga Bogor 16680 (Indonesia); Sumaryada, Tony, E-mail: tsumaryada@ipb.ac.id [Theoretical Physics Division, Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB Dramaga Bogor 16680 (Indonesia); Computational Biophysics and Molecular Modeling Research Group (CBMoRG), Department of Physics, Bogor Agricultural University, Jalan Meranti Kampus IPB Dramaga Bogor 16680 (Indonesia)

    2016-03-11

    The Morse potential is a potential model that is used to describe the anharmonic behavior of molecular vibration between atoms. The BaO and SrO molecules, which are two almost similar diatomic molecules, were investigated in this research. Some of their properties like the value of the dissociation energy, the energy eigenvalues of each energy level, and the profile of the wavefunctions in their correspondence vibrational states were presented in this paper. Calculation of the energy eigenvalues and plotting the wave function’s profiles were performed using Numerov method combined with the shooting method. In general we concluded that the Morse potential solved with numerical methods could accurately produce the vibrational properties and the wavefunction behavior of BaO and SrO molecules from the ground state to the higher states close to the dissociation level.

  7. A verification of quantum field theory – measurement of Casimir force

    Indian Academy of Sciences (India)

    journal of. Feb. & Mar. 2001 physics pp. 239–243. A verification of quantum field theory ... minum coated a sphere and flat plate using an atomic force microscope. ... where R is the radius of curvature of the spherical surface. The finite .... sured by AFM) of 60% Au/40% Pd, to form a nonreactive and conductive top layer. For.

  8. Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

    Science.gov (United States)

    Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-10-08

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

  9. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor.

    Science.gov (United States)

    Dennis, John Ojur; Ahmad, Farooq; Khir, M Haris Bin Md; Bin Hamid, Nor Hisham

    2015-07-27

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT.

  10. Steady state models for filamentary plasma structures associated with force free magnetic fields

    International Nuclear Information System (INIS)

    Marklund, G.

    1978-05-01

    This paper presents a model for filamentary plasma structures associated with force-free magnetic fields. A homogenous electric field parallel to the symmetry axis of the magnetic field is assumed. Under the influence of these fields, the plasma will drift radially inwards resulting in an accumulation of plasma in the central region. We assume recombination losses to keep the central plasma density at a finite value, and the recombined plasma i.e. the neutrals to diffuse radially outwards. Plasma density and some neutral gas density distributions for a steady state situation are calculated for various cases

  11. The influence of inhomogeneous magnetic field over a NdFeB guideway on levitation force of the HTS bulk maglev system

    Science.gov (United States)

    Zhao, Lifeng; Deng, Jiangtao; Li, Linbo; Feng, Ning; Wei, Pu; Lei, Wei; Jiang, Jing; Wang, Xiqin; Zhang, Yong; Zhao, Yong

    2018-04-01

    Dynamic responses of high temperature superconducting bulk to inhomogeneous magnetic field distribution of permanent magnet guideway, as well as enlarged amplitude of magnetic field obtained by partially covering the permanent magnet guideway (PMG) with iron sheets in different thickness, are investigated. Experiments show that the instantaneous levitation force increases with the increase of the variation rate of magnetic field (dB/dt). Meanwhile, inhomogeneous magnetic field from PMG causes the decay of levitation force. The decay of levitation force almost increases linearly with the increase of alternating magnetic field amplitude. It should be very important for the application of high-speed maglev system.

  12. Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

    International Nuclear Information System (INIS)

    Haydock, David

    2005-01-01

    We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important

  13. Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

    Energy Technology Data Exchange (ETDEWEB)

    Haydock, David [Unilever R and D Colworth, Sharnbrook, Bedford MK44 1LQ (United Kingdom); Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

    2005-04-15

    We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important.

  14. Rigorous force field optimization principles based on statistical distance minimization

    Energy Technology Data Exchange (ETDEWEB)

    Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)

    2015-10-14

    We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.

  15. Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

    International Nuclear Information System (INIS)

    Abdoli, A; Mirzaee, I; Purmahmod, N; Anvari, A

    2008-01-01

    Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s -1 at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A b and D c , have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications

  16. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

    Science.gov (United States)

    Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke

    2015-06-25

    Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

  17. Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.

    Science.gov (United States)

    Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo

    2013-03-21

    The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

  18. Calculation of magnetic field and electromagnetic forces in MHD superconducting magnets

    International Nuclear Information System (INIS)

    Martinelli, G.; Morini, A.; Moisio, M.F.

    1992-01-01

    The realization of a superconducting prototype magnet for MHD energy conversion is under development in Italy. Electromechanical industries and University research groups are involved in the project. The paper deals with analytical methods developed at the Department of Electrical Engineering of Padova University for calculating magnetic field and electromagnetic forces in MHD superconducting magnets and utilized in the preliminary design of the prototype

  19. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

    Science.gov (United States)

    Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

    2010-07-28

    Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

  20. Small strain multiphase-field model accounting for configurational forces and mechanical jump conditions

    Science.gov (United States)

    Schneider, Daniel; Schoof, Ephraim; Tschukin, Oleg; Reiter, Andreas; Herrmann, Christoph; Schwab, Felix; Selzer, Michael; Nestler, Britta

    2018-03-01

    Computational models based on the phase-field method have become an essential tool in material science and physics in order to investigate materials with complex microstructures. The models typically operate on a mesoscopic length scale resolving structural changes of the material and provide valuable information about the evolution of microstructures and mechanical property relations. For many interesting and important phenomena, such as martensitic phase transformation, mechanical driving forces play an important role in the evolution of microstructures. In order to investigate such physical processes, an accurate calculation of the stresses and the strain energy in the transition region is indispensable. We recall a multiphase-field elasticity model based on the force balance and the Hadamard jump condition at the interface. We show the quantitative characteristics of the model by comparing the stresses, strains and configurational forces with theoretical predictions in two-phase cases and with results from sharp interface calculations in a multiphase case. As an application, we choose the martensitic phase transformation process in multigrain systems and demonstrate the influence of the local homogenization scheme within the transition regions on the resulting microstructures.

  1. Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

    Science.gov (United States)

    Carbogno, Christian; Scheffler, Matthias

    In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

  2. Airy function approach and Numerov method to study the anharmonic oscillator potentials V(x) = Ax{sup 2α} + Bx{sup 2}

    Energy Technology Data Exchange (ETDEWEB)

    Al Sdran, N. [King Khalid University, Faculty of Science, Physics Department P.O. Box 9004 Abha (Saudi Arabia); Najran University, Faculty of Sciences and Arts, Najran (Saudi Arabia); Maiz, F., E-mail: fethimaiz@gmail.com [King Khalid University, Faculty of Science, Physics Department P.O. Box 9004 Abha (Saudi Arabia); Thermal Process Laboratory Research and Technologies Centre of Energy, BP 95, 2050 Hammam-lif (Tunisia)

    2016-06-15

    The numerical solutions of the time independent Schrödinger equation of different one-dimensional potentials forms are sometime achieved by the asymptotic iteration method. Its importance appears, for example, on its efficiency to describe vibrational system in quantum mechanics. In this paper, the Airy function approach and the Numerov method have been used and presented to study the oscillator anharmonic potential V(x) = Ax{sup 2α} + Bx{sup 2}, (A>0, B<0), with (α = 2) for quadratic, (α =3) for sextic and (α =4) for octic anharmonic oscillators. The Airy function approach is based on the replacement of the real potential V(x) by a piecewise-linear potential v(x), while, the Numerov method is based on the discretization of the wave function on the x-axis. The first energies levels have been calculated and the wave functions for the sextic system have been evaluated. These specific values are unlimited by the magnitude of A, B and α. It’s found that the obtained results are in good agreement with the previous results obtained by the asymptotic iteration method for α =3.

  3. Tuning the Mass of Chameleon Fields in Casimir Force Experiments

    CERN Document Server

    Brax, Ph; Davis, A C; Shaw, D J; Iannuzzi, D

    2010-01-01

    We have calculated the chameleon pressure between two parallel plates in the presence of an intervening medium that affects the mass of the chameleon field. As intuitively expected, the gas in the gap weakens the chameleon interaction mechanism with a screening effect that increases with the plate separation and with the density of the intervening medium. This phenomenon might open up new directions in the search of chameleon particles with future long range Casimir force experiments.

  4. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  5. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

    Science.gov (United States)

    Lee, Kuo Hao; Chen, Jianhan

    2017-06-15

    Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

    2018-03-01

    The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

  7. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  8. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    Science.gov (United States)

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  9. Scalar field collapse in a conformally flat spacetime

    Energy Technology Data Exchange (ETDEWEB)

    Chakrabarti, Soumya; Banerjee, Narayan [Indian Institute of Science Education and Research, Kolkata, Department of Physical Sciences, Mohanpur, West Bengal (India)

    2017-03-15

    The collapse scenario of a scalar field along with a perfect fluid distribution was investigated for a conformally flat spacetime. The theorem for the integrability of an anharmonic oscillator has been utilized. For a pure power-law potential of the form φ{sup n+1}, it was found that a central singularity is formed which is covered by an apparent horizon for n > 0 and n < -3. Some numerical results have also been presented for a combination of two different powers of φ in the potential. (orig.)

  10. Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

    International Nuclear Information System (INIS)

    Zhang Longcai; Wang Suyu; Wang Jiasu

    2009-01-01

    Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

  11. Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Longcai, E-mail: zhlcai2000@163.co [College of Air Traffic Management, Civil Aviation Flight University of China, Guanghan, Sichuan 618307 (China); Wang Suyu; Wang Jiasu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)

    2009-07-01

    Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

  12. The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

    2017-01-01

    of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...

  13. The scaled-charge additive force field for amino acid based ionic liquids

    DEFF Research Database (Denmark)

    Fileti, E. E.; Chaban, V. V.

    2014-01-01

    Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs...... comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions were taken into account by computing electrostatic potential for ion pairs. The van der Waals interactions were adopted from...

  14. Determination of the viscous acoustic field for liquid drop positioning/forcing in an acoustic levitation chamber in microgravity

    Science.gov (United States)

    Lyell, Margaret J.

    1992-01-01

    The development of acoustic levitation systems has provided a technology with which to undertake droplet studies as well as do containerless processing experiments in a microgravity environment. Acoustic levitation chambers utilize radiation pressure forces to position/manipulate the drop. Oscillations can be induced via frequency modulation of the acoustic wave, with the modulated acoustic radiation vector acting as the driving force. To account for tangential as well as radial forcing, it is necessary that the viscous effects be included in the acoustic field. The method of composite expansions is employed in the determination of the acoustic field with viscous effects.

  15. Calculation of electromagnetic fields and forces in coil systems of arbitrary geometry

    International Nuclear Information System (INIS)

    Sackett, S.J.

    1975-01-01

    A computer program, EFFI, is described which calculates the electric and magnetic fields due to an arbitrary spatial distribution of current-carrying circular loops, circular arcs, and straight lines. The electric field is assumed to arise solely from the time variation of the magnetic field, and the magnetic field due to the changing electric field is assumed to be negligible. In addition, the conductor bundle elements (loops, arcs, lines) are assumed to be absent. Electric and magnetic flux lines and magnetic forces and inductances are also calculated by the program. The algorithm used in the code, which is based on a combination of direct and numerical integration using the Biot-Savart law, is discussed. The methods used to maintain accuracy in calculating fields within the conductor bundle, in particular, are detailed. Several examples are then presented to illustrate the input and output features as well as the accuracy obtained and the running time required

  16. Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

    Science.gov (United States)

    Kolmann, Stephen J.; Jordan, Meredith J. T.

    2010-02-01

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol-1 at the CCSD(T)/6-31G∗ level of theory, has a 4 kJ mol-1 dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol-1 lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol-1 lower in energy at the CCSD(T)/6-31G∗ level of theory. Ideally, for sub-kJ mol-1 thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

  17. Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: application to SSSH.

    Science.gov (United States)

    Kolmann, Stephen J; Jordan, Meredith J T

    2010-02-07

    One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.

  18. Accurate energy levels for the anharmonic oscillator and a summable series for the double-well potential in perturbation theory

    International Nuclear Information System (INIS)

    Caswell, W.E.

    1979-01-01

    We introduce a generalization of Wick-ordering which maps the anharmonic oscillator (AO) Hamiltonian for mass m and coupling lambda exactly into a ''Wick-ordered'' Hamiltonian with an effective mass M which is a simple analytic function of lambda and m. The effective coupling Λ=lambda/M 3 is bounded. We transform the AO perturbation series in lambda into one in Λ. This series may then be summed using Borel summation methods. We also introduce a new summation method for the AO series (which is a practical necessity to obtain accurate energy levels of the excited states). We obtain a numerical accuracy for (E/sub P/T--E/sub e/xact)/ E/sub e/xact of at least 10 -7 (using 20 orders of perturbation theory) and 10 -3 (using only 2 orders of perturbation theory) for all couplings and all energy levels of the anharmonic oscillator. The methods are applicable also to the double-well potential (DWP, the AO with a negative mass-squared). The only change is that now the effective coupling is unbounded as lambda→0. The series in Λ is, however, still summable. The relative accuracy in the energy levels for 20 orders of perturbation theory varies from 10 -7 for large coupling to 1% at lambda=0.1 and to 10% at lambda=.05. We also present results for the sextic oscillator

  19. Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

    Energy Technology Data Exchange (ETDEWEB)

    Abdoli, A; Mirzaee, I; Purmahmod, N [Faculty of Engineering, Urmia University, Urmia (Iran, Islamic Republic of); Anvari, A [Department of Physics, Sharif University of Technology, Tehran (Iran, Islamic Republic of)], E-mail: ab.abdoli@gmail.com

    2008-09-07

    Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s{sup -1} at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A{sub b} and D{sub c}, have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications.

  20. Theoretical Kinetic Study of the Formic Acid Catalyzed Criegee Intermediate Isomerization: Multistructural Anharmonicity and Atmospheric Implications

    KAUST Repository

    Monge Palacios, Manuel

    2018-01-29

    We performed a theoretical study on the double hydrogen shift isomerization reaction of a six carbon atom Criegee intermediate (C6-CI), catalyzed by formic acid (HCOOH), to produce vinylhydroperoxide (VHP), C6-CI+HCOOH→VHP+HCOOH. This Criegee intermediate can serve as a surrogate for larger CIs derived from important volatile organic compounds like monoterpenes, whose reactivity is not well understood and are difficult to handle computationally. The reactant HCOOH exerts a pronounced catalytic effect on the studied reaction by lowering the barrier height, but the kinetic enhancement is hindered by the multistructural anharmonicity. First, the rigid ring-structure adopted by the saddle point to facilitate simultaneous transfer of two atoms does not allow formation of as many conformers as those formed by the reactant C6-CI. And second, the flexible carbon chain of C6-CI facilitates the formation of stabilizing intramolecular C–H···O hydrogen bonds; this stabilizing effect is less pronounced in the saddle point structure due to its tightness and steric effects. Thus, the contribution of the reactant C6-CI conformers to the multistructural partition function is larger than that of the saddle point conformers. The resulting low multistructural anharmonicity factor partially cancels out the catalytic effect of the carboxylic acid, yielding in a moderately large rate coefficient, k(298 K) = 4.9·10-13 cm3 molecule-1 s-1. We show that carboxylic acids may promote the conversion of stabilized Criegee intermediates into vinylhydroperoxides in the atmosphere, which generates OH radicals and leads to secondary organic aerosol, thereby affecting the oxidative capacity of the atmosphere and ultimately the climate.

  1. Gravitomagnetic Field of the Universe and Coriolis Force on the Rotating Earth

    Science.gov (United States)

    Veto, B.

    2011-01-01

    The Machian effect of distant masses of the universe in the frame of reference of the rotating Earth is demonstrated using the gravitomagnetic approach of general relativity. This effect appears in the form of a gravitomagnetic Lorentz force acting on moving bodies on the Earth. The gravitomagnetic field of the universe--deduced from a simple…

  2. Self-consistent ansatz for energy levels of the anharmonic oscillator with an application to channeling radiation

    Energy Technology Data Exchange (ETDEWEB)

    Rath, Biswanath

    1988-01-01

    An ansatz is developed to find out an analytical expression for energy levels of anharmonic oscillators of the type V(X) X/sup 2//2 + lambdaXsup(2m) (m = 2,3) which is valid for all values of n and all regimes of parameter space. The procedure is extended to find out an analytical expression for the energy levels of the oscillator V(X) X/sup 2//2 + lambda/sub 1/ X/sup 4/ + lambda/sub 2/ X/sup 6/. As a practical application, it has been applied to calculate the characteristics of radiation emitted due to channeling of relativistic positrons between (100) planes in silicon.

  3. Dynamical instability, strong anharmonicity and electron-phonon coupling in KOs2O6: First-principles calculations

    Science.gov (United States)

    Wang, Wei; Sun, Jiafa; Li, Bin; He, Junqi

    2017-09-01

    First-principles pseudopotential calculations on phonon and electronic properties of β -pyrochlore superconductor KOs2O6 are performed. The imaginary soft-phonon modes with a special double-well potential for the lowest Eu(1) mode and the second lowest T1u(1) mode are reported, which indicates the dynamical instability in KOs2O6. However, the double wells are too small to induce a structural phase transformation in KOs2O6. The strong anharmonicity especially for K T2g(1) phonon mode is got, which is approved to be from the strong electron-phonon coupling that supports the superconductivity in KOs2O6.

  4. Unsteady hydrodynamic forces acting on a hand and its flow field during sculling motion.

    Science.gov (United States)

    Takagi, Hideki; Shimada, Shohei; Miwa, Takahiro; Kudo, Shigetada; Sanders, Ross; Matsuuchi, Kazuo

    2014-12-01

    The goal of this research is to clarify the mechanism by which unsteady forces are generated during sculling by a skilled swimmer and thereby to contribute to improving propulsive techniques. We used particle image velocimetry (PIV) to acquire data on the kinematics of the hand during sculling, such as fluid forces and flow field. By investigating the correlations between these data, we expected to find a new propulsion mechanism. The experiment was performed in a flow-controlled water channel. The participant executed sculling motions to remain at a fixed position despite constant water flow. PIV was used to visualize the flow-field cross-section in the plane of hand motion. Moreover, the fluid forces acting on the hand were estimated from pressure distribution measurements performed on the hand and simultaneous three-dimensional motion analysis. By executing the sculling motion, a skilled swimmer produces large unsteady fluid forces when the leading-edge vortex occurs on the dorsal side of the hand and wake capture occurs on the palm side. By using a new approach, we observed interesting unsteady fluid phenomena similar to those of flying insects. The study indicates that it is essential for swimmers to fully exploit vortices. A better understanding of these phenomena might lead to an improvement in sculling techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

    Science.gov (United States)

    Xu, Dong; Zhang, Yang

    2012-07-01

    Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

  6. Zero mass field quantization and Kibble's long-range force criterion for the Goldstone theorem

    International Nuclear Information System (INIS)

    Wright, S.H.

    1981-01-01

    The central theme of the dissertation is an investigation of the long-range force criterion used by Kibble in his discussion of the Goldstone Theorem. This investigation is broken up into the following sections: I. Introduction. Spontaneous symmetry breaking, the Goldstone Theorem and the conditions under which it holds are discussed. II. Massless Wave Expansions. In order to make explicit calculations of the operator commutators used in applying Kibble's criterion, it is necessary to work out the operator expansions for a massless field. Unusual results are obtained which include operators corresponding to classical macroscopic field modes. III. The Kibble Criterion for Simple Models Exhibiting Spontaneously Broken Symmetries. The results of the previous section are applied to simple models with spontaneously broken symmetries, namely, the real scalar massless field and the Goldstone model without gauge coupling. IV. The Higgs Mechanism in Classical Field Theory. It is shown that the Higgs Mechanism has a simple interpretation in terms of classical field theory, namely, that it arises from a derivative coupling term between the Goldstone fields and the gauge fields. V. The Higgs Mechanism and Kibble's Criterion. This section draws together the material discussed in sections II to IV. Explicit calculations are made to evaluate Kibble's criterion on a Goldstone-Higgs type of model in the Coulomb gauge. It is found, as expected, that the criterion is not met, but not for reasons relating to the range of the mediating force. By referring to the findings of sections III and IV, it is concluded that the common denominator underlying both the Higgs Mechanism and the failure of Kibble's criterion is a structural aspect of the field equations: derivative coupling between fields

  7. First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

    Science.gov (United States)

    Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

    2014-01-01

    Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

  8. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

    Directory of Open Access Journals (Sweden)

    A. V. Sulimov

    2017-01-01

    Full Text Available Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

  9. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

    Science.gov (United States)

    Sulimov, A V; Kutov, D C; Katkova, E V; Sulimov, V B

    2017-01-01

    Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

  10. Near-field Light Scattering Techniques for Measuring Nanoparticle-Surface Interaction Energies and Forces.

    Science.gov (United States)

    Schein, Perry; Ashcroft, Colby K; O'Dell, Dakota; Adam, Ian S; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David

    2015-08-15

    Nanoparticles are quickly becoming commonplace in many commercial and industrial products, ranging from cosmetics to pharmaceuticals to medical diagnostics. Predicting the stability of the engineered nanoparticles within these products a priori remains an important and difficult challenge. Here we describe our techniques for measuring the mechanical interactions between nanoparticles and surfaces using near-field light scattering. Particle-surface interfacial forces are measured by optically "pushing" a particle against a reference surface and observing its motion using scattered near-field light. Unlike atomic force microscopy, this technique is not limited by thermal noise, but instead takes advantage of it. The integrated waveguide and microfluidic architecture allow for high-throughput measurements of about 1000 particles per hour. We characterize the reproducibility of and experimental uncertainty in the measurements made using the NanoTweezer surface instrument. We report surface interaction studies on gold nanoparticles with 50 nm diameters, smaller than previously reported in the literature using similar techniques.

  11. Resonance oscillations of nonreciprocal long-range van der Waals forces between atoms in electromagnetic fields

    Science.gov (United States)

    Sherkunov, Yury

    2018-03-01

    We study theoretically the van der Waals interaction between two atoms out of equilibrium with an isotropic electromagnetic field. We demonstrate that at large interatomic separations, the van der Waals forces are resonant, spatially oscillating, and nonreciprocal due to resonance absorption and emission of virtual photons. We suggest that the van der Waals forces can be controlled and manipulated by tuning the spectrum of artificially created random light.

  12. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  13. Moessbauer study of the fast magnetization reversal forced in permalloy and invar by an external rf magnetic field

    International Nuclear Information System (INIS)

    Kopcewicz, M.

    1978-01-01

    The effect of fast magnetization reversal leading to fast relaxation of the hyperfine field (collapse effect) forced by an external rf magnetic field is studied using the Moessbauer technique for permalloy and invar. The rf collapse and sideband effects are investigated as a function of external rf field, frequency, and intensity. The collapse of the hfs spectrum through unresolved hfs spectrum, triangular shape to a single line, as well as the formation of sidebands is observed. The rf collapse effect is attributed to the rf forced uniform rotation of internal magnetization which causes fast magnetization reversal leading to fast relaxation of the hyperfine field as a result of which the average field at the Moessbauer nuclei is reduced to zero. The difference of the magnetization reversal process in permalloy and invar are discussed. It is shown that the origin of collapse and sideband effects is totaly different: the collapse effect being of purely magnetic origin while the formation of sidebands is due to the rf induced mechanical vibrations of iron atoms within the sample. It is possible to damp sidebands without affecting the collapse effect. The results obtained show that the application of the rf field to ferromagnetic materials gives a unique possibility to force, simulate, and control the relaxation effects in ferromagnetic materials. (author)

  14. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

    Science.gov (United States)

    Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

    2012-01-10

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats

  15. Projection and nested force-gradient methods for quantum field theories

    Energy Technology Data Exchange (ETDEWEB)

    Shcherbakov, Dmitry

    2017-07-26

    For the Hybrid Monte Carlo algorithm (HMC), often used to study the fundamental quantum field theory of quarks and gluons, quantum chromodynamics (QCD), on the lattice, one is interested in efficient numerical time integration schemes which preserve geometric properties of the flow and are optimal in terms of computational costs per trajectory for a given acceptance rate. High order numerical methods allow the use of larger step sizes, but demand a larger computational effort per step; low order schemes do not require such large computational costs per step, but need more steps per trajectory. So there is a need to balance these opposing effects. In this work we introduce novel geometric numerical time integrators, namely, projection and nested force-gradient methods in order to improve the efficiency of the HMC algorithm in application to the problems of quantum field theories.

  16. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Ye [Sanford-Burnham-Prebys Medical Discovery Institute (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham-Prebys Medical Discovery Institute (United States)

    2017-01-15

    Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

  17. Air Force Officer Accession Planning: Addressing Key Gaps in Meeting Career Field Academic Degree Requirements for Nonrated Officers

    Science.gov (United States)

    2016-06-09

    C O R P O R A T I O N Research Report Air Force Officer Accession Planning Addressing Key Gaps in Meeting Career Field Academic Degree Requirements...potential performance, and how to include these quality measures in the classification process. The research sponsor asked us to focus on academic ...Andrew P., and James K. Lowe, “Decision Support for the Career Field Selection Process at the US Air Force Academy,” European Journal of Operational

  18. Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

    Science.gov (United States)

    Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

    2018-04-05

    Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

  19. Magnetic Field Equivalent Current Analysis-Based Radial Force Control for Bearingless Permanent Magnet Synchronous Motors

    Directory of Open Access Journals (Sweden)

    Huangqiu Zhu

    2015-05-01

    Full Text Available Bearingless permanent magnet synchronous motors (BPMSMs, with all advantages of permanent magnet motors (PMSMs and magnetic bearings, have become an important research direction in the bearingless motor field. To realize a stable suspension for the BPMSM, accurate decoupling control between the electromagnetic torque and radial suspension force is indispensable. In this paper, a concise and reliable analysis method based on a magnetic field equivalent current is presented. By this analysis method, the operation principle is analyzed theoretically, and the necessary conditions to produce a stable radial suspension force are confirmed. In addition, mathematical models of the torque and radial suspension force are established which is verified by the finite element analysis (FEA software ANSYS. Finally, an experimental prototype of a 2-4 poles surface-mounted BPMSM is tested with the customized control strategy. The simulation and experimental results have shown that the motor has good rotation and suspension performance, and validated the accuracy of the proposed analysis method and the feasibility of the control strategy.

  20. Compatibility of the Chameleon-Field Model with Fifth-Force Experiments, Cosmology, and PVLAS and CAST Results

    International Nuclear Information System (INIS)

    Brax, Philippe; Bruck, Carsten van de; Davis, Anne-Christine

    2007-01-01

    We analyze the PVLAS results using a chameleon field whose properties depend on the environment. We find that, assuming a runaway bare potential V(φ) and a universal coupling to matter, the chameleon potential is such that the scalar field can act as dark energy. Moreover, the chameleon-field model is compatible with the CERN Axion Solar Telescope results, fifth-force experiments, and cosmology

  1. Influence of AC external magnetic field perturbation on the guidance force of HTS bulk over a NdFeB guideway

    International Nuclear Information System (INIS)

    Zhang Longcai; Wang Jiasu; Wang Suyu; He Qingyong

    2007-01-01

    Superconducting maglev vehicle system requires that the surface magnetic field of the guideway is uniform along the forward direction. But in practice the surface magnetic field of the NdFeB permanent magnet guideway is not always immutable. So the HTS bulks in this case are exposed to AC external magnetic field, which may induce the energy loss in the bulk and influence the guidance force between the HTS bulks and the NdFeB guideway. In this paper, we experimentally studied the influence of the AC external magnetic field perturbation on the guidance force of a HTS bulk over the NdFeB guideway. The experimental results showed that the guidance force was influenced by the application of the AC external magnetic. The guidance fore hysteresis became more evident with the amplitude of the AC field and was independent of the frequency in the range 90-400 Hz. We attributed the reason to magnetic hysteresis loss in the superconductor

  2. Influence of AC external magnetic field perturbation on the guidance force of HTS bulk over a NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Longcai [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)]. E-mail: zhlcai2000@163.com; Wang Jiasu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China); Wang Suyu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China); He Qingyong [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)

    2007-08-01

    Superconducting maglev vehicle system requires that the surface magnetic field of the guideway is uniform along the forward direction. But in practice the surface magnetic field of the NdFeB permanent magnet guideway is not always immutable. So the HTS bulks in this case are exposed to AC external magnetic field, which may induce the energy loss in the bulk and influence the guidance force between the HTS bulks and the NdFeB guideway. In this paper, we experimentally studied the influence of the AC external magnetic field perturbation on the guidance force of a HTS bulk over the NdFeB guideway. The experimental results showed that the guidance force was influenced by the application of the AC external magnetic. The guidance fore hysteresis became more evident with the amplitude of the AC field and was independent of the frequency in the range 90-400 Hz. We attributed the reason to magnetic hysteresis loss in the superconductor.

  3. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

    Science.gov (United States)

    Wu, Xiaojing; Clavaguera, Carine; Lagardère, Louis; Piquemal, Jean-Philip; de la Lande, Aurélien

    2018-04-16

    We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.

  4. An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-02-10

    A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.

  5. The influence of anharmonic vibrations of the core to M2-transition between low-lying states in 115Sn

    International Nuclear Information System (INIS)

    Sy Savane, Y.

    1995-12-01

    The influence of the anharmonicity of the core vibration, on the magnetic transition 11/2 - 1 → 7/2 + 1 in 115 Sn have been investigated in the frame of the quasiparticle-phonon nuclear model. The model wave function includes a ''quasiparticle + two phonons'' component. The performed numerical calculations show that those effects cannot explain the strong reduction of the M2-transition observed in the experiment. A full agreement with the experimental value is obtained with g eff s = 0.42g free s . (author). 10 refs, 2 figs, 1 tab

  6. Drastic fall-off of the thermal conductivity for disordered lattices in the limit of weak anharmonic interactions

    International Nuclear Information System (INIS)

    Huveneers, François

    2013-01-01

    We study the thermal conductivity, at fixed positive temperature, of a disordered lattice of harmonic oscillators, weakly coupled to each other through anharmonic potentials. The interaction is controlled by a small parameter ϵ > 0. We rigorously show, in two slightly different setups, that the conductivity has a non-perturbative origin. This means that it decays to zero faster than any polynomial in ϵ as ϵ → 0. It is then argued that this result extends to a disordered chain studied by Dhar and Lebowitz (2008 Phys. Rev. Lett. 100 134301), and to a classic spin chain recently investigated by Oganesyan, Pal and Huse (2009 Phys. Rev. B 80 115104). (paper)

  7. An automated analysis workflow for optimization of force-field parameters using neutron scattering data

    Energy Technology Data Exchange (ETDEWEB)

    Lynch, Vickie E.; Borreguero, Jose M. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Bhowmik, Debsindhu [Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Ganesh, Panchapakesan; Sumpter, Bobby G. [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Proffen, Thomas E. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Goswami, Monojoy, E-mail: goswamim@ornl.gov [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)

    2017-07-01

    Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.

  8. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    Science.gov (United States)

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

  9. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-01-01

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities

  10. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  11. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

    Science.gov (United States)

    Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

    2009-10-01

    This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

  12. On the Shape of Force-Free Field Lines in the Solar Corona

    KAUST Repository

    Prior, C.

    2012-02-02

    This paper studies the shape parameters of looped field lines in a linear force-free magnetic field. Loop structures with a sufficient amount of kinking are generally seen to form S or inverse S (Z) shapes in the corona (as viewed in projection). For a single field line, we can ask how much the field line is kinked (as measured by the writhe), and how much neighbouring flux twists about the line (as measured by the twist number). The magnetic helicity of a flux element surrounding the field line can be decomposed into these two quantities. We find that the twist helicity contribution dominates the writhe helicity contribution, for field lines of significant aspect ratio, even when their structure is highly kinked. These calculations shed light on some popular assumptions of the field. First, we show that the writhe of field lines of significant aspect ratio (the apex height divided by the footpoint width) can sometimes be of opposite sign to the helicity. Secondly, we demonstrate the possibility of field line structures which could be interpreted as Z-shaped, but which have a helicity value sign expected of an S-shaped structure. These results suggest that caution should be exercised in using two-dimensional images to draw conclusions on the helicity value of field lines and flux tubes. © 2012 Springer Science+Business Media B.V.

  13. Numerical-analytic implementation of the higher-order canonical Van Vleck perturbation theory for the interpretation of medium-sized molecule vibrational spectra.

    Science.gov (United States)

    Krasnoshchekov, Sergey V; Isayeva, Elena V; Stepanov, Nikolay F

    2012-04-12

    Anharmonic vibrational states of semirigid polyatomic molecules are often studied using the second-order vibrational perturbation theory (VPT2). For efficient higher-order analysis, an approach based on the canonical Van Vleck perturbation theory (CVPT), the Watson Hamiltonian and operators of creation and annihilation of vibrational quanta is employed. This method allows analysis of the convergence of perturbation theory and solves a number of theoretical problems of VPT2, e.g., yields anharmonic constants y(ijk), z(ijkl), and allows the reliable evaluation of vibrational IR and Raman anharmonic intensities in the presence of resonances. Darling-Dennison and higher-order resonance coupling coefficients can be reliably evaluated as well. The method is illustrated on classic molecules: water and formaldehyde. A number of theoretical conclusions results, including the necessity of using sextic force field in the fourth order (CVPT4) and the nearly vanishing CVPT4 contributions for bending and wagging modes. The coefficients of perturbative Dunham-type Hamiltonians in high-orders of CVPT are found to conform to the rules of equality at different orders as earlier proven analytically for diatomic molecules. The method can serve as a good substitution of the more traditional VPT2.

  14. Simulation of a force on force exercise

    International Nuclear Information System (INIS)

    Terhune, R.; Van Slyke, D.; Sheppard, T.; Brandrup, M.

    1988-01-01

    The Security Exercise Evaluation System (SEES) is under development for use in planning Force on Force exercises and as an aid in post-exercise evaluation. This study is part of the development cycle where the simulation results are compared to field data to provide guidance for further development of the model. SEES is an event-driven stochastic computer program simulating individual movement and combat within an urban terrain environment. The simulator models the physics of movement, line of sight, and weapon effects. It relies on the controllers to provide all knowledge of security tactics, which are entered by the controllers during the simulation using interactive color graphic workstations. They are able to develop, modify and implement plans promptly as the simulator maintains real time. This paper reports on how SEES will be used to develop an intrusion plan, test the security response tactics and develop observer logistics. A Force on Force field exercise will then be executed to follow the plan with observations recorded. An analysis is made by first comparing the plan and events of the simulation with the field exercise, modifying the simulation plan to match the actual field exercise, and then running the simulation to develop a distribution of possible outcomes

  15. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    Energy Technology Data Exchange (ETDEWEB)

    MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  16. Dispersion Forces

    CERN Document Server

    Buhmann, Stefan Yoshi

    2012-01-01

    In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

  17. Novel System for Bite-Force Sensing and Monitoring Based on Magnetic Near Field Communication

    Directory of Open Access Journals (Sweden)

    Jesús Sanz Maudes

    2012-08-01

    Full Text Available Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID technology (NFC. The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient’s dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system’s operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials.

  18. Quantum theory of anharmonic oscillators - a variational and systematic general approximation method

    International Nuclear Information System (INIS)

    Yamazaki, K.; Kyoto Univ.

    1984-01-01

    The paper investigates the energy levels and wavefunctions of an anharmonic oscillator characterised by the potential 1/2ω 2 q 2 +lambdaq 4 . As a lowest-order approximation an extremely simple formula for energy levels, Esub(i)sup(0) = (i+1/2)1/4(3/αsub(i)+αsub(i)), is derived (i being the quantum number of the energy level). This formula reproduces the exact energy levels within an error of about 1%. Systematically higher orders of the present perturbation theory are developed. The present second-order perturbation theory reduces the errors of the lowest-order results by a factor of about 1/5 in general. Various ranges (large, intermediate, small) of (i, lambda) are investigated and compared with the exact values obtained by other workers. For i = 0, 1, even the fourth-order perturbation calculation can be elaborated explicitly, which reduces the error to about 0.01% for any lambda. For small lambda it gives correct numerical coefficients up to lambda 4 terms, as it should. (author)

  19. Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

    International Nuclear Information System (INIS)

    Kim, S H; Hashi, S; Ishiyama, K

    2011-01-01

    This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and 19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

  20. Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

    Science.gov (United States)

    Kim, S. H.; Hashi, S.; Ishiyama, K.

    2011-01-01

    This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

  1. Mapping the global football field: a sociological model of transnational forces within the world game.

    Science.gov (United States)

    Giulianotti, Richard; Robertson, Roland

    2012-06-01

    This paper provides a sociological model of the key transnational political and economic forces that are shaping the 'global football field'. The model draws upon, and significantly extends, the theory of the 'global field' developed previously by Robertson. The model features four quadrants, each of which contains a dominant operating principle, an 'elemental reference point', and an 'elemental theme'. The quadrants contain, first, neo-liberalism, associated with the individual and elite football clubs; second, neo-mercantilism, associated with nation-states and national football systems; third, international relations, associated with international governing bodies; and fourth, global civil society, associated with diverse institutions that pursue human development and/or social justice. We examine some of the interactions and tensions between the major institutional and ideological forces across the four quadrants. We conclude by examining how the weakest quadrant, featuring global civil society, may gain greater prominence within football. In broad terms, we argue that our four-fold model may be utilized to map and to examine other substantive research fields with reference to globalization. © London School of Economics and Political Science 2012.

  2. Theory and numerical calculation of the acoustic field exerted by eddy-current forces

    Energy Technology Data Exchange (ETDEWEB)

    Kawashima, K.

    1976-01-01

    The equations for calculating the acoustic field produced within a nonmagnetic metal by interaction of eddy currents with a static magnetic field were obtained on the assumptions (1) an ultrasonic wave is generated by the electromagentic force through classical and macroscopic phenomena; (2) the electric, magnetic, and elastic properties of the metal are linear, isotropic, and homogeneous throughout the metal, which occupies semi-infinite space; (3) the whole system is axially symmetric; and (4) eddy currents and elastic waves show a steady-state sinusoidal variation. The acoustic field produced by a specific electromagnetic ultrasonic transducer with axial symmetry was calculated numerically, and the results showed a well-defined ultrasonic wave beam, which was narrower than had been expected from the size of the transducer. (auth)

  3. Influence of Complete Coriolis Force on the Dispersion Relation of Ocean Internal-wave in a Background Currents Field

    Directory of Open Access Journals (Sweden)

    Liu Yongjun

    2015-01-01

    Full Text Available In this thesis, the influence of complete Coriolis force (the model includes both the vertical and horizontal components of Coriolis force on the dispersion relation of ocean internal-wave under background currents field are studied, it is important to the study of ocean internal waves in density-stratified ocean. We start from the control equation of sea water movement in the background of the non-traditional approximation, and the vertical velocity solution is derived where buoyancy frequency N(z gradually varies with the ocean depth z. The results show that the influence of complete Coriolis force on the dispersion relation of ocean internal-wave under background currents field is obvious, and these results provide strong evidence for the understanding of dynamic process of density stratified ocean internal waves.

  4. Atomic force and scanning near-field optical microscopy study of carbocyanine dye J-aggregates

    Czech Academy of Sciences Publication Activity Database

    Prokhorov, V.V.; Petrova, M.G.; Kovaleva, Natalia; Demikhov, E.I.

    2014-01-01

    Roč. 10, č. 5 (2014), s. 700-704 ISSN 1573-4137 Institutional support: RVO:68378271 Keywords : carbocyanine dye * elementary fibri * high-resolution atomic force microscopy * J-aggregate * probe microscopy * scanning near-field optical microscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.096, year: 2014

  5. Construction of an accurate quartic force field by using generalised least-squares fitting and experimental design

    International Nuclear Information System (INIS)

    Carbonniere, Philippe; Begue, Didier; Dargelos, Alain; Pouchan, Claude

    2004-01-01

    In this work we present an attractive least-squares fitting procedure which allows for the calculation of a quartic force field by jointly using energy, gradient, and Hessian data, obtained from electronic wave function calculations on a suitably chosen grid of points. We use the experimental design to select the grid points: a 'simplex-sum' of Box and Behnken grid was chosen for its efficiency and accuracy. We illustrate the numerical implementations of the method by using the energy and gradient data for H 2 O and H 2 CO. The B3LYP/cc-pVTZ quartic force field performed from 11 and 44 simplex-sum configurations shows excellent agreement in comparison to the classical 44 and 168 energy calculations

  6. Force-free fields in the vicinity of a Reissner-Nordstroem black hole

    International Nuclear Information System (INIS)

    Evangelidis, E.

    1978-01-01

    The behaviour of a force-free field has been studied in a Reissner-Nordstroem metric. An expansion in tensor harmonics of even-odd parity reduced the radial equations in a differential equation of the Sturm-Liouville system which was solved asymptotically in a conveniently defined space coordinate. Further, it has been possible to regularize the singular behaviour of the Reissner-Nordstroem metric at the event horizon and the modified metric to be given explicitly. (Auth.)

  7. Mean-field theory for a ferroelectric transition

    International Nuclear Information System (INIS)

    Dobry, A.; Greco, A.; Stachiotti, M.

    1990-01-01

    For the treatment of anharmonic models of solids presenting structural transitions, a commonly used approximation is that of self-consistent phonons. Rather than the usual site decoupling, this mean-field theory is based on decoupling of modes in reciprocal space. A self-consistent phonon approximation for the non-linear polarizability model is developed in this work. The model describes the dynamical properties of ferroelectric materials. Phase diagrams as a function of relevant model parameters are presented. An analysis is made of critical behaviour and it is shown that the approximation leads to the same anomalies found in other models. (Author). 9 refs., 3 figs

  8. An electric field in a gravitational field

    International Nuclear Information System (INIS)

    Harpaz, Amos

    2005-01-01

    The behaviour of an electric field in a gravitational field is analysed. It is found that due to the mass (energy) of the electric field, it is subjected to gravity and it falls in the gravitational field. This fall curves the electric field, a stress force (a reaction force) is created, and the interaction of this reaction force with the static charge gives rise to the creation of radiation

  9. On the use of quartic force fields in variational calculations

    Science.gov (United States)

    Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.

    2013-06-01

    Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine (-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods.

  10. Baryonic forces and hyperons in nuclear matter from SU(3) chiral effective field theory

    Energy Technology Data Exchange (ETDEWEB)

    Petschauer, Stefan Karl

    2016-02-12

    In this work the baryon-baryon interaction is studied at next-to-leading order in SU(3) chiral effective field theory and applied to hyperon-nucleon scattering. The properties of hyperons in isospin-symmetric as well as asymmetric nuclear matter are calculated within the Bruecker-Hartree-Fock formalism. Moreover, the leading three-baryon interaction is derived and its low-energy constants are estimated from decuplet intermediate states. We conclude, that chiral effective field theory is a well-suited tool to describe the baryonic forces.

  11. Recent Progress in Molecular Simulation of Aqueous Electrolytes: Force Fields, Chemical Potentials and Solubility.

    Czech Academy of Sciences Publication Activity Database

    Nezbeda, Ivo; Moučka, F.; Smith, W.R.

    2016-01-01

    Roč. 114, č. 11 (2016), s. 1665-1690 ISSN 0026-8976 R&D Projects: GA ČR GA15-19542S Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : force fields * chemical potentials * aqueous electrolytes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.870, year: 2016

  12. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

    Science.gov (United States)

    Miller, Mark S.; Lay, Wesley K.

    2016-01-01

    Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

  13. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    International Nuclear Information System (INIS)

    Morante, S.; Rossi, G.C.

    2017-01-01

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  14. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)

    2017-02-15

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  15. Hearing the zero locus of a magnetic field

    International Nuclear Information System (INIS)

    Montgomery, R.

    1995-01-01

    We investigate the ground state of a two-dimensional quantum particle in a magnetic field where the field vanishes nondegenerately along a closed curve. We show that the ground state concentrates on this curve as e/h tends to infinity, where e is the charge, and that the ground state energy grows like (e/h) 2/3 . These statements are true for any energy level, the level being fixed as the charge tends to infinity. If the magnitude of the gradient of the magnetic field is a constant b 0 along its zero locus, then we get the precise asymptotics (e/h) 2/3 (b 0 ) 2/3 E * + O(1) for every energy level. The constant E * ≅ .5698 is the infimum of the ground state energies E(β) of the anharmonic oscillator family -d 2 /dy 2 + (1/2 y 2 - β) 2 . (orig.)

  16. Feedforward compensation for novel dynamics depends on force field orientation but is similar for the left and right arms.

    Science.gov (United States)

    Reuter, Eva-Maria; Cunnington, Ross; Mattingley, Jason B; Riek, Stephan; Carroll, Timothy J

    2016-11-01

    There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153-167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. Copyright © 2016 the American Physiological Society.

  17. ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

    International Nuclear Information System (INIS)

    Zhang, X. M.; Zhang, M.; Su, J. T.

    2017-01-01

    It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such as limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.

  18. Reconsidering harmonic and anharmonic coherent states: Partial differential equations approach

    Energy Technology Data Exchange (ETDEWEB)

    Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

    2015-02-15

    This article presents a new approach to dealing with time dependent quantities such as autocorrelation function of harmonic and anharmonic systems using coherent states and partial differential equations. The approach that is normally used to evaluate dynamical quantities involves formidable operator algebra. That operator algebra becomes insurmountable when employing Morse oscillator coherent states. This problem becomes even more complicated in case of Morse oscillator as it tends to exhibit divergent dynamics. This approach employs linear partial differential equations, some of which may be solved exactly and analytically, thereby avoiding the cumbersome noncommutative algebra required to manipulate coherent states of Morse oscillator. Additionally, the arising integrals while using the herein presented method feature stability and high numerical efficiency. The correctness, applicability, and utility of the above approach are tested by reproducing the partition and optical autocorrelation function of the harmonic oscillator. A closed-form expression for the equilibrium canonical partition function of the Morse oscillator is derived using its coherent states and partial differential equations. Also, a nonequilibrium autocorrelation function expression for weak electron–phonon coupling in condensed systems is derived for displaced Morse oscillator in electronic state. Finally, the utility of the method is demonstrated through further simplifying the Morse oscillator partition function or autocorrelation function expressions reported by other researchers in unevaluated form of second-order derivative exponential. Comparison with exact dynamics shows identical results.

  19. Momentum distribution, vibrational dynamics, and the potential of mean force in ice

    Science.gov (United States)

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

    2011-06-01

    By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.

  20. Neutron scattering techniques for betaine calcium chloride dihydrate under applied external field (temperature, electric field and hydrostatic pressure)

    International Nuclear Information System (INIS)

    Hernandez, O.

    1997-01-01

    We have studied with neutron scattering techniques betaine calcium chloride dihydrate (BCCD), a dielectric aperiodic crystal which displays a Devil's staircase type phase diagram made up of several incommensurate and commensurate phases, having a range of stability very sensitive to temperature, electric field and hydrostatic pressure. We have measured a global hysteresis of δ(T) of about 2-3 K in the two incommensurate phases. A structural study of the modulated commensurate phases 1/4 and 1/5 allows us to evidence that the atomic modulation functions are anharmonic. The relevance of the modelization of the modulated structure by polar Ising pseudo-spins is then directly established. On the basis of group theory calculation in the four dimensional super-space, we interpret this anharmonic modulation as a soliton regime with respect to the lowest-temperature non modulated ferroelectric phase. The continuous character of the transition to the lowest-temperature non modulated phase and the diffuse scattering observed in this phase are accounted for the presence of ferroelectric domains separated by discommensurations. Furthermore, we have shown that X-rays induce in BCCD a strong variation with time of irradiation of the intensity of satellite peaks, and more specifically for third order ones. This is why the 'X-rays' structural model is found more harmonic than the 'neutron' one. Under electric field applied along the vector b axis, we confirm that commensurate phases with δ = even/odd are favoured and hence are polar along this direction. We have evidenced at 10 kV / cm two new higher order commensurate phases in the phase INC2, corroborating the idea of a 'complete' Devil's air-case phase diagram. A phenomenon of generalized coexistence of phases occurs above 5 kV / cm. We have characterized at high field phase transitions between 'coexisting' phases, which are distinguishable from classical lock-in transitions. Under hydrostatic pressure, our results contradict

  1. Influence of grain size and upper critical magnetic field on global pinning force of bronze-processed Nb/sub 3/Sn compound

    International Nuclear Information System (INIS)

    Ochiai, S.; Osamura, K.

    1986-01-01

    In order to know the dependency of global pinning force of Nb/sub 3/Sn compound on grain size and upper critical magnetic field, the global pinning force was measured at 3-15 T using bronze-processed multifilamentary composites. The grain size and upper critical magnetic field were varied by two types of annealing treatment: one is the isothermal annealing at 873, 973 and 1073 K up to 1730 ks and another is the two-stage annealing (low temperature annealing to form fine grains at 873 K for 1730 ks + high temperature annealing to raise upper critical magnetic field at 1073 K up to 18 ks). In the case of isothermal annealing treatment, both of grain size and upper critical magnetic field increased with increasing annealing temperature and time except for the annealing treatments at high temperature for prolonged times. In the case of two-stage annealing, both of them increased with second stage annealing time. The increase in grain size led to decrease in the pinning force but the increase in upper critical magnetic field to increase in it. From the analysis of the present data based on the Suenaga's speculation concerning with the density of pinning site and the Kramer's equation, it was suggested that the pinning force is, to a first approximation, proportional to the product of inverse grain size and (1-h)/sup 2/h/sup 1/2/ where h is the reduced magnetic field

  2. The force analysis for superparamagnetic nanoparticles-based gene delivery in an oscillating magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jiajia [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Shi, Zongqian, E-mail: zqshi@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Jia, Shenli [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Zhang, Pengbo [Department of Anesthesiology, Second Affiliated Hospital of Xi’an Jiaotong University School of Medicine, No.157 West 5 Road, Xi’an, Shaanxi Province 710004 (China)

    2017-04-01

    Due to the peculiar magnetic properties and the ability to function in cell-level biological interaction, superparamagnetic nanoparticles (SMNP) have been being the attractive carrier for gene delivery. The superparamagnetic nanoparticles with surface-bound gene vector can be attracted to the surface of cells by the Kelvin force provided by external magnetic field. In this article, the influence of the oscillating magnetic field on the characteristics of magnetofection is studied in terms of the magnetophoretic velocity. The magnetic field of a cylindrical permanent magnet is calculated by equivalent current source (ECS) method, and the Kelvin force is derived by using the effective moment method. The results show that the static magnetic field accelerates the sedimentation of the particles, and drives the particles inward towards the axis of the magnet. Based on the investigation of the magnetophoretic velocity of the particle under horizontally oscillating magnetic field, an oscillating velocity within the amplitude of the magnet oscillation is observed. Furthermore, simulation results indicate that the oscillating amplitude plays an important role in regulating the active region, where the particles may present oscillating motion. The analysis of the magnetophoretic velocity gives us an insight into the physical mechanism of the magnetofection. It's also helpful to the optimal design of the magnetofection system. - Highlights: • We compare the results of the ECS method and FEA method with the commercial software, Ansys. • We analyze the physic mechanism of the oscillating motion of the particles in the presence of an oscillating magnet. • We discuss the influence of the oscillating amplitude of the magnet on the behavior of the particle.

  3. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

    Science.gov (United States)

    2016-01-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  4. Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes

    DEFF Research Database (Denmark)

    Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus

    2015-01-01

    The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical...

  5. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  6. Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

    DEFF Research Database (Denmark)

    Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

    2004-01-01

    of the (gg, gt and tg) rotamers of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol. respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error...

  7. The empirical equilibrium structure of diacetylene

    OpenAIRE

    Thorwirth, S.; Harding, M. E.; Muders, D.; Gauss, J.

    2008-01-01

    High-level quantum-chemical calculations are reported at the MP2 and CCSD(T) levels of theory for the equilibrium structure and the harmonic and anharmonic force fields of diacetylene, HCCCCH. The calculations were performed employing Dunning's hierarchy of correlation-consistent basis sets cc-pVXZ, cc-pCVXZ, and cc-pwCVXZ, as well as the ANO2 basis set of Almloef and Taylor. An empirical equilibrium structure based on experimental rotational constants for thirteen isotopic species of diacety...

  8. Confinement of plasma along shaped open magnetic fields from the centrifugal force of supersonic plasma rotation.

    Science.gov (United States)

    Teodorescu, C; Young, W C; Swan, G W S; Ellis, R F; Hassam, A B; Romero-Talamas, C A

    2010-08-20

    Interferometric density measurements in plasmas rotating in shaped, open magnetic fields demonstrate strong confinement of plasma parallel to the magnetic field, with density drops of more than a factor of 10. Taken together with spectroscopic measurements of supersonic E × B rotation of sonic Mach 2, these measurements are in agreement with ideal MHD theory which predicts large parallel pressure drops balanced by centrifugal forces in supersonically rotating plasmas.

  9. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

    Science.gov (United States)

    Pavlova, Anna; Parks, Jerry M; Gumbart, James C

    2018-02-13

    Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

  10. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field

    National Research Council Canada - National Science Library

    Bunte, Steven

    2000-01-01

    To investigate the mechanical and other condensed phase properties of energetic materials using atomistic simulation techniques, the COMPASS force field has been expanded to include high-energy nitro functional groups...

  11. On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters.

    Science.gov (United States)

    Bachmann, Stephan J; Lin, Zhixiong; Stafforst, Thorsten; van Gunsteren, Wilfred F; Dolenc, Jožica

    2014-01-14

    The technique of one-step perturbation to explore the relation between particular force-field parameters on the one hand and particular properties of a biomolecular system on the other hand from one or a few molecular dynamics simulations is applied to investigate the dependence of the free enthalpy of dimer formation and of crystal dissolution of a self-complementary fragment (H-CGTACG-NH2) of peptide nucleic acid, PNA, a mimic of DNA. The simulations show that PNA dimer formation in aqueous solution is favored by a decrease in the base charges with respect to values of the GROMOS 45A4 force field, while it is disfavored by a decrease in the backbone charges. In contrast, crystal dissolution of the PNA dimer is favored by a decrease in base charges, while a variation of backbone charges has a minor effect on this free enthalpy change. These opposite effects in a crystalline versus aqueous solution environment can be understood from the different water contents for these systems and have consequences for biomolecular force-field development.

  12. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  13. Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

    Science.gov (United States)

    Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

    2012-12-01

    Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

  14. Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

    Science.gov (United States)

    Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David

    2016-12-12

    For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. NONLINEAR FORCE-FREE MAGNETIC FIELD FITTING TO CORONAL LOOPS WITH AND WITHOUT STEREOSCOPY

    International Nuclear Information System (INIS)

    Aschwanden, Markus J.

    2013-01-01

    We developed a new nonlinear force-free magnetic field (NLFFF) forward-fitting algorithm based on an analytical approximation of force-free and divergence-free NLFFF solutions, which requires as input a line-of-sight magnetogram and traced two-dimensional (2D) loop coordinates of coronal loops only, in contrast to stereoscopically triangulated three-dimensional loop coordinates used in previous studies. Test results of simulated magnetic configurations and from four active regions observed with STEREO demonstrate that NLFFF solutions can be fitted with equal accuracy with or without stereoscopy, which relinquishes the necessity of STEREO data for magnetic modeling of active regions (on the solar disk). The 2D loop tracing method achieves a 2D misalignment of μ 2 = 2.°7 ± 1.°3 between the model field lines and observed loops, and an accuracy of ≈1.0% for the magnetic energy or free magnetic energy ratio. The three times higher spatial resolution of TRACE or SDO/AIA (compared with STEREO) also yields a proportionally smaller misalignment angle between model fit and observations. Visual/manual loop tracings are found to produce more accurate magnetic model fits than automated tracing algorithms. The computation time of the new forward-fitting code amounts to a few minutes per active region.

  16. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

    Directory of Open Access Journals (Sweden)

    Kenichi Dedachi

    2013-01-01

    Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

  17. A Simple Model of Fields Including the Strong or Nuclear Force and a Cosmological Speculation

    Directory of Open Access Journals (Sweden)

    David L. Spencer

    2016-10-01

    Full Text Available Reexamining the assumptions underlying the General Theory of Relativity and calling an object's gravitational field its inertia, and acceleration simply resistance to that inertia, yields a simple field model where the potential (kinetic energy of a particle at rest is its capacity to move itself when its inertial field becomes imbalanced. The model then attributes electromagnetic and strong forces to the effects of changes in basic particle shape. Following up on the model's assumption that the relative intensity of a particle's gravitational field is always inversely related to its perceived volume and assuming that all black holes spin, may create the possibility of a cosmic rebound where a final spinning black hole ends with a new Big Bang.

  18. Ionization induced by strong electromagnetic field in low dimensional systems bound by short range forces

    Energy Technology Data Exchange (ETDEWEB)

    Eminov, P.A., E-mail: peminov@mail.ru [Moscow State University of Instrument Engineering and Computer Sciences, 20 Stromynka Street, Moscow 2107996 (Russian Federation); National Research University Higher School of Economics, 3/12 Bolshoy Trekhsvyatskiy pereulok, Moscow 109028 (Russian Federation)

    2013-10-01

    Ionization processes for a two dimensional quantum dot subjected to combined electrostatic and alternating electric fields of the same direction are studied using quantum mechanical methods. We derive analytical equations for the ionization probability in dependence on characteristic parameters of the system for both extreme cases of a constant electric field and of a linearly polarized electromagnetic wave. The ionization probabilities for a superposition of dc and low frequency ac electric fields of the same direction are calculated. The impulse distribution of ionization probability for a system bound by short range forces is found for a superposition of constant and alternating fields. The total probability for this process per unit of time is derived within exponential accuracy. For the first time the influence of alternating electric field on electron tunneling probability induced by an electrostatic field is studied taking into account the pre-exponential term.

  19. Three-dimensional computation of magnetic fields and Lorentz forces of an LHC dipole magnet

    International Nuclear Information System (INIS)

    Daum, C.; Avest, D. ter

    1989-07-01

    Magnetic fields and Lorentz forces of an LHC dipole magnet are calculated using the method of image currents to represent the effect of the iron shield. The calculation is performed for coils of finite length using a parametrization for coil heads of constant perimeter. A comparison with calculations based on POISSON and TOSCA is made. (author). 5 refs.; 31 figs.; 6 tabs

  20. Source evaluation report phase 2 investigation: Limited field investigation. Final report: United States Air Force Environmental Restoration Program, Eielson Air Force Base, Alaska

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

    This report describes the limited field investigation work done to address issues and answer unresolved questions regarding a collection of potential contaminant sources at Eielson Air Force Base (AFB), near Fairbanks, Alaska. These sources were listed in the Eielson AFB Federal Facility Agreement supporting the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) cleanup of the base. The limited field investigation began in 1993 to resolve all remaining technical issues and provide the data and analysis required to evaluate the environmental hazard associated with these sites. The objective of the limited field investigation was to allow the remedial project managers to sort each site into one of three categories: requiring remedial investigation/feasibility study, requiring interim removal action, or requiring no further remedial action.

  1. Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

    Science.gov (United States)

    Müller, Erich A; Jackson, George

    2014-01-01

    A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

  2. Researching Refugee and Forced Migration Studies: An Introduction to the Field and the Reference Literature.

    Science.gov (United States)

    Mason, Elisa

    1999-01-01

    Describes the evolution of refugee and forced migration studies, identifies factors that render it a challenging field to research, and highlights a variety of Internet-based and other electronic resources that can be used to locate monographs, periodicals, grey literature, and current information. Provides a bibliography of reference materials in…

  3. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

    DEFF Research Database (Denmark)

    Rossi, G.; Monticelli, L.; Puisto, S. R.

    2011-01-01

    We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....

  4. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  5. A Multiposture Locomotor Training Device with Force-Field Control

    Directory of Open Access Journals (Sweden)

    Jianfeng Sui

    2014-11-01

    Full Text Available This paper introduces a multiposture locomotor training device (MPLTD with a closed-loop control scheme based on joint angle feedback, which is able to overcome various difficulties resulting from mechanical vibration and the weight of trainer to achieve higher accuracy trajectory. By introducing the force-field control scheme used in the closed-loop control, the device can obtain the active-constrained mode including the passive one. The MPLTD is mainly composed of three systems: posture adjusting and weight support system, lower limb exoskeleton system, and control system, of which the lower limb exoskeleton system mainly includes the indifferent equilibrium mechanism with two degrees of freedom (DOF and the driving torque is calculated by the Lagrangian function. In addition, a series of experiments, the weight support and the trajectory accuracy experiment, demonstrate a good performance of mechanical structure and the closed-loop control.

  6. Prediction of Low-Thermal-Conductivity Compounds with First-Principles Anharmonic Lattice-Dynamics Calculations and Bayesian Optimization

    Science.gov (United States)

    Seko, Atsuto; Togo, Atsushi; Hayashi, Hiroyuki; Tsuda, Koji; Chaput, Laurent; Tanaka, Isao

    2015-11-01

    Compounds of low lattice thermal conductivity (LTC) are essential for seeking thermoelectric materials with high conversion efficiency. Some strategies have been used to decrease LTC. However, such trials have yielded successes only within a limited exploration space. Here, we report the virtual screening of a library containing 54 779 compounds. Our strategy is to search the library through Bayesian optimization using for the initial data the LTC obtained from first-principles anharmonic lattice-dynamics calculations for a set of 101 compounds. We discovered 221 materials with very low LTC. Two of them even have an electronic band gap <1 eV , which makes them exceptional candidates for thermoelectric applications. In addition to those newly discovered thermoelectric materials, the present strategy is believed to be powerful for many other applications in which the chemistry of materials is required to be optimized.

  7. Different forces

    CERN Multimedia

    1982-01-01

    The different forces, together with a pictorial analogy of how the exchange of particles works. The table lists the relative strength of the couplings, the quanta associated with the force fields and the bodies or phenomena in which they have a dominant role.

  8. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    International Nuclear Information System (INIS)

    Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; Gunsteren, W. F. van

    2004-01-01

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, 3 J NHα and 3 J αβ coupling constants, and 1 5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone 3 J HNα -coupling constants and 1 H- 1 5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain 3 J αβ -coupling constants and 1 H- 1 5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result

  9. Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas

    International Nuclear Information System (INIS)

    Ebihara, Ken-ichi; Watanabe, Tadashi

    2000-10-01

    The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)

  10. Theoretical Investigation of Hydrogen Adsorption and Dissociation on Iron and Iron Carbide Surfaces Using the ReaxFF Reactive Force Field Method

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Chenyu; van Duin, Adri C.T.; Sorescu, Dan C.

    2012-06-01

    We have developed a ReaxFF reactive force field to describe hydrogen adsorption and dissociation on iron and iron carbide surfaces relevant for simulation of Fischer–Tropsch (FT) synthesis on iron catalysts. This force field enables large system (>>1000 atoms) simulations of hydrogen related reactions with iron. The ReaxFF force field parameters are trained against a substantial amount of structural and energetic data including the equations of state and heats of formation of iron and iron carbide related materials, as well as hydrogen interaction with iron surfaces and different phases of bulk iron. We have validated the accuracy and applicability of ReaxFF force field by carrying out molecular dynamics simulations of hydrogen adsorption, dissociation and recombination on iron and iron carbide surfaces. The barriers and reaction energies for molecular dissociation on these two types of surfaces have been compared and the effect of subsurface carbon on hydrogen interaction with iron surface is evaluated. We found that existence of carbon atoms at subsurface iron sites tends to increase the hydrogen dissociation energy barrier on the surface, and also makes the corresponding hydrogen dissociative state relatively more stable compared to that on bare iron. These properties of iron carbide will affect the dissociation rate of H{sub 2} and will retain more surface hydride species, thus influencing the dynamics of the FT synthesis process.

  11. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    NARCIS (Netherlands)

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  12. Edge effects on forces and magnetic fields produced by a conductor moving past a magnet

    Energy Technology Data Exchange (ETDEWEB)

    Mulcahy, T.M.; Hull, J.R.; Almer, J.D. (Argonne National Lab., IL (United States)); Rossing, T.D. (Northern Illinois Univ., De Kalb, IL (United States))

    1992-01-01

    Experiments have been performed to further understand the forces acting on magnets moving along and over the edge of a continuous conducting sheet and to produce a comprehensive data set for the validation of analysis methods. Mapping the magnetic field gives information about the eddy currents induced in the conductor, which agrees with numerical calculations.

  13. Edge effects on forces and magnetic fields produced by a conductor moving past a magnet

    Energy Technology Data Exchange (ETDEWEB)

    Mulcahy, T.M.; Hull, J.R.; Almer, J.D. [Argonne National Lab., IL (United States); Rossing, T.D. [Northern Illinois Univ., De Kalb, IL (United States)

    1992-04-01

    Experiments have been performed to further understand the forces acting on magnets moving along and over the edge of a continuous conducting sheet and to produce a comprehensive data set for the validation of analysis methods. Mapping the magnetic field gives information about the eddy currents induced in the conductor, which agrees with numerical calculations.

  14. On a role of the Bsub(z) component of interplanetary magnetic field in a force balance in the day time magnetopause

    International Nuclear Information System (INIS)

    Kuznetsova, T.V.

    1980-01-01

    The role of interplanetary magnetic field (IMF) in the force balance in the day time magnetopause is discussed. The effect of the circular DR-current on the balance of pressures in the magnetopause is taken into account in the calculations. It is shown that IMF plays a significant role in the balance of forces in the day time magnetopause. The ratio of magnetic pressure to the thermal pressure of solar wind in subsolar point is k=0.5. The field observed in magnetosphere near the neutral line is lower by the value of transition region field. All the conclusions are obtained for Bsub(z) [ru

  15. Similarity-transformed equation-of-motion vibrational coupled-cluster theory

    Science.gov (United States)

    Faucheaux, Jacob A.; Nooijen, Marcel; Hirata, So

    2018-02-01

    A similarity-transformed equation-of-motion vibrational coupled-cluster (STEOM-XVCC) method is introduced as a one-mode theory with an effective vibrational Hamiltonian, which is similarity transformed twice so that its lower-order operators are dressed with higher-order anharmonic effects. The first transformation uses an exponential excitation operator, defining the equation-of-motion vibrational coupled-cluster (EOM-XVCC) method, and the second uses an exponential excitation-deexcitation operator. From diagonalization of this doubly similarity-transformed Hamiltonian in the small one-mode excitation space, the method simultaneously computes accurate anharmonic vibrational frequencies of all fundamentals, which have unique significance in vibrational analyses. We establish a diagrammatic method of deriving the working equations of STEOM-XVCC and prove their connectedness and thus size-consistency as well as the exact equality of its frequencies with the corresponding roots of EOM-XVCC. We furthermore elucidate the similarities and differences between electronic and vibrational STEOM methods and between STEOM-XVCC and vibrational many-body Green's function theory based on the Dyson equation, which is also an anharmonic one-mode theory. The latter comparison inspires three approximate STEOM-XVCC methods utilizing the common approximations made in the Dyson equation: the diagonal approximation, a perturbative expansion of the Dyson self-energy, and the frequency-independent approximation. The STEOM-XVCC method including up to the simultaneous four-mode excitation operator in a quartic force field and its three approximate variants are formulated and implemented in computer codes with the aid of computer algebra, and they are applied to small test cases with varied degrees of anharmonicity.

  16. An atomistic fingerprint algorithm for learning ab initio molecular force fields

    Science.gov (United States)

    Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

    2018-01-01

    Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

  17. Mapping in vitro local material properties of intact and disrupted virions at high resolution using multi-harmonic atomic force microscopy.

    Science.gov (United States)

    Cartagena, Alexander; Hernando-Pérez, Mercedes; Carrascosa, José L; de Pablo, Pedro J; Raman, Arvind

    2013-06-07

    Understanding the relationships between viral material properties (stiffness, strength, charge density, adhesion, hydration, viscosity, etc.), structure (protein sub-units, genome, surface receptors, appendages), and functions (self-assembly, stability, disassembly, infection) is of significant importance in physical virology and nanomedicine. Conventional Atomic Force Microscopy (AFM) methods have measured a single physical property such as the stiffness of the entire virus from nano-indentation at a few points which severely limits the study of structure-property-function relationships. We present an in vitro dynamic AFM technique operating in the intermittent contact regime which synthesizes anharmonic Lorentz-force excited AFM cantilevers to map quantitatively at nanometer resolution the local electro-mechanical force gradient, adhesion, and hydration layer viscosity within individual φ29 virions. Furthermore, the changes in material properties over the entire φ29 virion provoked by the local disruption of its shell are studied, providing evidence of bacteriophage depressurization. The technique significantly generalizes recent multi-harmonic theory (A. Raman, et al., Nat. Nanotechnol., 2011, 6, 809-814) and enables high-resolution in vitro quantitative mapping of multiple material properties within weakly bonded viruses and nanoparticles with complex structure that otherwise cannot be observed using standard AFM techniques.

  18. Recent advances toward a general purpose linear-scaling quantum force field.

    Science.gov (United States)

    Giese, Timothy J; Huang, Ming; Chen, Haoyuan; York, Darrin M

    2014-09-16

    Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to

  19. Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

    Science.gov (United States)

    Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

    2018-03-01

    Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

  20. The effect of magnet size on the levitation force and attractive force of single-domain YBCO bulk superconductors

    International Nuclear Information System (INIS)

    Yang, W M; Chao, X X; Bian, X B; Liu, P; Feng, Y; Zhang, P X; Zhou, L

    2003-01-01

    The levitation forces between a single-domain YBCO bulk and several magnets of different sizes have been measured at 77 K to investigate the effect of the magnet size on the levitation force. It is found that the levitation force reaches a largest (peak) value when the size of the magnet approaches that of the superconductor when the other conditions are fixed. The absolute maximum attractive force (in the field-cooled state) increases with the increasing of the magnet size, and is saturated when the magnet size approaches that of the superconductor. The maximum attractive force in the field-cooled (FC) state is much higher than that of the maximum attractive force in the zero field-cooled (ZFC) state. The results indicate that the effects of magnetic field distribution on the levitation force have to be considered during the designing and manufacturing of superconducting devices