Sample records for force field ff

  1. 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

  2. Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

    PubMed

    Zheng, Mo; Li, Xiaoxia; Guo, Li

    2013-04-01

    Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. PMID:23454611

  3. Development of a ReaxFF reactive force field for tetrabutylphosphonium glycinate/CO2 mixtures.

    PubMed

    Zhang, Bo; van Duin, Adri C T; Johnson, J Karl

    2014-10-16

    Carbon dioxide interacts with the ionic liquid tetrabutylphosphonium glycinate, [P(C4)4][Gly], through both physical and chemical absorption. We present a parametrization of the ReaxFF force field for this system that accounts for both chemical and physical interactions. The parametrization was developed from an extensive training set including periodic density functional theory (DFT) calculations of reaction pathways between CO2 and the anion [Gly](-) in the condensed phase, condensed-phase molecular dynamics (MD) configurations, gas-phase CO2-anion and CO2-cation interactions, and gas-phase cluster calculations for intra-ion interactions. The optimized ReaxFF parameters capture the essential features of both physical and chemical interactions between CO2 and [P(C4)4][Gly] as compared with experiments, van der Waals-corrected DFT calculations, or, in the case of physical interactions, classical force field calculations. The probability distributions of the distance between C (from CO2) and N (from the anion) and the CO2 bend angles calculated from MD simulations with the optimized ReaxFF force field are in good general agreement with those from DFT-based MD simulations. We predict that the density of CO2/[P(C4)4][Gly] mixtures increases with increasing CO2 concentration up to at least 50 mol % CO2. We attribute the significant increase in density to the small effective volume occupied by chemically bound CO2 in the mixture. The predicted increase in density may be tested experimentally. PMID:25285669

  4. 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

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

    E-print Network

    Goddard III, William A.

    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, angle and dihedral distortions, and reactions between hydrocarbons and vanadium oxide clusters

  6. Dynamics of the Dissociation of Hydrogen on Stepped Platinum Surfaces Using the ReaxFF Reactive Force Field

    E-print Network

    Dynamics of the Dissociation of Hydrogen on Stepped Platinum Surfaces Using the ReaxFF Reactive Force Field Jeffery Ludwig and Dionisios G. Vlachos* Department of Chemical Engineering and Center of hydrogen on eight platinum surfaces, Pt(111), Pt(100), Pt(110), Pt(211), Pt(311), Pt(331), Pt(332), and Pt

  7. ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Kimberly Chenoweth, Adri C. T. van Duin, and William A. Goddard, III*

    E-print Network

    Goddard III, William A.

    and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, weReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation Kimberly-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include

  8. 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.

    Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures Elodie Salmon a , Adri C.T. van Duin b , François Lorant Brown coal using the ReaxFF reactive force field. We find that these reactive MD simulations

  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. QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

    PubMed

    Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

    2015-05-15

    QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. PMID:25740170

  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.

    structure, as would be predicted from the Jahn-Teller effect for a d9 electronic configurationDevelopment and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended

  13. Formation of water at a Pt(111) surface: A study using reactive force fields (ReaxFF) Markus J. Buehler1

    E-print Network

    Barr, Al

    Formation of water at a Pt(111) surface: A study using reactive force fields (ReaxFF) Markus J temperature, we describe the dynamics of water formation at a Pt catalyst using a new reactive Reax formation, which is found to be in reasonable agreement with the activation barrier calculated by restraint

  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. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

    E-print Network

    Das, Rhiju

    , tripeptides, tetra-alanine, and ubiquitin. Of the force fields examined (ff96, ff99, ff03, ff03*, ff03w, ff99sb*, ff99sb-ildn, ff99sb-ildn-phi, ff99sb-ildn-NMR, CHARMM27, and OPLS-AA), two force fields (ff99sb-ildn- phi, ff99sb-ildn-NMR) combining recent side chain and backbone torsion modifications achieved high

  18. Development and validation of a ReaxFF reactive force field for Fe/Al/Ni alloys: molecular dynamics study of elastic constants, diffusion, and segregation.

    PubMed

    Shin, Yun Kyung; Kwak, Hyunwook; Zou, Chenyu; Vasenkov, Alex V; van Duin, Adri C T

    2012-12-13

    We have developed a ReaxFF force field for Fe/Al/Ni binary alloys based on quantum mechanical (QM) calculations. In addition to the various bulk phases of the binary alloys, the (100), (110) and (111) surface energies and adatom binding energies were included in the training set for the force field parametrization of the Fe/Al/Ni binary alloys. To validate these optimized force fields, we studied (i) elastic constants of the binary alloys at finite temperatures, (ii) diffusivity of alloy components in Al/Ni alloy, and (iii) segregation on the binary alloy surfaces. First, we calculated linear elastic constants of FeAl, FeNi(3), and Ni(3)Al in the temperature range 300 to 1100 K. The temperature dependences of the elastic constants of these three alloys, showing a decrease in C(11), C(12), and C(44) as temperature increases, were in good agreement with the experimental results. We also performed ReaxFF molecular dynamics (MD) simulations for Al or Ni diffusion in the system modeled as Al/Ni mixed layers with the linear composition gradients. At 1000 K, Al diffusivity at the pure Al end was 2 orders of magnitude larger than that in the Al trace layers, probably explaining the nature of different diffusion behavior between molten metals and alloys. However, the diffusivity of Ni at the pure Ni end was only slightly larger than that in the Ni trace layers at the system temperature much lower than the melting temperature of Ni. Third, we investigated the surface segregation in L1(2)-Fe(3)Al, Fe(3)Ni, and Ni(3)Al clusters at high temperature (2500 K). From the analysis of composition distribution of the alloy components from the bulk to the surface layer, it was found that the degree of segregation depended on the chemical composition of the alloy. Al surface segregation occurred most strongly in Fe(3)Al, whereas it occurred most weakly in Ni(3)Al. These results may support the segregation mechanism that surface segregation results from the interplay between the energetic stability of the ordered bulk phase and the surface reconstruction. In addition, the surface segregation induced the depletion layers of segregating metal species (Al in Fe(3)Al and Ni(3)Al, and Ni in Fe(3)Ni) next to the segregation layers. These simulation results qualitatively agreed with early experimental observations of segregation in Fe/Al/Ni binary alloys. PMID:23167515

  19. 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

  20. ReaxFF: A Reactive Force Field for Hydrocarbons Adri C. T. van Duin,,| Siddharth Dasgupta, Francois Lorant, and William A. Goddard III*,

    E-print Network

    van Duin, Adri

    ) to quickly evaluate the forces and other dynamical properties such as the effects of mechanical shock waves, particularly when coupled to charge equilibration6 (QEq) or other methods for predicting charges. However repairing the fundamental problems in the shapes of the dissociation and reactive potential curves. Two

  1. 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.

  2. = =ff M =ff M =ff M =ff M

    E-print Network

    Quigg, Chris

    Z 3 2 2 2 2 2 3 2 2 2 3 2 15 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 = =ff M =ff M Ã? M u u M Ã? =ff M =ff M : M : =c =ff M : =ff M : u : : SU =ff =ff M Ã? u M : : x M ff M Ã? M u x M : : x : M ff M x =ff M x M =ff M =ff M : : =ff M =ff M =ff M =ff M : =ff M =ff M : : Four Memos for the Next Millennium

  3. Radial field retrieval in spherical scanning for current reconstruction and NF-FF transformation

    Microsoft Academic Search

    Fernando Las-Heras; Tapan K. Sarkar

    2002-01-01

    A near-field to far-field (NF-FF) transformation is addressed for the case of spherical scanning using equivalent magnetic currents (EMCs) and matrix methods. It is based on the decoupling of the field components and the iterative retrieval of the radial component of the electric field. The technique is applied for far-field calculation as well as for the estimation of the current

  4. Carbohydrate force fields

    PubMed Central

    Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.

    2014-01-01

    Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813

  5. Force field development for cofactors in the photosystem II.

    PubMed

    Zhang, Lu; Silva, Daniel-Adriano; Yan, Yijing; Huang, Xuhui

    2012-09-30

    We present a set of force field (FF) parameters compatible with the AMBER03 FF to describe five cofactors in photosystem II (PSII) of oxygenic photosynthetic organisms: plastoquinone-9 (three redox forms), chlorophyll-a, pheophytin-a, heme-b, and ?-carotene. The development of a reliable FF for these cofactors is an essential step for performing molecular dynamics simulations of PSII. Such simulations are important for the calculation of absorption spectrum and the further investigation of the electron and energy transfer processes. We have derived parameters for partial charges, bonds, angles, and dihedral-angles from solid theoretical models using systematic quantum mechanics (QM) calculations. We have shown that the developed FF parameters are in good agreement with both ab initio QM and experimental structural data in small molecule crystals as well as protein complexes. PMID:22685077

  6. Molecular dynamics simulation of HIV-protease with polarizable and non-polarizable force fields

    Microsoft Academic Search

    B. R. Meher; M. V. Satish Kumar; Pradipta Bandyopadhyay

    2009-01-01

    The effect of polarization in biomolecular force field is investigated by performing Molecular Dynamics (MD) simulation of\\u000a HIV-protease by using two AMBER force fields, namely ff99 (non-polarizable) and ff02 (polarizable). The results of simulation\\u000a show that the overall structural fluctuation of HIV-protease is reduced in the polarizable simulation. Comparison with the\\u000a NMR order parameters with the calculated values shows that

  7. Approximate photochemical dynamics of azobenzene with reactive force fields

    SciTech Connect

    Li, Yan; Hartke, Bernd [Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098 Kiel (Germany)] [Institute for Physical Chemistry, Christian-Albrechts-University, Olshausenstr. 40, 24098 Kiel (Germany)

    2013-12-14

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

  8. Approximate photochemical dynamics of azobenzene with reactive force fields

    NASA Astrophysics Data System (ADS)

    Li, Yan; Hartke, Bernd

    2013-12-01

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

  9. Approximate photochemical dynamics of azobenzene with reactive force fields.

    PubMed

    Li, Yan; Hartke, Bernd

    2013-12-14

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis?trans- and trans?cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work). PMID:24329064

  10. Force field of monoethanolamine

    SciTech Connect

    Alejandre, J.; Rivera, J.L.; Mora, M.A.; Garza, V. de la

    2000-02-17

    Ab initio calculations and canonical molecular dynamics simulations were performed to obtain a force field of monoethanolamine (MEA). The molecule is modeled by seven charged sites, and the force field includes intramolecular degrees of freedom and intermolecular interactions. The charges obtained in the energy minimization procedure reproduce the experimental geometry, dipole moment, and the most stable conformation. Molecular dynamics simulations were carried out in the liquid phase and in the liquid-vapor equilibrium state. Simulations in the liquid region give information about hydrogen bond formation, while simulations in the two-phase region allow the determination of coexisting densities and surface tension as functions of temperature. The hydrogen bond is favored when the hydrogen of the hydroxyl group is close to a nitrogen or to an oxygen of another molecule, and the strength in both cases is the same. Radial distribution functions involving hydrogens and oxygen in the hydroxyl group of MEA are compared with those of water at 298 K, and a similar structure is found for the first neighbor of atoms. The proposed force field gives a good description of the liquid-vapor coexistence of MEA. The liquid density obtained in simulations of the liquid-vapor equilibrium at 298 K is 1.003 g/cm{sup 3} versus the experimental value of 1.012 g/cm{sup 3}. The estimated critical point is located at 583.9 K and 0.32 g/cm{sup 3} in comparison with the experimental result of 614 K and 0.3116 g/cm{sup 3}, respectively. At 323 K the calculated surface tension if 43.2 {+-} 2.5 nM/m while the experimental value is 44.81 mN/m.

  11. The MSXX Force Field for the Barium Sulfate-Water Interface Yun Hee Jang,, Xiao Yan Chang, Mario Blanco, Sungu Hwang,, Yongchun Tang,

    E-print Network

    Goddard III, William A.

    The MSXX Force Field for the Barium Sulfate-Water Interface Yun Hee Jang,, Xiao Yan Chang, Mario, 2001; In Final Form: April 3, 2002 A new force field (MSXX FF) was developed for barium sulfate (BaSO4

  12. 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.

  13. The scaled-charge additive force field for amino acid based ionic liquids

    NASA Astrophysics Data System (ADS)

    Fileti, Eudes Eterno; Chaban, Vitaly V.

    2014-11-01

    Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions were taken into account by computing electrostatic potential for ion pairs. The van der Waals interactions were adopted from the CHARMM36 FF with minor modifications. Compatibility between our parameters and CHARMM36 parameters is preserved.

  14. Validation Of A Reactive Force Field Included With An Open Source, Massively Parallel Code For Molecular Dynamics Simulations Of RDX

    NASA Astrophysics Data System (ADS)

    Warrier, M.; Pahari, P.; Chaturvedi, S.

    2010-12-01

    Molecular dynamics (MD) simulations of RDX is carried out using the ReaxFF force field supplied with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Validation of ReaxFF to model RDX is carried out by extracting the (i) crystal unit cell parameters, (ii) bulk modulus and (iii) thermal expansion coefficient and comparing with reported values from both experiments and simulations.

  15. ff ff fi!ff A predicative classification of the elementary functions

    E-print Network

    Covino, Emanuele

    1 0 S j j 3 3 0 0 ffl G ff T T T Abstract. Ÿ G G T G E E T E ff ff fi!ff ff ff ff ffl ffl â?? â?? ff ff ff ff ff fi!ff ff n ff ff ff ffl ffl ff ff ffl T T T â?? â?? ffl S S â?? E n E n G G n G n E : E G E

  16. 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.

  17. 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.

  18. A reactive force field for lithium-aluminum silicates with applications to eucryptite phases

    NASA Astrophysics Data System (ADS)

    Narayanan, Badri; van Duin, Adri C. T.; Kappes, Branden B.; Reimanis, Ivar E.; Ciobanu, Cristian V.

    2012-01-01

    We have parameterized a reactive force field (ReaxFF) for lithium-aluminum silicates using density functional theory (DFT) calculations of structural properties of a number of bulk phase oxides, silicates and aluminates, as well as of several representative clusters. The force field parameters optimized in this study were found to predict lattice parameters and heats of formation of selected condensed phases in excellent agreement with previous DFT calculations and with experiments. We have used the newly developed force field to study the eucryptite phases in terms of their thermodynamic stability and their elastic properties. We have found that (a) these ReaxFF parameters predict the correct order of stability of the three crystalline polymorphs of eucryptite, ?, ? and ?, and (b) that upon indentation, a new phase appears at applied pressures >=7 GPa. The high-pressure phase obtained upon indentation is amorphous, as illustrated by the radial distribution functions calculated for different pairs of elements. In terms of elastic properties analysis, we have determined the elements of the stiffness tensor for ?- and ?-eucryptite at the level of ReaxFF, and discussed the elastic anisotropy of these two polymorphs. Polycrystalline average properties of these eucryptite phases are also reported to serve as ReaxFF predictions of their elastic moduli (in the case of ?-eucryptite), or as tests against values known from experiments or DFT calculations (?-eucrypite). The ReaxFF potential reported here can also describe well single-species systems (e.g. Li-metal, Al-metal and condensed phases of silicon), which makes it suitable for investigating structure and properties of suboxides, atomic-scale mechanisms responsible for phase transformations, as well as oxidation-reduction reactions.

  19. Reactive Force Fields Based on Quantum Mechanics for Applications to Materials at Extreme Conditions

    NASA Astrophysics Data System (ADS)

    van Duin, Adri C. T.; Zybin, Sergey V.; Chenoweth, Kimberley; Zhang, Luzheng; Han, Si-Ping; Strachan, Alejandro; Goddard, William A.

    2006-07-01

    Understanding the response of energetic materials (EM) to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of multimillion-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, we developed the ReaxFF reactive force fields based on quantum mechanics (QM) calculations of reactants, products, high-energy intermediates and transition states, but using functional forms suitable for large-scale molecular dynamics simulations of chemical reactions under extreme conditions. The elements of ReaxFF are: - charge distributions change instantaneously as atomic coordinates change, - all valence interactions use bond orders derived uniquely from the bond distances which in turn describe uniquely the energies and forces, - three body (angle) and four body (torsion and inversion) terms are allowed but not required, - a general "van der Waals" term describes short range Pauli repulsion and long range dispersion interactions, which with Coulomb terms are included between all pairs of atoms (no bond or angle exclusions), - no environmental distinctions are made of atoms involving the same element; thus every carbon has the same parameters whether in diamond, graphite, benzene, porphyrin, allyl radical, HMX or TATP. ReaxFF uses the same functional form and parameters for reactive simulations in hydrocarbons, polymers, metal oxides, and metal alloys, allowing mixtures of all these systems into one simulation. We will present an overview of recent progress in ReaxFF developments, including the extension of ReaxFF to nitramine-based (nitromethane, HMX) and peroxide-based (TATP) explosives. To demonstrate the versatility and transferability of ReaxFF, we also present applications to silicone polymer poly-dimethylsiloxane (PDMS).

  20. Polarization effects in molecular mechanical force fields

    PubMed Central

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2014-01-01

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594

  1. Force field feature extraction for ear biometrics

    Microsoft Academic Search

    David J. Hurley; Mark S. Nixon; John N. Carter

    2005-01-01

    The overall objective in defining feature space is to reduce the dimensionality of the original pattern space, whilst maintaining discriminatory power for classification. To meet this objec- tive in the context of ear biometrics a new force field transformation treats the image as an array of mutually attracting particles that act as the source of a Gaussian force field. Under-

  2. 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

  3. MODELING OF GAMMA-RAY PULSAR LIGHT CURVES USING THE FORCE-FREE MAGNETIC FIELD

    SciTech Connect

    Bai Xuening; Spitkovsky, Anatoly, E-mail: xbai@astro.princeton.ed, E-mail: anatoly@astro.princeton.ed [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    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.

  4. The Force Field for Amino Acid Based Ionic Liquids: Polar Residues

    E-print Network

    Fileti, Eudes Eterno

    2015-01-01

    Ionic liquids (ILs) constitute one of the most active fields of research nowadays. Many organic and inorganic molecules can be converted into ions via relatively simple procedures. These ions can be combined into ILs. Amino acid based ILs (AAILs) represent a specific interest due to solubilization of biological species, participation in enzymatic catalysis, and capturing toxic gases. We develop a new force field (FF) for the seven selected AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions with polar residues. The anions were obtained via deprotonation of carboxyl group. We account for peculiar interactions between the anion and the cation by fitting electrostatic potential for an ion pair, in contrast to isolated ions. The van der Waals interactions were transferred from the CHARMM36 FF with minor modifications, as suggested by hybrid density functional theory. Compatibility between our parameters and CHARMM36 parameters is preserved. The developed interaction model fosters computation...

  5. Characterization of wet pad surface in chemical mechanical polishing (CMP) process with full-field optical coherence tomography (FF-OCT).

    PubMed

    Choi, Woo June; Jung, Sung Pyo; Shin, Jun Geun; Yang, Danning; Lee, Byeong Ha

    2011-07-01

    Chemical mechanical polishing (CMP) is a key process for global planarization of silicon wafers for semiconductors and AlTiC wafers for magnetic heads. Removal rate of wafer material is directly dependent on the surface roughness of a CMP pad, thus the structure of the pad surface has been evaluated with variable techniques. However, under in situ CMP process, the measurements have been severely limited due to the existence of polishing fluids including the slurry on the pad surface. In here, we newly introduce ultra-high resolution full-field optical coherence tomography (FF-OCT) to investigate the surface of wet pads. With FF-OCT, the wet pad surface could be quantitatively characterized in terms of the polishing pad lifetime, and also be three-dimensionally visualized. We found that reasonable polishing span could be evaluated from the surface roughness measurement and the groove depth measurement made by FF-OCT. PMID:21747489

  6. Molecular simulations: Force fields for carbon capture

    NASA Astrophysics Data System (ADS)

    Getman, Rachel B.

    2012-10-01

    Force fields have been generated that enable accurate simulations of interactions occurring between CO2 molecules and metal-organic frameworks featuring 'open' metal sites, which are promising for carbon capture applications.

  7. Common Force Field Thermodynamics of Cholesterol

    PubMed Central

    Giangreco, Francesco; Yamamoto, Eiji; Hirano, Yoshinori; di Giosia, Matteo; Zerbetto, Francesco; Yasuoka, Kenji; Narumi, Tetsu; Yasui, Masato; Höfinger, Siegfried

    2013-01-01

    Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field independence. Moreover, charge assignments for membrane-embedded compounds are revealed to be critical with significant impact on biological reasoning. PMID:24302856

  8. Field-regulated force by grafted polyelectrolytes

    E-print Network

    Christian Seidel; Yury A. Budkov; Nikolay V. Brilliantov

    2014-11-08

    Generation of mechanical force regulated by external electric field is studied both theoretically and by molecular dynamics (MD) simulations. The force arises in deformable bodies linked to the free end of a grafted polyelectrolyte chain which is exposed to electric field that favours its adsorption. We consider a few target bodies with different force-deformation relations including (i) linear and (ii) cubic dependences as well as (iii) Hertzian-like force. Such force-deformation relations mimic the behaviour of (i) coiled and (ii) stretched polymer chains, respectively, or (iii) that of a squeezed colloidal particle. The magnitude of the arising force varies over a wide interval although the electric field alters within a relatively narrow range only. The predictions of our theory agree quantitatively well with the results of numerical simulations. Both cases of zero and finite electrical current are investigated and we do not obtain substantial differences in the force generated. The phenomenon studied could possibly be utilised to design, e.g., vice-like devices to fix nano-sized objects.

  9. Evaluating force field accuracy with long-time simulations of a ?-hairpin tryptophan zipper peptide

    NASA Astrophysics Data System (ADS)

    Hayre, N. R.; Singh, R. R. P.; Cox, D. L.

    2011-01-01

    We have combined graphics processing unit-accelerated all-atom molecular dynamics with parallel tempering to explore the folding properties of small peptides in implicit solvent on the time scale of microseconds. We applied this methodology to the synthetic ?-hairpin, trpzip2, and one of its sequence variants, W2W9. Each simulation consisted of over 8 ?s of aggregated virtual time. Several measures of folding behavior showed good convergence, allowing comparison with experimental equilibrium properties. Our simulations suggest that the intramolecular interactions of tryptophan side chains are responsible for much of the stability of the native fold. We conclude that the ff99 force field combined with ff96 ? and ? dihedral energies and an implicit solvent can reproduce plausible folding behavior in both trpzip2 and W2W9.

  10. Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids

    PubMed Central

    2012-01-01

    An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The parametrization has been largely based on high-level ab initio calculations in order to keep the empirical input to a minimum. Parameters for the lipid chains have been developed based on knowledge about bulk alkane liquids, for which thermodynamic and dynamic data are excellently reproduced. The FFs ability to simulate lipid bilayers in the liquid crystalline phase in a tensionless ensemble was tested in simulations of three lipids: 1,2-diauroyl-sn-glycero-3-phospocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1,2-dipalmitoyl-sn-glycero-3-phospcholine (DPPC). Computed areas and volumes per lipid, and three different kinds of bilayer thicknesses, have been investigated. Most importantly NMR order parameters and scattering form factors agree in an excellent manner with experimental data under a range of temperatures. Further, the compatibility with the AMBER FF for biomolecules as well as the ability to simulate bilayers in gel phase was demonstrated. Overall, the FF presented here provides the important balance between the hydrophilic and hydrophobic forces present in lipid bilayers and therefore can be used for more complicated studies of realistic biological membranes with protein insertions. PMID:22352995

  11. Thermal Decomposition of Hydrazines from Reactive Dynamics Using the ReaxFF Reactive Force Field

    E-print Network

    Goddard III, William A.

    the decomposition of hydrazine is affected by temperature, pressure, and heating rate. We analyzed chemical reaction is decreased, the onset for hydrazine decomposition shifts to lower temperatures. Using a constant heating rate of chemical reactions in these systems for a variety of reaction conditions in order to show

  12. eFF, a force field with electrons Julius Su and William A. Goddard III

    E-print Network

    Goddard III, William A.

    2 ^ ^12 21 12 21 12 21 12 21 12 21 12 21 12 21 12 21 3 41 1 3 4 1 deform H H E r r r S r r Sr r-row hydrides and hydrocarbons 1.508 (1.335) 1.060 (1.084) 1.371 (1.216) 1.022 (1.065) 1.527 (1.497) 1.513 (1

  13. LABORATORY I ELECTRIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    of the object. (The magnitude of the gravitational field near the earth's surface is g = 9.8 m/s2 .) In the case as "action-at-a-distance". This means that an object can exert a force on another object that require some getting used to. First, it is hard to visualize objects interacting when

  14. Development of non-standard arginine residue parameters for use with the AMBER force fields

    NASA Astrophysics Data System (ADS)

    Wu, Min; Strid, Åke; Eriksson, Leif A.

    2013-10-01

    Amino acid radicals are often involved as intermediates in biological processes, but are difficult to capture by experiment. Computational modeling can be employed to study the features of the species involved. The neutral arginyl radical has previously been detected experimentally using ECD and ETD spectroscopy. Protonation of the radical can occur on the guanidinium carbon, depending on the peptide structure and protein environment. Accurate force fields are essential for reproducing the conformational and dynamic behavior of these intermediates. New AMBER ff99 parameters for the arginyl radical and hydrogenated arginyl side chains are presented based on ab initio quantum chemical calculations.

  15. 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.

  16. Extension of the CHARMM General Force Field to Sulfonyl-Containing Compounds and Its Utility in Biomolecular Simulations

    PubMed Central

    Yu, Wenbo; He, Xibing; Vanommeslaeghe, Kenno; MacKerell, Alexander D.

    2012-01-01

    Presented is an extension of the CHARMM General force field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest. PMID:22821581

  17. Limited Field Investigation Report for Uranium Contamination in the 300 Area, 300-FF-5 Operable Unit, Hanford Site, Washington

    SciTech Connect

    Williams, Bruce A.; Brown, Christopher F.; Um, Wooyong; Nimmons, Michael J.; Peterson, Robert E.; Bjornstad, Bruce N.; Lanigan, David C.; Serne, R. Jeffrey; Spane, Frank A.; Rockhold, Mark L.

    2007-11-01

    Four new CERCLA groundwater monitoring wells were installed in the 300-FF-5 Operable Unit in FY 2006 to fulfill commitments for well installations proposed in the Hanford Federal Facility Agreement and Consent Order Milestone M-24-57. Wells were installed to collect data to determine the distribution of process uranium and other contaminants of potential concern in groundwater. These data will also support uranium contaminant transport simulations and the wells will supplement the water quality monitoring network for the 300-FF-5 OU. This report supplies the information obtained during drilling, characterization, and installation of the new groundwater monitoring wells. This document also provides a compilation of hydrogeologic, geochemical, and well construction information obtained during drilling, well development, and sample collection/analysis activities.

  18. 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

  19. Self-forces from generalized Killing fields

    NASA Astrophysics Data System (ADS)

    Harte, Abraham I.

    2008-12-01

    A non-perturbative formalism is developed that simplifies the understanding of self-forces and self-torques acting on extended scalar charges in curved spacetimes. Laws of motion are locally derived using momenta generated by a set of generalized Killing fields. Self-interactions that may be interpreted as arising from the details of a body's internal structure are shown to have very simple geometric and physical interpretations. Certain modifications to the usual definition for a center-of-mass are identified that significantly simplify the motions of charges with strong self-fields. A derivation is also provided for a generalized form of the Detweiler Whiting axiom that pointlike charges should react only to the so-called regular component of their self-field. Standard results are shown to be recovered for sufficiently small charge distributions.

  20. Magnetic Fields and Forces in Permanent Magnet Levitated Bearings

    Microsoft Academic Search

    Kevin D. Bachovchin; James F. Hoburg; Richard F. Post

    2012-01-01

    Magnetic fields and magnetic forces from magnetic bearings made of circular Halbach permanent-magnet arrays are computed and analyzed. The magnetic fields are calculated using superposition of fields due to patches of magnetization charge at surfaces where the magnetization is discontinuous. The magnetic force from the magnetic bearing is computed using superposition of forces on each patch of magnetization charge. The

  1. 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

  2. Recent Developments and Applications of the CHARMM force fields

    PubMed Central

    Zhu, Xiao; Lopes, Pedro E.M.; MacKerell, Alexander D.

    2011-01-01

    Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields. PMID:23066428

  3. The Energetics of Motivated Cognition: A Force-Field Analysis

    ERIC Educational Resources Information Center

    Kruglanski, Arie W.; Belanger, Jocelyn J.; Chen, Xiaoyan; Kopetz, Catalina; Pierro, Antonio; Mannetti, Lucia

    2012-01-01

    A force-field theory of motivated cognition is presented and applied to a broad variety of phenomena in social judgment and self-regulation. Purposeful cognitive activity is assumed to be propelled by a "driving force" and opposed by a "restraining force". "Potential" driving force represents the maximal amount of energy an individual is prepared…

  4. Total screening and finite range forces from ultramassive scalar fields

    NASA Astrophysics Data System (ADS)

    Arod?, H.; Karkowski, J.; ?wierczy?ski, Z.

    2013-06-01

    Force between static point particles coupled to a classical ultramassive scalar field is calculated. The field potential is proportional to the modulus of the field. It turns out that the force exactly vanishes when the distance between the particles exceeds certain finite value. Moreover, each isolated particle is surrounded by a compact cloud of the scalar field that completely screens its scalar charge.

  5. Evaluation of the OPLS-AA Force Field for the Study of Structural and Energetic Aspects of Molecular Organic Crystals.

    PubMed

    Bernardes, Carlos E S; Joseph, Abhinav

    2015-03-26

    Motivated by the need for reliable experimental data for the assessment of theoretical predictions, this work proposes a data set of enthalpies of sublimation determined for specific crystalline structures, for the validation of molecular force fields (FF). The selected data were used to explore the ability of the OPLS-AA parametrization to investigate the properties of solid materials in molecular dynamics simulations. Furthermore, several approaches to improve this parametrization were also considered. These modifications consisted in replacing the original FF atomic point charges (APC), by values calculated using quantum chemical methods, and by the implementation of a polarizable FF. The obtained results indicated that, in general, the best agreement between theoretical and experimental data is found when the OPLS-AA force field is used with the original APC or when these are replaced by ChelpG charges, computed at the MP2/aug-cc-pVDZ level of theory, for isolated molecules in the gaseous phase. If a good description of the energetic relations between the polymorphs of a compound is required then either the use of polarizable FF or the use of charges determined taking into account the vicinity of the molecules in the crystal (combining the ChelpG and MP2/cc-pVDZ methods) is recommended. Finally, it was concluded that density functional theory methods, like B3LYP or B3PW91, are not advisable for the evaluation of APC of organic compounds for molecular dynamic simulations. Instead, the MP2 method should be considered. PMID:25733134

  6. 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.)

  7. MolStruc: a force field calculation program allowing interactive modifications of the force field parameters.

    PubMed

    Siri, D; Pèpe, G; Bernassau, J M

    1990-12-01

    To analyze the influence of parameters and functions on the energy and geometry obtained through different force field calculations, we have developed program MolStruc. This software allows the user to choose between two sets of functions and parameters, MM2 and AMBER. The MM2 option of the program was developed to compute the coulombic energy in a dipole or monopole approximation. To establish comparisons between the energy values, the coulombic contribution is computed in the same way in the Amber and MM2 options of the program. The force field parameters can be handled interactively (through addition or modification). The program was used to study molecules of a representative sample displaying most of the problems encountered in molecular mechanics (MM). PMID:2282362

  8. Reactive Force Fields via Explicit Valency

    NASA Astrophysics Data System (ADS)

    Kale, Seyit

    Computational simulations are invaluable in elucidating the dynamics of biological macromolecules. Unfortunately, reactions present a fundamental challenge. Calculations based on quantum mechanics can predict bond formation and rupture; however they suffer from severe length- and time-limitations. At the other extreme, classical approaches provide orders of magnitude faster simulations; however they regard chemical bonds as immutable entities. A few exceptions exist, but these are not always trivial to adopt for routine use. We bridge this gap by providing a novel, pseudo-classical approach, based on explicit valency. We unpack molecules into valence electron pairs and atomic cores. Particles bear ionic charges and interact via pairwise-only potentials. The potentials are informed of quantum effects in the short-range and obey dissociation limits in the long-range. They are trained against a small set of isolated species, including geometries and thermodynamics of small hydrides and of dimers formed by them. The resulting force field captures the essentials of reactivity, polarizability and flexibility in a simple, seamless setting. We call this model LEWIS, after the chemical theory that inspired the use of valence pairs. Following the introduction in Chapter 1, we initially focus on the properties of water. Chapter 2 considers gas phase clusters. To transition to the liquid phase, Chapter 3 describes a novel pairwise long-range compensation that performs comparably to infinite lattice summations. The approach is suited to ionic solutions in general. In Chapters 4 and 5, LEWIS is shown to correctly predict the dipolar and quadrupolar response in bulk liquid, and can accommodate proton transfers in both acid and base. Efficiency permits the study of proton defects at dilutions not accessible to experiment or quantum mechanics. Chapter 6 discusses explicit valency approaches in other hydrides, forming the basis of a reactive organic force field. Examples of simple proton transfer and more complex reactions are discussed. Chapter 7 provides a framework for variable electron spread. This addition resolves some of the inherent limitations of the former model which implicitly assumed that electron spread was not affected by the environment. A brief summary is provided in Chapter 8.

  9. 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

  10. Three-body Forces from a Classical Nonlinear Field

    NASA Astrophysics Data System (ADS)

    Arod?, H.; Karkowski, J.; ?wierczy?ski, Z.

    Forces in the systems of two opposite sign and three identical charges coupled to the dynamical scalar field of the signum-Gordon model are investigated. Three-body force is present, and the exact formula for it is found. Flipping the sign of one of the two charges changes not only the sign but also the magnitude of the force. Both effects are due to nonlinearity of the field equation.

  11. Three-body forces from a classical nonlinear field

    E-print Network

    Arodz, H; Swierczynski, Z

    2013-01-01

    Forces in the systems of two opposite sign and three identical charges coupled to the dynamical scalar field of the signum-Gordon model are investigated. Three-body force is present, and the exact formula for it is found. Flipping the sign of one of the two charges changes not only the sign but also the magnitude of the force. Both effects are due to nonlinearity of the field equation.

  12. Three-body forces from a classical nonlinear field

    E-print Network

    H. Arodz; J. Karkowski; Z. Swierczynski

    2013-10-02

    Forces in the systems of two opposite sign and three identical charges coupled to the dynamical scalar field of the signum-Gordon model are investigated. Three-body force is present, and the exact formula for it is found. Flipping the sign of one of the two charges changes not only the sign but also the magnitude of the force. Both effects are due to nonlinearity of the field equation.

  13. Force-Free Magnetic Fields of Closed Configuration Having More Energy Than Open Fields

    NASA Astrophysics Data System (ADS)

    Choe, G.; Cheng, C.

    2002-05-01

    Observations of CMEs show an apparent opening of a coronal magnetic field which has assumed a closed configuration before the eruption. In order for this transition of field configuration to occur spontaneously, the pre-eruption closed field must have more energy than the open field. However, as far as force-free fields are concerned, such a transition is energetically forbidden according to the Aly-Sturrock theorem. The theorem states that the maximum energy of the closed force-free fields with the same boundary-normal field distribution and the same field topology is the energy of the corresponding open field. The force-free fields treated in Aly and Sturrock's proofs of the theorem are force-free fields that can be generated from closed potential fields by footpoint motions conserving the boundary normal field distribution and the field topology. The force-free fields investigated in this paper are force-free fields which are not governed by Aly and Sturrock's proofs. We have constructed force-free fields in weak equilibrium, which can be generated in multiple flux systems by a footpoint motion not conserving the boundary normal field distribution. It is found that there exist force-free fields having more magnetic energy than the corresponding open fields. The relevance with observations and the possible mechanisms of CMEs will be discussed.

  14. Can a Closed Force-Free Field Have More Energy Than the Open Field?

    NASA Astrophysics Data System (ADS)

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

    2001-12-01

    Observations of CMEs show an apparent opening of a coronal magnetic field which has assumed a closed configuration before the eruption. In order for this transition of field configuration to occur spontaneously, the pre-eruption closed field must have more energy than the open field. However, as far as force-free fields are concerned, such a transition is energetically forbidden according to the Aly-sturrock theorem. The theorem states that the maximum energy of the closed force-free fields with the same boundary-normal field distribution and the same field topology is the energy of the corresponding open field. The force-free fields treated in Aly and Sturrock's proofs of the theorem are force-free fields that can be generated from closed potential fields by footpoint motions conserving the boundary normal field distribution and the field topology. The force-free fields investigated in this paper are force-free fields which are not governed by Aly and Sturrock's proofs. We will construct force-free fields in weak equilibrium by a footpoint motion not conserving the boundary normal field distribution and show that there exist force-free fields having more magnetic energy than the corresponding open fields. The relevance with observations and the possible mechanisms of CMEs will also be discussed.

  15. Magnetic Forces and Field Line Density

    NSDL National Science Digital Library

    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.

  16. Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields

    SciTech Connect

    Matthews, J. F.; Beckham, G. T.; Bergenstrahle, M.; Brady, J. W.; Himmel, M. E.; Crowley, M. F.

    2012-02-14

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

  17. 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

  18. 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.

  19. Models of force-free magnetic fields in resistive media

    Microsoft Academic Search

    Rolf Boström

    1973-01-01

    A review is given of some of the basic properties of force-free fields under circumstances when the conductivity of the medium is finite. Then the electric current density is related not only to the magnetic field, but also by Ohm's law to the electric field and plasma velocity, which must be considered in the solutions. It is pointed out that

  20. 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 total azimuthal flux with a power-law distribution over the poloidal field. Particular attention is paid

  1. Generation of Dielectrophoretic Force under Uniform Electric Field

    E-print Network

    Kua, C.H.

    Effective dipole moment method has been widely accepted as the de facto technique in predicting the dielectrophoretic force due to the non-uniform electric field. In this method, a finite-particle is modeled as an equivalent ...

  2. LABORATORY V MAGNETIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    's technology. Magnets are used today to image parts of the body, to explore the mysteries of the human brain to combine magnets to change the magnetic field at any point. You decide to determine the form

  3. LABORATORY V MAGNETIC FIELDS AND FORCES

    E-print Network

    Minnesota, University of

    's technology. Magnets are used today to image parts of the body, to explore the mysteries of the human brain to combine magnets to change the magnetic field at any point. You must determine the map of the magnetic

  4. Fields Institute Communications Volume 00, 0000

    E-print Network

    to a fixed algebraic closure K of K. For any ff belonging to K \\ K, let K (ff) (resp. !K (ff)) denote the invarian* *ts defined to be the minimum (resp. maximum) of the set {~v(ff - ff0) | ff06= ff runs over K-conjugates of}ff. In 1998, it was proved that (K, * *v) is a tame field

  5. Vibrational spectrum and force field of dimethyldimethoxysilane

    SciTech Connect

    Tenisheva, T.F.; Lazarev, A.N.

    1986-01-01

    Experimental data is presented on the spectra of (CH/sub 3/)/sub 2/Si(OCH/sub 3/)/sub 2/ (I), (CH/sub 3/)/sub 2/Si(OCD/sub 3/)/sub 2/ (II), and (CD/sub 3/)/sub 2/Si(OCH/sub 3/)/sub 2/ (III). The results of the determination of the force constants on the basis of the optimization of the solution of the inverse mechanical problem of the theory of molecular vibrations with consideration of all the internal degrees of freedom with the exception of the coordinates corresponding to internal rotations are discussed. Raman spectra of I, II, and III in the liquid phase is shown and the IR spectra of amorphous films of I, II, and III are illustrated.

  6. 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.

  7. 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.

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

    NASA Technical Reports Server (NTRS)

    El-Kaddah, N.; Szekely, J.

    1982-01-01

    A mathematical representation was developed for the electromagnetic force field, the flow field, the temperature field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was employed for the calculation of the electromagnetic force field, while the turbulent Navier - Stokes equations and the turbulent convective transport equations were used to represent the fluid flow field, the temperature field and the concentration field. The governing differential equations, written in spherical coordinates, were solved numerically. The computed results were in good agreement with measurements, regarding the lifting force, and the average temperature of the specimen and carburization rates, which were transport controlled.

  9. Particle-Particle Interaction in Electromagnetic Fields for Force-Field Tailoring

    Microsoft Academic Search

    Sameh S. Wanis; Thilini Rangedera; Narayanan M. Komerath

    2007-01-01

    Tailored electromagnetic force fields offer the possibility of forming structures having diverse geometries at various length scales from loose particles. The analogy of the responses of a neutral particle placed in an acoustic or electromagnetic field pointed to the existence of a unified governing force field expression. This was shown to be based on a dipole model of the particle

  10. Force-Field Compensation in a Manual Tracking Task

    PubMed Central

    Squeri, Valentina; Masia, Lorenzo; Casadio, Maura; Morasso, Pietro; Vergaro, Elena

    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 force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%), which is a function of the implicit accuracy of the tracking task. PMID:20567516

  11. 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

  12. Pattern forced geophysical vector field segmentation based on Clifford FFT

    NASA Astrophysics Data System (ADS)

    Yuan, Linwang; Yu, Zhaoyuan; Luo, Wen; Yi, Lin; Hu, Yong

    2013-10-01

    Vector field segmentation is gaining increasing importance in geophysics research. Existing vector field segmentation methods usually can only handle the statistical characteristics of the original data. It is hard to integrate the patterns forced by certain geophysical phenomena. In this paper, a template matching method is firstly constructed on the foundation of the Clifford Fourier Transformation (CFT). The geometric meanings of both inner and outer components can provide more attractive information about the similarities between original vector field and template data. A composed similarity field is constructed based on the coefficients fields. After that, a modified spatial consistency preserving K-Means cluster algorithm is proposed. This algorithm is applied to the similarity fields to extract the template forced spatial distribution pattern. The complete algorithm for the overall processing is given and the experiments of ENSO forced global ocean surface wind segmentation are configured to test our method. The results suggest that the pattern forced segmentation can extract more latent information that cannot be directly measured from the original data. And the spatial distribution of ENSO influence on the surface wind field is clearly given in the segmentation result. All the above suggest that the method we proposed provides powerful and new thoughts and tools for geophysical vector field data analysis.

  13. Tracing optical force fields within graded-index media

    NASA Astrophysics Data System (ADS)

    Akbarzadeh, Alireza; Danesh, Mohammad; Qiu, Cheng-Wei; Danner, Aaron J.

    2014-05-01

    The mechanical interaction between light and graded index media (both isotropic and anisotropic) is presented from the geometrical optics (GO) perspective. Utilizing Hamiltonian equations to determine ray trajectories combined with a description of the Lorentz force exerted on bound currents and charges, we provide a general method that we denote ‘force tracing’ for determining the direction and magnitude of the bulk and surface force density in arbitrarily anisotropic and inhomogeneous media. This technique provides the optical community with machinery which can give a good estimation of the force field distribution in different complex media, and with significantly faster computation speeds than full-wave methods allow. Comparison of force tracing against analytical solutions shows some unusual limitations of GO, which we also illustrate.

  14. E-Government Field Force Automation: Promises, Challenges, and Stakeholders

    Microsoft Academic Search

    Hans Jochen Scholl; Raya Fidel; Michael Paulsmeyer; Kristene Unsworth

    2007-01-01

    With the growing pervasiveness and maturity of fully mobile and wirelessly connected technologies (FMWC), many organizations\\u000a have begun to equip their field workforce with such information and communication technologies (ICT). The aim of these projects\\u000a is to automate fieldwork operations, that is, to make them more effective, to improve field force responsiveness, and to speed\\u000a up the field processes, while

  15. 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.

  16. Simulation of Forces between Humid Amorphous Silica Surfaces: A Comparison of Empirical Atomistic Force Fields

    PubMed Central

    2012-01-01

    Atmospheric humidity strongly influences the interactions between dry granular particles in process containers. To reduce the energy loss in industrial production processes caused by particle agglomeration, a basic understanding of the dependence of particle interactions on humidity is necessary. Hence, in this study, molecular dynamic simulations were carried out to calculate the adhesion between silica surfaces in the presence of adsorbed water. For a realistic description, the choice of force field is crucial. Because of their frequent use and transferability to biochemical systems, the Clay and CWCA force fields were investigated with respect to their ability to describe the water–silica interface in comparison to the more advanced Reax force field, ab initio calculations, and experiments. PMID:23378869

  17. 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.

  18. Interaction Forces Between Multiple Bodies in a Magnetic Field

    NASA Technical Reports Server (NTRS)

    Joffe, Benjamin

    1996-01-01

    Some of the results from experiments to determine the interaction forces between multiple bodies in a magnetic field are presented in this paper. It is shown how the force values and the force directions depend on the configuration of the bodies, their relative positions to each other, and the vector of the primary magnetic field. A number of efficient new automatic loading and assembly machines, as well as manipulators and robots, have been created based on the relationship between bodies and magnetic fields. A few of these patented magnetic devices are presented. The concepts involved open a new way to design universal grippers for robot and other kinds of mechanisms for the manipulation of objects. Some of these concepts can be used for space applications.

  19. 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.

  20. 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

  1. 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.

  2. Einstein's osmotic equilibrium of colloidal suspensions in conservative force fields

    NASA Astrophysics Data System (ADS)

    Fu, Jinxin; Ou-Yang, H. Daniel

    2014-09-01

    Predicted by Einstein in his 1905 paper on Brownian motion, colloidal particles in suspension reach osmotic equilibrium under gravity. The idea was demonstrated by J.B. Perrin to win Nobel Prize in Physics in 1926. We show Einstein's equation for osmotic equilibrium can be applied to colloids in a conservative force field generated by optical gradient forces. We measure the osmotic equation of state of 100nm Polystyrene latex particles in the presence of KCl salt and PEG polymer. We also obtain the osmotic compressibility, which is important for determining colloidal stability and the internal chemical potential, which is useful for predicting the phase transition of colloidal systems. This generalization allows for the use of any conservative force fields for systems ranging from colloidal systems to macromolecular solutions.

  3. Introduction of periodic boundary conditions into UNRES force field.

    PubMed

    Sieradzan, Adam K

    2015-05-01

    In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the ??? hetero tetramer 1 protein system. © 2015 Wiley Periodicals, Inc. PMID:25753584

  4. Frequency-dependent force fields for QMMM calculations.

    PubMed

    Harczuk, Ignat; Vahtras, Olav; Ågren, Hans

    2015-03-11

    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

  5. Comparison of different force fields for the study of disaccharides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ß-cellobiose, a-maltose, and a-galabiose [a-D-Galp-(1'4)-a-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl and glycosidic linkage orientatio...

  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. Force Field Modeling of Conformational Energies: Importance of Multipole

    E-print Network

    Ponder, Jay

    Force Field Modeling of Conformational Energies: Importance of Multipole Moments and Intramolecular the correlation, and both contributions are of similar importance. © 2006 Wiley Periodicals, Inc. Int J Quantum little influence on con- formational degrees of freedom. The nonbonded Correspondence to: F. Jensen; e

  8. ADVANCES IN FORCE FIELD TAILORING FOR CONSTRUCTION IN SPACE

    E-print Network

    reports the status of adapting this new technology to a mission plan to build a 5-module, 1-G radiation a reference mission architecture and engineering solutions to the other issues in building large1 ADVANCES IN FORCE FIELD TAILORING FOR CONSTRUCTION IN SPACE Sam Wanis, Narayanan Komerath School

  9. Cylindrical Magnets and Coils: Fields, Forces, and Inductances

    Microsoft Academic Search

    R. Ravaud; G. Lemarquand; S. Babic; V. Lemarquand; C. Akyel

    2010-01-01

    This paper presents a synthesis of analytical calculations of magnetic parameters (field, force, torque, stiffness) in cylindrical magnets and coils. By using the equivalence between the amperian current model and the coulombian model of a magnet, we show that a thin coil or a cylindrical magnet axially magnetized have the same mathematical model. Consequently, we present first the analytical expressions

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

    PubMed

    Geng, Yanan; Wu, Weida

    2014-05-01

    We present the realization of a mesoscopic imaging technique, namely, the Magnetoelectric Force Microscopy (MeFM), for visualization of local magnetoelectric effect. The basic principle of MeFM is the lock-in detection of local magnetoelectric response, i.e., the electric field-induced magnetization, using magnetic force microscopy. We demonstrate MeFM capability by visualizing magnetoelectric domains on single crystals of multiferroic hexagonal manganites. Results of several control experiments exclude artifacts or extrinsic origins of the MeFM signal. The parameters are tuned to optimize the signal to noise ratio. PMID:24880381

  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. Particle energization in a chaotic force-free magnetic field

    NASA Astrophysics Data System (ADS)

    Li, Xiaocan; Li, Gang; Dasgupta, Brahmananda

    2015-04-01

    A force-free field (FFF) is believed to be a reasonable description of the solar corona and in general a good approximation for low-beta plasma. The equations describing the magnetic field of FFF is similar to the ABC fluid equations which has been demonstrated to be chaotic. This implies that charged particles will experience chaotic magnetic field in the corona. Here, we study particle energization in a time-dependent FFF using a test particle approach. An inductive electric field is introduced by turbulent motions of plasma parcels. We find efficient particle acceleration with power-law like particle energy spectra. The power-law indices depend on the amplitude of plasma parcel velocity field and the spatial scales of the magnetic field fluctuation. The spectra are similar for different particle species. This model provide a possible mechanism for seed population generation for particle acceleration by, e.g., CME-driven shocks. Generalization of our results to certain non-force-free-field (NFFF) is straightforward as the sum of two or multiple FFFs naturally yield NFFF.

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

    PubMed Central

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

    2014-01-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism. PMID:24875276

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  16. 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

  17. Magnetic forces for type II superconductors in a levitation field

    NASA Astrophysics Data System (ADS)

    Torng, Terry; Chen, Q. Y.

    1993-02-01

    A complete loop of hysteretic force has been calculated for hard superconductors in an almost-constant-gradient magnetic suspension system, which consists of a pair of oppositely wound superconducting coils. The dependences of levitation forces on the sample size, critical current density, external field strength, field gradient, and the magnetic history were investigated. Dynamic spring constants as well as magnetic damping coefficients were inferred from minor loop calculations. The minor loops, similar to the Rayleigh loops for ferromagnetic materials, could be described in quadratic terms. The major loops strongly depend on the magnetic passage, a flux-trap effect which is responsible for the subtlety in obtaining reproducible hysteresis loop. The basic physics of levitation and inverse levitation will be quantitatively illustrated.

  18. Lost at Sea: Hurricane Force Wind Fields and the North Pacific Ocean Environment

    E-print Network

    Businger, Steven

    Lost at Sea: Hurricane Force Wind Fields and the North Pacific Ocean Environment 1 Steven Businger: Hurricane Force Wind Fields and the North Pacific Ocean Environment 2 Hurricane Force (HF) Wind Fields in this talk is to help raise awareness of the hazards created by hurricane force winds in extratropical

  19. 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.

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

    PubMed Central

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

    2013-01-01

    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 × 106 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

  1. Four-nucleon force in chiral effective field theory

    SciTech Connect

    Evgeny Epelbaum

    2005-10-25

    We derive the leading contribution to the four--nucleon force within the framework of chiral effective field theory. It is governed by the exchange of pions and the lowest--order nucleon--nucleon contact interaction and includes effects due to the nonlinear pion--nucleon couplings and the pion self interactions constrained by the chiral symmetry of QCD. The resulting 4NF does not contain any unknown parameters and can be tested in future few--and many--nucleon studies.

  2. 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

  3. Modeling High Rate Impact Sensitivity of Perfect RDX and HMX Crystals by ReaxFF Reactive Dynamics

    Microsoft Academic Search

    Luzheng Zhang; Sergey V. Zybin; Adri C. T. Van Duin; William A. Goddard III

    2010-01-01

    We report a methodology for rapid assessment of impact sensitivity of energetic materials which uses the ReaxFF reactive force field in reactive dynamics (RD) simulations of the high rate compression\\/expansion of a perfect energetic crystal. This approach is validated here to study the high rate impact sensitivity of 1,3,5-trinitrohexahydro-s-triazine (RDX) crystal and octahydro-1,3,5,7-tetrazocine (HMX) crystal at different phases (?, ?,

  4. Current Practices in Field Force Automation: Decision Support and Information Management for the Field Force

    Microsoft Academic Search

    Gwen Trentham; Hans Jochen Scholl

    2008-01-01

    Abstract Inthe past, field operations have mostly been a stepchild,of information ,and ,communication technology,(ICT) enabled ,organizational ,overhaul and process re-design. Recently, increased technological,(mobile ,wirelessly ,connected) capability, economic necessity, and new external factors (such as the ,higher frequency of large-scale emergencies, for example, of the magnitude of hurricanes Katrina and Rita in the US) have raised interest in and ,commitment ,to

  5. 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

  6. 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

  7. Loftin Collection - Grumman FF-1

    NASA Technical Reports Server (NTRS)

    1936-01-01

    A civil version of the Grumman FF-1 navy fighter is shown in this photograph. This particular aircraft was used by the Grumman company as an executive transport. The occasion for this photograph was probably an NACA Annual Inspection.

  8. Lost at Sea: Hurricane Force Wind Fields and the North Pacific Ocean Environment

    E-print Network

    Lost at Sea: Hurricane Force Wind Fields and the North Pacific Ocean Environment 1 Unidata Policy Lost at Sea: Hurricane Force Wind Fields and the North Pacific Ocean Environment 2 Hurricane Force (HF to help raise awareness of the hazards created by hurricane force winds in extratropical cyclones

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

    NASA Astrophysics Data System (ADS)

    Pound, Adam

    2012-10-01

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

  10. Transferability of coarse-grained force fields: the polymer case.

    PubMed

    Carbone, Paola; Varzaneh, Hossein Ali Karimi; Chen, Xiaoyu; Müller-Plathe, Florian

    2008-02-14

    A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80 K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at different temperatures agrees very well with the experimental one. We find that the polymer chain length does not affect the transferability of the force field and we attribute such transferability mainly to the finer model used in describing the polyamide-6,6 than the polystyrene. PMID:18282071

  11. 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.

  12. A Single Universal Force Field Can Uniquely Orient Non-Symmetric Parts

    E-print Network

    Richardson, David

    grippers, conveyor belts, or vibratory bowl feeders, these devices generate force fields in which the parts with trans- versely vibrating plates. The flexibility and dexter- ity that programmable force fields offer

  13. Relativistic ponderomotive forces in the field of intense laser radiation

    NASA Astrophysics Data System (ADS)

    Castillo, A. J.; Milant'ev, V. P.

    2014-09-01

    The motion of a relativistic charged particle in the presence of the field of high-power laser radiation represented in the form of a Gaussian beam of arbitrary mode is analyzed. The vector potential of the radiation field is expanded in terms of a small parameter (the ratio of the wavelength to the Gaussian beam waist). A specific feature of averaging with respect to the phases of the high-mode Gaussian beams is demonstrated. The averaged equations for the motion of particle and a general expression for the ponderomotive relativistic force for the circularly polarized radiation are derived. It is demonstrated that relativistic effects suppress the averaged action of high-power laser radiation on the particle.

  14. 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...

  15. On the controllability of the Vlasov-Poisson system in the presence of external force fields

    E-print Network

    Paris-Sud XI, Université de

    On the controllability of the Vlasov-Poisson system in the presence of external force fields Olivier Glass Daniel Han-Kwan May 3, 2011 Abstract In this work, we are interested in the controllability of Vlasov-Poisson systems in the presence of an external force field (namely a bounded force field

  16. Quantum Chemistry Based Force Field for Simulations of HMX Grant D. Smith* and Rishikesh K. Bharadwaj

    E-print Network

    Utah, University of

    Quantum Chemistry Based Force Field for Simulations of HMX Grant D. Smith* and Rishikesh K kcal/mol. The force field, parametrized to reproduce the quantum chemistry geometries and energies the quantum chemistry based force field accurately reproduced the gas-phase structure of DMNA as determined

  17. Developing Force Fields from the Microscopic Structure of Solutions.

    PubMed

    Ploetz, Elizabeth A; Bentenitis, Nikolaos; Smith, Paul E

    2010-03-25

    We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach. PMID:20161692

  18. Why the OPLS-AA force field cannot produce the ?-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field?

    PubMed

    Cao, Zanxia; Liu, Lei; Wang, Jihua

    2011-12-01

    The optimal combination of force field and water model is an essential problem that is able to increase molecular dynamics simulation quality for different types of proteins and peptides. In this work, an attempt has been made to explore the problem by studying H1 peptide using four different models based on different force fields, water models and electrostatic schemes. The driving force for H1 peptide conformation transition and the reason why the OPLS-AA force field cannot produce the ?-hairpin structure of H1 peptide in solution while the GROMOS 43A1 force field can do were investigated by temperature replica exchange molecular dynamics simulation (T-REMD). The simulation using the GROMOS 43A1 force field preferred to adopt a ?-hairpin structure, which was in good agreement with the several other simulations and the experimental evidences. However, the simulation using the OPLS-AA force field has a significant difference from the simulations with the GROMOS 43A1 force field simulation. The results show that the driving force in H1 peptide conformation transition is solvent exposure of its hydrophobic residues. However, the subtle balances between residue-residue interactions and residue-solvent interaction are disrupted by using the OPLS-AA force field, which induced the reduction in the number of residue-residue contact. Similar solvent exposure of the hydrophobic residues is observed for all the conformations sampled using the OPLS-AA force field. For H1 peptide which exhibits large solvent exposure of the hydrophobic residues, the GROMOS 43A1 force field with the SPC water model can provide more accurate results. PMID:22066538

  19. ff (Z ff) 2 E F Correction to Hyperfine Splitting in Hydrogenic Atoms

    E-print Network

    Pachucki, Krzysztof

    ff (Z ff) 2 E F Correction to Hyperfine Splitting in Hydrogenic Atoms Krzysztof Pachucki \\Lambda­energy correction of the order ff (Z ff) 2 EF to the ground state hyperfine splitting in hydrogenic atoms energy is of the order m ff 2 , and the effective hyperfine interaction is given by ffi 3 (r

  20. Electromagnetic self-forces and generalized Killing fields

    NASA Astrophysics Data System (ADS)

    Harte, Abraham I.

    2009-08-01

    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.

  1. 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.

  2. 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 ...

  3. Adaptation and generalization in acceleration dependent force fields

    PubMed Central

    Hwang, Eun Jung; Smith, Maurice A.; Shadmehr, Reza

    2005-01-01

    Any passive rigid inertial object that we hold in our hand, e.g., a tennis racquet, imposes a field of forces on the arm that depends on limb position, velocity, and acceleration. A fundamental characteristic of this field is that the forces due to acceleration and velocity are linearly separable in the intrinsic coordinates of the limb. In order to learn such dynamics with a collection of basis elements, a control system would generalize correctly and therefore perform optimally if the basis elements that were sensitive to limb velocity were not sensitive to acceleration, and vice versa. However, in the mammalian nervous system proprioceptive sensors like muscle spindles encode a nonlinear combination of all components of limb state, with sensitivity to velocity dominating sensitivity to acceleration. Therefore, limb state in the space of proprioception is not linearly separable despite the fact that this separation is a desirable property of control systems that form models of inertial objects. In building internal models of limb dynamics, does the brain use a representation that is optimal for control of inertial objects, or a representation that is closely tied to how peripheral sensors measure limb state? Here we show that in humans, patterns of generalization of reaching movements in acceleration dependent fields are strongly inconsistent with basis elements that are optimized for control of inertial objects. Unlike a robot controller that models the dynamics of the natural world and represents velocity and acceleration independently, internal models of dynamics that people learn appear to be rooted in the properties of proprioception, nonlinearly responding to the pattern of muscle activation and representing velocity more strongly than acceleration. PMID:16292640

  4. ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces

    SciTech Connect

    Henson, Neil Jon [Los Alamos National Laboratory; Waldher, Benjamin [WSU; Kuta, Jadwiga [WSU; Clark, Aurora [WSU; Clark, Aurora E [NON LANL

    2009-01-01

    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.

  5. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential.

    PubMed

    Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand

    2015-03-19

    The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ?340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed. PMID:25650885

  6. 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).

  7. Modification of the CHARMM force field for DMPC lipid bilayer.

    PubMed

    Högberg, Carl-Johan; Nikitin, Alexei M; Lyubartsev, Alexander P

    2008-11-15

    The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids. PMID:18512235

  8. Derivation of a Molecular Mechanics Force Field for Cholesterol

    SciTech Connect

    Cournia, Zoe; Vaiana, Andrea C.; Smith, Jeremy C.; Ullmann, G. Matthias M.

    2004-01-01

    As a necessary step toward realistic cholesterol:biomembrane simulations, we have derived CHARMM molecular mechanics force-field parameters for cholesterol. For the parametrization we use an automated method that involves fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. Results for another polycyclic molecule, rhodamine 6G, are also given. The usefulness of the method is thus demonstrated by the use of reference data from two molecules at different levels of theory. The frequency-matching plots for both cholesterol and rhodamine 6G show overall agreement between the CHARMM and quantum chemical normal modes, with frequency matching for both molecules within the error range found in previous benchmark studies.

  9. Forces due to fluctuations in the anisotropic phase-field model of solidification

    Microsoft Academic Search

    Stanislav G. Pavlik; Robert F. Sekerka

    1999-01-01

    Stochastic forces due to thermodynamic fluctuations are derived for the anisotropic phase-field model of solidification. The stochastic forces turn out to be anisotropic. The derivation utilizes the general principles of irreversible thermodynamics. One of the forces is the divergence of the stochastic heat flux derived by Landau and Lifshitz (Statistical Physics, Pergamon Press, Oxford, 1958). The other force is the

  10. Neuropeptide FF, pain and analgesia

    Microsoft Academic Search

    Michel Roumy; Jean-Marie Zajac

    1998-01-01

    Neuropeptide FF (Phe–Leu–Phe–Gln–Pro–Gln–Arg–Phe–NH2) and the octadecapeptide neuropeptide AF (Ala–Gly–Glu–Gly–Leu–Ser–Ser–Pro–Phe–Trp–Ser–Leu–Ala–Ala–Pro–Gln–Arg–Phe–NH2) were isolated from bovine brain, and were initially characterized as anti-opioid peptides. They can oppose the acute effects of opioids and an increase in their brain concentrations may be responsible for the development of tolerance and dependence to opioids. Numerous experiments suggest a possible neuromodulatory role for neuropeptide FF. A precursor

  11. Accounting for electronic polarization in non-polarizable force fields.

    PubMed

    Leontyev, Igor; Stuchebrukhov, Alexei

    2011-02-21

    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 ?? 3D reported in recent ab initio and experimental studies with the value ?(eff)? 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value ?(eff) = ?/??(el), where ?(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes. PMID:21212894

  12. Comparison of ReaxFF, DFTB, and DFT for phenolic pyrolysis. 2. Elementary reaction paths.

    PubMed

    Bauschlicher, Charles W; Qi, Tingting; Reed, Evan J; Lenfant, Antonin; Lawson, John W; Desai, Tapan G

    2013-11-01

    Reaction paths for the loss of CO, H2, and H2O from atomistic models of phenolic resin are determined using the hybrid B3LYP approach. B3LYP energetics are confirmed using CCSD(T). The energetics along the B3LYP paths are also evaluated using the PW91 generalized gradient approximation (GGA), the more approximate self-consistent charge density functional tight binding (SCC-DFTB), and the reactive force field (ReaxFF). Compared with the CCSD(T)/cc-pVTZ level for bond and reaction energies and barrier heights, the B3LYP, PW91, DFTB(mio), DFTB(pbc), and ReaxFF have average absolute errors of 3.8, 5.1, 17.4, 13.2, and 19.6 kcal/mol, respectively. The PW91 is only slightly less accurate than the B3LYP approach, while the more approximate approaches yield somewhat larger errors. The SCC-DFTB paths are in better agreement with B3LYP than are those obtained with ReaxFF. PMID:24093151

  13. Structure of liquid ethylene glycol: A molecular dynamics simulation study with different force fields

    E-print Network

    Saiz, Leonor

    of the studied force fields have the same intermolecular parameters and different intramolecular interactionsStructure of liquid ethylene glycol: A molecular dynamics simulation study with different force simulation studies for several different liquid phase force fields. We compare the properties obtained

  14. Optimization of protein force-field parameters with the Protein Data Bank

    NASA Astrophysics Data System (ADS)

    Sakae, Yoshitake; Okamoto, Yuko

    2003-12-01

    We propose a novel method to optimize existing force-field parameters for protein systems. The method consists of minimizing the summation of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank. We performed this optimization to the partial-charge and torsion-energy parameters of the AMBER parm94 force field, using 100 molecules from the Protein Data Bank. We then performed folding simulations of ?-helical and ?-hairpin peptides. The optimized force-field parameters gave structures more consistent with the experimental implications than the original AMBER force field.

  15. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

    Discusses pupil misconceptions concerning forces. Summarizes some of Assessment of Performance Unit's findings on meaning of (1) force, (2) force and motion in one dimension and two dimensions, and (3) Newton's second law. (YP)

  16. A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers

    PubMed Central

    2015-01-01

    Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ? 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ? 0.93 on average). The RSMEs do not exceed 3.2 kcal mol–1 for the UBDB and are in the range of 3.7–7.6 kcal mol–1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications to macromolecules. PMID:24803869

  17. Critical Casimir forces in the presence of random surface fields

    NASA Astrophysics Data System (ADS)

    Macio?ek, A.; Vasilyev, O.; Dotsenko, V.; Dietrich, S.

    2015-03-01

    We study critical Casimir forces (CCFs) fC for films of thickness L which in the three-dimensional bulk belong to the Ising universality class and which are exposed to random surface fields (RSFs) on both surfaces. We consider the case in which, in the absence of RSFs, the surfaces of the film belong to the surface universality class of the so-called ordinary transition. We carry out a finite-size scaling analysis and show that for weak disorder, CCFs still exhibit scaling, acquiring a random field scaling variable w that is zero for pure systems. We confirm these analytic predictions by Monte Carlo (MC) simulations. Moreover, our MC data show that fC varies as fC(w ?0 ) -fC(w =0 ) ˜w2 . Asymptotically, for large L , w scales as w ˜L-0.26?0 , indicating that this type of disorder is an irrelevant perturbation of the ordinary surface universality class. However, for thin films such that w ?1 , we find that the presence of RSFs with vanishing mean value increases significantly the strength of CCFs, as compared to systems without them, and it shifts the extremum of the scaling function of fC toward lower temperatures. But fC remains attractive.

  18. Spatial confinement of ultrasonic force fields in microfluidic channels Otto Manneberg a

    E-print Network

    Spatial confinement of ultrasonic force fields in microfluidic channels Otto Manneberg a , S: 43.25.Gf Keywords: Ultrasonic manipulation Acoustic radiation force Microfluidic chip Particle image localized ultrasonic manipulation functions in series in micro- fluidic chips. The manipulation functions

  19. instructions HisTrap FF crude,

    E-print Network

    Lebendiker, Mario

    · p1 instructions HisTrap FF crude, 1 ml and 5 ml i 11-0012-38 Edition AA HisTrapTM FF crude, such as degradation and oxidation of sensitive target proteins, and is therefore of great importance. HisTrap FF crude properties HisTrap FF crude 1-ml and 5-ml columns are prepacked with the affinity medium Ni Sepharose 6 Fast

  20. Competition among Li(+), Na(+), K(+), and Rb(+) Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields.

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2015-03-26

    In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li(+), Na(+), K(+), and Rb(+), and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

  1. 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

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

    PubMed

    Orban de Xivry, Jean-Jacques; 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

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

    NASA Astrophysics Data System (ADS)

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

    2002-05-01

    In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. In order for this transition of field configuration to occur spontaneously, the pre-eruption closed magnetic field must have more energy than the post-eruption open field. In force-free fields, however, such a possibility is denied by the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. Here we note that the theorem implicitly assumes the existence of the maximum energy configuration. However, this may not be taken for granted because the limiting configuration of energy-increasing sequences of force-free fields does not necessarily have an energy equal to the energy supremum. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed.

  4. Force field independent metal parameters using a nonbonded dummy model.

    PubMed

    Duarte, Fernanda; Bauer, Paul; Barrozo, Alexandre; Amrein, Beat Anton; Purg, Miha; Aqvist, Johan; Kamerlin, Shina Caroline Lynn

    2014-04-24

    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 Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-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

  5. 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

  6. 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

  7. BE.430J Fields, Forces, and Flows in Biological Systems, Fall 2004

    E-print Network

    Grodzinsky, Alan J.

    This course covers the following topics: conduction, diffusion, convection in electrolytes; fields in heterogeneous media; electrical double layers; Maxwell stress tensor and electrical forces in physiological systems; and ...

  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. 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 ...

  10. Cell Separation by Non-Inertial Force Fields in Microfluidic Systems

    PubMed Central

    Tsutsui, Hideaki; Ho, Chih-Ming

    2009-01-01

    Cell and microparticle separation in microfluidic systems has recently gained significant attention in sample preparations for biological and chemical studies. Microfluidic separation is typically achieved by applying differential forces on the target particles to guide them into different paths. This paper reviews basic concepts and novel designs of such microfluidic separators with emphasis on the use of non-inertial force fields, including dielectrophoretic force, optical gradient force, magnetic force, and acoustic primary radiation force. Comparisons of separation performances with discussions on physiological effects and instrumentation issues toward point-of-care devices are provided as references for choosing appropriate separation methods for various applications. PMID:20046897

  11. A Mechanical Force Accompanies Fluorescence Resonance Energy Transfer (FRET) Adam E. Cohen*, and Shaul Mukamel

    E-print Network

    Mukamel, Shaul

    the FF is as a generalization of optical trapping. A polarizable particle (atom, molecule, colloid, etc.) experiences a force along an electric field gradient. In laser tweezers, tight focusing of the laser beam be thought of as optical trapping of the acceptor by the near-field of the excited donor. This electrodynamic

  12. Total screening and finite range forces from ultra-massive scalar fields

    E-print Network

    H. Arodz; J. Karkowski; Z. Swierczynski

    2013-04-11

    Force between static point particles coupled to a classical ultra-massive scalar field is calculated. The field potential is proportional to the modulus of the field. It turns out that the force exactly vanishes when the distance between the particles exceeds certain finite value. Moreover, each isolated particle is surrounded by a compact cloud of the scalar field that completely screens its scalar charge.

  13. Total screening and finite range forces from ultra-massive scalar fields

    E-print Network

    Arodz, H; Swierczynski, Z

    2013-01-01

    Force between static point particles coupled to a classical ultra-massive scalar field is calculated. The field potential is proportional to the modulus of the field. It turns out that the force exactly vanishes when the distance between the particles exceeds certain finite value. Moreover, each isolated particle is surrounded by a compact cloud of the scalar field that completely screens its scalar charge.

  14. A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters

    SciTech Connect

    Iftner, Christophe; Simon, Aude; Korchagina, Kseniia; Rapacioli, Mathias; Spiegelman, Fernand [Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse (France)] [Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse (France)

    2014-01-21

    We propose in the present paper a SCC-DFTB/FF (Self-Consistent-Charge Density Functional based Tight Binding/Force-Field) scheme adapted to the investigation of molecules trapped in rare gas environments. With respect to usual FF descriptions, the model involves the interaction of quantum electrons in a molecule with rare gas atoms in an anisotropic scheme. It includes polarization and dispersion contributions and can be used for both neutral and charged species. Parameters for this model are determined for hydrocarbon-argon complexes and the model is validated for small hydrocarbons. With the future aim of studying polycyclic aromatic hydrocarbons in Ar matrices, extensive benchmark calculations are performed on (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters against DFT and CCSD(T) calculations for the smaller sizes, and more generally against other experimental and theoretical data. Results on the structures and energetics (isomer ordering and energy separation, cohesion energy per Ar atom) are presented in detail for n = 1–8, 13, 20, 27, and 30, for both neutrals and cations. We confirm that the clustering of Ar atoms leads to a monotonous decrease of the ionization potential of benzene for n ? 20, in line with previous experimental and FF data.

  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. Quantum Chemistry Based Force Field for Simulations of Poly(vinylidene fluoride)

    E-print Network

    Utah, University of

    Quantum Chemistry Based Force Field for Simulations of Poly(vinylidene fluoride) Oleksiy G. Byutner geometries and confor- mational energies of the PVDF oligomers as well as intermolecular interactions between CH4 and CF4. To validate the force field, molecular dynamics simulations of a PVDF melts have been

  17. New design of a superconducting magnet for generation of quasi-uniform magnetic force field

    Microsoft Academic Search

    L. Quettier; A. Mailfert

    2003-01-01

    The generation of uniform field of magnetic forces exerted on diamagnetic or paramagnetic particles is a problem with various applications: magnetic separation of particles with small differential magnetic susceptibility, diamagnetic levitation, material processing crystallization of proteins, etc. Superconducting magnets that are usually investigated to generate uniform field of magnetic forces are solenoids but unfortunately these designs lead necessarily to a

  18. Modeling of Hydrogen Storage Materials: A Reactive Force Field for NaH

    E-print Network

    Goddard III, William A.

    Modeling of Hydrogen Storage Materials: A Reactive Force Field for NaH Ojwang' J.G.O.*, Rutger van is the fall in potential energy surface during heating. Keywords: hydrogen storage, reactive force field governing hydrogen desorption in NaH. During the abstraction process of surface molecular hydrogen charge

  19. 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

  20. Energy of Force-free Magnetic Fields in Relation to Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

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

    SciTech Connect

    G.S. Choe; C.Z. Cheng

    2002-05-09

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

  2. 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

  3. Mechanical Forces between Electric Currents and Saturated Magnetic Fields

    Microsoft Academic Search

    Vladimir Karapetoff

    1927-01-01

    The general case considered is that of N independent electric circuits placed in a medium of variable permeability and subject to saturation, in parts or as a whole. The problem is to determine the component (in a given direction) of the mechanical force acting upon one of the electric circuits, upon a group of circuits, or upon a group of

  4. FF: The Fast-Forward Planning System

    Microsoft Academic Search

    Jörg Hoffmann

    2001-01-01

    Fast-Forward, abbreviated FF, was the most successfulautomatic planner in the AIPS-2000 planningsystems competition. Like the well knownHSP system, FF relies on forward search in thestate space, guided by a heuristic that estimatesgoal distances by ignoring delete lists. It differsfrom HSP in a number of important details. Thisarticle describes the algorithmic techniques usedin FF in comparison to HSP, and evaluates theirbenefits

  5. Development of Field Excavator with Embedded Force Measurement

    NASA Technical Reports Server (NTRS)

    Johnson, K.; Creager, C.; Izadnegahdar, A.; Bauman, S.; Gallo, C.; Abel, P.

    2012-01-01

    A semi-intelligent excavation mechanism was developed for use with the NASA-built Centaur 2 rover prototype. The excavator features a continuously rotatable large bucket supported between two parallel arms, both of which share a single pivot axis near the excavator base attached to the rover. The excavator is designed to simulate the collection of regolith, such as on the Moon, and to dump the collected soil into a hopper up to one meter tall for processing to extract oxygen. Because the vehicle can be autonomous and the terrain is generally unknown, there is risk of damaging equipment or using excessive power when attempting to extract soil from dense or rocky terrain. To minimize these risks, it is critical for the rover to sense the digging forces and adjust accordingly. It is also important to understand the digging capabilities and limitations of the excavator. This paper discusses the implementation of multiple strain gages as an embedded force measurement system in the excavator's arms. These strain gages can accurately measure and resolve multi-axial forces on the excavator. In order to validate these sensors and characterize the load capabilities, a series of controlled excavation tests were performed at Glenn Research Center with the excavator at various depths and cut angles while supported by a six axis load cell. The results of these tests are both compared to a force estimation model and used for calibration of the embedded strain gages. In addition, excavation forces generated using two different types of bucket edge (straight vs. with teeth) were compared.

  6. 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.

    phases in cement paste and has also been associated with severe cracking in cured hardened cement aluminate (C3A) column in ettringite during uniaxial compression and tension and that hydrogen bond re has also been associated spatially with severe cracking in cured hardened concrete1 during what

  7. 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.

  8. Shape-induced force fields in optical trapping

    NASA Astrophysics Data System (ADS)

    Phillips, D. B.; Padgett, M. J.; Hanna, S.; Ho, Y.-L. D.; Carberry, D. M.; Miles, M. J.; Simpson, S. H.

    2014-05-01

    Advances in optical tweezers, coupled with the proliferation of two-photon polymerization systems, mean that it is now becoming routine to fabricate and trap non-spherical particles. The shaping of both light beams and particles allows fine control over the flow of momentum from the optical to mechanical regimes. However, understanding and predicting the behaviour of such systems is highly complex in comparison with the traditional optically trapped microsphere. In this Article, we present a conceptually new and simple approach based on the nature of the optical force density. We illustrate the method through the design and fabrication of a shaped particle capable of acting as a passive force clamp, and we demonstrate its use as an optically trapped probe for imaging surface topography. Further applications of the design rules highlighted here may lead to new sensors for probing biomolecule mechanics, as well as to the development of optically actuated micromachines.

  9. Force-Free Fields Having More Energy Than Open Fields and Their Role in Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

    In typical CME observations, a CME loop expands outward and a radially stretched open field structure is eventually formed. For this transition of field configuration to occur spontaneously, the closed field configuration before the eruption must have more energy than the open field configuration. This possibility is, however, precluded by the Aly-Sturrock theorem, according to which closed force-free fields with the same boundary normal field distribution do not have more energy than the corresponding open field. Here we note that in their proofs of the theorem, Aly and Sturrock assume that a limiting configuration of energy increasing sequences should exist and that the energy of this configuration is the energy supremum. These two conditions are far from trivial. In this paper, we report counterexamples in which the Aly-Sturrock theorem is invalid. We have constructed force-free fields in multiple flux systems with current sheets and found that some of them have more energy than the open field. We investigate how the geometrical properties of those force-free solutions depend on the imposed field connectivity. A comparison of our solutions with observational features is presented, and the dynamical evolution of those force-free fields toward eruption is discussed.

  10. Numerical derivation of forces on particles and agglomerates in a resonant acoustic field

    NASA Astrophysics Data System (ADS)

    Knoop, Claas; Fritsching, Udo

    2013-10-01

    Particles and agglomerates are investigated in gaseous acoustic flow fields. Acoustic fields exert forces on solid objects, which can influence the shape of the exposed bodies, even to the point of breakage of the structures. Motivated by experimentally observed breakage of agglomerates in an acoustic levitator (f = 20 kHz), a numerical study is presented that derives the acoustic forces on a complex model agglomerate from the pressure and velocity fields of a resonant standing ultrasound wave, calculated by computational fluid dynamics (CFD). It is distinguished between the drag and lift/lateral forces on the overall agglomerate and on the different primary particles of the model.

  11. Nonlinear force-free magnetic fields: Calculation and applicatin to astrophysics. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Yang, Wei-Hong

    1987-01-01

    The problem concerned in this work is that of calculating magnetic field configurations in which the Lorentz force (vector)j x (vector)B is everywhere zero, subject to specified boundary conditions. The magnetic field is represented in terms of Clebsch variables in the form (vector)B = del alpha x del beta. These variables are constant on any field line. The most appropriate choice of boundary conditions is to specify the values of alpha and beta on the bounding surface. It is proposed that the field lines move in the direction of local Lorentz force and relax towards a force-free field configuration. This concept leads to an iteration procedure for modifying the variables alpha and beta that tends asymptotically towards the force-free state. This method is first applied to a simple problem in two rectangular dimensions; the calculation shows that the convergence of magnetic field energy to a minimum state (force-free) is close to exponential. This method is then applied to study some astrophysical force-free magnetic fields, such as the structures and evolution of magnetic fields of rotating sunspots and accretion disks. The implication of the results, as related to the mechanisms of solar flares, extragalactic radio sources and radio jets, are discussed.

  12. Nonredundant Nf-Ff Transformation With Helicoidal Scanning

    Microsoft Academic Search

    O. M. Bucci; C. Gennarelli; G. Riccio; C. Savarese

    2001-01-01

    A probe compensated near-field-far-field (NF-FF) transformation technique with helicoidal scanning, which makes use of a minimum number of probe output voltage samples, is developed in this paper. This target is achieved by using a nonuniform helix as scanning curve, i.e., a circular helix with a constant angular elevation step, and by developing an efficient sampling representation over it. Then, by

  13. Preprocessing of vector magnetograph data for a non-linear force-free magnetic field reconstruction

    E-print Network

    Thomas Wiegelmann; Bernd Inhester; Takashi Sakurai

    2006-12-21

    Knowledge regarding the coronal magnetic field is important for the understanding of many phenomena, like flares and coronal mass ejections. Because of the low plasma beta in the solar corona the coronal magnetic field is often assumed to be force-free and we use photospheric vector magnetograph data to extrapolate the magnetic field into the corona with the help of a non-linear force-free optimization code. Unfortunately the measurements of the photospheric magnetic field contain inconsistencies and noise. In particular the transversal components (say Bx and By) of current vector magnetographs have their uncertainties. Furthermore the magnetic field in the photosphere is not necessary force-free and often not consistent with the assumption of a force-free field above. We develop a preprocessing procedure to drive the observed non force-free data towards suitable boundary conditions for a force-free extrapolation. As a result we get a data set which is as close as possible to the measured data and consistent with the force-free assumption.

  14. 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.

  15. Transferable next-generation force fields from simple liquids to complex materials.

    PubMed

    Schmidt, J R; Yu, Kuang; McDaniel, Jesse G

    2015-03-17

    Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as physically motivated. We find that these physically motivated force fields exhibit both high accuracy and transferability, with the latter deriving from the universality of the fundamental physical laws governing intermolecular interactions. This basic methodology has been applied to a diverse set of systems, ranging from simple liquids to nanoporous metal-organic framework materials. A key conclusion is that, in many cases, it is feasible to account for nearly all of the relevant physics of intermolecular interactions within the context of the force field. In such cases, the structural, thermodynamic, and dynamic properties of the system become naturally emergent, even in the absence of explicit parameterization to bulk properties. We also find that, quite generally, the three-body contributions to the dispersion and exchange energies in bulk liquids are crucial for quantitative accuracy in a first-principles force field, although these contributions are almost universally neglected in existing empirical force fields. PMID:25688596

  16. Models of force-free magnetic fields in resistive media

    Microsoft Academic Search

    Bostroem

    1973-01-01

    A review is given of some of the basic properties of forcefree fields ; under circumstances when the conductivity of the medium is finite. Then the ; electric current density is related not only to the magnetic field, but also by ; Ohm's law to the electric fleld and plasma velocity, which must be considered in ; the solutions. It

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

    Microsoft Academic Search

    T. Emig; R. L. Jaffe

    2007-01-01

    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

  18. Forces and movement of water droplets in oil caused by applied electric field

    Microsoft Academic Search

    A. Pedersen; E. Ildstad; A. Nysveen

    2004-01-01

    The effect of applying an electric field to an emulsion of water and oil is to induce attractive forces and enhance the coalescence of adjacent water droplets. In the oil industry, it is common to utilize this process, called electrocoalescense, to enhance oil-water separation by enlarging the water droplets. The work presented here describes the forces influencing the kinematics of

  19. Accurate Prediction of Magnetic Field and Magnetic Forces in Permanent Magnet Motors Using an Analytical Solution

    Microsoft Academic Search

    Z. J. Liu; J. T. Li

    2008-01-01

    This paper presents an analytical model suitable for analyzing permanent magnet motors with slotted stator core. By including the effect of the interaction between the pole transitions and slot openings, the model is able to predict the airgap field and magnetic forces with high accuracy, which cannot be achieved using the previously available analytical methods. The results of electromagnetic forces,

  20. Choices and challenges in e-government field force automation projects: insights from case studies

    Microsoft Academic Search

    Raya Fidel; Kristene Unsworth

    2007-01-01

    Field Force Automation (FFA) has been introduced as the summary term for the redesign of workflows and business processes in the field by means of fully mobile wirelessly connected technologies and applications. In practice, governments around the world have increasingly begun to explore the potential of FFA by equipping field crews with mobile technologies and applications. FFA in government promises

  1. 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

  2. Extending FF to Numerical State Variables

    Microsoft Academic Search

    Jörg Hoffmann

    2002-01-01

    The FF system obtains a heuristic estimate for each state during a forward search by solving a relaxed version of the planning t ask, where the re- laxation is to assume that all delete lists are empty. We show how this relax- ation, and FF' s heuristic function, can naturally be extend ed to planning tasks with constraints and effects

  3. Excitation of forced ion acoustic waves, large plasma sheets, and magnetic field fluctuations over Gakona, Alaska

    E-print Network

    Cohen, Joel (Joel A.)

    2009-01-01

    Two research subjects: (1) excitation of "forced ion acoustic waves", and (2) "simultaneous excitation of plasma density fluctuations and geomagnetic field fluctuations" are reported in my M.S. thesis. The data was acquired ...

  4. Design of a multi-axis force transducer with applications in track and field

    E-print Network

    Traina, Zachary J

    2005-01-01

    The objective of this thesis is the design and implementation of a multi-axis force transducer to be integrated into a set of track and field starting blocks. The feedback from this transducer can be used by athletes and ...

  5. Evaluation of unsteady pressure fields and forces in rotating airfoils from time-resolved PIV

    NASA Astrophysics Data System (ADS)

    Villegas, A.; Diez, F. J.

    2014-04-01

    The instantaneous pressure fields and aerodynamic loads are obtained for rotating airfoils from time-resolved particle image velocimetry (TR-PIV) measurements. These allowed evaluating the contribution from the local acceleration (unsteady acceleration) to the instantaneous forces. Traditionally, this term has been neglected for wind turbines with quasi-steady flows, but results show that it is a dominant term in the wake where high temporal variations in the flow field are present due to vortex shedding. Briefly, time-resolved particle image velocimetry TR-PIV measurements are used to calculate flow velocity fields and corresponding spatial and temporal derivatives. These derivatives are then used in the Poisson equation to solve for the pressure field and later used in the integral momentum equation to solve for the instantaneous forces. The robustness of the measurements is analyzed by calculating the PIV uncertainty and the independence of the calculated forces. The experimental mean aerodynamic forces are compared with theoretical predictions from the blade element momentum theory showing good agreement. The instantaneous pressure field showed dependence with time in the wake due to vortex shedding. The contribution to the instantaneous forces from each term in the integral momentum equation is evaluated. The analysis shows that the larger contributions to the normal force coefficient are from the unsteady and the pressure terms, and the larger contribution to the tangential force coefficient is from the convective term.

  6. 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.

  7. 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.

  8. 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

  9. Force field parametrization by weak coupling. Re-engineering SPC water

    Microsoft Academic Search

    Christian D. Berweger; Wilfred F. van Gunsteren; Florian Müller-Plathe

    1995-01-01

    A recently developed scheme for the automatic adjustment of force field parameters to experimentally observed properties is applied to the simple-point-charge (SPC) water model. The refinement procedure is based on a first-order coupling of a force-field parameter (say, an atomic charge) to the deviation of a calculated bulk liquid property (e.g. the heat of vaporization) from its ideal value. I.e.

  10. Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

    NASA Astrophysics Data System (ADS)

    Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

    2014-11-01

    The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

  11. Force on a heated sphere in a horizontal plane acoustic standing wave field

    NASA Technical Reports Server (NTRS)

    Leung, E. W.; Wang, T. G.

    1985-01-01

    The force on a heated sphere in a horizontal plane acoustic standing wave field is the subject of this investigation. The heated sphere produces a thermal gradient in the resonance chamber. The force on the sphere in a direction perpendicular to that of gravity is measured. This force is enhanced in the region near the pressure node, and is weakened in the region near the pressure antinode. Measurements of the force on a heated sphere with sound pressure levels between 148 and 156 dB are presented.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. Thermal decomposition of energetic materials by ReaxFF reactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, L.

    2005-07-01

    Understanding the complex physicochemical processes that govern the initiation and decomposition kinetics of energetic materials can pave the way for modifying the explosive or propellant formulation to improve their performance and reduce the sensitivity. In this work, we used molecular dynamics (MD) simulations with the reactive force field (ReaxFF) to study the thermal decomposition of pure crystals (RDX, HMX) as well as crystals bonded with polyurethane chains (Estane). The preliminary simulation results show that pure RDX and HMX crystals exhibit similar decomposition kinetics with main products (e.g., N2, H2O, CO2, and CO) and intermediates (NO2, NO, HONO, OH) in a good agreement with experiment. We also studied the effect of temperature on decomposition rate which increases at higher temperatures. With addition of polymer binders, we found that the reactivity of these energetic materials is reduced, and the polymer chains packing along different planes may also influence their thermal decomposition. In addition, we studied the thermal decomposition of TATP and hydrazine which are examples of ReaxFF development for non- nitramine based energetic materials.

  15. 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.

  16. A Voltage-Input-Based Field Reconstruction Technique for Efficient Modeling of the Fields and Forces Within Induction Machines

    Microsoft Academic Search

    Dezheng Wu; Steven D. Pekarek; Babak Fahimi

    2010-01-01

    In recent research, a field reconstruction (FR) technique was developed to enable more efficient evaluation of the magnetic fields and forces within induction machines. By using the FR, the results of two finite-element (FE) solutions (in which stator current is used as the input to the FE model) are used to establish basis functions for the flux densities in the

  17. 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...

  18. MAGNETIC HELICITY OF SELF-SIMILAR AXISYMMETRIC FORCE-FREE FIELDS

    SciTech Connect

    Zhang Mei [Key Laboratory of Solar Activity, National Astronomical Observatory, Chinese Academy of Sciences, Datun Road A20, Chaoyang District, Beijing 100012 (China); Flyer, Natasha [Institute for Mathematics Applied to Geosciences, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307 (United States); Low, Boon Chye [High Altitude Observatory, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307 (United States)

    2012-08-10

    In this paper, we continue our theoretical studies addressing the possible consequences of magnetic helicity accumulation in the solar corona. Our previous studies suggest that coronal mass ejections (CMEs) are natural products of coronal evolution as a consequence of magnetic helicity accumulation and that the triggering of CMEs by surface processes such as flux emergence also have their origin in magnetic helicity accumulation. Here, we use the same mathematical approach to study the magnetic helicity of axisymmetric power-law force-free fields but focus on a family whose surface flux distributions are defined by self-similar force-free fields. The semi-analytical solutions of the axisymmetric self-similar force-free fields enable us to discuss the properties of force-free fields possessing a huge amount of accumulated magnetic helicity. Our study suggests that there may be an absolute upper bound on the total magnetic helicity of all bipolar axisymmetric force-free fields. With the increase of accumulated magnetic helicity, the force-free field approaches being fully opened up with Parker-spiral-like structures present around a current-sheet layer as evidence of magnetic helicity in the interplanetary space. It is also found that among the axisymmetric force-free fields having the same boundary flux distribution, the one that is self-similar is the one possessing the maximum amount of total magnetic helicity. This gives a possible physical reason why self-similar fields are often found in astrophysical bodies, where magnetic helicity accumulation is presumably also taking place.

  19. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-19

    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

  20. Comparison of oxidation resistance of UHMWPE and POM in H2O2 solution from ReaxFF reactive molecular dynamics simulations.

    PubMed

    Chen, Wu; Duan, Hai-tao; Hua, Meng; Gu, Ka-li; Shang, Hong-fei; Li, Jian

    2014-08-28

    The oxidation mechanism of ultra-high-molecular-weight polyethylene (UHMWPE) and polyoxymethylene (POM) in hydrogen peroxide solution was investigated by molecular dynamics (MD) simulations via reactive force field (ReaxFF) method. MD results from ReaxFF suggested that UHMWPE provided better antioxidation activity at high temperature (>373 K) than its POM counterpart in the same concentration of hydrogen peroxide solution. Furthermore, POM was relatively more susceptible to erosion and swelling because of the infiltration of H2O2 solution. Calculations of the diffusion coefficient at different temperatures permit further understanding of the chemical phenomena involved in the level of oxidation in the course of MD simulations. Results of the simulations are generally consistent with the previous experimental available in literature. The simulations also provide new insights into understanding the mechanism resulting oxidation products among the interested polymers. PMID:25133290

  1. On the representation of inhomogeneous linear force-free fields

    NASA Astrophysics Data System (ADS)

    Clegg, J. R.; Browning, P. K.; Laurence, P.; Bromage, B. J. I.; Stredulinsky, E.

    2000-10-01

    It is shown that there is a false assumption hidden in the description of a relaxed state with inhomogeneous boundary conditions as the vector sum of a potential field, satisfying the boundary conditions, and a sum of eigenfunctions of the associated eigenvalue problem expanded by certain coefficients. In particular, although the Jensen and Chu formula (1984) can provide the correct expansion coefficients, it contains an implicit paradox in its derivation according to a general vector theorem. The same paradox led Chu et al. (1999) to be concerned about a contradiction obtained by taking the curl of their magnetic field expansion which, if permitted, becomes inconsistent with a current normal to the surface. The assumption that the curl can be commuted across an infinite sum of terms is the mechanism leading to these, apparently paradoxical, conclusions. Two mechanisms for resolving this apparent paradox are possible, one of which will be described in some detail below and the other discussed further in a forthcoming, more theoretical paper (Laurence et al., 2000). The decomposition of the magnetic field above is valid with convergence in the mean squared sense, but a decomposition of the current needs to be reinterpreted in terms of negative Sobolev spaces. To avoid this, and remain in a more easily managable and familiar setting, we derive the expansion coefficients in a way that involves the commuting of the inverse curl (as opposed to the curl) and the series. The resulting series converges in a mean square sense. When this is done the calculation can conform to the general vector theorem and a new gauge-invariant expression for the coefficients is obtained. However the consequence of the non-commutability is nullified in the Jensen and Chu formula, in both simply and multiply connected domains, by the important extra requirement of a boundary condition on the vector potential eigenfunctions; this excludes magnetic field eigenfunctions that carry flux, but there remains a complete set for the expansion and all flux is carried by the potential field. The two formulas are then identical. On a different issue, it is shown that if the general expansion is taken over a half-space, by combining positive and negative eigenvalue terms, then the coefficients are anisotropic, that is they are tensors except when evaluated at the first eigenvalue. A specific example is presented to illustrate the situation and to validate the new method of deriving the coefficients.

  2. 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

  3. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

    PubMed

    Lupyan, Dmitry; Abramov, Yuriy A; Sherman, Woody

    2012-11-01

    The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130 small molecules from the CSD containing an intramolecular sulfur-oxygen distance less than the sum of their van der Waals (vdW) radii. Close S···O distances are observed in several important medicinal chemistry motifs (e.g. a carbonyl oxygen connected by a carbon or nitrogen linker to a sulfur) and are not treated well with existing parameters in the MMFFs or OPLS_2005 force fields, resulting in suboptimal geometries and energetics. In this work, we develop modified parameters for the OPLS_2005 force field to better treat this specific interaction in order to generate conformations close to those found in the CSD structures. We use a combination of refitting a force field torsional parameter, adding a specific atom pair vdW term, and attenuating the electrostatic interactions to obtain an improvement in the accuracy of geometry minimizations and conformational searches for these molecules. Specifically, in a conformational search 58 % of the cases produced a conformation less than 0.25 Å from the CSD crystal conformation with the modified OPLS force field parameters developed in this work. In contrast, 25 and 37 % produced a conformation less than 0.25 Å with the MMFFs and OPLS_2005 force fields, respectively. As an application of the new parameters, we generated conformations for the tyrosine kinase inhibitor axitinib (trade name Inlyta) that could be correctly repacked into three observed polymorphic structures, which was not possible with conformations generated using MMFFs or OPLS_2005. The improved parameters can be mapped directly onto physical characteristics of the systems that are treated inadequately with the molecular mechanics force fields used in this study and potentially other force fields as well. PMID:23053737

  4. Vibrational spectroscopy and the development of new force fields for biological molecules.

    PubMed

    Gerber, R B; Chaban, G M; Gregurick, S K; Brauer, B

    2003-03-01

    The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy. PMID:12601796

  5. Comparison of Cross-Field Matching and Forced-Choice Identification in Hemispatial Neglect

    Microsoft Academic Search

    M. Verfaellie; W. P. Milberg; R. McGlinchey-Berroth; L. Grande

    1995-01-01

    The ability of patients with neglect to process information in the contralateral field was examined by comparing performance on a cross-field matching and a forced-choice identification task. The matching task required participants to judge whether 2 laterally presented pictures were the same or different. The identification task required selection of 1 of 2 centrally presented pictures that were identical to

  6. First-principles calculation of electrical forces among nanospheres in a uniform applied electric field

    Microsoft Academic Search

    David J. Bergman; Xiangting Li; Kwangmoo Kim; David Stroud

    2005-01-01

    We present a unified framework for a first-principles calculation of the electric force acting on dielectric or metallic nanospheres suspended in a dielectric host and subject to a uniform external electric field. This framework is based on the spectral representation of the local electric field in a composite medium. The quasi-static (or \\

  7. BIOREMEDIATION FIELD EVALUATION: EIELSON AIR FORCE BASE, ALASKA (EPA/540/R-95/533)

    EPA Science Inventory

    This publication, one of a series presenting the findings of the Bioremediation Field Initiatives bioremediation field evaluations, provides a detailed summary of the evaluation conducted at the Eielson Air Force Base (AFB) Superfund site in Fairbanks, Alaska. At this site, the ...

  8. 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.

  9. 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.

  10. POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins.

    PubMed

    Li, Xinbi; Ponomarev, Sergei Y; Sigalovsky, Daniel L; Cvitkovic, John P; Kaminski, George A

    2014-11-11

    Previously, we reported development of a fast polarizable force field and software named POSSIM (POlarizable Simulations with Second order Interaction Model). The second-order approximation permits the speed up of the polarizable component of the calculations by ca. an order of magnitude. We have now expanded the POSSIM framework to include a complete polarizable force field for proteins. Most of the parameter fitting was done to high-level quantum mechanical data. Conformational geometries and energies for dipeptides have been reproduced within average errors of ca. 0.5 kcal/mol for energies of the conformers (for the electrostatically neutral residues) and 9.7° for key dihedral angles. We have also validated this force field by running Monte Carlo simulations of collagen-like proteins in water. The resulting geometries were within 0.94 Å root-mean-square deviation (RMSD) from the experimental data. We have performed additional validation by studying conformational properties of three oligopeptides relevant in the context of N-glycoprotein secondary structure. These systems have been previously studied with combined experimental and computational methods, and both POSSIM and benchmark OPLS-AA simulations that we carried out produced geometries within ca. 0.9 Å RMSD of the literature structures. Thus, the performance of POSSIM in reproducing the structures is comparable with that of the widely used OPLS-AA force field. Furthermore, our fitting of the force field parameters for peptides and proteins has been streamlined compared with the previous generation of the complete polarizable force field and relied more on transferability of parameters for nonbonded interactions (including the electrostatic component). The resulting deviations from the quantum mechanical data are similar to those achieved with the previous generation; thus, the technique is robust, and the parameters are transferable. At the same time, the number of parameters used in this work was noticeably smaller than that of the previous generation of our complete polarizable force field for proteins; thus, the transferability of this set can be expected to be greater, and the danger of force field fitting artifacts is lower. Therefore, we believe that this force field can be successfully applied in a wide variety of applications to proteins and protein-ligand complexes. PMID:25400518

  11. 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.

  12. Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids.

    PubMed

    Starovoytov, Oleg N; Torabifard, Hedieh; Cisneros, G Andrés

    2014-06-26

    The development of AMOEBA (a multipolar polarizable force field) for imidazolium based ionic liquids is presented. Our parametrization method follows the AMOEBA procedure and introduces the use of QM intermolecular total interactions as well as QM energy decomposition analysis (EDA) to fit individual interaction energy components. The distributed multipoles for the cation and anions have been derived using both the Gaussian distributed multipole analysis (GDMA) and Gaussian electrostatic model-distributed multipole (GEM-DM) methods.1 The intermolecular interactions of a 1,3-dimethylimidazolium [dmim(+)] cation with various anions, including fluoride [F(-)], chloride [Cl(-)], nitrate [NO(3)(-)], and tetraflorouborate [BF(4)(-)], were studied using quantum chemistry calculations at the MP2/6-311G(d,p) level of theory. Energy decomposition analysis was performed for each pair using the restricted variational space decomposition approach (RVS) at the HF/6-311G(d,p) level. The new force field was validated by running a series of molecular dynamic (MD) simulations and by analyzing thermodynamic and structural properties of these systems. A number of thermodynamic properties obtained from MD simulations were compared with available experimental data. The ionic liquid structure reproduced using the AMOEBA force field is also compared with the data from neutron diffraction experiment and other MD simulations. Employing GEM-DM force fields resulted in a good agreement on liquid densities ?, enthalpies of vaporization ?H(vap), and diffusion coefficients D(±) in comparison with conventional force fields. PMID:24901255

  13. Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

    NASA Astrophysics Data System (ADS)

    Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

    2004-12-01

    Secondary-structure forming tendencies are examined for six well-known protein force fields: AMBER94, AMBER96, AMBER99, CHARMM22, OPLS-AA/L, and GROMOS96. We performed generalized-ensemble molecular dynamics simulations of two peptides. One of these peptides is C-peptide of ribonuclease A, and the other is the C-terminal fragment from the B1 domain of streptococcal protein G. The former is known to form ?-helix structure and the latter ?-hairpin structure by experiments. The simulation results revealed significant differences of the secondary-structure forming tendencies among the force fields. Of the six force fields, the results of AMBER99 and CHARMM22 were in accord with experiments for C-peptide. For G-peptide, on the other hand, the results of OPLS-AA/L and GROMOS96 were most consistent with experiments. Therefore, further improvements on the force fields are necessary for studying the protein folding problem from the first principles, in which a single force field can be used for all cases.

  14. Force-free magnetosphere of an aligned rotator with differential rotation of open magnetic field lines

    E-print Network

    Andrey N. Timokhin

    2006-09-07

    Here we briefly report on results of self-consistent numerical modeling of a differentially rotating force-free magnetosphere of an aligned rotator. We show that differential rotation of the open field line zone is significant for adjusting of the global structure of the magnetosphere to the current density flowing through the polar cap cascades. We argue that for most pulsars stationary cascades in the polar cap can not support stationary force-free configurations of the magnetosphere.

  15. Quasi-static evolution of sheared force-free fields and the solar flare problem

    NASA Technical Reports Server (NTRS)

    Aly, J. J.

    1985-01-01

    Some new results are given showing the possible evolution of a two-dimensional force-free field in the half-space z greater than 0 toward an open field. This evolution is driven by shearing motions applied to the feet of the field lines on the boundary z = 0. The consequences of these results for a model of the two-ribbon solar flare are discussed.

  16. 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.

  17. 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.

  18. 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

  19. 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.

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

    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 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.

  1. Use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields.

    PubMed

    Huang, Wei; Lin, Zhixiong; van Gunsteren, Wilfred F

    2014-06-19

    The predictive power of biomolecular simulation critically depends on the quality of the force field or molecular model used and on the extent of conformational sampling that can be achieved. Both issues are addressed. First, it is shown that widely used force fields for simulation of proteins in aqueous solution appear to have rather different propensities to stabilize or destabilize ?-, ?-, and 3(10)- helical structures, which is an important feature of a biomolecular force field due to the omni-presence of such secondary structure in proteins. Second, the relative stability of secondary structure elements in proteins can only be computationally determined through so-called free-energy calculations, the accuracy of which critically depends on the extent of configurational sampling. It is shown that the method of enveloping distribution sampling is a very efficient method to extensively sample different parts of configurational space. PMID:24410325

  2. 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).

  3. Force field parametrization by weak coupling. Re-engineering SPC water

    NASA Astrophysics Data System (ADS)

    Berweger, Christian D.; van Gunsteren, Wilfred F.; Müller-Plathe, Florian

    1995-01-01

    A recently developed scheme for the automatic adjustment of force field parameters to experimentally observed properties is applied to the simple-point-charge (SPC) water model. The refinement procedure is based on a first-order coupling of a force-field parameter (say, an atomic charge) to the deviation of a calculated bulk liquid property (e.g. the heat of vaporization) from its ideal value. I.e. the method is very similar in spirit to the weak-coupling scheme used to implement constant-temperature or constant-pressure molecular dynamics. With the method we have refined the charges and the Lennard-Jones diameter of the SPC water model at several state points of high temperature and high pressure. We also have studied how these force-field parameters have to be reoptimized as the cutoff distance is varied.

  4. 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...

  5. 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.

  6. Forces and torque on a pair of uncharged conducting spheres in an external electric field

    NASA Astrophysics Data System (ADS)

    Lekner, John

    2013-12-01

    Exact results are given for the forces acting on two conducting spheres in an applied electric field E. The torque acting on the two-sphere system is proportional to the difference between the longitudinal and transverse polarizabilities: ? =(??-?t)E2 sin? cos? (? is the angle between the applied field and the line-of-centers of the spheres). The forces acting on the two spheres are equal and opposite, and given by the derivatives of ?? and ?t with respect to the sphere separation. Simple analytic forms for the torque and forces are found at small and at large separations. At all separations, the torque always acts to align the line of centers of the spheres with the external field. Possible applications are to colloidal suspensions of spherical conducting particles.

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

    NASA Astrophysics Data System (ADS)

    He, Han; Wang, Huaning

    2008-05-01

    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 the bottom boundary surface. On the basis of this new method, we devised a practical calculation scheme for the nonlinear force-free field extrapolation above solar active regions. The code of the scheme was tested by the analytical solutions of Low and Lou (1990) and was applied to the observed vector magnetogram of solar active region NOAA 9077. The results of the calculations show that the improvement of the new computational scheme to the scheme of Yan and Li (2006) is significant, and the force-free and divergence-free constraints are well satisfied in the extrapolated fields. The calculated field lines for NOAA 9077 present the X-shaped structure and can be helpful for understanding the magnetic configuration of the filament channel as well as the magnetic reconnection process during the Bastille Day flare on 14 July 2000.

  8. Multi-phase-field analysis of short-range forces between diffuse interfaces.

    PubMed

    Wang, N; Spatschek, R; Karma, A

    2010-05-01

    We characterize both analytically and numerically short-range forces between spatially diffuse interfaces in multi-phase-field models of polycrystalline materials. During late-stage solidification, crystal-melt interfaces may attract or repel each other depending on the degree of misorientation between impinging grains, temperature, composition, and stress. To characterize this interaction, we map the multiphase-field equations for stationary interfaces to a multidimensional classical mechanical scattering problem. From the solution of this problem, we derive asymptotic forms for short-range forces between interfaces for distances larger than the interface thickness. The results show that forces are always attractive for traditional models where each phase-field represents the phase fraction of a given grain. Those predictions are validated by numerical computations of forces for all distances. Based on insights from the scattering problem, we propose a multi-phase-field formulation that can describe both attractive and repulsive forces in real systems. This model is then used to investigate the influence of solute addition and a uniaxial stress perpendicular to the interface. Solute addition leads to bistability of different interfacial equilibrium states, with the temperature range of bistability increasing with strength of partitioning. Stress in turn, is shown to be equivalent to a temperature change through a standard Clausius-Clapeyron relation. The implications of those results for understanding grain boundary premelting are discussed. PMID:20866233

  9. Acquisition and contextual switching of multiple internal models for different viscous force fields.

    PubMed

    Wada, Yasuhiro; Kawabata, Yasuhiro; Kotosaka, Shinya; Yamamoto, Kenji; Kitazawa, Shigeru; Kawato, Mitsuo

    2003-07-01

    Humans can learn an enormous number of motor behaviors in different environments. To explain this, the MOSAIC model proposes that multiple internal models are acquired in the brain, which can be switched. However, previous behavioral studies that examined arm-movement adaptations to multiple environments reported a rather limited learning capability. Hitherto, humans have been believed incapable of learning two opposite viscous force fields, which are both dynamic transformations and depend on the same state variable, presented in a random order with only a visual cue. In contrast, this study found that humans are capable of this. Elbow joint movements to specified targets were perturbed by either resistive or assistive viscous force fields generated by a single degree-of-freedom manipulandum. The resistive or assistive viscous force fields were cued by a blue or red color on a CRT screen, respectively. The squared distance between the end point and the target, and the variance of the joint angular velocities were used as kinematic performance indices. These movement errors decreased significantly as a function of the training days. Aftereffects and learning consolidation were demonstrated in the random presentation of the two force fields. Consequently, humans were able to learn the multiple and distinct internal models of the two force fields and appropriately switch them even for a random presentation cued only by color after several days of training. This study suggests that none of the previously proposed conditions for multiple internal model learning are necessary prerequisites, and indicates that the difficulty in learning is determined by the balance between the effectiveness of contextual information and the similarity of force fields. PMID:12804793

  10. 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.

  11. Higher-Order Nonlocal Effects of a Relativistic Ponderomotive Force in High-Intensity Laser Fields

    NASA Astrophysics Data System (ADS)

    Iwata, Natsumi; Kishimoto, Yasuaki

    2014-01-01

    We have developed a new formula for a relativistic ponderomotive force of transversely localized laser fields based on the noncanonical Lie perturbation method by finding proper coordinates and gauges in the variational principle. The formula involves new terms represented by second and third spatial derivatives of the field amplitude, so that the ponderomotive force depends not only on the local field gradient, but also on the curvature and its variation. The formula is then applicable to a regime in which the conventional formula is hardly applied such that nonlocal and/or global extent of the field profile becomes important. The result can provide a theoretical basis for describing nonlinear laser-plasma interaction including such nonlocal effects, which is examined via particle-in-cell simulation of laser propagation in a plasma with a super Gaussian transverse field profile.

  12. Higher-order nonlocal effects of a relativistic ponderomotive force in high-intensity laser fields.

    PubMed

    Iwata, Natsumi; Kishimoto, Yasuaki

    2014-01-24

    We have developed a new formula for a relativistic ponderomotive force of transversely localized laser fields based on the noncanonical Lie perturbation method by finding proper coordinates and gauges in the variational principle. The formula involves new terms represented by second and third spatial derivatives of the field amplitude, so that the ponderomotive force depends not only on the local field gradient, but also on the curvature and its variation. The formula is then applicable to a regime in which the conventional formula is hardly applied such that nonlocal and/or global extent of the field profile becomes important. The result can provide a theoretical basis for describing nonlinear laser-plasma interaction including such nonlocal effects, which is examined via particle-in-cell simulation of laser propagation in a plasma with a super Gaussian transverse field profile. PMID:24484146

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

    SciTech Connect

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

    1993-04-01

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

  14. Experimental and ab Initio Equilibrium Structure and Harmonic Force Field of 1,2,5-Oxadiazole

    Microsoft Academic Search

    J. Vázquez; J. Demaison; J. J. López-González; James E Boggs; H. D Rudolph

    2001-01-01

    The equilibrium structure of 1,2,5-oxadiazole has been calculated ab initio at the CCSD(T) level using a polarized valence quadruple ? basis set. The harmonic force field has also been calculated at the MP2\\/cc-pVTZ, B3LYP\\/6-311++G(3df, 2pd), and B3LYP\\/cc-pVQZ levels. These force fields have been subsequently scaled and further refined by fitting them to the experimental values of the vibrational fundamentals of

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

    PubMed

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

    2014-09-16

    Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis. PMID:25098651

  16. 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.

  17. Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent.

    PubMed

    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. PMID:25793854

  18. FF-Replan: A Baseline for Probabilistic Planning Sungwook Yoon

    E-print Network

    Givan, Bob

    FF-Replan: A Baseline for Probabilistic Planning Sungwook Yoon Computer Science & Engineering Engineering Purdue University West Lafayette, IN 47907 givan@purdue.edu Abstract FF-Replan was the winner- prising, due to the simplicity of the approach. In particular, FF-Replan calls FF on a carefully

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

    NASA Astrophysics Data System (ADS)

    Lerche, I.; Low, B. C.

    2014-10-01

    An axisymmetric force-free magnetic field B(r, ?) in spherical coordinates is defined by a function r sin ? B ? = Q ( A ) relating its azimuthal component to its poloidal flux-function A. The power law r sin ? B ? = a A | A | 1/ n, n a positive constant, admits separable fields with A = An/(?)rn, posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and An(?) 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/(? ,?)rn+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.

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

    SciTech Connect

    Ram, Abhay K. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Dasgupta, Brahmananda [Center for Space Plasma and Aeronomic Research, University of Alabama in Huntsville, Huntsville, Alabama 35805 (United States); Krishnamurthy, V. [Center for Ocean-Land-Atmosphere Studies, George Mason University, Fairfax, Virginia 22030 (United States); Mitra, Dhrubaditya [Nordita, KTH Royal Institute of Technology and Stockholm University, 10691 Stockholm (Sweden)

    2014-07-15

    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 t{sup 2}, 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{sup ?}, 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.

  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. Scalar field self-force effects on orbits about a Schwarzschild black hole

    SciTech Connect

    Diaz-Rivera, Luz Maria; Whiting, Bernard F.; Detweiler, Steven [Department of Physics, PO Box 118440, University of Florida, Gainesville, Florida 32611-8440 (United States); Messaritaki, Eirini [Department of Physics, PO Box 118440, University of Florida, Gainesville, Florida 32611-8440 (United States); Department of Physics, PO Box 413, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53201 (United States)

    2004-12-15

    For a particle of mass {mu} and scalar charge q, we compute the effects of the scalar field self-force upon circular orbits, upon slightly eccentric orbits and upon the innermost stable circular orbit (ISCO) of a Schwarzschild black hole of mass m. For circular orbits the self-force is outward and causes the angular frequency at a given radius to decrease. For slightly eccentric orbits the self-force decreases the rate of the precession of the orbit. The effect of the self-force moves the radius of the innermost stable circular orbit inward by 0.122 701xq{sup 2}/{mu}, and it increases the angular frequency of the ISCO by the fraction 0.029 165 7xq{sup 2}/{mu}m.

  3. Scalar field self-force effects on orbits about a Schwarzschild black hole

    E-print Network

    Luz Maria Diaz-Rivera; Eirini Messaritaki; Bernard F. Whiting; Steven Detweiler

    2004-10-04

    For a particle of mass mu and scalar charge q, we compute the effects of the scalar field self-force upon circular orbits, upon slightly eccentric orbits and upon the innermost stable circular orbit of a Schwarzschild black hole of mass M. For circular orbits the self force is outward and causes the angular frequency at a given radius to decrease. For slightly eccentric orbits the self force decreases the rate of the precession of the orbit. The effect of the self force moves the radius of the innermost stable circular orbit inward by 0.122701 q^2/mu, and it increases the angular frequency of the ISCO by the fraction 0.0291657 q^2/mu M.

  4. EXCLUSIVE STUDY OF REACTIONS p(ff; ff 0 )X AND p( ~ IN THE REGION OF THE ROPER RESONANCE

    E-print Network

    Titov, Anatoly

    EXCLUSIVE STUDY OF REACTIONS p(ff; ff 0 )X AND p( ~ d; d 0 )X IN THE REGION OF THE ROPER RESONANCE that this resonance might correspond to a hybrid structure. The study of inelastic scattering of ff mechanism and the properties of baryon resonances. The fact that the ff­particle has the isospin I = 0

  5. 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

  6. 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).

  7. The Pulsation Mode and Distance of the Cepheid FF Aquilae

    E-print Network

    Turner, D G; Luck, R E; Berdnikov, L N

    2013-01-01

    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 4.47d s-Cepheid FF Aql. Line ratios in high dispersion spectra of the variable yield values of =-3.40+-0.02 s.e.(+-0.04 s.d.), average effective temperature Teff=6195+-24 K, and intrinsic color (-)o = +0.506+-0.007, corresponding to a reddening of E(B-V)=0.25+-0.01, or E(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 =39.0+-0.7 Rsun inferred from its luminosity and effective temperature. The dust extinction towards FF Aql is described by a ratio of total-to-selective extinction of R...

  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. Simulation of the Brownian motion of the domain wall in a nonlinear force field of nanowires

    NASA Astrophysics Data System (ADS)

    Ivanov, Anatoly A.; Orlov, Vitaly A.

    2015-02-01

    The paper proposes a computer simulation method of the thermo-fluctuational motion of domain walls in ferromagnetic polycrystalline nanowires, taking into account a non-linear force field of magnetic inhomogeneities. The method makes use of stochastic Langevin function. Into the Langevin equation we added a member describing random force pattern of domain wall fixation on magnetic inhomogeneities. A variety of statistic characteristics of domain wall propagation process have been obtained: magnetization jumps distribution, activation energies distribution, distribution of magnetization switch waiting times and distribution of magnetization jump times. Paper shows that it is incorrect to apply Einstein-Smoluchowski equation for particle's thermo-fluctuational motion in non-linear force field pattern.

  10. All-atom CHARMM force field and bulk properties of perfluorozinc phthalocyanines.

    PubMed

    Dwyer, Patrick J; Vander Valk, Rory J; Caltaldo, Vito; Demianicz, David; Kelty, Stephen P

    2014-12-11

    Classical force fields within the CHARMM parametrized model are developed for zinc phthalocyanines including the parent per-hydro molecule and per-fluoro-alkyl substituted derivatives. Partial atomic charges, 2-body bond lengths, and 3-body angle parameters were obtained from B3LYP-level density functional calculations. Force constants for 2-, 3-, and 4-body interactions were derived from existing fluoroalkane models and incorporated assuming transferability. The force fields were validated by comparing equilibrium molecular geometries from molecular dynamics simulations with density functional theory (DFT) calculations and, where available, published experimental XRD refinements. The models produce molecular geometries for the target materials within 1-2% of expected values. Intermolecular interaction geometries were also investigated using molecular dynamics simulations. The results provide new insight and predictions of the equilibrium stacking and orientational intermolecular interactions of this novel class of modified phthalocyanines. PMID:25390623

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

    PubMed

    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

  12. 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

  13. High Force Magnetic Levitation Using Magnetized Superconducting Bulks as a Field Source for Bearing Applications

    NASA Astrophysics Data System (ADS)

    Patel, A.; Giunchi, G.; Albisetti, A. Figini; Shi, Y.; Hopkins, S. C.; Palka, R.; Cardwell, D. A.; Glowacki, B. A.

    The ability of high temperature superconducting bulks to trap magnetic fields of several tesla allows them to generate very high levitation force. This paper reports the development of a bulk-bulk superconducting rotary bearing design which uses superconducting bulks on both the rotor and the stator. An evaluation is made of the effectiveness of pulsed fields for magnetizing bulks. Modeling of the bulks using the perfectly trapped flux model is also reported to assess the limits of the bearing design. The results demonstrate the feasibility of a (RE)BCO-MgB2 bulk bearing capable of force densities of the order of 100N/cm2. The design and construction of a unique system capable of magnetizing a 25 mm (RE)BCO bulk and measuring levitation force between this bulk and a coaxial MgB2 hollow cylinder is outlined.

  14. 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...

  15. 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.

  16. 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

  17. Visualization of Force Fields in Protein Structure Clark Crawford, Oliver Kreylos, Bernd Hamann, Silvia Crivelli

    E-print Network

    Hamann, Bernd

    , it is an unfortunate reality that only a small fraction of those structures have been solved due to their cost and time surface. Therefore, the protein structure prediction problem is often approached as a highVisualization of Force Fields in Protein Structure Prediction Clark Crawford, Oliver Kreylos, Bernd

  18. Self-force of a scalar field for circular orbits about a Schwarzschild black hole

    E-print Network

    Steven Detweiler; Eirini Messaritaki; Bernard F. Whiting

    2003-02-22

    The foundations are laid for the numerical computation of the actual worldline for a particle orbiting a black hole and emitting gravitational waves. The essential practicalities of this computation are here illustrated for a scalar particle of infinitesimal size and small but finite scalar charge. This particle deviates from a geodesic because it interacts with its own retarded field $\\psi^\\ret$. A recently introduced Green's function $G^\\SS$ precisely determines the singular part, $\\psi^\\SS$, of the retarded field. This part exerts no force on the particle. The remainder of the field $\\psi^\\R = \\psi^\\ret - \\psi^\\SS$ is a vacuum solution of the field equation and is entirely responsible for the self-force. A particular, locally inertial coordinate system is used to determine an expansion of $\\psi^\\SS$ in the vicinity of the particle. For a particle in a circular orbit in the Schwarzschild geometry, the mode-sum decomposition of the difference between $\\psi^\\ret$ and the dominant terms in the expansion of $\\psi^\\SS$ provide a mode-sum decomposition of an approximation for $\\psi^\\R$ from which the self-force is obtained. When more terms are included in the expansion, the approximation for $\\psi^\\R$ is increasingly differentiable, and the mode-sum for the self-force converges more rapidly.

  19. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field

    NASA Astrophysics Data System (ADS)

    Mareš, Ji?í; Vaara, Juha

    2014-10-01

    An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6 ] 2 + complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  20. Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs

    E-print Network

    Varshney, Amitabh

    Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs (Accepted in JCISE 2012) Robert Patro Graduate Student Inst. for Advanced Computer Studies Department of Computer Science Assistant Inst. for Advanced Computer Studies University of Maryland College Park, Maryland 20742 Email

  1. 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…

  2. IN SITU BIOVENTING: TWO USEPA AND AIR FORCE SPONSORED FIELD STUDIES

    EPA Science Inventory

    Bioventing is the process of delivering oxygen by forced air movement through organically contaminated unsaturated soils in order to stimulate in situ biodegradation in an otherwise oxygen-limited environment. his paper is a report on progress of two ongoing bioventing field stud...

  3. Analysis of Three-Phase Power Transformer Short Circuit Magnetic Field and Forces

    Microsoft Academic Search

    Hongkui Li; Gang Cheng

    2010-01-01

    This research studies the magnetic field and forces on the windings of transformer due to short circuit. Three dimensional finite element computation of three-phase power transformer is carried out. The model developed have been applied to power transformer and the results are verified experimentally. To verify the computation results, they are compared with those obtained using ANSYS software simulation.

  4. 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

  5. The SPASIBA force field as an essential tool for studying the structure and dynamics of saccharides.

    PubMed

    Vergoten, G; Mazur, I; Lagant, P; Michalski, J C; Zanetta, J P

    2003-01-01

    The SPASIBA force field has been applied to the determination of the structure and dynamical properties of various disaccharides. It has been shown that the experimental properties (structure, dipole moment, conformational relative energies) are satisfactorily predicted. The anomeric and exo-anomeric effects are confidently reproduced without specific terms for the alpha and beta anomers and the type of glycosidic linkages. PMID:12765776

  6. A field construction technique to efficiently model the dynamic vector forces within induction machines

    Microsoft Academic Search

    Dezheng Wu

    2008-01-01

    Using finite element (FE) analysis to model the dynamic vector fields and forces within induction machines requires significant computational effort. Numerous researchers have proposed techniques to reduce the effort such as taking advantage of machine symmetry. Although these techniques have been effective, the required computation remains relatively high, particularly if it is desired to use the model as an integral

  7. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  8. Chapter 5 Development of Adiabatic Force Field for Polyvinyl Chloride PVC

    E-print Network

    Goddard III, William A.

    73 Chapter 5 Development of Adiabatic Force Field for Polyvinyl Chloride PVC and Chlorinated PVC, dielectric, and ame and smoke properties, chemical inertness, and low sensitivity to hydrocarbon costs would be to determine the non-adiabatic surface by xing all bonds and angles so that only the torsional

  9. Theoretical Studies on VPI5. 3. The MSQ Force Field for Alu minophosphate Zeolites

    E-print Network

    Çagin, Tahir

    9/22/98 Theoretical Studies on VPI­5. 3. The MS­Q Force Field for Alu­ minophosphate Zeolites Osamu 91125 Abstract Aluminophosphate zeolite is an artificial material which shows strange hydrophilic­ ity of this zeolite depended on the local geometric deformation, and speculated that the site­specific hydrophilicity

  10. 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.

  11. First use of synoptic vector magnetograms for global nonlinear, force-free coronal magnetic field models

    NASA Astrophysics Data System (ADS)

    Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

    2014-02-01

    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 three-dimensional magnetic fields are used to estimate the magnetic free energy content Efree = Enlfff - Epot, 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.

  12. Dependence of A-RNA simulations on the choice of the force field and salt strength.

    PubMed

    Besseová, Ivana; Otyepka, Michal; Réblová, Kamila; Sponer, Jirí

    2009-12-01

    We present an extensive molecular dynamics study (0.6 micros in total) on three A-RNA duplexes. The dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions (approximately 0.18 M net-neutralizing Na(+) and approximately 0.3 M KCl) was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alpha/gamma t/t flips common in Parm99 simulations. Nevertheless, since the alpha/gamma t/t sub-state occurs to certain extent in experimental A-RNA structures, we consider both force fields as viable. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form. Further narrowing of the deep major groove is observed in excess salt simulations, again accompanied by larger roll, inclination and twist. The cumulative difference between Parm99/lower-salt and Parmbsc0/higher-salt simulations is approximately 4-8 A for the average PP distances, and -0.7 to -2.5 degrees, -2.0 to -5.4 degrees, -2.6 to -8.6 degrees and 1.7 to 7.0 degrees for the twist, roll, inclination and propeller, respectively. The effects of the force field and salt condition are sequence-dependent. Thus, the compactness of A-RNA is sensitive to the sequence and the salt strength which may, for example, modulate the end-to-end distance of the A-RNA helix. The simulations neatly reproduce the known base pair roll re-distribution in alternating purine-pyrimidine A-RNA helices. PMID:20145814

  13. 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.

  14. 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.

  15. Streaming and removal forces due to second-order sound field during megasonic cleaning of silicon wafers

    E-print Network

    Deymier, Pierre

    Streaming and removal forces due to second-order sound field during megasonic cleaning of silicon September 2000 We calculate the second-order streaming force in a fluid in the vicinity of the solid. It is composed of one silicon slab wafer immersed in water. The components of the streaming force parallel

  16. Solution of variational equations of the problem of the motion of a mass point in a central force field

    Microsoft Academic Search

    Iu. S. Aleksandrov

    1980-01-01

    The problem of obtaining a general solution of the variational equations describing the motion of a mass point under the action of a central force is examined, assuming that the force modulus is a function of the distance to the force center. From the results obtained, a solution for the case of motion in a Newtonian gravitational field derives (in

  17. 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.

  18. 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.

  19. The Effect of Electric Fields In A Classic Introductory Physics Treatment of Eddy Current Forces

    E-print Network

    P. J. Salzman; John Robert Burke; Susan M. Lea

    2006-07-23

    A simple model of eddy currents in which current is computed solely from magnetic forces acting on electrons proves accessible to introductory students and gives a good qualitative account of eddy current forces. However, this model cannot be complete; it ignores the electric fields that drive current outside regions of significant magnetic field. In this paper we show how to extend the model to obtain a boundary value problem for current density. Solution of this problem in polar coordinates shows that the electric field significantly affects the quantitative results and presents an exercise suitable for upper division students. We apply elliptic cylindrical coordinates to generalize the result and offer an exercise useful for teaching graduate students how to use non-standard coordinate systems.

  20. Experimental and ab Initio Equilibrium Structure and Harmonic Force Field of 1,2,5-Oxadiazole.

    PubMed

    Vázquez, J.; Demaison, J.; López-González, J. J.; Boggs, James E.; Rudolph, H. D.

    2001-06-01

    The equilibrium structure of 1,2,5-oxadiazole has been calculated ab initio at the CCSD(T) level using a polarized valence quadruple zeta basis set. The harmonic force field has also been calculated at the MP2/cc-pVTZ, B3LYP/6-311++G(3df, 2pd), and B3LYP/cc-pVQZ levels. These force fields have been subsequently scaled and further refined by fitting them to the experimental values of the vibrational fundamentals of three isotopomers and the centrifugal distortion constants of the parent molecule. The specific refinement of those scaled force constants particularly sensitive to the experimental data set was decisive for obtaining a more reliable harmonic potential. The resulting force fields are presented and used, together with the ground state rotational constants, to calculate an r(z) structure. The experimental r(0), r(s), and r(m) structures have also been determined. The different results have been compared and it is concluded that the ab initio structure is a good approximation of the equilibrium structure. It is also shown that the magnetic correction is not negligible, particularly for the inertial defect. Another interesting conclusion is that the anharmonicity of the C-H stretching might be unusually small. Copyright 2001 Academic Press. PMID:11397111

  1. A research on the force-freeness of photosphere magnetic field

    NASA Astrophysics Data System (ADS)

    Liu, S.; Hao, J.

    2015-03-01

    In this paper, the statistical studies on the force-freeness of photosphere magnetic fields are given. The studies are based on the vector magnetic fields observed by Solar Optical Telescope/Spectro-Polarimeter (SOT/SP) on board Hinode. Three parameters (Fx /Fp,Fy /Fp , and Fz /Fp) are introduced to investigate the force-freeness of active regions photosphere magnetic field. Various thresholds and reductions of original resolutions are selected to calculated parameters. As for the resolutions, the reductions of original resolution data by a factor of 2, 4 and 8 are applied. While for thresholds, they are calculated from individual active region with the average of 75/77/57 G for Bx /By /Bz for all original data. When the resolution are reduced by 2, 4 and 8, the corresponding averages are 72/75/55, 66/68/49 and 57/59/41 G for Bx /By /Bz , respectively. It is found that the forces indicated by Fx /Fp and Fy /Fp increase as thresholds/resolutions increase/decrease. While for Fz /Fp the trends become more complex. For low threshold, when the resolution decrease the trends of Fz /Fp are similar as those of Fx /Fp and Fy /Fp , while for high threshold the trends of Fz /Fp are different from those of Fx /Fp and Fy /Fp . For original resolution, the forces indicated by Fy /Fp increase as thresholds increase, while for others resolution they decrease as the thresholds increase contrarily.

  2. Ab initio and density functional studies of the structure, vibrational spectra and force field of trimethylsilane

    NASA Astrophysics Data System (ADS)

    McKean, D. C.

    1999-07-01

    Ab initio and density functional Q-M treatments have been carried out on trimethylsilane, SiHMe 3. The harmonic force fields so obtained are scaled to frequencies selected from four isotopic species, SiH(CH 3) 3, SiD(CH 3) 3, SiH(CD 3) 3 and SiD(CD 3) 3, some new infrared data for the d 0 species being employed. The region 250-200 cm -1 is reinterpreted in terms of the skeletal bending modes ?8( a1) and ?23( e), with ?8> ?23. Microwave information regarding the positions of the methyl torsions apparently conflicts with evidence both from the Q-M calculations and from infrared combination bands, which favour values less than 160 cm -1. All the scaled force fields give a poor fit to frequencies in the E symmetry species and nine force constants there are further refined. The spread of scale factors narrows when a larger basis set or density functional theory is employed, but widens slightly when electron correlation is introduced through an MP2 calculation. Valence interaction constants are reported for bond stretching motions and their significance assessed. Coriolis and centrifugal distortion constants are listed for the preferred B3LYP/6-311G** based force field. Electrical properties of the atoms and bonds are discussed.

  3. 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.

  4. Three-dimensional approximation of the total force on uncharged spheres in electric fields

    NASA Astrophysics Data System (ADS)

    Langemann, Dirk

    2007-02-01

    Droplets on outdoor high-voltage equipment suffer a total force which is non-vanishing in general. We consider a model problem of an uncharged and conductive sphere. We show that the total force can be given as a series of inhomogeneity indicators of the undisturbed electric field in the absence of the droplet. The proof of the series involves several aspects of the spherical harmonics in the three-dimensional Fourier technique. The series expansion establishes a relation between the solutions of two Poisson's equations on different domains. It is found that the expansion converges fast. The results are applied for droplets on a realistically shaped insulator.

  5. On some properties of force-free magnetic fields in infinite regions of space

    NASA Technical Reports Server (NTRS)

    Aly, J. J.

    1984-01-01

    Techniques for solving boundary value problems (BVP) for a force free magnetic field (FFF) in infinite space are presented. A priori inequalities are defined which must be satisfied by the force-free equations. It is shown that upper bounds may be calculated for the magnetic energy of the region provided the value of the magnetic normal component at the boundary of the region can be shown to decay sufficiently fast at infinity. The results are employed to prove a nonexistence theorem for the BVP for the FFF in the spatial region. The implications of the theory for modeling the origins of solar flares are discussed.

  6. Effects of external force fields on peptide self-assembly and biomimetic silica synthesis

    NASA Astrophysics Data System (ADS)

    Yu, Jun; Wang, Qinrong; Zhang, Xin

    2014-08-01

    This study investigated the influence of physical parameters on the dynamic self-assembly of short peptide amphiphiles (A6K and V6K) and the peptide-mediated silica morphologies by applying external force fields (electric and flow fields). Diverse self-assembled structures (nanofibers, nanorods, or lamellar stacks) can be obtained depending on field intensities and molecular architectures. Although the trend in the structural transitions observed from the electrostatic stimulation differed from that obtained in flow field, the common features indicate that the formed structures exhibit a higher extent of end-to-end merging or lateral association. These self-assembled peptide-based nanostructures then were used as organic templates to tailor silica deposition. It was found that the application of flow fields can stably produce fibril morphology. However, in the case of electric fields, different silica structures were obtained by using different systems. The silica morphologies directed by V6K peptide were transformed from fibrils to plate-like structures, and A6K peptide produced fibril silica materials. The difference may be attributed to different biomimetic conditions, including external forces, solubility of hydrophobic blocks, and intensity of peptide-silicate interactions. This understanding of the mechanism by which external fields affect the self-assembled amphiphilic peptide nanostructures and the silicification process allows us to manipulate the role of short amphiphilic peptides in silica formation in vitro.

  7. A Comparison Between Nonlinear Force-Free Field and Potential Field Models Using Full-Disk SDO/HMI Magnetogram

    NASA Astrophysics Data System (ADS)

    Tadesse, Tilaye; Wiegelmann, T.; MacNeice, P. J.; Inhester, B.; Olson, K.; Pevtsov, A.

    2014-03-01

    Measurements of magnetic fields and electric currents in the pre-eruptive corona are crucial to the study of solar eruptive phenomena, like flares and coronal mass ejections (CMEs). However, spectro-polarimetric measurements of certain photospheric lines permit a determination of the vector magnetic field only at the photosphere. Therefore, there is considerable interest in accurate modeling of the solar coronal magnetic field using photospheric vector magnetograms as boundary data. In this work, we model the coronal magnetic field above multiple active regions with the help of a potential field and a nonlinear force-free field (NLFFF) extrapolation code over the full solar disk using Helioseismic and Magnetic Imager (SDO/HMI) data as boundary conditions. We compare projections of the resulting magnetic field lines with full-disk coronal images from the Atmospheric Imaging Assembly (SDO/AIA) for both models. This study has found that the NLFFF model reconstructs the magnetic configuration closer to observation than the potential field model for full-disk magnetic field extrapolation. We conclude that many of the trans-equatorial loops connecting the two solar hemispheres are current-free.

  8. Mean Field with Tensor Force and Shell Structure of Exotic Nuclei

    SciTech Connect

    Otsuka, Takaharu [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Center for Nuclear Study, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 (Japan); Matsuo, Toshiaki [Software Division, Hitachi Ltd., Yokohama, Kanagawa (Japan); Abe, Daisuke [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan)

    2006-10-20

    The tensor force is implemented into the mean-field model so that the evolution of nuclear shells can be described for exotic nuclei as well as stable ones. Besides the tensor-force part simulating the meson exchange, the model is an extension of the successful Gogny model. One of the major issues of rare-isotope beam physics is a reduced spin-orbit splitting in neutron-rich exotic nuclei. It will be shown that the effect of the tensor force on this splitting is larger than or about equal to the one due to the neutron skin. We will present predictions for stable and exotic nuclei with comparisons to conventional results and experimental data.

  9. A New Code for Nonlinear Force-free Field Extrapolation of the Global Corona

    NASA Astrophysics Data System (ADS)

    Jiang, Chaowei; Feng, Xueshang; Xiang, Changqing

    2012-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

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

  11. Relationship between the present-day stress field and plate boundary forces in the Pacific Northwest

    USGS Publications Warehouse

    Geist, E.L.

    1996-01-01

    The relationship between plate boundary forces and the observed stress field in the Pacific Northwest is established using numerical models of continental deformation. Because the orientation of the greatest horizontal principal stress throughout the Pacific Northwest differs considerably from the direction of convergence between the Juan de Fuca and North American plates, the relationship between the stress field and forces acting along the subduction zone has been unclear. To address this relationship, a two-dimensional finite element model developed by Bird [1989] is used that incorporates critical aspects of continental deformation such as a stratified rheology and interaction between thermal and mechanical components of deformation. Boundary conditions are specified in terms of either velocity or shear traction, depending on whether the computed shear stress at the plate boundary is less than or exceeds, respectively, a prescribed limit. Shear-stress limits on the subduction and transform plate boundaries are independently varied to determine the relative effect of forces along these boundaries on intraplate deformation. Results from this study indicate that the shear stress limit of both subduction and transform boundaries is low, and that the intraplate stress field is attributed, in part, to the normal component of relative plate motion along the transform boundaries. However, the models also indicate that although the subduction zone fault is weak, a minimum shear strength ( ??? 10 MPa) for the fault is necessary to explain the observed stress field. The balance among forces along the tectonic boundaries of North America results in a surprising degree of variation in the present-day stress field.

  12. Forced and free variations of the surface temperature field in a general circulation model

    SciTech Connect

    North, G.R.; Yip, K.J.J.; Laiyung Leung (Texas A M Univ., College Station (United States)); Chervin, R.M. (National Center for Atmospheric Research, Boulder, CO (United States))

    1992-03-01

    The concept of forced' and free' variations of large-scale surface temperature is examined by analyzing several long runs of the Community Climate Model (CCM0) with idealized boundary conditions and forcing. (1) The planet is all land with uniform sea-level topography and fixed soil moisture. (2) The planetary surface and prescribed ozone are reflection symmetric across the equator and there is no generation of snow. (3) The obliquity is set to zero so that the climate is for a perpetual equinox solar insolation (i.e., sun fixed over the equator). After examining some relevant aspects of the undisturbed climate (surface temperature field) such as temporal and spatial autocorrelations and the corresponding spectra, two types of changes in external forcing are imposed to study the model response: (1) sinusoidal changes of the solar constant (5%, 10%, 20%, and 40% amplitudes) at periods of 15 and 30 days (the latter is the autocorrelation time for the global average surface temperature) and 20% at 60 days and (2) insertion of steady heat sources (points and zonal bands) of variable strength at the surface. Then the temporal spectra of large scales for the periodically forced climate and the ensemble-averaged influence functions are examined for the point source disturbed climates. In each class of experiments the response of ensemble-averaged amplitudes was found to be proportional to the amplitude of the forcing. These results suggest that the lowest moments of the surface temperature field have a particularly simple dependence on forcing. Furthermore, the apparent finiteness of the variance spectrum at low frequencies suggest that estimates of long-term statistics are stable in this type of atmospheric general circulation model. 31 refs., 17 figs.

  13. Students' conceptions and reasoning models of the electric force and field related questions in the interviewed CSEM test

    Microsoft Academic Search

    M Saarelainen; A Laaksonen; P E Hirvonen

    This study explores undergraduate students' conceptions and reasoning models of electric forces and fields. It is based on their answers and explanations given in the interviewed CSEM test questions 6 and 13. The results indicate that the students are able to apply Coulombian force only in relatively simple problems, but they fail in using appropriate electric field models in cases

  14. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

    Microsoft Academic Search

    William L. Jorgensen; David S. Maxwell; Julian Tirado-Rives

    1996-01-01

    The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio

  15. Faraday's law of induction and the force on a body due to change in its magnetization in an electric field

    Microsoft Academic Search

    K. G. Ramanathan

    1962-01-01

    From arguments based on Faraday's Law of induction, it is shown that a body whose intensity of magnetization is changing should, in general, experience a force when situated in an electrostatic field in a manner analogous to the force experienced by a conductor carrying an electric current in a magnetic field.

  16. Neuropeptide FF and modulation of pain

    Microsoft Academic Search

    Pertti Panula; Eija Kalso; Maija-Liisa Nieminen; Vesa K Kontinen; Annika Brandt; Antti Pertovaara

    1999-01-01

    Neuropeptide FF (NPFF) and the related longer peptide neuropeptide AF (NPAF) derive from a single gene in several mammalian species. The gene product is expressed mainly in the CNS, where the posterior pituitary and dorsal spinal cord contain the highest concentrations. Evidence from biochemical and immunohistochemical studies combined with in situ hybridization using NPFF gene-specific probes suggest that all NPFF-like

  17. Liberty ID-FF Architecture Overview

    Microsoft Academic Search

    Thomas Wason; Jeff Hodges; John Kemp; Peter Thompson

    This is a non-normative document describing the basic structure and operation of the Liberty Alliance architecture. Examples are provided to illustrate the operation of systems using the architecture. It is intended that this document provide a general introduction to the Liberty ID-FF architecture. Filename: draft-liberty-idff-arch-overview-1.2-errata-v1.0.pdf

  18. Dielectrophoresis Force and Deflection of Dielectric Elastomers and Blends under AC field

    NASA Astrophysics Data System (ADS)

    Kunanuraksapong, Ruksapong; Sirivat, Anuvat

    2010-03-01

    The effects of frequency and amplitude of AC electric field on the deflection distance and the dielectrophoresis force of the of acrylic elastomers (AR71), styrene copolymers (SAR and SBR), and blends with poly(p-phenylene) (AR71:PPP and SAR:PPP) were investigated. The dielectrophoresis forces of the dielectric elastomers and blends were measured by a vertical cantilever under various frequencies (0.3-60 Hz) and at the amplitudes of 200, 300, 500, 600 and 800 Vpp/mm. In addition, the effect of thickness of specimens and the particle concentration on the dielectrophoresis force were studied. Poly(p-phenylene) particles were added into AR71 and SAR with particle concentrations of 5, 10, 15 and 20 vol%. The forces were calculated from the non-linear deflection theory of the cantilever. The dielectrophoresis forces and deflection distances of the dielectric elastomers and blends generally increase with increasing amplitude but slightly decrease with increasing frequency, and they dramatically drop at the cut-off frequency. The cutoff frequencies are 12.0, 1.5 and 1.5 Hz for AR71, SAR, and SBR, at E = 800 Vpp/mm, respectively.

  19. Dynamic evolution of welding residual stress field under noncontact electromagnetic force

    NASA Astrophysics Data System (ADS)

    Xu, Da; Liu, Xuesong; Wang, Ping; Yang, Jianguo; Xu, Wei; Fang, Hongyuan

    2010-03-01

    Controlling welding residual stress and distortion has still been a challenging problem due to the complexity of welding process. In this paper, a new technique with inductive electromagnetic forces has been reported for controlling welding residual stresses and distortion in welded thin plate. In order to get better understanding the associated mechanism, a hybrid three-dimensional finite element analysis, including electromagnetic force induction, welding, and electromagnetic force impact processes, has been performed to investigate the dynamic evolution of stress and strain in the welded plate under electromagnetic force impact. It is found that transient electromagnetic impact causes the mechanical response with the obvious strain rate sensitivity, and complex variation in stress and strain states in the welded plate occurs due to combination action of electromagnetic force and welding residual stress. As a result, the incompatible degree of strain field, arising from welding thermal cycle, is reduced. The residual stresses also finally fall, although the flow stress rises during electromagnetic impact. The measurement results of microhardness also indicate that the plastic strain state in local weld region is indeed changed under electromagnetic impact. Finally, continuous electromagnetic impacts experiments are conducted, and results show that this approach is very successful for reducing welding residual stresses and distortion in welded thin plates, without any impairment of appearance and performance.

  20. 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

  1. Force-Free Magnetic Fields Calculated from Automated Tracing of Coronal Loops with AIA/SDO

    NASA Astrophysics Data System (ADS)

    Aschwanden, M. J.

    2013-12-01

    One of the most realistic magnetic field models of the solar corona is a nonlinear force-free field (NLFFF) solution. There exist about a dozen numeric codes that compute NLFFF solutions based on extrapolations of photospheric vector magnetograph data. However, since the photosphere and lower chromosphere is not force-free, a suitable correction has to be applied to the lower boundary condition. Despite of such "pre-processing" corrections, the resulting theoretical magnetic field lines deviate substantially from observed coronal loop geometries. - Here we developed an alternative method that fits an analytical NLFFF approximation to the observed geometry of coronal loops. The 2D coordinates of the geometry of coronal loop structures observed with AIA/SDO are traced with the "Oriented Coronal CUrved Loop Tracing" (OCCULT-2) code, an automated pattern recognition algorithm that has demonstrated the fidelity in loop tracing matching visual perception. A potential magnetic field solution is then derived from a line-of-sight magnetogram observed with HMI/SDO, and an analytical NLFFF approximation is then forward-fitted to the twisted geometry of coronal loops. We demonstrate the performance of this magnetic field modeling method for a number of solar active regions, before and after major flares observed with SDO. The difference of the NLFFF and the potential field energies allows us then to compute the free magnetic energy, which is an upper limit of the energy that is released during a solar flare.

  2. 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.

  3. Vibrational spectra of alkali metal cyclopentadienides and force field calculation of free cyclopentadienyl anion

    NASA Astrophysics Data System (ADS)

    Garkusha, O. G.; Garbuzova, I. A.; Lokshin, B. V.; Mink, J.

    1988-05-01

    Raman and IR spectra have been studied in detail for lithium, sodium and potassium cyclopentadienides in solid state and their tetrahydrofuran (THF) and hexamethylphosphoric triamide (HMPA) solutions. The vibrational frequencies of cyclopentadienyl (Cp) anion have been obtained. The normal coordinate analysis of Cp-anion is presented. The force field of Cp-anion have been calculated by variation to a small extent of benzene force field, which reveals proximity of their electronic structures. Analysis of the low-frequency spectrum has shown that the interion stretching vibration dependent upon the cation mass is observed only in the IR spectrum, while the Raman spectrum exhibits the tilt doubly-degenerate vibration of Cp-ring in spite of the fact that both vibrations are allowed in both IR and Raman spectra.

  4. 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

  5. Artifact or reality? Force field issues in the simulation proteins and nucleic acids

    NASA Astrophysics Data System (ADS)

    Cheatham, Thomas

    2008-03-01

    Access to ever-increasing computational power is providing the means to critically evaluate the performance of atomistic force fields of biomolecules. With greater sampling, and more detailed comparisons to experiment, limitations and artifacts in the applied simulation protocols and force fields can be discovered and ultimately overcome. Additionally, we are able to more carefully validate and assess the performance of the simulations in comparison with experiment. In this talk, we will outline our experiences in large-scale simulations of protein and nucleic acid systems in the context of the AMBER biomolecular simulation program. Issues related to salt and dihedral parameters will be highlighted in applications ranging from ligand-induced remodeling of dihydrofolate reductase and cytochrome P450 2B4 protein structures to large-scale decoy sets and NMR comparisons of various RNA structures.

  6. A Field Reconstruction Technique for Efficient Modeling of the Fields and Forces within Induction Machines

    Microsoft Academic Search

    Dezheng Wu; S. D. Pekarek; B. Fahimi

    2007-01-01

    Traditional analysis and design of induction machines have been largely based upon lumped-parameter models. An alternative tool used for fields-based evaluations of an induction machine is the finite-element method. Although useful, its computational complexity limits its use as a design tool. In this paper, a field reconstruction (FR) method for induction machine simulation is introduced The FR method utilizes a

  7. A Field Reconstruction Technique for Efficient Modeling of the Fields and Forces Within Induction Machines

    Microsoft Academic Search

    Dezheng Wu; Steven D. Pekarek; Babak Fahimi

    2009-01-01

    Traditional analysis and design of induction machines have been largely based upon lumped-parameter models. An alternative tool used for field-based evaluations of an induction machine is the finite-element method. Although useful, its computational complexity limits its use as a design tool. In this paper, a field reconstruction (FR) method for induction machine simulation is introduced. The FR method utilizes a

  8. Force fields for divalent cations based on single-ion and ion-pair properties.

    PubMed

    Mamatkulov, Shavkat; Fyta, Maria; Netz, Roland R

    2013-01-14

    We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) 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 MgY(2), CaY(2), BaY(2), SrY(2) 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 Ca(2+), Ba(2+), and Sr(2+) such LJ parameters exist. On the other hand, for Mg(2+) 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. PMID:23320702

  9. 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

  10. Force model identification for magnetic suspension systems via magnetic field measurement

    Microsoft Academic Search

    Chin E. Lin; Huei L. Jou

    1993-01-01

    In magnetic suspension analysis, a simplified model of the current-to-distance relationship is not sufficient to design an optimal control. Due to the nonlinearity of the magnetic field, an accurate model, which is a function of the suspended object, suspension distance, core material, and operation conditions, is difficult to obtain. An improved force-model-identification method for magnetic suspension systems establishes reliable parameters

  11. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble.

    PubMed

    Coimbra, João T S; Sousa, Sérgio F; Fernandes, Pedro A; Rangel, Maria; Ramos, Maria J

    2014-01-01

    The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. However, the absence of a specific set of parameters for lipids has been limiting the widespread application of this force field in biomembrane simulations, including membrane protein simulations and drug-membrane simulations. Here, we report the systematic parameterization of 12 common lipid types consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6-31G(d) level of theory, to be consistent with AMBER. The accuracy of the scheme was evaluated by comparing predicted and experimental values for structural lipid properties in MD simulations in an NPT ensemble with explicit solvent in 100:100 bilayer systems. Globally, a consistent agreement with experimental reference data on membrane structures was achieved for some lipid types when using the typical MD conditions normally employed when handling membrane proteins and drug-membrane simulations (a tensionless NPT ensemble, 310?K), without the application of any of the constraints often used in other biomembrane simulations (such as the surface tension and the total simulation box area). The present set of parameters and the universal approach used in the parameterization of all the lipid types described here, as well as the consistency with the AMBER force field family, together with the tensionless NPT ensemble used, opens the door to systematic studies combining lipid components with small drug-like molecules or membrane proteins and show the potential of GAFF in dealing with biomembranes. PMID:23730894

  12. Relationship between coercive force and anisotropy field for oriented barium ferrite tapes and magnets

    Microsoft Academic Search

    R. E. Fayling

    1978-01-01

    The approximate anisotropy field (Han) has been determined for twelve experimental oriented barium ferrite recording tapes and magnets with coercive force (Hc) between 715 Oe and 5250 Oe, and squareness ratio greater than 0.80. The Han values were taken as the ratio of saturation magnetic moment (ms) to the initial hard-axis susceptibility (m\\/H). Han values were generally within the 12.6–19.8

  13. Relationship between coercive force and anisotropy field for oriented barium ferrite tapes and magnets

    Microsoft Academic Search

    R. E. Fayling

    1978-01-01

    The approximate anisotropy field (Han) has been determined for twelve experimental oriented barium ferrite recording tapes and magnets with coercive force (Hc) between 715 Oe and 5250 Oe, and squareness ratio greater than 0.80. The Han values were taken as the ratio of saturation magnetic moment (ms) to the initial hard-axis susceptibility (m\\/H). Han values were generally within the 12.6-19.8

  14. 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

  15. 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.

  16. Calculation of Fields, Forces, and Mutual Inductances of Current Systems by Elliptic Integrals

    Microsoft Academic Search

    Milan Wayne Garrett

    1963-01-01

    A minimum-ordered set of elliptic integral equations is given for magnetic vector potential, axial and radial fields, the mixed gradient ?B&rgr;??z for axially symmetric iron-free current systems, and for mutual inductance and force between coaxial units. The units may be circular loops, cylindrical or plane annular current sheets, or coils of thick section. With full use of correlations, six basic

  17. Aerodynamic forces and flow fields of a two-dimensional hovering wing

    Microsoft Academic Search

    K. B. Lua; T. T. Lim; K. S. Yeo

    2008-01-01

    This paper reports the results of an experimental investigation on a two-dimensional (2-D) wing undergoing symmetric simple\\u000a harmonic flapping motion. The purpose of this investigation is to study how flapping frequency (or Reynolds number) and angular\\u000a amplitude affect aerodynamic force generation and the associated flow field during flapping for Reynolds number (Re) ranging from 663 to 2652, and angular amplitudes

  18. Molecular dynamics simulation of protein crystal with polarized protein-specific force field.

    PubMed

    Li, Yongxiu; Zhang, John Z H; Mei, Ye

    2014-10-30

    Two 250 ns molecular simulations have been carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing the polarized protein-specific charge (PPC), as well as the standard AMBER99SB force field, to investigate the electrostatic polarization on the simulated crystal stability. Results show that under PPC, the monomers in unit cell as well as the lattice in supercell are more stable with smaller root-mean-square deviations and more accurate lattice atomic fluctuations compared with the crystallographic B-factors than under AMBER99SB force field. Most of the interactions at interfaces in the X-ray structure are quite well-preserved, underscoring the important effect of polarization on maintaining the crystal stability. However, the results also show that the hydrogen bond between Asp53 and Gln37 and the cation-? interaction between Arg56 and His64 are not stable, indicating that further optimization of force field, especially the van der Waals interaction parameters, is desired. PMID:25285919

  19. Markov model-based polymer assembly from force field-parameterized building blocks.

    PubMed

    Durmaz, Vedat

    2015-03-01

    A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very work-intensive and time-consuming. Using the example of polyglycerol, I present a polymer decomposition strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantum-chemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. PMID:25428569

  20. The Design of a Next Generation Force Field: The X-POL Potential

    PubMed Central

    Xie, Wangshen; Gao, Jiali

    2008-01-01

    An electronic structure-based polarization method, called the X-POL potential, has been described for the purpose of constructing an empirical force field for modeling polypeptides. In the X-POL potential, the internal, bonded interactions are fully represented by an electronic structure theory augmented with some empirical torsional terms. Non-bonded interactions are modeled by an iterative, combined quantum mechanical and molecular mechanical method, in which the molecular mechanical partial charges are derived from the molecular wave functions of the individual fragments. In this paper, the feasibility of such an electronic structure force field is illustrated by small model compounds. A method has been developed for separating a polypeptide chain into peptide units and its parameterization procedure in the X-POL potential is documented and tested on glycine dipeptide. We envision that the next generation of force fields for biomolecular polymer simulations will be developed based on electronic structure theory, which can adequately define and treat many-body polarization and charge delocalization effects. PMID:18985172

  1. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    PubMed

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site. PMID:25410708

  2. Development of a force field for zeolitic imidazolate framework-8 with structural flexibility

    NASA Astrophysics Data System (ADS)

    Hu, Zhongqiao; Zhang, Liling; Jiang, Jianwen

    2012-06-01

    A force field is developed for zeolitic imidazolate framework-8 (ZIF-8) with structural flexibility by combining quantum chemical calculations and classical Amber force field. The predicted crystalline properties of ZIF-8 (lattice constants, bond lengths, angles, dihedrals, and x-ray diffraction patterns) agree well with experimental results. A structural transition from crystalline to amorphous as found in experiment is observed. The mechanical properties of ZIF-8 are also described fairly well by the force field, particularly the Young's modulus predicted matches perfectly with measured value. Furthermore, the heat capacity of ZIF-8 as a typical thermophysical property is predicted and close to experimental data available for other metal-organic frameworks. It is revealed the structural flexibility of ZIF-8 exerts a significant effect on gas diffusion. In rigid ZIF-8, no diffusive behavior is observed for CH4 within the simulation time scale of current study. With the structural flexibility, however, the predicted diffusivities of CH4 and CO2 are close to reported data in the literature. The density distributions and free energy profiles of CH4 and CO2 in the pore of ZIF-8 are estimated to analyze the mechanism of gas diffusion.

  3. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

    PubMed Central

    2015-01-01

    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

  4. 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

  5. A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

    PubMed Central

    Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

    2012-01-01

    Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the C? root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

  6. Observation of force-detected nuclear magnetic resonance in a homogeneous field.

    PubMed

    Madsen, L A; Leskowitz, G M; Weitekamp, D P

    2004-08-31

    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 microm-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 microm and nm scales. PMID:15326302

  7. Studying electric field profiles in GaAs-based detector structures by Kelvin probe force microscopy

    NASA Astrophysics Data System (ADS)

    Vilisova, M. D.; Germogenov, V. P.; Kaztaev, O. Zh.; Novikov, V. A.; Ponomarev, I. V.; Titkov, A. N.

    2010-05-01

    The method of scanning Kelvin probe force microscopy has been used to study the electric field distribution in GaAs-based p +-?- n- n + detector structures. In the active layer volume, two maxima in the field strength profiles have been found, which are localized in the regions of p +-? and ?- n junctions. A volt-age drop on the ?- n junction expands the region of collection of nonequilibrium holes, thus increasing the charge collection efficiency for the absorption of ? photons with an energy of 59.5 keV.

  8. 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

  9. Materials Bound by Non-Chemical Forces: External Fields and the Quantum Vacuum

    E-print Network

    John Swain; Allan Widom; Yogendra Srivastava

    2014-04-29

    We discuss materials which owe their stability to external fields. These include: 1) external electric or magnetic fields, and 2) quantum vacuum fluctuations in these fields induced by suitable boundary conditions (the Casimir effect). Instances of the first case include the floating water bridge and ferrofluids in magnetic fields. An example of the second case is taken from biology where the Casimir effect provides an explanation of the formation of stacked aggregations or "rouleaux" by negatively charged red blood cells. We show how the interplay between electrical and Casimir forces can be used to drive self-assembly of nano-structured materials, and could be generalized both as a probe of Casimir forces and as a means of manufacturing nanoscale structures. Interestingly, all the cases discussed involve the generation of the somewhat exotic negative pressures. We note that very little is known about the phase diagrams of most materials in the presence of external fields other than those represented by the macroscopic scalar quantities of pressure and temperature. Many new and unusual states of matter may yet be undiscovered.

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

    SciTech Connect

    Weening, R. H. [Department of Radiologic Sciences, Thomas Jefferson University, 130 S. 9th Street, Philadelphia, Pennsylvania 19107-5233 (United States)

    2011-12-15

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

  11. 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.

  12. Structure of kinematic and force fields in the Riemannian continuum model

    NASA Astrophysics Data System (ADS)

    Guzev, M. A.

    2011-09-01

    In this paper, we consider a non-Euclidean continuum model for which the structure of defects in the material is characterized by an internal metric and scalar curvature. It is shown that the irrotational displacement field for points of this medium is composed of elastic displacements (in the absence of defects) and the field which characterizes the deviation of the internal geometry of the model from Euclidean geometry. The corresponding components of the internal stresses are the sum of elastic stresses and the self-equilibrated stresses determined by the scalar curvature. The exact solution for the vortex field of dislocations is constructed, and conditions of the existence of a nonzero stress field parametrized by a scalar curvature in the absence of external forces are formulated.

  13. A Bidirectional Brain-Machine Interface Algorithm That Approximates Arbitrary Force-Fields

    PubMed Central

    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

  14. What Makes The Difference Between HSP and FF? Jorg Hoffmann

    E-print Network

    Nebel, Bernhard

    What Makes The Difference Between HSP and FF? J¨org Hoffmann and Bernhard Nebel Institute for Computer Science ¡ last-name¢ @informatik.uni-freiburg.de Abstract The HSP and FF systems are state-of-the-art domain independent planners. FF can his- torically be seen as a successor of HSP. It is based on the same

  15. 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.

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

    PubMed

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

    2015-02-11

    Direct measurements of particle-surface interactions are important for characterizing the stability and behavior of colloidal and nanoparticle suspensions. Current techniques are limited in their ability to measure pico-Newton scale interaction forces on submicrometer particles due to signal detection limits and thermal noise. Here we present a new technique for making measurements in this regime, which we refer to as nanophotonic force microscopy. Using a photonic crystal resonator, we generate a strongly localized region of exponentially decaying, near-field light that allows us to confine small particles close to a surface. From the statistical distribution of the light intensity scattered by the particle we are able to map out the potential well of the trap and directly quantify the repulsive force between the nanoparticle and the surface. As shown in this Letter, our technique is not limited by thermal noise, and therefore, we are able to resolve interaction forces smaller than 1 pN on dielectric particles as small as 100 nm in diameter. PMID:25625877

  17. 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.

  18. Trans-1-chloro-2-fluoroethylene: Microwave spectra and anharmonic force field

    NASA Astrophysics Data System (ADS)

    Cazzoli, Gabriele; Puzzarini, Cristina; Gambi, Alberto

    2004-04-01

    For the first time the millimeter-wave spectra of the trans-35ClHC=CHF and trans-37ClHC=CHF isotopomers have been observed in natural abundance. Many ?J=0, ±1 ?K-1=+1 transitions for 35ClHC=CHF and ?J=0 ?K-1=+1 transitions for 37ClHC=CHF have been detected and assigned. This allowed us to accurately determine the vibrational ground-state rotational constants, quartic and some sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for both 35Cl and 37Cl. The experimental investigation has been supported by highly accurate theoretical predictions. As far as ab initio computations are concerned, the complete set of cubic and quartic force constants have been evaluated by numerical differentiation of the analytic second-order Møller-Plesset many-body perturbation theory/correlation consistent polarized valence triple zeta second derivatives. The anharmonic part of the force field completes the theoretical study on the equilibrium structure, dipole moment, chlorine quadrupolar tensor, and harmonic force field previously carried out by the same authors.

  19. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

    PubMed Central

    Xu, Dong; Zhang, Yang

    2012-01-01

    Ab initio protein folding is one of the major unsolved problems in computational biology due 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 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) 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 (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  20. Neuropeptide FF reduces food intake in rats

    Microsoft Academic Search

    Takashi Murase; Hiroshi Arima; Kunikazu Kondo; Yutaka Oiso

    1996-01-01

    The effect of neuropeptide FF (NPFF), a mammalian FMRFamide-like peptide with antiopioid activity, on food intake was investigated in food-deprived rat. The ICV administration of NPFF (5 or 10 ?g\\/rat) reduced food intake during the first 60 min after administration. ICV injection of naloxone (10 or 100 ?g\\/rat), an opioid antagonist, also decreased food intake. However, the combination of NPFF

  1. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

    PubMed Central

    Luo, Yun; Jiang, Wei; Yu, Haibo; MacKerell, Alexander D.; Roux, Benoît

    2012-01-01

    The accuracy of the empirical force fields is critical for meaningful molecular dynamics simulations of concentrated ionic solutions. Current models are typically developed on the basis of single ion properties such as the monohydrate energy in the gas phase, or the absolute hydration free energy at infinite dilution. However, failure of these models to accurately represent the properties of concentrated solutions cannot be excluded. Here, these issues are illustrated for a polarizable potential based on classical Drude oscillators. To accurately model concentrated ionic solutions, the parameters of the potential functions are optimized to reproduce osmotic pressure data. The sodium-chloride potential of mean force in solution calculated from the empirically-adjusted model is consistent with the results from that calculated from ab initio CPMD simulations. PMID:23795497

  2. The fast multipole method and point dipole moment polarizable force fields.

    PubMed

    Coles, Jonathan P; Masella, Michel

    2015-01-14

    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. PMID:25591340

  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. Novel system for bite-force sensing and monitoring based on magnetic near field communication.

    PubMed

    Lantada, Andres Diaz; Bris, Carlos González; Morgado, Pilar Lafont; Maudes, Jesús Sanz

    2012-01-01

    Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient's dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system's operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials. PMID:23112669

  5. Novel System for Bite-Force Sensing and Monitoring Based on Magnetic Near Field Communication

    PubMed Central

    Lantada, Andres Diaz; Bris, Carlos González; Morgado, Pilar Lafont; Maudes, Jesús Sanz

    2012-01-01

    Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient's dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system's operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials. PMID:23112669

  6. 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.

  7. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field

    PubMed Central

    Schnieders, Michael J.; Baltrusaitis, Jonas; Shi, Yue; Chattree, Gaurav; Zheng, Lianqing; Yang, Wei; Ren, Pengyu

    2012-01-01

    An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure–property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies ?Gsolubilityo=?Gsubo+?Gsolvo, which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals. PMID:22582032

  8. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    PubMed

    Petrov, Drazen; Zagrovic, Bojan

    2014-05-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

  9. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

    PubMed Central

    Petrov, Drazen; Zagrovic, Bojan

    2014-01-01

    The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

  10. Exploring Solvent Effects upon the Menshutkin Reaction using a Polarizable Force Field

    PubMed Central

    Acevedo, Orlando; Jorgensen, William L.

    2010-01-01

    The energetics of the Menshutkin reaction between triethylamine and ethyl iodide have been computed using B3LYP and MP2 with the LANL2DZ, LANL2DZd, SVP, MIDI!, 6–311G(d,p), and aug-cc-PVTZ basis sets. Small- and large-core energy-consistent relativistic pseudopotentials were employed. Solvent effect corrections were computed from QM/MM Monte Carlo simulations utilizing free-energy perturbation theory, PDDG/PM3, and both a non-polarizable OPLS and polarizable OPLS-AAP force field. The B3LYP/MIDI! theory level provided the best ?G‡ values with a mean absolute error (MAE) of 4.9 kcal/mol from experiment in cyclohexane, CCl4, THF, DMSO, acetonitrile, water, and methanol. However, the relative rates in cyclohexane, and to a certain extent CCl4, were determined to be greatly underestimated when using the non-polarizable OPLS force field. An overall reduction in the MAE to 3.1 kcal/mol using B3LYP/MIDI!/OPLS-AAP demonstrated the need for a fully polarizable force field when computing solvent effects for highly dipolar transition structures in low-dielectric media. The MAEs obtained with PDDG/PM3/OPLS and OPLS-AAP of 5.3 and 3.8 kcal/mol, respectively, provided comparable results to B3LYP at a fraction of the computational resources. The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions. PMID:20527873

  11. 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

  12. Magnetic force microscopy measurements in external magnetic fields-comparison between coated probes and an iron filled carbon nanotube probe

    Microsoft Academic Search

    F. Wolny; T. Mühl; U. Weissker; A. Leonhardt; U. Wolff; D. Givord; B. Büchner

    2010-01-01

    We performed magnetic force microscopy (MFM) measurements in external magnetic fields parallel to the sample plane to qualitatively study their effect on the magnetization of different kinds of MFM probes. As a test structure we used an array of rectangular ferromagnetic thin film elements aligned with the external magnetic field direction. MFM images were taken while the field was increased

  13. Analysis of the magnetic field and force of LSM with permanent magnet Halbach array and ironless coil

    Microsoft Academic Search

    Xiao Zhang; Yungang Li; Hengkun Liu

    2011-01-01

    The LSM, or linear synchronous motor, with permanent magnet Halbach array and ironless coil possesses the dominant advantages of direct linear movement and being energy-saving. To analytically investigate the characteristics of this innovative LSM, its magnetic field and magnetic force are analyzed in this work. Based on the magnetic field of a single surface current, the field of a single

  14. ON THE INTERSECTION OF TRANSLATION OF MIDDLE-ff CANTOR SETS

    E-print Network

    Li, Wenxia

    ON THE INTERSECTION OF TRANSLATION OF MIDDLE-ff CANTOR SETS Wuhan 430079, P.R. China Abstract Let ffbe the middle-ff Cantor set andTlet ff+ t = {x + t : xT2 ff} * *for -1 t 1. Let Hp = {t 2 ff: dimH ( ff

  15. The current mechanism of emission of Ellermann "bombs" in a force-free magnetic field.

    NASA Astrophysics Data System (ADS)

    den, O. E.

    1990-06-01

    Due to a variation of the magnetic field in an active region inductive currents emerge along the closed circuits, consisting of a chain of "bombs" and linking arch fibrils. The currents are channeled in fine magnetic force tubes along the fibril axes. Heating of a "bomb" takes place due to Ohm dissipation of energy, mainly, electron component of the current. The proton component of the current causes the observed asymmetry of intensity peaks "moustaches" and forms a fibril. The lag in time of the attainment of the maximum length of the fibril and the time of maximum emission of the "bomb" is explained.

  16. Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9.

    PubMed

    Guerra, Federico; Adam, Suliman; Bondar, Ana-Nicoleta

    2015-05-01

    Biological photosynthetic machineries, such as photosystem I, photosystem II, or the bacterial reaction center, use cofactor molecules that absorb light or directly participate in chemical reactions. Accurate description of the structure of the cofactors, and of their interactions with protein groups, is an important step toward understanding how photosynthetic machineries work. Here we revisit the classical force field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9. We present systematic quantum mechanical and classical mechanical computations that lead to a good description of the structure and non-bonded interactions of these cofactors. PMID:25829096

  17. 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.

  18. Finding fields and self-force in a gauge appropriate to separable wave equations

    NASA Astrophysics Data System (ADS)

    Keidl, Tobias S.; Friedman, John L.; Wiseman, Alan G.

    2007-06-01

    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 ?0 (or ?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 ?0 and ?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 ?0 (or ?4) is a source-free solution to the Teukolsky equation; and one can therefore reconstruct a nonsingular renormalized metric in a radiation gauge.

  19. The shortest time and/or the shortest path strategies in a CA FF pedestrian dynamics model

    E-print Network

    Ekaterina Kirik; Tat'yana Yurgel'yan; Dmitriy Krouglov

    2009-06-23

    This paper deals with a mathematical model of a pedestrian movement. A stochastic cellular automata (CA) approach is used here. The Floor Field (FF) model is a basis model. FF models imply that virtual people follow the shortest path strategy. But people are followed by a strategy of the shortest time as well. This paper is focused on how to mathematically formalize and implement to a model these features of the pedestrian movement. Some results of a simulation are presented.

  20. Polycarbonate Simulations with a Density Functional Based Force Field P. Ballone, B. Montanari, and R. O. Jones*

    E-print Network

    Polycarbonate Simulations with a Density Functional Based Force Field P. Ballone, B. Montanari properties of molecules related to polycarbonate have been used to optimize the parameters describing dynamics simulations of crystalline, amorphous, and liquid polycarbonate systems. Applications include

  1. 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.

  2. 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.

  3. Trapping and micromanipulation using ultrasonic fields and dual ultrasonic/magnetic forces

    NASA Astrophysics Data System (ADS)

    Hill, Martyn; Glynne-Jones, Peter; Harris, Nicholas R.; Boltryk, Rosemary J.; Stanley, Christopher; Bond, Damian

    2010-08-01

    Ultrasonic fields can be used to trap and manipulate micron-scale particles and second-phase fluids, utilising energy densities that do not impair cell viability. The technology can be seen as complementary to optical trapping as the size of the potential wells generated can be relatively large, making ultrasound suitable for the formation and manipulation of cell agglomerates, but less suitable for the manipulation of individual cells. This paper discusses physical phenomena associated with ultrasonic manipulation, including radiation forces, cavitation, and acoustic streaming. The technology is well suited to integration within "Lab on a Chip" devices and can involve excitation by plane, focussed, flexural, or surface acoustic waves. Example applications of resonators are discussed including particle filtration and concentration, cell washing, and biosensor enhancement. A recently developed device that uses both ultrasonic and magnetic forces to enhance the detection of tuberculosis bacteria using magnetic beads is discussed in detail. This approach uses ultrasonic levitation forces to overcome some of the issues associated with purely magnetic trapping. The technology has been implemented in a device in which the main fluidic components are disposable to allow for low production costs and improved control of biohazards.

  4. Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

    PubMed

    Jiang, Fan; Zhou, Chen-Yang; Wu, Yun-Dong

    2014-06-26

    Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil library were used as the target data. The dihedral angle (torsion) potentials and some local nonbonded (1-4/1-5/1-6) interactions in OPLS-AA/L force field were modified such that the target data can be excellently reproduced by molecular dynamics simulations of dipeptides (blocked AAs) in explicit water, resulting in a new force field with AA-specific parameters, RSFF1. An efficient free energy decomposition approach was developed to separate the corrections on ? and ? from the two-dimensional Ramachandran plots. RSFF1 is shown to reproduce the experimental NMR (3)J-coupling constants of AA dipeptides better than other force fields. It has a good balance between ?-helical and ?-sheet secondary structures. It can successfully fold a set of ?-helix proteins (Trp-cage and Homeodomain) and ?-hairpins (Trpzip-2, GB1 hairpin), which cannot be consistently stabilized by other state-of-the-art force fields. Interestingly, the RSFF1 force field systematically overestimates the melting temperature (and the stability of native state) of these peptides/proteins. It has a potential application in the simulation of protein folding and protein structure refinement. PMID:24815738

  5. 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.

  6. 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.

  7. Effects of AC Electrical Field on the Dielectrophoresis Force of Dielectric Elastomers and Blends

    NASA Astrophysics Data System (ADS)

    Sirivat, Anuvat; Kunanuruksapong, Ruksapong

    2011-03-01

    The effects of frequency and amplitude of AC electric field on the deflection and the dielectrophoresis force of an acrylic elastomer (AR71), styrene copolymers (SAR and SBR), and the blends of doped PPP and AR71 are investigated. The dielectrophoresis forces of the dielectric elastomers and blends were measured by using a vertical cantilever fixture at various frequencies (0.3 to 60 Hz) and at AC electric field strengths of 200-800 Vpp/mm. The effects of the thicknesses of the specimens and the particle concentration are studied. The doped PPP particles are embedded in the AR71 with concentrations of 1, 10, and 20 %vol. The dielectrophoresis forces and deflection distance of the dielectric elastomers and blends generally increase with increasing amplitude but slightly decrease with increasing frequency; and they dramatically drop at the cut-off frequency. The cut-off frequencies are 7.84, 1.45, and 0.74 Hz for AR71, SAR, and SBR, respectively, at E of 800 Vpp/mm and a thickness of 0.7 to 0.8 mm. After blending the AR71 with doped PPP, the cut-off frequencies of the 1 %vol, 10 %vol and 20 %vol of doped PPP are 18.51, 15.28, and 10.67 Hz, respectively, at an E of 800 Vpp/mm and a thickness of 0.2 to 0.3 mm. The conductive polymer particles are shown here to improve the electromechanical responses at high frequency.

  8. A New Charge Model in The Valence Force Field Model for Phonon Calculations

    NASA Astrophysics Data System (ADS)

    Barrett, Christopher; Wang, Lin-Wang

    2013-03-01

    The classical ball and spring Valence Force Field model is useful to determine the elastic relaxation of thousand-atom nanosystems. We have also used it to calculate the phonon spectra of nanosystems. However, we found that the conventional point charge model in the Valence Force Field model can cause artificial instability in nanostructures. In this talk, we will present a new charge model which represents the electron cloud feature of the Born charge in a real crystal. More specifically, we have two opposite-signed point charges assigned to each atom, one at its real position, another at a position determined by its neighbor atoms. This innovation allows both electrostatic charges and Born charges to be accurately represented while retaining extreme efficiency. This customized VFF method is developed to be fittable to the results of density functional theory (DFT) calculation. We will present the results of CdSe bulk, surface, and nanowire calculations and compare them with the equivalent ab-initio calculations, for both in their accuracies and their costs.

  9. DOE Task Force meeting on Electrical Breakdown of Insulating Ceramics in a High Radiation Field

    SciTech Connect

    Green, P.H. (comp.) [comp.

    1991-08-01

    This volume contains the abstracts and presentation material from the Research Assistance Task Force Meeting Electrical Breakdown of Insulating Ceramics in a High-Radiation Field.'' The meeting was jointly sponsored by the Office of Basic Energy Sciences and the Office of Fusion Energy of the US Department of Energy in Vail, Colorado, May 28--June 1, 1991. The 26 participants represented expertise in fusion, radiation damage, electrical breakdown, ceramics, and semiconductor and electronic structures. These participants came from universities, industries, national laboratories, and government. The attendees represented eight nations. The Task Force meeting was organized in response to the recent discovery that a combination of temperature, electric field, and radiation for an extended period of time has an unexplained adverse effect in ceramics, termed radiation-enhanced electrical degradation (REED). REED occurs after an incubation period and continues to accelerate with irradiation until the ceramics can no longer be regarded as insulators. It appears that REED is irreversible and the ceramic insulators cannot be readily annealed or otherwise repaired for future services. This effect poses a serious threat for fusion reactors, which require electrical insulators in diagnostic devices, in radio frequency and neutral beam systems, and in magnetic assemblies. The problem of selecting suitable electrical insulating materials in thus far more serious than previously anticipated.

  10. 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

  11. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

    PubMed Central

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.

    2013-01-01

    Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand’s electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered. PMID:24015114

  12. The Outflows Accelerated by the Magnetic Fields and Radiation Force of Accretion Disks

    NASA Astrophysics Data System (ADS)

    Cao, Xinwu

    2014-03-01

    The inner region of a luminous accretion disk is radiation-pressure-dominated. We estimate the surface temperature of a radiation-pressure-dominated accretion disk, \\Theta =c_s^2/r^2\\Omega _K^2\\ll (H/r)^2, which is significantly lower than that of a gas-pressure-dominated disk, ? ~ (H/r)2. This means that the outflow can be launched magnetically from the photosphere of the radiation-pressure-dominated disk only if the effective potential barrier along the magnetic field line is extremely shallow or no potential barrier is present. For the latter case, the slow sonic point in the outflow will probably be in the disk, which leads to a slow circular dense flow above the disk. This implies that hot gas (probably in the corona) is necessary for launching an outflow from the radiation-pressure-dominated disk, which provides a natural explanation for the observational evidence that the relativistic jets are related to hot plasma in some X-ray binaries and active galactic nuclei. We investigate the outflows accelerated from the hot corona above the disk by the magnetic field and radiation force of the accretion disk. We find that with the help of the radiation force, the mass loss rate in the outflow is high, which leads to a slow outflow. This may be why the jets in radio-loud narrow-line Seyfert galaxies are in general mildly relativistic compared with those in blazars.

  13. Anharmonic force field, vibrational energies, and barrier to inversion of SiH{sub 3}{sup -}

    SciTech Connect

    Aarset, Kirsten [Department of Theoretical Chemistry, Eoetvoes University, P.O. Box 32, H-1518 Budapest 112, (Hungary)] [Department of Theoretical Chemistry, Eoetvoes University, P.O. Box 32, H-1518 Budapest 112, (Hungary); Csaszar, Attila G. [Department of Theoretical Chemistry, Eoetvoes University, P.O. Box 32, H-1518 Budapest 112, (Hungary)] [Department of Theoretical Chemistry, Eoetvoes University, P.O. Box 32, H-1518 Budapest 112, (Hungary); Sibert, Edwin L. III [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)] [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States); Allen, Wesley D. [Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602 (United States)] [Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602 (United States); Schaefer, Henry F. III [Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602 (United States)] [Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602 (United States); Klopper, Wim [Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, (Norway) [Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, (Norway); Theoretical Chemistry Group, Debye Institute, Utrecht University, Padualaan 14, NL-3584 CH Utrecht, The Netherlands (Netherlands); Noga, Jozef [Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, (Slovakia)] [Institute of Inorganic Chemistry, Slovak Academy of Sciences, SK-84236 Bratislava, (Slovakia)

    2000-03-01

    The full quartic force field of the ground electronic state of the silyl anion (SiH{sub 3}{sup -}) has been determined at the CCSD(T)-R12 level employing a [Si/H]=[16s11p6d5f/7s5p4d] basis set. The vibrational energy levels, using the quartic force field as a representation of the potential energy hypersurface around equilibrium, have been determined by vibrational perturbation theory carried out to second, fourth, and sixth order. The undetected vibrational fundamental for the umbrella mode, {nu}{sub 2}, is predicted to be 844 cm-1. High-quality ab initio quantum chemical methods, including higher-order coupled cluster (CC) and many-body perturbation (MP) theory with basis sets ranging from [Si/H] [5s4p2d/3s2p] to [8s7p6d5f4g3h/7s6p5d4f3g] have been employed to obtain the best possible value for the inversion barrier of the silyl anion. The rarely quantified effects of one- and two-particle relativistic terms, core correlation, and the diagonal Born-Oppenheimer correction (DBOC) have been included in the determination of the barrier for this model system. The final electronic (vibrationless) extrapolated barrier height of this study is 8351{+-}100 cm{sup -1}. (c) 2000 American Institute of Physics.

  14. Matching of additive and polarizable force fields for multiscale condensed phase simulations.

    PubMed

    Baker, Christopher M; Best, Robert B

    2013-06-11

    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

  15. 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.

  16. Distortion of magnetic field and magnetic force of a brushless dc motor due to deformed rubber magnet

    NASA Astrophysics Data System (ADS)

    Lee, C. J.; Jang, G. H.

    2008-04-01

    This paper investigates the distortion of magnetic field of a brushless dc (BLDC) motor due to deformed rubber magnet. Global or local deformation of rubber magnet in the BLDC motor is mathematically modeled by using the Fourier series. Distorted magnetic field is calculated by using the finite element method, and unbalanced magnetic force is calculated by using the Maxwell stress tensor. When the rubber magnet is globally or locally deformed, the unbalanced magnetic force has the frequencies with the first harmonic and the harmonics of slot number ±1. However, the harmonic deformation with multiple of common divisor of pole and slot does not generate unbalanced magnetic force due to the rotational symmetry.

  17. Optical forces on Y-type four-level atoms by a few-cycle pulsed focused vector field

    NASA Astrophysics Data System (ADS)

    Cai, Xunming; Lin, Qiang

    2013-11-01

    The optical force in a Y-type four level atomic system induced by a few-cycle pulsed focused vector field is studied. The expressions for pulsed focused vector beams are used to calculate the optical force. The Bloch equation of the Y-type four-level sodium atom is numerically solved without the rotating-wave approximation. The transverse optical force can change from focusing force to defocusing force depending on the initially state of atom and the detuning of the light frequency. An acceleration of atom that is 11 orders of magnitude higher than the Earth's gravitational acceleration g can be obtained. It is shown that the focusing and defocusing of real sodium atoms can be possible in an atomic beam just by a few-cycle-pulse laser field.

  18. Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

    PubMed Central

    Baker, Christopher M.; Anisimov, Victor M.; MacKerell, Alexander D.

    2010-01-01

    A polarizable force field for nucleic acid bases based on the classical Drude oscillator model is presented. Parameter optimization was performed to reproduce crystallographic geometries, crystal unit cell parameters, heats of sublimation, vibrational frequencies and assignments, dipole moments, molecular polarizabilities and quantum mechanical base-base and base-water interaction energies. The training and validation data included crystals of unsubstituted and alkyl-substituted adenine, guanine, cytosine, uracil, and thymine bases, hydrated crystals, and hydrogen bonded base pairs. Across all compounds, the RMSD in the calculated heats of sublimation is 4.1%. This equates to an improvement of more than 2.5 kcal/mol in accuracy compared to the non-polarizable CHARMM27 force field. However, the level of agreement with experimental molecular volume decreased from 1.7% to 2.1% upon moving from the non-polarizable to the polarizable model. The representation of dipole moments is significantly improved with the Drude polarizable force field. Unlike in additive force fields, there is no requirement for the gas-phase dipole moments to be overestimated, illustrating the ability of the Drude polarizable force field to treat accurately differently dielectric environments and indicating the improvements in the electrostatic model. Validation of the model was performed based on the calculation of the gas phase binding enthalpies of base pairs obtained via potential of mean force calculations; the additive and polarizable models both performed satisfactorily with average differences of 0.2 and 0.9 kcal/mol, respectively, and RMS differences of 1.3 and 1.7 kcal/mol, respectively. Overall, considering the number of significant improvements versus the additive CHARMM force field, the incorporation of explicit polarizability into the force field for nucleic acid bases represents an additional step toward accurate computational modeling of biological systems. PMID:21166469

  19. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical forces are reviewed culminating with the research manuscript in section 3.4 of the development of the two-state worm-like chain, modeling the overstretching transition of B-DNA to S-DNA. Chapter 4 considers the behavior of DNA in an electric field, first reviewing DNA as a polyelectrolyte and of DNA electrophoresis in free solution and it's polarization and resulting stretched conformation as context for the study of the contrasting behavior of DNA in an AC electric field presented in the research manuscripts of the final two sections of chapter 4. In section 4.3 the collapse of DNA in ac electric fields is investigated with the experimental results and possible models for collapse presented with a scaling analysis of the frequency- and confinement-dependent critical field for collapse presented in section 4.4, contrasting a mean-field Flory-type model and a continuum, wormlike chain model. Chapter 5 investigates viral RNA; reviewing the encapsidation, life cycle and the evolutionary dynamics of single-stranded RNA viruses including the quasispecies model and it's prediction of the information or error catastrophe, providing context for the models developed in the research manuscripts presented in sections 2.5 and 5.3. In section 5.3, a simple ODE model of the evolution of positive-sense single-stranded RNA viruses is developed, adopting the two-state mean-field quasispecies model, to characterize the selection pressure associated with the encapsidation and independently, the degradation by RNAi of the wild-type relative to the mutant population and demonstrate their capacity to induce an information catastrophe and consequently support the evolution of intermediate encapsidation rates and of viral suppressors of RNA silencing, in addition to providing support for antiviral therapeutic pathways.

  20. REVIEWS OF TOPICAL PROBLEMS Gravitational radiation of systems and the role of their force field

    NASA Astrophysics Data System (ADS)

    Nikishov, Anatolii I.; Ritus, Vladimir I.

    2011-02-01

    Gravitational radiation (GR) from compact relativistic systems with a known energy-momentum tensor (EMT) and GR from two masses elliptically orbiting their common center of inertia are considered. In the ultrarelativistic limit, the GR spectrum of a charge rotating in a uniform magnetic field, a Coulomb field, a magnetic moment field, and a combination of the last two fields differs by a factor 4?Gm2?2/e2 (? being of the order of the charge Lorentz factor) from its electromagnetic radiation (EMR) spectrum. This factor is independent of the radiation frequency but does depend on the wave vector direction and the way the field behaves outside of the orbit. For a plane wave external field, the proportionality between the gravitational and electromagnetic radiation spectra is exact, whatever the velocity of the charge. Qualitative estimates of ? are given for a charge moving ultrarelativistically in an arbitrary field, showing that it is of the order of the ratio of the nonlocal and local source contributions to the GR. The localization of external forces near the orbit violates the proportionality of the spectra and reduces GR by about the Lorentz factor squared. The GR spectrum of a rotating relativistic string with masses at the ends is given, and it is shown that the contributions by the masses and string are of the same order of magnitude. In the nonrelativistic limit, the harmonics of GR spectra behave universally for all the rotating systems considered. A trajectory method is developed for calculating the GR spectrum. In this method, the spatial (and hence polarization) components of the conserved EMT are calculated in the long wavelength approximation from the time component of the EMTs of the constituent masses of the system. Using this method, the GR spectrum of two masses moving in elliptic orbits about their common center of inertia is calculated, as are the relativistic corrections to it.

  1. Formation of magnetic discontinuities through superposition of force-free magnetic fields: Periodic boundaries

    SciTech Connect

    Kumar, Dinesh; Bhattacharyya, R. [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur-313001 (India)] [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur-313001 (India); Smolarkiewicz, P. K. [European Centre for Medium-Range Weather Forecasts, Reading RG2 9AX (United Kingdom)] [European Centre for Medium-Range Weather Forecasts, Reading RG2 9AX (United Kingdom)

    2013-11-15

    In ideal magnetohydrodynamics characterized by an infinite electrical conductivity, the magnetic flux across an arbitrary fluid surface is conserved in time. The magnetofluid then can be partitioned into contiguous subvolumes of fluid, each of which entraps its own subsystem of magnetic flux. During dynamical evolution of the magnetofluid, these subvolumes press into each other; and in the process, two such subvolumes may come into direct contact while ejecting a third interstitial subvolume. Depending on the orientations of magnetic fields of the two interacting subvolumes, the magnetic field at the common surface of interaction may become discontinuous and a current sheet is formed there. This process of current sheet formation and their subsequent decay is believed to be a plausible mechanism for coronal heating and may also be responsible for various eruptive phenomena at the solar corona. In this work, we explore this theoretical concept through numerical simulations of a viscous, incompressible magnetofluid characterized by infinite electrical conductivity. In particular, we show that if the initial magnetic field is prescribed by superposition of two linear force-free fields with different torsion coefficients, then formation of current sheets are numerically realizable in the neighborhood of magnetic nulls.

  2. Time Evolution of Relativistic Force-Free Fields Connecting a Neutron Star and its Disk

    E-print Network

    Eiji Asano; Toshio Uchida; Ryoji Matsumoto

    2005-02-18

    We study the magnetic interaction between a neutron star and its disk by solving the time-dependent relativistic force-free equations. At the initial state, we assume that the dipole magnetic field of the neutron star connects the neutron star and its equatorial disk, which deeply enters into the magnetosphere of the neutron star. Magnetic fields are assumed to be frozen to the star and the disk. The rotation of the neutron star and the disk is imposed as boundary conditions. We apply Harten-Lax-van Leer (HLL) method to simulate the evolution of the star-disk system. We carry out simulations for (1) a disk inside the corotation radius, in which the disk rotates faster than the star, and (2) a disk outside the corotation radius, in which the neutron star rotates faster than the disk. Numerical results indicate that for both models, the magnetic field lines connecting the disk and the star inflate as they are twisted by the differential rotation between the disk and the star. When the twist angle exceeds pi radian, the magnetic field lines expand with speed close to the light speed. This mechanism can be the origin of relativistic outflows observed in binaries containing a neutron star.

  3. 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.

  4. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

    PubMed Central

    Maisuradze, Gia G.; Senet, Patrick; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

    2010-01-01

    Coarse-grained molecular-dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-?-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel ?-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes which are unimodal. In addition, a comparison, between the structures that are representative of the minima in the free-energy profile along the essential collective coordinates of protein folding (computed by principal component analysis) and the free-energy profile projected along the virtual-bond dihedral angles ? of the backbone, revealed the key residues involved in the transitions between the different basins of the folding free-energy profile, in agreement with existing experimental data for 1E0L. PMID:20166738

  5. Force Field for Peptides and Proteins based on the Classical Drude Oscillator

    PubMed Central

    Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

    2013-01-01

    Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone ?, ? conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

  6. Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

    PubMed

    Lopes, Pedro E M; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; Mackerell, Alexander D

    2013-12-10

    Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone ?, ? conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1(st) generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S(2) order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

  7. 300-FF-1 remedial design report/remedial action work plan

    SciTech Connect

    Gustafson, F.W.

    1997-02-01

    The 300 Area has been divided into three operable units 300-FF-1, 300-FF-2, and 300-FF-5 all of which are in various stages of the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) process. The 300-FF-1 Operable Unit, the subject of this report, includes liquid waste disposal sites, landfills, and a burial ground. This Remedial Design Report/Remedial Action Work Plan (RDR/RAWP) provides a summary description of each waste site included in the 300-FF-1 Operable Unit, the basis for remedial actions to be taken, and the remedial action approach and management process for implementing these actions. The remedial action approach and management sections provide a description of the remedial action process description, the project schedule, the project team, required planning documentation, the remedial action change process, the process for verifying attainment of the remedial action goals, and the required CERCLA and RCRA closeout documentation. Appendix A provides additional details on each waste site. In addition to remediation of the waste sites, waste generated during the remedial investigation/feasibility study portions of the project will also be disposed at the Environmental Restoration Disposal Facility (ERDF). Appendix B provides a summary of the modeling performed in the 300-FF-1 Phase 3 FS and a description of the modeling effort to be used to show attainment of the remedial action goals. Appendix C provides the sampling and analysis plan (SAP) for all sampling and field-screening activities performed during remediation and for verification of attainment with the remedial action goals. Appendix D provides the public involvement plan, prepared to ensure information is provided to the public during remedial design and remedial action processes.

  8. FF-Replan: A Baseline for Probabilistic Planning

    Microsoft Academic Search

    Sung Wook Yoon; Alan Fern; Robert Givan

    2007-01-01

    FF-Replan was the winner of the 2004 International Proba- bilistic Planning Competition (IPPC-04) (Younes & Littman 2004a) and was also the top performer on IPPC-06 domains, though it was not an official entry. This success was quite sur- prising, due to the simplicity of the approach. In particular, FF-Replan calls FF on a carefully constructed deterministic variant of the planning

  9. ff = 0:3427812069 a = 1:5614141543

    E-print Network

    Zingg, David W.

    Scheme C: ff = 0:3427812069 a = 1:5614141543 b = 0:124148259 In Fig. 4, the pentadiagonal 7­point scheme has ff = 0:5801818925 fi = 0:0877284887 a = 1:3058941939 b = 0:9975884963 c = 0:0323380724 The tridiagonal 7­point scheme has ff = 0:3904091387 fi = 0 a = 1:5638887738 b = 0:2348222711 c = \\Gamma0

  10. 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.

  11. Biopolymers Under Large External Forces and Mean-field RNA Virus Evolutionary Dynamics

    E-print Network

    Ahsan, Syed Amir

    2013-01-01

    with single molecule atomic force microscopy. Naturesingle-molecule force detection and measurement technologies, methods such as magnetic and optical tweezers, atomic force microscopy (single-molecule level ii through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy,

  12. A program to compute magnetic fields, forces, and inductances due to solid rectangular conductors arbitrarily positioned in space

    Microsoft Academic Search

    R. T. Honjo; R. M. del Vecchio

    1986-01-01

    The computer program BUS3D was developed to compute the magnetic field and vector potential produced by a collection of rectangular busbars carrying dc current and arbitrarily oriented in space, using exact analytic expressions. The field and vector potential expressions are used in numerical integrations to obtain forces on individual busbars and inductances or mutual inductances between collections of busbars. The

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

    E-print Network

    Ian Vega; Steven Detweiler

    2008-01-15

    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 non-singular source. Solving this wave equation for the remainder completely avoids the calculation of the singular retarded field along with the attendant difficulties associated with numerically modeling a delta function source. From this differentiable remainder one may compute the self-force, the energy flux, and also a waveform which reflects the effects of the self-force. As a test of principle, we implement this method using a 4th-order (1+1) code, and calculate the self-force for the simple case of a scalar charge moving in a circular orbit around a Schwarzschild black hole. We achieve agreement with frequency-domain results to ~ 0.1% or better.

  14. Single nanowire manipulation within dielectrophoretic force fields in the sub-crossover frequency regime

    NASA Astrophysics Data System (ADS)

    Palapati, N. K. R.; Pomerantseva, E.; Subramanian, A.

    2015-02-01

    This paper presents the quantitative relationship between the control parameters of a dielectrophoretic (DEP) force field and the resulting electrokinetic region of influence experienced by individual nanowires (NWs) in colloidal suspensions. Our results show that DEP operation at sub-crossover frequencies, which are defined as frequencies slightly below the transition from positive-to-negative DEP, offers a suitable but previously unexplored performance regime for single NW manipulation and assembly. The low-magnitude DEP forces at these frequencies, which are estimated to be 8 orders of magnitude smaller as compared to near-DC frequencies, provide an efficient avenue to controllably extend electrokinetic influence on suspension volumes that present isolated NWs. These results are demonstrated using ?-phase manganese dioxide NWs as a model one-dimensional construct. Based on experimentally extracted values for the NW intrinsic conductivity and dielectric permittivity, we employ computational models to explain each of the performance regimes observed in this nanoassembly system. In addition, we use a new approach to estimate the concentration of a NW suspension from experimentally observed data for deposition yields.

  15. Effects of polymer surface molecular structure and force-field characteristics on blood interfacial phenomena.

    PubMed

    Nyilas, E; Morton, W A; Cumming, R D; Lederman, D M; Chiu, T H

    1977-01-01

    To quantify the effects of major surface structural factors influencing interfacial reactions induced by polymers in native blood, model surfaces of solvent-cast films of two analogous poly(ether urethanes) and three homologous polyamides (nylon 4, 6/6, and 12) were exposed ex vivo to canine blood under the well-defined hemodynamic conditions of the Stagnation Point Flow Experiment. The selected surfaces allow for incremental changes in properties and were characterized by their "Composite Surface Free ENergy Function," gamma'S, which describes the surface force field as the sum of the mean dispersion (gammaSd) and polar (gammaSp) contributions and is computed from wettability spectra obtained with ultrapure diagnostic liquids. Blood interfacial effects were measured by the shear-limited diameter of the white cell circle formed around the stagnation point, the flow parameter at which symmetric aggregation occurred, and the surface-number density of platelets, [P s], remaining adherent under fixed conditions. At identical flows, within each group of polymers, both the WBC-circle diameter and [P s] scale with gamma Sp/gamma'S, implying that 1) only the magnitude but not the interaction mechanism varies as a function of incremental structural and surface changes, 2) the primary determinant of surface-induced effects is the polar force contribution, and 3) the magnitude of gamma'S is secondary if gammaSd/gamma'S is sufficiently great. PMID:557479

  16. Determination of the instantaneous forces on flapping wings from a localized fluid velocity field

    NASA Astrophysics Data System (ADS)

    Minotti, F. O.

    2011-11-01

    Expressions are derived to relate the instantaneous pressure force on a flapping wing to the velocity field on a plane at the trailing edge and on a highly localized region around and near the wing, valid when the vortex sheet is thin. In its more practical version, the formalism is applicable to wings with close to two-dimensional geometry and has the advantage of not using spatial derivatives, but only a time derivative of a surface integral of the velocity. In the purely two-dimensional case, the expression obtained is used to justify a much simpler one that only requires the evaluation of the time derivative of the wing circulation. A comparison with a numerical simulation in a two-dimensional case shows a good representation of the forces, even with the most simplified expression, when the condition of a thin wake is met. Other examples are shown in which the wake is not thin in order to explore the limitations of the formalism. It is found in these cases that the thrust is sometimes not so well reproduced, with a tendency to be overestimated, while the lift is generally better reproduced. Remarkably, the simpler expression reproduces rather acceptably the phase and amplitude of both thrust and lift in all cases.

  17. Scanning near-field optical/atomic-force microscopy for biomedical applications

    NASA Astrophysics Data System (ADS)

    Tamiya, Eiichi; Iwabuchi, Shinichiro; Murakami, Yuji; Sakaguchi, Toshifumi; Yokoyama, Kenji; Chiba, Norio; Muramatsu, Hiroshi

    1996-12-01

    We have developed scanning near-field optical/atomic force microscopy (SNOM/AFM). The SNOM/AFM uses a bent optical fiber simultaneously as a dynamic force AFM cantilever and a SNOM probe. Resonant frequency of the optical fiber cantilever is 15 - 40 kHz. Optical resolution of the SNOM/AFM images shows less than 50 nm. The SNOM/AFM system contains photon counting system and polychrometer/ICCD system to observe fluorescence image and spectrograph of micro areas, respectively. A SNOM-AFM system was newly applied to analyses of biological samples. In this system a feedback signal from AFM in the noncontact mode was used to scan the probe tip along the surface contour of the sample. An optical fiber with a sharp tip on one end was bent for use as cantilever, and ac amplitude of the cantilever deflection was held constant during scanning by moving the stage. Green fluorescent protein (GFP) absorbs blue light and emits green light. GFP should be a convenient indicator of transformation and one that could allow cells to be separated with fluorescence-activated cell sorting. The gene coding to GFP was cloned in recombinant E.coli and plant cells. Spatial distribution of GFP gene expression was clarified using a SNOM-AFM system. Fluorescent spectroscopic analyses supported GFP was surely produced in E.coli and plant cells. Applications to gene identification in human genomes were also discussed.

  18. Stochastic Force Due to a Quantum Scalar Field in Minkowski Spacetime

    E-print Network

    Jason D. Bates

    2013-03-07

    A method is presented for computing approximate expressions for the stochastic force term $\\xi_{ab}$ which appears in the Einstein-Langevin equation of stochastic gravity. Within this framework, $\\xi_{ab}$ is a stochastic tensor field whose probability distribution mimics the probability distribution of the fluctuations of the quantum stress tensor operator; it is defined to be a random tensor field of zero mean whose correlation function is given by the expectation value of the symmetrized two point function of the stress energy fluctuation operator, called the noise kernel. Approximate expressions are obtained by means of a truncated Karhunen-Loeve transform defined on a random lattice of spacetime points. Due to the singular nature of the noise kernel, a coarse graining procedure is used to regulate divergences; as a result, the expressions obtained for $\\xi_{ab}$ approximate values which might be seen by a probe measuring fluctuations in the stress energy using a sampling profile of finite width. Two realizations of $\\xi_{ab}$ in Minkowski spacetime for the conformally invariant quantum scalar field in the Minkowski vacuum state are presented.

  19. Mean force on a finite-sized spherical particle due to an acoustic field in a viscous compressible medium.

    PubMed

    Annamalai, Subramanian; Balachandar, S; Parmar, Manoj K

    2014-05-01

    An analytical expression to evaluate the second-order mean force (acoustic radiation force) on a finite-sized, rigid, spherical particle due to an acoustic wave is presented. The medium in which the particle is situated is taken to be both viscous and compressible. A far-field derivation approach has been used in determining the force, which is a function of the particle size, acoustic wavelength, and viscous boundary-layer thickness. It is assumed that the viscous length scale is negligibly small compared to the acoustic wavelength. The force expression presented here (i) reduces to the correct inviscid behavior (for both small- and finite-sized particles) and (ii) is identical to recent viscous results [M. Settnes and H. Bruus, Phys. Rev. E 85, 016327 (2012)] for small-sized particles. Further, the computed force qualitatively matches the computational fluid dynamics (finite-element) results [D. Foresti, M. Nabavi, and D. Poulikakos, J. Fluid Mech. 709, 581 (2012)] for finite-sized particles. Additionally, the mean force is interpreted in terms of a multipole expansion. Subsequently, considering the fact that the force expansion is an infinite series, the number of terms that are required or adequate to capture the force to a specified accuracy is also provided as a function of the particle size to acoustic wavelength ratio. The dependence of the force on particle density, kinematic viscosity, and bulk viscosity of the fluid is also investigated. Here, both traveling and standing waves are considered. PMID:25353881

  20. Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields

    PubMed Central

    Dahlgren, Markus K.; Schyman, Patric; Tirado-Rives, Julian; Jorgensen, William L.

    2013-01-01

    The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parameterization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and non-planar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 C) are also reported. PMID:23621692

  1. Predictions for water clusters from a first-principles two- and three-body force field

    NASA Astrophysics Data System (ADS)

    Góra, Urszula; Cencek, Wojciech; Podeszwa, Rafa?; van der Avoird, Ad; Szalewicz, Krzysztof

    2014-05-01

    A new rigid-monomer three-body potential has been developed for water by fitting it to more than 70 thousand trimer interaction energies computed ab initio using coupled-cluster methods and augmented triple-zeta-quality basis sets. This potential was used together with a modified form of a previously developed two-body potential and with a polarization model of four- and higher-body interactions to predict the energetics of the water trimer, hexamer, and 24-mer. Despite using the rigid-monomer approximation, these predictions agree better with flexible-monomer benchmarks than published results obtained with flexible-monomer force fields. An unexpected finding of our work is that simple polarization models predict four-body interactions to within a few percent, whereas for three-body interactions these models are known to have errors on the order of 50%.

  2. Mind as a force field: comments on a new interactionistic hypothesis.

    PubMed

    Lindahl, B I; Arhem, P

    1994-11-01

    The survival and development of consciousness in biological evolution call for an explanation. An interactionistic mind-brain theory seems to have the greatest explanatory value in this context. An interpretation of an interactionistic hypothesis, recently proposed by Karl Popper, is discussed both theoretically and based on recent experimental data. In the interpretation, the distinction between the conscious mind and the brain is seen as a division into what is subjective and what is objective, and not as an ontological distinction between something immaterial and something material. The interactionistic hypothesis is based on similarities between minds and physical forces. The conscious mind is understood to interact with randomly spontaneous spatio-temporal patterns of action potentials through an electromagnetic field. Consequences and suggestions for future studies are discussed. PMID:7844991

  3. 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.

  4. 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.

  5. Current sheet scattering and ion isotropic boundary under 3-D empirical force-balanced magnetic field

    NASA Astrophysics Data System (ADS)

    Yue, Chao; Wang, Chih-Ping; Lyons, Larry; Liang, Jun; Donovan, Eric F.; Zaharia, Sorin G.; Henderson, Michael

    2014-10-01

    To determine statistically the extent to which current sheet scattering is sufficient to account for the observed ion isotropic boundaries (IBs) for <30 keV ions, we have computed IBs from our 3-D empirical force-balanced magnetic field, identified IBs in FAST observations, and investigated the model-observation consistency. We have found in both model and FAST results the same dependences of IB latitudes on magnetic local time, ion energy, Kp, and solar wind dynamic pressure (PSW) levels: IB moves to higher latitudes from midnight toward dawn/dusk and to lower latitudes as energy increases and as Kp or PSW increases. The model predicts well the observed energy dependence, and the modeled IB latitudes match fairly well with those from FAST for Kp = 0. As Kp increases, the latitude agreement at midnight remains good but a larger discrepancy is found near dusk. The modeled IBs at the equator are located around the earthward boundary of highly isotropic ions observed by Time History of Events and Macroscale Interactions during Substorms at midnight and postmidnight, but with some discrepancy near dusk under high Kp. Thus, our results indicate that current sheet scattering generally plays the dominant role. The discrepancies suggest the importance of pitch angle scattering by electromagnetic ion cyclotron waves, which occur more often from dusk to noon and are more active during higher Kp. The comparison with the observed IBs is better with our model than under the nonforce-balanced T89, indicating that using a forced-balanced model improves the description of the magnetic field configuration and reinforces our conclusions regarding the role of current sheet scattering.

  6. The effect of low force chiropractic adjustments on body surface electromagnetic field

    PubMed Central

    Zhang, John; Snyder, Brian J; Vernor, Lori

    2004-01-01

    Objective The purpose of this study was to investigate the body surface electromagnetic field (EMF) changes using a sensitive magnetometer before and after a specific Toftness chiropractic adjustment in asymptomatic human subjects. Method Forty-four subjects were randomly assigned into control (20 subjects) and experimental groups (24 subjects) in a pre and post-test design. The Triaxial Fluxgate Magnetometer FGM-5DTAA (Walker Scientific, Worcester, Massachusetts) with five digit display and resolution of 1 nanotesla (nT) was used for EMF detection. The EMF in the research room and on the adjustment table was monitored and recorded. The subjects’ body surface (cervical, thoracic, lumbar and sacral areas) EMF was determined in the prone position before and after the chiropractic adjustment. A low force Toftness chiropractic adjustment was applied to the cervical, thoracic, lumbar and sacral areas as determined by the practitioner. Results The EMF in the research room was recorded as 41611 nT at the Z axis (earth field), 13761 nT at the X axis and 7438 nT at the Y axis. The EMF on the adjusting table changed minimally during the 15 minute observation period. The EMF on the subjects’ body surface decreased at 4 spinal locations after chiropractic adjustment. The EMF (mean ± SD in nT) decreased significantly at the cervical region from 42449 ± 907 to 41643 ± 1165 (p < 0.01) and at the sacral regions from 43206 ± 760 to 42713 ± 552 (p < 0.01). The EMF at the lumbar and thoracic regions decreased but did not reach a statistically significant level. No significant changes of the body surface EMF were found in the control group. Conclusion A low force Toftness chiropractic adjustment in the cervical and sacral areas resulted in a significant reduction of the cervical and sacral surface EMF. No significant body surface EMF changes were observed in the lumbar and thoracic regions. The mechanisms of the EMF reduction after chiropractic adjustment are not known. PMID:17549217

  7. A Critical Assessment of Nonlinear Force-Free Field Modeling of the Solar Corona for Active Region 10953

    E-print Network

    DeRosa, Marc L; Barnes, Graham; Leka, K D; Lites, Bruce W; Aschwanden, Markus J; Amari, Tahar; Canou, Aurelien; McTiernan, James M; Regnier, Stephane; Thalmann, Julia K; Valori, Gherardo; Wheatland, Michael S; Wiegelmann, Thomas; Cheung, Mark C M; Conlon, Paul A; Fuhrmann, Marcel; Inhester, Bernd; Tadesse, Tilaye

    2009-01-01

    Nonlinear force-free field (NLFFF) models are thought to be viable tools for investigating the structure, dynamics and evolution of the coronae of solar active regions. In a series of NLFFF modeling studies, we have found that NLFFF models are successful in application to analytic test cases, and relatively successful when applied to numerically constructed Sun-like test cases, but they are less successful in application to real solar data. Different NLFFF models have been found to have markedly different field line configurations and to provide widely varying estimates of the magnetic free energy in the coronal volume, when applied to solar data. NLFFF models require consistent, force-free vector magnetic boundary data. However, vector magnetogram observations sampling the photosphere, which is dynamic and contains significant Lorentz and buoyancy forces, do not satisfy this requirement, thus creating several major problems for force-free coronal modeling efforts. In this article, we discuss NLFFF modeling o...

  8. A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set.

    PubMed

    Rajgaria, R; McAllister, S R; Floudas, C A

    2006-11-15

    This work presents a novel C(alpha)--C(alpha) distance dependent force field which is successful in selecting native structures from an ensemble of high resolution near-native conformers. An enhanced and diverse protein set, along with an improved decoy generation technique, contributes to the effectiveness of this potential. High quality decoys were generated for 1489 nonhomologous proteins and used to train an optimization based linear programming formulation. The goal in developing a set of high resolution decoys was to develop a simple, distance-dependent force field that yields the native structure as the lowest energy structure and assigns higher energies to decoy structures that are quite similar as well as those that are less similar. The model also includes a set of physical constraints that were based on experimentally observed physical behavior of the amino acids. The force field was tested on two sets of test decoys not in the training set and was found to excel on all the metrics that are widely used to measure the effectiveness of a force field. The high resolution force field was successful in correctly identifying 113 native structures out of 150 test cases and the average rank obtained for this test was 1.87. All the high resolution structures (training and testing) used for this work are available online and can be downloaded from http://titan.princeton.edu/HRDecoys. PMID:16981202

  9. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues

    PubMed Central

    Sieradzan, Adam K.; Hansmann, Ulrich H.E.; Scheraga, Harold A.; Liwo, Adam

    2013-01-01

    Coarse-grained force fields for protein simulations are usually designed and parameterized to treat proteins composed of natural L-amino-acid residues. However, D-amino-acid residues occur in bacterial, fungal (e.g., gramicidins), as well as human-designed proteins. For this reason, we have extended the UNRES coarse-grained force field developed in our laboratory to treat systems with D-amino-acid residues. We developed the respective virtual-bond-torsional and double-torsional potentials for rotation about the C? · · · C? virtual-bond axis and two consecutive C? · · · C? virtual-bond axes, respectively, as functions of virtual-bond-dihedral angles ?. In turn, these were calculated as potentials of mean force (PMFs) from the diabatic energy surfaces of terminally-blocked model compounds for glycine, alanine, and proline. The potential-energy surfaces were calculated by using the ab initio method of molecular quantum mechanics at the Møller-Plesset (MP2) level of theory and the 6-31G(d,p) basis set, with the rotation angles of the peptide groups about Ci-1??Ci?(?(1)) and Ci??Ci+1?(?(2)) used as variables, and the energy was minimized with respect to the remaining degrees of freedom. The PMFs were calculated by numerical integration for all pairs and triplets with all possible combinations of types (glycine, alanine, and proline) and chirality (D or L); however, symmetry relations reduce the number of non-equivalent torsional potentials to 13 and the number of double-torsional potentials to 63 for a given C-terminal blocking group. Subsequently, one- (for torsional) and two-dimensional (for double-torsional potentials) Fourier series were fitted to the PMFs to obtain analytical expressions. It was found that the torsional potentials of the x-Y and X-y types, where X and Y are Ala or Pro, respectively, and a lowercase letter denotes D-chirality, have global minima for small absolute values of ?, accounting for the double-helical structure of gramicidin A, which is a dimer of two chains, each possessing an alternating D-Tyr-L-Tyr sequence, and similar peptides. The side-chain and correlation potentials for D-amino-acid residues were obtained by applying the reflection about the Ci-1??Ci??Ci+1? plane to the respective potentials for the L-amino-acid residues. PMID:24729761

  10. A finite-element analysis of the electrostatic force on a uniformly charged dielectric sphere resting on a dielectric-coated electrode in a detaching electric field

    Microsoft Academic Search

    James Q. Feng; Dan A. Hays

    1998-01-01

    In the electrophotographic process, charged toner particles are transferred from one surface to another with an electric field. To enable electric field transfer of toner, the externally applied field strength must be greater than a threshold value, so that the Coulomb force can overcome the toner adhesion force at the supporting surface. In this paper, the threshold field strength to

  11. @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 ' Ã?f 2 @||@^ @?| *i t)t| i4i t @?| G ++I#12; +I#12; ;W#12; ;W#12; ;W#12;

  12. @h|i* _i 5|@|t|^ i Vi?_hi_ #iUi4Mhi 2ff2c e ffS ff

    E-print Network

    Tourneret, Jean-Yves

    @h|i* _i 5|@|t|^ i Vi?_hi_ #12; #iUi4Mhi 2ff2c e ffS ff , ihUUi w@ _i?t|i _ iU|i h E%c c %c tiUh| s E%c c %c( b '~} f d ciicdc|it c\\ 9 s E%( b ' bc e3 S? ' 7 ,? TLt@?| UL44i _i 7% ' c Sc 9 %c L? LM|i?| *? s E%c c %c( b ' ? *? b ?b7% #L?U Y *? s E%c c %c( b Yb f / ? b ?% f / % b N? Ti

  13. 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.

  14. Compatibility of the chameleon-field model with fifth-force experiments, cosmology, and PVLAS and CAST results.

    PubMed

    Brax, Philippe; van de Bruck, Carsten; Davis, Anne-Christine

    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. PMID:17930493

  15. 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.

  16. 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.

  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. An integrated microparticle sorting system based on near-field optical forces and a structural perturbation.

    PubMed

    Lin, Shiyun; Crozier, Kenneth B

    2012-02-13

    We demonstrate an integrated microparticle passive sorting system based on the near-field optical forces exerted by a 3-dB optical splitter that consists of a slot waveguide and a conventional channel waveguide. We show that 320 nm and 2 µm polystyrene particles brought into the splitter are sorted so that they exit along the slot waveguide and channel waveguide, respectively. Electromagnetic simulations and precise position tracking experiments are carried out to investigate the sorting mechanism. As the waveguides are separated by 200 nm, they provide two potential wells for the smaller particles, but only one broad potential well for the larger particles, since their diameters exceed the distance between the two field maxima. A structural perturbation consisting of a stuck bead transfers the smaller particles to the second well associated with the slot waveguide, while the larger particles are brought to the region between the two waveguides and eventually follow the channel waveguide, as it is associated with a deeper potential well. This label-free passive particle sorting system requires low guided power (20 mW in these experiments), and provides a new technique for sorting sub-micron particles. PMID:22418095

  19. Lorentz force time-optimal transfer trajectory design in Jovian magnetic field

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiguo; Gong, Shengping; Li, Junfeng

    2015-02-01

    In this paper, the Lorentz force in Jupiter's magnetic field is used to design the transfer trajectory between Galileo moons' Lagrange points. The equatorial orbits of charged spacecraft in three-body axis-aligned nontilted-dipole magnetic field model are analyzed and the results show that the libration point L1 and L2 become nearer or further away from Europa with the variable size and polarity of the charge. The bang-bang charge control with the variable size and polarity of the charge can be used to change orbit's direction and shape. Analytical and numerical iteration methods give the fast and accurate bang-bang charge control to send the spacecraft to the L2 point of Europa, respectively. Finally, two numerical methods, the indirect and direct methods, give the time-optimal charge controls which are similar to but different from the semi-revolution variable polarity control maneuver. The optimal results achieve the final position and the flight angle at the same time, and need less time and less magnitude of charge compared with the numerical iteration method.

  20. 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.

  1. A vibrational analysis of the 7-azaindole-water complex: Anharmonicities using the quartic force field

    NASA Astrophysics Data System (ADS)

    Taketsugu, Tetsuya; Yagi, Kiyoshi; Gordon, Mark S.

    Vibrational frequencies for the 7-azaindole and 7-azaindole-water complex are calculated by the vibrational self-consistent field (VSCF) and correlation-corrected VSCF (cc-VSCF) methods using second-order perturbation theory (MP2), with the 6-31G(d) basis set, and density functional theory with the B3LYP functional and the same basis set. The potential energies at quadrature points for VSCF calculations are estimated from the quartic force field (QFF) determined by the respective electronic structure methods. The comparison with experimental fundamentals for 7-azaindole indicates that MP2 gives better results for NH and CH stretching modes than B3LYP, while B3LYP gives better results for CC stretching and ring deforming modes. The vibrational modes for the 7-azaindole-water complex are discussed in terms of those of the isolated 7-azaindole and water. This VSCF/QFF approach will help quantitative evaluations of vibrational energies of a general polyatomic molecule with a reasonable computational cost.

  2. Simulation of mesogenic diruthenium tetracarboxylates: Development of a force field for coordination polymers of the MMX type.

    PubMed

    Castro, Maria Ana; Roitberg, Adrian E; Cukiernik, Fabio D

    2013-06-01

    A classical molecular mechanics force field, able to simulate coordination polymers (CP) based on ruthenium carboxylates (Ru2 (O2CReq )4 Lax) (eq = equatorial group containing aliphatic chains, Lax = axial ligand), has been developed. New parameters extracted from experimental data and quantum calculations on short aliphatic chains model systems were included in the generalized AMBER force field. The proposed parametrization was evaluated using model systems with known structure, containing either short or long aliphatic chains; experimental results were reproduced satisfactorily. This modified force field, although in a preliminary stage, could then be applied to long chain liquid crystalline compounds. The resulting atomistic simulations allowed assessing the relative influence of the factors determining the CP conformation, determinant for the physical properties of these materials. PMID:23436725

  3. Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

    PubMed

    Schmid, Nathan; Eichenberger, Andreas P; Choutko, Alexandra; Riniker, Sereina; Winger, Moritz; Mark, Alan E; van Gunsteren, Wilfred F

    2011-07-01

    New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new ?/? torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl(-) ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained. PMID:21533652

  4. Combined influences of gravitoinertial force level and visual field pitch on visually perceived eye level

    NASA Technical Reports Server (NTRS)

    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.

  5. 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

  6. 6. FF coal pulverizer (ball mill inside). GG building in ...

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

    6. FF coal pulverizer (ball mill inside). GG building in background did preliminary crushing; pulverizer to left, coal conveyor and air cleaning towers to right; conveyor on left brought crushed coal to FF. Looking north/northeast - Rouge Steel Company, 3001 Miller Road, Dearborn, Wayne County, MI

  7. The FF Planning System: Fast Plan Generation Through Heuristic Search

    Microsoft Academic Search

    Jörg Hoffmann; Bernhard Nebel

    2001-01-01

    We describe and evaluate the algorithmic techniques that are used in the ff planningsystem. Like the HSP system, ff relies on forward state space search, using a heuristic thatestimates goal distances by ignoring delete lists. Unlike HSP's heuristic, our method doesnot assume facts to be independent. We introduce a novel search strategy that combinesHill-climbing with systematic search, and we show

  8. Proof. By Theorem 2.30 and the choice of K + 0 , every model of T ff is

    E-print Network

    Baldwin, John T.

    Proof. By Theorem 2.30 and the choice of K + 0 , every model of T ff is (K ff ; Ÿ ff )­semigeneric. By Corollary 1.31, T ff is nearly model complete. By Corollary 1.32 and Lemma 2.31, T ff is complete. Since the generic model for K ff is semigeneric, T ff = T ff . [1] shows that T ff is stable. Since each theorem

  9. 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.

  10. Measurements of the force fields within an acoustic standing wave using holographic optical tweezers

    NASA Astrophysics Data System (ADS)

    Bassindale, P. G.; Phillips, D. B.; Barnes, A. C.; Drinkwater, B. W.

    2014-04-01

    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 pNpp) 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.

  11. Source evaluation report phase 2 investigation: Limited field investigation. Final report: United States Air Force Environmental Restoration Program, Eielson Air Force Base, Alaska

    SciTech Connect

    Not Available

    1994-10-01

    This report describes the limited field investigation work done to address issues and answer unresolved questions regarding a collection of potential contaminant sources at Eielson Air Force Base (AFB), near Fairbanks, Alaska. These sources were listed in the Eielson AFB Federal Facility Agreement supporting the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) cleanup of the base. The limited field investigation began in 1993 to resolve all remaining technical issues and provide the data and analysis required to evaluate the environmental hazard associated with these sites. The objective of the limited field investigation was to allow the remedial project managers to sort each site into one of three categories: requiring remedial investigation/feasibility study, requiring interim removal action, or requiring no further remedial action.

  12. 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...

  13. 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...

  14. Electric-field-induced forces between two surfaces filled with an insulating liquid: the role of adsorbed water

    NASA Astrophysics Data System (ADS)

    Wang, Yong Jian; Xu, Zuli; Sheng, Ping; Tong, Penger

    2014-06-01

    A systematic study of the electric-field-induced forces between a solid glass sphere and a flat gold-plated substrate filled with an insulating liquid has been carried out. Using atomic force microscopy, we measure the electrostatic force f(s, V) between the sphere and substrate as a function of the surface separation s and applied voltage V. The measured f(s, V) is found to be well described by an equation for a conducting sphere. Further force measurements for the "wet" porous glass spheres filled with an aqueous solution of urea and the dried porous glass spheres filled with (dry) air suggest that there is a water layer of a few nanometers in thickness adsorbed on the hydrophilic glass surface under ambient conditions. This adsorbed water layer is more conductive than the dielectric core of the glass sphere, making the sphere surface to be at a potential close to that of the cantilever electrode. As a result, the electric field is strongly concentrated in the gap region between the glass sphere and gold-plate substrate and thus their electrostatic attraction is enhanced. This surface conductivity effect is further supported by the thermal gravimetric analysis (TGA) and force response measurements to a time-dependent electric field. The experiment clearly demonstrates that the adsorption of a conductive water layer on a hydrophilic surface plays a dominant role in determining the electrostatic interaction between the dielectric sphere and substrate.

  15. 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.

  16. Testing non-linear force-free coronal magnetic field extrapolations with the Titov-Demoulin equilibrium

    E-print Network

    Thomas Wiegelmann; Bernd Inhester; Bernhard Kliem; Gherardo Valori; Thomas Neukirch

    2006-12-21

    CONTEXT: As the coronal magnetic field can usually not be measured directly, it has to be extrapolated from photospheric measurements into the corona. AIMS: We test the quality of a non-linear force-free coronal magnetic field extrapolation code with the help of a known analytical solution. METHODS: The non-linear force-free equations are numerically solved with the help of an optimization principle. The method minimizes an integral over the force-free and solenoidal condition. As boundary condition we use either the magnetic field components on all six sides of the computational box in Case I or only on the bottom boundary in Case II. We check the quality of the reconstruction by computing how well force-freeness and divergence-freeness are fulfilled and by comparing the numerical solution with the analytical solution. The comparison is done with magnetic field line plots and several quantitative measures, like the vector correlation, Cauchy Schwarz, normalized vector error, mean vector error and magnetic energy. RESULTS: For Case I the reconstructed magnetic field shows good agreement with the original magnetic field topology, whereas in Case II there are considerable deviations from the exact solution. This is corroborated by the quantitative measures, which are significantly better for Case I. CONCLUSIONS: Despite the strong nonlinearity of the considered force-free equilibrium, the optimization method of extrapolation is able to reconstruct it; however, the quality of reconstruction depends significantly on the consistency of the input data, which is given only if the known solution is provided also at the lateral and top boundaries, and on the presence or absence of flux concentrations near the boundaries of the magnetogram.

  17. Importance of local force fields on lattice thermal conductivity reduction in PbTe1-xSex alloys

    NASA Astrophysics Data System (ADS)

    Murakami, Takuru; Shiga, Takuma; Hori, Takuma; Esfarjani, Keivan; Shiomi, Junichiro

    2013-05-01

    Lattice thermal conductivity of PbTe1-xSex alloyed crystals has been calculated by molecular-dynamics simulations with anharmonic interatomic force constants (a-IFCs) obtained from first principles. The a-IFCs of pure PbTe and PbSe were calculated by the real-space displacement method with care of the stability for molecular-dynamics simulations. An empirical mixing rule of a-IFCs has been developed to account for both mass and local force-field differences in alloys. The obtained alloy-fraction dependence of lattice thermal conductivity reduction agrees well with the experiments. The comparative study shows that the local force-field difference significantly impacts the lattice thermal conductivity.

  18. 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

  19. 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.

  20. On finding fields and self-force in a gauge appropriate to separable wave equations

    NASA Astrophysics Data System (ADS)

    Friedman, John; Keidl, Tobias; Wiseman, Alan

    2007-04-01

    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. We report progress on finding the renormalized self-force from the Teukolsky equation. The method is related to the MiSaTaQuWa renormalization and to the Detweiler-Whiting construction of the singular field. It relies on the fact that the renormalized ?0 (or ?4) is a sourcefree solution to the Teukolsky equation; and, following Chrzanowski, Cohen and Kegeles, one can therefore reconstruct a nonsingular renormalized metric in a radiation gauge. References: [1] T. S. Keidl, J. L. Friedman, and A. G. Wiseman, Phys. Rev. D., in press; gr-qc/0611072. [2] Y. Mino, M. Sasaki, and T. Tanaka, Phys. Rev. D 55, 3457 (1997); T. C. Quinn and R. M. Wald, Phys. Rev. D 56, 3381 (1997); S. Detweiler and B. F.Whiting, Phys. Rev. D 67, 024025 (2003).

  1. A robust force field based method for calculating conformational energies of charged drug-like molecules.

    PubMed

    Poehlsgaard, Jacob; Harpsøe, Kasper; Jørgensen, Flemming Steen; Olsen, Lars

    2012-02-27

    The binding affinity of a drug-like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, then the molecule is unlikely to bind to its target. Determination of the global minimum energy conformation and calculation of conformational penalties of binding is a prerequisite for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic compounds generated by conformational analysis with modified electrostatics are good approximations of the conformational distributions predicted by experimental data and with molecular dynamics performed in explicit solvent. Finally the method is used to calculate conformational penalties for zwitterionic GluA2 agonists and to filter false positives from a docking study. PMID:21985436

  2. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field.

    PubMed

    Xiang, Jin Yu; Ponder, Jay W

    2014-01-01

    An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies. PMID:25045338

  3. Digital control of force microscope cantilevers using a field programmable gate array

    NASA Astrophysics Data System (ADS)

    Jacky, Jonathan P.; Garbini, Joseph L.; Ettus, Matthew; Sidles, John A.

    2008-12-01

    This report describes a cantilever controller for magnetic resonance force microscopy based on a field programmable gate array, along with the hardware and software used to integrate the controller into an experiment. The controller is assembled from a low-cost commercially available software defined radio device and libraries of open-source software. The controller includes a digital filter comprising two cascaded second-order sections ("biquads"), which together can implement transfer functions for optimal cantilever controllers. An appendix in this report shows how to calculate filter coefficients for an optimal controller from measured cantilever characteristics. The controller also includes an input multiplexer and adder used in calibration protocols. Filter coefficients and multiplexer settings can be set and adjusted by control software while an experiment is running. The input is sampled at 64 MHz; the sampling frequency in the filters can be divided down under software control to achieve a good match with filter characteristics. Data reported here were sampled at 500 kHz, chosen for acoustic cantilevers with resonant frequencies near 8 kHz. Inputs are digitized with 12 bit resolution, and outputs are digitized with 14 bits. The experiment software is organized as a client and server to make it easy to adapt the controller to different experiments. The server encapsulates the details of controller hardware organization, connection technology, filter architecture, and number representation. The same server could be used in any experiment, while a different client encodes the particulars of each experiment.

  4. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

    PubMed

    Mazack, Michael J M; Gao, Jiali

    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. PMID:24880295

  5. 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

  6. Digital control of force microscope cantilevers using a field programmable gate array.

    PubMed

    Jacky, Jonathan P; Garbini, Joseph L; Ettus, Matthew; Sidles, John A

    2008-12-01

    This report describes a cantilever controller for magnetic resonance force microscopy based on a field programmable gate array, along with the hardware and software used to integrate the controller into an experiment. The controller is assembled from a low-cost commercially available software defined radio device and libraries of open-source software. The controller includes a digital filter comprising two cascaded second-order sections ("biquads"), which together can implement transfer functions for optimal cantilever controllers. An appendix in this report shows how to calculate filter coefficients for an optimal controller from measured cantilever characteristics. The controller also includes an input multiplexer and adder used in calibration protocols. Filter coefficients and multiplexer settings can be set and adjusted by control software while an experiment is running. The input is sampled at 64 MHz; the sampling frequency in the filters can be divided down under software control to achieve a good match with filter characteristics. Data reported here were sampled at 500 kHz, chosen for acoustic cantilevers with resonant frequencies near 8 kHz. Inputs are digitized with 12 bit resolution, and outputs are digitized with 14 bits. The experiment software is organized as a client and server to make it easy to adapt the controller to different experiments. The server encapsulates the details of controller hardware organization, connection technology, filter architecture, and number representation. The same server could be used in any experiment, while a different client encodes the particulars of each experiment. PMID:19123567

  7. 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

  8. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  9. Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator

    PubMed Central

    Lopes, Pedro E. M.; Lamoureux, Guillaume; Roux, Benoit; MacKerell, Alexander D.

    2008-01-01

    The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene. Parameters were optimized for benzene and then transferred directly to toluene, with parameters for the methyl moiety of toluene taken from the previously published work on the alkanes. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters. The absolute values of the Lennard-Jones parameters were determined by comparing computed and experimental heats of vaporization, molecular volumes, free energies of hydration and dielectric constants. The newly developed parameter set was extensively tested against additional experimental data such as vibrational spectra in the condensed phase, diffusion constants, heat capacities at constant pressure and isothermal compressibilities including data as a function of temperature. Moreover, the structure of liquid benzene, liquid toluene and of solutions of each in water were studied. In the case of benzene, the computed and experimental total distribution function were compared, with the developed model shown to be in excellent agreement with experiment. PMID:17388420

  10. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization

    NASA Astrophysics Data System (ADS)

    Mazack, Michael J. M.; Gao, Jiali

    2014-05-01

    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.

  11. Computational simulation of blood flow in human systemic circulation incorporating an external force field.

    PubMed

    Sheng, C; Sarwal, S N; Watts, K C; Marble, A E

    1995-01-01

    A quasi-one-dimensional non-linear mathematical model for the computation of the blood flow in the human systemic circulation is constructed. The morphology and physical modelling of the whole system (arteries, capillaries and veins) are completed by different methods for the different vessel generations. A hybrid method is used to solve the problem numerically, based on the governing equation (continuity, momentum and state equations), the input boundary conditions and the predetermined initial conditions. The two-step Lax-Wendroff finite-difference method is used to compute variables for each individual vessel, and the characteristic method is employed for the computation of internal boundary conditions of the vessel connection and the input and output system boundary conditions. Using this approach, blood flow, transmural pressure and blood velocity are computed at all vessel sites and for each time step. The pressure and flow waveforms obtained show reasonable agreement with clinical data and results reported in the literature. When an external conservative force field is applied to the system, the results computed from the model are intuitively correct. The term representing the external pressure added to the system by the muscle, which represents active control on the cardiovascular system, is also embodied in this model. PMID:7616787

  12. 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.

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

    PubMed

    Ramakrishnan, Raghunathan; Rauhut, Guntram

    2015-04-21

    Semi-quartic force fields (QFF) rely on a Taylor-expansion of the multi-dimensional Born-Oppenheimer potential energy surface (PES) and are frequently used within the calculation of anharmonic vibrational frequencies based on 2nd order vibrational perturbation theory (VPT2). As such they are usually determined by differentiation of the electronic energy with respect to the nuclear coordinates. Alternatively, potential energy surfaces can be expanded in terms of multi-mode expansions, which typically do not require any derivative techniques. The computational effort to retrieve QFF from size-reduced multi-mode expansions has been studied and has been compared with standard Taylor-expansions. As multi-mode expansions allow for the convenient introduction of subtle approximations, these will be discussed in some detail. In addition, a preliminary study about the applicability of a generalized Duschinsky transformation to QFFs is provided. This transformation allows for the efficient evaluation of VPT2 frequencies of isotopologues from the PES of the parent compound and thus avoids the recalculation of PESs in different axes systems. PMID:25903877

  14. Density functional theory calculations of the molecular force field of L-ascorbic acid, vitamin C.

    PubMed

    Bichara, Laura C; Lanús, Hernán E; Nieto, Carlos G; Brandán, Silvia A

    2010-04-15

    We have studied L-ascorbic acid and characterized it by infrared spectroscopy in solid and aqueous solution phases. The density functional theory (DFT) method together with Pople's basis set show that three stable molecules for the compound have been theoretically determined in the gas phase, and that an average of only two more stable conformations are present in the solid phase, as it was experimentally observed. The harmonic vibrational wavenumbers for the optimized geometries of both structures were calculated at B3LYP/6-31G*and B3LYP/6-311++G** levels at the proximity of the isolated molecule. For a complete assignment of the vibrational spectra in the compound solid and aqueous solution phases, DFT calculations were combined with Pulay's scaled quantum mechanics force field methodology in order to fit the theoretical wavenumber values to the experimental ones. In this way, a complete assignment of all the observed bands in the infrared spectrum for l-ascorbic acid was performed. The natural bond orbital study reveals the characteristics of the electronic delocalization of the three structures while the corresponding topological properties of electronic charge density are analyzed by employing Bader's atoms-in-molecules theory. PMID:20297843

  15. Reactive Force Field for Proton Diffusion in BaZrO3

    E-print Network

    Raiteri, Paolo; Bussi, Giovanni

    2011-01-01

    A new reactive force field to describe proton diffusion within the solid-oxide fuel cell material BaZrO3 has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO3 have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 e...

  16. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

    PubMed Central

    Xiang, Jin Yu; Ponder, Jay W.

    2014-01-01

    An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies. PMID:25045338

  17. 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

  18. 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. © 2015 Wiley Periodicals, Inc. PMID:25706623

  19. Magnetic Field-Assisted Piezoelectric Force Microscopy Investigation of PbTiO$_{3}$–TbDyFe Bilayered Nanocomposites

    Microsoft Academic Search

    Amin Yourdkhani; Ezra Garza; Luis Zaldivar; Leonard Spinu; Gabriel Caruntu

    2011-01-01

    The magnetoelectric coupling in a bilayered composite consisting of a polycrystalline PbTiO and an amorphous TbDyFe layer was investigated by magnetic field-assisted piezoelectric force microscopy. Both the phase and the amplitude components of the piezoelectric signal undergo substantial changes upon applying an in-plane magnetic field, demonstrating the existence of a magnetoelectric coupling between the magnetic and electrostrictive layers. Consequently, the

  20. A CRITICAL ASSESSMENT OF NONLINEAR FORCE-FREE FIELD MODELING OF THE SOLAR CORONA FOR ACTIVE REGION 10953

    SciTech Connect

    DeRosa, Marc L.; Schrijver, Carolus J.; Aschwanden, Markus J.; Cheung, Mark C. M. [Lockheed Martin Solar and Astrophysics Laboratory, 3251 Hanover St. B/252, Palo Alto, CA 94304 (United States); Barnes, Graham; Leka, K. D. [North West Research Associates, Colorado Research Associates Division, 3380 Mitchell Ln., Boulder, CO 80301 (United States); Lites, Bruce W. [High Altitude Observatory, National Center for Atmospheric Research , P.O. Box 3000, Boulder, CO 80307 (United States); Amari, Tahar; Canou, Aurelien [CNRS, Centre de Physique Theorique de l'Ecole Polytechnique, 91128 Palaiseau Cedex (France); McTiernan, James M. [Space Sciences Laboratory, University of California at Berkeley, 7 Gauss Way, Berkeley, CA 94720 (United States); Regnier, Stephane [Mathematics Institute, University of St Andrews, St Andrews, Fife KY16 9SS (United Kingdom); Thalmann, Julia K.; Wiegelmann, Thomas; Inhester, Bernd; Tadesse, Tilaye [Max-Planck-Institut fuer Sonnensystemforschung, Max-Planck-Strasse 2, 37191 Katlenburg-Lindau (Germany); Valori, Gherardo [Astrophysikalisches Institut Potsdam, An der Sternwarte 16, 14482 Potsdam (Germany); Wheatland, Michael S. [School of Physics, University of Sydney, Sydney, NSW 2006 (Australia); Conlon, Paul A. [Astrophysics Research Group, School of Physics, Trinity College Dublin, Dublin 2 (Ireland); Fuhrmann, Marcel [Institut fuer Physik, Universitaet Potsdam, Am Neuen Palais 10, 14469 Potsdam (Germany)

    2009-05-10

    Nonlinear force-free field (NLFFF) models are thought to be viable tools for investigating the structure, dynamics, and evolution of the coronae of solar active regions. In a series of NLFFF modeling studies, we have found that NLFFF models are successful in application to analytic test cases, and relatively successful when applied to numerically constructed Sun-like test cases, but they are less successful in application to real solar data. Different NLFFF models have been found to have markedly different field line configurations and to provide widely varying estimates of the magnetic free energy in the coronal volume, when applied to solar data. NLFFF models require consistent, force-free vector magnetic boundary data. However, vector magnetogram observations sampling the photosphere, which is dynamic and contains significant Lorentz and buoyancy forces, do not satisfy this requirement, thus creating several major problems for force-free coronal modeling efforts. In this paper, we discuss NLFFF modeling of NOAA Active Region 10953 using Hinode/SOT-SP, Hinode/XRT, STEREO/SECCHI-EUVI, and SOHO/MDI observations, and in the process illustrate three such issues we judge to be critical to the success of NLFFF modeling: (1) vector magnetic field data covering larger areas are needed so that more electric currents associated with the full active regions of interest are measured, (2) the modeling algorithms need a way to accommodate the various uncertainties in the boundary data, and (3) a more realistic physical model is needed to approximate the photosphere-to-corona interface in order to better transform the forced photospheric magnetograms into adequate approximations of nearly force-free fields at the base of the corona. We make recommendations for future modeling efforts to overcome these as yet unsolved problems.

  1. The ultrasonic/shear-force microscope: Integrating ultrasonic sensing into a near-field scanning optical microscope

    E-print Network

    La Rosa, Andres H.

    The ultrasonic/shear-force microscope: Integrating ultrasonic sensing into a near-field scanning 2005; published online 15 September 2005 An ultrasonic transducer is incorporated into a near adsorbed to a sample's surface. Working under typical NSOM operation conditions, the ultrasonic transducer

  2. Vibrational Information Extracted from Inertial Defects: The Complete General Valence Force Field for 1,1-Difluoroethene

    Microsoft Academic Search

    Dines Christen

    1998-01-01

    The method of extracting harmonic information from inertial defect differences has been used to obtain sufficient information for a determination of the complete force field for 1,1-difluoroethylene. The presumption that inertial defect differences for non-totally-symmetric vibrations of orthorhombic molecules contain purely harmonic information (1992. D. Christen,J. Mol. Spectrosc.151,1–11) must be revoked, however.

  3. 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.

  4. Molecular force fields for aqueous electrolytes: SPC/E-compatible charged LJ sphere models and their limitations.

    PubMed

    Mou?ka, Filip; Nezbeda, Ivo; Smith, William R

    2013-04-21

    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. Mouc?ka, M. Li?sal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)]. 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. PMID:23614407

  5. 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

  6. Measurement of the effects of the localized field of a magnetic force microscope tip on a 180° domain wall

    Microsoft Academic Search

    Sheryl Foss; E. Dan Dahlberg; Roger Proksch; Bruce M. Moskowitz

    1997-01-01

    Opposite polarity magnetic force microscope (MFM) profiles of domain walls (DWs) in magnetite were measured with a commercial MFM tip magnetized in opposite directions perpendicular to the sample surface. The influence of the tip field on a DW resulted in an overall more attractive interaction. The difference between opposite polarity DW profiles provided a qualitative measurement of the reversible changes

  7. 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

  8. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ?/? Force Field Reparametrizations.

    PubMed

    Mlýnský, Vojt?ch; Kührová, Petra; Zgarbová, Marie; Jure?ka, Petr; Walter, Nils G; Otyepka, Michal; Šponer, Ji?í; Banáš, Pavel

    2015-03-19

    X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme's active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozyme's active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used. Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of ?/? torsions significantly improves the description of the hairpin ribozyme's scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH contributes to the conformational behavior observed for the scissile phosphate in the presence of a deprotonated G8(-). On the basis of the new force field, we obtain a reactive conformation for the hairpin ribozyme active site that is consistent with the most recent mechanistic and structural data. PMID:25692537

  9. Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene.

    PubMed

    Abramyan, Tigran M; Snyder, James A; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

    2015-01-01

    Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG-X-GTGT host-guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5?kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard-Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid-liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122

  10. 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.

  11. EFFI: a code for calculating the electromagnetic field, force, and inductance in coil systems of arbitrary geometry. User's manual

    Microsoft Academic Search

    1977-01-01

    EFFI calculates magnetic flux lines, fields, forces, and inductance for an arbitrary system of coils made from circular arc and\\/or straight segments of rectangular cross section conductor. The preparation of input to the code and the output options available are described. Several examples, including the magnet design for MFTF and a divertor design for a Tokamak are used for illustration.

  12. High-field magnetic force microscopy as susceptibility imaging Casey Israel, Weida Wu, and Alex de Lozannea

    E-print Network

    Wu, Weida

    High-field magnetic force microscopy as susceptibility imaging Casey Israel, Weida Wu, and Alex de into a superconducting mag- net in a liquid He dewar.17 The tip on the MFM cantilever was sputter coated with Co85Cr15

  13. Prominence sheets supported by constant-current force-free fields. II - Imposition of normal photospheric field component and prominence surface current

    NASA Astrophysics Data System (ADS)

    Ridgway, C.; Priest, E. R.; Amari, T.

    1992-02-01

    Attention is given to a method of constructing longitudinally invariant magnetic field configurations in which a symmetric finite vertical current sheet is in magnetohydrostatic equilibrium between the combined forces exerted by a background constant-current force-free field and a uniform gravitational field. Both the normal magnetic field component along the photosphere and the current density along the prominence sheet are imposed as functions of position. The method is used to generate both N- and I-type configurations by selecting a convenient form for the imposed functions. Consideration is given to the evolution of these configurations as the strength of the current (and hence the mass) is increased while all other parameters are held fixed. It is shown that in general the sheet loses equilibrium near its upper extremity as I is increased beyond a certain value.

  14. Ionic velocities in an ionic liquid under high electric fields using all-atom and coarse-grained force field molecular dynamics

    Microsoft Academic Search

    John W. Daily; Michael M. Micci

    2009-01-01

    Molecular dynamics has been used to estimate ionic velocities and electrical conductivity in the ionic liquid 1-ethyl-3-methylimidazolium\\/tetraflouroborate (EMIM-BF4). Both an all-atom and coarse grained force fields were explored. The simulations were carried out at high electric fields where one might expect the Wien effect to become important in conventional electrolytes and that effect is observed. While the original Wilson theory

  15. Data validation summary report 300-FF-5 round 5 groundwater

    SciTech Connect

    Hulstrom, L.C.

    1993-07-15

    Laboratory data for Fifth Round Groundwater samples collected during the 300-FF-5 Operable Unit Remedial Investigation have been reviewed and validated to ensure that they are of sufficient quality to support decisions regarding further actions to be taken at the 300-FF-5 Operable Unit. Table 1-1 is a summary of the validated samples. This report summarizes the results previously presented to Westinghouse Hanford in a series of Preliminary Quality Assurance Reports (PQAR) for the 300-FF-5 Fifth Round Groundwater samples. In some instances, the data qualifiers originally presented in the PQARs have been changed based upon further review of the data; these changes are highlighted in the text.

  16. Polyhedra Formation and Transient Cone Ejection of a Resonant Microdrop Forced by an ac Electric Field

    E-print Network

    Chang, Hsueh-Chia

    Polyhedra Formation and Transient Cone Ejection of a Resonant Microdrop Forced by an ac Electric of the diffuse layer. The selected polyhedra possess symmetries that ensure a global force balance of the Maxwell and frequencies, specific spherical har- monics are shown to evolve into specific polyhedra at comparatively low

  17. Nonlinear force-free magnetic field extrapolations: comparison of the Grad-Rubin and Wheatland-Sturrock-Roumeliotis algorithm

    E-print Network

    B. Inhester; T. Wiegelmann

    2008-01-23

    We compare the performance of two alternative algorithms which aim to construct a force-free magnetic field given suitable boundary conditions. For this comparison, we have implemented both algorithms on the same finite element grid which uses Whitney forms to describe the fields within the grid cells. The additional use of conjugate gradient and multigrid iterations result in quite effective codes. The Grad-Rubin and Wheatland-Sturrock-Roumeliotis algorithms both perform well for the reconstruction of a known analytic force-free field. For more arbitrary boundary conditions the Wheatland-Sturrock-Roumeliotis approach has some difficulties because it requires overdetermined boundary information which may include inconsistencies. The Grad-Rubin code on the other hand loses convergence for strong current densities. For the example we have investigated, however, the maximum possible current density seems to be not far from the limit beyond which a force free field cannot exist anymore for a given normal magnetic field intensity on the boundary.

  18. Shock initiated thermal and chemical responses of HMX crystal from ReaxFF molecular dynamics simulation.

    PubMed

    Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei

    2014-07-21

    To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. ?-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions. PMID:24899535

  19. Modelling the interaction of several bisphosphonates with hydroxyapatite using the generalised AMBER force field

    NASA Astrophysics Data System (ADS)

    Robinson, Janine; Cukrowski, Ignacy; Marques, Helder M.

    2006-12-01

    The ability of the Generalised AMBER Force Field (GAFF) of Kollman and co-workers to model the structures of bisphosphonate ligands, C(R 1)(R 2)(PO 32-) 2, important compounds in the treatment of bone cancer, by molecular mechanics methods is evaluated. The structure of 50 bisphosphonates and nine bisphosphonate esters were predicted and compared to their crystal structures. Partial charges were assigned from a RHF/6-31G ? single point calculation at the geometry of the crystal structure. Additional parameters required for GAFF were determined using the methods of the force field's developers. The structures were found to be well replicated with virtually all bond lengths reproduced to within 0.015 Å, or within 1.2 ? of the crystallographic mean. Bond angles were reproduced to within 1.9° (0.8 ?). The observed gauche or anti conformation of the molecules was reproduced, although in several instances gauche conformations observed in the solid state energy-minimised into anti conformations, and vice versa. The interaction of MDP (R 1 = R 2 = H), HEDP (R 1 = OH, R 2 = CH 3), APD (R 1 = OH, R 2 = (CH 2) 2NH 3+), alendronate (R 1 = OH, R 2 = (CH 2) 3NH 3+) and neridronate (R 1 = OH, R 2 = (CH 2) 5NH 3+) with the (001), (010) and (100) faces of hydroxyapaptite was examined by energy-minimising 20 random orientations of each ligand 20 Å from the mineral (where there is no interaction), and then at about 8 Å from the surface whereupon the ligand relaxes onto the surface. The difference in energy between the two systems is the interaction energy. In all cases interaction with hydroxyapatite caused a decrease in energy. When modelled with a dielectric constant of 78 ?o, non-bonded interactions dominate; electrostatic interactions become important when the dielectric constant is <10 ?o. Irrespective of the value of the dielectric constant used, the structure of the ligands on the hydroxyapatite surface is very similar. On the (001) face, both phosphonate groups interact near a surface Ca 2+ ion. The magnitude of the exothermic interaction energy varies with molecular volume (MDP

  20. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    SciTech Connect

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France)] [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)] [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.