Sample records for force field ff

  1. Development and Application of a ReaxFF Reactive Force Field for Oxidative Dehydrogenation on Vanadium Oxide Catalysts

    E-print Network

    Goddard III, William A.

    Development and Application of a ReaxFF Reactive Force Field for Oxidative Dehydrogenation on Vanadium Oxide Catalysts Kimberly Chenoweth, Adri C.T. van Duin, Petter Persson, Mu-Jeng Cheng, Jonas of hydrocarbons with vanadium oxide catalysts. The ReaxFF force field parameters have been fit to a large quantum

  2. Development and application of a ReaxFF reactive force field for hydrogen combustion.

    PubMed

    Agrawalla, Satyam; van Duin, Adri C T

    2011-02-17

    To investigate the reaction kinetics of hydrogen combustion at high-pressure and high-temperature conditions, we constructed a ReaxFF training set to include reaction energies and transition states relevant to hydrogen combustion and optimized the ReaxFF force field parameters against training data obtained from quantum mechanical calculations and experimental values. The optimized ReaxFF potential functions were used to run NVT MD (i.e., molecular dynamics simulation with fixed number of atoms, volume, and temperature) simulations for various H(2)/O(2) mixtures. We observed that the hydroperoxyl (HO(2)) radical plays a key role in the reaction kinetics at our input conditions (T ? 3000 K, P > 400 atm). The reaction mechanism observed is in good agreement with predictions of existing continuum-scale kinetic models for hydrogen combustion, and a transition of reaction mechanism is observed as we move from high pressure, low temperature to low pressure, high temperature. Since ReaxFF derives its parameters from quantum mechanical data and can simulate reaction pathways without any preconditioning, we believe that atomistic simulations through ReaxFF could be a useful tool in enhancing existing continuum-scale kinetic models for prediction of hydrogen combustion kinetics at high-pressure and high-temperature conditions, which otherwise is difficult to attain through experiments. PMID:21261320

  3. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.

    PubMed

    Cerutti, David S; Swope, William C; Rice, Julia E; Case, David A

    2014-10-14

    We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on ?-helical and ?-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

  4. ReaxFF(MgH) reactive force field for magnesium hydride systems.

    PubMed

    Cheung, Sam; Deng, Wei-Qiao; van Duin, Adri C T; Goddard, William A

    2005-02-10

    We have developed a reactive force field (ReaxFF(MgH)) for magnesium and magnesium hydride systems. The parameters for this force field were derived from fitting to quantum chemical (QM) data on magnesium clusters and on the equations of states for condensed phases of magnesium metal and magnesium hydride crystal. The force field reproduces the QM-derived cell parameters, density, and the equations of state for various pure Mg and MgH(2) crystal phases as well as and bond dissociation, angle bending, charge distribution, and reaction energy data for small magnesium hydride clusters. To demonstrate one application of ReaxFF(MgH), we have carried out MD simulations on the hydrogen absorption/desorption process in magnesium hydrides, focusing particularly on the size effect of MgH(2) nanoparticles on H(2) desorption kinetics. Our results show a clear relationship between grain size and heat of formation of MgH(2); as the particle size decreases, the heat of formation increases. Between 0.6 and 2.0 nm, the heat of formation ranges from -16 to -19 kcal/Mg and diverges toward that of the bulk value (-20.00 kcal/Mg) as the particle diameter increases beyond 2 nm. Therefore, it is not surprising to find that Mg nanoparticles formed by ball milling (20-100 nm) do not exhibit any significant change in thermochemical properties. PMID:16838956

  5. Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups

    PubMed Central

    Hegazy, Lamees; Richards, Nigel G. J.

    2013-01-01

    We report an optimized set of CGenFF parameters that can be used to model small molecules containing acylphosphate and N-phosphonosulfonimidoyl functional groups in combination with the CHARMM force field. Standard CGenFF procedures were followed to obtain bonded interaction parameters, which were validated by geometry optimizations, comparison to the results of calculations at the MP2/6-31+G(d) level of theory, and molecular dynamics simulations. In addition, partial atomic charges were assigned so that the energy of hydrogen bonding of the model compounds with water was correctly reproduced. The availability of these parameters will facilitate computational studies of enzymes that generate acyladenylate intermediates during catalytic turnover. In addition, given that the N-phosphonosulfonimidoyl moiety is a stable transition state analog for the reaction of ammonia with an acyladenylate, the parameters developed in this study should find use in efforts to develop novel and potent inhibitors of various glutamine-dependent amidotransferases that have been validated as drug targets. Topology and parameter files for the model compounds used in this study, which can be combined with other CGenFF parameters in computational studies of more complicated acylphosphates and N-phosphonosulfonimidates are made available. PMID:24085536

  6. ReaxFF-lg: correction of the ReaxFF reactive force field for London dispersion, with applications to the equations of state for energetic materials.

    PubMed

    Liu, Lianchi; Liu, Yi; Zybin, Sergey V; Sun, Huai; Goddard, William A

    2011-10-13

    The practical levels of density functional theory (DFT) for solids (LDA, PBE, PW91, B3LYP) are well-known not to account adequately for the London dispersion (van der Waals attraction) so important in molecular solids, leading to equilibrium volumes for molecular crystals ~10-15% too high. The ReaxFF reactive force field is based on fitting such DFT calculations and suffers from the same problem. In the paper we extend ReaxFF by adding a London dispersion term with a form such that it has low gradients (lg) at valence distances leaving the already optimized valence interactions intact but behaves as 1/R(6) for large distances. We derive here these lg corrections to ReaxFF based on the experimental crystal structure data for graphite, polyethylene (PE), carbon dioxide, and nitrogen and for energetic materials: hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX), pentaerythritol tetranitrate (PETN), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), and nitromethane (NM). After this dispersion correction the average error of predicted equilibrium volumes decreases from 18.5 to 4.2% for the above systems. We find that the calculated crystal structures and equation of state with ReaxFF-lg are in good agreement with experimental results. In particular, we examined the phase transition between ?-RDX and ?-RDX, finding that ReaxFF-lg leads to excellent agreement for both the pressure and volume of this transition occurring at ~4.8 GPa and ~2.18 g/cm(3) density from ReaxFF-lg vs 3.9 GPa and ~2.21 g/cm(3) from experiment. We expect ReaxFF-lg to improve the descriptions of the phase diagrams for other energetic materials. PMID:21888351

  7. ReaxFF reactive force field development and applications for molecular dynamics simulations of ammonia borane dehydrogenation and combustion.

    PubMed

    Weismiller, Michael R; van Duin, Adri C T; Lee, Jongguen; Yetter, Richard A

    2010-05-01

    Ammonia borane (AB) has attracted significant attention due to its high hydrogen content (19.6% by mass). To investigate the reaction mechanism associated with the combustion of AB, a reactive force field (ReaxFF) has been developed for use in molecular dynamics (MD) simulations. The ReaxFF parameters have been derived directly from quantum mechanical data (QM). NVT-MD simulations of single- and polymolecular AB thermolysis were conducted in order to validate the force field. The release of the first equivalent H(2) is a unimolecular reaction, and MD simulations show an activation energy of 26.36 kcal mol(-1), which is in good agreement with experimental results. The release of the second H(2) is also a unimolecular reaction; however, the release of a third H(2) requires the formation of a B-N polymer. Similar simulations were conducted with a boron and oxygen system, since the oxidation of boron will be an integral step in AB combustion, and show good agreement with the established mechanism for this system. At low temperatures, boron atoms agglomerate into a cluster, which is oxidized at higher temperatures, eventually forming condensed and gas phase boron-oxide-species. These MD results provide confidence that ReaxFF can properly model the oxidation of AB and provide mechanistic insight into the AB dehydrogenation and combustion reactions. PMID:20384351

  8. Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.

    PubMed

    Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

    2014-02-27

    We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings. PMID:24479769

  9. High-temperature high-pressure phases of lithium from electron force field (eFF) quantum electron dynamics simulations.

    PubMed

    Kim, Hyungjun; Su, Julius T; Goddard, William A

    2011-09-13

    We recently developed the electron force field (eFF) method for practical nonadiabatic electron dynamics simulations of materials under extreme conditions and showed that it gave an excellent description of the shock thermodynamics of hydrogen from molecules to atoms to plasma, as well as the electron dynamics of the Auger decay in diamondoids following core electron ionization. Here we apply eFF to the shock thermodynamics of lithium metal, where we find two distinct consecutive phase changes that manifest themselves as a kink in the shock Hugoniot, previously observed experimentally, but not explained. Analyzing the atomic distribution functions, we establish that the first phase transition corresponds to (i) an fcc-to-cI16 phase transition that was observed previously in diamond anvil cell experiments at low temperature and (ii) a second phase transition that corresponds to the formation of a new amorphous phase (amor) of lithium that is distinct from normal molten lithium. The amorphous phase has enhanced valence electron-nucleus interactions due to localization of electrons into interstitial locations, along with a random connectivity distribution function. This indicates that eFF can characterize and compute the relative stability of states of matter under extreme conditions (e.g., warm dense matter). PMID:21873210

  10. High-temperature high-pressure phases of lithium from electron force field (eFF) quantum electron dynamics simulations

    PubMed Central

    Kim, Hyungjun; Su, Julius T.; Goddard, William A.

    2011-01-01

    We recently developed the electron force field (eFF) method for practical nonadiabatic electron dynamics simulations of materials under extreme conditions and showed that it gave an excellent description of the shock thermodynamics of hydrogen from molecules to atoms to plasma, as well as the electron dynamics of the Auger decay in diamondoids following core electron ionization. Here we apply eFF to the shock thermodynamics of lithium metal, where we find two distinct consecutive phase changes that manifest themselves as a kink in the shock Hugoniot, previously observed experimentally, but not explained. Analyzing the atomic distribution functions, we establish that the first phase transition corresponds to (i) an fcc-to-cI16 phase transition that was observed previously in diamond anvil cell experiments at low temperature and (ii) a second phase transition that corresponds to the formation of a new amorphous phase (amor) of lithium that is distinct from normal molten lithium. The amorphous phase has enhanced valence electron-nucleus interactions due to localization of electrons into interstitial locations, along with a random connectivity distribution function. This indicates that eFF can characterize and compute the relative stability of states of matter under extreme conditions (e.g., warm dense matter). PMID:21873210

  11. Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization

    PubMed Central

    Rahaman, Obaidur; van Duin, Adri C.T.; Goddard, William A.; Doren, Douglas J.

    2011-01-01

    Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF?ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment. PMID:21166434

  12. Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases

    E-print Network

    Goddard III, William A.

    Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases Adri C. T. van Duin,*, Vyacheslav S. Bryantsev-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended

  13. Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures

    Microsoft Academic Search

    Elodie Salmon; Adri C. T. van Duin; François Lorant; Paul-Marie Marquaire; William A. Goddard III

    2009-01-01

    This paper reports reactive dynamics (RD) simulations of a macro-model of Morwell Brown coal using the ReaxFF reactive force field. We find that these reactive MD simulations successfully reproduce thermal decomposition processes of defunctionalization, depolymerization and rearrangement of the residual structure observed in various experimental studies. For example, our simulations indicate that the decarboxylation and dehydroxylation of the lignin side

  14. Theoretical Investigation of Hydrogen Adsorption and Dissociation on Iron and Iron Carbide Surfaces Using the ReaxFF Reactive Force Field Method

    SciTech Connect

    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.

  15. Development of a ReaxFF reactive force field for ettringite and study of its mechanical failure modes from reactive dynamics simulations.

    PubMed

    Liu, Lianchi; Jaramillo-Botero, Andres; Goddard, William A; Sun, Huai

    2012-04-19

    Ettringite is a hexacalcium aluminate trisulfate hydrate mineral that forms during Portland cement hydration. Its presence plays an important role in controlling the setting rate of the highly reactive aluminate phases in cement paste and has also been associated with severe cracking in cured hardened cement. To understand how it forms and how its properties influence those of hardened cement and concrete, we have developed a first-principles-based ReaxFF reactive force field for Ca/Al/H/O/S. Here, we report on the development of this ReaxFF force field and on its validation and application using reactive molecular dynamics (RMD) simulations to characterize and understand the elastic, plastic, and failure response of ettringite at the atomic scale. The ReaxFF force field was validated by comparing the lattice parameters, pairwise distribution functions, and elastic constants of an ettringite crystal model obtained from RMD simulations with those from experiments. The predicted results are in close agreement with published experimental data. To characterize the atomistic failure modes of ettringite, we performed stress-strain simulations to find that Ca-O bonds are responsible for failure of the calcium sulfate and tricalcium aluminate (C3A) column in ettringite during uniaxial compression and tension and that hydrogen bond re-formation during compression induces an increase in plastic strain beyond the material's stress-strain proportionality limit. These results provide essential insight into understanding the mechanistic role of this mineral in cement and concrete degradation, and the ReaxFF potential developed in this work serves as a fundamental tool to further study the kinetics of hydration in cement and concrete. PMID:22413941

  16. Development and validation of a ReaxFF reactive force field for Cu-cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases

    PubMed Central

    van Duin, Adri C.T.; Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; Goddard, William A.; Rahaman, Obaidur; Doren, Douglas J.; Raymand, David; Hermansson, Kersti

    2010-01-01

    In order to enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H2O)n]2+-cluster structures and energies) is augmented by single-point QM-energies from [Cu(H2O)n]2+-clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu2+/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion and inversion in [Cu(H2O)6]2+-clusters, and first- and second shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution and surface catalysis. PMID:20707333

  17. A reactive force-field (ReaxFF) Monte Carlo study of surface enrichment and step structure on yttria-stabilized zirconia

    NASA Astrophysics Data System (ADS)

    Mayernick, Adam D.; Batzill, Matthias; van Duin, Adri C. T.; Janik, Michael J.

    2010-08-01

    To investigate surface segregation in yttria-stabilized zirconia (YSZ), DFT energies describing surface energy as a function of yttrium lattice position were used to parameterize a reactive-force field (ReaxFF). We used ReaxFF to perform Monte Carlo (MC) simulated annealing to sample structural configurations of flat YSZ (111) and vicinal YSZ (111) stepped surfaces. We evaluated yttrium surface segregation, oxygen vacancy position, and surface step composition for flat and stepped YSZ surfaces. It is thermodynamically favorable for yttrium atoms to segregate to the surface of YSZ, and specifically to step edge sites. Surface saturation of yttrium occurs at approximately 40% (40:60 Y:Zr ratio) while yttrium concentration at the step edge does not approach a saturation value, suggesting that steps on the YSZ surface are mainly yttria-terminated. We found that it is thermodynamically favorable for oxygen vacancies to occupy positions in the subsurface layer of YSZ, and a higher fraction of vacancies occupy positions NN to Y than NN to Zr. Yttrium segregation to step edges on the YSZ surface does not lower the surface formation energy of the stepped surface below that of the flat (111) termination, suggesting that the stability of YSZ surface steps observed experimentally is due to kinetic barriers for surface re-ordering.

  18. Molecular-dynamics-based study of the collisions of hyperthermal atomic oxygen with graphene using the ReaxFF reactive force field.

    PubMed

    Srinivasan, Sriram Goverapet; van Duin, Adri C T

    2011-11-24

    In this work, we have investigated the hyperthermal collisions of atomic oxygens with graphene through molecular dynamics simulations using the ReaxFF reactive force field. First, following Paci et al. (J. Phys. Chem. A 2009, 113, 4677 - 4685), 5-eV energetic collisions of atomic oxygen with a 24-atom pristine graphene sheet and a sheet with a single vacancy defect, both functionalized with oxygen atoms in the form of epoxides, were studied. We found that the removal of an O(2) molecule from the surface of the graphene sheet occurs predominantly through an Eley-Rideal-type reaction mechanism. Our results, in terms of the number of occurrences of various reactive events, compared well with those reported by Paci et al. Subsequently, energetic collisions of atomic oxygen with a 25-times-expanded pristine sheet were investigated. The steady-state oxygen coverage was found to be more than one atom per three surface carbon atoms. Under an oxygen impact, the graphene sheet was always found to buckle along its diagonal. In addition, the larger sheet exhibited trampoline-like behavior, as a result of which we observed a much larger number of inelastic scattering events than those reported by Paci et al. for the smaller system. Removal of O(2) from the larger sheet occurred strictly through an Eley-Rideal-type reaction. Investigation of the events leading to the breakup of a pristine unfunctionalized graphene sheet and the effects of the presence of a second layer beneath the graphene sheet in an AB arrangement was done through successive impacts with energetic oxygen atoms on the structures. Breakup of a graphene sheet was found to occur in two stages: epoxide formation, followed by the creation and growth of defects. Events leading to the breakup of a two-layer graphene stack included epoxide formation, transformation from an AB to an AA arrangement as a result of interlayer bonding, defect formation and expansion in the top layer, and finally erosion of the bottom layer. We observed that the breakup of the two-layer stack occurred through a sequential, layer-by-layer, erosion process. PMID:21942282

  19. Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures

    E-print Network

    Goddard III, William A.

    force field on Morwell Brown coal structures Elodie Salmon a , Adri C.T. van Duin b , François Lorant 2009 a b s t r a c t This paper reports reactive dynamics (RD) simulations of a macro-model of Morwell indicate that the decar- boxylation and dehydroxylation of the lignin side chain of the Morwell model

  20. Development of the ReaxFF reactive force field for mechanistic studies of catalytic selective oxidation processes on BiMoOx

    E-print Network

    van Duin, Adri

    report the use of ReaxFF to study the activation and conversion of propene to acrolein by various metal acrolein. The propene reations on V2O5 occur at lower temperatures than on Bi2O3 or Bi2Mo3O12. The results-metal­ oxide (MMO) catalysts, accounts for the majority of the 8 billion pounds of acrolein produced annually

  1. Reactive molecular dynamics simulation on the disintegration of Kapton, POSS polyimide, amorphous silica, and teflon during atomic oxygen impact using the ReaxFF reactive force-field method.

    PubMed

    Rahnamoun, A; van Duin, A C T

    2014-04-17

    Atomic oxygen (AO) is the most abundant element in the low Earth orbit (LEO). It is the result of the dissociation of molecular oxygen by ultraviolet radiation from the sun. In the LEO, it collides with the materials used on spacecraft surfaces and causes degradation of these materials. The degradation of the materials on the surface of spacecrafts at LEO has been a significant problem for a long time. Kapton polyimide, polyhedral oligomeric silsesquioxane (POSS), silica, and Teflon are the materials extensively used in spacecraft industry, and like many other materials used in spacecraft industry, AO collision degradation is an important issue in their applications on spacecrafts. To investigate the surface chemistry of these materials in exposure to space AO, a computational chemical evaluation of the Kapton polyimide, POSS, amorphous silica, and Teflon was performed in separate simulations under similar conditions. For performing these simulations, the ReaxFF reactive force-field program was used, which provides the computational speed required to perform molecular dynamics (MD) simulations on system sizes sufficiently large to describe the full chemistry of the reactions. Using these simulations, the effects of AO impact on different materials and the role of impact energies, the content of material, and temperature of material on the behavior of the materials are studied. The ReaxFF results indicate that Kapton is less resistant than Teflon toward AO damage. These results are in good agreement with experiment. These simulations indicate that the amorphous silica shows the highest stability among these materials before the start of the highly exothermic silicon oxidation. We have verified that adding silicon to the bulk of the Kapton structure enhances the stability of the Kapton against AO impact. Our canonical MD simulations demonstrate that an increase in the heat transfer in materials during AO impact can provide a considerable decrease in the disintegration of the material. This effect is especially relevant in silica AO collision. Considerable experimental efforts have been undertaken to minimize such AO-based degradations. As our simulations demonstrate, ReaxFF can provide a cost-effective screening tool for future material optimization. PMID:24679339

  2. Simulating the Initial Stage of Phenolic Resin Carbonization via the ReaxFF Reactive Force De-en Jiang,*,

    E-print Network

    Goddard III, William A.

    Simulating the Initial Stage of Phenolic Resin Carbonization via the ReaxFF Reactive Force Field DeVed: May 7, 2009 Pyrolysis of phenolic resins leads to carbon formation. Simulating this resin atomistically. 1. Introduction Phenolic resins are a good source of carbon. Direct pyrolysis of neat phenolic

  3. Dynamic properties of force fields

    NASA Astrophysics Data System (ADS)

    Vitalini, F.; Mey, A. S. J. S.; Noé, F.; Keller, B. G.

    2015-02-01

    Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.

  4. Hessian biased force field for polysilane polymers

    SciTech Connect

    Musgrave, C.B.; Dasgupta, S.; Goddard, W.A. III [California Inst. of Technology, Pasadena, CA (United States)

    1995-09-07

    We report a force field (FF) suitable for molecular dynamics simulations of polysilane polymers. This FF, denoted MSXX, was developed using the Hessian biased method to describe accurately the vibrational states, the ab initio torsional potential energy surface, and the ab initio electrostatic charges of polysilane oligomers. This MSXX FF was used to calculate various spectroscopic and mechanical properties of the polysilane crystal. Stress-strain curves and surface energies are reported. Gibbs molecular dynamics calculations (Nose, Rahman-Parrinello) were used to predict various materials properties at higher temperatures. Phonon dispersion curves and elastic constants were calculated at various temperatures. Although this polymer is of increasing industrial interest, we could find no experimental data with which to compare these predictions. 20 refs., 6 figs., 16 tabs.

  5. Development of a united-atom force field for 1-ethyl-3-methylimidazolium tetracyanoborate ionic liquid

    Microsoft Academic Search

    Thomas Koller; Javier Ramos; Nuno M. Garrido; Andreas P. Fröba; Ioannis G. Economou

    2012-01-01

    Three united-atom (UA) force fields are presented for the ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, abbreviated as [EMIM][B(CN)4]. The atomistic charges were calculated based on the restrained electrostatic potential (RESP) of the isolated ions (abbreviated as force field 1, FF-1) and the ensemble averaged RESP (EA-RESP) method from the most stable ion pair configurations obtained by MP2\\/6-31G*+ calculations (abbreviated as FF-2 and

  6. Efficient global optimization of reactive force-field parameters.

    PubMed

    Dittner, Mark; Müller, Julian; Aktulga, Hasan Metin; Hartke, Bernd

    2015-07-30

    Reactive force fields make low-cost simulations of chemical reactions possible. However, optimizing them for a given chemical system is difficult and time-consuming. We present a high-performance implementation of global force-field parameter optimization, which delivers parameter sets of the same quality with much less effort and in far less time than before, and also offers excellent parallel scaling. We demonstrate these features with example applications targeting the ReaxFF force field. © 2015 Wiley Periodicals, Inc. PMID:26085201

  7. The Early Universe $f^{2}FF$ Model of Primordial Magnetic Field in Natural Inflation

    E-print Network

    AlMuhammad, Anwar S

    2015-01-01

    We study the simple gauge invariant model ${f^2}FF$ as a way to generate primordial magnetic fields (PMF) in Natural Inflation (NI). We compute both magnetic and electric spectra generated by the ${f^2}FF$ model in NI for different values of model parameters and find that both de Sitter and power law expansion lead to the same results at sufficiently large number of e-foldings. We also find that the necessary scale invariance property of the PMF cannot be obtained in NI in first order of slow roll limits under the constraint of inflationary potential, $V\\left( 0 \\right) \\simeq 0$. Furthermore, if this constraint is relaxed to achieve scale invariance, then the model suffers from the backreaction problem for almost all values of model parameters. We show that there is a narrow range of the height of the potential $\\Lambda $ around ${\\Lambda _{\\min }} \\approx 0.00874{M_{{\\rm{Pl}}}}$ and of the co-moving wave number $k$ around ${k_{\\min }} \\sim 0.0173{\\rm{Mp}}{{\\rm{c}}^{ - 1}}$, at which the problem of backreact...

  8. Force field-dependent solution properties of glycine oligomers.

    PubMed

    Drake, Justin A; Pettitt, B Montgomery

    2015-06-30

    Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 ?s, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. © 2015 Wiley Periodicals, Inc. PMID:25952623

  9. An Assessment of Molecular Dynamic Force Fields for Silica for Use in Simulating Laser Damage Mitigation

    SciTech Connect

    Soules, T F; Gilmer, G H; Matthews, M J; Stolken, J S; Feit, M D

    2010-10-21

    We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important to laser mitigation experiments.

  10. Development of the CHARMM Force Field for Lipids

    PubMed Central

    Pastor, R.W.; MacKerell, A.D.

    2011-01-01

    The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990’s to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed. PMID:21760975

  11. Physics 2000: Electric Force Fields

    NSDL National Science Digital Library

    This page illustrates and describes electric fields and forces through a simulation. The explanation is given in the form of a conversation between two people. There is also a simple simulation which helps understand the concept better. This web page is part of a tutorial that introduces electric forces and fields.

  12. The Scaled-Charge Additive Force Field for Amino Acid Based Ionic Liquids

    E-print Network

    Fileti, Eudes Eterno

    2014-01-01

    Abstract. Ionic liquids (ILs) constitute an emerging field of research. New ILs are continuously introduced involving 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 have been taken into account by computing electrostatic potential for ion pairs, in contrast to isolated ions. The van der Waals interactions have been transferred from the CHARMM36 FF with minor modifications. Therefore, compatibility between our parameters and CHARMM36 parameters is preserved. Our FF can be easily implemented using a variety of popular molecular dynamics programs. It will find broad applications in computational investigation of ILs.

  13. Atomistic force field for pyridinium-based ionic liquids: reliable transport properties.

    PubMed

    Voroshylova, Iuliia V; Chaban, Vitaly V

    2014-09-11

    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 cation-anion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove that three parameters per interaction site (atom diameter, depth of potential well, point electrostatic charge) provide a sufficient basis to predict thermodynamics (heat of vaporization, density), structure (radial distributions), and transport (diffusion, viscosity, conductivity) of ILs at room conditions and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia Lopes-Pádua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids. PMID:25144141

  14. J. Phys. Chem. 1995,99, 13321-13333 13321 Hessian Biased Force Field for Polysilane Polymers

    E-print Network

    Goddard III, William A.

    :May 16, 1995@ We report a force field (FF)suitable for molecular dynamics simulations of polysilane of the polysilane crystal. Stress-strain curves and surface energies are reported. Gibbs molecular dynamics. Phonon dispersion curves and elastic constants were calculated at various temperatures. Although

  15. Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.; Dayton, James A.

    1998-01-01

    In a previous study using a fully three-dimensional (3D) helical slow-wave circuit cold- test model it was found, contrary to classical helical circuit analyses, that transverse FF electric fields have significant amplitudes compared with the longitudinal component. The RF fields obtained using this helical cold-test model have been scaled to correspond to those of an actual TWT. At the output of the tube, RF field forces reach 61%, 26% and 132% for radial, azimuthal and longitudinal components, respectively, compared to radial space charge forces indicating the importance of considering them in the design of electron beam focusing.

  16. A reactive force field for aqueous-calcium carbonate systems.

    PubMed

    Gale, Julian D; Raiteri, Paolo; van Duin, Adri C T

    2011-10-01

    A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water. PMID:21850319

  17. Modeling of Gamma-ray Pulsar Light Curves Using the Force-free Magnetic Field

    NASA Astrophysics Data System (ADS)

    Bai, Xue-Ning; Spitkovsky, Anatoly

    2010-06-01

    Gamma-ray emission from pulsars has long been modeled using a vacuum dipole field. This approximation ignores changes in the field structure caused by the magnetospheric plasma and strong plasma currents. We present the first results of gamma-ray pulsar light-curve modeling using the more realistic field taken from three-dimensional force-free (FF) magnetospheric simulations. Having the geometry of the field, we apply several prescriptions for the location of the emission zone, comparing the light curves to observations. We find that when the emission region is chosen according to the conventional slot-gap (or two-pole caustic) prescription, the model fails to produce double-peak pulse profiles, mainly because the size of the polar cap in the FF magnetosphere is larger than the vacuum field polar cap. This suppresses caustic formation in the inner magnetosphere. The conventional outer-gap model is capable of producing only one peak under general conditions because a large fraction of open field lines does not cross the null charge surface. We propose a novel "separatrix layer" model, where the high-energy emission originates from a thin layer on the open field lines just inside of the separatrix that bounds the open flux tube. The emission from this layer generates two strong caustics on the sky map due to the effect we term "Sky Map Stagnation" (SMS). It is related to the fact that the FF field asymptotically approaches the field of a rotating split monopole, and the photons emitted on such field lines in the outer magnetosphere arrive to the observer in phase. The double-peak light curve is a natural consequence of SMS. We show that most features of the currently available gamma-ray pulsar light curves can be reasonably well reproduced and explained with the separatrix layer model using the FF field. Association of the emission region with the current sheet will guide more detailed future studies of the magnetospheric acceleration physics.

  18. HOVEDOPPGAVE Polarizable force fields for flexible molecules

    E-print Network

    Izaguirre, Jesús A.

    HOVEDOPPGAVE 2004 Polarizable force fields for flexible molecules Kandidatens navn Asbjørn Holt interactions. In this study a force field for flexible water molecules is constructed. To describe the electrostatic properties of the water molecules in this force fields, atomic charges and dipole moments are used

  19. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

    PubMed

    Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana

    2015-06-25

    Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various ?-hairpin states, reminiscent of the first ?-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher ?-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known ? preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to ?-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions. PMID:26020564

  20. LABORATORY I ELECTRIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    LABORATORY I ELECTRIC FIELDS AND FORCES Lab I - 1 The most fundamental forces are characterized as "action-at-a-distance". This means that an object can exert a force on another object that is not in contact with it. You have already learned about the gravitational force, which is of this type. You

  1. The MS-Q Force Field for Clay Minerals: Application to Oil Production Sungu Hwang, Mario Blanco, Ersan Demiralp, Tahir Cagin, and William A. Goddard, III*

    E-print Network

    Çagin, Tahir

    The MS-Q Force Field for Clay Minerals: Application to Oil Production Sungu Hwang, Mario Blanco to model kaolinite and pyrophyllite clay minerals and their interactions with representative organic molecules. The MS-Q FF reproduces the structural parameters for these clay minerals and gives accurate

  2. Development and Validation of ReaxFF Reactive Force Field for Hydrocarbon Chemistry Catalyzed by Nickel

    E-print Network

    Goddard III, William A.

    by Nickel Jonathan E. Mueller, Adri C. T. van Duin, and William A. Goddard III*, Materials and Process reactions catalyzed by nickel surfaces and particles using reactive molecular dynamics on thousands of atoms adsorption, decomposition, reformation and desorption of hydrocarbons as they interact with the nickel

  3. Atomistic-scale simulations of energetic materials with ReaxFF reactive force fields

    Microsoft Academic Search

    W. A. Goddard III; A. Strachan

    2005-01-01

    Understanding the response of energetic materials to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of million atom systems to capture the complex chemical and mechanical behavior involved: nonequilibrium energy\\/mass transfer, molecule excitation and decomposition under high strain\\/heat rates, formation of defects, plastic flow, and phase transitions. To enable such simulations,

  4. Lipid14: The Amber Lipid Force Field

    PubMed Central

    2015-01-01

    The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 ?s each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields. PMID:24803855

  5. Simulations of the quart (101-bar1)/water interface: A comparison of classical force fields, ab initi molecular dynamics, and x-ray reflectivity experiments.

    SciTech Connect

    Skelton, Adam [ORNL; Fenter, Paul [Argonne National Laboratory (ANL); Kubicki, James D. [Pennsylvania State University; Wesolowski, David J [ORNL; Cummings, Peter T [ORNL

    2011-01-01

    Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.

  6. Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

    NASA Astrophysics Data System (ADS)

    de M. Seabra, Gustavo; Walker, Ross C.; Roitberg, Adrian E.

    2009-07-01

    The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (?, ?) dihedral angle space, 3J(HN,H?) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.

  7. LABORATORY IV ELECTRIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    , electric, and magnetic) make up a common part of your everyday experiences. These forces are difficult energy as residing in the field. Using fields to study interactions solves the intellectual puzzle. The only reason we use field theory is because it leads us to a deeper understanding of natural phenomena

  8. Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF)

    PubMed Central

    Peters, Martin B.; Yang, Yue; Wang, Bing; Füsti-Molnár, László; Weaver, Michael N.; Merz, Kenneth M.

    2010-01-01

    Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262–8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement. PMID:20856692

  9. Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).

    PubMed

    Peters, Martin B; Yang, Yue; Wang, Bing; Füsti-Molnár, László; Weaver, Michael N; Merz, Kenneth M

    2010-09-14

    Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement. PMID:20856692

  10. LABORATORY VI MAGNETIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    . · Calculate the motion of a particle with a constant acceleration. · Calculate the motion of a particle of the universe, the atomic structure of materials, and the quark structure of elementary particles. Magnetic; · Calculate the magnetic force on a charged particle moving in a uniform magnetic field and describe its

  11. Field study on moving force identification

    NASA Astrophysics Data System (ADS)

    Chan, Hung-tin Tommy; Yung, Tak H.; Law, S. S.

    2001-08-01

    A field measurement to validate a moving force identification method was carried out on an existing prestressed concrete highway bridge with a span length of 28 m. The test bridge is located at Ma Tau Wai, Kowloon, Hong Kong. A heavy 2-axle truck with known axle loads was used as a control vehicle. Besides the control vehicle, axle load data of in-service vehicles were also collected. The bridge responses acquired for the identification were indirectly measured using strain gauges. Results show that dynamic axle loads induced from both control and in-service vehicles can be identified indicating the method is valid for identification of moving forces.

  12. Forces in Optical Near-Fields

    Microsoft Academic Search

    Lukas Novotny

    2001-01-01

    In this article we use classical electrodynamics to derive the conservation law for linear momentum in an optical field. The\\u000a net force exerted on an arbitrary object is determined by Maxwell’s stress tensor. It is shown that in the limiting case of\\u000a an infinitely extended object, the formalism renders the known expressions for radiation pressure. Similarly, in the small\\u000a object

  13. A compact high field magnetic force microscope.

    PubMed

    Zhou, Haibiao; Wang, Ze; Hou, Yubin; Lu, Qingyou

    2014-12-01

    We present the design and performance of a simple and compact magnetic force microscope (MFM), whose tip-sample coarse approach is implemented by the piezoelectric tube scanner (PTS) itself. In brief, a square rod shaft is axially spring-clamped on the inner wall of a metal tube which is glued inside the free end of the PTS. The shaft can thus be driven by the PTS to realize image scan and inertial stepping coarse approach. To enhance the inertial force, each of the four outer electrodes of the PTS is driven by an independent port of the controller. The MFM scan head is so compact that it can easily fit into the 52mm low temperature bore of a 20T superconducting magnet. The performance of the MFM is demonstrated by imaging a manganite thin film at low temperature and in magnetic fields up to 15T. PMID:25189114

  14. Effects of temperature on the properties of glycerol: a computer simulation study of five different force fields.

    PubMed

    Jahn, David A; Akinkunmi, Frederick O; Giovambattista, Nicolas

    2014-09-25

    We perform molecular dynamics simulations of glycerol (propane-1,2,3-triol) at normal pressure and a wide range of temperatures (300-460 K) and study the sensitivity of simulation results to the force field (FF) considered. We employ five commonly used FFs: (i) AMBER, (ii) CHARMM22, and (iii) three versions of the OPLS-AA FF (OPLS1, OPLS2, and OPLS3). We study thermodynamic (density ?(T), thermal expansion coefficient ?P(T), isobaric specific heat cP(T)), dynamic (diffusion coefficient D(T)), as well as structural properties (molecular conformations and hydrogen-bond statistics). In comparison with experiments, FFs i and iii provide reasonable estimations of ?(T) with deviations of ?4.5%; for FF ii, deviations in density are more pronounced, ?9%. Values of ?P(T) vary considerably among the FFs; e.g., deviations are ?9% for OPLS1-FF and ?60% for FF ii. For all models studied, values of cP(T) are approximately twice the corresponding experimental values. Diffusion coefficients are very sensitive to the FFs considered. Specifically, for FFs i and ii and OPLS3, the values of D(T) are remarkably close to the experimental values over the whole range of temperatures studied. Instead, in the cases of OPLS1 and OPLS2-FFs, D(T) is underestimated by approximately 2 orders of magnitude. Interestingly, in all cases, D(T) can be well described by a Vogel-Tamman-Fulcher equation, as observed in experiments. We present a detailed characterization of glycerol backbone conformation based on the traditional classification introduced by Bastiansen, defined in terms of glycerol's OCCC dihedral angles. All FFs indicate that the conformer population varies smoothly with temperature. However, the FFs provide very different conformer distributions. This implies that, from the microscopic point of view, these glycerol models may provide very different liquid environments for, for example, guest biomolecules and hence may play a relevant role in interpreting simulation results involving glycerol-based solutions. We also discuss the statistics of inter- and intramolecular hydrogen bonds (HBs). The FFs are qualitatively comparable regarding HB statistics; however, quantitative differences remain. For example, molecules form a total of 5.5-7 HBs at T = 350 K, depending on the FF considered, including at least one intramolecular HB. PMID:25188739

  15. The Introduction of Fields in Relation to Force

    ERIC Educational Resources Information Center

    Brunt, Marjorie; Brunt, Geoff

    2012-01-01

    The introduction of force at age 14-16 years is considered, starting with elementary student experiments using magnetic force fields. The meaningless use of terms such as "action" and "reaction", or "agent" and "receiver" is discussed. (Contains 6 figures.)

  16. Dislocation core fields and forces in FCC metals

    SciTech Connect

    Henager, Charles H.; Hoagland, Richard G.

    2004-04-01

    Atomistic models were used to obtain dislocation core fields for edge, screw, and mixed dislocations in Al and Cu using EAM. Core fields are analyzed using a line force dipole representation, with dilatant and dipole terms. The core field contribution to the force between dislocations is shown to be significant for interactions within 50b.

  17. Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

    PubMed Central

    2015-01-01

    Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

  18. Forces between Dislocations due to Dislocation Core Fields

    SciTech Connect

    Henager, Charles H.; Hoagland, Richard G.

    2001-11-21

    Atomistic dislocation models were used to determine the properties of dislocation core fields in Al using an EAM potential. Equilibrium atom configurations were compared with initial configurations displaced according to the Volterra field to determine core displacement fields for edge, screw, and mixed (60? and 30?) geometries. The core field was approximated by a line force defect field lying parallel to the dislocation line direction. Best-fit parameters for the core fields were obtained in terms of the anisotropic elastic solution for a line force defect, from which the line force strengths and the origin of the line forces were determined. The line force stress fields were then used to compute the forces between dislocations for several dislocation configurations. The Volterra field dominates beyond 50b but core field forces modify the equilibrium angle of edge dislocation dipoles and determine the force between otherwise non-interacting edge and screw dislocations at distances out to 50b compared to the Volterra-only forces.

  19. Friction forces arising from fluctuating thermal fields

    SciTech Connect

    Zurita-Sanchez, Jorge R.; Greffet, Jean-Jacques; Novotny, Lukas [Institute of Optics, University of Rochester, Rochester, New York 14627 (United States); Laboratoire Energetique Moleculaire et Macroscopique, Combustion, Ecole Centrale Paris, 92295 Chatenay-Malabry Cedex (France); Institute of Optics, University of Rochester, Rochester, New York 14627 (United States)

    2004-02-01

    We calculate the damping of a classical oscillator induced by the electromagnetic field generated by thermally fluctuating currents in the environment. The fluctuation-dissipation theorem is applied to derive the linear-velocity damping coefficient {gamma}. It turns out that {gamma} is the result of fourth-order correlation functions. The theory is applied to a particle oscillating parallel to a flat substrate and numerical values for {gamma} are evaluated for particle and substrate materials made of silver and glass. We find that losses are much higher for dielectric materials than for metals because of the higher resistivity. We predict that measurements performed on metal films are strongly affected by the underlying dielectric substrate and we show that our theory reproduces existing theoretical results in the nonretarded limit. The theory provides an explanation for the observed distance-dependent damping in shear-force microscopy and it gives guidance for future experiments. Also, the theory should be of importance for the design of nanoscale mechanical systems and for understanding the trade-offs of miniaturization.

  20. Application of the ReaxFF Reactive Force Field to Reactive Dynamics of Hydrocarbon Chemisorption and Decomposition

    E-print Network

    Goddard III, William A.

    of higher hydrocarbons.2 In addition, nickel catalysts are used in high temperature solid oxide fuel cells in such important industrial processes as the Haber Bosch synthesis of ammonia and the Fischer-Tropsch formation using hydrocarbon fuels, and more recently nickel has been used to catalyze the formation and growth

  1. Reaction analysis and visualization of ReaxFF molecular dynamics simulations.

    PubMed

    Liu, Jian; Li, Xiaoxia; Guo, Li; Zheng, Mo; Han, Junyi; Yuan, Xiaolong; Nie, Fengguang; Liu, Xiaolong

    2014-09-01

    ReaxFF MD (Reactive Force Field Molecular Dynamics) is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents the algorithms, implementation strategies, features, and applications of VARxMD, a tool for Visualization and Analysis of Reactive Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by determination of atomic connectivity for recognizing connected molecular fragments, perception of bond types in the connected fragments for molecules or radicals, indexing of all these molecules or radicals (chemical species) based on their 3D coordinates and recognition of bond breaking or forming in the chemical species for reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (high-density polyethylene) pyrolysis show that VARxMD provides the capabilities in exploring the reaction mechanism in large systems with complex chemical reactions involved that are difficult to access manually. PMID:25064439

  2. Empirical force fields for biological macromolecules: Overview and issues

    Microsoft Academic Search

    Alexander D. MacKerell Jr.

    2004-01-01

    Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force

  3. Polarizable and nonpolarizable force fields for alkyl nitrates.

    PubMed

    Borodin, Oleg; Smith, Grant D; Sewell, Thomas D; Bedrov, Dmitry

    2008-01-24

    Quantum-chemistry-based many-body polarizable and two-body nonpolarizable atomic force fields were developed for alkyl nitrate liquids and pentaerythritol tetranitrate (PETN) crystal. Bonding, bending, and torsional parameters, partial charges, and atomic polarizabilities for the polarizable force field were determined from gas-phase quantum chemistry calculations for alkyl nitrate oligomers and PETN performed at the MP2/aug-cc-pvDz level of theory. Partial charges for the nonpolarizable force field were determined by fitting the dipole moments and electrostatic potential to values for PETN molecules in the crystal phase obtained from molecular dynamics simulations using the polarizable force field. Molecular dynamics simulations of alkyl nitrate liquids and two polymorphs of PETN crystal demonstrate the ability of the quantum-chemistry-based force fields to accurately predict thermophysical and mechanical properties of these materials. PMID:18085767

  4. MAGNETIC FIELD CONFINEMENT IN THE SOLAR CORONA. I. FORCE-FREE MAGNETIC FIELDS B. Fornberg,2

    E-print Network

    Fornberg, Bengt

    MAGNETIC FIELD CONFINEMENT IN THE SOLAR CORONA. I. FORCE-FREE MAGNETIC FIELDS N. Flyer,1 B Axisymmetric force-free magnetic fields external to a unit sphere are studied as solutions to boundary value to the formation of an azimuthal rope of twisted magnetic field embedded within the global field, and to the energy

  5. Ponderomotive force in the presence of electric fields

    NASA Astrophysics Data System (ADS)

    Khazanov, G. V.; Krivorutsky, E. N.

    2013-02-01

    This paper presents averaged equations of particle motion in an electromagnetic wave of arbitrary frequency with its wave vector directed along the ambient magnetic field. The particle is also subjected to an E?×B? drift and a background electric field slowly changing in space and acting along the magnetic field line. The fields, wave amplitude, and the wave vector depend on the coordinate along the magnetic field line. The derivations of the ponderomotive forces are done by assuming that the drift velocity in the ambient magnetic field is comparable to the particle velocity. Such a scenario leads to new ponderomotive forces, dependent on the wave magnetic field intensity, and, as a result, to the additional energy exchange between the wave and the plasma particles. It is found that the parallel electric field can lead to the change of the particle-wave energy exchange rate comparable to that produced by the previously discussed ponderomotive forces.

  6. Nanoscale Piezoelectric Properties of Self-Assembled Fmoc-FF Peptide Fibrous Networks.

    PubMed

    Ryan, Kate; Beirne, Jason; Redmond, Gareth; Kilpatrick, Jason I; Guyonnet, Jill; Buchete, Nicolae-Viorel; Kholkin, Andrei L; Rodriguez, Brian J

    2015-06-17

    Fibrous peptide networks, such as the structural framework of self-assembled fluorenylmethyloxycarbonyl diphenylalanine (Fmoc-FF) nanofibrils, have mechanical properties that could successfully mimic natural tissues, making them promising materials for tissue engineering scaffolds. These nanomaterials have been determined to exhibit shear piezoelectricity using piezoresponse force microscopy, as previously reported for FF nanotubes. Structural analyses of Fmoc-FF nanofibrils suggest that the observed piezoelectric response may result from the noncentrosymmetric nature of an underlying ?-sheet topology. The observed piezoelectricity of Fmoc-FF fibrous networks is advantageous for a range of biomedical applications where electrical or mechanical stimuli are required. PMID:25994251

  7. LABORATORY V MAGNETIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    of a particle with a constant acceleration. · Calculate the motion of a particle with an acceleration structure of materials, and the quark structure of elementary particles. The magnetic interaction can best current-carrying wires, and coils of wire. · Calculate the magnetic force on a charged particle moving

  8. LABORATORY V MAGNETIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    with a constant acceleration. · Calculate the motion of a particle with an acceleration of constant magnitude, the atomic structure of materials, and the quark structure of elementary particles. In this set of laboratory-carrying wires, and coils of wire. · Calculate the magnetic force on a charged particle moving in a uniform

  9. Chapter 19: Electric Charges, Forces, and Fields

    E-print Network

    Kioussis, Nicholas

    of gravity on the proton. Set the magnitudes of the two forces equal to each other and solve for r. Set of electrons and protons are collected together into a single system. Use the total number of charges and the net electrical charge of the system to determine the number of protons and electrons. Sum the product

  10. Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.

    PubMed

    Chang, Le; Ishikawa, Takeshi; Kuwata, Kazuo; Takada, Shoji

    2013-05-30

    Accurate computational estimate of the protein-ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein-ligand simulations, we use a protein-specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO-RESP method to two proteins, dodecin, and lysozyme, we found that protein-specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO-RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. PMID:23420697

  11. ForceFit: a code to fit classical force fields to quantum mechanical potential energy surfaces.

    PubMed

    Waldher, Benjamin; Kuta, Jadwiga; Chen, Samuel; Henson, Neil; Clark, Aurora E

    2010-09-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. PMID:20340109

  12. Magnetic Forces and Field Line Density

    NSDL National Science Digital Library

    2012-08-03

    This is an activity about depicting the relative strength of magnetic fields using field line density. Learners will use the magnetic field line drawing of six magnetic poles created in a previous activity and identify the areas of strong, weak, and medium magnetic intensity using the density of magnetic field lines. This is the fifth activity in the Magnetic Math booklet; this booklet can be found on the Space Math@NASA website. How to Draw Magnetic Fields - II in the Magnetic Math booklet must be completed prior to this activity.

  13. Prediction of Mechanical Properties of Polymers With Various Force Fields

    NASA Technical Reports Server (NTRS)

    Odegard, Gregory M.; Clancy, Thomas C.; Gates, Thomas S.

    2005-01-01

    The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

  14. Solutions and symmetries of force-free magnetic fields

    SciTech Connect

    Tassi, E. [Burning Plasma Research Group, Dipartimento di Energetica and CNISM, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Pegoraro, F. [Dipartimento di Fisica, E. Fermi and CNISM, Pisa (Italy); Cicogna, G. [Dipartimento di Fisica, E. Fermi and INFN, Pisa (Italy)

    2008-09-15

    New analytical results concerning force-free magnetic fields are presented. A number of examples of exact solutions for two-dimensional nonlinear force-free fields described by the Liouville equation are shown. These include classical solutions, such as, the Gold-Hoyle field and the force-free Harris sheet as special cases. The connection between these solutions and the Lie point symmetries of the Liouville equation is illustrated. Lie point symmetries of the equation describing force-free magnetic fields in helical symmetry in cylindrical geometry are also investigated and an infinitesimal generator that, in the vicinity of the cylinder axis, makes it possible to transform purely radially dependent solutions into helically symmetric solutions, is found. Finally we point out the existence of a formal analogy between the equations for the vector potential components of a class of force-free fields and the equations of motion of a charged particle in a magnetic field. This analogy makes it possible to transfer known results from the theory of the motion of a charged particle, into the context of force-free magnetic fields. Explicit examples of such application are given.

  15. Generative morphologies of architectural organization in matter force field

    E-print Network

    Mutlu, Murat

    2010-01-01

    This thesis investigates generative methods of architectural form finding in matter force fields that produce spatial subdivision and organizational variation. Unlike the style driven contemporary free-form architecture ...

  16. ReaxFF Study of the Oxidation of Softwood Lignin in View of Carbon Fiber Production

    SciTech Connect

    Beste, Ariana [ORNL

    2014-01-01

    We investigate the oxidative, thermal conversion of softwood lignin by performing molecular dynamics simulations based on a reactive force field (ReaxFF). The lignin samples are constructed from coniferyl alcohol units, which are connected through linkages that are randomly selected from a natural distribution of linkages in softwood. The goal of this work is to simulate the oxidative stabilization step during carbon fiber production from lignin precursor. We find that at simulation conditions where stabilization reactions occur, the lignin fragments have already undergone extensive degradation. The 5-5 linkage shows the highest reactivity towards cyclization and dehydrogenation.

  17. Brownian motion in a non-homogeneous force field and photonic force microscope

    E-print Network

    Giorgio Volpe; Giovanni Volpe; Dmitri Petrov

    2007-08-03

    The Photonic Force Microscope (PFM) is an opto-mechanical technique based on an optical trap that can be assumed to probe forces in microscopic systems. This technique has been used to measure forces in the range of pico- and femto-Newton, assessing the mechanical properties of biomolecules as well as of other microscopic systems. For a correct use of the PFM, the force field to measure has to be invariable (homogeneous) on the scale of the Brownian motion of the trapped probe. This condition implicates that the force field must be conservative, excluding the possibility of a rotational component. However, there are cases where these assumptions are not fulfilled Here, we show how to improve the PFM technique in order to be able to deal with these cases. We introduce the theory of this enhanced PFM and we propose a concrete analysis workflow to reconstruct the force field from the experimental time-series of the probe position. Furthermore, we experimentally verify some particularly important cases, namely the case of a conservative or rotational force-field.

  18. Imaging the C black formation by acetylene pyrolysis with molecular reactive force field simulations.

    PubMed

    Zhang, Chaoyang; Zhang, Chi; Ma, Yu; Xue, Xianggui

    2015-04-21

    C black is a class of substantial materials with a long history of applications. However, apart from some descriptions of primary reactions, subsequent processes leading up to the final formation mechanism remain unclear. This mechanism is also crucial for understanding the formation of other carbonaceous materials. In this work, we visualize C black formation by acetylene pyrolysis using molecular dynamics simulations with a molecular reactive force field named ReaxFF. We find that the formation undergoes four stages: (1) chain elongation by H abstraction and polymerization of small C species, (2) chain branching, (3) cyclization and ring densification, and (4) condensed ring folding. The simulated C black particle possesses a structure of folded graphite layers, which is in good accordance with experimental observations. Cyclization and condensation are derived from fusion between neighboring chains, significantly varying from common experimental observations at relatively low temperatures that abide by the mechanism of H abstraction and C2H2 addition. Moreover, polyyne and polyene are usually found during acetylene pyrolysis, suggesting that the pyrolysis of acetylene and other hydrocarbons may be a feasible method of obtaining carbyne, a novel carbonaceous material with a high value. PMID:25854895

  19. Simulating the Initial Stage of Phenolic-resin Carbonization via the Reactive Force Field

    SciTech Connect

    Jiang, Deen [ORNL; Van Duin, Adri C. T. [Pennsylvania State University, University Park, PA; GoddardIII, William A [California Institute of Technology, Pasadena; Dai, Sheng [ORNL

    2009-01-01

    Pyrolysis of phenolic resins leads to carbon formation. Simulating this resin-to-carbon process atomistically is a daunting task. In this paper, we attempt to model the initial stage of this process by using the ReaxFF reactive force field, which bridges quantum mechanical and molecular mechanical methods. We run molecular dynamics simulations to examine the evolution of small molecules at different temperatures. The main small-molecule products found include H{sub 2}O, H{sub 2}, CO, and C{sub 2}H{sub 2}. We find multiple pathways leading to H{sub 2}O formation, including a frequent channel via {beta}-H elimination, which has not been proposed before. We determine the reaction barrier for H{sub 2}O formation from the reaction rates obtained at different temperatures. We also discuss the relevance of our simulations to previous experimental observations. This work represents a first attempt to model the resin-to-carbon process atomistically.

  20. Acceleration of particles in an isotropic random force field

    E-print Network

    Hector Javier Durand-Manterola

    2012-04-18

    If we have a particle immersed in a field of random forces, each interaction of the particle with the field can enlarge or diminish its kinetic energy. In this work is shown that in general, for any field of random force with uniform distribution of directions, the probability to gain kinetic energy is larger that the probability to lose it. Therefore, if the particle is submitted to a great number of interactions with the force stochastic field, the final result will be that the particle will gain energy. The probability to gain energy in each interaction is Pg=1/2 (1+T/(2Po)), where T is the impulse given by the field and Po is the momentum of the particle before the interaction. The probability to lose energy in each interaction is Pl=1/2 (1-T/(2Po)).

  1. Alternating Magnetic Field Forces for Satellite Formation Flying

    NASA Technical Reports Server (NTRS)

    Youngquist, Robert C.; Nurge, Mark A.; Starr, Stnaley O.

    2012-01-01

    Selected future space missions, such as large aperture telescopes and multi-component interferometers, will require the precise positioning of a number of isolated satellites, yet many of the suggested approaches for providing satellites positioning forces have serious limitations. In this paper we propose a new approach, capable of providing both position and orientation forces, that resolves or alleviates many of these problems. We show that by using alternating fields and currents that finely-controlled forces can be induced on the satellites, which can be individually selected through frequency allocation. We also show, through analysis and experiment, that near field operation is feasible and can provide sufficient force and the necessary degrees of freedom to accurately position and orient small satellites relative to one another. In particular, the case of a telescope with a large number of free mirrors is developed to provide an example of the concept. We. also discuss the far field extension of this concept.

  2. Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants

    SciTech Connect

    Smith, R.; Chung, P.S; Steckel, J.A.; Jhon, M.S; Biegler, L.T.

    2011-01-01

    The head disk interface in hard disk drive can be considered one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models .In this paper, we investigate beyond molecular level and perform ab-initio calculations to obtain the force field parameters. Intramolecular force field parameters for the Zdol and Ztetraol were evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.

  3. Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants

    SciTech Connect

    Smith, R.; Chung, P.S.; Steckel, J; Jhon, M.S.; Biegler, L.T.

    2011-01-01

    The head disk interface in a hard disk drive can be considered to be one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models. In this paper, we investigate beyond molecular level and perform ab initio calculations to obtain the force field parameters. Intramolecular force field parameters for Zdol and Ztetraol were evaluated with truncated PFPE molecules to allow for feasible quantum calculations while still maintaining the characteristic chemical structure of the end groups. Using the harmonic approximation to the bond and angle potentials, the parameters were derived from the Hessian matrix, and the dihedral force constants are fit to the torsional energy profiles generated by a series of constrained molecular geometry optimization.

  4. Apparatus having reduced mechanical forces for supporting high magnetic fields

    DOEpatents

    Prueitt, Melvin L. (Los Alamos, NM); Mueller, Fred M. (Los Alamos, NM); Smith, James L. (Los Alamos, NM)

    1991-01-01

    The present invention identifies several configurations of conducting elements capable of supporting extremely high magnetic fields suitable for plasma confinement, wherein forces experienced by the conducting elements are significantly reduced over those which are present as a result of the generation of such high fields by conventional techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency.

  5. Comparing Molecular Dynamics Force Fields in the Essential Subspace

    PubMed Central

    Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2015-01-01

    The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their “unbalanced” counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178

  6. On force-field models of the spacecraft flyby anomaly

    Microsoft Academic Search

    Wolfgang Hasse; Emrah Birsin; Philipp Haehnel

    2009-01-01

    Recently, Anderson et al. published an empirical prediction formula for the so far unexplained parts of the velocity changes of spacecrafts during Earth flybys. In the framework of a perturbational approach, we show that there is no velocity-independent force field of the Earth - in addition to its Newtonian gravity field - that is to reproduce this formula. However, we

  7. Classical motion in force fields with short range correlations

    E-print Network

    B. Aguer; S. De Bievre; P. Lafitte; P. Parris

    2009-06-25

    We study the long time motion of fast particles moving through time-dependent random force fields with correlations that decay rapidly in space, but not necessarily in time. The time dependence of the averaged kinetic energy and mean-squared displacement is shown to exhibit a large degree of universality; it depends only on whether the force is, or is not, a gradient vector field. When it is, p^{2}(t) ~ t^{2/5} independently of the details of the potential and of the space dimension. Motion is then superballistic in one dimension, with q^{2}(t) ~ t^{12/5}, and ballistic in higher dimensions, with q^{2}(t) ~ t^{2}. These predictions are supported by numerical results in one and two dimensions. For force fields not obtained from a potential field, the power laws are different: p^{2}(t) ~ t^{2/3} and q^{2}(t) ~ t^{8/3} in all dimensions d\\geq 1.

  8. First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface.

    PubMed

    Yamada, Takahiro; Phelps, Donald K; van Duin, Adri C T

    2013-09-01

    Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from -22.9 to -33.9 kcal/mol for formaldehyde, and from -44.3 to -66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde ? HCO + H, HCO ? H + CO, and CO ? C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST-based rates are consistent with HREELS observation. PMID:23804527

  9. Deriving forces from 2D velocity field measurements

    NASA Astrophysics Data System (ADS)

    Albrecht, Thomas; del Campo, Vanessa; Weier, Tom; Metzkes, Hans; Stiller, Jörg

    2013-03-01

    We discuss how to derive a force or a force density from a measured velocity field. The first part focuses on the integral force a fluid exerts on a body, e.g. lift and drag on an airfoil. Obtaining the correct pressure is crucial; however, it cannot be measured within the flow non-intrusively. Using numerical and experimental test cases, we compare the accuracy achievable with three methods: pressure reconstruction from velocity fields via (1) the differential momentum equation, or (2) the Poisson equation, furthermore, (3) Noca's momentum equation [Noca, JFS 13(5), 1999], which does not require pressure explicitly. The latter gives the best results for the lift, whereas the first or second approach should be used for the drag. The second part deals with obtaining the distribution of a body force density generated by an actuator. Using a stream function ansatz, we obtain a Laplace equation that allows us to compute the solenoidal part of the force distribution; however, the irrotational part is lost. Furthermore, the wall pressure must be known. We validate this approach using numerical data from a wall jet flow in a rectangular box, driven by a fictitious, solenoidal body force. Reconstructing the force distribution yields an error of less than 10-2 for most of the domain.

  10. On force-field models of the spacecraft flyby anomaly

    E-print Network

    Hasse, Wolfgang; Haehnel, Philipp

    2009-01-01

    Recently, Anderson et al. published an empirical prediction formula for the so far unexplained parts of the velocity changes of spacecrafts during Earth flybys. In the framework of a perturbational approach, we show that there is no velocity-independent force field of the Earth - in addition to its Newtonian gravity field - that is to reproduce this formula. However, we give examples for fields modeling exactly the flyby anomaly which are quadratic functions of the velocity of the spacecraft.

  11. On force-field models of the spacecraft flyby anomaly

    E-print Network

    Wolfgang Hasse; Emrah Birsin; Philipp Haehnel

    2009-02-28

    Recently, Anderson et al. published an empirical prediction formula for the so far unexplained parts of the velocity changes of spacecrafts during Earth flybys. In the framework of a perturbational approach, we show that there is no velocity-independent force field of the Earth - in addition to its Newtonian gravity field - that is to reproduce this formula. However, we give examples for fields modeling exactly the flyby anomaly which are quadratic functions of the velocity of the spacecraft.

  12. Average Lorentz Self-Force From Electric Field Lines

    E-print Network

    Aashish, Sandeep

    2014-01-01

    We generalize the derivation of electromagnetic fields of a charged particle moving with a constant acceleration [1] to a variable acceleration (piecewise constants) over a small finite time interval using Coulomb's law, relativistic transformations of electromagnetic fields and Thomson's construction [2]. We derive the average Lorentz self-force for a charged particle in arbitrary non-relativistic motion via averaging the fields at retarded time.

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

    SciTech Connect

    Behunin, Ryan O. [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Hu, Bei-Lok [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States)

    2010-08-15

    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.

  14. Imaging Nanoscale Electromagnetic Near-Field Distributions Using Optical Forces.

    PubMed

    Huang, Fei; Ananth Tamma, Venkata; Mardy, Zahra; Burdett, Jonathan; Kumar Wickramasinghe, H

    2015-01-01

    We demonstrate the application of Atomic Force Microscopy (AFM) for mapping optical near-fields with nanometer resolution, limited only by the AFM probe geometry. By detecting the optical force between a gold coated AFM probe and its image dipole on a glass substrate, we profile the electric field distributions of tightly focused laser beams with different polarizations. The experimentally recorded focal force maps agree well with theoretical predictions based on a dipole-dipole interaction model. We experimentally estimate the aspect ratio of the apex of gold coated AFM probe using only optical forces. We also show that the optical force between a sharp gold coated AFM probe and a spherical gold nanoparticle of radius 15?nm, is indicative of the electric field distribution between the two interacting particles. Photo Induced Force Microscopy (PIFM) allows for background free, thermal noise limited mechanical imaging of optical phenomenon over wide range of wavelengths from Visible to RF with detection sensitivity limited only by AFM performance. PMID:26073331

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

    NASA Technical Reports Server (NTRS)

    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.

  16. Simulations of a protein crystal with a high resolution X-ray structure: Evaluation of force fields and water models

    PubMed Central

    Cerutti, David S.; Freddolino, Peter L.; Duke, Robert E.; Case, David A.

    2010-01-01

    We use classical molecular dynamics and sixteen combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96Å) and the simplicity of the crystallization solution (nearly pure water) makes it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100ns of production dynamics, permitting some long-timescale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can be modified to improve their representations of protein structure and thermodynamics. PMID:20860388

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

    PubMed

    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. PMID:25717155

  18. The electromagnetic force field, fluid flow field, and temperature profiles in levitated metal droplets

    Microsoft Academic Search

    N. El-Kaddah; J. Szekely

    1983-01-01

    A mathematical representation has been developed for the electromagnetic force field, the fluid flow field, the temperature\\u000a field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was\\u000a employed for the calculation of the electromagnetic force field, while the turbulent Navier-Stokes equations and the turbulent\\u000a convective transport equations were used to represent the

  19. Ponderomotive force in the presence of electric fields

    SciTech Connect

    Khazanov, G. V.; Krivorutsky, E. N. [NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States)

    2013-02-15

    This paper presents averaged equations of particle motion in an electromagnetic wave of arbitrary frequency with its wave vector directed along the ambient magnetic field. The particle is also subjected to an E(vector sign) Multiplication-Sign B(vector sign) drift and a background electric field slowly changing in space and acting along the magnetic field line. The fields, wave amplitude, and the wave vector depend on the coordinate along the magnetic field line. The derivations of the ponderomotive forces are done by assuming that the drift velocity in the ambient magnetic field is comparable to the particle velocity. Such a scenario leads to new ponderomotive forces, dependent on the wave magnetic field intensity, and, as a result, to the additional energy exchange between the wave and the plasma particles. It is found that the parallel electric field can lead to the change of the particle-wave energy exchange rate comparable to that produced by the previously discussed ponderomotive forces.

  20. Comparison of pharmacological activities of Neuropeptide FF 1 and Neuropeptide FF 2 receptor agonists

    Microsoft Academic Search

    Isabelle Quelven; Anne Roussin; Jean-marie Zajac

    2005-01-01

    The pharmacological effects of Neuropeptide FF (NPFF) analogs exhibiting different selectivities towards Neuropeptide FF1 (NPFF1) and Neuropeptide FF2 (NPFF2) receptors were investigated after supraspinal administration in mice. Injected into the third ventricle, VPNLPQRF-NH2, which is selective for Neuropeptide FF1 receptor induced a hypothermia while EFWSLAAPQRF-NH2 and SPAFLFQPQRF-NH2 which are selective for Neuropeptide FF2 receptor, did not. Furthermore, EFWSLAAPQRF-NH2 significantly increased

  1. The force exerting on cosmic bodies in a quaternionc field

    E-print Network

    V. Majernik

    2003-09-03

    The expression of a time-dependent cosmological constant $\\lambda \\propto 1/t^2$ is interpreted as the energy density of a special type of the quaternionic field. The Lorenz-like force acting on the moving body in the presence of this quaternionic field is determined. The astronomical and terrestrial effects of this field are presented, and the ways how it can be observably detected is discussed. Finally, a new mechanism of the particle creation and an alternative cosmological scenario in the presence of the cosmic quatertionic field is suggested.

  2. Mitigated-force carriage for high magnetic field environments

    DOEpatents

    Ludtka, Gerard M; Ludtka, Gail M; Wilgen, John B; Murphy, Bart L

    2014-05-20

    A carriage for high magnetic field environments includes a first work-piece holding means for holding a first work-piece, the first work-piece holding means being disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla. The first work-piece holding means is further disposed in operable connection with a second work-piece holding means for holding a second work-piece so that, as the first work-piece is inserted into the magnetic field, the second work-piece is simultaneously withdrawn from the magnetic field, so that an attractive magnetic force imparted on the first work-piece offsets a resistive magnetic force imparted on the second work-piece.

  3. Quantum chemistry based force fields for soft matter

    Microsoft Academic Search

    Matthew A. Glaser; Noel A. Clark; Edgardo Garcia; David M. Walba

    1997-01-01

    We describe the use of ab initio electronic structure calculations in the development of high-quality classical interaction potentials for liquid crystal modeling. Our focus is on methods for the rapid, on-demand creation of force fields for use in mean field theory based calculations of materials properties, employed for routine pre-synthesis evaluation of novel liquid crystalline materials. The role of quantum

  4. Subdiffusion in a time-dependent force field

    SciTech Connect

    Shkilev, V. P., E-mail: shkilevv@ukr.net [National Academy of Sciences of Ukraine, Institute of Surface Chemistry (Ukraine)

    2012-05-15

    Based on the random-barrier model and using the mean-field approximation, we derive an equation that describes the subdiffusion of particles in an external time-varying force field. The derived equation predicts the frequency dependence of the conductivity and, in this regard, is consistent with the experiment. We show that the response of the system to an external perturbation depends significantly on the structure of the inhomogeneous medium.

  5. Force field development from first principles for materials design

    NASA Astrophysics Data System (ADS)

    Chan, Maria; Kinaci, Alper; Narayanan, Badri; Sen, Fatih; Gray, Stephen; Davis, Michael; Sankaranaryanan, Subramanian

    2015-03-01

    The ability to perform accurate calculations efficiently is crucial for computational materials design. In this talk, we will discuss a stream-lined approach to force field development using first principles density functional theory training data and machine learning algorithms. We will also discuss the validation of this approach on precious metal nanoparticles.

  6. Force, current and field effects in single atom manipulation

    E-print Network

    Hla, Saw-Wai

    Force, current and field effects in single atom manipulation K.-F. Braun , S.-W. Hla , N. Pertaya present a detailed investigation of the manipulation of Ag and Au atoms with a STM tip on the Ag(111 of the atom during manipulation. The threshold tunnelling resistance and tip-height to move a Au/Ag atom have

  7. Evaluation of DNA Force Fields in Implicit Solvation

    PubMed Central

    Gaillard, Thomas; Case, David A.

    2011-01-01

    DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

  8. Frequency-dependent force fields for QMMM calculations.

    PubMed

    Harczuk, Ignat; Vahtras, Olav; Ågren, Hans

    2015-03-28

    We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean [small alpha, Greek, macron] is determined with respect to the size of the QM and MM parts of the total system. PMID:25714984

  9. Energy buildup in sheared force-free magnetic fields

    NASA Technical Reports Server (NTRS)

    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.

  10. Benchmark Database on Isolated Small Peptides Containing an Aromatic Side Chain: Comparison Between Wave Function and Density Functional Theory Methods and Empirical Force Field

    SciTech Connect

    Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel

    2008-03-13

    A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

  11. Atomistic force field for alumina fit to density functional theory

    SciTech Connect

    Sarsam, Joanne [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom) [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Thomas Young Centre, Imperial College London, London SW7 2AZ (United Kingdom); Finnis, Michael W.; Tangney, Paul, E-mail: p.tangney@imperial.ac.uk [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom) [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Thomas Young Centre, Imperial College London, London SW7 2AZ (United Kingdom); Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom)

    2013-11-28

    We present a force field for bulk alumina (Al{sub 2}O{sub 3}), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.

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

    USGS Publications Warehouse

    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 differences in appearance and bulk?flow density. These results demonstrate that debris flows can have strong control on rates of steepland evolution and contribute to a foundation needed for modeling debris?flow incision stochastically.

  13. An attempt in assessing contact forces from a kinematic field

    NASA Astrophysics Data System (ADS)

    Richefeu, Vincent; Combe, Gaël; Maurin, Raphaël

    2013-06-01

    In granular materials, it is not so simple to assess experimentally the contact forces. Photoelasticity is generally used for this purpose but this technique involves some constraints that may limit its use. We propose a different solution, which implements both the digital image correlation (DIC) technique and the non-smooth contact dynamics (NSCD) formalism. In a nutshell, the technique aims to find a set of contact forces mechanically admissible given a set of measured contact velocities. We used photographs of a simple shear test of a two-dimensional analogue granular material (about 1000 aluminum rods) to apply the solution, and we showed that valuable information about the contact forces can be extracted from the kinematic field provided that no major rearrangement occurs for at least five image shots.

  14. Particle Energization in a Chaotic Force-free/Non-Force-free Magnetic field

    NASA Astrophysics Data System (ADS)

    Li, X.; Dasgupta, B.; Li, G.

    2014-12-01

    Force-free field is believed to be a reasonable description of the quiet sun and a good approximation for low-beta plasma, like the lower region of solar corona. This field is similar to ABC field, which has been demonstrated to be chaotic. Here, we study the particle transport behavior in this field. We are particularly interested in particle energization if there is an electric field, which can be introduced by turbulent motion of plasma parcels. We expect a second order Fermi acceleration. Different spectra for turbulent motions are used, and particles with various mass-to-charge ratio are investigated. This process can provide a seed population generation mechanism for CME-driven shocks.

  15. Advancement of polarizable force field and its use for molecular modeling and design.

    PubMed

    Xu, Peijun; Wang, Jinguang; Xu, Yong; Chu, Huiying; Liu, Jiahui; Zhao, Meixia; Zhang, Depeng; Mao, Yingchen; Li, Beibei; Ding, Yang; Li, Guohui

    2015-01-01

    The most important requirement of biomolecular modeling is to deal with electrostatic energies. The electrostatic polarizability is an important part of electrostatic interaction for simulation systems. However, AMBER, CHARMM, OPLS, GROMOS, MMFF force fields etc. used in the past mostly apply fixed atomic center point charge to describe electrostatic energies, and are not sufficient for considering the influence of the electrostatic polarization. The emergence of polarizable force fields has solved this problem. In recent years, quickly developed polarizable force fields have involved a lot of fields. The chapter relating to polarizable force fields spread over several aspects. Firstly, we reviewed the history of the classical force fields and compared with polarizable force fields to elucidate the advancements of polarizable force fields. Secondly, it is introduced that the application of polarizable force fields to small molecules and biological macromolecules simulation, including molecular design. Finally, a brief development trend and perspective is given on rapidly growing polarizable force fields. PMID:25387957

  16. Force-free configurations in reversed-field pinches

    SciTech Connect

    Emets, Y.P.; Zamidra, A.I.; Kovbasenko, Y.P.

    1988-03-01

    The structure of reversed-field pinches is analyzed on the basis of analytic solutions of equations describing force-free configurations. A model with a constant coefficient of the proportionality between the current density and the magnetic field is used to analyze the effect of the toroidal geometry on the field distribution and the F--THETA diagrams. A modified model is proposed in which the ratio of the current density to the magnetic field tends toward zero near the wall of the discharge chamber. This model yields a more accurate description of the experiments F--THETA diagrams and of the field distributions. It is preferable to the Bessel-function model from the energy standpoint.

  17. Direct computation of parameters for accurate polarizable force fields.

    PubMed

    Verstraelen, Toon; Vandenbrande, Steven; Ayers, Paul W

    2014-11-21

    We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields. PMID:25416881

  18. Double-charge model for classical force-field simulations

    NASA Astrophysics Data System (ADS)

    Barrett, Christopher; Wang, Lin-Wang

    2015-06-01

    In a traditional classical force-field model, the atomic point charge that generates the electrostatic potential, and the Born charge induced by atomic movement, are represented by the same charge parameter. But their actual values can be very different, and correct values for both of them are needed in order to yield the correct atomic structure (electrostatic charge) and phonon spectrum (Born charge). This is particularly true for nanostructure calculations. Here, we introduce a double-charge model (DCM) to reconcile the difference between the electrostatic charge and Born charge. The DCM allows us to reproduce the accurate ab initio phonon spectrum not only in bulk systems, but also for nanostructures (slabs and nanowires). This enables the use of classical force fields to study phonon spectra of large nanostructures, which are important for many phenomena from carrier dynamics to thermo conductivities.

  19. Efficient parametrization of complex molecule-surface force fields.

    PubMed

    Gao, David Z; Federici Canova, Filippo; Watkins, Matthew B; Shluger, Alexander L

    2015-06-15

    We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. © 2015 Wiley Periodicals, Inc. PMID:25891018

  20. Force-Field Compensation in a Manual Tracking Task

    Microsoft Academic Search

    Valentina Squeri; Lorenzo Masia; Maura Casadio; Pietro Morasso; Elena Vergaro; Paul L. Gribble

    2010-01-01

    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

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

    SciTech Connect

    Han, Jaebeom; Mazack, Michael J. M.; Zhang, Peng; Truhlar, Donald G.; Gao, Jiali [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States)] [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States)

    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{sup 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 biological ion channels through membranes.

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

    PubMed

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

    2013-08-01

    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 biological ion channels through membranes. PMID:23927266

  3. Current Status of the AMOEBA Polarizable Force Field

    PubMed Central

    Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu; Pande, Vijay S.; Chodera, John D.; Schnieders, Michael J.; Haque, Imran; Mobley, David L.; Lambrecht, Daniel S.; DiStasio, Robert A.; Head-Gordon, Martin; Clark, Gary N. I.; Johnson, Margaret E.

    2010-01-01

    Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical. PMID:20136072

  4. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

    PubMed Central

    2011-01-01

    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, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968

  5. Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon

    NASA Technical Reports Server (NTRS)

    DasGupta, Sunando; Plawsky, Joel L.; Wayner, Peter C., Jr.

    1995-01-01

    Isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth's gravitational field using an image-analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. These profiles are a function of the stress field. Experimentally, the augmented Young-Laplace equation is an excellent model for the force field at the solid-liquid-vapor interfaces for heptane and pentane menisci on quartz and tetradecane on SFL6. The effects of refractive indices of the solid and liquid on the measurement techniques were demonstrated. Experimentally obtained values of the disjoining pressure and dispersion constants were compared to those predicted from the Dzyaloshinskii - Lifshitz - Pilaevskii theory for an ideal surface and reasonable agreements were obtained. A parameter introduced gives a quantitative measurement of the closeness of the system to equilibrium. The nonequilibrium behavior of this parameter is also presented

  6. Coupling ReaxFF with Temperature Accelerated

    E-print Network

    Goddard III, William A.

    Coupling ReaxFF with Temperature Accelerated Dynamics CMDF: Summer 2005 Daniel Yi, Caltech `07 #12: TAD standalone code - FORTRAN 77 CMDF - Python based #12;CMDF Module: TADTOOLS #12;Seamless;TAD ReaxFF Coupled Example: Hydrogen adatom on Platinum min = 5 x 1011 sec-1 , = .01 [100] Platinum

  7. Continuum Polarizable Force Field within the Poisson-Boltzmann Framework

    PubMed Central

    Tan, Yu-Hong; Tan, Chunhu; Wang, Junmei; Luo, Ray

    2008-01-01

    We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation of dielectric environment. Comparison with experiment also shows that the new continuum polarizable model is reasonable, with similar accuracy as B3LYP/cc-pVTZ in reproduction of dipole moments of selected organic molecules in the gas phase. We have further tested the validity to interchange the Amber van der Waals parameters between the explicit and continuum polarizable force fields with a series of dimers. It can be found that the continuum polarizable model agrees well with MP2/cc-pVTZ, with deviations in dimer binding energies less than 0.9 kcal/mol in the aqueous dielectric environment. Finally we have optimized atomic cavity radii with respect to experimental solvation free energies of 177 training molecules. To validate the optimized cavity radii, we have tested these parameters against 176 test molecules. It is found that the optimized PB atomic cavity radii transfer well from the training set to the test set, with an overall root-mean-squared deviation of 1.30 kcal/mol, unsigned average error of 1.07 kacl/mol, and correlation coefficient of 92% for all 353 molecules in both the training and test sets. Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework. PMID:18507452

  8. Micro-gravity: current distributions creating a uniform force field

    NASA Astrophysics Data System (ADS)

    Vincent-Viry, O.; Mailfert, A.; Colteu, A.; Dael, A.; Gourdin, C.; Quettier, L.

    2001-02-01

    This paper presents two structures of superconducting coils able to give satisfactory solutions to the problem of generation of uniform field of high magnetic forces. The first structure is modeled by the use of purely surface current densities, whereas the second one can be described with volume current densities. Both of these structures proceed from the study of a particular expression of the complex magnetic potential introduced for structures with two-dimensional geometry. This work is carried out in a research collaboration between the GREEN and the DSM-DAPNIA department of the CEA Saclay.

  9. On the force fields which are homogeneous of degree $-3$

    E-print Network

    Alain Albouy

    2014-12-12

    The dynamics defined by a force field which is positively homogeneous of degree $-3$ can always be reduced, by simply constraining it. The dimension of the phase space is reduced by two dimensions, while it may only be reduced by one dimension if the degree of homogeneity is different from $-3$. This remark is an elegant foundation of Appell's projective dynamics. We show how it relates to Kn\\"orrer's remark on the correspondence between the Neumann potential on a sphere and the geodesic motion on an ellipsoid.

  10. The Anharmonic Force Field of BeH2 Revisited

    NASA Technical Reports Server (NTRS)

    Martin, Jan M. L.; Lee, Timothy J.

    2003-01-01

    The anharmonic force field of BeH2 has been calculated near the basis set and n-particle space limits. The computed antisymmetric stretch frequencies of BeH2 and BeD2 are in excellent agreement with recent high-resolution gas-phase measurements. The agreement between theory and experiment for the other spectroscopic constants is also excellent, except for omega(sub 3) and X(sub 33) for BeH2 and G(sub 22) for BeD2. It is concluded that further experimental work is needed in order to resolve these discrepancies.

  11. Validating empirical force fields for molecular-level simulation of cellulose dissolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

  12. Molecules as a Basis'for Modeling the Force Field of

    E-print Network

    Downs, Robert T.

    6 Molecules as a Basis'for Modeling the Force Field of Silica G. v. Gibbs, F. C. Hill, M. B. Boisen in small molecules'. More recent studies indicate that a similar connection exists between the force field CONNECTION BETWEEN THE FORCE FIELD OF SILICA AND SMALL MOLECULES 2.1 Structural Evidence There is a wealth

  13. Accounting for electronic polarization in nonpolarizable force fields

    E-print Network

    Leontyev, Igor

    2015-01-01

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole $\\mu$~3D reported in recent ab initio and experimental s...

  14. Thermomechanical properties of graphene: valence force field model approach.

    PubMed

    Lajevardipour, A; Neek-Amal, M; Peeters, F M

    2012-05-01

    Using the valence force field model of Perebeinos and Tersoff (2009 Phys. Rev. B 79 241409(R)), different energy modes of suspended graphene subjected to tensile or compressive strain are studied. By carrying out Monte Carlo simulations it is found that: (i) only for small strains (|?| force field model results in a temperature independent bending modulus for graphene, and (viii) the Grüneisen parameter is estimated to be 0.64. PMID:22475745

  15. Development of force field parameters for molecular simulation of polylactide

    PubMed Central

    McAliley, James H.; Bruce, David A.

    2011-01-01

    Polylactide is a biodegradable polymer that is widely used for biomedical applications, and it is a replacement for some petroleum based polymers in applications that range from packaging to carpeting. Efforts to characterize and further enhance polylactide based systems using molecular simulations have to this point been hindered by the lack of accurate atomistic models for the polymer. Thus, we present force field parameters specifically suited for molecular modeling of PLA. The model, which we refer to as PLAFF3, is based on a combination of the OPLS and CHARMM force fields, with modifications to bonded and nonbonded parameters. Dihedral angle parameters were adjusted to reproduce DFT data using newly developed CMAP dihedral cross terms, and the model was further adjusted to reproduce experimentally resolved crystal structure conformations, melt density, volume expansivity, and the glass transition temperature of PLA. We recommend the use of PLAFF3 in modeling PLA in its crystalline or amorphous states and have provided the necessary input files required for the publicly available molecular dynamics code GROMACS. PMID:22180734

  16. 6.641 Electromagnetic Fields, Forces, and Motion, Spring 2003

    E-print Network

    Zahn, Markus, 1946-

    Electric and magnetic quasistatic forms of Maxwell's equations applied to dielectric, conduction, and magnetization boundary value problems. Electromagnetic forces, force densities, and stress tensors, including magnetization ...

  17. Electromagnetic self-forces and generalized Killing fields

    E-print Network

    Abraham I. Harte

    2009-07-20

    Building upon previous results in scalar field theory, a formalism is developed that uses generalized Killing fields to understand the behavior of extended charges interacting with their own electromagnetic fields. New notions of effective linear and angular momenta are identified, and their evolution equations are derived exactly in arbitrary (but fixed) curved spacetimes. A slightly modified form of the Detweiler-Whiting axiom that a charge's motion should only be influenced by the so-called "regular" component of its self-field is shown to follow very easily. It is exact in some interesting cases, and approximate in most others. Explicit equations describing the center-of-mass motion, spin angular momentum, and changes in mass of a small charge are also derived in a particular limit. The chosen approximations -- although standard -- incorporate dipole and spin forces that do not appear in the traditional Abraham-Lorentz-Dirac or Dewitt-Brehme equations. They have, however, been previously identified in the test body limit.

  18. Unified Field Theory and Force Formulas of Interactions

    NASA Astrophysics Data System (ADS)

    Ma, Tian; Wang, Shouhong

    2013-04-01

    The main objective of this talk is to drive a unified field model coupling four interactions, based on the principle of interaction dynamics (PID) and the principle of representation invariance (PID). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint. PRI requires that physical laws be independent of representations of the gauge groups. One important outcome of this unified field model is a natural duality between the interacting fields (g, A, W^a, S^k), corresponding to graviton, photon, intermediate vector bosons W^± and Z and gluons, and the adjoint bosonic fields (?,, ^aw, ^ks). This duality predicts two Higgs particles of similar mass with one due to weak interaction and the other due to strong interaction. PID and PRI can be applied directly to individual interactions, leading to 1) modified Einstein equations, giving rise to a unified theory for dark matter and dark energy, 2) three levels of strong interaction potentials for quark, nucleon/hadron, and atom respectively, and 3) a weak interaction potential. These potential/force formulas offer a clear mechanism for both quark confinement and asymptotic freedom.

  19. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of ?\\/ ? Conformers

    Microsoft Academic Search

    Alberto Pérez; Iván Marchán; Daniel Svozil; Jiri Sponer; Thomas E. Cheatham; Charles A. Laughton; Modesto Orozco

    2007-01-01

    We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the ?\\/? concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the ?\\/?=(g+,t) backbone that were seen in long (more than 10ns) simulations with previous AMBER parameter sets (parm94-99). The force

  20. Field emission study of diamond like carbon films with scanned probe field emission force microscopy

    SciTech Connect

    Inoue, Takahito; Ogletree, D.Frank; Salmeron, Miquel

    1999-12-07

    Using a tip as an anode, a scanning force microscope (SFM) with an electrically conducting tip allows simultaneous measurement of both field emitted currents and surface electronic properties with high lateral resolution. The principle of the method and its application to field emission from CVD diamond-like carbon films are presented. By simultaneously imaging the topography and field emission current distribution with a 100 nm tip-surface separation, we correlated emission, topography and dielectric properties. Subsequent contact SFM images of the same regions correlated topography and conductivity on the nanometer scale. The electrostatic force between tip and surface showed fluctuations on a millisecond time scale during field emission. This is probably due to charging and discharging of deep traps in the diamond film.

  1. Application of polarizable ellipsoidal force field model to pnicogen bonds.

    PubMed

    Liu, Fang; Du, Likai; Gao, Jun; Wang, Lili; Song, Bo; Liu, Chengbu

    2015-03-15

    Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono- and polysubstituted PH3 -NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self-assembly structures. PMID:25565043

  2. Electromagnetic Forces and Fields in a Rotating Reference Frame

    E-print Network

    Paul N. Arendt, Jr

    1998-01-20

    Maxwell's equations and the equations governing charged particle dynamics are presented for a rotating coordinate system with the global time coordinate of an observer on the rotational axis. Special care is taken in defining the relevant entities in these equations. Ambiguities in the definitions of the electromagnetic fields are pointed out, and in fact are shown to be essential in such a system of coordinates. The Lorentz force is found to have an extra term in this frame, which has its origins in relativistic mass. A related term in the energy equation, which allows inertia to be gained even during strict corotation, suggests ways existing pulsar magnetosphere models may be modified to match observed `braking indices' more closely.

  3. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

    PubMed Central

    2015-01-01

    Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein–water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance. PMID:24955078

  4. On the Use of Quartic Force Fields in Variational Calculations

    NASA Technical Reports Server (NTRS)

    Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.

    2013-01-01

    The use of quartic force fields (QFFs) has been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this paper we outline and 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 effectively describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system. 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. Cases are referenced where variational computations coupled with transformed QFFs produce accuracies compared to experiment for fundamental frequencies on the order of 5 cm(exp -1) and often as good as 1 cm(exp -1).

  5. The Eccentric Frame Decomposition of Central Force Fields

    E-print Network

    Jared M. Maruskin; Daniel J. Scheeres; Fred C. Adams; Anthony M. Bloch

    2007-12-20

    The rosette-shaped motion of a particle in a central force field is known to be classically solvable by quadratures. We present a new approach of describing and characterizing such motion based on the eccentricity vector of the two body problem. In general, this vector is not an integral of motion. However, the orbital motion, when viewed from the nonuniformly rotating frame defined by the orientation of the eccentricity vector, can be solved analytically and will either be a closed periodic circulation or libration. The motion with respect to inertial space is then given by integrating the argument of periapsis with respect to time. Finally we will apply the decomposition to a modern central potential, the spherical Hernquist-Newton potential, which models dark matter halos of galaxies with central black holes.

  6. Non-bonded force field for the interaction between metals and organic molecules

    E-print Network

    Mueser, Martin

    Non-bonded force field for the interaction between metals and organic molecules: A case study to parameterize the non-bonded force field for the interaction between organic molecules and metal surfaces. After reaching a local equilibration, molecules near the metal surfaces are isolated and the forces

  7. Field measurements of interactions between furnaces and forced air distribution systems

    E-print Network

    LBNL 40587 Field measurements of interactions between furnaces and forced air distribution systems Vol. 104 Part 1 Field measurements of interactions between furnaces and forced air distribution performance of these furnaces and their interactions with their forced-air distribution systems

  8. Lipidbook: a public repository for force field parameters used in membrane simulations

    E-print Network

    Beckstein, Oliver

    Lipidbook: a public repository for force field parameters used in membrane. P. Sansom, and Oliver Beckstein. Lipidbook: a public repository for force via PubMed identifier and digital object identifier (DOI), and users can

  9. Calculation of three-dimensional electromagnetic force field during arc welding

    NASA Astrophysics Data System (ADS)

    Kumar, A.; DebRoy, T.

    2003-07-01

    Electromagnetic force is an important driving force for convection in the weld pool during arc welding. Accurate calculation of the electromagnetic force field requires complex numerical calculations of three-dimensional current density and magnetic flux fields. Several simplifying assumptions have been suggested to avoid the complex calculations. The resulting analytical expressions for the electromagnetic force field have been widely used without any critical evaluation of their intrinsic merit, since accurate numerical calculations were difficult in the past because of lack of fast computers. A numerical model has been developed to accurately calculate the current density and magnetic flux fields and the resulting electromagnetic force field in three dimensions in the entire weldment. The model can take into account any current distribution on the work piece surface and evaluate the effects of different arc locations and work piece geometry on the electromagnetic force field. Contributions of the electrode current, arc plasma, and current distribution inside the three-dimensional work piece to the magnetic field and the electromagnetic force field are determined. The electromagnetic force field computed from the model is compared with those obtained from the commonly used simplified expressions of electromagnetic force to examine the accuracy of the commonly used simplifying assumptions. The accuracy of the computed electromagnetic force field can be significantly improved by using the proposed numerical model.

  10. Comparison of Nonlinear Force-Free Field and Potential Field in the Quiet Sun

    NASA Astrophysics Data System (ADS)

    Liu, S.; Zhang, H. Q.; Su, J. T.

    2011-05-01

    In this paper, a potential field extrapolation and three nonlinear force-free (NLFF) field extrapolations (optimization, direct boundary integral (DBIE), and approximate vertical integration (AVI) methods) are used to study the spatial configuration of magnetic field in the quiet Sun. It is found that differences in the computed field strengths among the three NLFF and potential fields exist in the low layers. However, they tend to disappear as the height increases, and the differences are of the order of 0.1 gauss when the height exceeds ? 2000 km above the photosphere. The difference in azimuth angles between each NLFF field model and the potential field is as follows: for the optimization field, it decreases evidently as the height increases; for the DBIE field, it almost stays constant and shows no significant change as the height increases; for the AVI field, it increases slowly as the height increases. Our analysis shows that the reconstructed NLFF fields deviate significantly from the potential field in the quiet Sun.

  11. Soil washing physical separations test procedure - 300-FF-1 operable unit

    SciTech Connect

    Belden, R.D.

    1993-10-08

    This procedure provides the operations approach, a field sampling plan, and laboratory procedures for a soil washing test to be conducted by Alternative Remedial Technologies, Inc. (ART) in the 300-FF-1 area at the Hanford site. The {open_quotes}Quality Assurance Project Plan for the Soil Washing Physical Separations Test, 300-FF-1 Operable Unit,{close_quotes} Hanford, Washington, Alternative Remedial Technologies, Inc., February 1994 (QAPP) is provided in a separate document that presents the procedural and organizational guidelines for this test. This document describes specifications, responsibilities, and general procedures to be followed to conduct physical separation soil treatability tests in the North Process Pond of the 300-FF-1 Operable Unit (OU) at the Hanford Site. These procedures are based on the {open_quotes}300-FF-1 Physical Separations CERCLA Treatability Test Plan, DOE/RL 92-2l,{close_quotes} (DOE-RL 1993).

  12. Diffusion through ordered force fields in nanopores represented by Smoluchowski equation

    SciTech Connect

    Wang, F.Y.; Zhu, Z.H.; Rudolph, V. [University of Queensland, Brisbane, Qld. (Australia). School of Engineering

    2009-06-15

    The classical Einstein or Fick diffusion equation was developed in random force fields. When the equation is applied to gas transport through coal, significant discrepancies are observed between experimental and simulation results. The explanation may be that the random force field assumption is violated. In this article, we analyze molecular transport driven by both random and ordered (directional) forces in nanopores. When applied to CO{sub 2} transport through cone-shaped carbon nano-tubes (CNTs) and Li{sup +} doped graphite pores, computational results show that directional force fields may significantly affect porous media flow. Directional forces may be generated by potential gradients arising from a range of non-uniform characteristics, such as variations in the pore-sizes and in local surface compositions. On the basis of the simulation and experimental results, the Smoluchowski and Fokker-Planck equations, which account for the directional force fields, are recommended for diffusion through ordered force fields in nanopores.

  13. Thermal decomposition process in algaenan of Botryococcus braunii race L. Part 2: Molecular dynamics simulations using the ReaxFF reactive force field

    E-print Network

    Goddard III, William A.

    Thermal decomposition process in algaenan of Botryococcus braunii race L. Part 2: Molecular simulation results on pyrolysis of a molecular model of the algaenan Botryococcus braunii race L biopolymer cracking process within algaenan race L biopolymers. The simulations indicate that the thermal

  14. Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure Modes from Reactive Dynamics

    E-print Network

    Goddard III, William A.

    ,*, and Huai Sun Computational Chemistry Group, School of Chemistry and Chemical Engineering, Shanghai Jiao Center (MC 139-74), Chemistry and Chemical Engineering Division, California Institute of Technology, 1200

  15. Nonlinear force-free coronal magnetic field extrapolation scheme based on the direct boundary integral formulation

    Microsoft Academic Search

    Han He; Huaning Wang

    2008-01-01

    The boundary integral equation (BIE) method was first proposed by Yan and Sakurai (2000) and used to extrapolate the nonlinear force-free magnetic field in the solar atmosphere. Recently, Yan and Li (2006) improved the BIE method and proposed the direct boundary integral equation (DBIE) formulation, which represents the nonlinear force-free magnetic field by direct integration of the magnetic field on

  16. Unified Field Theory and Force Formulas of Interactions Tian Ma, Shouhong Wang

    E-print Network

    Wang, Shouhong

    Unified Field Theory and Force Formulas of Interactions Tian Ma, Shouhong Wang Supported in part by NSF, ONR and Chinese NSF http://www.indiana.edu/~fluid I. Two Roads to a Unified Field Theory II. Unified Field Theory of Four Interactions III. Potential and Force Formulas for Strong Interaction IV

  17. Unified Field Equations Coupling Four Forces and Theory of Dark Matter and Dark Energy

    E-print Network

    Wang, Shouhong

    Unified Field Equations Coupling Four Forces and Theory of Dark Matter and Dark Energy Tian Ma II. Principle of Interaction Dynamics III. Unified Field Equations Coupling Four Forces IV. Duality V, June, 2012, http://arxiv.org/abs/1206.5078 2. Tian Ma & Shouhong Wang, Unified Field Equations Coupling

  18. THE PULSATION MODE AND DISTANCE OF THE CEPHEID FF AQUILAE

    SciTech Connect

    Turner, D. G. [Department of Astronomy and Physics, Saint Mary's University, Halifax, NS B3H 3C3 (Canada); Kovtyukh, V. V. [Astronomical Observatory, Odessa National University, and Isaac Newton Institute of Chile, Odessa Branch, T. G. Shevkenko Park, 65014 Odessa (Ukraine); Luck, R. E. [Department of Astronomy, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-7215 (United States); Berdnikov, L. N., E-mail: turner@ap.smu.ca, E-mail: val@deneb1.odessa.ua, E-mail: rel2@case.edu, E-mail: leonid.berdnikov@gmail.com [Sternberg Astronomical Institute, Moscow M. V. Lomonosov State University, Moscow 119992 (Russian Federation)

    2013-07-20

    The determination of pulsation mode and distance for field Cepheids is a complicated problem best resolved by a luminosity estimate. For illustration a technique based on spectroscopic luminosity discrimination is applied to the 4.47 day s-Cepheid FF Aql. Line ratios in high dispersion spectra of the variable yield values of (M{sub V} ) = -3.40 {+-} 0.02 s.e. ({+-}0.04 s.d.), average effective temperature T{sub eff} = 6195 {+-} 24 K, and intrinsic color ((B) - (V)){sub 0} = +0.506 {+-} 0.007, corresponding to a reddening of E{sub B-V} = 0.25 {+-} 0.01, or E{sub B-V}(B0) = 0.26 {+-} 0.01. The skewed light curve, intrinsic color, and luminosity of FF Aql are consistent with fundamental mode pulsation for a small-amplitude classical Cepheid on the blue side of the instability strip, not a sinusoidal pulsator. A distance of 413 {+-} 14 pc is estimated from the Cepheid's angular diameter in conjunction with a mean radius of (R) = 39.0 {+-} 0.7 R{sub Sun} inferred from its luminosity and effective temperature. The dust extinction toward FF Aql is described by a ratio of total-to-selective extinction of R{sub V} = A{sub V} /E(B - V) = 3.16 {+-} 0.34 according to the star's apparent distance modulus.

  19. Modelling of ?- d-glucopyranose ring distortion in different force fields: a metadynamics study

    Microsoft Academic Search

    Vojt?ch Spiwok; Blanka Králová; Igor Tvaroška

    2010-01-01

    Modelling of carbohydrate conformations is a challenging task for force field developers. Three carbohydrate force fields, namely GLYCAM06, GROMOS 45a4 and OPLS were evaluated. Free energies of different ring conformations of ?-d-glucopyranose were calculated using metadynamics in vacuum as well as in explicitly modelled water. All three force fields model the 4C1 conformation as the most stable by at least

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

    PubMed

    Focke, Anne; Stockinger, Christian; Diepold, Christina; Taubert, Marco; Stein, Thorsten

    2013-01-01

    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 N·s/m). Moreover, the arm of the subjects was not supported. A total of 46 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 is needed. PMID:23898319

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

    PubMed Central

    Focke, Anne; Stockinger, Christian; Diepold, Christina; Taubert, Marco; Stein, Thorsten

    2013-01-01

    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 N·s/m). Moreover, the arm of the subjects was not supported. A total of 46 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 is needed. PMID:23898319

  2. FF/C SCRUBBER DEMONSTRATION ON A SECONDARY METALS RECOVERY FURNACE

    EPA Science Inventory

    The paper describes a flux force/condensation (FF/C) scrubbing system that was built to control particulate emissions from a secondary metals recovery furnace. Total mass penetration and fractional penetration measurements were made under several different operating modes. The pe...

  3. Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields

    E-print Network

    Leontyev, Igor

    2015-01-01

    Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM,...

  4. Changes in corticospinal excitability during reach adaptation in force fields

    PubMed Central

    Ahmadi-Pajouh, Mohammad Ali; Harran, Michelle D.; Salimpour, Yousef; Shadmehr, Reza

    2013-01-01

    Both abrupt and gradually imposed perturbations produce adaptive changes in motor output, but the neural basis of adaptation may be distinct. Here, we measured the state of the primary motor cortex (M1) and the corticospinal network during adaptation by measuring motor-evoked potentials (MEPs) before reach onset using transcranial magnetic stimulation of M1. Subjects reached in a force field in a schedule in which the field was introduced either abruptly or gradually over many trials. In both groups, by end of the training, muscles that countered the perturbation in a given direction increased their activity during the reach (labeled as the on direction for each muscle). In the abrupt group, in the period before the reach toward the on direction, MEPs in these muscles also increased, suggesting a direction-specific increase in the excitability of the corticospinal network. However, in the gradual group, these MEP changes were missing. After training, there was a period of washout. The MEPs did not return to baseline. Rather, in the abrupt group, off direction MEPs increased to match on direction MEPs. Therefore, we observed changes in corticospinal excitability in the abrupt but not gradual condition. Abrupt training includes the repetition of motor commands, and repetition may be the key factor that produces this plasticity. Furthermore, washout did not return MEPs to baseline, suggesting that washout engaged a new network that masked but did not erase the effects of previous adaptation. Abrupt but not gradual training appears to induce changes in M1 and/or corticospinal networks. PMID:23034365

  5. The FoldX web server: an online force field

    PubMed Central

    Schymkowitz, Joost; Borg, Jesper; Stricher, Francois; Nys, Robby; Rousseau, Frederic; Serrano, Luis

    2005-01-01

    FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed. PMID:15980494

  6. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

    PubMed Central

    2014-01-01

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+–O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers. PMID:24670003

  7. The stability properties of cylindrical force-free fields - Effect of an external potential field

    NASA Technical Reports Server (NTRS)

    Chiuderi, C.; Einaudi, G.; Ma, S. S.; Van Hoven, G.

    1980-01-01

    A large-scale potential field with an embedded smaller-scale force-free structure gradient x B equals alpha B is studied in cylindrical geometry. Cases in which alpha goes continuously from a constant value alpha 0 on the axis to zero at large r are considered. Such a choice of alpha (r) produces fields which are realistic (few field reversals) but not completely stable. The MHD-unstable wavenumber regime is found. Since the considered equilibrium field exhibits a certain amount of magnetic shear, resistive instabilities can arise. The growth rates of the tearing mode in the limited MHD-stable region of k space are calculated, showing time-scales much shorter than the resistive decay time.

  8. Acoustic radiation force in tissue-like solids due to modulated sound field

    E-print Network

    Guzina, Bojan

    Acoustic radiation force in tissue-like solids due to modulated sound field Egor V. Dontsov, Bojan April 2012 Available online 23 May 2012 Keywords: Acoustic radiation force Nonlinear acoustics Modulated-called acoustic radiation force) in homogeneous tissue-like solids generated by an elevated-intensity, focused

  9. An optimal direct thrust force control for interior Permanent Magnet Linear Synchronous Motors incorporating field weakening

    Microsoft Academic Search

    M. Abroshan; K. Malekian; J. Milimonfared; B. A. Varmiab

    2008-01-01

    This paper presents an optimum direct thrust force control for interior permanent magnet linear synchronous motor (PMLSM) over wide velocity range in which the maximum thrust force per ampere (MTPA) strategy is used below the base velocity and field weakening strategy is used above the base velocity. Using MTPA strategy, copper losses is minimized in constant force region, and using

  10. Influence of the water layer on the shear force damping in near-field microscopy

    E-print Network

    La Rosa, Andres H.

    Influence of the water layer on the shear force damping in near-field microscopy S. Davy,a) M control by shear force detection. © 1998 American Institute of Physics. S0003-6951 98 03244-6 One to the so-called ``shear forces,'' whose exact na- ture is still unclear. They seem to be a combination

  11. PROGRAMMABLE FORCE FIELDS FOR DISTRIBUTED MANIPULATION, AND THEIR IMPLEMENTATION USING

    E-print Network

    in Partial Ful llment of the Requirements for the Degree of Doctor of Philosophy by Karl-Friedrich Bohringer, the programmed force eld induces a force and moment upon it. Over time, the part may come to rest in a dynamic equilibrium analysis. We demon- strate lower bounds i.e., impossibility results on what the devices cannot do

  12. Inertia as a zero-point-field Lorentz force

    Microsoft Academic Search

    Bernhard Haisch; Alfonso Rueda; H. E. Puthoff

    1994-01-01

    Under the hypothesis that ordinary matter is ultimately made of subelementary constitutive primary charged entities or partons'' bound in the manner of traditional elementary Planck oscillators (a time-honored classical technique), it is shown that a heretofore uninvestigated Lorentz force (specifically, the magnetic component of the Lorentz force) arises in any accelerated reference frame from the interaction of the partons with

  13. Force

    NSDL National Science Digital Library

    Mrs. Brownie

    2010-04-07

    Instructions: This is a webquest designed to help students understand force. It is specifically meant to teach the idea that the greater the force applied to an object the greater the change in speed or direction of the object depending on the mass. This is also known as Newton's Second Law of Motion. Lets Learn about Force! For this project your students will understand force. They will use Newton's second law to solve the problem presented. UT Core Curriculum: Science 3rd Grade. Standard 3- Students will understand the relationship between the force applied to an object and resulting motion of the ...

  14. ReaxFF reactive molecular dynamics on silicon pentaerythritol tetranitrate crystal validates the mechanism for the colossal sensitivity.

    PubMed

    Zhou, Tingting; Liu, Lianchi; Goddard, William A; Zybin, Sergey V; Huang, Fenglei

    2014-11-21

    Recently quantum mechanical (QM) calculations on a single Si-PETN (silicon-pentaerythritol tetranitrate) molecule were used to explain its colossal sensitivity observed experimentally in terms of a unique Liu carbon-silyl nitro-ester rearrangement (R3Si-CH2-O-R2? R3Si-O-CH2-R2). In this paper we expanded the study of Si-PETN from a single molecule to a bulk system by extending the ReaxFF reactive force field to describe similar Si-C-H-O-N systems with parameters optimized to reproduce QM results. The reaction mechanisms and kinetics of thermal decomposition of solid Si-PETN were investigated using ReaxFF reactive molecular dynamics (ReaxFF-RMD) simulations at various temperatures to explore the origin of the high sensitivity. We find that at lower temperatures, the decomposition of Si-PETN is initiated by the Liu carbon-silyl nitro-ester rearrangement forming Si-O bonds which is not observed in PETN. As the reaction proceeds, the exothermicity of Si-O bond formation promotes the onset of NO2 formation from N-OC bond cleavage which does not occur in PETN. At higher temperatures PETN starts to react by the usual mechanisms of NO2 dissociation and HONO elimination; however, Si-PETN remains far more reactive. These results validate the predictions from QM that the significantly increased sensitivity of Si-PETN arises from a unimolecular process involving the unusual Liu rearrangement but not from multi-molecular collisions. It is the very low energy barrier and the high exothermicity of the Si-O bond formation providing energy early in the decomposition process that is responsible. PMID:25272955

  15. The lift forces acting on a submarine composite pipeline in a wave-current coexisting field

    SciTech Connect

    Li, Y.C.; Zhang, N.C. [Dalian Univ. of Technology (China). Dept. of Civil Engineering

    1994-12-31

    The composite pipeline is defined as a main big pipe composed with one or several small pipes. The flow behavior around a submarine composite pipeline is more complicated than that around a single submarine pipeline. A series model test of composite pipelines in a wave-current coexisting field was conducted by the authors. Both in-line and lift forces were measured, and the resultant forces are also analyzed. The results of lift forces and resultant forces are reported in this paper. It is found that the lift force coefficients for composite pipelines are well related to the KC number. The lift force coefficients in an irregular wave-current coexisting field are smaller than those in regular wave-current coexisting field. The frequency of lift force is usually the twice or higher than the wave frequency. It is indicated by the authors` test that the resultant forces are larger than in-line forces (horizontal forces) about 10 to 20 percent. The effect of water depth was analyzed. Finally, the relationship between lift force coefficient C{sub l} and KC number, the statistical characteristics of lift and resultant forces, are given in this paper, which may be useful for practical engineering application.

  16. Topology-based inequalities and inverse problems for near force-free magnetic fields

    Microsoft Academic Search

    P. Robert Kotiuga

    2004-01-01

    We review a conjecture characterizing the knotting of current paths arising as solutions to an inverse problem involving near force-free magnetic fields. Results about the nonexistence of solutions involving force-free fields supported in a finite domain are then considered, as are explicit constructions of force-free solutions in unbounded domains. This shows why truncating solutions defined on unbounded domains has proven

  17. Crystallization of aluminum alloys in the presence of vertical electromagnetic force fields

    Microsoft Academic Search

    Charles Vivès

    1997-01-01

    The influence of vertical and steady electromagnetic force fields applied during the solidification of representative aluminum alloys was investigated. The experiments were performed both in the absence and in the presence of electromagnetic body force fields, oriented either upward or downward, and for various degrees of heat extraction rate. Several physical mechanisms of magnetohydrodynamic origin, acting on the macro- and

  18. A reactive force field simulation of liquidliquid phase transitions in phosphorus

    E-print Network

    A reactive force field simulation of liquid­liquid phase transitions in phosphorus P. Ballone 2004; accepted 6 August 2004 A force field model of phosphorus has been developed based on density-ray diffraction measurements1 have identified a liquid-liquid phase transition in phosphorus occurring at high

  19. ENHANCED THERMAL CONDUCTIVITY IN NANOFLUIDS UNDER THE ACTION OF OSCILLATING FORCE FIELDS

    E-print Network

    Paris-Sud XI, Université de

    ENHANCED THERMAL CONDUCTIVITY IN NANOFLUIDS UNDER THE ACTION OF OSCILLATING FORCE FIELDS Clément Le the transportation and energy production to promising fluidic cooling technologies. Considerable efforts have been in what extent the motion of nanoparticles, submit to the action of an external oscillating force field

  20. Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field

    E-print Network

    Buehler, Markus J.

    Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field Alfonso Gautieri, Massachusetts Received January 9, 2010 Abstract: Collagen is the most abundant protein in the human body of collagen molecules. We identify MARTINI force field parameters to describe hydroxyproline amino acid

  1. The forces on small diameter piles in wave-current field

    Microsoft Academic Search

    Huang Ting; Gong Weiming; Dai Guoliang

    2011-01-01

    In the construction process of building great bridge, steel pipe pile is often damaged by wave force. The research on the dynamic response of pile in wave-current field is attractive for practicing engineers. Base on indoor model test, the forces on small diameter piles in the wave-current field were studied in this paper. The model test was carried into execution

  2. Fort Future: Virtual Installation supports rapidly changing needs of armed forces in the field

    E-print Network

    Kemner, Ken

    Fort Future: Virtual Installation supports rapidly changing needs of armed forces in the field FORT quickly to meet rapidly changing support needs of forces in the field. Argonne National Laboratory sup, to determine at any time the level of contamination infiltrating specific buildings based on air-exchange rates

  3. Gait Rehabilitation Therapy Using Robot Generated Force Fields Applied at the Pelvis

    E-print Network

    Mavroidis, Constantinos

    Gait Rehabilitation Therapy Using Robot Generated Force Fields Applied at the Pelvis ABSTRACT The Robotic Gait Rehabilitation (RGR) Trainer was designed and built to target secondary gait deviations tissue dynamics. KEYWORDS: Force field, robotic gait rehabilitation, pelvis. 1 INTRODUCTION Each year

  4. External driver Forced harmonic motion the damped and driven harmonic oscillator

    E-print Network

    Luettmer-Strathmann, Jutta

    m 0 cos fF t External driver Forced harmonic motion ­ the damped and driven harmonic oscillator Restoring force: Fs = ­kx Damping force: Fd = ­cv Driving force: Ff = F0 cos ft Net force: Fnet = ­kx ­cv, driving period Natural frequency of the undamped oscillator Frequency of the underdamped oscillator Assume

  5. Charge Equilibration Force Fields for Molecular Dynamics Simulations of Lipids, Bilayers, and Integral Membrane Protein Systems

    PubMed Central

    Lucas, Timothy R.; Bauer, Brad A.; Patel, Sandeep

    2014-01-01

    With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogues across the water-bilayer interface. PMID:21967961

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

    PubMed

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H

    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. PMID:26178083

  7. 7. FF. Note vertical ribs indicating storage bin inside; conveyor ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. FF. Note vertical ribs indicating storage bin inside; conveyor to left brings pulverized coal from GG to FF; 8 sisters in background. Looking northeast - Rouge Steel Company, 3001 Miller Road, Dearborn, Wayne County, MI

  8. instructions HisTrap FF crude,

    E-print Network

    Lebendiker, Mario

    , and convenient purifications. Short purification time generally minimizes deleterious effects. coli lysates. Table 1. HisTrap FF crude characteristics Matrix Highly cross-linked spherical agarose, 6. Tested for 30 min Avoid in buffers Chelating agents, e.g. EDTA, EGTA, citrate (see Table 2) pH stability

  9. The accurate measurement of a micromechanical force using force-sensitive capacitances

    SciTech Connect

    Wolffenbuttel, M.R.; Regtien, P.P.L. [Delft Univ. of Technology (Netherlands)

    1994-12-31

    A sensor for the precise and accurate measurement of micro-mechanical forces is presented. The sensor is used to detect a tactile image and has capacitive force sensing elements which are detected by charge readout. The mechanical performance of the force sensor is evaluated and verified with experiments. The force-to-deflection and deflection measurements have been separated in order to result in a sensor structure in which the response is linear with force and little affected by fringe fields. The sensor is 0.25 mm{sup 2} in size, it has a force range of 0.25 mN and a capacitance of 2 pF. The amplifier detects capacitance changes of 15 fF with a maximum non-linearity of 0.01 % over the 1.25-2.5 pF range.

  10. J. Phys. Chem. Generalized Extended Empirical BondOrder Dependent Force Fields

    E-print Network

    Çagin, Tahir

    deposition (CVD) of diamond films. 5 Despite its successes, the current form of the Brenner FF has Institute of Technology, Pasadena, California 91125 We present a general approach for describing chemical and hydrocarbon systems. 3\\Gamma5 The Brenner FF has been used for reactions of hydrocarbon species on diamond

  11. Catch trials in force field learning influence adaptation and consolidation of human motor memory

    PubMed Central

    Stockinger, Christian; Focke, Anne; Stein, Thorsten

    2014-01-01

    Force field studies are a common tool to investigate motor adaptation and consolidation. Thereby, subjects usually adapt their reaching movements to force field perturbations induced by a robotic device. In this context, so-called catch trials, in which the disturbing forces are randomly turned off, are commonly used to detect after-effects of motor adaptation. However, catch trials also produce sudden large motor errors that might influence the motor adaptation and the consolidation process. Yet, the detailed influence of catch trials is far from clear. Thus, the aim of this study was to investigate the influence of catch trials on motor adaptation and consolidation in force field experiments. Therefore, 105 subjects adapted their reaching movements to robot-generated force fields. The test groups adapted their reaching movements to a force field A followed by learning a second interfering force field B before retest of A (ABA). The control groups were not exposed to force field B (AA). To examine the influence of diverse catch trial ratios, subjects received catch trials during force field adaptation with a probability of either 0, 10, 20, 30, or 40%, depending on the group. First, the results on motor adaptation revealed significant differences between the diverse catch trial ratio groups. With increasing amount of catch trials, the subjects' motor performance decreased and subjects' ability to accurately predict the force field—and therefore internal model formation—was impaired. Second, our results revealed that adapting with catch trials can influence the following consolidation process as indicated by a partial reduction to interference. Here, the optimal catch trial ratio was 30%. However, detection of consolidation seems to be biased by the applied measure of performance. PMID:24795598

  12. Catch trials in force field learning influence adaptation and consolidation of human motor memory.

    PubMed

    Stockinger, Christian; Focke, Anne; Stein, Thorsten

    2014-01-01

    Force field studies are a common tool to investigate motor adaptation and consolidation. Thereby, subjects usually adapt their reaching movements to force field perturbations induced by a robotic device. In this context, so-called catch trials, in which the disturbing forces are randomly turned off, are commonly used to detect after-effects of motor adaptation. However, catch trials also produce sudden large motor errors that might influence the motor adaptation and the consolidation process. Yet, the detailed influence of catch trials is far from clear. Thus, the aim of this study was to investigate the influence of catch trials on motor adaptation and consolidation in force field experiments. Therefore, 105 subjects adapted their reaching movements to robot-generated force fields. The test groups adapted their reaching movements to a force field A followed by learning a second interfering force field B before retest of A (ABA). The control groups were not exposed to force field B (AA). To examine the influence of diverse catch trial ratios, subjects received catch trials during force field adaptation with a probability of either 0, 10, 20, 30, or 40%, depending on the group. First, the results on motor adaptation revealed significant differences between the diverse catch trial ratio groups. With increasing amount of catch trials, the subjects' motor performance decreased and subjects' ability to accurately predict the force field-and therefore internal model formation-was impaired. Second, our results revealed that adapting with catch trials can influence the following consolidation process as indicated by a partial reduction to interference. Here, the optimal catch trial ratio was 30%. However, detection of consolidation seems to be biased by the applied measure of performance. PMID:24795598

  13. HiTrapTM Phenyl FF (high sub), HiTrap Phenyl FF (low sub), HiTrap Phenyl HP, HiTrap Butyl FF, HiTrap Butyl-S FF, and HiTrap Octyl FF are prepacked 1 ml and 5 ml,

    E-print Network

    Lebendiker, Mario

    HiTrapTM Phenyl FF (high sub), HiTrap Phenyl FF (low sub), HiTrap Phenyl HP, HiTrap Butyl FF, Hi. Instructions 11-0034-52 AB HiTrap HIC columns GE Healthcare HiTrap HIC Columns HiTrap Phenyl FF (high sub), 1 ml and 5 ml HiTrap Phenyl FF (low sub), 1 ml and 5 ml HiTrap Phenyl HP, 1 ml and 5 ml HiTrap Butyl FF

  14. Combustion of 1,5-dinitrobiuret (DNB) in the presence of nitric acid using ReaxFF molecular dynamics simulations.

    PubMed

    Russo, Michael F; Bedrov, Dmitry; Singhai, Shashank; van Duin, Adri C T

    2013-09-26

    In this study we have examined the combustion dynamics of 1,5-dinitrobiuret (DNB) and nitric acid using reactive molecular dynamics simulations. Simulations were performed using the ReaxFF force field with parameters that were fitted against quantum mechanical calculations on model compounds/clusters relevant for this particular chemical system. Several different compositions were investigated, at densities of 0.5 and 1.0 g/mL, to examine the reaction kinetics in a dense vapor and liquid phase of these mixtures. Our simulations show that at certain compositions of the mixture reaction kinetics result in a very sharp release of thermal energy, which we associate with spontaneous ignition or hypergolicity. Analysis of key reaction mechanisms responsible for this process is discussed. PMID:23985064

  15. The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube.

    PubMed

    Jensen, Benjamin D; Wise, Kristopher E; Odegard, Gregory M

    2015-08-01

    As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon-based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress-strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress-strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed. © 2015 Wiley Periodicals, Inc. PMID:26096628

  16. Error analysis regarding the calculation of nonlinear force-free field

    NASA Astrophysics Data System (ADS)

    Liu, S.; Zhang, H. Q.; Su, J. T.

    2012-02-01

    Magnetic field extrapolation is an alternative method to study chromospheric and coronal magnetic fields. In this paper, two semi-analytical solutions of force-free fields (Low and Lou in Astrophys. J. 352:343, 1990) have been used to study the errors of nonlinear force-free (NLFF) fields based on force-free factor ?. Three NLFF fields are extrapolated by approximate vertical integration (AVI) Song et al. (Astrophys. J. 649:1084, 2006), boundary integral equation (BIE) Yan and Sakurai (Sol. Phys. 195:89, 2000) and optimization (Opt.) Wiegelmann (Sol. Phys. 219:87, 2004) methods. Compared with the first semi-analytical field, it is found that the mean values of absolute relative standard deviations (RSD) of ? along field lines are about 0.96-1.19, 0.63-1.07 and 0.43-0.72 for AVI, BIE and Opt. fields, respectively. While for the second semi-analytical field, they are about 0.80-1.02, 0.67-1.34 and 0.33-0.55 for AVI, BIE and Opt. fields, respectively. As for the analytical field, the calculation error of <| RSD|> is about 0.1˜0.2. It is also found that RSD does not apparently depend on the length of field line. These provide the basic estimation on the deviation of extrapolated field obtained by proposed methods from the real force-free field.

  17. The influence of centrifugal forces on the B field structure of an axially symmetric equilibrium magnetosphere

    NASA Technical Reports Server (NTRS)

    Ye, Gang; Voigt, Gerd-Hannes

    1989-01-01

    A model is presented of an axially symmetric pole-on magnetosphere in MHD force balance, in which both plasma thermal pressure gradients and centrifugal force are taken into account. Assuming that planetary rotation leads to differentially rotating magnetotail field lines, the deformation of magnetotail field lines under the influence of both thermal plasma pressure and centrifugal forces was calculated. Analytic solutions to the Grad-Shafranov equation are presented, which include the centrifugal force term. It is shown that the nonrotational magnetosphere with hot thermal plasma leads to a field configuration without a toroidal B(phi) component and without field-aligned Birkeland currents. The other extreme, a rapidly rotating magnetosphere with cold plasma, leads to a configuration in which plasma must be confined within a thin disk in a plane where the radial magnetic field component B(r) vanishes locally.

  18. Developing the Pulsed Fission-Fusion (PuFF) Engine

    NASA Technical Reports Server (NTRS)

    Adams, Robert B.; Cassibry, Jason; Bradley, David; Fabisinski, Leo; Statham, Geoffrey

    2014-01-01

    In September 2013 the NASA Innovative Advanced Concept (NIAC) organization awarded a phase I contract to the PuFF team. Our phase 1 proposal researched a pulsed fission-fusion propulsion system that compressed a target of deuterium (D) and tritium (T) as a mixture in a column, surrounded concentrically by Uranium. The target is surrounded by liquid lithium. A high power current would flow down the liquid lithium and the resulting Lorentz force would compress the column by roughly a factor of 10. The compressed column would reach criticality and a combination of fission and fusion reactions would occur. Our Phase I results, summarized herein, review our estimates of engine and vehicle performance, our work to date to model the fission-fusion reaction, and our initial efforts in experimental analysis.

  19. Pull-in control due to Casimir forces using external magnetic fields

    NASA Astrophysics Data System (ADS)

    Esquivel-Sirvent, R.; Palomino-Ovando, M. A.; Cocoletzi, G. H.

    2009-08-01

    We present a theoretical calculation of the pull-in control in capacitive microswitches actuated by Casimir forces using external magnetic fields. The external magnetic fields induce an optical anisotropy due to the excitation of magnetoplasmons that reduces the Casimir force. The calculations are performed in the Voigt configuration and the results show that as the magnetic field increases the system becomes more stable. The detachment length for a cantilever is also calculated for a cantilever, showing that it increases with increasing magnetic field. At the pull-in separation, the stiffness of the system decreases with the increasing magnetic field.

  20. Global constant-alpha force-free magnetic fields and coronal structures

    NASA Technical Reports Server (NTRS)

    Nakagawa, Y.; Wu, S. T.; Tandberg-Hanssen, E.

    1978-01-01

    Nakagawa's (1973) general formulation of constant-alpha global force-free magnetic fields is used to examine the topological characteristics of axisymmetric constant-alpha fields with specific reference to solar EUV, XUV, and X-ray structures observed from Skylab. The theoretical formulation is briefly summarized, and topological characteristics of the field lines are analyzed. The results are compared with X-ray observations of a large coronal arch and white-light observations of a coronal transient. It is concluded that global-scale force-free magnetic fields are present in the solar atmosphere and that their topological characteristics differ significantly from those of potential fields.

  1. Pull-in control due to Casimir forces using external magnetic fields

    E-print Network

    R. Esquivel-Sirvent; M. A. Palomino-Ovando; G. H. Cocoletzi

    2009-07-13

    We present a theoretical calculation of the pull-in control in capacitive micro switches actuated by Casimir forces, using external magnetic fields. The external magnetic fields induces an optical anisotropy due to the excitation of magneto plasmons, that reduces the Casimir force. The calculations are performed in the Voigt configuration, and the results show that as the magnetic field increases the system becomes more stable. The detachment length for a cantilever is also calculated for a cantilever, showing that it increases with increasing magnetic field. At the pull-in separation, the stiffness of the system decreases with increasing magnetic field.

  2. Dynamics of a rigid body in an inhomogenous force field

    Microsoft Academic Search

    Andreas Resch; Claus Laemmerzahl; Dennis Lorek; Isabell Schaffer

    2008-01-01

    Extended rigid bodies do not move on geodesics but couple to the space-time curvature. We discuss this effect at the Newtonian level where the deviation from the ordinary Keplerian orbits occurs in two ways: we obtain an additional force in the equation of motion for the center-of-mass and a torque acting on the rotational degrees of freedom. We give a

  3. Introducing dielectrophoresis as a new force field for field-flow fractionation.

    PubMed Central

    Huang, Y; Wang, X B; Becker, F F; Gascoyne, P R

    1997-01-01

    We present the principle of cell characterization and separation by dielectrophoretic field-flow fractionation and show preliminary experimental results. The operational device takes the form of a thin chamber in which the bottom wall supports an array of microelectrodes. By applying appropriate AC voltage signals to these electrodes, dielectrophoretic forces are generated to levitate cells suspended in the chamber and to affect their equilibrium heights. A laminar flow profile is established in the chamber so that fluid flows faster with increasing distance from the chamber walls. A cell carried in the flow stream will attain an equilibrium height, and a corresponding velocity, based on the balance of dielectrophoretic, gravitational, and hydrodynamic lift forces it experiences. We describe a theoretical model for this system and show that the cell velocity is a function of the mean fluid velocity, the voltage and frequency of the signals applied to the electrodes, and, most significantly, the cell dielectric properties. The validity of the model is demonstrated with human leukemia (HL-60) cells subjected to a parallel electrode array, and application of the device to separating HL-60 cells from peripheral blood mononuclear cells is shown. PMID:9251828

  4. Electromagnetic Field Tensor and Lorentz Force as Consequence of the Geometry of Minkowskian Spacetime

    E-print Network

    J. Buitrago; Chus Martin

    1999-05-20

    We show that the electromagnetic field tensor and the Lorentz Force are both a natural consequence of the geometric structure of Minkowskian space, being related to infinitesimal boosts and rotations in spacetime. The longstanding issue about the apparent empirical origin of the Lorentz Force is clarified.

  5. Electromagnetic Forces on a Metal Disk in an Alternating Magnetic Field

    Microsoft Academic Search

    Samir Basu; K. D. Srivastava

    1969-01-01

    Many fast-acting electromechanical devices utilize the repulsion forces produced on a metal disk subjected to a transient magnetic field. Coupled circuit theory yields a simple expression for this force in terms of an equivalent inductance. The equivalent inductance, however, is difficult to evaluate by theoretical and\\/or experimental methods when the metal disk is very close to the magnet coil. A

  6. The force acting on a polarizable nanoparticle in the quantized electromagnetic field

    E-print Network

    Vanik E. Mkrtchian

    2009-01-14

    In this letter we derive an expression for the force acting on a small (still macroscopic) particle in the field of the quantized electromagnetic radiation in any arbitrary quantum state. This result unifies in one simple formula all known expressions for the forces (i.e. van der Waals or frictional) acting on a small particle.

  7. A STUDY OF FORCE IN A STEADY MAGNETIC FIELD WITH ASYMPTOTIC BOUNDARY CONDITIONS

    Microsoft Academic Search

    Saul PASARE

    In this paper there is performed a comparative study of the force that acts over a mobile coil pierced by current when it is placed in an external steady magnetic field. Firstly the determination of force is performed through analytic calculations and by experiments over a physical model from the Faculty of Electrotechnics, University of Craiova. The determined values are

  8. Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields

    Microsoft Academic Search

    Toby W. Allen; Turgut Ba?tu?; Serdar Kuyucak; Shin-Ho Chung

    2003-01-01

    We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K+ ion is calculated along

  9. Management of Social Incentives in Air Force Technical Training: A Field Experiment. Final Report.

    ERIC Educational Resources Information Center

    Hakel, Milton D.; And Others

    The report is a study of the utility of social reinforcement for improving Air Force training. It was conducted through a field evaluation of social incentive instructional systems which would serve to improve student motivation, classroom performance, and attitudes. The participants included a total of 300 trainees from two Air Force bases; 25…

  10. The Sensitivity of Simulated Ocean Biogeochemistry to Forcing Fields Derived from NCEP and MERRA Reanalysis Products

    Microsoft Academic Search

    W. W. Gregg

    2010-01-01

    Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in

  11. Nonlinear restoring forces and geometry influence on stability in near-field acoustic levitation

    E-print Network

    Cao, Wenwu

    Nonlinear restoring forces and geometry influence on stability in near-field acoustic levitation; published online 22 April 2011) Stability is a key factor in near-field acoustic levitation (NFAL), which is preferred. Near- field acoustic levitation (NFAL) is one of the most suitable methods for noncontact

  12. Nonideal evolution of nonaxisymmetric, force-free magnetic fields in a magnetar

    E-print Network

    Alpha Mastrano; Andrew Melatos

    2008-04-25

    Recent numerical magnetohydrodynamic calculations by Braithwaite and collaborators support the `fossil field' hypothesis regarding the origin of magnetic fields in compact stars and suggest that the resistive evolution of the fossil field can explain the reorganisation and decay of magnetar magnetic fields. Here, these findings are modelled analytically by allowing the stellar magnetic field to relax through a quasistatic sequence of nonaxisymmetric, force-free states, by analogy with spheromak relaxation experiments, starting from a random field. Under the hypothesis that the force-free modes approach energy equipartition in the absence of resistivity, the output of the numerical calculations is semiquantitatively recovered: the field settles down to a linked poloidal-toroidal configuration, which inflates and becomes more toroidal as time passes. A qualitatively similar (but not identical) end state is reached if the magnetic field evolves by exchanging helicity between small and large scales according to an $\\alpha$-dynamo-like, mean-field mechanism, arising from the fluctuating electromotive force produced by the initial random field. The impossibility of matching a force-free internal field to a potential exterior field is discussed in the magnetar context.

  13. UNIFIED FIELD EQUATIONS COUPLING FOUR FORCES AND PRINCIPLE OF INTERACTION DYNAMICS

    E-print Network

    Wang, Shouhong

    UNIFIED FIELD EQUATIONS COUPLING FOUR FORCES AND PRINCIPLE OF INTERACTION DYNAMICS TIAN MA dynamics (PID) and to derive unified field equations coupling the four fundamental interactions based) principle of principle of representation invari- ance (PRI), introduced in [11]. The unified field equations

  14. 78 FR 29378 - Aquatic Nuisance Species Task Force; Public Teleconference/Webinar

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-20

    ...FXFR133609ANS09-FF09F14000-134] Aquatic Nuisance Species Task Force; Public Teleconference/ Webinar AGENCY: Fish...teleconference/webinar of the Aquatic Nuisance Species Task Force (ANS Task Force). The ANS Task Force's purpose is to...

  15. Water properties from first principles: Simulations by a general-purpose quantum mechanical polarizable force field

    PubMed Central

    Donchev, A. G.; Galkin, N. G.; Illarionov, A. A.; Khoruzhii, O. V.; Olevanov, M. A.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, V. I.

    2006-01-01

    We have recently introduced a quantum mechanical polarizable force field (QMPFF) fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here, we present an improved form of the force field, QMPFF2, and apply it to simulations of liquid water. The results of the simulations show excellent agreement with a variety of experimental thermodynamic and structural data, as good or better than that provided by specialized water potentials. In particular, QMPFF2 is the only ab initio force field to accurately reproduce the anomalous temperature dependence of water density to our knowledge. The ability of the same force field to successfully simulate the properties of both organic molecules and water suggests it will be useful for simulations of proteins and protein–ligand interactions in the aqueous environment. PMID:16723394

  16. Numerical Investigation of Flow Fields and Forces for 2-D Squeeze Film Dampers

    E-print Network

    Neadkratoke, Terdsak

    2011-08-08

    A numerical method is used to predict flow fields and forces for squeeze film dampers (SFDs). A two dimensional SFD is modeled with different amplitudes and frequencies of the journal orbiting inside the wall. In addition to the typical circular...

  17. Magnetic field effects in the Casimir force between two parallel anti-ferromagnetic slabs

    NASA Astrophysics Data System (ADS)

    Palomino-Ovando, M.; Kinto-Ramírez, H.; Cocoletzi, Gregorio H.

    2008-03-01

    We study the Casimir force F between two parallel anti-ferromagnetic slabs taking into account an external magnetic field in the Voigt configuration. Using a frequency and magnetic field dependent magnetic permeability tensor and a frequency independent dielectric permittivity, to describe the slabs, we calculate the Casimir force using non-normal incidence reflectivity of the electromagnetic waves in the free space between the slabs. We determine the Casimir force by performing two-dimensional calculations. F is investigated as a function of the layer thickness d, the vacuum gap width L between slabs, and the external magnetic field strength H. Features of F as function of the external field include the presence of sharp dips and peaks, which appear in the vicinity of the resonance frequency, and are consequences of the interaction of the external magnetic field with the electron spin. In addition, an external field may diminish F, which is an important effect not found in any other system.

  18. Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field

    Microsoft Academic Search

    J. Sarzy?ska; T. Kuli?ski

    2005-01-01

    A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acids was developed for 2-thiouracil and 4-thiouracil, two naturally modified RNA bases. The new parameters allow for molecular modeling and molecular dynamics simulations of RNA containing 2-thiouracil and 4-thiouracil. Over the last several years, the main goal of molecular biology became the understanding

  19. The 1B2u excited state of benzene: Force field and normal coordinates

    Microsoft Academic Search

    M. J. Robey; E. W. Schlag

    1977-01-01

    A complete valence force field is presented for the 1B2u excited state of benzene. Perprotonated and perdeuterated isotopes were used in the refinement which matches known frequencies to within one half percent. New excited state vibrational frequencies from two-photon spectroscopy enable reliable planar and out-of-plane force fields to be calculated. The frequencies of experimentally unobserved vibrational modes are given with

  20. Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

    Microsoft Academic Search

    Matthias Buck; Sabine Bouguet-Bonnet; Richard W. Pastor; Alexander D. MacKerell Jr.

    2006-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25ns 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

  1. Forces

    NSDL National Science Digital Library

    The representation depicts what forces are and how they can change the motion and shape of objects in an animated slide show. This resource also includes an interactive test and review of the material, and can be downloaded for offline use.

  2. Refining classical force fields for ionic liquids: theory and application to [MMIM][Cl].

    PubMed

    Dommert, Florian; Holm, Christian

    2013-02-14

    Most of the force fields for ionic liquids cannot properly describe statics and dynamics. In this context, we propose an efficient method to adapt force fields, the basis of any classical molecular dynamics simulation. In the parameterisation process, a target function is minimized by a conjugate gradient based approach that vastly accelerates the tuning of the force field parameters through parallelization. As the description of the dynamics is captured in the parameterisation of the partial charges, we fit the short range parameters using only static properties, thus avoiding long simulations for the force field refinement. In the validation of the final parameterisation, the force field gives a good description of the dynamics in terms of the conductivity, especially in the temperature regime where the reference properties are matched very accurately. This method is sufficiently general and easily altered to fit an arbitrary set of reference properties, such that it can be considered for the construction of a versatile, transferable force field for ionic liquids. PMID:23262645

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

    PubMed

    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

    2014-12-28

    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. PMID:25554163

  4. Casimir forces between arbitrary compact objects: Scalar and electromagnetic field

    E-print Network

    T. Emig; R. L. Jaffe

    2007-10-26

    We develop an exact method for computing the Casimir energy between arbitrary compact objects, both with boundary conditions for a scalar field and dielectrics or perfect conductors for the electromagnetic field. The energy is obtained as an interaction between multipoles, generated by quantum source or current fluctuations. The objects' shape and composition enter only through their scattering matrices. The result is exact when all multipoles are included, and converges rapidly. A low frequency expansion yields the energy as a series in the ratio of the objects' size to their separation. As examples, we obtain this series for two spheres with Robin boundary conditions for a scalar field and dielectric spheres for the electromagnetic field. The full interaction at all separations is obtained for spheres with Robin boundary conditions and for perfectly conducting spheres.

  5. Force acting on an atom and a classical oscillator in an electromagnetic field

    SciTech Connect

    Makarov, V. P., E-mail: vpmac@ran.gpi.ru; Rukhadze, A. A., E-mail: rukh@fpl.gpi.ru [Russian Academy of Sciences, Prokhorov General Physics Institute (Russian Federation)

    2010-01-15

    The expression for the force exerted by the field on an atom and averaged over the field period is derived in quantum-mechanical perturbation theory, in which a quasi-monochromatic electromagnetic field plays the role of a perturbation. An approximate solution is obtained to the classical (Newton) equation of motion in the same field for a harmonic isotropic oscillator. In both problems, the expressions for the force acting on a particle are completely identical if they are written in terms of the polarizability (of the atom and the oscillator). These results conform with the data obtained in macroscopic electrodynamics for rarefied media.

  6. Asymptotic analysis of force-free magnetic fields of cylindrical symmetry

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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, in the process, the energy of the field increases progressively. Analysis of a simple model of force-free fields of cylindrical symmetry leads to simple asymptotic expressions for the extent and energy of such a configuration. The analysis is carried through for both spherical and planar source surfaces. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.

  7. Controlling the optical dipole force for molecules with field-induced alignment

    SciTech Connect

    Purcell, S. M.; Barker, P. F. [Department of Physics and Astronomy, University College London, London, WC1E 6BT (United Kingdom)

    2010-09-15

    We measure the role of field-induced alignment on the dipole force for molecules using a single focused nonresonant laser beam. We show that through the alignment process we can modify the effective polarizability by field polarization and thus control the center-of-mass motion of the molecule. We observe a maximum change of 20% in the dipole force on CS{sub 2} molecules when changing from linearly to circularly polarized light. Additionally, the effect of the dipole force on different vibrational states is also studied.

  8. Cluster evolution during the early stages of heating explosives and its relationship to sensitivity: a comparative study of TATB, ?-HMX and PETN by molecular reactive force field simulations.

    PubMed

    Wen, Yushi; Zhang, Chaoyang; Xue, Xianggui; Long, Xinping

    2015-04-29

    Clustering is experimentally and theoretically verified during the complicated processes involved in heating high explosives, and has been thought to influence their detonation properties. However, a detailed description of the clustering that occurs has not been fully elucidated. We used molecular dynamic simulations with an improved reactive force field, ReaxFF_lg, to carry out a comparative study of cluster evolution during the early stages of heating for three representative explosives: 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), ?-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and pentaerythritol tetranitrate (PETN). These representatives vary greatly in their oxygen balance (OB), molecular structure, stability and experimental sensitivity. We found that when heated, TATB, HMX and PETN differ in the size, amount, proportion and lifetime of their clusters. We also found that the clustering tendency of explosives decreases as their OB becomes less negative. We propose that the relationship between OB and clustering can be attributed to the role of clustering in detonation. That is, clusters can form more readily in a high explosive with a more negative OB, which retard its energy release, secondary decomposition, further decomposition to final small molecule products and widen its detonation reaction zone. Moreover, we found that the carbon content of the clusters increases during clustering, in accordance with the observed soot, which is mainly composed of carbon as the final product of detonation or deflagration. PMID:25872486

  9. Analysis of degradation mechanism of disperse orange 25 in supercritical water oxidation using molecular dynamic simulations based on the reactive force field.

    PubMed

    Zhang, Jinli; Gu, Jintao; Han, You; Li, Wei; Gan, Zhongxue; Gu, Junjie

    2015-03-01

    4-[N-(2-cyanoethyl)-N-ethylamino]-4'-nitroazo-benzene (disperse orange 25, DO25) is one of the main components in dyeing wastewater. In this work, supercritical water oxidation (SCWO) process of DO25 has been investigated using the molecular dynamic simulations based on the reactive force field (ReaxFF). For the SCWO system, the effects of temperature, the molecular ratio of DO25, O2 and H2O as well as the reaction time have been analyzed. The simulated results showed that the aromatic rings in DO25 could be attacked by hydroxyl radical, oxygen molecule, and hydroxyl radical together with oxygen molecule, respectively, which caused the aromatic ring-opening reaction to happen mainly through three different pathways. The hydroxyl radicals were mainly from water clusters and H2O2 (which was produced from oxygen molecules reacting with water clusters). However, for the SCW system as comparison, the aromatic rings in DO25 could be attacked by hydroxyl radical only, and the OH radicals just come from water clusters. During the DO25 SCWO degradation process, we also found that N elements in one DO25 molecule were difficult to be converted into environmentally friendly N2 molecules because of steric hindrance, but increasing the number of DO25 molecules could improve the possibility for the connection of N elements, thus promoting N element converting into N2. Extending reaction time could also improve N elements in DO25 to transform into N2 rather than carbonitride. PMID:25701086

  10. Particle diffusion and energization in Arnold-Beltrami-Childress force-free helical magnetic fields

    NASA Astrophysics Data System (ADS)

    Dasgupta, B.; Holguin, F.; Ram, A. K.; Mitra, D.

    2013-10-01

    It has long been considered that the cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The Arnold-Beltrami-Childress (ABC) field is an example of a force-free helical magnetic field. The ABC magnetic field lines exhibit a complex and varied structure and can be chaotic. The motion of charged particles in regions of spatially chaotic ABC magnetic field lines displays a variety of dynamical behavior depending on the particle's energy and its initial direction of motion with respect to the local magnetic field vector. Particles started on chaotic magnetic field lines do not necessarily follow chaotic orbits. A class of particles executes periodic motion. For steady-state ABC fields the particles diffuse in space. For time-dependent ABC fields the particles gain energy for extended time periods-the mean kinetic energy has a power-law behavior in time. We present results on the dynamics of particles, and on their spatial diffusion and velocity space energization in ABC fields. It has long been considered that the cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The Arnold-Beltrami-Childress (ABC) field is an example of a force-free helical magnetic field. The ABC magnetic field lines exhibit a complex and varied structure and can be chaotic. The motion of charged particles in regions of spatially chaotic ABC magnetic field lines displays a variety of dynamical behavior depending on the particle's energy and its initial direction of motion with respect to the local magnetic field vector. Particles started on chaotic magnetic field lines do not necessarily follow chaotic orbits. A class of particles executes periodic motion. For steady-state ABC fields the particles diffuse in space. For time-dependent ABC fields the particles gain energy for extended time periods-the mean kinetic energy has a power-law behavior in time. We present results on the dynamics of particles, and on their spatial diffusion and velocity space energization in ABC fields. Supported by DoE, NSF, European Research Council, and Swedish Research Council.

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

    PubMed Central

    2015-01-01

    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 subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

  12. BIOREMEDIATION FIELD EVALUATION - HILL AIR FORCE BASE, UTAH

    EPA Science Inventory

    In 1990, the U.S. Environmental Protection Agency (EPA) established the Bioremediation Field Initiative as part of its overall strategy to increase the use of bioremediation to treat hazardous wastes at Comprehensive Environmental Response, Compensation, and Liabil- ity Act (C...

  13. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy

    NASA Astrophysics Data System (ADS)

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-07-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results.

  14. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy.

    PubMed

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-08-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results. PMID:24953042

  15. Strong gravitational force induced by static electromagnetic fields

    E-print Network

    B. V. Ivanov

    2004-07-13

    It is argued that static electric or magnetic fields induce Weyl-Majumdar-Papapetrou solutions for the metric of spacetime. Their gravitational acceleration includes a term many orders of magnitude stronger than usual perturbative terms. It gives rise to a number of effects, which can be detected experimentally. Four electrostatic and four magnetostatic examples of physical set-ups with simple symmetries are proposed. The different ways in which mass sources enter and complicate the pure electromagnetic picture are described.

  16. Phase-field simulations of dendritic crystal growth in a forced flow C. Beckermann,1,

    E-print Network

    Beckermann, Christoph

    by crystal- line anisotropy in the tip selection, and this theory has been confirmed by phase-fieldPhase-field simulations of dendritic crystal growth in a forced flow X. Tong,1 C. Beckermann,1, * A; published 15 May 2001 Convective effects on free dendritic crystal growth into a supercooled melt in two

  17. FIELD EXPERIMENTATION OF COTS-BASED UAV NETWORKING Air Force Research Laboratory

    E-print Network

    Kung, H. T.

    1 of 7 FIELD EXPERIMENTATION OF COTS-BASED UAV NETWORKING Dan Hague Air Force Research Laboratory Vehicles (UAVs). This new capability has inspired many novel application ideas in UAV networking. We argue that field experimentation of UAV networking is essential in collecting link meas- urement data, developing

  18. Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force

    PubMed Central

    Cheng, Hsiao-Bing; Cheng, Li-Tien; Li, Bo

    2013-01-01

    A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends non-trivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability, and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation. PMID:23853423

  19. Forcing a Global, Offline Land Surface Modeling System with Observation-Based Fields

    NASA Technical Reports Server (NTRS)

    Rodell, Matthew; Houser, Paul R.; Jambor, U.; Gottschalck, J.; Radakovich, J.; Arsenault, K.; Meng, C.-J.; Mitchell, K. E.

    2002-01-01

    The Global Land Data Assimilation System (GLDAS) drives multiple uncoupled land surface models in order to produce optimal output fields of surface states in near-real time, globally, at 1/4 degree spatial resolution. These fields are then made available for coupled atmospheric model initialization and further research. One of the unique aspects of GLDAS is its ability to ingest both modeled and observation-derived forcing for running global scale land surface models. This paper compares results of runs forced by modeled and observed precipitation and shortwave radiation fields. Differences are examined and the impact of the observations on model skill is assessed.

  20. Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

    SciTech Connect

    Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

    2012-05-09

    Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

  1. Unsteady hydrodynamic forces acting on a robotic hand and its flow field.

    PubMed

    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. PMID:23764175

  2. Modeling of Centrifugal Force Field and the Effect on Filling and Solidification in Centrifugal Casting

    NASA Astrophysics Data System (ADS)

    Sheng, Wenbin; Ma, Chunxue; Gu, Wanli

    2011-06-01

    Based on the steady flow in a tube, a mathematical model has been established for the consideration of centrifuging force field by combining the equations of continuity, conservation of momentum and general energy. Effects of centrifugal field on the filling and solidification are modeled by two accessional terms: centrifugal force and Chorios force. In addition, the transfer of heat by convection is considered to achieve a coupling calculation of velocity field and temperature field. The solution of pressure item is avoided by introducing the stream function ?(x,y) and the eddy function ?(x,y). Corresponding difference formats for the simultaneous equations of centrifugal filling, the accessional terms and the solidifying latent heat have been established by the finite difference technique. Furthermore, the centrifugal filling and solidification processes in a horizontal tube are summarized to interpret the mechanism by which internal defects are formed in centrifugal castings.

  3. Tethyan collision forces and the stress field of the Eurasian Plate

    NASA Astrophysics Data System (ADS)

    Warners-Ruckstuhl, Karin N.; Govers, Rob; Wortel, Rinus

    2013-10-01

    Resistive forces along convergent plate boundaries have a major impact on surface deformation, most visibly at collisional plate boundaries. Although quantification of these forces is key to understanding the evolution and present state of mountain belts, they remain highly uncertain due to the complexity of plate boundary structures and rheologies. In previous studies of the Eurasian Plate, we have analysed the balance of plate boundary forces, tractions resulting from lithosphere-mantle coupling, and intraplate variations in topography and density structure. This yielded a range of acceptable force distributions. In this study, we investigate to which extent the observed present-day stress field provides further constraints on the distribution of forces. We address the dynamics of the Eurasian Plate as a whole. This enables us to base our analysis on mechanical equilibrium of a tectonic plate and to evaluate all forces as part of an internally consistent set of forces driving and deforming Eurasia. We incorporate tractions from convective mantle flow modelling in a lithospheric model in which edge and lithospheric body forces are modelled explicitly and compute resulting stresses in a homogeneous elastic thin shell. Intraplate stress observations used are from the World Stress Map project. Eurasia's stress field turns out to be particularly sensitive to the distribution of collision forces on the plate's southern margin and, to a much lesser extent, to lithospheric density structure and tractions from mantle flow. Stress observations require collision forces on the India-Eurasia boundary of 7.0-10.5 TN m-1 and on the Arabia-Eurasia boundary of 1.3-2.7 TN m-1. Implication of mechanical equilibrium of the plate is that forces on the contacts with the African and Australian plates amount to 1.0-2.5 and 0-1.3 TN m-1, respectively. We use our results to assess the validity of the classical view that the mean elevation of an orogenic plateau can be taken as a measure of the magnitude of the compressive (in this case: collision-related) forces involved. For both the Tibetan and the Iranian plateaus, two plateaus with significantly different average elevations, we find that the horizontal force derived from the excess gravitational potential energy (collapse force) is in balance with the collision force.

  4. Vacuum force for a massive scalar field in a multiply warped braneworld

    NASA Astrophysics Data System (ADS)

    Ceron, V. E.; Hernández, Héctor H.; López, L. A.; Pedraza, Omar

    2014-11-01

    We determine the finite temperature Casimir force for a scalar massive field for a pair of parallel plates in a 6D non-factorizable geometry. In this contribution we use the Green's function method to determine the Casimir force. It can be expressed in terms of two four-dimensional Casimir force contributions: one for the zero mode and the other for a tower of massive modes associated with the extra dimensions. An uncertainty band of 10% around the theoretical standard 4D Casimir force was set up, by limiting the effective 4D Casimir force within such band yields the bound k/rz gg 1.97 × 106 TeV.

  5. The Sensitivity of Simulated Ocean Biogeochemistry to Forcing Fields Derived from NCEP and MERRA Reanalysis Products

    NASA Technical Reports Server (NTRS)

    Gregg, Watson; Casey, Nancy

    2010-01-01

    Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in addition to aerosol and cloud information which is derived from satellite data). The question posed here is, does the choice of reanalysis products make a difference in the representation of ocean biology and biogeochemistry? NOBM was forced by NCEP and MERRA reanalysis products for the period 2002-2009. We find that in 2009 global distributions and abundances of biological variables (total chlorophyll and nutrients) and carbon (dissolved inorganic and organic carbon and surface pCO2) were similar between the two different forcing fields. Global statistical comparisons with satellite and in situ data also showed negligible differences.

  6. Force-field parameterization of the galactic cosmic ray spectrum: Validation for Forbush decreases

    NASA Astrophysics Data System (ADS)

    Usoskin, I. G.; Kovaltsov, G. A.; Adriani, O.; Barbarino, G. C.; Bazilevskaya, G. A.; Bellotti, R.; Boezio, M.; Bogomolov, E. A.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bruno, A.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; De Donato, C.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A. M.; Karelin, A. V.; Koldashov, S. V.; Koldobskiy, S.; Krutkov, S. Y.; Kvashnin, A. N.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A. G.; Menn, W.; Mergé, M.; Mikhailov, V. V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Pizzolotto, C.; Ricci, M.; Ricciarini, S. B.; Rossetto, L.; Sarkar, R.; Scotti, V.; Simon, M.; Sparvoli, R.; Spillantini, P.; Stozhkov, Y. I.; Vacchi, A.; Vannuccini, E.; Vasilyev, G. I.; Voronov, S. A.; Yurkin, Y. T.; Zampa, G.; Zampa, N.; Zverev, V. G.

    2015-06-01

    A useful parametrization of the energy spectrum of galactic cosmic rays (GCR) near Earth is offered by the so-called force-field model which describes the shape of the entire spectrum with a single parameter, the modulation potential. While the usefulness of the force-field approximation has been confirmed for regular periods of solar modulation, it was not tested explicitly for disturbed periods, when GCR are locally modulated by strong interplanetary transients. Here we use direct measurements of protons and ? -particles performed by the PAMELA space-borne instrument during December 2006, including a major Forbush decrease, in order to directly test the validity of the force-field parameterization. We conclude that (1) The force-field parametrization works very well in describing the energy spectra of protons and ? -particles directly measured by PAMELA outside the Earths atmosphere; (2) The energy spectrum of GCR can be well parameterized by the force-field model also during a strong Forbush decrease; (3) The estimate of the GCR modulation parameter, obtained using data from the world-wide neutron monitor network, is in good agreement with the spectra directly measured by PAMELA during the studied interval. This result is obtained on the basis of a single event analysis, more events need to be analyzed.

  7. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.

    PubMed

    Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

    2015-07-01

    Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results. PMID:26009297

  8. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.

    PubMed

    Götz, Andreas W; Bucher, Denis; Lindert, Steffen; McCammon, J Andrew

    2014-04-01

    The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem. 2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks. PMID:24803868

  9. The rate of separation of magnetic lines of force in a random magnetic field.

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.

    1973-01-01

    The mixing of magnetic lines of force, as represented by their rate of separation, as a function of distance along the magnetic field, is considered with emphasis on neighboring lines of force. This effect is particularly important in understanding the transport of charged particles perpendicular to the average magnetic field. The calculation is carried out in the approximation that the separation changes by an amount small compared with the correlation scale normal to the field, in a distance along the field of a few correlation scales. It is found that the rate of separation is very sensitive to the precise form of the power spectrum. Application to the interplanetary and interstellar magnetic fields is discussed, and it is shown that in some cases field lines, much closer together than the correlation scale, separate at a rate which is effectively as rapid as if they were many correlation lengths apart.

  10. Electromagnetic field and force analyses of a noncontacting conveyance system for steel mill application

    Microsoft Academic Search

    Cheng-Tsung Liu; Sung-Yi Yao

    2002-01-01

    Based on the design concepts of linear induction motors, an electromagnetic device has been constructed to investigate its feasibility for noncontacting steel-plate conveyance system applications. The system is intended to provide the desired lift, propulsive, and guidance forces to the steel plate simultaneously. Three-dimensional (3-D) field distributions and force characteristics have been investigated through a system state model and finite

  11. Gravitational self-force in non-vacuum spacetimes: an effective field theory derivation

    E-print Network

    Peter Zimmerman

    2015-07-13

    In this paper we investigate the motion of small compact objects in non-vacuum spacetimes using methods from effective field theory in curved spacetime. Although a vacuum formulation is sufficient in many astrophysical contexts, there are applications such as the role of the self-force in enforcing cosmic-censorship in the context of the overcharging problem, which necessitate an extension into the non-vacuum regime. The defining feature of the self-force problem in non-vacuum spacetimes is the coupling between gravitational and non-gravitational field perturbations. The formulation of the self-force problem for non-vacuum spacetimes was recently provided in simultaneous papers by Zimmerman and Poisson [1] and Linz, Friedmann, Wiseman [2]. Here we distinguish ourselves by working with the effective action rather than the field equations. The formalism utilizes the multi-index notation developed by Zimmerman and Poisson [1] to accommodate the coupling between the different fields. Using dimensional regularization, we arrive at a finite expression for the local self-force expressed in terms of multi-index quantities evaluated in the background spacetime. We then apply the formalism to compute the coupled gravitational self-force in two explicit cases. First, we calculate the self-force on a massive particle possessing scalar charge and moving in an scalarvac spacetime. We then derive an expression for the self-force on an electrically charged, massive particle moving in an electrovac spacetime. In both cases, the force is expressed as a sum of local terms involving tensors defined in the background spacetime and evaluated at the current position of the particle, as well as tail integrals that depend on the past history of the particle.

  12. Gravitational self-force in non-vacuum spacetimes: an effective field theory derivation

    E-print Network

    Peter Zimmerman

    2015-05-14

    In this paper we investigate the motion of small compact objects in non-vacuum spacetimes using methods from effective field theory in curved spacetime. Although a vacuum formulation is sufficient in many astrophysical contexts, there are applications such as the role of the self-force in enforcing cosmic-censorship in the context of the overcharging problem, which necessitate an extension into the non-vacuum regime. The defining feature of the self-force problem in non-vacuum spacetimes is the coupling between gravitational and non-gravitational field perturbations. The formulation of the self-force problem for non-vacuum spacetimes was recently provided in simultaneous papers by Zimmerman and Poisson [1] and Linz, Friedmann, Wiseman [2]. Here we distinguish ourselves by working with the effective action rather than the field equations. The formalism utilizes the multi-index notation developed by Zimmerman and Poisson [1] to accommodate the coupling between the different fields. Using dimensional regularization, we arrive at a finite expression for the local self-force expressed in terms of multi-index quantities evaluated in the background spacetime. We then apply the formalism to compute the coupled gravitational self-force in two explicit cases. First, we calculate the self-force on a massive particle possessing scalar charge and moving in an scalarvac spacetime. We then derive an expression for the self-force on an electrically charged, massive particle moving in an electrovac spacetime. In both cases, the force is expressed as a sum of local terms involving tensors defined in the background spacetime and evaluated at the current position of the particle, as well as tail integrals that depend on the past history of the particle.

  13. Superadiabatic optical forces on a dipole: exactly solvable model for a vortex field

    NASA Astrophysics Data System (ADS)

    Berry, M. V.; Shukla, Pragya

    2014-03-01

    The forces exerted by light on a small particle are modified by the particle's motion, giving a series of superadiabatic corrections to the lowest-order approximation in which the motion is neglected. The correction forces can be calculated recursively for an electric dipole modelled as a damped oscillator. In lowest order, there is, as is known, a non-potential though non-dissipative ‘curl force’, in addition to the familiar gradient force. In the next order, there are forces of geometric magnetism and friction, related to the geometric phase 2-form and the metric of the driving field. For the paraxial field of an optical vortex, the hierarchy of superadiabatic forces can be calculated explicitly, revealing a four-sheeted Riemann surface on which fast and slow dynamics are connected. This leads to an exact ‘slow manifold’, on which the dipole is driven without oscillations by the same forces as in the first two adiabatic orders, but with frequency-renormalized strengths.

  14. Computation of the Wind by Forced Adjustment to the Height Field

    Microsoft Academic Search

    Fedor Mesinger

    1972-01-01

    The problem of the forced adjustment of the wind field to the height field is experimentally studied with the Mintz-Arakawa two-level atmospheric general circulation model.In all but one of the experiments, the height field was assumed to be perfectly observed at 6-hr intervals, over a time period of one day or less, and from this height data the vector wind

  15. Centrifugal and electric field forces dual-pumping CD-like microfluidic platform for biomedical separation.

    PubMed

    Wang, Gou-Jen; Hsu, Wen-Haw; Chang, Yau-Zin; Yang, Hsiharng

    2004-03-01

    In this article, we propose a versatile CD-like multi-channel electrophoresis-based biomedical separation system that is driven by the interactive forces between the centrifugal force and the electric field force. The centrifugal force control of this system is realized through the velocity control of a DC servo motor, while the electric field is governed through the concentric conducting circuits, which are suitably designed and fabricated by sputtering on metal mask method, and can be adjusted to provide multi-stage voltages. Experimental results demonstrate that the electro-osmotic flow (EOF) effect can be effectively reduced when the electric field force and centrifugal force are in the opposite direction. Benefits from this are that the electrophoresis separation time can be prolonged and the length of the microfluidic channels can be shortened; therefore, more effective separation efficiency can be obtained. Moreover, other advantages, such as lower joule-heat generation, low-chemistry reaction, and no variation on the ion concentration during processes, make this biomedical separation system more useful. PMID:15307444

  16. Experimental studies of protozoan response to intense magnetic fields and forces

    NASA Astrophysics Data System (ADS)

    Guevorkian, Karine

    Intense static magnetic fields of up to 31 Tesla were used as a novel tool to manipulate the swimming mechanics of unicellular organisms. It is shown that homogenous magnetic fields alter the swimming trajectories of the single cell protozoan Paramecium caudatum, by aligning them parallel to the applied field. Immobile neutrally buoyant paramecia also oriented in magnetic fields with similar rates as the motile ones. It was established that the magneto-orientation is mostly due to the magnetic torques acting on rigid structures in the cell body and therefore the response is a non-biological, passive response. From the orientation rate of paramecia in various magnetic field strengths, the average anisotropy of the diamagnetic susceptibility of the cell was estimated. It has also been demonstrated that magnetic forces can be used to create increased, decreased and even inverted simulated gravity environments for the investigation of the gravi-responses of single cells. Since the mechanisms by which Earth's gravity affects cell functioning are still not fully understood, a number of methods to simulate different strength gravity environments, such as centrifugation, have been employed. Exploiting the ability to exert magnetic forces on weakly diamagnetic constituents of the cells, we were able to vary the gravity from -8 g to 10 g, where g is Earth's gravity. Investigations of the swimming response of paramecia in these simulated gravities revealed that they actively regulate their swimming speed to oppose the external force. This result is in agreement with centrifugation experiments, confirming the credibility of the technique. Moreover, the Paramecium's swimming ceased in simulated gravity of 10 g, indicating a maximum possible propulsion force of 0.7 nN. The magnetic force technique to simulate gravity is the only earthbound technique that can create increased and decreased simulated gravities in the same experimental setup. These findings establish a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

  17. Anomalous diffusion of field lines and charged particles in Arnold-Beltrami-Childress force-free magnetic fields

    NASA Astrophysics Data System (ADS)

    Dasgupta, B.; Ram, A. K.; Holguin, F.; Krishnamurthy, V.

    2014-10-01

    The cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The three-dimensional Arnold-Beltrami-Childress (ABC) field is an example of a force-free, helical magnetic field. The ABC magnetic field lines exhibit a complex and varied structure that is a mix of regular and chaotic trajectories in phase space. The characteristic features of field line trajectories are illustrated through the phase space distribution of finite-distance and asymptotic-distance Lyapunov exponents. In regions of chaotic trajectories, the field lines are superdiffusive. The time evolution of an ensemble of charged particles moving in the chaotic ABC fields is divided into three time domains. For short times, the motion of the particles is essentially ballistic. The intermediate times are characterized by a decay of the velocity autocorrelation function. For longer times, the particles undergo anomalous superdiffusion. Detailed theoretical and numerical results will be presented. Supported by DoE, NSF, U. Alabama.

  18. Subthalamic Nucleus Local Field Potential Activity Helps Encode Motor Effort Rather Than Force in Parkinsonism

    PubMed Central

    Pogosyan, Alek; Ashkan, Keyoumars; Cheeran, Binith; FitzGerald, James J.; Green, Alexander L.; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Brown, Peter

    2015-01-01

    Local field potential (LFP) recordings from patients with deep brain stimulation electrodes in the basal ganglia have suggested that frequency-specific activities correlate with force or effort, but previous studies have not been able to disambiguate the two. Here, we dissociated effort from actual force generated by contrasting the force generation of different fingers while recording LFP activity from the subthalamic nucleus (STN) in patients with Parkinson's disease who had undergone functional surgery. Patients were studied while on their normal dopaminergic medication. We investigated the relationship between frequency-specific oscillatory activity in the STN and voluntary flexion of either the index or little finger at different effort levels. At each tested effort level (10%, 25%, and 40% of the maximal voluntary contraction force of each individual finger), the index finger generated larger force than the little finger. Movement-related suppression of beta-band power in the STN LFP was significantly modulated by effort, but not by which finger was used, suggesting that the beta suppression in the STN LFP during sustained contraction serves as a proxy for effort. The absolute force scaled with beta power suppression, but with the scaling determined by the maximal voluntary contraction force of the motor effector. Our results argue against the hypothesis that the basal ganglia are directly involved in the parameterization of force during movement and support a role of the STN in the control of motor effort to be attributed to a response. PMID:25878267

  19. Subthalamic nucleus local field potential activity helps encode motor effort rather than force in parkinsonism.

    PubMed

    Tan, Huiling; Pogosyan, Alek; Ashkan, Keyoumars; Cheeran, Binith; FitzGerald, James J; Green, Alexander L; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Brown, Peter

    2015-04-15

    Local field potential (LFP) recordings from patients with deep brain stimulation electrodes in the basal ganglia have suggested that frequency-specific activities correlate with force or effort, but previous studies have not been able to disambiguate the two. Here, we dissociated effort from actual force generated by contrasting the force generation of different fingers while recording LFP activity from the subthalamic nucleus (STN) in patients with Parkinson's disease who had undergone functional surgery. Patients were studied while on their normal dopaminergic medication. We investigated the relationship between frequency-specific oscillatory activity in the STN and voluntary flexion of either the index or little finger at different effort levels. At each tested effort level (10%, 25%, and 40% of the maximal voluntary contraction force of each individual finger), the index finger generated larger force than the little finger. Movement-related suppression of beta-band power in the STN LFP was significantly modulated by effort, but not by which finger was used, suggesting that the beta suppression in the STN LFP during sustained contraction serves as a proxy for effort. The absolute force scaled with beta power suppression, but with the scaling determined by the maximal voluntary contraction force of the motor effector. Our results argue against the hypothesis that the basal ganglia are directly involved in the parameterization of force during movement and support a role of the STN in the control of motor effort to be attributed to a response. PMID:25878267

  20. Relativistic mean field model based on realistic nuclear forces

    NASA Astrophysics Data System (ADS)

    Hirose, S.; Serra, M.; Ring, P.; Otsuka, T.; Akaishi, Y.

    2007-02-01

    In order to predict properties of asymmetric nuclear matter, we construct a relativistic mean field (RMF) model consisting of one-meson exchange (OME) terms and point coupling (PC) terms. In order to determine the density dependent parameters of this model, we use properties of isospin symmetric nuclear matter in combination with the information on nucleon-nucleon scattering data, which are given in the form of the density dependent G-matrix derived from Brueckner calculations based on the Tamagaki potential. We show that the medium- and long-range components of this G-matrix can be described reasonably well by our effective OME interaction. In order to take into account the short-range part of the nucleon-nucleon interaction, which cannot be described well in this manner, a point coupling term is added. Its analytical form is taken from a model based on chiral perturbation theory. It contains only one additional parameter, which does not depend on the density. It is, together with the parameters of the OME potentials adjusted to the equation of state of symmetric nuclear matter. We apply this model for the investigation of asymmetric nuclear matter and find that the results for the symmetry energy as well as for the equation of state of pure neutron matter are in good agreement with either experimental data or with presently adopted theoretical predictions. In order to test the model at higher density, we use its equation of state for an investigation of properties of neutron stars.

  1. Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage.

    PubMed

    Sattar, Sadia; Bennett, Nicholas J; Wen, Wesley X; Guthrie, Jenness M; Blackwell, Len F; Conway, James F; Rakonjac, Jasna

    2015-01-01

    F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70(?)C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative "dipstick" lateral flow diagnostic assay for human plasma fibronectin. PMID:25941520

  2. Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage

    PubMed Central

    Sattar, Sadia; Bennett, Nicholas J.; Wen, Wesley X.; Guthrie, Jenness M.; Blackwell, Len F.; Conway, James F.; Rakonjac, Jasna

    2015-01-01

    F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70?C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative “dipstick” lateral flow diagnostic assay for human plasma fibronectin. PMID:25941520

  3. Anharmonic force field and vibrational frequencies of tetrafluoromethane (CF4) and tetrafluorosilane (SiF4)

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Gang; Sibert, Edwin L.; Martin, Jan M. L.

    2000-01-01

    Accurate quartic anharmonic force fields for CF4 and SiF4 have been calculated using the CCSD(T) method and basis sets of spdf quality. Based on the ab initio force field with a minor empirical adjustment, the vibrational energy levels of these two molecules and their isotopomers are calculated by means of high order Canonical Van Vleck Perturbation Theory (CVPT) based on curvilinear coordinates. The calculated energies agree very well with the experimental data. The full quadratic force field of CF4 is further refined to the experimental data. The symmetrization of the Cartesian basis for arbitrary combination bands of Td group molecules is discussed using the circular promotion operator for the doubly degenerate modes, together with tabulated vector coupling coefficients. The extraction of the spectroscopic constants from our second order transformed Hamiltonian in curvilinear coordinates is discussed, and compared to a similar procedure in rectilinear coordinates.

  4. Controlling dispersion forces between small particles with artificially created random light fields

    E-print Network

    Georges Bruegger; Luis Froufe-Perez; Frank Scheffold; Juan Jose Saenz

    2015-01-22

    Appropriate combinations of laser beams can be used to trap and manipulate small particles with "optical tweezers" as well as to induce significant "optical binding" forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir-Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light induced interactions open a path towards the control of translationally invariant interactions with tuneable strength and range in colloidal systems.

  5. Controlling dispersion forces between small particles with artificially created random light fields

    E-print Network

    Bruegger, Georges; Scheffold, Frank; Saenz, Juan Jose

    2015-01-01

    Appropriate combinations of laser beams can be used to trap and manipulate small particles with "optical tweezers" as well as to induce significant "optical binding" forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir-Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light induced interactions open a path towards...

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

    NASA Astrophysics Data System (ADS)

    Yao, Shuang; Zhang, Yang; Guan, Baiou

    2015-05-01

    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.

  7. Analysis of the electric field induced forces in erythrocyte membrane pores using a realistic cell model.

    PubMed

    Sebastián, J L; Muñoz, S; Sancho, M; Miranda, J M

    2006-12-01

    We calculate the induced electric stress forces on transient hydrophobic pores in the membrane of an erythrocyte exposed to an electric field. For this purpose, we use a finite element numerical technique and a realistic shape for the biconcave erythrocyte represented by a set of parametric equations in terms of Jacobi elliptic functions. The results clearly show that the electrical forces on the base and sidewalls of the pore favour the opening of the pore. A comparison of the force densities obtained for an unstretched flat membrane and for the realistic erythrocyte model shows that the thinning and curvature of the membrane cannot be neglected. We also show that the pore deformation depends strongly on the orientation of the pore with respect to the external field, and in particular is very small when the field is tangent to the membrane surface. PMID:17110781

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

    NASA Technical Reports Server (NTRS)

    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).

  9. Apparatus for storing high magnetic fields having reduced mechanical forces and reduced magnetic pollution

    DOEpatents

    Prueitt, M.L.; Mueller, F.M.; Smith, J.L.

    1991-04-09

    The present invention identifies several configurations of conducting elements capable of storing extremely high magnetic fields for the purpose of energy storage or for other uses, wherein forces experienced by the conducting elements and the magnetic field pollution produced at locations away from the configuration are both significantly reduced over those which are present as a result of the generation of such high fields by currently proposed techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency. 15 figures.

  10. Super resolution mapping of the near optical field and the gradient optical force

    NASA Astrophysics Data System (ADS)

    Gelfand, Ryan M.; Bonakdar, Alireza; Memis, O. Gokalp; Mohseni, Hooman

    2013-09-01

    We have developed a NSOM technique that can map both the near optical field and the optical force using an atomic force microscope. This technique could be very useful for characterizing MEMs/NEMs devices, plasmonic nanoantennas, nano-photonic devices and biologically active substrates. Unlike conventional NSOM techniques that rely on an aperture fabricated on the end of an AFM tip to collect the optical signal this apertureless technique uses a lockin amplifier locked to the AFM tip vibrational frequency, to correlate the amplitude modulation of the back reflected optical signal to the strength of the optical field. And since we are not limited by the fabrication of an aperture the spatial resolution of the map is limited only by the size of a sharp AFM tip which for metallic coated tips can have a radius of curvature of 10 to 20 nm. For optical force mapping the incident laser is modulated and the lock-in amplifier is used to correlate the amplitude modulation of the vibrating AFM tip to strength of the optical gradient force. And in this way one can get a very accurate mapping of both the optical force and the optical field for any substrate of interest as long as it can be back illuminated. Lastly with an electrically monolithic substrate it is possible to correlate the amplitude modulation of the tunneling current to the optical field and obtain a spatial mapping that has a resolution of an STM, about 1 nm or maybe less.

  11. Field emission study of diamond-like carbon films with scanned-probe field-emission force microscopy

    SciTech Connect

    Inoue, Takahito [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)] [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States); Ogletree, D. Frank [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)] [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States); Salmeron, Miquel [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)] [Materials Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)

    2000-05-15

    Using a tip as an anode, a scanning force microscope (SFM) with an electrically conducting tip allows simultaneous measurement of both field-emitted currents and surface electronic properties with high lateral resolution. The principle of the method and its application to field emission from chemical vapor deposition diamond-like carbon films are presented. By simultaneously imaging the topography and field-emission current distribution with a 100 nm tip-surface separation, we correlated emission, topography, and dielectric properties. Subsequent contact SFM images of the same regions correlated topography and conductivity on the nanometer scale. The electrostatic force between tip and surface showed fluctuations on a millisecond time scale during field emission. This is probably due to charging and discharging of deep traps in the diamond-like carbon film. (c) 2000 American Institute of Physics.

  12. @h|i* _i A iLhi _ 5}?@* Vi?_hi_ 22 4@ht 2ff2c f ff2 ff

    E-print Network

    Tourneret, Jean-Yves

    @h|i* _i A iLhi _ 5}?@* Vi?_hi_ 22 4@ht 2ff2c f ff2 ff @h|i* t@?t _LU 4i?|t EN?i ui **i e hiU|L ihtL it| @ |Lhtii , ihUUi 5L| fE| ? Mh | M*@?U t|@|L??@hi _i _i?t|i tTiU|h@*i rfEs ' Çf 2 @||@^ @?| *i t; ,? t TTLt@?| sf :: {s i| i? hi4@h^ @?| ^ i t EA @ *@ uLh4i _

  13. @h|i* _i A iLhi _ 5}?@* Vi?_hi_ e @h* 2ff c f ff2 ff

    E-print Network

    Tourneret, Jean-Yves

    @h|i* _i A iLhi _ 5}?@* Vi?_hi_ e @h* 2ff#12;c f ff2 ff @h|i* t@?t _LU 4i?|t EN?i ui **i e hi| it| *hi _ Thi4ih Lh_hi _i uL?U|L? _i |h@?tuih| MEs ' @n2Zs E@iU @ : f @||@^ i T@h ? t}?@* %E| ' rE| n KE|c L KE| it| ? Mh | M*@?U t|@|L??@hi

  14. Magnetic Field, Force, and Inductance Computations for an Axially Symmetric Solenoid

    NASA Technical Reports Server (NTRS)

    Lane, John E.; Youngquist, Robert C.; Immer, Christopher D.; Simpson, James C.

    2001-01-01

    The pumping of liquid oxygen (LOX) by magnetic fields (B field), using an array of electromagnets, is a current topic of research and development at Kennedy Space Center, FL. Oxygen is paramagnetic so that LOX, like a ferrofluid, can be forced in the direction of a B field gradient. It is well known that liquid oxygen has a sufficient magnetic susceptibility that a strong magnetic gradient can lift it in the earth's gravitational field. It has been proposed that this phenomenon can be utilized in transporting (i.e., pumping) LOX not only on earth, but on Mars and in the weightlessness of space. In order to design and evaluate such a magnetic pumping system, it is essential to compute the magnetic and force fields, as well as inductance, of various types of electromagnets (solenoids). In this application, it is assumed that the solenoids are air wrapped, and that the current is essentially time independent.

  15. Variational Scheme to Compute Protein Reaction Pathways Using Atomistic Force Fields with Explicit Solvent

    NASA Astrophysics Data System (ADS)

    a Beccara, S.; Fant, L.; Faccioli, P.

    2015-03-01

    We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an ? and a ? protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.

  16. Non-mean-field effects in systems with long-range forces in competition.

    PubMed

    Bachelard, R; Staniscia, F

    2012-11-01

    We investigate the canonical equilibrium of systems with long-range forces in competition. These forces create a modulation in the interaction potential and modulated phases appear at the system scale. The structure of these phases differentiate this system from monotonic potentials, where only the mean-field and disordered phases exist. With increasing temperature, the system switches from one ordered phase to another through a first-order phase transition. Both mean-field and modulated phases may be stable, even at zero temperature, and the long-range nature of the interaction will lead to metastability characterized by extremely long time scales. PMID:23214765

  17. FORCED FIELD EXTRAPOLATION: TESTING A MAGNETOHYDRODYNAMIC (MHD) RELAXATION METHOD WITH A FLUX-ROPE EMERGENCE MODEL

    SciTech Connect

    Zhu, X. S.; Wang, H. N.; Du, Z. L.; Fan, Y. L., E-mail: xszhu@bao.ac.cn [Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2013-05-10

    We undertake an attempt to reconstruct the Sun's non-force-free magnetic field. The solar corona is often considered to be magnetohydrostatic. We solve the full MHD equations with a semi-realistic atmosphere model to attain this stationary state. Our method is tested with a Sun-like model which simulates the emergence of a magnetic flux rope passing from below the photosphere into the corona. Detailed diagnostics shows that our method can model the forced field more successfully than the optimization and potential method, but it still needs to be applied to real data.

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

    SciTech Connect

    Behunin, Ryan O. [Center for Nonlinear Studies (CNLS) and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States); Hu, Bei-Lok [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States)

    2011-07-15

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

    SciTech Connect

    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. [Centre for Interdisciplinary Plasma Science, Max-Planck-Institut fuer extraterrestrische Physik, D-85741 Garching (Germany); Institute for High Energy Densities, Russian Academy of Sciences, Izhorskaya 13/19, 125412 Moscow (Russian Federation); RSC 'Energia' Korolev, 141070 Moscow Region (Russian Federation)

    2005-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

    2005-05-01

    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.

  1. Anomalous diffusion of field lines and charged particles in Arnold-Beltrami-Childress force-free magnetic fields

    NASA Astrophysics Data System (ADS)

    Ram, Abhay K.; Dasgupta, Brahmananda; Krishnamurthy, V.; Mitra, Dhrubaditya

    2014-07-01

    The cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The three-dimensional Arnold-Beltrami-Childress (ABC) field is an example of a force-free, helical magnetic field. In fluid dynamics, ABC flows are steady state solutions of the Euler equation. The ABC magnetic field lines exhibit a complex and varied structure that is a mix of regular and chaotic trajectories in phase space. The characteristic features of field line trajectories are illustrated through the phase space distribution of finite-distance and asymptotic-distance Lyapunov exponents. In regions of chaotic trajectories, an ensemble-averaged variance of the distance between field lines reveals anomalous diffusion—in fact, superdiffusion—of the field lines. The motion of charged particles in the force-free ABC magnetic fields is different from the flow of passive scalars in ABC flows. The particles do not necessarily follow the field lines and display a variety of dynamical behavior depending on their energy, and their initial pitch-angle. There is an overlap, in space, of the regions in which the field lines and the particle orbits are chaotic. The time evolution of an ensemble of particles, in such regions, can be divided into three categories. For short times, the motion of the particles is essentially ballistic; the ensemble-averaged, mean square displacement is approximately proportional to t2, where t is the time of evolution. The intermediate time region is defined by a decay of the velocity autocorrelation function—this being a measure of the time after which the collective dynamics is independent of the initial conditions. For longer times, the particles undergo superdiffusion—the mean square displacement is proportional to t?, where ? > 1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics, both of magnetic field lines and of particles moving in these fields, strongly suggest that theories of transport in three-dimensional chaotic magnetic fields need a shift from the usual paradigm of quasilinear diffusion.

  2. Ampere force based magnetic field sensor using dual-polarization fiber laser.

    PubMed

    Cheng, Linghao; Guo, Zhenzhen; Han, Jianlei; Jin, Long; Guan, Bai-Ou

    2013-06-01

    A magnetic field sensor is proposed by placing a dual-polarization fiber grating laser under a copper wire. With a perpendicular magnetic field applied, an electrical current flowing through the copper wire can generate Ampere force to squeeze the fiber grating laser, resulting in the birefringence change inside the laser cavity and hence the change of the beat note frequency. When an alternating current is injected into the copper wire, the magnetic field induced beat note frequency change can be discriminated from environment disturbances. A novel fiber-optic magnetic field sensor is therefore demonstrated with high sensitivity and inherent immunity to disturbances. PMID:23736594

  3. Application of superconductivity for magnetic force control in medical and industrial fields

    NASA Astrophysics Data System (ADS)

    Nishijima, S.

    2008-09-01

    The magnetic force control technique has expanded the applied field with developing a superconductivity because a high magnetic field and a high magnetic field gradient can be produced using the superconducting magnet. The magnetic force control technique has been applied to industrial fields such as recycling of abrasives, removing ferromagnetic particles from powdered products and purifying waste water. The technique is also applied to the drug delivery system as the medical application. Open gradient of magnetic separation was used for the recycling of the abrasives in wasted slurry from solar battery factory. For the removing the ferromagnetic particles from powdered products the magnetic filters were designed not to be blocked with the aggregated powder. In the water purification system, the superconducting high gradient magnetic separation was employed. For the magnetic drug delivery system the superconducting bulk magnet was used to navigate the nanometer-sized ferromagnetic particles in the blood vessel.

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

    NASA Technical Reports Server (NTRS)

    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. Active control of sound fields in elastic cylinders by multi-control forces

    NASA Technical Reports Server (NTRS)

    Jones, J. D.; Fuller, C. R.

    1987-01-01

    An unstiffened cylindrical model was used to study the control of sound transmission into aircraft cabins by the use of multi-control forces applied directly to the cylinder wall. External acoustic monopoles were located on each side of the cylinder to approximate the propeller noise source. This allowed the study of a dual control system utilizing multi-control forces in conjunction with synchrophasing of the twin acoustic monopole sources. For acoustic resonant conditions within the cavity, a spatially averaged noise reduction of approximately 30 dB was achieved using the active control system for both in-phase and out-of-phase monopoles; however, effective reduction of the sound field was dependent upon judiciously positioning the control forces for optimal control of the sound field.

  6. Mean first-passage time for an overdamped particle in a disordered force field

    NASA Astrophysics Data System (ADS)

    Denisov, S. I.; Horsthemke, Werner

    2000-09-01

    We derive a rigorous expression for the mean first-passage time of an overdamped particle subject to a constant bias in a force field with quenched disorder. Depending on the statistics of the disorder, the disorder-averaged mean first-passage time can undergo a transition from an infinite value for small bias to a finite value for large bias. This corresponds to a depinning transition of the particle. We obtain exact values for the depinning threshold for Gaussian disorder and also for a class of piecewise constant random forces, which we call generalized kangaroo disorder. For Gaussian disorder, we investigate how the correlations of the random force field affect the average motion of the particle. For kangaroo disorder, we apply the general results for the depinning transition to two specific examples, viz., dichotomous disorder and random fractal disorder.

  7. Physical forces exerted by microbubbles on a surface in a traveling wave field.

    PubMed

    Brems, S; Hauptmann, M; Camerotto, E; Mertens, P W; Heyns, M; Struyf, H; De Gendt, S

    2014-02-01

    The effect of a wave with a varying traveling component on the bubble activity as well as the physical force generated by microbubbles on a surface has been studied. The acoustic emission from a collection of bubbles is measured in a 928 kHz sound field. Particle removal tests on a surface, which actually measures the applied physical force by the bubbles on that surface, indicate a very strong dependence on the angle of incidence. In other words, when the traveling wave component is maximized, the average physical force applied by microbubbles reaches a maximum. Almost complete particle removal for 78 nm silica particles was obtained for a traveling wave, while particle removal efficiency was reduced to only a few percent when a standing wave was applied. This increase in particle removal for a traveling wave is probably caused by a decrease in bubble trapping at nodes and antinodes in a standing wave field. PMID:24091148

  8. Spinmotive force due to motion of magnetic bubble arrays driven by magnetic field gradient

    PubMed Central

    Yamane, Yuta; Hemmatiyan, Shayan; Ieda, Jun'ichi; Maekawa, Sadamichi; Sinova, Jairo

    2014-01-01

    Interaction between local magnetization and conduction electrons is responsible for a variety of phenomena in magnetic materials. It has been recently shown that spin current and associated electric voltage can be induced by magnetization that depends on both time and space. This effect, called spinmotive force, provides for a powerful tool for exploring the dynamics and the nature of magnetic textures, as well as a new source for electromotive force. Here we theoretically demonstrate the generation of electric voltages in magnetic bubble array systems subjected to a magnetic field gradient. It is shown by deriving expressions for the electric voltages that the present system offers a direct measure of phenomenological parameter ? that describes non-adiabaticity in the current induced magnetization dynamics. This spinmotive force opens a door for new types of spintronic devices that exploit the field-gradient. PMID:25365971

  9. Equilibrium of magnetic fields with arbitrary interweaving of the lines of force. II - Discontinuities in the field

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1986-01-01

    The surfaces of discontinuity (SDs) identified by Parker (1986) in the torsion of a force-free magnetic field in an infinitely conducting fluid contained betweeen two fixed boundary planes are characterized analytically. It is shown that field discontinuities (current sheets) occur whenever an SD terminates within the fluid or intersects with another SD, that intersections occur in most cases, and that the resulting current sheets are responsible for most field dissipation in highly conducting fluids. The astrophysical implications of these findings and a number of unresolved problems are discussed.

  10. COMPARISON OF FORCE-FREE CORONAL MAGNETIC FIELD MODELING USING VECTOR FIELDS FROM HINODE AND SOLAR DYNAMICS OBSERVATORY

    SciTech Connect

    Thalmann, J. K.; Tiwari, S. K.; Wiegelmann, T., E-mail: thalmann@mps.mpg.de [Max-Plank-Institut fuer Sonnensystemforschung, Max-Planck-Str. 2, D-37191 Katlenburg-Lindau (Germany)

    2013-05-20

    Photospheric magnetic vector maps from two different instruments are used to model the nonlinear force-free coronal magnetic field above an active region. We use vector maps inferred from polarization measurements of the Solar Dynamics Observatory/Helioseismic and Magnetic Imager (HMI) and the Solar Optical Telescope's Spectropolarimeter (SP) on board Hinode. Besides basing our model calculations on HMI data, we use both SP data of original resolution and scaled down to the resolution of HMI. This allows us to compare the model results based on data from different instruments and to investigate how a binning of high-resolution data affects the model outcome. The resulting three-dimensional magnetic fields are compared in terms of magnetic energy content and magnetic topology. We find stronger magnetic fields in the SP data, translating into a higher total magnetic energy of the SP models. The net Lorentz forces of the HMI and SP lower boundaries verify their force-free compatibility. We find substantial differences in the absolute estimates of the magnetic field energy but similar relative estimates, e.g., the fraction of excess energy and of the flux shared by distinct areas. The location and extension of neighboring connectivity domains differ and the SP model fields tend to be higher and more vertical. Hence, conclusions about the magnetic connectivity based on force-free field models are to be drawn with caution. We find that the deviations of the model solution when based on the lower-resolution SP data are small compared to the differences of the solutions based on data from different instruments.

  11. The Forces Exerted on Dislocations and the Stress Fields Produced by Them

    Microsoft Academic Search

    M. Peach; J. S. Koehler

    1950-01-01

    It is shown that the force dF exerted on a line element nudsigma of a dislocation with Burgers vector f by a stress tau is given by dF=-nu×(f.tau)dsigma. An analogy is drawn between the behavior of a closed line dislocation in a stress field and the behavior of a closed current-carrying loop in a field of magnetic induction. Then formulas

  12. Field forced antiferroelectric-to-ferroelectric switching in modified lead zirconate titanate stannate ceramics

    Microsoft Academic Search

    Wuyi Pan; Qiming Zhang; Amar Bhalla; Leslie E. Cross

    1989-01-01

    Electric-field-forced antiferroelectric- to-ferroelectric phase transitions in several compositions of modified lead zirconate titanate stannate antiferroelectric ceramics are studied for ultra-high-field-induced strain actuator applications. Two types of fatigue effects are observed in these ceramic compositions. In one, the fatigue effects only proceed to a limited extent and the properties may be restored by annealing above the Curie temperature, while in the

  13. Turbulent relaxation to a force-free field-reversed state

    NASA Technical Reports Server (NTRS)

    Dahlburg, J. P.; Montgomery, D.; Doolen, G. D.; Turner, L.

    1986-01-01

    The evolution of nonequilibrium initial conditions of an incompressible magnetohydrodynamic Z pinch is described by a three-dimensional, pseudospectral numerical code. Magnetohydrodynamic turbulence develops in the resistive, nonviscous magnetofluid, resulting in the selective decay of the energy relative to the magnetic helicity, at Lundquist numbers of only a few hundred. An interior force-free region grows with time and achieves spontaneous reversal of the toroidal magnetic field at the wall, without the necessity of an external electric field.

  14. Confinement of Plasma along Shaped Open Magnetic Fields from the Centrifugal Force of Supersonic Plasma Rotation

    SciTech Connect

    Teodorescu, C.; Young, W. C.; Swan, G. W. S.; Ellis, R. F.; Hassam, A. B.; Romero-Talamas, C. A. [University of Maryland, College Park, Maryland 20742 (United States)

    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 ExB 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.

  15. Nonlinear Force-Free Modeling of Coronal Magnetic Fields Part I: A Quantitative Comparison of Methods

    NASA Astrophysics Data System (ADS)

    Schrijver, Carolus J.; De Rosa, Marc L.; Metcalf, Thomas R.; Liu, Yang; McTiernan, Jim; Régnier, Stéphane; Valori, Gherardo; Wheatland, Michael S.; Wiegelmann, Thomas

    2006-05-01

    We compare six algorithms for the computation of nonlinear force-free (NLFF) magnetic fields (including optimization, magnetofrictional, Grad Rubin based, and Green's function-based methods) by evaluating their performance in blind tests on analytical force-free-field models for which boundary conditions are specified either for the entire surface area of a cubic volume or for an extended lower boundary only. Figures of merit are used to compare the input vector field to the resulting model fields. Based on these merit functions, we argue that all algorithms yield NLFF fields that agree best with the input field in the lower central region of the volume, where the field and electrical currents are strongest and the effects of boundary conditions weakest. The NLFF vector fields in the outer domains of the volume depend sensitively on the details of the specified boundary conditions; best agreement is found if the field outside of the model volume is incorporated as part of the model boundary, either as potential field boundaries on the side and top surfaces, or as a potential field in a skirt around the main volume of interest. For input field (B) and modeled field (b), the best method included in our study yields an average relative vector error E n = < |B-b|>/< |B|> of only 0.02 when all sides are specified and 0.14 for the case where only the lower boundary is specified, while the total energy in the magnetic field is approximated to within 2%. The models converge towards the central, strong input field at speeds that differ by a factor of one million per iteration step. The fastest-converging, best-performing model for these analytical test cases is the Wheatland, Sturrock, and Roumeliotis (2000) optimization algorithm as implemented by Wiegelmann (2004).

  16. ON THE FORCE-FREE NATURE OF PHOTOSPHERIC SUNSPOT MAGNETIC FIELDS AS OBSERVED FROM HINODE (SOT/SP)

    SciTech Connect

    Tiwari, Sanjiv Kumar, E-mail: tiwari@mps.mpg.de [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur 313 001 (India)

    2012-01-01

    A magnetic field is force-free if there is no interaction between it and the plasma in the surrounding atmosphere, i.e., electric currents are aligned with the magnetic field, giving rise to zero Lorentz force. The computation of various magnetic parameters, such as magnetic energy (using the virial theorem), gradient of twist of sunspot magnetic fields (computed from the force-free parameter {alpha}), and any kind of extrapolation, heavily hinges on the force-free approximation of the photospheric sunspot magnetic fields. Thus, it is of vital importance to inspect the force-free behavior of sunspot magnetic fields. The force-free nature of sunspot magnetic fields has been examined earlier by some researchers, ending with incoherent results. Accurate photospheric vector field measurements with high spatial resolution are required to inspect the force-free nature of sunspots. For this purpose, we use several vector magnetograms of high spatial resolution obtained from the Solar Optical Telescope/Spectro-Polarimeter on board Hinode. Both the necessary and sufficient conditions for force-free nature are examined by checking the global and local nature of equilibrium magnetic forces over sunspots. We find that sunspot magnetic fields are not very far from the force-free configuration, although they are not completely force-free on the photosphere. The umbral and inner penumbral fields are more force-free than the middle and outer penumbral fields. During their evolution, sunspot magnetic fields are found to maintain their proximity to force-free field behavior. Although a dependence of net Lorentz force components is seen on the evolutionary stages of the sunspots, we do not find a systematic relationship between the nature of sunspot magnetic fields and the associated flare activity. Further, we examine whether the fields at the photosphere follow linear or nonlinear force-free conditions. After examining this in various complex and simple sunspots, we conclude that, in either case, photospheric sunspot magnetic fields are closer to satisfying the nonlinear force-free field approximation.

  17. Antibody-Antigen Equilibria in a Field of Magnetic Forces: Design of Reagentless Christopher F. Monsona

    E-print Network

    Majda, Marcin

    Antibody-Antigen Equilibria in a Field of Magnetic Forces: Design of Reagentless Biosensors of an analyte with two-component molecular tethers attaching superparamagnetic microspheres (4 microns-antigen complex and are designed to selectively detect either specific ssDNA or antigenic proteins, respectively

  18. Gravitomagnetic Field of the Universe and Coriolis Force on the Rotating Earth

    ERIC Educational Resources Information Center

    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…

  19. Charged particles in higher dimensional homogeneous gravitational field: self-energy and self-force

    NASA Astrophysics Data System (ADS)

    Frolov, Valeri P.; Zelnikov, Andrei

    2014-10-01

    A problem of self-energy and self-force for a charged point-like particle in a higher dimensional homogeneous gravitational field is considered. We study two cases, when a particle has the usual electric charge, and when it has a scalar charge, which is a source of a scalar massless minimally coupled field. We assume that a particle is at rest in the gravitational field, so that its motion is not geodesic, and it has an acceleration a directed away from the horizon. The self-energy of a point charge is divergent and the strength of the divergence grows with the number of dimensions. In order to obtain a finite contribution to the self-energy, we use a covariant regularization method which is a modification of the proper time cut-off and other covariant regularizations. We analyze the relation between the self-energy and the self-force and obtain explicit expressions for the self-forces for the electric and the scalar charge in spacetimes with the number of dimensions up to eight. General expressions for the case of higher dimensions are also obtained. We discuss special logarithmic factors ln a, which are present in both the self-energy and the self-force in odd dimensions. Finally, we compare the obtained results with the earlier known results both for the homogeneous gravitational field and for particles near black holes.

  20. Author's personal copy A reactive force-field for Zirconium and Hafnium Di-Boride

    E-print Network

    Sharma, Pradeep

    flights, rocket propulsion systems, thermal protection for space vehicles, present ­ for instance material systems that are of critical importance for applications in ultra-high temperature environments. The parameters of the reactive force field are derived by fitting to detailed quantum mechanical simulations

  1. Exploring the Needs for Competency Measures in Eight Occupational Fields: Position Reports of Task Forces.

    ERIC Educational Resources Information Center

    Bergquist, William H.; And Others

    These position reports describe the findings of task forces which focused on the need to translate work-related experience into degree or certificate credit at postsecondary institutions. The eight occupational fields examined included Accounting, Agribusiness, Data Processing, Day Care, Electronics Technology, Management, Police Science and…

  2. Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems

    Microsoft Academic Search

    Sandeep Patel; Charles L. Brooks III

    2006-01-01

    The past decade has seen intense development of what are anticipated to be the next generation of classical force fields to be used in computational statistical mechanical approaches to studying a broad class of physical and biological systems. Among the several approaches being actively pursued currently is the fluctuating charge (or equivalently charge equilibration or electronegativity equalization) method. Within this

  3. The Lorentz forces on an electrically conducting sphere in an alternating magnetic field

    Microsoft Academic Search

    Udaya B. Sathuvalli; Yildiz Bayazitoglu

    1996-01-01

    A method to calculate the Lorentz force on an electrically conducting sphere placed in an arbitrary sinusoidally varying magnetic field is developed. The crux of this method lies in expressing the external magnetic held and the eddy current density in the sphere in terms of a “source function” of the current sources and a “skin depth dependent function”. The general

  4. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

    PubMed Central

    Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.

    2015-01-01

    The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan ?, ?, ?1, and ?2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.

  5. Charged particles in higher dimensional homogeneous gravitational field: Self-energy and self-force

    E-print Network

    Valeri P. Frolov; Andrei Zelnikov

    2014-09-11

    A problem of self-energy and self-force for a charged point-like particle in a higher dimensional homogeneous gravitational field is considered. We study two cases, when a particle has usual electric charge and a case when it has a scalar charge, which is a source of a scalar massless minimally coupled field. We assume that a particle is at rest in the gravitational field, so that its motion is not geodesic and it has an acceleration a directed from the horizon. The self-energy of a point charge is divergent and the strength of the divergence grows with the number of dimensions. In order to obtain a finite contribution to the self- energy we use a covariant regularization method which is a modification of the proper time cut-off and other covariant regularizations. We analyze a relation between the self-energy and self-force and obtain explicit expressions for the self-forces for the electric and scalar charge in the spacetimes with the number of dimensions up to eight. General expressions for the case of higher dimensions are also obtained. We discuss special logarithmic factors ln(a), which are present both in the self-energy and self-force in odd dimensions. Finally, we compare the obtained results with the earlier known results both for the homogeneous gravitational field and for particles near black holes.

  6. ON GENERAL TRANSPORT EQUATIONS WITH ABSTRACT BOUNDARY CONDITIONS. THE CASE OF DIVERGENCE FREE FORCE FIELD.

    E-print Network

    Lods, Bertrand

    ON GENERAL TRANSPORT EQUATIONS WITH ABSTRACT BOUNDARY CONDITIONS. THE CASE OF DIVERGENCE FREE FORCE with general external fields and general measures associated to boundary conditions modeled by abstract boundary oper- ators H. Fine properties of the traces are investigated, extending well-known results by M

  7. Researching Refugee and Forced Migration Studies: An Introduction to the Field and the Reference Literature.

    ERIC Educational Resources Information Center

    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…

  8. Study of electric fields parallel to the magnetic lines of force using artificially injected energetic electrons

    NASA Technical Reports Server (NTRS)

    Wilhelm, K.; Bernstein, W.; Whalen, B. A.

    1980-01-01

    Electron beam experiments using rocket-borne instrumentation will be discussed. The observations indicate that reflections of energetic electrons may occur at possible electric field configurations parallel to the direction of the magnetic lines of force in an altitude range of several thousand kilometers above the ionosphere.

  9. Active contour external force using vector field convolution for image segmentation.

    PubMed

    Li, Bing; Acton, Scott T

    2007-08-01

    Snakes, or active contours, have been widely used in image processing applications. Typical roadblocks to consistent performance include limited capture range, noise sensitivity, and poor convergence to concavities. This paper proposes a new external force for active contours, called vector field convolution (VFC), to address these problems. VFC is calculated by convolving the edge map generated from the image with the user-defined vector field kernel. We propose two structures for the magnitude function of the vector field kernel, and we provide an analytical method to estimate the parameter of the magnitude function. Mixed VFC is introduced to alleviate the possible leakage problem caused by choosing inappropriate parameters. We also demonstrate that the standard external force and the gradient vector flow (GVF) external force are special cases of VFC in certain scenarios. Examples and comparisons with GVF are presented in this paper to show the advantages of this innovation, including superior noise robustness, reduced computational cost, and the flexibility of tailoring the force field. PMID:17688214

  10. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    PubMed

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

  11. Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force field Parameters for Calcite

    E-print Network

    Goddard III, William A.

    ARTICLES Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force field energetics for the various surfaces of interest are predicted. 1. Introduction Corrosion inhibitors for oil mechanism for corrosion inhibition of iron by imidazolines.1 Atomistic simulations have also been made

  12. Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids

    E-print Network

    Nielsen, Steven O.

    Versity of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080, United States, and Department dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown experiments have suggested a connection to solubility in water.14 These experiments have focused on so

  13. J. Phys. Chem. 1990, 94, 8897-8909 DREIDING: A Generic Force Field for Molecular Simulations

    E-print Network

    Goddard III, William A.

    , 1982; ACS Monograph 177. (3) (a) Weiner, S.J.; Kollman, P. A.; Case, D. A,;Singh, U.C.; Ghio, C accurately determined crystal structures of organic compounds involving H, C, N, 0,F, P, S, CI, and Br, (ii which have been useful for a variety of organic and inorganic systems, the AMBER force field of Kollman

  14. Nonlinear generation of large-scale magnetic fields in forced spherical shell dynamos

    SciTech Connect

    Livermore, P. W.; Hughes, D. W.; Tobias, S. M. [Department of Applied Mathematics, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2010-03-15

    In an earlier paper [P. W. Livermore, D. W. Hughes, and S. M. Tobias, ''The role of helicity and stretching in forced kinematic dynamos in a spherical shell'', Phys. Fluids 19, 057101 (2007)], we considered the kinematic dynamo action resulting from a forced helical flow in a spherical shell. Although mean field electrodynamics suggests that the resulting magnetic field should have a significant mean (axisymmetric) component, we found no evidence for this; the dynamo action was distinctly small scale. Here we extend our investigation into the nonlinear regime in which the magnetic field reacts back on the velocity via the Lorentz force. Our main result is somewhat surprising, namely, that nonlinear effects lead to a considerable change in the structure of the magnetic field, its final state having a significant mean component. By investigating the dominant flow-field interactions, we isolate the dynamo mechanism and show schematically how the generation process differs between the kinematic and nonlinear regimes. In addition, we are able to calculate some components of the transport coefficient {alpha} and thus discuss our results within the context of mean field electrodynamics.

  15. First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

    NASA Technical Reports Server (NTRS)

    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.

  16. Force Field for Mica-Type Silicates and Dynamics of Octadecylammonium Chains Grafted to Montmorillonite

    SciTech Connect

    Heinz,H.; Koerner, H.; Anderson, K.; Vaia, R.; Farmer, B.

    2005-01-01

    Layered silicates are widely used in nanotechnology and composite materials. We describe a force field for phyllosilicates (mica, montmorillonite, and pyrophyllite) on the basis of physically justified atomic charges, van der Waals parameters, vibrational constants, and distributions of charge defects in agreement with solid state {sup 29}Si NMR data. Unit cell parameters deviate only {approx}0.5% relative to experimental X-ray measurements and surface (respectively cleavage) energies deviate less than 10% from experimental data, including the partition between Coulomb and van der Waals contributions. Reproduction of surface energies facilitates quantitative simulations of hybrid interfaces with water, organics, and biomolecules for which accurate force fields are available. Parameters are consistent with the force fields PCFF (polymer consistent force field), CVFF (consistent valence force field), CHARMM (chemistry at Harvard macromolecular mechanics), and GROMACS (Groningen machine for chemical simulations). As an example of interest, we investigate the structure and dynamics of octadecylammonium montmorillonite ('C{sub 18}'-montmorillonite, cation exchange capacity = 91 mmol/100 g) by molecular dynamics simulation. The surfactant chains assemble essentially as a bilayer with minimal interpenetration within the gallery while the ammonium headgroups are hydrogen-bonded to cavities in the montmorillonite surface. In contrast to quaternary ammonium ions, no rearrangements on the surface have been observed (cavity crossing barrier >5 kcal/mol). The alkyl chains are in a liquidlike state with approximately 30% gauche conformations, in agreement with previous Fourier-transform infrared and solid-state NMR measurements. Computed X-ray diffraction patterns of sodium and C18-montmorillonite agree very well with X-ray patterns from experiment, and the computational model can assist in the assignment of complex reflections.

  17. An improved DNA force field for ssDNA interactions with gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

    2014-06-01

    The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

  18. Reparameterization of RNA ? Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine

    PubMed Central

    2010-01-01

    A reparameterization of the torsional parameters for the glycosidic dihedral angle, ?, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99?. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99? force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99? force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) 1H, steady-state 1D 1H nuclear Overhauser effect (NOE), and transient 1D 1H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2?-endo sugar puckering of the pyrimidines, while the AMBER99? force field’s predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310° for the base orientation of purines. The AMBER99? force field prefers anti conformations around 185°, which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99? force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures. PMID:20463845

  19. The stochastic design of force-minimized compact magnets for high-field magnetic resonance imaging applications

    Microsoft Academic Search

    Stuart Crozier; Christopher J. Snape-Jenkinson; Larry K. Forbes

    2001-01-01

    New designs for force-minimized compact high-field clinical MRI magnets are described. The design method is a modified simulated annealing (SA) procedure which includes Maxwell forces in the error function to be minimized. This permits an automated force reduction in the magnet designs while controlling the overall dimensions of the system. As SA optimization requires many iterations to achieve a final

  20. Multiscale analysis of the electromagnetic self-force in a weak gravitational field

    SciTech Connect

    Pound, Adam; Poisson, Eric [Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1 (Canada)

    2008-02-15

    We examine the motion of a charged particle in a weak gravitational field. In addition to the Newtonian gravity exerted by a large central body, the particle is subjected to an electromagnetic self-force that contains both a conservative piece and a radiation-reaction piece. This toy problem shares many of the features of the strong-field gravitational self-force problem, and it is sufficiently simple that it can be solved exactly with numerical methods, and approximately with analytical methods. We submit the equations of motion to a multiscale analysis, and we examine the roles of the conservative and radiation-reaction pieces of the self-force. We show that the radiation-reaction force drives secular changes in the orbit's semilatus rectum and eccentricity, while the conservative force drives a secular regression of the periapsis and affects the orbital time function; neglect of the conservative term can hence give rise to an important phasing error. We next examine what might be required in the formulation of a reliable secular approximation for the orbital evolution; this would capture all secular changes in the orbit and discard all irrelevant oscillations. We conclude that such an approximation would be very difficult to formulate without prior knowledge of the exact solution.

  1. Multi-scale analysis of the electromagnetic self-force in a weak gravitational field

    E-print Network

    Adam Pound; Eric Poisson

    2007-12-18

    We examine the motion of a charged particle in a weak gravitational field. In addition to the Newtonian gravity exerted by a large central body, the particle is subjected to an electromagnetic self-force that contains both a conservative piece and a radiation-reaction piece. This toy problem shares many of the features of the strong-field gravitational self-force problem, and it is sufficiently simple that it can be solved exactly with numerical methods, and approximately with analytical methods. We submit the equations of motion to a multi-scale analysis, and we examine the roles of the conservative and radiation-reaction pieces of the self-force. We show that the radiation-reaction force drives secular changes in the orbit's semilatus rectum and eccentricity, while the conservative force drives a secular regression of the periapsis and affects the orbital time function; neglect of the conservative term can hence give rise to an important phasing error. We next examine what might be required in the formulation of a reliable adiabatic approximation for the orbital evolution; this would capture all secular changes in the orbit and discard all irrelevant oscillations. We conclude that such an approximation would be very difficult to formulate without prior knowledge of the exact solution.

  2. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  3. PHYSICS OF ELEMENTARY PARTICLES AND FIELDS: Casimir Force on a Piston in Randall-Sundrum Models

    NASA Astrophysics Data System (ADS)

    Cheng, Hong-Bo

    2010-06-01

    The Casimir effect of a piston for massless scalar fields which satisfy Dirichlet boundary conditions in the context of five-dimensional Randall-Sundrum models is studied. In these scenarios we derive and calculate the expression for the Casimir force on the piston. We also discuss the Casimir force in the limit that one outer plate is moved to the remote place to show that the nature of the reduced force between the parallel plates left. In the Randall-Sundrum model involving two branes the two plates attract each other when they locate very closely, but the reduced Casimir force turns to be repulsive as the plates separation is not extremely tiny, which is against the experimental phenomena, meaning that the RSI model can not be acceptable. In the case of one brane model the shape of the reduced Casimir force is similar to that of the standard two-parallel-system in the four-dimensional flat spacetimes while the sign of force remains negative.

  4. ReaxFF Study of the Oxidation of Lignin Model Compounds for the Most Common Linkages in Softwood in View of Carbon Fiber Production

    SciTech Connect

    Beste, Ariana [ORNL] [ORNL

    2014-01-01

    Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic, and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers.

  5. Modeling of Lorentz forces and radiated wave fields for bulk wave electromagnetic acoustic transducers

    NASA Astrophysics Data System (ADS)

    Zhai, Guofu; Wang, Kaican; Wang, Yakun; Su, Riliang; Kang, Lei

    2013-08-01

    Currently, the finite element method (FEM) and analytical calculation are widely employed for the modeling of electromagnetic acoustic transducers (EMATs). However, it takes long time for finite element calculation. Previous analytical models for bulk wave EMATs are generally considered separately and incompletely, and expressions of radiated wave fields contain infinite integrations and multiple singular points, which result in complex numerical computation. A complete model containing the Lorentz force and radiated wave field calculation for the EMAT with a spiral coil and a NdFeB permanent magnet is established. By introducing a current loop instead of the permanent magnet and adopting the truncated region eigenfunction expansion (TREE) method, the distributions of static and dynamic magnetic fields and their generated Lorentz forces are calculated. A series expansion method is proposed for the computation of radiated wave fields, which replaces the integration by series operation and avoids the solutions of singular points effectively. The Lorentz forces and radiated wave fields of a typical transducer are computed. The validity of the model is verified by FEM and experiments. Their good agreements verify the accuracy and validity of the model.

  6. The thermal near-field: Coherence, spectroscopy, heat-transfer, and optical forces

    NASA Astrophysics Data System (ADS)

    Jones, Andrew C.; O'Callahan, Brian T.; Yang, Honghua U.; Raschke, Markus B.

    2013-12-01

    One of the most universal physical processes shared by all matter at finite temperature is the emission of thermal radiation. The experimental characterization and theoretical description of far-field black-body radiation was a cornerstone in the development of modern physics with the groundbreaking contributions from Gustav Kirchhoff and Max Planck. With its origin in thermally driven fluctuations of the charge carriers, thermal radiation reflects the resonant and non-resonant dielectric properties of media, which is the basis for far-field thermal emission spectroscopy. However, associated with the underlying fluctuating optical source polarization are fundamentally distinct spectral, spatial, resonant, and coherence properties of the evanescent thermal near-field. These properties have been recently predicted theoretically and characterized experimentally for systems with thermally excited molecular, surface plasmon polariton (SPP), and surface phonon polariton (SPhP) resonances. We review, starting with the early historical developments, the emergence of theoretical models, and the description of the thermal near-field based on the fluctuation-dissipation theory and in terms of the electromagnetic local density of states (EM-LDOS). We discuss the optical and spectroscopic characterization of distance dependence, magnitude, spectral distribution, and coherence of evanescent thermal fields. Scattering scanning near-field microscopy proved instrumental as an enabling technique for the investigations of several of these fundamental thermal near-field properties. We then discuss the role of thermal fields in nano-scale heat transfer and optical forces, and the correlation to the van der Waals, Casimir, and Casimir-Polder forces. We conclude with an outlook on the possibility of intrinsic and extrinsic resonant manipulation of optical forces, control of nano-scale radiative heat transfer with optical antennas and metamaterials, and the use of thermal infrared near-field spectroscopy (TINS) for broadband chemical nano-spectroscopic imaging, where the thermally driven vibrational optical dipoles provide their own intrinsic light source.

  7. Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting

    NASA Astrophysics Data System (ADS)

    Pan, Bing-Yi; Zhang, Ling-Yun; Dou, Shuo-Xing; Wang, Peng-Ye

    2010-07-01

    We propose a physics method to study the effect of laser field and mechanical force on the melting process of double-stranded deoxyribonucleic acid (DNA). A two-dimensional lattice model is established for DNA molecules stuck on the surface, and the stretching energy of the hydrogen bond and stacking energy for each DNA molecule are calculated by using a nonlinear potential. A real-time algorithm is employed to deal with the dynamics process of DNA melting. Numerical results explain the experimental observations. The spatial distribution of the laser field determines the sequences of DNA melting. The simulation has shown the dependence of the final number of melted DNA on the laser field and mechanical force.

  8. How to treat the confined QCD force field as a massless relativistic string

    NASA Astrophysics Data System (ADS)

    Andersson, B.

    2001-02-01

    I will discuss the Lund String Fragmentation process, in particular some new results that I have obtained together with two bright graduate students, Fredrik Söderberg and Sandipan Mohanty. We have been able to provide a complete analytical solution of the 1 + 1-dimensional model (only containing quarks and anti-quarks together with a constant force field in between them) and we have by now come a long way towards an understanding of the situation when we add gluonic degrees of freedom as internal excitations on the string field. Then we obtain the force field as a 1 + 1-dimensional surface (with a "geography" defined by the gluonic excitations) embedded in 1 + 3-dimensional space-time (or in a dual way into energy-momentum space).

  9. Electromagnetic and gravitational self-force on a relativistic particle from quantum fields in curved space

    E-print Network

    Chad R. Galley; B. L. Hu; Shih-Yuin Lin

    2006-03-24

    We provide a quantum field theoretical derivation of the Abraham-Lorentz-Dirac (ALD) equation, describing the motion of an electric point charge sourcing an electromagnetic field, which back-reacts on the charge as a self-force, and the Mino-Sasaki-Tanaka-Quinn-Wald (MSTQW) equation describing the motion of a point mass with self-force interacting with the linearized metric perturbations caused by the mass off an otherwise vacuous curved background spacetime. We regularize the formally divergent self-force by smearing the direct part of the retarded Green's function and using a quasilocal expansion. We also derive the ALD-Langevin and the MSTQW-Langevin equations with a classical stochastic force accounting for the effect of the quantum fluctuations in the field, which causes small fluctuations on the particle trajectory. These equations will be useful for studying the stochastic motion of charges and small masses under the influence of both quantum and classical noise sources, derived either self-consistently or put in by hand phenomenologically. We also show that history-dependent noise-induced drift motions could arise from such stochastic sources on the trajectory that could be a hidden feature of gravitational wave forms hitherto unknown.

  10. Analytical solutions and validation of electric field and dielectrophoretic force in a bio-microfluidic channel.

    PubMed

    Nerguizian, Vahé; Alazzam, Anas; Roman, Dacian; Stiharu, Ion; Burnier, Miguel

    2012-02-01

    In a microbiological device, cell or particle manipulation and characterization require the use of electric field on different electrodes in several configurations and shapes. To efficiently design microelectrodes within a microfluidic channel for dielectrophoresis focusing, manipulation and characterization of cells, the designer will seek the exact distribution of the electric potential, electric field and hence dielectrophoresis force exerted on the cell within the microdevice. In this paper we describe the approach attaining the analytical solution of the dielectrophoretic force expression within a microchannel with parallel facing same size electrodes present on the two faces of channel substrates, with opposite voltages on the pair electrodes. Simple Fourier series mathematical expressions are derived for electric potential, electric field and dielectric force between two distant finite-size electrodes. Excellent agreement is found by comparing the analytical results calculated using MATLAB™ with numerical ones obtained by Comsol. This analytical result can help the designer to perform simple design parametric analysis. Bio-microdevices are also designed and fabricated to illustrate the theoretical solution results with the experimental data. Experiments with red blood cells show the dielectrophoretic force contour plots of the analytical data matched to the experimental results. PMID:22287173

  11. Molecular Dynamics Simulation of Tri-n-Butyl-Phophate Liquid: A Force Field Comparative Study

    SciTech Connect

    Cui, Shengting [ORNL; de Almeida, Valmor F [ORNL; Hay, Benjamin [ORNL; Ye, Xianggui [ORNL; Khomami, Bamin [ORNL

    2012-01-01

    Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near the atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has been demonstrated that the electric dipole moment can be approximated within 1% of the average experimental value by virtue of scaled atomic partial charges. The liquid mass density can be predicted within 0.5-1% of its experimentally determined value when using the corresponding charge scaling. However, in all cases the predicted self- diffusion coefficient is significantly smaller than a commonly quoted experimental measurement; this result is qualified by the fact that the uncertainty of the experimental value was not available.

  12. The elastodynamic Liénard-Wiechert potentials and elastic fields of non-uniformly moving point and line forces

    E-print Network

    Markus Lazar

    2012-05-23

    The purpose of this paper is to investigate the fundamental problem of the non-uniform subsonic motion of a point force and line forces in an unbounded, homogeneous, isotropic medium in analogy to the electromagnetic Li\\'enard-Wiechert potentials. The exact closed-form solutions of the displacement and elastic fields produced by the point force and line forces are calculated. The displacement fields can be identified with the elastodynamic Li\\'enard-Wiechert tensor potentials. For a non-uniformly moving point force, we decompose the elastic fields into a radiation part and a non-radiation part. We show that the solution of a non-uniformly moving point force is the generalization of the Stokes solution towards the non-uniform motion. For line forces the mathematical solutions are given in the form of time-integrals and, therefore, their motion depends on the history.

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

    SciTech Connect

    Guo, Y.; Ding, M. D. [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China); Liu, Y.; Sun, X. D. [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States); DeRosa, M. L. [Lockheed Martin Advanced Technology Center, 3251 Hanover Street, Palo Alto, CA 94304 (United States); Wiegelmann, T., E-mail: guoyang@nju.edu.cn [Max-Planck-Institut fuer Sonnensystemforschung, Max-Planck-Strasse 2, D-37191 Katlenburg-Lindau (Germany)

    2012-11-20

    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 Degree-Sign Multiplication-Sign 20 Degree-Sign . 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.

  14. Burgers Velocity Fields and the Electromagnetic Forcing in Schroedinger's Interpolating Dynamics

    E-print Network

    P. Garbaczewski; G. Kondrat; R. Olkiewicz

    1996-04-03

    We explore a connection of the deterministically forced Burgers equation for local velocity fields with probabilistic solutions of the Schr\\"{o}dinger boundary data problem. An issue of deducing the most likely interpolating dynamics from the given initial and terminal probability density data is here investigated to give account of the perturbation by external electromagnetic fields. A suitable extension of the Hopf-Cole logarithmic transformation allows to deal with nonconservative drift fields and implies the validity of appropriately generalised heat equations, which completely determine the dynamics.

  15. Ground-water resources of the Holloman Air Force Base well field area, 1967, New Mexico

    USGS Publications Warehouse

    Ballance, W.C.; Mattick, Robert E.

    1976-01-01

    Water consumption at Holloman Air Force Base (HAFB), N. Mex., reached an all time high in 1964 and 1965. Further increases in withdrawal without expansion of pumping facilities will hasten the chemical deterioration of the ground water pumped from the well fields. Saline water in the well-field area is present on the north and west sides of the potable-water area and in a thin shallow zone that overlies the potable-water sands in part of the potable-water area. The latter source is affecting quality of the water produced from most wells. The saturated thickness of material underlying the Boles well field ranges from about 3 ,500 feet in the western part of the field to about 1,200 feet in the eastern part of the field. In the Douglass and San Andres well fields, the saturated thickness ranges from 3,500 feet to about 300 feet. Expansion of the Boles and San Andres well fields to the east and southeast would move the center of pumping away from the highly saline water to the north and west. This would eliminate overpumping of the present wells that has resulted from the expanded facilities at Holloman Air Force Base. (Woodard-USGS)

  16. Shear-force distance control at megahertz frequencies for near-field scanning optical microscopy

    NASA Astrophysics Data System (ADS)

    Simon, A.; Brunner, R.; White, J. O.; Hollricher, O.; Marti, O.

    2001-11-01

    We show that the use of fiber overtone resonance modes up to 3 MHz for shear-force distance control has two advantages for near-field microscopy. The higher dither frequency allows a shorter feedback loop time delay, which in turn allows scanning speeds of 100 ?m/s on a sample with, for example, a 150 nm height variation over a 1 ?m distance. Experiments on a hard semiconductor device and on a soft polymer sample demonstrate a factor of 5 improvement in scanning speed when the dither frequency is increased by a factor of 20. The second advantage is a reduction of the minimum lateral force required for height regulation, which is important for soft samples. Modeling the piezoelectric detection system as a harmonic oscillator indicates a factor of 33 increase in lateral force sensitivity when using the third overtone resonance of a typical fiber tip. This result is confirmed experimentally by immersing the tip into water.

  17. Vibrational analysis and valence force field for nitrotoluenes, dimethylanilines and some substituted methylbenzenes.

    PubMed

    Ojha, Jai Kishan; Venkatram Reddy, B; Ramana Rao, G

    2012-10-01

    The Fourier transform infrared (FTIR) and Raman spectra of 2-amino-4-nitrotoluene; 2-amino-5-nitrotoluene; 2,4-dimethylaniline; 2,5-dimethylaniline; 2,6-dimethylaniline; 1,2,4-trimethylbenzene; 1,3,5-trimethylbenzene and pentamethylbenzene have been recorded in the range 4000-400 cm(-1) and 4000-30 cm(-1), respectively. A normal coordinate analysis was carried out for both in-plane and out-of-plane vibrations of these molecules using an 81-parameter modified valence force field. The force constants were refined using 369 frequencies of eight molecules in the overlay least-squares technique. The reliability of the force constants was tested by making a zero-order calculation for both in-plane and out-of-plane vibrations for five related molecules. The potential energy distributions and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamentals. PMID:22868336

  18. Vibrational Analysis and Valence Force Field for Nitrotoluenes, Dimethylanilines and Some Substituted Methylbenzenes

    NASA Astrophysics Data System (ADS)

    Reddy, B. Venkatram; Ojha, Jai Kishan; Rao, G. Ramana

    2011-06-01

    The Fourier transform infrared (FTIR) and Raman spectra of 2-amino-4-nitro-toluene; 2-amino-5-nitrotoluene; 2,4-dimethylaniline; 2,5-dimethylaniline; 2,6-dimethylaniline; 1,2,4-trimethylbenzene; 1,3,5-trimethylbenzene and pentamethyl-benzene have been recorded in the range 4000-400 Cm-1 and 4000-30 Cm-1, respectively. A normal coordinate analysis was carried out for both in-plane and out-of-plane vibrations of these molecules using an 81-parameter modified valence force field. The force constants were refined using 251 frequencies of eight molecules in the Overlay least-square technique. The reliability of force constants was tested by making zero-order calculations for both in-plane and out-of plane vibrations for five related molecules. The potential energy distribution (PED) and eigen vectors calculated in the process were used to make unambiguous vibrational assignment of all the fundamentals.

  19. Vibrational analysis and valence force field for nitrotoluenes, dimethylanilines and some substituted methylbenzenes

    NASA Astrophysics Data System (ADS)

    Ojha, Jai Kishan; Venkatram Reddy, B.; Ramana Rao, G.

    2012-10-01

    The Fourier transform infrared (FTIR) and Raman spectra of 2-amino-4-nitrotoluene; 2-amino-5-nitrotoluene; 2,4-dimethylaniline; 2,5-dimethylaniline; 2,6-dimethylaniline; 1,2,4-trimethylbenzene; 1,3,5-trimethylbenzene and pentamethylbenzene have been recorded in the range 4000-400 cm-1 and 4000-30 cm-1, respectively. A normal coordinate analysis was carried out for both in-plane and out-of-plane vibrations of these molecules using an 81-parameter modified valence force field. The force constants were refined using 369 frequencies of eight molecules in the overlay least-squares technique. The reliability of the force constants was tested by making a zero-order calculation for both in-plane and out-of-plane vibrations for five related molecules. The potential energy distributions and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamentals.

  20. STUDY OF HORIZONTAL-SPRAY FLUX FORCE/CONDENSATION SCRUBBER

    EPA Science Inventory

    The report gives results of a laboratory pilot-scale evaluation of a Flux Force/Condensation (FF/C) scrubber for collecting fine particles, those smaller than 2 micrometers in diameter. FF/C scrubbing includes the effects of diffusiophoresis, thermophoresis, Stefan flow, and part...

  1. PARTICULATE CONTROL HIGHLIGHTS: FLUX FORCE/CONDENSATION WET SCRUBBING

    EPA Science Inventory

    The report gives highlights of EPA's flux force/condensation (FF/C) program, a system that involves the use of water vapor condensation effects to enhance fine particle collection. FF/C scrubbing offers significant cost advantages over conventional control equipment for a large n...

  2. Heat Transfer Control in Quiescent Air with Thermal Gradient by Magnetizing Force Under both Gravitational and Nongravitational Fields

    Microsoft Academic Search

    Masato Akamatsu; Mitsuo Higano; Yoshio Takahashi; Hiroyuki Ozoe

    2005-01-01

    Two-dimensional numerical computations were carried out to clarify the influence of magnetizing force on quiescent air with thermal gradient in a vertical cylindrical container under both gravitational and nongravitational fields. Several sizes and axial positions of a circular electric coil were tested so that the magnetizing force depended on the magnetic gradient. Under both gravitational and nongravitational fields, the convection

  3. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

    PubMed

    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. PMID:22411565

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

    SciTech Connect

    Jiang Chaowei; Feng Xueshang; Xiang Changqing, E-mail: cwjiang@spaceweather.ac.cn [SIGMA Weather Group, State Key Laboratory for Space Weather, Center for Space Science and Applied Research, Chinese Academy of Sciences, Beijing 100190 (China)

    2012-08-10

    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 Multiplication-Sign 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.

  5. Effects of auroral-particle anisotropies and mirror forces on high-latitude electric fields

    NASA Technical Reports Server (NTRS)

    Chiu, Y. T.; Schulz, M.; Cornwall, J. M.

    1981-01-01

    It is noted that, for most of the mechanisms for the strong electric fields that characterize the narrow regions in which there is acceleration and precipitation of ring current and/or plasma-sheet plasma, certain effects must be taken into account in simulations of auroral electric fields. The effects are those of auroral particle anisotropy, of mirror forces due to the inhomogeneous geomagnetic field, of auroral electron backscatter by the atmosphere, and of electron trapping by the combination of magnetic mirroring and electrostatic forces. What is more, the effects of the very strong perpendicular electric field must also be taken into account in a kinetic description of the Poisson equation in order to achieve a unified theory of the auroral electrostatic structure. Progress in these areas during the past few years is reviewed. It is shown that particle anisotropies and mirror forces can account for some basic electrostatic features of the quiet arc, while additional effects may be occurring in strong events in which the parallel potential drop is more than about 10 kV.

  6. Unsteady hydrodynamic forces acting on a hand and its flow field during sculling motion.

    PubMed

    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. PMID:25310026

  7. Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction

    PubMed Central

    Dagdeviren, Omur E; Schwendemann, Todd C; Mönig, Harry; Altman, Eric I

    2012-01-01

    Summary Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation. In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface. PMID:23019560

  8. Statement of Work for Drilling Five CERCLA Groundwater Monitoring Wells During Fiscal Year 2006, 300-FF-5 Operable Unit

    SciTech Connect

    Williams, Bruce A.

    2005-08-01

    Pacific Northwest National Laboratory, the U.S. Department of Energy (DOE), and the regulators have agreed that two characterization wells along with three additional performance monitoring wells shall be installed in the 300-FF-5 Operable Unit as defined in the proposed Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement [TPA]) Milestone M-24-57 and the 300-FF-5 Limited Field Investigation plan (DOE/RL-2005-47). This document contains the statement of work required to drill, characterize, and construct the proposed groundwater monitoring wells during FY 2006.

  9. Simulations of room temperature ionic liquids: From polarizable to coarse-grained force fields

    E-print Network

    Salanne, Mathieu

    2015-01-01

    Room temperature ionic liquids (RTILs) are solvent with unusual properties, which are difficult to characterize experimentally because of their intrinsic complexity (large number of atoms, strong Coulomb interactions). Molecular simulations have therefore been essential in our understanding of these systems. Depending on the target property and on the necessity to account for fine details of the molecular structure of the ions, a large range of simulation techniques are available. Here I focus on classical molecular dynamics, in which the level of complexity of the simulation, and therefore the computational cost, mostly depends on the force field. Depending on the representation of the ions, these are either classified as all-atom or coarse-grained. In addition, all-atom force fields may account for polarization effects if necessary. The most widely used methods for RTILs are described together with their main achievements and limitations.

  10. Brownian motion in a designer force field: dynamical effects of negative refraction on nanoparticles.

    PubMed

    Cuche, A; Stein, B; Canaguier-Durand, A; Devaux, E; Genet, C; Ebbesen, T W

    2012-08-01

    Photonic crystals (PC) have demonstrated unique features that have renewed the fields of classical and quantum optics. Although holding great promises, associated mechanical effects have proven challenging to observe. We demonstrate for the first time that one of the most salient properties of PC, namely negative refraction, can induce specific forces on metal nanoparticles. By integrating a periodically patterned metal film in a fluidic cell, we show that near-field optical forces associated with negatively refracted surface plasmons are capable of controlling particle trajectories. Coupling particle motions to PC band structures draws new approaches and strategies for parallel and high resolution all-optical control of particle flows with applications for micro- and nanofluidic systems. PMID:22793687

  11. Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator

    PubMed Central

    2015-01-01

    A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute–water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins. PMID:24564643

  12. Anisotropic nonadditive ab initio force field for noncovalent interactions of H2

    NASA Astrophysics Data System (ADS)

    Donchev, A. G.; Galkin, N. G.; Tarasov, V. I.

    2007-05-01

    A quantum mechanical polarizable force field (QMPFF) has been applied to the noncovalent interactions of molecular hydrogen as well as closed-shell monoatomic species (CSMS): rare gases, alkali cations, and halide anions. The importance of all the main energy components is demonstrated: electrostatics (including penetration effect), exchange repulsion, dispersion, and induction. As the MP2 level of quantum mechanics, which is used to parametrize QMPFF, significantly underestimates the H2-H2 dimer binding energy, the force field was refined using state-of-the-art CCSD(T) data. The approach demonstrates excellent transferability, which is confirmed by accurate reproduction of mixed H2-CSMS dimers and the second virial coefficient of hydrogen vapor.

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

    SciTech Connect

    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, ?) in spherical coordinates is defined by a function r?sin??B{sub ?}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r?sin??B{sub ?}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(?))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(?) 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(?,?))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for ?-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 ??=?4/3 as discussed in the Appendix.

  14. Numerical calculation of 3D eddy current field and short circuit electromagnetic force in large transformers

    Microsoft Academic Search

    Renyuan Tang; Yan Li; Dake Li; Lijian Tian

    1992-01-01

    The improved T-? method is employed to calculate the three-dimensional transient eddy current field in large transformers, as well as the short-circuit electromagnetic forces acting on the transformer windings. The effects of the magnetic shielding and initial angles of currents are studied, and the nonuniform distribution of ampere-turn along the height of the windings is taken into account. Thus, a

  15. A cryogenic scanning near-field optical microscope with shear-force gapwidth control

    Microsoft Academic Search

    A. Kramer; J.-M. Segura; A. Hunkeler; A. Renn; B. Hecht

    2002-01-01

    We present a scanning near-field optical microscope designed for nanoscale optical imaging and spectroscopy as well as simultaneous tuning fork shear-force topographic imaging at cryogenic temperatures. The whole setup is immersed in superfluid helium (T=1.8 K). In this medium we observe resonance frequency fluctuations of the tuning fork sensor with an amplitude of Delta][nu][approximately5%-10% of the full width at half-maximum

  16. Determining force field parameters using a physically based equation of state.

    PubMed

    van Westen, Thijs; Vlugt, Thijs J H; Gross, Joachim

    2011-06-23

    Force field parameters used in classical molecular simulations can be estimated from quantum mechanical calculations or spectroscopic measurements. This especially applies to bonded interactions such as bond-stretching, bond-bending, and torsional interactions. However, it is difficult and computational expensive to obtain accurate parameters describing the nonbonded van der Waals interactions from quantum mechanics. In many studies, these parameters are adjusted to reproduce experimental data, such as vapor-liquid equilibria (VLE) data. Adjusting these force field parameters to VLE data is currently a cumbersome and computationally expensive task. The reason is that the result of a calculation of the vapor-liquid equilibria depends on the van der Waals interactions of all atom types in the system, therefore requiring many time-consuming iterations. In this work, we use an analytical equation of state, the perturbed chain statistical associating fluid theory (PC-SAFT), to predict the results of molecular simulations for VLE. The analytical PC-SAFT equation of state is used to approximate the objective function f(p) as a function of the array of force field parameters p. The objective function is here for example defined as the deviations of vapor pressure, enthalpy of vaporization and liquid density data, with respect to experimental data. The parameters are optimized using the analytical PC-SAFT equation of state, which is orders of magnitude quicker to calculate than molecular simulation. The solution is an excellent approximation of the real objective function, so that the resulting method requires only very few molecular simulation runs to converge. The method is here illustrated by optimizing transferable Lennard-Jones parameters for the n-alkane series. Optimizing four force field parameters p = (?(CH(2))(CH(2)), ?(CH(3))(CH(3)), ?(CH(2))(CH(2)), ?(CH(3))(CH(3))) we obtain excellent agreement of coexisting densities, vapor pressure and caloric properties within only 2 -3 molecular simulation runs. PMID:21568280

  17. Ab initio based force field and molecular dynamics simulations of crystalline TATB

    Microsoft Academic Search

    Richard H. Gee; Szczepan Roszak; Krishnan Balasubramanian; Laurence E. Fried

    2004-01-01

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular

  18. Fields and forces in flywheel energy storage with high-temperature superconducting bearings

    Microsoft Academic Search

    Larry R. Turner

    1997-01-01

    The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet

  19. The prediction of spectroscopic properties from quartic correlated force fields - HCCF, HFCO, SiH3(+)

    Microsoft Academic Search

    William H. Green; Dylan Jayatilaka; Andrew Willetts; Roger D. Amos; Nicholas C. Handy

    1990-01-01

    The harmonic and anharmonic IR spectroscopic properties of the HCCF, HFCO, and SiH3(+) molecules are determined by means of ab initio quantum-chemistry calculations using the computer program SPECTRO (Gaw et al., 1990). The derivation of the quartic force fields in second-order Moller-Plesset theory is explained; the application of the method to the three molecules investigated is discussed; and the results

  20. Force fields for divalent cations based on single-ion and ion-pair properties

    NASA Astrophysics Data System (ADS)

    Mamatkulov, Shavkat; Fyta, Maria; Netz, Roland R.

    2013-01-01

    We develop force field parameters for the divalent cations Mg2+, Ca2+, Sr2+, and Ba2+ for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the divalent cations as the relevant single-ion property. As a probe for ion-pair properties we compute the activity derivatives of the salt solutions. The optimization of the ionic force fields is done in two consecutive steps. First, the cation solvation free energy is determined as a function of the Lennard-Jones (LJ) parameters. The peak in the ion-water radial distribution function (RDF) is used as a check of the structural properties of the ions. Second, the activity derivatives of the electrolytes MgY2, CaY2, BaY2, SrY2 are determined through Kirkwood-Buff solution theory, where Y = Cl-, Br-, I-. The activity derivatives are determined for the restricted set of LJ parameters which reproduce the exact solvation free energy of the divalent cations. The optimal ion parameters are those that match the experimental activity data and therefore simultaneously reproduce single-ion and ion-pair thermodynamic properties. For Ca2+, Ba2+, and Sr2+ such LJ parameters exist. On the other hand, for Mg2+ the experimental activity derivatives can only be reproduced if we generalize the combination rule for the anion-cation LJ interaction and rescale the effective cation-anion LJ radius, which is a modification that leaves the cation solvation free energy invariant. The divalent cation force fields are transferable within acceptable accuracy, meaning the same cation force field is valid for all halide ions Cl-, Br-, I- tested in this study.

  1. A force field for 3,3,3-fluoro-1-propenes, including HFO-1234yf.

    PubMed

    Raabe, Gabriele; Maginn, Edward J

    2010-08-12

    The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field. PMID:20684636

  2. Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator

    PubMed Central

    He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D.

    2014-01-01

    A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments, results in significant improvement in the treatment of the conformational energies, and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules. PMID:23703219

  3. Observation of force-detected nuclear magnetic resonance in a homogeneous field

    PubMed Central

    Madsen, L. A.; Leskowitz, G. M.; Weitekamp, D. P.

    2004-01-01

    We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to ?m-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the ?m and nm scales. PMID:15326302

  4. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field

    PubMed Central

    Schyman, Patric; Jorgensen, William L.

    2013-01-01

    Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C6H6) and coronene (C24H12) well; however, for acenes larger than circumcoronene (C54H18) and especially for C60, the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces. PMID:23440601

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions.

    PubMed

    Giese, Timothy J; Chen, Haoyuan; Huang, Ming; York, Darrin M

    2014-03-11

    We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein-ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O-O radial distribution functions similar to TIP4P-EW. PMID:24803856

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

    PubMed

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-21

    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. PMID:26093545

  8. Ionic force field optimization and modified ion-pair mixing rules

    NASA Astrophysics Data System (ADS)

    Fyta, Maria; Netz, Roland R.

    2012-02-01

    We propose an optimization scheme to obtain good ionic force fields for classical simulations of salt solutions, also of biological relevance. Our work is based on Molecular Dynamics simulations with explicit (SPC/E) water for different halide and alkali ions forming salt solutions at finite ion concentration. The force field derivation technique we propose is based on a simultaneous optimization of single-ion and ion-pair properties and the determination of the cation-anion interaction parameters (traditionally given by the mixing rules). From the finite-concentration simulations, thermodynamic properties of the salt solutions are derived, using the Kirkwood-Buff theory of solutions, and compared to relevant experimental data. For the rather size-symmetric salt solutions involving bromide and chloride ions, this scheme using the standard mixing rules works fine. For the iodide and fluoride solutions, corresponding to the largest and smallest anion we have considered, a rescaling of the mixing rules was necessary. In this respect, we have introduced scaling factors for the cation-anion Lennard-Jones interaction that quantify deviations from the standard mixing rules. We discuss the efficiency and complications of the proposed ionic force field optimization scheme.

  9. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field.

    PubMed

    Schyman, Patric; Jorgensen, William L

    2013-02-01

    Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces. PMID:23440601

  10. Field forced antiferroelectric-to-ferroelectric switching in modified lead zirconate titanate stannate ceramics

    SciTech Connect

    Pan, W.; Zhang, Q.; Bhalla, A.; Cross, L.E. (Materials Research Lab., Pennsylvania State Univ., University Park, PA (US))

    1989-04-01

    Electric-field-forced antiferroelectric- to-ferroelectric phase transitions in several compositions of modified lead zirconate titanate stannate antiferroelectric ceramics are studied for ultra-high-field-induced strain actuator applications. Two types of fatigue effects are observed in these ceramic compositions. In one, the fatigue effects only proceed to a limited extent and the properties may be restored by annealing above the Curie temperature, while in the other, the fatigue effects proceed to a large extent and the properties cannot be restored completely by heat treatment.

  11. Computation of the wind by forced adjustment to the height field.

    NASA Technical Reports Server (NTRS)

    Mesinger, F.

    1972-01-01

    Experimental study of the problem of the forced adjustment of the wind field to the height field with the Mintz-Arakawa two-level atmospheric general circulation model. In all but one of the experiments, the height field was assumed to be perfectly observed at 6-hr intervals, over a time period of one day or less, and from these height data the vector wind field was computed by forced dynamical adjustment. In one experiment, the temperature alone was prescribed. The winds computed in these experiments were compared with the 'control' winds of the general circulation simulation. The best agreement between the computed and the control winds was obtained when the time-differencing scheme in the governing finite-difference equations of motion had a large rate of damping of high-frequency motions. This damping rate also determined the optimum fraction and frequency of restoration of the height (or temperature) fields. With strong damping, total restoration at every time step gave the most rapid rate of wind error reduction and the smallest asymptotic limit of the wind error.

  12. Study on Two Methods for Nonlinear Force-Free Extrapolation Based on Semi-Analytical Field

    NASA Astrophysics Data System (ADS)

    Liu, S.; Zhang, H. Q.; Su, J. T.; Song, M. T.

    2011-03-01

    In this paper, two semi-analytical solutions of force-free fields (Low and Lou, Astrophys. J. 352, 343, 1990) have been used to test two nonlinear force-free extrapolation methods. One is the boundary integral equation (BIE) method developed by Yan and Sakurai ( Solar Phys. 195, 89, 2000), and the other is the approximate vertical integration (AVI) method developed by Song et al. ( Astrophys. J. 649, 1084, 2006). Some improvements have been made to the AVI method to avoid the singular points in the process of calculation. It is found that the correlation coefficients between the first semi-analytical field and extrapolated field using the BIE method, and also that obtained by the improved AVI method, are greater than 90% below a height 10 of the 64×64 lower boundary. For the second semi-analytical field, these correlation coefficients are greater than 80% below the same relative height. Although differences between the semi-analytical solutions and the extrapolated fields exist for both the BIE and AVI methods, these two methods can give reliable results for heights of about 15% of the extent of the lower boundary.

  13. Using the atomic force microscope as a nanomechanical partner to support evanescent field imaging

    NASA Astrophysics Data System (ADS)

    Amini, S.; Sun, Z.; Meininger, G. A.; Meissner, K. E.

    2014-09-01

    Quantum Dot (QD)/microsphere structures supporting Whispering Gallery Modes (WGMs) are attached to Atomic Force Microscope (AFM) cantilevers for characterization of the evanescent field around the QD/microsphere and utilization of the evanescent field for sensing at the apical surface of live cells. Following laser excitation, QD emission couples to WGMs that circumnavigate the microsphere via total internal reflection at the internal surfaces of the microsphere. The resulting evanescent field is characterized utilizing the high spatial control of an AFM in approaching a dye monolayer on a test surface. The measured evanescent field extends approximately 50 nm from the microsphere surface, matching theoretical predictions. This system was then used to sense the accumulation of integrin and formation of focal adhesions at the apical surface of cells.

  14. CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

    PubMed Central

    Guvench, Olgun; Hatcher, Elizabeth R.; Venable, Richard M.; Pastor, Richard W.; MacKerell, Alexander D.

    2009-01-01

    We present an extension of the CHARMM hexopyranose monosaccharide additive all-atom force field to enable modeling of glycosidic-linked hexopyranose polysaccharides. The new force field parameters encompass 1?1, 1?2, 1?3, 1?4, and 1?6 hexopyranose glycosidic linkages, as well as O-methylation at the C1 anomeric carbon, and are developed to be consistent with the CHARMM all-atom biomolecular force fields for proteins, nucleic acids, and lipids. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates, in particular O-methyl-tetrahydropyran and glycosidic-linked dimers consisting of two molecules of tetrahyropyran or one of tetrahydropyran and one of cyclohexane. Target data for parameter optimization include full two-dimensional energy surfaces defined by the ?/? glycosidic dihedral angles in the disaccharide analogs as determined by quantum mechanical MP2/cc-pVTZ single point energies on MP2/6-31G(d) optimized structures (MP2/cc-pVTZ//MP2/6-31G(d)). In order to achieve balanced, transferable dihedral parameters for the ?/? glycosidic dihedral angles, surfaces for all possible chiralities at the ring carbon atoms involved in the glycosidic linkages are considered, resulting in over 5000 MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. Also included as target data are vibrational frequencies, pair interaction energies and distances with water molecules, and intramolecular geometries including distortion of the glycosidic valence angle as a function of the glycosidic dihedral angles. The model-compound optimized force field parameters are validated on full disaccharides through comparison of molecular dynamics results to available experimental data. Good agreement is achieved with experiment for a variety of properties including crystal cell parameters and intramolecular geometries, aqueous densities, and aqueous NMR coupling constants associated with the glycosidic linkage. The newly-developed parameters allow for the modeling of linear, branched, and cyclic hexopyranose glycosides both alone and in heterogenous systems including proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:20161005

  15. Non-uniform spatial distributions of both the magnitude and phase of AC electric fields determine dielectrophoretic forces

    Microsoft Academic Search

    X.-B Wang; M. P Hughes; Y Huang; F. F Becker; P. R. C Gascoyne

    1995-01-01

    It is well known that the conventional dielectrophoretic force acting on a polarised particle in a non-uniform AC electric field is proportional to the in-phase component of the induced dipole moment and the non-uniformity of the field strength. In contrast, the travelling-wave-dielectrophoretic force that acts on a particle subjected to a travelling electric field is proportional to the out-of-phase component

  16. Acoustic radiation force in tissue-like solids due to modulated sound field

    NASA Astrophysics Data System (ADS)

    Dontsov, Egor V.; Guzina, Bojan B.

    2012-10-01

    The focus of this study is the sustained body force (the so-called acoustic radiation force) in homogeneous tissue-like solids generated by an elevated-intensity, focused ultrasound field (Mach number=O(10-3)) in situations when the latter is modulated by a low-frequency signal. This intermediate-asymptotics problem, which bears relevance to a number of emerging biomedical applications, is characterized by a number of small (but non-vanishing) parameters including the Mach number, the ratio between the modulation and ultrasound frequency, the ratio of the shear to bulk modulus, and the dimensionless attenuation coefficient. On approximating the response of soft tissues as that of a nonlinear viscoelastic solid with heat conduction, the featured second-order problem is tackled via a scaling paradigm wherein the transverse coordinates are scaled by the width of the focal region, while the axial and temporal coordinate are each split into a "fast" and "slow" component with the twin aim of: (i) canceling the linear terms from the field equations governing the propagation of elevated-intensity ultrasound, and (ii) accounting for the effect of ultrasound modulation. In the context of the focused ultrasound analyses, the key feature of the proposed study revolves around the dual-time-scale treatment of the temporal variable, which allows one to parse out the contribution of ultrasound and its modulation in the nonlinear solution. In this way the acoustic radiation force (ARF), giving rise to the mean tissue motion, is exacted by computing the "fast" time average of the germane field equations. A comparison with the existing theory reveals a number of key features that are brought to light by the new formulation, including the contributions to the ARF of ultrasound modulation and thermal expansion, as well as the precise role of constitutive nonlinearities in generating the sustained body force in tissue-like solids by a focused ultrasound beam.

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

    PubMed

    Vato, Alessandro; Szymanski, Francois D; Semprini, Marianna; Mussa-Ivaldi, Ferdinando A; Panzeri, Stefano

    2014-01-01

    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. PMID:24626393

  18. How Should One Optimize Nonlinear Force-Free Coronal Magnetic Field Extrapolations from SDO/HMI Vector Magnetograms?

    NASA Astrophysics Data System (ADS)

    Wiegelmann, T.; Thalmann, J. K.; Inhester, B.; Tadesse, T.; Sun, X.; Hoeksema, J. T.

    2012-11-01

    The Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) provides photospheric vector magnetograms with a high spatial and temporal resolution. Our intention is to model the coronal magnetic field above active regions with the help of a nonlinear force-free extrapolation code. Our code is based on an optimization principle and has been tested extensively with semianalytic and numeric equilibria and applied to vector magnetograms from Hinode and ground-based observations. Recently we implemented a new version which takes into account measurement errors in photospheric vector magnetograms. Photospheric field measurements are often affected by measurement errors and finite nonmagnetic forces inconsistent for use as a boundary for a force-free field in the corona. To deal with these uncertainties, we developed two improvements: i) preprocessing of the surface measurements to make them compatible with a force-free field, and ii) new code which keeps a balance between the force-free constraint and deviation from the photospheric field measurements. Both methods contain free parameters, which must be optimized for use with data from SDO/HMI. In this work we describe the corresponding analysis method and evaluate the force-free equilibria by how well force-freeness and solenoidal conditions are fulfilled, by the angle between magnetic field and electric current, and by comparing projections of magnetic field lines with coronal images from the Atmospheric Imaging Assembly (SDO/AIA). We also compute the available free magnetic energy and discuss the potential influence of control parameters.

  19. Motion in classical field theories and the foundations of the self-force problem

    E-print Network

    Abraham I. Harte

    2014-05-20

    This article serves as a pedagogical introduction to the problem of motion in classical field theories. The primary focus is on self-interaction: How does an object's own field affect its motion? General laws governing the self-force and self-torque are derived using simple, non-perturbative arguments. The relevant concepts are developed gradually by considering motion in a series of increasingly complicated theories. Newtonian gravity is discussed first, then Klein-Gordon theory, electromagnetism, and finally general relativity. Linear and angular momenta as well as centers of mass are defined in each of these cases. Multipole expansions for the force and torque are then derived to all orders for arbitrarily self-interacting extended objects. These expansions are found to be structurally identical to the laws of motion satisfied by extended test bodies, except that all relevant fields are replaced by effective versions which exclude the self-fields in a particular sense. Regularization methods traditionally associated with self-interacting point particles arise as straightforward perturbative limits of these (more fundamental) results. Additionally, generic mechanisms are discussed which dynamically shift --- i.e., renormalize --- the apparent multipole moments associated with self-interacting extended bodies. Although this is primarily a synthesis of earlier work, several new results and interpretations are included as well.

  20. The Analog-Method: Reconstruction of highly resolved Atmospheric Forcing Fields

    NASA Astrophysics Data System (ADS)

    Schenk, Frederik; Zorita, Eduardo

    2010-05-01

    In this study we test and apply a new method to reconstruct highly resolved atmospheric forcing fields for Northern Europe since 1850 AD. As a simple statistical upscaling method, the analog-method is used to find best fitting atmospheric fields (predictand) to a given variable from long historical station measurements (predictor). The atmospheric fields are taken from a regional climate simulation and serve as a pool of analogs to match the local climate information of station measurements. An important advantage of this non-linear approach is the conservation of full variability in the reconstruction which is generally underestimated by linear regression methods by more than a factor of two. In a first step, the analog method is tested within the model domain serving as surrogate climate. Atmospheric fields (0.25° x 0.25°) of SLP, wind components, temperature, relative humidity, total cloud cover and precipitation are reconstructed by the analog-method using different amounts of grid points (5-25) as synthetic stations. Within the regional model, reconstructions of atmospheric forcing fields for the variables SLP and wind components show excellent skills (r ~ 0.8) when being reconstructed by daily SLP as predictor. For temperature, rel. humidity, total cloud cover and precipitation, SLP is a weak physical predictor leading to lower skills but significantly better than their climatological mean. Using daily air temperature as predictor instead of SLP, temperature fields are reconstructed with very good skills (r > 0.5 for summer and >0.7 in winter). In a second step, the same approach is repeated with real daily SLP data from 23 stations as predictor spanning the period from 1850 to 2009. Limited by the length of the model simulations, 25 years (1958-1982, 1983-2007) are used as calibration and validation periods. The forcing fields for SLP and wind (u,v) show correlations >0.7 for the validation periods. Although the physical link between SLP and relative humidity, total cloud cover and precipitation is weak, the analog-method is able to reconstruct these fields with significantly better skills than their climatological means. Precipitation fields show generally high regional differences in their skill with a mean correlation of about 0.5. In contrast, the temperature fields are only insufficiently explained by SLP as predictor. Hence, long historical monthly station temperatures since 1850 are used as predictor to reconstruct monthly temperature fields. To retain the consistent daily variability, the daily temperature anomalies reconstructed by SLP are projected on the reconstructed monthly means of temperature. This procedure makes also sure that effects on temperature are taken into account which are not explained by SLP (like e.g. changes in the solar forcing). It can be concluded that the analog-method is a very good non-linear upscaling method to reconstruct highly resolved atmospheric fields from local station data (or proxies) on the basis of a pool of regionally downscaled analogs of atmospheric fields.

  1. Force Field Analysis Suggests a Lowering of Diffusion Barriers in Atomic Manipulation Due to Presence of STM Tip

    NASA Astrophysics Data System (ADS)

    Emmrich, Matthias; Schneiderbauer, Maximilian; Huber, Ferdinand; Weymouth, Alfred J.; Okabayashi, Norio; Giessibl, Franz J.

    2015-04-01

    We study the physics of atomic manipulation of CO on a Cu(111) surface by combined scanning tunneling microscopy and atomic force microscopy at liquid helium temperatures. In atomic manipulation, an adsorbed atom or molecule is arranged on the surface using the interaction of the adsorbate with substrate and tip. While previous experiments are consistent with a linear superposition model of tip and substrate forces, we find that the force threshold depends on the force field of the tip. Here, we use carbon monoxide front atom identification (COFI) to characterize the tip's force field. Tips that show COFI profiles with an attractive center can manipulate CO in any direction while tips with a repulsive center can only manipulate in certain directions. The force thresholds are independent of bias voltage in a range from 1 to 10 mV and independent of temperature in a range of 4.5 to 7.5 K.

  2. Penetration and radial force balance in field-reversed configuration with large rotating magnetic field

    SciTech Connect

    Ohnishi, M.; Fukuhara, M.; Masaki, T.; Osawa, H.; Chikano, T. [Department of Electrical Engineering and Computer Science, Kansai University, 3-3-35 Yamate-cho, Suita-shi, Osaka 564-8680 (Japan); Hugrass, W. [School of Computing, University of Tasmania, Locked Bag 1359, Launceston, Tasmania 7250 (Australia)

    2008-10-15

    A field-reversed configuration (FRC) is formed by applying a rotating magnetic field (RMF) much larger than the axial magnetic field to a cylindrical glass vacuum chamber filled with 10 Pa argon gas without a preionization. The FRC with the plasma density 2.2x10{sup 19} m{sup -3}, the temperature 8.0 eV, the separatrix length 0.45 m, and the separatrix radius 0.035 m is sustained for the notably long period of 40 ms. It is observed that the antenna current which produces the RMF is reduced by about half after the FRC is formed. The interaction between the plasma and the antenna circuit increases the antenna resistance and changes the inductance of the antenna so that the circuit becomes nonresonant. The RMF is sufficiently large to fully penetrate to the center during the period and drive the current with a rigid rotor profile. The RMF is shown to play a major role in sustaining the plasma pressure.

  3. The fast multipole method and point dipole moment polarizable force fields

    NASA Astrophysics Data System (ADS)

    Coles, Jonathan P.; Masella, Michel

    2015-01-01

    We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.

  4. Active control of structurally-coupled sound fields in elastic cylinders by vibrational force inputs

    NASA Technical Reports Server (NTRS)

    Jones, J. D.; Fuller, C. R.

    1990-01-01

    Active control of structurally-coupled sound fields in elastic cylinders is analytically and experimentally studied. The primary (noise) field in the cylinder model is generated by the coupled dynamic response of the shell under loading by a single exterior acoustic source. Control of the interior sound field is achieved by applying vibrational force inputs directly to the shell wall. Action of the point controllers serve to increase the input impedance of select structural modes of the shell which are well-coupled to the interior acoustic cavity, thus substantially reducing sound transmission into the cavity. Spatially-averaged noise reductions in excess of 30 dB are demonstrated for acoustic resonant conditions within the cavity. Twin controller configurations are presented which demonstrate the ability to independently control orthogonal modes of the interior acoustic space. Benefits and drawbacks of this new methodology for noise control are discussed and clearly demonstrated.

  5. Lorentz Force on Sodium and Chlorine Ions in a Salt Water Solution Flow under a Transverse Magnetic Field

    ERIC Educational Resources Information Center

    De Luca, R.

    2009-01-01

    It is shown that, by applying elementary concepts in electromagnetism and electrochemistry to a system consisting of salt water flowing in a thin rectangular pipe at an average velocity v[subscript A] under the influence of a transverse magnetic field B[subscript 0], an electromotive force generator can be conceived. In fact, the Lorentz force

  6. Rational design of ion force fields based on thermodynamic solvation properties

    NASA Astrophysics Data System (ADS)

    Horinek, Dominik; Mamatkulov, Shavkat I.; Netz, Roland R.

    2009-03-01

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H3O+) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the problem is almost underdetermined, i.e., there is a whole set of degenerate parameters that equally well describe, e.g., chloride and bromide ions. (iii) For the heavy cations the problem is overdetermined, i.e., no combination of Lennard-Jones parameters is able to reproduce simultaneously energy and entropy of solvation. We discuss various possibilities to deal with these problems and finally present an optimized force field for the halide anions that reproduces the free energy and the entropy of solvation. For the alkali metal cations there is no unambiguous choice of parameters. Therefore, we give three different parameter sets for every ion with a small, intermediate, or large Lennard-Jones interaction strength, where the Lennard-Jones diameters are optimized to reproduce the solvation free energy. The ionic radius is reproduced with acceptable accuracy by this optimization strategy, meaning that the proposed force fields are reliable beyond the target observables (i.e., free energy and entropy of solvation).

  7. Rational design of ion force fields based on thermodynamic solvation properties.

    PubMed

    Horinek, Dominik; Mamatkulov, Shavkat I; Netz, Roland R

    2009-03-28

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H(3)O(+)) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the problem is almost underdetermined, i.e., there is a whole set of degenerate parameters that equally well describe, e.g., chloride and bromide ions. (iii) For the heavy cations the problem is overdetermined, i.e., no combination of Lennard-Jones parameters is able to reproduce simultaneously energy and entropy of solvation. We discuss various possibilities to deal with these problems and finally present an optimized force field for the halide anions that reproduces the free energy and the entropy of solvation. For the alkali metal cations there is no unambiguous choice of parameters. Therefore, we give three different parameter sets for every ion with a small, intermediate, or large Lennard-Jones interaction strength, where the Lennard-Jones diameters are optimized to reproduce the solvation free energy. The ionic radius is reproduced with acceptable accuracy by this optimization strategy, meaning that the proposed force fields are reliable beyond the target observables (i.e., free energy and entropy of solvation). PMID:19334851

  8. Advances in damage control resuscitation and surgery: implications on the organization of future military field forces

    PubMed Central

    Tien, Col Homer; Beckett, Maj Andrew; Garraway, LCol Naisan; Talbot, LCol Max; Pannell, Capt Dylan; Alabbasi, Thamer

    2015-01-01

    Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future.

  9. Perspectives on the simulation of protein-surface interactions using empirical force field methods.

    PubMed

    Latour, Robert A

    2014-12-01

    Protein-surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein-surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242

  10. Interfacial force field characterization of a constrained vapor bubble thermosyphon using IAI

    NASA Technical Reports Server (NTRS)

    Dasgupta, Sunando; Plawsky, Joel L.; Wayner, Peter C., Jr.

    1994-01-01

    The isothermal profiles of the extended meniscus in a quartz cuvette were measured in a gravitational field using IAI (image analyzing interferometer) which is based on computer enhanced video microscopy of the naturally occurring interference fringes. The experimental results for heptane and pentane menisci were analyzed using the extended Young-Laplace Equation. These isothermal results characterized the interfacial force field in-situ at the start of the heat transfer experiments by quantifying the dispersion constant for the specific liquid-solid system. The experimentally obtained values of the disjoining pressures and the dispersion constants are compared to the subsequent non-isothermal experiments because one of the major variables in the heat sink capability of the CVBT is the dispersion constant. In all previous studies of micro heat pipes the value of the dispersion constant has been 'guesstimated'. The major advantages of the current glass cell is the ability to view the extended meniscus at all times. Experimentally, we find that the extended Young-Laplace Equation is an excellent model for for the force field at the solid-liquid vapor interfaces.

  11. Effects of the field dependent Jc on the vertical levitation force between a superconductor and a magnet

    Microsoft Academic Search

    Gang Li; Meng Jun Qin; Hua Kun Liu; Shi Xue Dou

    2003-01-01

    The vertical levitation force between a superconductor disk (SC) and a permanent magnet disk (PM) has been calculated from first principles using different Jc(B) relationships of the magnetic field. Based upon the first principles, the current distribution inside the SC induced by the applied inhomogeneous magnetic field generated by the PM and the field profiles have been calculated with a

  12. Future Force and First Responders: Building Ties for Collaboration and

    E-print Network

    Hammer, Joachim

    peacekeeping roles · First Responders (FR) and Future Force warriors (FF) have similar information needs sources United States Army Web Site, http://www.natick.army.mil/soldier/WSIT/ Similarities #12;Joachim

  13. CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450

  14. The global regulator FfSge1 is required for expression of secondary metabolite gene clusters but not for pathogenicity in Fusarium fujikuroi.

    PubMed

    Michielse, Caroline B; Studt, Lena; Janevska, Slavica; Sieber, Christian M K; Arndt, Birgit; Espino, Jose Juan; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

    2014-08-12

    The plant pathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F.?fujikuroi is able to produce several other secondary metabolites (SMs). Although much progress has been made in the field of secondary metabolism, the transcriptional regulation of SM biosynthesis is complex and still incompletely understood. Environmental conditions, global as well as pathway-specific regulators and chromatin remodelling have been shown to play major roles. Here, the role of FfSge1, a homologue of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for formation of conidia and pathogenicity but is involved in vegetative growth. Transcriptome analysis of the mutant ?ffsge1 compared with the wild type, as well as comparative chemical analysis between the wild type, ?ffsge1 and OE:FfSGE1, revealed that FfSge1 functions as a global activator of secondary metabolism in F.?fujikuroi. Double mutants of FfSGE1 and other SM regulatory genes brought insights into the hierarchical regulation of secondary metabolism. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a non-canonical non-ribosomal peptide synthetase. PMID:25115968

  15. Equilibrium of magnetic fields with arbitrary interweaving of the lines of force. I - Discontinuities in the torsion

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1986-01-01

    Consideration is given to the static force-free equilibrium of a magnetic field in which all of the lines of force connect without knotting between parallel planes. The field is formed by continuous deformation from an initial uniform field, and is conventiently described in terms of the scalar function psi, which is the stream function for the incompressible wrapping and interweaving of the lines of force. Local compression and expansion of the lines of force is described in terms of the scalar function Phi. Equilibrium in the field requires satisfaction of two independent equations which cannot be accomplished without the full freedom of both psi and Phi. It is shown that discontinuities in the torsional characteristics of the lines occur when psi is predetermined by an arbitrary pattern. Discontinuities in the winding pattern of the lines can lead to discontinuities in the associated current sheets.

  16. Role of external magnetic field and current closure in the force balance mechanism of a magnetically stabilized plasma torch

    NASA Astrophysics Data System (ADS)

    G, Ravi; Goyal, Vidhi

    2012-10-01

    Experimental investigations on the role of applied external magnetic field and return current closure in the force balance mechanism of a plasma torch are reported. The plasma torch is of low power and has wall, gas and magnetic stabilization mechanisms incorporated in it. Gas flow is divided into two parts: axial-central and peripheral-shroud, applied magnetic field is axial and return current is co-axial. Results indicate that application of large external magnetic field gives rise to not only J x B force but also, coupled with gas flow, to a new drag-cum-centrifugal force that acts on the plasma arc root and column. The magnetic field also plays a role in the return current closure dynamics and thus in the overall force balance mechanism. This in turn affects the electro-thermal efficiency of the plasma torch. Detailed experimental results, analytical calculations and physical model representing the processes will be presented and discussed.

  17. On the representation of potential energy surfaces of polyatomic molecules in normal coordinates: II. Parameterisation of the force field

    NASA Astrophysics Data System (ADS)

    Burcl, Rudolf; Carter, Stuart; Handy, Nicholas C.

    2003-05-01

    By substituting the standard mass-weighted normal coordinates with either Morse-like or Gauss-like coordinates, it is demonstrated that significant improvements can be made to the vibrational spectra of polyatomic molecules calculated variationally. Quartic force fields in the form of Taylor expansions are generated by density functional theory for water, formaldehyde and methane, and their vibrational spectra calculated by the perturbation normal coordinate code SPECTRO. These are then compared with three sets of spectra arising from the variational code MULTIMODE. Initial spectra are obtained using the identical Taylor expansion force fields. A subsequent set of spectra are then obtained for which the symmetric normal coordinates of the force fields are replaced by Morse-like coordinates and a final set of spectra are obtained for which the asymmetric normal coordinates of the force field are replaced by Gauss-like coordinates. The restriction is imposed that the complete set of derivatives to quartic are preserved under these coordinate transformations.

  18. Solutions of the Helmholtz equation with boundary conditions for force-free magnetic fields

    NASA Technical Reports Server (NTRS)

    Rasband, S. N.; Turner, L.

    1981-01-01

    It is shown that the solution, with one ignorable coordinate, for the Taylor minimum energy state (resulting in a force-free magnetic field) in either a straight cylindrical or a toroidal geometry with arbitrary cross section can be reduced to the solution of either an inhomogeneous Helmholtz equation or a Grad-Shafranov equation with simple boundary conditions. Standard Green's function theory is, therefore, applicable. Detailed solutions are presented for the Taylor state in toroidal and cylindrical domains having a rectangular cross section. The focus is on solutions corresponding to the continuous eigenvalue spectra. Singular behavior at 90 deg corners is explored in detail.

  19. Fields and forces in flywheel energy storage with high-temperature superconducting bearings

    SciTech Connect

    Turner, L.R. [Argonne National Lab., IL (United States). Energy Technology Div.] [Argonne National Lab., IL (United States). Energy Technology Div.

    1997-03-01

    The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stability subsystems.

  20. Fields and forces in flywheel energy storage with high-temperature superconducting bearings

    SciTech Connect

    Turner, L.R. [Argonne National Lab., IL (United States). Energy Technology Div.

    1996-05-01

    The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stabilization subsystem.

  1. Accurate ab initio quartic force fields for borane and BeH2

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.; Lee, Timothy J.

    1992-01-01

    The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

  2. Finding fields and self-force in a gauge appropriate to separable wave equations

    SciTech Connect

    Keidl, Tobias S.; Friedman, John L.; Wiseman, Alan G. [Department of Physics, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, Wisconsin 53201 (United States)

    2007-06-15

    Gravitational waves from the inspiral of a stellar-size black hole to a supermassive black hole can be accurately approximated by a point particle moving in a Kerr background. This paper presents progress on finding the electromagnetic and gravitational field of a point particle in a black-hole spacetime and on computing the self-force in a 'radiation gauge.' The gauge is chosen to allow one to compute the perturbed metric from a gauge-invariant component {psi}{sub 0} (or {psi}{sub 4}) of the Weyl tensor and follows earlier work by Chrzanowski, Cohen, and Kegeles (we correct a minor, but propagating, error in the Cohen-Kegeles formalism). The electromagnetic field tensor and vector potential of a static point charge and the perturbed gravitational field of a static point mass in a Schwarzschild geometry are found, surprisingly, to have closed-form expressions. The gravitational field of a static point charge in the Schwarzschild background must have a strut, but {psi}{sub 0} and {psi}{sub 4} are smooth except at the particle, and one can find local radiation gauges for which the corresponding spin {+-}2 parts of the perturbed metric are smooth. Finally a method for finding the renormalized self-force from the Teukolsky equation is presented. The method is related to the Mino, Sasaki, Tanaka and Quinn and Wald (MiSaTaQuWa) renormalization and to the Detweiler-Whiting construction of the singular field. It relies on the fact that the renormalized {psi}{sub 0} (or {psi}{sub 4}) is a source-free solution to the Teukolsky equation; and one can therefore reconstruct a nonsingular renormalized metric in a radiation gauge.

  3. MSX Force Field and Vibrational Frequencies for BEDT-TTF (Neutral and Cation) Ersan Demiralp, Siddharth Dasgupta, and William A. Goddard III*

    E-print Network

    Goddard III, William A.

    MSX Force Field and Vibrational Frequencies for BEDT-TTF (Neutral and Cation) Ersan Demiralp and available experimental frequencies, we used Hessian-biased methods to develop the MSX force fields frequencies, we develop the MSX force fields for the neutral and cation ET molecules. These frequen- cies

  4. Optical gecko toe: Optically controlled attractive near-field forces between plasmonic metamaterials and dielectric or metal surfaces

    NASA Astrophysics Data System (ADS)

    Zhang, J.; MacDonald, K. F.; Zheludev, N. I.

    2012-05-01

    On the mesoscopic scale, electromagnetic forces are of fundamental importance to an enormously diverse range of systems, from optical tweezers to the adhesion of gecko toes. Here we show that a strong light-driven force may be generated when a plasmonic metamaterial is illuminated in close proximity to a dielectric or metal surface. This near-field force can exceed radiation pressure and Casimir forces to provide an optically controlled adhesion mechanism mimicking the gecko toe: At illumination intensities of just a few tens of nW/?m2 it is sufficient to overcome the Earth's gravitational pull.

  5. Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

    SciTech Connect

    Gao, Weimin; Niu, Haitao; Lin, Tong; Wang, Xungai; Kong, Lingxue [Institute for Frontier Materials, Deakin University, Waurn Ponds VIC 3216 (Australia)] [Institute for Frontier Materials, Deakin University, Waurn Ponds VIC 3216 (Australia)

    2014-01-28

    The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

  6. Evidence that transduction of electromagnetic field is mediated by a force receptor.

    PubMed

    Marino, Andrew A; Carrubba, Simona; Frilot, Clifton; Chesson, Andrew L

    2009-03-13

    Low-strength magnetic fields triggered onset and offset evoked potentials, indicating that the detection process was a form of sensory transduction; whether the field interacted directly with an ion channel or indirectly via a signaling cascade is unknown. By analogy with electrosensory transduction in lower life forms, we hypothesized that the evoked potentials were initiated by a force exerted by the induced electric field on an ion channel in the plasma membrane. We applied a rapid magnetic stimulus (0.2 ms) and found that it produced evoked potentials indistinguishable in latency, magnitude, and frequency from those found previously when the stimulus was 50 times slower. The ability of the field-detection system in human subjects to respond to the rapid stimulus supported the theory that the receptor potentials necessary for production of evoked potentials originated from a direct interaction between the field and an ion channel in the plasma membrane that resulted in a change in the average probability of the channel to be in the open state. PMID:19383425

  7. A Non-Linear Force-Free Field Model for the Solar Magnetic Carpet

    NASA Astrophysics Data System (ADS)

    Meyer, Karen; Mackay, D.; van Ballegooijen, A.; Parnell, C.

    2013-07-01

    The magnetic carpet is defined to be the small-scale photospheric magnetic field of the quiet-Sun. Recent high resolution, high cadence observations have shown that although small-scale, the magnetic carpet is far from 'quiet', it is continually evolving in a complex and dynamic manner. I will present a two-component model for the dynamic evolution of the Sun's magnetic carpet. The first component is a 2D model for the photospheric evolution of the small-scale solar magnetic field, that reproduces many observed parameters. The basic evolution of magnetic elements within the model is governed by a supergranular flow profile. In addition, magnetic elements may evolve through the processes of emergence, cancellation, coalescence and fragmentation. The synthetic magnetograms produced by the 2D model are then applied as photospheric boundary data to drive the continuous evolution of a 3D non-linear force-free coronal field. We studied the resultant complex, small-scale coronal magnetic field, in particular the energetics of the field.

  8. Field evidence of the viscous sublayer in a tidally forced developing boundary layer

    NASA Astrophysics Data System (ADS)

    Wengrove, M. E.; Foster, D. L.

    2014-07-01

    Field observations of boundary layer development within a tidally forced estuary revealed evidence of an observable viscous sublayer. Evidence is provided by several independent measures of the flow field, including hydrodynamic smoothness, an immobile bed, and characteristic velocity, constant stress, and higher-order moment structures. This investigation reports what may be the second comprehensive observation of the viscous sublayer in a marine environment, and what could be the first observation of a momentum balance that includes the viscous sublayer within a shallow estuarine environment. Hydrodynamic observations were made in a straight channel within the Great Bay Estuary of New Hampshire over a flat sandy mud with low water depth of 1.5 m at the sampling location. Beyond quantifying the role of the benthic boundary layer in nutrient dynamics, these observations are useful to provide insight into very near boundary stress estimates leading to incipient motion in estuarine and coastal environments.

  9. Determination of the viscous acoustic field for liquid drop positioning/forcing in an acoustic levitation chamber in microgravity

    NASA Technical Reports Server (NTRS)

    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.

  10. Gravitational forces in the Randall-Sundrum model with a scalar stabilizing field

    SciTech Connect

    Arnowitt, R.; Dent, J. [Center For Theoretical Physics, Department of Physics, Texas A and M University, College Station, Texas 77843-4242 (United States)

    2007-03-15

    We consider the problem of gravitational forces between point particles on the branes in a five-dimensional (5D) Randall-Sundrum model with two branes (at y{sub 1} and y{sub 2}) and S{sup 1}/Z{sub 2} symmetry of the fifth dimension. The matter on the branes is viewed as a perturbation on the vacuum metric and treated to linear order. In a previous work [R. Arnowitt and J. Dent, Phys. Rev. D 71, 124024 (2005).] it was seen that the trace of the transverse part of the 4D metric on the TeV brane, f{sup T}(y{sub 2}), contributed a Newtonian potential enhanced by e{sup 2{beta}y{sub 2}} congruent with 10{sup 32} and thus produced gross disagreement with the experiment. In this work we include a scalar stabilizing field {phi} and solve the coupled Einstein and scalar equations to leading order for the case where {phi}{sub 0}{sup 2}/M{sub 5}{sup 3} is small and the vacuum field {phi}{sub 0}(y) is a decreasing function of y. f{sup T} then grows a mass factor e{sup -{mu}}{sup r} where, however, {mu} is suppressed from its natural value, O(M{sub Pl}), by an exponential factor e{sup -(1+{lambda}{sub b}){beta}y{sub 2}}, {lambda}{sub b}>0. Thus agreement with the experiment depends on the interplay between the enhancing and decaying exponentials. Current data eliminates a significant part of the parameter space, and the Randall-Sundrum model will be sensitive to any improvements on the tests of the Newtonian force law at smaller distances. An example of coupling of the {phi} field to the Higgs field is examined and found to generally produce very small effects.

  11. Field investigation source area ST58 old Quartermaster service station, Eielson Air Force Base, Alaska

    SciTech Connect

    Liikala, T.L.; Evans, J.C.

    1995-01-01

    Source area ST58 is the site of the old Quartermaster service station at Eielson Air Force Base, Alaska. The source area is one of several Source Evaluation Report sites being investigated by Pacific Northwest Laboratory for the US Air Force as candidates for no further remedial action, interim removal action, or a remedial investigation/feasibility study under a Federal Facilities Agreement. The purpose of this work was to characterize source area ST58 and excavate the most contaminated soils for use in composting treatability studies. A field investigation was conducted to determine the nature and extent of soil contamination. The field investigation entailed a records search; grid node location, surface geophysical, and soil gas surveys; and test pit soil sampling. Soil excavation followed based on the results of the field investigation. The site was backfilled with clean soil. Results from this work indicate close spatial correlation between screening instruments, used during the field investigation and soil excavation, and laboratory analyses. Gasoline was identified as the main subsurface contaminant based on the soil gas surveys and test pit soil sampling. A center of contamination was located near the northcentral portion of the source area, and a center was located in the northwestern comer. The contamination typically occurred near or below a former soil horizon probably as a result of surface spills and leaks from discontinuities and/or breaks in the underground piping. Piping locations were delineated during the surface geophysical surveys and corresponded very well to unscaled drawings of the site. The high subsurface concentrations of gasoline detected in the northwestern comer of the source area probably reflect ground-water contamination and/or possibly floating product.

  12. Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

    PubMed

    Zhang, Jin; Tuguldur, Badamkhatan; van der Spoel, David

    2015-06-22

    Quantitative prediction of physical properties of liquids is a longstanding goal of molecular simulation. Here, we evaluate the predictive power of the Generalized Amber Force Field (Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) for the Gibbs energy of solvation of organic molecules in organic solvents using the thermodynamics integration (TI) method. The results are compared to experimental data, to a model based on quantitative structure property relations (QSPR), and to the conductor-like screening models for realistic solvation (COSMO-RS) model. Although the TI calculations yield slightly better correlation to experimental results than the other models, in all fairness we should conclude that the difference between the models is minor since both QSPR and COSMO-RS yield a slightly lower RMSD from that of the experiment (<3.5 kJ/mol). By analyzing which molecules (either as solvents or solutes) are outliers in the TI calculations, we can pinpoint where additional parametrization efforts are needed. For the force field based TI calculations, deviations from the experiment occur in particular when compounds containing nitro or ester groups are solvated into other liquids, suggesting that the interaction between these groups and solvents may be too strong. In the COSMO-RS calculations, outliers mainly occur when compounds containing (in particular aromatic) rings are solvated despite using a ring correction term in the calculations. PMID:26010106

  13. Predictive force-field calculations for the equilibrium dimerization of isoprene

    SciTech Connect

    Kar, M.; Lenz, T.G.; Vaughan, J.D. (Colorado State Univ., Fort Collins, CO (United States))

    1994-03-03

    The Diels-Alder dimerization of isoprene is an important reaction. In the present work, the QCFF force field program was used to calculate gas-phase thermodynamic properties of the monomer (isoprene) and the dimers 1-methyl-5-(1-methylethenyl)cyclohexene (diprene) and 1-methyl-4-(1-methylethenyl)cyclohexene (dipentene) for the temperature range 298.15-1000 K. These QCFF-calculated thermodynamic values were compared, when possible, with corresponding values obtained experimentally or from other force field programs, and the agreement was found to be satisfactory. The QCFF values were further used to derive gas-phase equilibrium properties--[Delta]H[sup o], [Delta]S[sup o], [Delta]G[sup o], and K[sub p]--for the isoprene dimerization reaction at various temperatures. These computational results suggest that, based upon thermodynamics, diprene and dipentene are about equally favored dimerization products of isoprene and that reported experimental data reflect kinetic control of dipentene formation at lower temperatures. The equilibrium thermodynamics data for the isoprene dimerization reaction presented in this paper are felt to be sufficiently reliable that they can be utilized in the absence of any additional experimental data. 13 refs., 4 figs., 7 tabs.

  14. Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface

    PubMed Central

    Lopes, Pedro E. M.; Murashov, Vladimir; Tazi, Mouhsine; Demchuk, Eugene; MacKerell, Alexander D.

    2008-01-01

    Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of ?-quartz, ab initio vibrational spectra and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of ?-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and space-time correlations of water oxygen atoms in terms of Van Hove self correlation functions. The Vibrational Density of States (VDOS) spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level. PMID:16471886

  15. Directly resolving particles in an electric field: local charge, force, torque, and applications

    NASA Astrophysics Data System (ADS)

    Liu, Qianlong

    2011-11-01

    Prosperetti's seminal Physalis method for fluid flows with suspended particles is extended to electric fields to directly resolve finite-sized particles and to investigate accurately the mutual fluid-particle, particle-particle, and particle-boundary interactions. The method can be used for uncharged/charged dielectrics, uncharged/charged conductors, conductors with specified voltage, and general weak and strong discontinuous interface conditions. These interface conditions can be in terms of field variable, its gradients, and surface integration which has not been addesed by other numerical methods. In addition, for the first time, we rigorously derive the force and torque on the finite-sized particles resulting from the interactions between harmonics. The method, for the first time, directly resolves the particles with accurate local charge distribution, force, and torque on the particles, making many applications in engineering, mechanics, physics, chemistry, and biology possible, such as heterogeneous materials, microfluidics, electrophotography, electric double layer capacitors, and microstructures of nanodispersions. The efficiency of the method is demonstrated with up to one hundred thousand 3D particles, which suggests that the method can be used for many important engineering applications of broad interest. This research is supported by the Department of Energy under funding for an EFRC (the HeteroFoaM Center), grant no. DE-SC0001061.

  16. NONLINEAR FORCE-FREE MAGNETIC FIELD FITTING TO CORONAL LOOPS WITH AND WITHOUT STEREOSCOPY

    SciTech Connect

    Aschwanden, Markus J., E-mail: aschwanden@lmsal.com [Lockheed Martin Advanced Technology Center, Solar and Astrophysics Laboratory, Org. ADBS, Bldg. 252, 3251 Hanover St., Palo Alto, CA 94304 (United States)

    2013-02-15

    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 {mu}{sub 2} = 2. Degree-Sign 7 {+-} 1. Degree-Sign 3 between the model field lines and observed loops, and an accuracy of Almost-Equal-To 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.

  17. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  18. Matching of additive and polarizable force fields for multiscale condensed phase simulations

    PubMed Central

    Baker, Christopher M.; Best, Robert B.

    2013-01-01

    Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 – 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures. PMID:23997691

  19. Investigation of force-freeness of a solar emerging magnetic field via application of the virial theorem to magnetohydrodynamic simulations

    NASA Astrophysics Data System (ADS)

    Kang, Jihye; Magara, Tetsuya

    2014-12-01

    Force-freeness of a solar magnetic field is a key to reconstructing the invisible coronal magnetic structure of an emerging flux region on the Sun where active phenomena such as flares and coronal mass ejections frequently occur. We have performed magnetohydrodynamic simulations which are adjusted to investigate force-freeness of an emerging magnetic field by using the virial theorem. Our focus is on how the force-free range of an emerging flux region develops and how it depends on the twist of a pre-emerged magnetic field. As an emerging flux region evolves, the upper limit of the force-free range continuously increases while the lower limit is asymptotically reduced to the order of a photospheric pressure scale height above the solar surface. As the twist becomes small the lower limit increases and then seems to be saturated. We also discuss the applicability of the virial theorem to an evolving magnetic structure on the Sun.

  20. Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation

    NASA Astrophysics Data System (ADS)

    Li, Zhenyu; Yu, Haibo; Zhuang, Wei; Mukamel, Shaul

    2008-02-01

    Molecular dynamics (MD) simulations are performed for N-methylacetamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the n?? and ??? transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue shifted n?? and ??? energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.

  1. Phase-field simulations of dendritic crystal growth in a forced flow

    SciTech Connect

    Tong, X.; Beckermann, C.; Karma, A.; Li, Q.

    2001-06-01

    Convective effects on free dendritic crystal growth into a supercooled melt in two dimensions are investigated using the phase-field method. The phase-field model incorporates both melt convection and thermal noise. A multigrid method is used to solve the conservation equations for flow. To fully resolve the diffuse interface region and the interactions of dendritic growth with flow, both the phase-field and flow equations are solved on a highly refined grid where up to 2.1 million control volumes are employed. A multiple time-step algorithm is developed that uses a large time step for the flow-field calculations while reserving a fine time step for the phase-field evolution. The operating state (velocity and shape) of a dendrite tip in a uniform axial flow is found to be in quantitative agreement with the prediction of the Oseen-Ivantsov transport theory if a tip radius based on a parabolic fit is used. Furthermore, using this parabolic tip radius, the ratio of the selection parameters without and with flow is shown to be close to unity, which is in agreement with linearized solvability theory for the ranges of the parameters considered. Dendritic sidebranching in a forced flow is also quantitatively studied. Compared to a dendrite growing at the same supercooling in a diffusive environment, convection is found to increase the amplitude and frequency of the sidebranches. The phase-field results for the scaled sidebranch amplitude and wavelength variations with distance from the tip are compared to linear Wentzel-Kramers-Brillouin theory. It is also shown that the asymmetric sidebranch growth on the upstream and downstream sides of a dendrite arm growing at an angle with respect to the flow can be explained by the differences in the mean shapes of the two sides of the arm.

  2. Compression and Suppression of Shifting Receptive Field Activity in Frontal Eye Field Neurons

    PubMed Central

    Cavanaugh, James; Wurtz, Robert H.

    2013-01-01

    Before each saccade, neurons in frontal eye field anticipate the impending eye movement by showing sensitivity to stimuli appearing where the neuron's receptive field will be at the end of the saccade, referred to as the future field (FF) of the neuron. We explored the time course of this anticipatory activity in monkeys by briefly flashing stimuli in the FF at different times before saccades. Different neurons showed substantial variation in FF time course, but two salient observations emerged. First, when we compared the time span of stimulus probes before the saccade to the time span of FF activity, we found a striking temporal compression of FF activity, similar to compression seen for perisaccadic stimuli in human psychophysics. Second, neurons with distinct FF activity also showed suppression at the time of the saccade. The increase in FF activity and the decrease with suppression were temporally independent, making the patterns of activity difficult to separate. We resolved this by constructing a simple model with values for the start, peak, and duration of FF activity and suppression for each neuron. The model revealed the different time courses of FF sensitivity and suppression, suggesting that information about the impending saccade triggering suppression reaches the frontal eye field through a different pathway, or a different mechanism, than that triggering FF activity. Recognition of the variations in the time course of anticipatory FF activity provides critical information on its function and its relation to human visual perception at the time of the saccade. PMID:24227735

  3. Acoustic Radiation Force on a Finite-Sized Particle due to an Acoustic Field in a Viscous Compressible Fluid

    NASA Astrophysics Data System (ADS)

    Annamalai, Subramanian; Parmar, Manoj; Balachandar, S.

    2013-11-01

    Particles when subjected to acoustic waves experience a time-averaged second-order force known as the acoustic radiation force, which is of prime importance in the fields of microfluidics and acoustic levitation. Here, the acoustic radiation force on a rigid spherical particle in a viscous compressible medium due to progressive and standing waves is considered. The relevant length scales include: particle radius (a), acoustic wavelength (?) and viscous penetration depth (?). While a / ? and a / ? are arbitrary, ? << ? . A farfield derivation approach has been used in determining the radiated force. Expressing the flow-field as a sum of the incident and scattered fields, an analytical expression for the force is obtained as a summation over infinite series (monopole, dipole and higher sources). These results indicate that the contributions from monopole, dipole and their cross-interaction are sufficient to describe the acoustic radiation force. Subsequently, the monopole and dipole strengths are represented in terms of the particle surface and volume averages of the incoming velocity. This generalization allows one to evaluate the radiation force for an incoming wave of any functional form. However acoustic streaming effects are neglected.

  4. NONLINEAR FORCE-FREE FIELD MODELING OF A SOLAR ACTIVE REGION USING SDO/HMI AND SOLIS/VSM DATA

    SciTech Connect

    Thalmann, J. K.; Wiegelmann, T. [Max-Plank-Institut fuer Sonnensystemforschung, Max-Planck-Str. 2, 37191 Katlenburg-Lindau (Germany); Pietarila, A. [National Solar Observatory, 950 N. Cherry Avenue, Tucson, AZ 85719 (United States); Sun, X., E-mail: thalmann@mps.mpg.de [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States)

    2012-08-15

    We use SDO/HMI and SOLIS/VSM photospheric magnetic field measurements to model the force-free coronal field above a solar active region, assuming magnetic forces dominate. We take measurement uncertainties caused by, e.g., noise and the particular inversion technique, into account. After searching for the optimum modeling parameters for the particular data sets, we compare the resulting nonlinear force-free model fields. We show the degree of agreement of the coronal field reconstructions from the different data sources by comparing the relative free energy content, the vertical distribution of the magnetic pressure, and the vertically integrated current density. Though the longitudinal and transverse magnetic flux measured by the VSM and HMI is clearly different, we find considerable similarities in the modeled fields. This indicates the robustness of the algorithm we use to calculate the nonlinear force-free fields against differences and deficiencies of the photospheric vector maps used as an input. We also depict how much the absolute values of the total force-free, virial, and the free magnetic energy differ and how the orientation of the longitudinal and transverse components of the HMI- and VSM-based model volumes compare to each other.

  5. Mechanism and kinetics for the initial steps of pyrolysis and combustion of 1,6-dicyclopropane-2,4-hexyne from ReaxFF reactive dynamics.

    PubMed

    Liu, Lianchi; Bai, Chen; Sun, Huai; Goddard, William A

    2011-05-19

    We report the kinetic analysis and mechanism for the initial steps of pyrolysis and combustion of a new fuel material, 1,6-dicyclopropane-2,4-hexyne, that has enormous heats of pyrolysis and combustion, making it a potential high-energy fuel or fuel additive. These studies employ the ReaxFF force field for reactive dynamics (RD) simulations of both pyrolysis and combustion processes for both unimolecular and multimolecular systems. We find that both pyrolysis and combustion initiate from unimolecular reactions, with entropy-driven reactions being most important in both processes. Pyrolysis initiates with extrusion of an ethylene molecule from the fuel molecule and is followed quickly by isomerization of the fuel molecule, which induces additional radicals that accelerate the pyrolysis process. In the combustion process, we find three distinct mechanisms for the O(2) attack on the fuel molecule: (1) attack on the cyclopropane, ring expanding to form the cyclic peroxide which then decomposes; (2) attack onto the central single bond of the diyne which then fissions to form two C(5)H(5)O radicals; (3) attack on the alkyne-cyclopropane moiety to form a seven-membered ring peroxide which then decomposes. Each of these unimolecular combustion processes releases energy that induces additional radicals to accelerate the combustion process. Here oxygen has major effects both as the radical acceptor and as the radical producer. We extract both the effective activation energy and the effective pre-exponential factor by kinetic analysis of pyrolysis and combustion from these ReaxFF simulations. The low value of the derived effective activation energy (26.18 kcal/mol for pyrolysis and 16.40 kcal/mol for combustion) reveals the high activity of this fuel molecule. PMID:21510658

  6. Sensitivity of an oceanic general circulation model forced by satellite wind stress fields

    NASA Astrophysics Data System (ADS)

    Grima, Nicolas; Bentamy, Abderrahim; Katsaros, Kristina; Quilfen, Yves; Delecluse, Pascale; Levy, Claire

    1999-04-01

    Satellite wind and wind stress fields at the sea surface, derived from the scatterometers on European Remote Sensing satellites 1 and 2 (ERS-1 and ERS-2) are used to drive the ocean general circulation model (OGCM) "OPA" in the tropical oceans. The results of the impact of ERS winds are discussed in terms of the resulting thermocline, current structures, and sea level anomalies. Their adequacy is evaluated on the one hand by comparison with simulations forced by the Arpege-Climat model and on the other hand by comparison with measurements of the Tropical Atmosphere-Ocean (TAO) buoy network and of the TOPEX/Poseidon altimeter. Regarding annual mean values, the thermal and current responses of the OGCM forced by ERS winds are in good agreement with the TAO buoy observations, especially in the central and eastern Pacific Ocean. In these regions the South Equatorial Current, the Equatorial Undercurrent, and the thermocline features simulated by the OGCM forced by scatterometer wind fields are described. The impact of the ERS-1 winds is particularly significant to the description of the main oceanic variability. Compared to the TAO buoy observations, the high-frequency (a few weeks) and the low-frequency of the thermocline and zonal current variations are described. The correlation coefficients between the time series of the thermocline simulated by ERS winds and that observed by the TAO buoy network are highly significant; their mean value is 0.73, over the whole basin width, while it is 0.58 between Arpege model simulation and buoy observations. At the equator the time series of the zonal current simulated by the ERS winds, at three locations (110°W, 140°W, and 165°E) and at two depths, are compared to the TAO current meter and acoustic Doppler current profiler (ADCP) measurements. The mean value of the significant correlation coefficients computed with the in situ measurements is 0.72 for ERS, while it is 0.51 for the Arpege-Climat model. Thus ERS wind fields through the OGCM generate more realistic current variations than those obtained with Arpege climate winds, and they are particularly efficient in capturing abrupt changes ("wind bursts") which may be important regarding ocean dynamics.

  7. Near-infrared contact mode collection near-field optical and normal force microscopy of modulated multiple quantum well lasers

    E-print Network

    Eisenstein, Gadi

    . Eisenstein,a) A. Lewis,b) J. M. Nielsen,c) and A. Mo"eller-Larsenc) Division of Applied Physics, The Hebrew is reported using bent normal force/near-field optical elements for simultaneous imaging of the light physics imaged with similar resolution. In this letter, we extend our development of bent near- field

  8. Comparison of objectively-analyzed SCM forcing fields with assimilated data from the June 1993 IOP for various siting scenarios

    SciTech Connect

    Cederwall, R.T.; Leach, M.J.; Dudhia, J. [National Center for Atmospheric Research, Boulder, CO (United States); Parsons, D.B. [National Center for Atmospheric Research, Boulder, CO (United States)

    1997-03-01

    The objective analysis method used for deriving Single-Column Model (SCM) forcing fields with ARM data has been evaluated for a variety of observation siting scenarios (Leach, et al., 1996). Our purpose was to assess the capability of the various siting scenarios to provide representative data for objective analysis and subsequent SCM forcing fields. That evaluation was performed with analytically prescribed input data, so that the results of the objective analysis could be compared with known analytic values. Here we extend that evaluation by using observed meteorological fields assimilated in a mesoscale model.

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

    SciTech Connect

    Vega, Ian; Detweiler, Steven [Institute for Fundamental Theory, Department of Physics, University of Florida, Gainesville, Florida 32611-8440 (United States)

    2008-04-15

    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 {approx}0.1% or better.

  10. Formal mathematical solutions of the force-free equations, spontaneous discontinuities, and dissipation in large-scale magnetic fields

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1990-01-01

    Direct integration of the force-free field equation del x B = alpha B, in the simple case of the local deformation of a laminar field, produces field configurations containing tangential discontinuities (current sheets). Whereas continuous solutions allow only restricted field topologies, the discontinuities provide the necessary release from those restrictions in more general topologies. Magnetic fields in nature are strongly deformed by convection, so as to contain significant internal discontinuities. The bipolar magnetic fields containing the active X-ray corona of the sun are a case in point. It appears that the dissipation caused by the discontinuities may be the primary heat source producing the X-ray corona.

  11. A Science Service Ff5ature Released upon receipt

    E-print Network

    A Science Service Ff5ature Released upon receipt but intended f o r use May 3, 1932 ? Wl, as well ae the distant blinking beacons far t o the northward along the two transcontinental airways acro, some airway stations located in auspicious places in this region frequently report v i s i b i l i t y

  12. 8. Elevation of west side of FF. Coal came from ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Elevation of west side of FF. Coal came from GG (breaker) to bins at top from which it dropped down in to ball mills and then sent it by conveyor to bunkers. Looking east - Rouge Steel Company, 3001 Miller Road, Dearborn, Wayne County, MI

  13. Vol. 45 No. 0 #ff#'##8# 2004 ###########~##### spi ##~##

    E-print Network

    Sumii, Eijiro

    Vol. 45 No. 0 #ff#'##š8# 2004 ###########~####�# spi ##¨~## up qw -- y z v t s yy x --- y r yy########### #####`0########Ÿ##fl##8######Abadi # Gordon # spi #### 6#53#\\Omega0 #2####spi ##############3 Security Protocols from Informal Notation into Spi Calculus Eijiro Sumii, y Hideaki Tatsuzawa yy

  14. MIT OpenCourseWare: Fields, Forces, and Flows in Biological Systems

    NSDL National Science Digital Library

    Materials from this intriguingly titled Massachusetts Institute of Technology (MIT) course about biological systems are freely available to students, educators, and others through MIT's OpenCourseWare. The course covers a variety of topics including "conduction, diffusion, convection in electrolytes; fields in heterogeneous media; electrical double layers; Maxwell stress tensor and electrical forces in physiological systems; and fluid and sold continua: equations of motion useful for porous, hydrated biological tissues. Case studies considered include membrane transport; electrode interfaces; electrical, mechanical, and chemical transduction in tissues; electrophoretic and electroosmotic flows; diffusion/reaction; and ECG." This OpenCourseWare website provides downloadable notes for 25 lectures; seven downloadable assignments with solutions; and a pdf version of the final exam. The site links to an open, online discussion group for the course as well.

  15. Generalized Valence-Force-Field Model of (Ga,In)(N,P) Ternary Alloys

    SciTech Connect

    Biswas, K.; Franceschetti, A.; Lany, S.

    2008-01-01

    We present a generalized valence-force-field (VFF) model for the ternary III-V alloys (III=Ga, In and V=N, P) to predict the formation energies and atomic structures of ordered and disordered alloy configurations. For each alloy (GaInN, GaInP, GaNP, and InNP) the VFF parameters, which include bond-angle/bond-length interactions, are fitted to the first-principles calculated formation energies of 30 ternary structures. Compared to standard approaches where the VFF parameters are transferred from the individual binary III-V compounds, our generalized VFF approach predicts alloy formation energies and atomic structures with considerably improved accuracy. Using this generalized approach and random realizations in large supercells (4096 atoms), we determine the temperature-composition phase diagram, i.e., the binodal and spinodal decomposition curves, of the (Ga, In) (N, P) ternary alloys.

  16. Trihydrogen cation with neon and argon: structural, energetic, and spectroscopic data from quartic force fields.

    PubMed

    Theis, Riley A; Fortenberry, Ryan C

    2015-05-21

    The argonium cation, ArH(+), has been previously detected in nature for the first time. This cation is believed to form through the gas-phase reaction of Ar(+) and H2. In this work, quantum chemical techniques show that the reaction of Ar and H3(+) may be a viable alternative or contributor to the creation of ArH(+) corroborating previous analysis. In order to further evaluate this claim, highly accurate quartic force field computations are used to produce spectroscopic data and anharmonic vibrational frequencies for ArH3(+) in its 18 isotopologues. NeH3(+) is also analyzed but has a low Ne-H3(+) dissociation barrier. Therefore, it less likely to be observed. Consequently, NeH(+) is also unlikely to be formed from NeH3(+) as it was also not from NeH2(+). PMID:25923978

  17. Nonlinear restoring forces and geometry influence on stability in near-field acoustic levitation

    NASA Astrophysics Data System (ADS)

    Li, Jin; Liu, Pinkuan; Ding, Han; Cao, Wenwu

    2011-04-01

    Stability is a key factor in near-field acoustic levitation (NFAL), which is a popular method for noncontact transportation of surface-sensitive objects. Since the physical principle of NFAL is based on nonlinear vibration and nonuniform pressure distribution of a plate resonator, traditional linearized stability analysis cannot address this problem correctly. We have performed a theoretical analysis on the levitation stability using a nonlinear squeeze film model including inertia effects and entrance pressure drop, and obtained nonlinear effective restoring force and moment. It was found that the nonuniform pressure distribution is mode-dependent, which determines the stability of the levitation system. Based on the theoretical understanding, we have designed a NFAL resonator with tapered cross section, which can provide higher stability for the levitating object than the rectangular cross-section resonator.

  18. A coarse-grain force-field for xylan and its interaction with cellulose.

    PubMed

    Li, Liang; Pérré, Patrick; Frank, Xavier; Mazeau, Karim

    2015-08-20

    We have built a coarse-grain (CG) model describing xylan and its interaction with crystalline cellulose surfaces. Each xylosyl or glucosyl unit was represented by a single grain. Our calculations rely on force-field parameters adapted from the atomistic description of short xylan fragments and their adsorption on cellulose. This CG model was first validated for xylan chains both isolated and in the bulk where a good match was found with its atomistic counterpart as well as with experimental measurements. A similar agreement was also found when short xylan fragments were adsorbed on the (110) surface of crystalline cellulose. The CG model, which was extended to the (100) and (1-10) surfaces, revealed that the adsorbed xylan, which was essentially extended in the atomistic situation, could also adopt coiled structures, especially when laying on the hydrophobic cellulose surfaces. PMID:25965503

  19. Electric-field-induced force on a charged spherical colloid embedded in an electrolyte-saturated Brinkman medium

    NASA Astrophysics Data System (ADS)

    Hill, Reghan J.

    2006-04-01

    When an electric field is applied to an electrolyte-saturated polymer gel immobilizing charged colloidal particles, the force that must be exerted by the hydrogel on each particle reflects a delicate balance of electrical and hydrodynamic stresses. This article adopts a simple boundary-layer analysis to derive a convenient formula for the force in terms of the particle, electrolyte and gel characteristics. Comparisons with numerically exact solutions of the full set of electrokinetic transport equations are presented. These reveal that a fortuitous cancellation of errors leads to reasonably accurate predictions of the force over a much wider range of the parameter space than should be expected. It is noteworthy that, in gels with low permeability, an adverse pressure gradient yields a net force that exceeds the bare electrical force. The analytical theory also provides a convenient formula for the incremental pore mobility, which is a convenient measure of the electro-osmotic pumping capacity of dilute random arrays of charged inclusions.

  20. Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

    PubMed Central

    Collier, Galen; Vellore, Nadeem A.; Yancey, Jeremy A.; Stuart, Steven J.; Latour, Robert A.

    2012-01-01

    All-atom empirical molecular mechanics protein force fields, which have been developed to represent the energetics of peptide folding behavior in aqueous solution, have not been parameterized for protein interactions with solid material surfaces. As a result, their applicability for representing the adsorption behavior of proteins with functionalized material surfaces should not be assumed. To address this issue, we conducted replica-exchange molecular dynamics simulations of the adsorption behavior of structured peptides to functionalized surfaces using three protein force fields that are widely used for the simulation of peptide adsorption behavior: CHARMM22, AMBER94, and OPLS-AA. Simulation results for peptide structure both in solution and when adsorbed to the surfaces were compared to experimental results for similar peptide-surface systems to provide a means of evaluating and comparing the performance of these three force fields for this type of application. Substantial differences in both solution and adsorbed peptide conformations were found amongst these three force fields, with the CHARMM22 force field found to most closely match experimental results. PMID:22589067

  1. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling

    PubMed Central

    Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu; Hatcher, Elizabeth; Vanommeslaeghe, Kenno; Foster, Theresa J.; Jamison, Francis W.; MacKerell, Alexander D.

    2011-01-01

    Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model. PMID:22125473

  2. Electro-elastic fields of piezoelectric materials with an elliptic hole under uniform internal shearing forces

    NASA Astrophysics Data System (ADS)

    Du, Yanliang; Liu, Shuhong; Duan, Shijie; Li, Yanqiang

    2013-05-01

    The existing investigations on piezoelectric materials containing an elliptic hole mainly focus on remote uniform tensile loads. In order to have a better understanding of the fracture behavior of piezoelectric materials under different loading conditions, theoretical and numerical solutions are presented for an elliptic hole in transversely isotropic piezoelectric materials subjected to uniform internal shearing forces based on the complex potential approach. By solving ten variable linear equations, the analytical solutions inside and outside the hole satisfying the permeable electric boundary conditions are obtained. Taking PZT-4 ceramic into consideration, numerical results of electro-elastic fields along the edge of the hole and axes, and the electric displacements in the hole are presented. Comparison with stresses in transverse isotropic elastic materials shows that the hoop stress at the ends of major axis in two kinds of material equals zero for the various ratios of major to minor axis lengths; If the ratio is greater than 1, the hoop stress in piezoelectric materials is smaller than that in elastic materials, and if the ratio is smaller than 1, the hoop stress in piezoelectric materials is greater than that in elastic materials; When it is a circle hole, the shearing stress in two materials along axes is the same. The distribution of electric displacement components shows that the vertical electric displacement in the hole and along axes in the material is always zero though under the permeable electric boundary condition; The horizontal and vertical electric displacement components along the edge of the hole are symmetrical and antisymmetrical about horizontal axis, respectively. The stress and electric displacement distribution tends to zero at distances far from the elliptical hole, which conforms to the conclusion usually made on the basis of Saint-Venant's principle. Unlike the existing work, uniform shearing forces acting on the edge of the hole, and the distribution of electro-elastic fields inside and outside the elliptic hole are considered.

  3. Infrared and Raman spectra of bicyclic molecules using scaled noncorrelated and correlated ab initio force fields

    NASA Astrophysics Data System (ADS)

    Collier, William B.; Magdó, Ildikó; Klots, Timothy D.

    1999-03-01

    This paper reports the application of a scaled ab initio calculated harmonic force field to predict the frequencies, infrared intensities, Raman intensities, and depolarization ratios of benzofuran, benzothiophene, indole, benzothiazole, and benzoxazole. The theoretical calculations were made using the Hartree-Fock HF/3-21G* and HF/6-31G* basis sets and density-functional theory (DFT)B3-LYP/6-31G* levels. The equilibrium calculated force constants are scaled according to the method of Pulay and compared with the experimentally determined frequencies, intensities, and depolarization ratios to assess the accuracy and fit of the theoretical calculation. Methods for quantitative comparison of intensities were developed. The double numerical differentiation algorithm of Komornicki and McIver was analyzed and used to calculate the Raman intensities for the (DFT)B3-LYP/6-31G* model. The (DFT)B3-LYP/6-31G* model is approaching the harmonic limit in the planar and nonplanar refinement of these bicyclics with wave number fits of 5 and 4 cm-1, respectively. It reduces the need for scale factors and increases their transfer accuracy, largely because the scale factors values cluster near unity. The Komornicki and McIver algorithm is still a viable method for calculating Raman intensity information for methods that do not have analytic routines programmed. The main shortcoming to this method may lie in the tighter self-consistent field (SCF) convergence criterion possibly needed to calculate Raman intensities for the totally symmetric modes of large molecules. The (DFT)B3-LYP/6-31G* model was superior for calculating the planar intensities, but equal to the HF methods for predicting the nonplanar intensities.

  4. Utilization of efficient gradient and Hessian computations in the force field optimization process of molecular simulations

    NASA Astrophysics Data System (ADS)

    Hülsmann, Marco; Kopp, Sonja; Huber, Markus; Reith, Dirk

    2013-01-01

    Computer simulations of chemical systems, especially systems of condensed matter, are highly important for both scientific and industrial applications. Thereby, molecular interactions are modeled on a microscopic level in order to study their impact on macroscopic phenomena. To be capable of predicting physical properties quantitatively, accurate molecular models are indispensable. Molecular interactions are described mathematically by force fields, which have to be parameterized. Recently, an automated gradient-based optimization procedure was published by the authors based on the minimization of a loss function between simulated and experimental physical properties. The applicability of gradient-based procedures is not trivial at all because of two reasons: firstly, simulation data are affected by statistical noise, and secondly, the molecular simulations required for the loss function evaluations are extremely time-consuming. Within the optimization process, gradients and Hessians were approximated by finite differences so that additional simulations for the respective modified parameter sets were required. Hence, a more efficient approach to computing gradients and Hessians is presented in this work. The method developed here is based on directional instead of partial derivatives. It is compared with the classical computations with respect to computation time. Firstly, molecular simulations are replaced by fit functions that define a functional dependence between specific physical observables and force field parameters. The goal of these simulated simulations is to assess the new methodology without much computational effort. Secondly, it is applied to real molecular simulations of the three chemical substances phosgene, methanol and ethylene oxide. It is shown that up to 75% of the simulations can be avoided using the new algorithm.

  5. Nanoscopic imaging of human chromosomes via a scanning near-field optical\\/atomic-force microscopy (SNOAM)

    Microsoft Academic Search

    Eiichi Tamiya; Masato Saito; Shinichirou Iwabuchi; Yasutaka Morita

    2003-01-01

    Scanning near-field optical\\/atomic-force microscopy (SNOAM) provided us with simultaneous topographic and fluorescence images of human chromosomes. The SNOAM uses a bent optical fiber simultaneously as a dynamic mode atomic force microscopy cantilever. Optical resolution was approximately 50–100 nm in fluorescence mode. Conventional karyotyping information was linked with SNOAM topographic analyses such as location of centromere and length of individual chromosomes.

  6. Compatibility of the Chameleon-Field Model with Fifth-Force Experiments, Cosmology, and PVLAS and CAST Results

    SciTech Connect

    Brax, Philippe; Bruck, Carsten van de; Davis, Anne-Christine [Service de Physique Theorique, Commissariat a l'Energie Atomique-Saclay, 91191 Gif-sur-Yvette Cedex (France); Department of Applied Mathematics, University of Sheffield, Hounsfield Road, Sheffield S3 7RH (United Kingdom); Department of Applied Mathematics and Theoretical Physics, Center for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 OWA (United Kingdom)

    2007-09-21

    We analyze the PVLAS results using a chameleon field whose properties depend on the environment. We find that, assuming a runaway bare potential V({phi}) 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.

  7. Characterization of magnetic force microscopy probe tip remagnetization for measurements in external in-plane magnetic fields

    SciTech Connect

    Weis, Tanja; Engel, Dieter; Ehresmann, Arno [Institute of Physics and Centre for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel (Germany); Krug, Ingo [DSM IRAMIS SPCSI, CEA-Saclay, 91191 Gif sur Yvette (France); Hoeink, Volker; Schmalhorst, Jan; Reiss, Guenter [Department of Physics, Thin Films and Nanostructures, Bielefeld University, P.O. Box 100131, 33501 Bielefeld (Germany)

    2008-12-15

    A quantitative analysis of magnetic force microscopy (MFM) images taken in external in-plane magnetic fields is difficult because of the influence of the magnetic field on the magnetization state of the magnetic probe tip. We prepared calibration samples by ion bombardment induced magnetic patterning with a topographically flat magnetic pattern magnetically stable in a certain external magnetic field range for a quantitative characterization of the MFM probe tip magnetization in point-dipole approximation.

  8. Accuracy analysis and application of extrapolation of force-free fields in solar active and quiet regions

    NASA Astrophysics Data System (ADS)

    Liu, Suo; Zhang, Hongqi; Su, Jiangtao; Song, Mutao

    2013-07-01

    In this paper, the availability, applicability and deviation of nonlinear force-free (NLFF) fields extrapolated by Approximate Vertical Integration (AVI), Boundary Integral Equation (BIE) and Optimization (Opt.) methods are studied based on the comparison with two semi-analytical fields (Low & Lou 1990). These NLFF extrapolations based on the observational vector magnetograms are used to study the spatial magnetic field in the quiet Sun.

  9. Evaluation of the Effect of Gravity Force on Transient Mass Diffusion Fields

    NASA Astrophysics Data System (ADS)

    Komiya, Atsuki; Maruyama, Shigenao

    In this study, the relationship between gravitational force and diffusion phenomena in aque-ous solutions is discussed. The microgravity environment gives a high quality crystal growth condition which produces high quality medicines or foods. In this condition, a natural con-vection can be neglected and diffusion phenomenon without convection is observed. The mass diffusion coefficient is one of the most important thermophysical properties to investigate that mass transport system. However, the available experimental data of mass diffusion coefficients in microgravity conditions is not enough. Because it is quite a few opportunity that exper-iments can be conducted using facilities which produce microgravity environment for a long time. Then we have developed an observation system of small transient diffusion fields within 20 seconds. The experimental apparatus is composed of phase shifting interferometer, special designed signal processing unit and recorder. The mechanism of test cell used in this study has a unique performance that the transient diffusion fields can be produced continuously with no change of solutions and cell. Therefore this system can be applied to short-time microgravity experiment which is generated by the parabolic flight of an airplane. By using this system, the transient diffusion field of Sodium Chloride (NaCl) solution in microgravity conditions could be clearly observed and the mass diffusion coefficient was estimated from the obtained data. In microgravity condition, the transient diffusion fields have different appearances from the normal gravity condition. A slight acceleration governs the transient diffusion fields because of no density difference, so vibrations applied the apparatus disturb the transient diffusion fields. The measured mass diffusion coefficient has been estimated as a smaller value compared with ones under normal gravity condition. Using the airplane as a facility, not only microgravity condition but also 0.8G, 1.5G or varied gravity level conditions can be generated during flight experiments. On the sudden change of gravity level from microgravity to 1.5G, different ap-pearances in the transient diffusion fields could be observed. The mass diffusion coefficient depends on measurement time. From this phenomenon, it is possible to guess that the dynamic re-clustering process may occur in the solutions.

  10. Atomic force microscope based near-field imaging for probing cell surface interactions

    NASA Astrophysics Data System (ADS)

    Amini, Sina

    Near-membrane and trans-membrane proteins and their interactions with the extracellular matrix (ECM) can yield valuable information about cell dynamics. However, advances in the field of nanoscale cellular processes have been hindered, in part, due to limits imposed by current technology. In this work, a novel evanescent field (EF) imaging technique is designed, modeled, created and tested for near-field imaging in the apical surface of cells. This technique and Forster resonance energy transfer (FRET) were used to investigate interactions between integrins on the cell surface and the ECM protein, fibronectin. The goal was to monitor changes in the integrin density at the cell surface as a function of clustering after binding to fibronectin on the microsphere surface. For the EF technique, quantum dot (QD)-embedded polystyrene microspheres were used to couple light into whispering gallery modes (WGMs) inside the microspheres; the resulting EF at the surface of the microsphere was used as a near-field excitation source with ~50 nm axial resolution for exciting fluorescently-labeled integrins. For FRET measurements (~10 nm axial resolution), QDs (donors) were coated on the surface of microspheres and energy transfer to red fluorescent protein (RFP)-integrin constructs (acceptors) studied. In both techniques, the QD-modified microspheres were mounted on atomic force microscope (AFM) cantilevers, functionalized with fibronectin, and brought into contact with fluorescently-labeled HeLa or vascular smooth muscle (VSM) cells. The results obtained from both methods show the clustering and activity of the integrins and are in good agreement with each other. Amsterdam discrete dipole approximation (ADDA) was used to study the effects of inhomogeneous surrounding refractive index on the quality factor and position of the WGMs due to the attachment of a microsphere to an AFM cantilever. WGMs of various QD-embedded microspheres mounted on AFM cantilevers were experimentally measured and shown to be consistent with the model.

  11. Capillary Force-Driven, Hierarchical Co-Assembly of Dandelion-Like Peptide Microstructures.

    PubMed

    Wang, Yuefei; Huang, Renliang; Qi, Wei; Xie, Yanyan; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2015-06-01

    The wetting and drying of drops on flexible fibers occurs ubiquitously in nature, and the capillary force underlying this phenomenon has motivated our great interest in learning how to direct supramolecular self-assembly. Here, the hierarchical co-assembly of two aromatic peptides, diphenylalanine (FF) and ferrocene-diphenylalanine (Fc-FF), is reported via sequential, combinatorial assembly. The resulting dandelion-like microstructures have highly complex architectures, where FF microtube arrays serve as the scapes and the Fc-FF nanofibers serve as the flower heads. Homogeneous FF microtubes with diameters tailored between 1 and 9 ?m and wall thickness ranging from 70 to 950 nm are initially formed by controlling the degree of supersaturation of the FF and the water content. Once the FF microtubes are formed, the growth of the dandelion-like microstructures is then driven by the capillary force, derived from the wetting and drying of the Fc-FF solution on the FF microtubes. This simple and ingenious strategy offers many opportunities to develop new and creative methods for controlling the hierarchical self-assembly of peptides and thus building highly complex nano and microstructures. PMID:25759325

  12. Molecular modelling of (? 6-arene)-Cr(CO) 3 complex systems: force field development of the monosubstituted complexes

    NASA Astrophysics Data System (ADS)

    Elass, A.; Mahieu, J.; Brocard, J.; Surpateanu, G.; Vergoten, G.

    1999-02-01

    In the present article we report our research on the (? 6-arene)-Cr(CO) 3 rotational barrier and its preferred stable conformation. We propose a molecular mechanics force field to describe the arene-Cr(CO) 3 rotation and the arene-metal bonding strength. The proposed torsional term is defined as both the contribution of the arene-(CO) 3 non-bonded barriers and the arene-Cr electrostatic energy. In order to allow reliable validation of the chosen model, we have first performed a vibrational calculation on the benzene-Cr(CO) 3 and durene-Cr(CO) 3 complexes. Our molecular mechanics parameters were implemented into the S YBYL force field. Comparison with other theoretical methods, S YBYL, M ERCK force fields and PM3(tm) semi-empirical method in the S PARTAN package is also given.

  13. Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride).

    PubMed

    Lachet, V; Teuler, J-M; Rousseau, B

    2015-01-01

    A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems. PMID:25479370

  14. Stess field in Brazil: First and Second-Order Stress Patterns: Examples of Regional Forces Controlling the Stress Field

    NASA Astrophysics Data System (ADS)

    Dias, F.; Assumpcao, M.

    2012-12-01

    The knowledge of stress field is fundamental not only to understand driving forces and plate deformation as also it helps in the study of intraplate seismicity. In Brazil, we find reverse, strike-slip and normal mechanisms that indicates a variable stress field. The stress field has been mainly obtained using focal mechanism results and a few breakout data and in-situ measurements. However the stress field is still poorly known in Brazil. Recent earthquake focal mechanisms were determinate using P-wave modeling of seismogram stacks of several teleseismic stations ( > 30°) grouped according to distance and azimuth and first motion polarities. Every record was visually inspected and those with a good signal/noise ratio (SNR) were grouped in latitude-longitude windows of ten degrees and stacked. We usually consider groups with at least two stations, but, in sometimes a good record of single station with different azimuth was also used to constrain the focal depth. The P, pP, sP wavetrains of the stacked signals were modelled using the hudson96 program of Herrman seismology package (Herrman, 2002). We also determinate moment tensor of same events in the central region. The major difficulty is to determinate focal mechanism of low magnitudes events (< 4.0 mb) using distants seismograph stations. The central region shows a purely compressional pattern which are predicted by regional theoretical models (Richardson & Coblentz, 1996 and the TD0 model of Lithgow& Bertelloni, 2004). Meanwhile in the Amazonic region we find a SHmax from E-W to SE-NW probably caused by Caribbean and South American plates interaction (Meijer, 1995). In NE region, the compression rotates following the coast line which indicates an important component regional present in stress field spreading effects due to the continental/oceanic crustal (Assumpção, 1998) and cases of stress caused by sedimentary load in Amazon Fan in agreement local theoretical models (Watts et al., 2009). We determinate the focal mechanism of several events in Brazil using different techniques according to the available data. We find examples of stress perturbations induced by local effects (e.g. flexure and continental spreading) . The results of this work should be useful for futures stress field numerical modeling. References: Assumpção,M.,1998.Seismicity and stresses in the Brazilian passive margin. Bull. Seism. Soc. Am., 88 (1),160-169. Coblentz, D.D. and Richardson, R.M. 1996. Analysis of the South America intraplate stress field. Journal of Geophysical Research 101: 8.643-8.657. Herrmann, R. B. (2002). Computer programs in seismology, St. Louis University Earthquake Center, St. Louis, Missouri, www.eas.slu .edu/eqc/eqccps.html. Lithgow-Bertelloni, C., & J.H. Guynn, 2004. Origin of the lithospheric stress field. J. Geophys. Res., 109, B01408, doi:10.1029/2003JB002467. Meijer, P.T., 1995. Dynamics of active continental margins: the Andes and the Aegean regions. PhD Thesis, Utrecht University, The Netherlands. Watts, A. B., M. Rodger, C. Peirce, C. J. Greenroyd, and R. W. Hobbs (2009), Seismic structure, gravity anomalies, and flexure of the Amazon continental margin, NE Brazil, J. Geophys. Res., 114, B07103, doi:10.1029/2008JB006259.

  15. Components of the gravitational force in the field of a gravitational wave

    E-print Network

    D. Baskaran; L. P. Grishchuk

    2004-07-14

    Gravitational waves bring about the relative motion of free test masses. The detailed knowledge of this motion is important conceptually and practically, because the mirrors of laser interferometric detectors of gravitational waves are essentially free test masses. There exists an analogy between the motion of free masses in the field of a gravitational wave and the motion of free charges in the field of an electromagnetic wave. In particular, a gravitational wave drives the masses in the plane of the wave-front and also, to a smaller extent, back and forth in the direction of the wave's propagation. To describe this motion, we introduce the notion of `electric' and `magnetic' components of the gravitational force. This analogy is not perfect, but it reflects some important features of the phenomenon. Using different methods, we demonstrate the presence and importance of what we call the `magnetic' component of motion of free masses. It contributes to the variation of distance between a pair of particles. We explicitely derive the full response function of a 2-arm laser interferometer to a gravitational wave of arbitrary polarization. We give a convenient description of the response function in terms of the spin-weighted spherical harmonics. We show that the previously ignored `magnetic' component may provide a correction of up to 10 %, or so, to the usual `electric' component of the response function. The `magnetic' contribution must be taken into account in the data analysis, if the parameters of the radiating system are not to be mis-estimated.

  16. Current sheet formation in a sheared force-free-magnetic field. [in sun

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard

    1989-01-01

    This paper presents the results of a study showing how continuous shearing motion of magnetic footpoints in a tenuous, infinitely conducting plasma can lead to the development of current sheets, despite the absence of such sheets or even of neutral points in the initial state. The calculations discussed here verify the earlier suggestion by Low and Wolfson (1988) that extended current sheets should form due to the shearing of a force-free quadrupolar magnetic field. More generally, this work augments earlier studies suggesting that the appearance of discontinuities - current sheets - may be a necessary consequence of the topological invariance imposed on the magnetic field geometry of an ideal MHD system by virtue of its infinite conductivity. In the context of solar physics, the work shows how the gradual and continuous motion of magnetic footpoints at the solar photosphere may lead to the buildup of magnetic energy that can then be released explosively when finite conductivity effects become important and lead to the rapid dissipation of current sheets. Such energy release may be important in solar flares, coronal mass ejections, and other eruptive events.

  17. Haptic Manipulation of Microspheres Using Optical Tweezers Under the Guidance of Artificial Force Fields

    E-print Network

    Bukusoglu, Ibrahim; Kiraz, Alper; Kurt, Adnan

    2007-01-01

    Using optical tweezers and a haptic device, microspheres having diameters ranging from 3 to 4 um (floating in a fluid solution) are manipulated in order to form patterns of coupled optical microresonators by assembling the spheres via chemical binding. For this purpose, biotin-coated microspheres trapped by a laser beam are steered and chemically attached to an immobilized streptavidin-coated sphere (i.e. anchor sphere) one by one using an XYZ piezo scanner controlled by a haptic device. The positions of all spheres in the scene are detected using a CCD camera and a collision-free path for each manipulated sphere is generated using the potential field approach. The forces acting on the manipulated particle due to the viscosity of the fluid and the artificial potential field are scaled and displayed to the user through the haptic device for better guidance and control during steering. In addition, a virtual fixture is implemented such that the desired angle of approach and strength are achieved during the bind...

  18. A modification of the force field approach to describe sub neutron monitor energies

    NASA Astrophysics Data System (ADS)

    Herbst, K.; Gieseler, J.; Heber, B.; Kühl, P.

    2014-12-01

    As they propagate through the heliosphere, Galactic Cosmic Rays (GCRs) are modulated by various effects before they are detected at Earth. This transport can be described by the Parker equation (Parker, 1965). It calculates the phase space distribution of GCRs depending on the main modulation processes: convection, drifts, diffusion and adiabatic energy changes. A first order approximation of this equation is the force field approach, reducing it to a one-parameter dependency, the solar modulation potential. Utilizing this approach, Usoskin et al. (2005; 2011) reconstructed the solar modulation potential between 1936 and 2010, which by now is commonly used in many fields. However, it has been shown previously e.g. by Herbst et al. (2010) that the solar modulation potential depends not only on the Local Interstellar Spectrum (LIS) but also on the energy range of interest. Using the LIS by Usoskin et al. (2005) together with published proton intensity spectra obtained by PAMELA as well as neutron monitor and spacecraft measurements, we have investigated this energy dependence further. As expected, the results show severe limitations at lower energies including a strong dependence on the solar magnetic epoch. Based on these results, we will present a tool to describe GCR proton spectra in the energy range from a few hundred MeV to 40 GeV over the last four solar cycles.

  19. Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields

    PubMed Central

    Allen, Toby W.; Andersen, Olaf S.; Roux, Benoit

    2006-01-01

    We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence of the PMF, finite size effects, and lipid hydrocarbon chain polarizability. When comparing the modern all-atom force fields of CHARMM27 and AMBER94, we found that a fairly consistent picture emerges, and that both AMBER94 and CHARMM27 predict observables that are in semiquantitative agreement with both the experimental conductance and dissociation coefficient. Even small changes in the force field, however, result in significant changes in permeation energetics. Furthermore, the full two-dimensional free-energy surface describing permeation reveals the location and magnitude of the central barrier and the location of two binding sites for K+ ion permeation near the channel entrance—i.e., an inner site on-axis and an outer site off-axis. We conclude that the MD-PMF approach is a powerful tool for understanding and predicting the function of narrow ion channels in a manner that is consistent with the atomic and thermally fluctuating nature of proteins. PMID:16500984

  20. Combined influences of gravitoinertial force level and visual field pitch on visually perceived eye level.

    PubMed

    DiZio, P; Li, W; Lackner, J R; Matin, L

    1997-01-01

    Psychophysical measurements of the level at which observers set a small visual target so as to appear at eye level (VPEL) were made on 13 subjects in 1.0 g and 1.5 g environments in the Graybiel Laboratory rotating room while they viewed a pitched visual field or while in total darkness. The gravitoinertial force was parallel to the z-axis of the head and body during the measurements. The visual field consisted of two 58 degrees high, luminous, pitched-from-vertical, bilaterally symmetric, parallel lines, viewed in otherwise total darkness. The lines were horizontally separated by 53 degrees and presented at each of 7 angles of pitch ranging from 30 degrees with the top of the visual field turned away from the subject (top backward) to 30 degrees with the top turned toward the subject (top forward). At 1.5 g, VPEL changed linearly with the pitch of the 2-line stimulus and was depressed with top backward pitch and elevated with top forward pitch as had been reported previously at 1.0 g (1,2); however, the slopes of the VPEL-vs-pitch functions at 1.0 g and 1.5 g were indistinguishable. As reported previously also (3,4), the VPEL in darkness was considerably lower at 1.5 g than at 1.0 g; however, although the y-intercept of the VPEL-vs-pitch function in the presence of the 2-line visual field (visual field erect) was also lower at 1.5 g than at 1.0 g as it was in darkness, the G-related difference was significantly attenuated by the presence of the visual field. The quantitative characteristics of the results are consistent with a model in which VPEL is treated as a consequence of an algebraic weighted average or a vector sum of visual and nonvisual influences although the two combining rules lead to fits that are equally good. PMID:9376912

  1. Simulation of near-field optical manipulator using the combination of a near-field scanning optical microscope probe and an atomic force microscope metallic probe

    NASA Astrophysics Data System (ADS)

    Liu, Binghui; Yang, Lijun; Wang, Yang

    2011-05-01

    We propose a physical model to calculate the trapping force on a nanoparticle trapped by the system using the combination of a near-field scanning optical microscope (NSOM) probe and an atomic force microscope (AFM) metallic probe. Such a near-field trap is produced by evanescent illumination from the NSOM probe and light scattering at the tip of the AFM metallic probe. By using the Maxwell stress tensor through the electric field distribution obtained with the three-dimensional finite difference time domain (3-D FDTD) method, the dependence of the trapping force on the system parameters is discussed, and trapping properties including near-field distribution, trapping position, and the role of other forces versus trapping force are revealed. The results indicate that a particle down to tens of nanometers in size can be trapped toward the tip of an AFM probe with a lower laser intensity (˜1040 W/mm2) than that required by conventional optical manipulators (˜105 W/mm2).

  2. Measurements of the force fields within an acoustic standing wave using holographic optical tweezers

    SciTech Connect

    Bassindale, P. G.; Drinkwater, B. W. [Faculty of Engineering, Queens building, University of Bristol, Bristol BS8 1TR (United Kingdom); Phillips, D. B. [Department of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Barnes, A. C. [Department of Physics, H.H.Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL (United Kingdom)

    2014-04-21

    Direct measurement of the forces experienced by micro-spheres in an acoustic standing wave device have been obtained using calibrated optical traps generated with holographic optical tweezers. A micro-sphere, which is optically trapped in three dimensions, can be moved through the acoustic device to measure forces acting upon it. When the micro-sphere is subjected to acoustic forces, it's equilibrium position is displaced to a position where the acoustic forces and optical forces are balanced. Once the optical trapping stiffness has been calibrated, observation of this displacement enables a direct measurement of the forces acting upon the micro-sphere. The measured forces are separated into a spatially oscillating component, attributed to the acoustic radiation force, and a constant force, attributed to fluid streaming. As the drive conditions of the acoustic device were varied, oscillating forces (>2.5 pN{sub pp}) and streaming forces (<0.2 pN) were measured. A 5??m silica micro-sphere was used to characterise a 6.8?MHz standing wave, ??=?220??m, to a spatial resolution limited by the uncertainty in the positioning of the micro-sphere (here to within 2?nm) and with a force resolution on the order of 10 fN. The results have application in the design and testing of acoustic manipulation devices.

  3. Natural frequencies of a pre-twisted blade in a centrifugal force field

    NASA Astrophysics Data System (ADS)

    Sinha, Sunil K.; Turner, Kevin E.

    2011-05-01

    In this paper, starting with the thin shell theory, the governing partial differential equation of motion for the transverse deflection of a rotating pre-twisted plate is derived. Strain-displacement relationships include the effect of warping of the cross-section due to twist-bend coupling effect introduced as a result of pre-twist in the plate of non-circular (rectangular) cross-section. Then the equation of motion, thus derived, is used to formulate the free vibration of a typical turbo-machinery cantilevered airfoil blade by considering it as a plate of an equivalent rectangular cross-section subjected to a quasi-static load due to centrifugal force field. The analytical derivation considers both the stress-stiffening as well as stress-softening effects of the centrifugal forces on the spinning airfoil. The partial differential equation governing the flexural motion of the plate is transformed into a matrix-eigenvalue form using a Rayleigh-Ritz technique. The plate deformations are represented by a set of 'admissible' sinusoidal trial functions, which fully satisfy all the clamped-end constrains as well as the free-edge boundary conditions. The results of the analytical model exhibit an excellent agreement with the previously published test data both for thin and thick plate geometries and even in highly twisted configurations. The results of the eigenvalue solution are presented in a non-dimensional form for plates of varying aspect ratios and different amounts of pre-twist in the plate. The numerical results are directly applicable in determining the static and running frequencies of typical blades used in turbo-machinery.

  4. Recent advances toward a general purpose linear-scaling quantum force field.

    PubMed

    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 simultaneously achieve very high accuracy and efficiency. The efficiency of the QMFF is made possible by partitioning the system into fragments and self-consistently solving for the fragment-localized molecular orbitals in the presence of the other fragment's electron densities. Unlike a LSQM, the QMFF introduces empirical parameters that are tuned to obtain very accurate intermolecular forces. The speed and accuracy of our QMFF is demonstrated through a series of examples ranging from small molecule clusters to condensed phase simulation, and applications to drug docking and protein-protein interactions. In these examples, comparisons are made to conventional molecular mechanical models, semiempirical methods, ab initio Hamiltonians, and a hybrid QM/MM method. The comparisons demonstrate the superior accuracy of our QMFF relative to the other models; nonetheless, we stress that the overarching role of QMFFs is not to supplant these established computational methods for problems where their use is appropriate. The role of QMFFs within the toolbox of multiscale modeling methods is to extend the range of applications to include problems that demand a fully quantum mechanical treatment of a large system with extensive configurational sampling. PMID:24937206

  5. Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

    PubMed Central

    2015-01-01

    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 simultaneously achieve very high accuracy and efficiency. The efficiency of the QMFF is made possible by partitioning the system into fragments and self-consistently solving for the fragment-localized molecular orbitals in the presence of the other fragment’s electron densities. Unlike a LSQM, the QMFF introduces empirical parameters that are tuned to obtain very accurate intermolecular forces. The speed and accuracy of our QMFF is demonstrated through a series of examples ranging from small molecule clusters to condensed phase simulation, and applications to drug docking and protein–protein interactions. In these examples, comparisons are made to conventional molecular mechanical models, semiempirical methods, ab initio Hamiltonians, and a hybrid QM/MM method. The comparisons demonstrate the superior accuracy of our QMFF relative to the other models; nonetheless, we stress that the overarching role of QMFFs is not to supplant these established computational methods for problems where their use is appropriate. The role of QMFFs within the toolbox of multiscale modeling methods is to extend the range of applications to include problems that demand a fully quantum mechanical treatment of a large system with extensive configurational sampling. PMID:24937206

  6. Vibrational analysis of helical poly-L-alanine: Improvement of an empirical harmonic force field for peptides and proteins

    NASA Astrophysics Data System (ADS)

    Lee, Sang-Ho

    1997-08-01

    Vibrational normal modes of regular helical polymers are characterized by A, E1, and E2 symmetry species where A and E1 modes are infrared active and A, E1, and E2 modes are Raman active. For uniaxially oriented ?-poly-L-alanine (?- PLA) samples and their N-deuterated analogues, polarized vibrational (Raman, infrared, and far-infrared) spectra corresponding to each of these optically active symmetry species were measured. Different from previous studies for ?-PLA, in addition to the usual ? I-helix conformation corresponding to the X-ray crystallographically determined structure, our excellent spectral data show another helical conformation occupying about 40% of the PLA sample. Meanwhile, recent advances in computational physics make it possible to compute the vibrational force field by ab initio quantum mechanical methods. In an effort to find a vibrational force field for polypeptides and proteins, based both on the ab initio force fields for small peptides like trans-N-methylacetamide and alanine dipeptides and on the new experimental data, a rigorous vibrational analysis has been done for the ? I-helix first. A compact vibrational formalism up to the cubic anharmonic terms for a regular helix was developed as well as analytic formulas for computation of higher order B-matrix elements. By using this, a more accurate Fermi- Dennison resonance analysis has been possible in the observed amide A band than was the case in previous studies. The direct nonbonded-interaction force constants, introduced to reproduce observed splittings among symmetry species for amide I and II modes, give a more accurate and simple transition-dipole coupling description than does the previous perturbation treatment. All the assigned bands are well reproduced within 5 cm-1 as a result of the least-squares refinement process on the initial force field taken from the ab initio peptide force fields, and the resulting refined force field for the ? I-helix also well explains the observed inelastic neutron scattering spectra for ?-PLA samples. In order to determine the unknown helical structure, the refined force field for the ? I-PLA structure has been applied to the candidate right-handed structures of ? II-, 310-B, and 310-P helices. The 310-helix is the most likely candidate for this additional structure.

  7. The combined use of SCF-MO calculations and frequency data in the evaluation of general harmonic force fields for molecules containing third row elements

    Microsoft Academic Search

    T. H. Arnold; B. I. Swanson; Y. Yamaguchi; D. J. Nelson

    1979-01-01

    The general harmonic force fields of several small molecules containing third row elements have been evaluated using a semiempirical method which combines SCF-MO calculations and limited frequency data. MOCIC (molecular orbital constraint using interaction coordinates) potential fields have been generated using the SCF-MO MNDO method which has recently been parameterized for third row elements. The general harmonic force field (GHFF)

  8. Constraining Carbonaceous Aerosol Climate Forcing by Bridging Laboratory, Field and Modeling Studies

    NASA Astrophysics Data System (ADS)

    Dubey, M. K.; Aiken, A. C.; Liu, S.; Saleh, R.; Cappa, C. D.; Williams, L. R.; Donahue, N. M.; Gorkowski, K.; Ng, N. L.; Mazzoleni, C.; China, S.; Sharma, N.; Yokelson, R. J.; Allan, J. D.; Liu, D.

    2014-12-01

    Biomass and fossil fuel combustion emits black (BC) and brown carbon (BrC) aerosols that absorb sunlight to warm climate and organic carbon (OC) aerosols that scatter sunlight to cool climate. The net forcing depends strongly on the composition, mixing state and transformations of these carbonaceous aerosols. Complexities from large variability of fuel types, combustion conditions and aging processes have confounded their treatment in models. We analyse recent laboratory and field measurements to uncover fundamental mechanism that control the chemical, optical and microphysical properties of carbonaceous aerosols that are elaborated below: Wavelength dependence of absorption and the single scattering albedo (?) of fresh biomass burning aerosols produced from many fuels during FLAME-4 was analysed to determine the factors that control the variability in ?. Results show that ? varies strongly with fire-integrated modified combustion efficiency (MCEFI)—higher MCEFI results in lower ? values and greater spectral dependence of ? (Liu et al GRL 2014). A parameterization of ? as a function of MCEFI for fresh BB aerosols is derived from the laboratory data and is evaluated by field data, including BBOP. Our laboratory studies also demonstrate that BrC production correlates with BC indicating that that they are produced by a common mechanism that is driven by MCEFI (Saleh et al NGeo 2014). We show that BrC absorption is concentrated in the extremely low volatility component that favours long-range transport. We observe substantial absorption enhancement for internally mixed BC from diesel and wood combustion near London during ClearFlo. While the absorption enhancement is due to BC particles coated by co-emitted OC in urban regions, it increases with photochemical age in rural areas and is simulated by core-shell models. We measure BrC absorption that is concentrated in the extremely low volatility components and attribute it to wood burning. Our results support enhanced light absorption by internally mixed BC parameterizations in models and identify mixed biomass and fossil combustion regions where this effect is large. We unify the treatment of carbonaceous aerosol components and their interactions to simplify and verify their representation in climate models, and re-evaluate their direct radiative forcing.

  9. Subwavelength particles in an inhomogeneous light field: optical forces associated with the spin and orbital energy flows

    NASA Astrophysics Data System (ADS)

    Bekshaev, A. Ya

    2013-04-01

    We analyse the ponderomotive action experienced by a small spherical particle immersed in an optical field, in relation to the internal energy flows (optical currents) and their spin and orbital constituents. The problem is studied analytically, on the basis of the dipole model, and numerically. The three sources of the field mechanical action—the energy density gradient and the orbital and spin parts of the energy flow—differ in their ponderomotive mechanisms, and their physical nature manifests itself in the dependence of the optical force on the particle radius a. If a ? ? (the radiation wavelength), the optical force behaves as a?, and integer ? can be used to classify the sources of the mechanical action. This classification correlates with the multipole representation of the field-particle interaction: the gradient force and the orbital momentum force appear due to the electric or magnetic dipole moments per se; the spin momentum force emerges due to interaction between the electric and magnetic dipoles or between the dipole and quadrupole moments (if the particle is polarizable electrically but not magnetically or vice versa). In principle, the spin and orbital currents can be measured separately through the probe particle motion, employing a special choice of particles with the necessary magnetic and/or electric properties.

  10. Targeting glioblastoma via intranasal administration of Ff bacteriophages

    PubMed Central

    Dor-On, Eyal; Solomon, Beka

    2015-01-01

    Bacteriophages (phages) are ubiquitous viruses that control the growth and diversity of bacteria. Although they have no tropism to mammalian cells, accumulated evidence suggests that phages are not neutral to the mammalian macro-host and can promote immunomodulatory and anti-tumorigenic activities. Here we demonstrate that Ff phages that do not display any proteins or peptides could inhibit the growth of subcutaneous glioblastoma tumors in mice and that this activity is mediated in part by lipopolysaccharide molecules attached to their virion. Using the intranasal route, a non-invasive approach to deliver therapeutics directly to the CNS, we further show that phages rapidly accumulate in the brains of mice and could attenuate progression of orthotopic glioblastoma. Taken together, this study provides new insight into phages non-bacterial activities and demonstrates the feasibility of delivering Ff phages intranasally to treat brain malignancies. PMID:26074908

  11. Primary motor cortical discharge during force field adaptation reflects muscle-like dynamics.

    PubMed

    Cherian, Anil; Fernandes, Hugo L; Miller, Lee E

    2013-08-01

    We often make reaching movements having similar trajectories within very different mechanical environments, for example, with and without an added load in the hand. Under these varying conditions, our kinematic intentions must be transformed into muscle commands that move the limbs. Primary motor cortex (M1) has been implicated in the neural mechanism that mediates this adaptation to new movement dynamics, but our recent experiments suggest otherwise. We have recorded from electrode arrays that were chronically implanted in M1 as monkeys made reaching movements under two different dynamic conditions: the movements were opposed by either a clockwise or counterclockwise velocity-dependent force field acting at the hand. Under these conditions, the preferred direction (PD) of neural discharge for nearly all neurons rotated in the direction of the applied field, as did those of proximal limb electromyograms (EMGs), although the median neural rotation was significantly smaller than that of muscles. For a given neuron, the rotation angle was very consistent, even across multiple sessions. Within the limits of measurement uncertainty, both the neural and EMG changes occurred nearly instantaneously, reaching a steady state despite ongoing behavioral adaptation. Our results suggest that M1 is not directly involved in the adaptive changes that occurred within an experimental session. Rather, most M1 neurons are directly related to the dynamics of muscle activation that themselves reflect the external load. It appears as though gain modulation, the differential recruitment of M1 neurons by higher motor areas, can account for the load and behavioral adaptation-related changes in M1 discharge. PMID:23657285

  12. The magnetic field, force and inductance of the system consisting of a thin ellipsoidal coil and a ferromagnetic ellipsoid

    Microsoft Academic Search

    Jan Purczynski; Pawel Rolicz; Ryszard Sikora

    1975-01-01

    The method of separation of variables has been applied to determine the magnetic field of the system consisting of a thin\\u000a ellipsoidal coil and a ferromagnetic ellipsoid of revolution. The inductance and the force acting between the coil and the\\u000a ellipsoid are also examined.

  13. AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

    PubMed Central

    2015-01-01

    Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer’s disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code. PMID:24931227

  14. The Gramicidin Channel Ion Permeation Free-Energy Profile: Direct and Indirect Effects of CHARMM Force Field Improvements

    PubMed Central

    Alawneh, Morad; Henderson, Douglas J.; Busath, David D.

    2009-01-01

    A revised CHARMM force field for tryptophan residues is studied as well as the effect of the new peptide torsion-energy cross-correlation correction algorithm (CMAP) using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl or 1 mol/kg KCl saline solution. The new tryptophan force field produces, in the decomposition, a Na+ PMFTrp that is consonant with the prediction from the experimental results, analyzed with rate theory by Durrant et al. (2006), in stark contrast to the prediction of the original CHARMM, version 22, tryptophan side-chain force field. However, the effect is lost in the complete PMF due to indirect effects mediated by other components of the system (peptide, lipid, ions, and water). CMAP reduces the excessive translocation barrier. Decomposition demonstrates that this effect is due to effects on the K+ PMFH2O rather than on K+ PMFgA. Both represent examples of indirect effects (i.e., consequences of the force field mediated by “innocent bystander” molecules). The results have been confirmed to be robust using an alternative umbrella potential method. PMID:20084184

  15. Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field

    E-print Network

    Jayaram, Bhyravabotla

    Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model provides rapid estimates of the electrostatic free energies of solvation for diverse molecules of parameters compatible with the AMBER force field is described. The method is used to estimate free energies

  16. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA

    PubMed Central

    Huang, Lei; Roux, Benoît

    2013-01-01

    Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out. PMID:24223528

  17. M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures

    E-print Network

    Goddard III, William A.

    M3B: A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water of malto-oligosaccharides (R(1f4) D-glucans) and their aqueous mixtures. This coarse grain model double-helical bulk structures of malto-oligosaccharides are feasible and of similar energy. The M3B

  18. Improvements in the LLNL objective analysis scheme for deriving forcing fields for single-column models using ARM data

    SciTech Connect

    Leach, M.J.; Yio, J.J.; Cederwall, R.T.

    1997-03-01

    The objective analysis method use for deriving Single-Column Model (SCM) forcing fields with ARM data (Leach, et al., 1996) is undergoing continual improvement. Several improvements were identified at the SCM Workshop held at LLNL in April 1996. These include incorporating large-scale analyses in the objective analysis, and time-filtering input data streams.

  19. Molecular force fields for aqueous electrolytes: SPC/E-compatible charged LJ sphere models and their limitations

    NASA Astrophysics Data System (ADS)

    Mou?ka, Filip; Nezbeda, Ivo; Smith, William R.

    2013-04-01

    Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Mou?ka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012), 10.1021/jp301447z]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.

  20. Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests

    Microsoft Academic Search

    George A. Kaminski; Harry A. Stern; Bruce J. Berne; Richard A. Friesner; Yixiang X. Cao; Robert B. Murphy; Ruhong Zhou; Thomas A. Halgren

    2002-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using

  1. Complementary Visualization of Mitotic Barley Chromatin by Field-Emission Scanning Electron Microscopy and Scanning Force Microscopy

    Microsoft Academic Search

    A. Schaper; M. Rößle; H. Formanek; T. M. Jovin; G. Wanner

    2000-01-01

    The surface structure of mitotic barley chromatin was studied by field-emission scanning electron microscopy (FESEM) and scanning force microscopy (SFM). Different stages of the cell cycle were accessible after a cell suspension was dropped onto a glass surface, chemical fixed, and critically point dried. Imaging was carried out with metal-coated specimen or uncoated specimen (only for SFM). The spatial contour

  2. A coarse-grained MARTINI-like force field for DNA unzipping in nanopores.

    PubMed

    Stachiewicz, Anna; Molski, Andrzej

    2015-05-15

    In nanopore force spectroscopy (NFS) a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. We present a new model that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The scaled conductivities in bulk solution are consistent with experimental results for NaCl for a wide range of electrolyte concentrations and temperatures. The dependence of the ionic current through a nanopore on the applied voltage is symmetric and, in the voltage range used in experiments (up to 2 V), linear and in good agreement with experimental data. The thermal stability and geometry of DNA is well represented. The model was applied to simulations of DNA hairpin unzipping in nanopores. The results are in good agreement with all-atom simulations: the scaled translocation times and unzipping sequence are similar. PMID:25706623

  3. Nano-imaging collagen by atomic force, near-field and nonlinear microscope

    NASA Astrophysics Data System (ADS)

    Lim, Ken Choong; Tang, Jinkai; Li, Hao; Ng, Boon Ping; Kok, Shaw Wei; Wang, Qijie; Zhang, Ying

    2015-03-01

    As the most abundant protein in the human body, collagen has a very important role in vast numbers of bio-medical applications. The unique second order nonlinear properties of fibrillar collagen make it a very important index in nonlinear optical imaging based disease diagnosis of the brain, skin, liver, colon, kidney, bone, heart and other organs in the human body. The second-order nonlinear susceptibility of collagen has been explored at the macroscopic level and was explained as a volume-averaged molecular hyperpolarizability. However, details about the origin of optical second harmonic signals from collagen fibrils at the molecular level are still not clear. Such information is necessary for accurate interpolation of bio-information from nonlinear optical imaging techniques. The later has shown great potential in collagen based disease diagnosis methodologies. In this paper, we report our work using an atomic force microscope (AFM), near field (SNOM) and nonlinear laser scanning microscope (NLSM) to study the structure of collagen fibrils and other pro-collagen structures.

  4. The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

    PubMed Central

    Orsi, Mario; Essex, Jonathan W.

    2011-01-01

    A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities. PMID:22194874

  5. Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

    PubMed Central

    He, Yi; Mozolewska, Magdalena A.; Krupa, Pawe?; Sieradzan, Adam K.; Wirecki, Tomasz K.; Liwo, Adam; Kachlishvili, Khatuna; Rackovsky, Shalom; Jagie?a, Dawid; ?lusarz, Rafa?; Czaplewski, Cezary R.; O?dziej, Stanis?aw; Scheraga, Harold A.

    2013-01-01

    The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our laboratory for the prediction of protein structure from amino acid sequence, is illustrated. Candidate models are selected, based on probabilities of the conformational families determined by multiplexed replica-exchange simulations, from the 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). For target T0663, classified as a new fold, which consists of two domains homologous to those of known proteins, UNRES predicted the correct symmetry of packing, in which the domains are rotated with respect to each other by 180° in the experimental structure. By contrast, models obtained by knowledge-based methods, in which each domain is modeled very accurately but not rotated, resulted in incorrect packing. Two UNRES models of this target were featured by the assessors. Correct domain packing was also predicted by UNRES for the homologous target T0644, which has a similar structure to that of T0663, except that the two domains are not rotated. Predictions for two other targets, T0668 and T0684_D2, are among the best ones by global distance test score. These results suggest that our physics-based method has substantial predictive power. In particular, it has the ability to predict domain–domain orientations, which is a significant advance in the state of the art. PMID:23980156

  6. Quantitative Interpretation of FRET Experiments via Molecular Simulation: Force Field and Validation.

    PubMed

    Best, Robert B; Hofmann, Hagen; Nettels, Daniel; Schuler, Benjamin

    2015-06-01

    Molecular simulation is a valuable and complementary tool that may assist with the interpretation of single-molecule Förster resonance energy transfer (FRET) experiments, if the energy function is of sufficiently high quality. Here we present force-field parameters for one of the most common pairs of chromophores used in experiments, AlexaFluor 488 and 594. From microsecond molecular-dynamics simulations, we are able to recover both experimentally determined equilibrium constants and association/dissociation rates of the chromophores with free tryptophan, as well as the decay of fluorescence anisotropy of a labeled protein. We find that it is particularly important to obtain a correct balance of solute-water interactions in the simulations in order to faithfully capture the experimental anisotropy decays, which provide a sensitive benchmark for fluorophore mobility. Lastly, by a combination of experiment and simulation, we address a potential complication in the interpretation of experiments on polyproline, used as a molecular ruler for FRET experiments, namely the potential association of one of the chromophores with the polyproline helix. Under conditions where simulations accurately capture the fluorescence anisotropy decay, we find at most a modest, transient population of conformations in which the chromophores associate with the polyproline. Explicit calculation of FRET transfer efficiencies for short polyprolines yields results in good agreement with experiment. These results illustrate the potential power of a combination of molecular simulation and experiment in quantifying biomolecular dynamics. PMID:26039173

  7. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

    PubMed Central

    Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D.

    2012-01-01

    Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein. PMID:22685386

  8. Two-phase Computerized Planning of Cryosurgery Using Bubble-packing and Force-field Analogy

    PubMed Central

    Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

    2007-01-01

    Background: Cryosurgery is the destruction of undesired tissues by freezing, as in prostate cryosurgery, for example. Minimally-invasive cryosurgery is currently performed by means of an array of cryoprobes, each in the shape of a long hypodermic needle. The optimal arrangement of the cryoprobes, which is known to have a dramatic effect on the quality of the cryoprocedure, remains an art held by the cryosurgeon, based on the cryosurgeon's experience and “rules of thumb.” An automated computerized technique for cryosurgery planning is the subject matter of the current report, in an effort to improve the quality of cryosurgery. Method of Approach: A two-phase optimization method is proposed for this purpose, based on two previous and independent developments by this research team. Phase I is based on a bubble-packing method, previously used as an efficient method for finite elements meshing. Phase II is based on a force-field analogy method, which has proven to be robust at the expense of a typically long runtime. Results: As a proof-of-concept, results are demonstrated on a 2D case of a prostate cross-section. The major contribution of this study is to affirm that in many instances cryosurgery planning can be performed without extremely expensive simulations of bioheat transfer, achieved in Phase I. Conclusions: This new method of planning has proven to reduce planning runtime from hours to minutes, making automated planning practical in a clinical time frame. PMID:16532617

  9. Predicting water uptake in poly(perfluorosulfonic acids) using force field simulation methods.

    PubMed

    Li, Xiaofeng; Li, Feng; Shi, Yue; Chen, Qing; Sun, Huai

    2010-11-21

    Free energy perturbation methods were applied to predict water contents in hydrated poly(perfluorosulfonic acids) (PPFSA). The simulations were based on the TEAM force field which was derived from quantum mechanical data calculated for small molecules using density functional theory (DFT) and thermodynamic data of molecular liquids and crystal. The equilibrium water contents in three PPFSA polymers (Nafion-117, Nafion-115 and Hyflon) were predicted by evaluating excess chemical potentials of water in hydrated polymers and in pure water. High level of precision measured by average uncertainty of ca. 0.1 kcal mol(-1), and accuracy in terms of deviation from experimental data by ca. 0.2 kcal mol(-1) were obtained in the predicted excess chemical potentials. The predicted amounts of water uptake agree well with experimental values. In addition, the equilibrium and dynamic properties of hydrated Nafion-117 were calculated and the results agree well with the existing experimental and computational data. The entropy and enthalpy contributions in the calculated excess chemical potentials are analyzed and the results are consistent with intuition. A linear correlation between the entropies and enthalpies is identified for the systems studied, which indicates that just increasing the interaction energies between water and host materials does not guarantee enhancement of the water uptake. PMID:20931118

  10. Non-polarizable force field of water based on the dielectric constant: TIP4P/?.

    PubMed

    Fuentes-Azcatl, Raúl; Alejandre, José

    2014-02-01

    The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/? force field of water. The TIP4P parameters are used as a starting point. The key step, to determine simultaneously both properties, is to perform simulations at 240 K where a molecular dipole moment of minimum density is found. The minimum is shifted to larger values of ? as the distance between the oxygen atom and site M, lOM, decreases. First, the parameters that define the dipole moment are adjusted to reproduce the experimental dielectric constant and then the Lennard-Jones parameters are varied to match the temperature of maximum density. The minimum on density at 240 K allows understanding why reported TIP4P models fail to reproduce the temperature of maximum density, the dielectric constant, or both properties. The new model reproduces some of the thermodynamic and transport anomalies of water. Additionally, the dielectric constant, thermodynamics, and dynamical and structural properties at different temperatures and pressures are in excellent agreement with experimental data. The computational cost of the new model is the same as that of the TIP4P. PMID:24422512

  11. A comparison of force fields and calculation methods for vibration intervals of isotopic H3(+) molecules

    NASA Astrophysics Data System (ADS)

    Carney, G. D.; Adler-Golden, S. M.; Lesseski, D. C.

    1986-04-01

    This paper reports (1) improved values for low-lying vibration intervals of H3(+), H2D(+), D2H(+), and D3(+) calculated using the variational method and Simons-Parr-Finlan (1973) representations of the Carney-Porter (1976) and Dykstra-Swope (1979) ab initio H3(+) potential energy surfaces, (2) quartic normal coordinate force fields for isotopic H3(+) molecules, (3) comparisons of variational and second-order perturbation theory, and (4) convergence properties of the Lai-Hagstrom internal coordinate vibrational Hamiltonian. Standard deviations between experimental and ab initio fundamental vibration intervals of H3(+), H2D(+), D2H(+), and D3(+) for these potential surfaces are 6.9 (Carney-Porter) and 1.2/cm (Dykstra-Swope). The standard deviations between perturbation theory and exact variational fundamentals are 5 and 10/cm for the respective surfaces. The internal coordinate Hamiltonian is found to be less efficient than the previously employed 't' coordinate Hamiltonian for these molecules, except in the case of H2D(+).

  12. Determination of a silane intermolecular force field potential model from an ab initio calculation

    SciTech Connect

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng [Institute of Applied Mechanics, National Taiwan University, Taipei 10617, Taiwan (China)

    2010-12-15

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  13. Conformational properties, torsional potential, and vibrational force field for methacryloyl fluoride - An ab initio investigation

    NASA Technical Reports Server (NTRS)

    Laskowski, B. C.; Jaffe, R. L.; Komornicki, A.

    1985-01-01

    The structure, torsional potentials, vibrational spectra, and harmonic force fields for s-cis and s-trans isomers of methacryloyl fluoride are examined to understand the conformational properties of the molecules and their relationship to macroscopic polymer properties. The structure is found to be in good agreement with experiment. It is shown by calculations that the energy difference between the cis and the transisomers is less than 1 kcal/mol at both the split valence and the split valence polarized levels, with the trans form favored. Analysis of the torsional potentials indicates that a rigid rotor model provides a reasonable description of the motion of the COF group in the molecule. The torsional barrier to interconvert the s-trans to the s-cis form is found to be 7.0 kcal/mol. A fit of the data to a three-term Fourier series shows that it is possible to reproduce the experimentally derived barrier, even though a direct determination indicates that the barrier is higher.

  14. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization

    SciTech Connect

    Mazack, Michael J. M., E-mail: mazack@mazack.org [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States); Gao, Jiali, E-mail: gao@jialigao.org [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States); State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, Jilin Province 130028 (China)

    2014-05-28

    The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

  15. Lipidbook: a public repository for force-field parameters used in membrane simulations.

    PubMed

    Doma?ski, Jan; Stansfeld, Phillip J; Sansom, Mark S P; Beckstein, Oliver

    2010-08-01

    Lipidbook is a public database for force-field parameters with a special emphasis on lipids, detergents and similar molecules that are of interest when simulating biological membrane systems. It stores parameter files that are supplied by the community. Topologies, parameters and lipid or whole bilayer structures can be deposited in any format for any simulation code, preferably under a license that promotes "open knowledge." A number of mechanisms are implemented to aid a user in judging the appropriateness of a given parameter set for a project. For instance, parameter sets are versioned, linked to the primary citation via PubMed identifier and digital object identifier (DOI), and users can publicly comment on deposited parameters. Licensing and, hence, the conditions for use and dissemination of academically generated data are often unclear. In those cases it is also possible to provide a link instead of uploading a file. A snapshot of the linked file is then archived using the WebCite(®) service without further involvement of the user or Lipidbook, thus ensuring a transparent and permanent history of the parameter set. Lipidbook can be accessed freely online at http://lipidbook.bioch.ox.ac.uk. Deposition of data requires online registration. PMID:20700585

  16. Modification of Bell Canyon Test (BCT) 1-FF grout. Final report

    SciTech Connect

    Buck, A.D.; Rhoderick, J.E.; Burkes, J.P.; Mather, K.; Reinhold, R.E.; Boa, J.A. Jr.

    1983-09-01

    Bell Canyon Test (BCT) 1-FF grout was developed as a candidate material for use in repository sealing applications and was actually used in two field tests in New Mexico. This grout and modifications of it were made in the laboratory and tested or examined for workability, compressive strength, restrained expansion, permeability, phase composition, and microstructure. Most of these were done to an age of 1 year. Compressive strength and expansion data were determined beyond this age (960 days). Modifications include use of three other cements, two other fly ashes, a silica fume, different water contents, and different amounts of expansive additive (plaster). Each cement and mineral admixture was characterized by conventional chemical and physical tests as well as by x-ray diffraction examination. In general, the results indicated that the modifcations to the basic BCT-1-FF grout produced other grouts that were as good as it. An exception to this was the grout mixture (M-8-C) made with shrinkage compensating expansive cement; it had an excessive flow time (>20 sec). Another grout mixture (M-9-C) also had excessive flow time and lower strength. It was thought that these problems could be solved with more modification to these two mixtures. 6 references, 24 figures, 7 tables.

  17. A Lagrangian description of nearshore hydrodynamics and rip currents forced by a random wave field

    NASA Astrophysics Data System (ADS)

    Leandro, S.; Cienfuegos, R.; Escauriaza, C. R.

    2011-12-01

    Nonlinear processes become important for waves propagating in the shoaling and surf zones. Wave shape changes when approaching the coast under the influence of bathymetry, becoming increasingly asymmetric until reaching the breaking limit. In the shoaling zone, non-linearities induce a net velocity in the direction of wave propagation, a phenomenon called Stokes drift, while in the surf zone, currents are mainly driven by spatio-temporal variations in energy dissipation gradients. In this work we aim at investigating and characterizing the nearshore circulation forced by a random wave field propagating over a variable bathymetry. We carry out numerical simulations over a laboratory experiment conducted in a wave basin over a realistic bathymetry [Michallet et al. 2010]. For the hydrodynamics, we use a 2D shock-capturing finite-volume model that solves the non-linear shallow water equations, taking into account energy dissipation by breaking, friction, bed-slope variations, and an accurate description for the moving shoreline in the swash zone [Marche et al. 2007;Guerra et al. 2010]. Model predictions are compared and validated against experimental data giving confidence for its use in the description of wave propagation in the surf/swash zone, together with mean eulerian velocities. The resulting wave propagation and circulation provided by the 2D model will then be used to describe drifter's patterns in the surf zone and construct Lagrangian particle tracking. The chosen experimental configuration is of great interest due to the random wave forcing (slowly modulated), the beach non-uniformities, and the existence of several bar-rip channels that enhance quasi-periodic rip instabilities. During the experiment, balloons filled with water, with a diameter between 5 and 10 cm, were placed in the surf zone in order to characterize circulation in a Lagrangian framework [Castelle et al. 2010]. The time-location of the balloons was continuously tracked by a shore-mounted video camera, and the images were processed to obtain the trajectories and mean velocities. The Lagrangian description provided by the numerical model will be thus confronted to experimental data, and then used to characterize circulation patterns, rip instabilities and infragravity wave pulsations.

  18. Dark-field full-field optical coherence tomography.

    PubMed

    Auksorius, Egidijus; Claude Boccara, A

    2015-07-15

    Full-field optical coherence tomography (FF-OCT) provides en face images from deep in the tissue with high spatial resolution. Specular reflections, however, may reduce image contrast as it can be much stronger than the backscattered signal from a specimen. To this end, we demonstrate dark-field FF-OCT (d-FF-OCT) that can block specular reflections by the help of an opaque disk in the pupil-conjugated plane. The reference mirror is replaced by a blazed grating, which eliminates a walk-off between the sample and the reference beams on a camera that otherwise limits the imaging field-of-view (FOV). We show that d-FF-OCT can suppress specular reflections efficiently from the glass-specimen interface by at least two orders of magnitude and yield higher contrast images compared to the conventional FF-OCT. PMID:26176447

  19. Potential Fields as an External Force and Algorithmic Improvements in Deformable Models

    Microsoft Academic Search

    Andrés Caro; Pablo G. Rodríguez; Eva Cernadas; Teresa Antequera; M. L. Duran

    2003-01-01

    Deformable Models are extensively used as a Pattern Recognition technique. They are curves defined within an image domain that can be moved under the influence of internal and external forces. Some trade-offs of standard deformable models algorithms are the selection of image energy function (external force), the location of initial snake and the attraction of contour points to local energy

  20. Current-induced magnetic field detection around fine current paths by magnetic force microscopy

    Microsoft Academic Search

    D. Saida; T. Edura; K. Tsutsui; Y. Wada; T. Takahashi

    2005-01-01

    A commercial magnetic force microscopy (MFM), combined with a potential feedback, is described. The MFM is operated in an intermittent contact mode, and a vertical displacement of the cantilever is used for observing a topography. Magnetic force images are obtained simultaneously with the topography with this setup. At total current of 200 ?A, topography, amplitude and phase difference of the