WorldWideScience

Sample records for systematic force field

  1. Systematic Parameterization of Lignin for the CHARMM Force Field

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-07-06

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

  2. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

    Energy Technology Data Exchange (ETDEWEB)

    Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)

    2010-09-15

    We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

  3. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

    International Nuclear Information System (INIS)

    Wang Zunjing; Deserno, Markus

    2010-01-01

    We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

  4. The Martini Coarse-Grained Force Field

    NARCIS (Netherlands)

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

    2013-01-01

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

  5. Forces in electromagnetic field and gravitational field

    OpenAIRE

    Weng, Zihua

    2008-01-01

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

  6. Consistent force fields for saccharides

    DEFF Research Database (Denmark)

    Rasmussen, Kjeld

    1999-01-01

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

  7. Deriving force field parameters for coordination complexes

    DEFF Research Database (Denmark)

    Norrby, Per-Ola; Brandt, Peter

    2001-01-01

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

  8. Nuclear Forces from Effective Field Theory

    International Nuclear Information System (INIS)

    Krebs, H.

    2011-01-01

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

  9. Ehrenfest force in inhomogeneous magnetic field

    International Nuclear Information System (INIS)

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

    2000-01-01

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

  10. Near field plasmon and force microscopy

    NARCIS (Netherlands)

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

    1995-01-01

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

  11. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-08-19

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

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

    NARCIS (Netherlands)

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

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

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  14. Transition States from Empirical Force Fields

    DEFF Research Database (Denmark)

    Jensen, Frank; Norrby, Per-Ola

    2003-01-01

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

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

    Science.gov (United States)

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

    2012-02-14

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

  16. Near field plasmon and force microscopy

    OpenAIRE

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

    1995-01-01

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

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

    African Journals Online (AJOL)

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

  18. Induced forces in the gravitational field

    International Nuclear Information System (INIS)

    Voracek, P.

    1979-01-01

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

  19. Martini Force Field Parameters for Glycolipids

    NARCIS (Netherlands)

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

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

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

    Directory of Open Access Journals (Sweden)

    Valentina Squeri

    2010-06-01

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

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

    Science.gov (United States)

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

    2018-03-01

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

  2. Controlling Casimir force via coherent driving field

    Science.gov (United States)

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

    2016-04-01

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

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

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2010-01-01

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

  4. Solitons in a random force field

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  5. Charm production and the confining force field

    International Nuclear Information System (INIS)

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

    1983-03-01

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

  6. Harmonic force field for nitro compounds.

    Science.gov (United States)

    Bellido, Edson P; Seminario, Jorge M

    2012-06-01

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

  7. Sultan - forced flow, high field test facility

    International Nuclear Information System (INIS)

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

    1981-01-01

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

  8. Building machine learning force fields for nanoclusters

    Science.gov (United States)

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

    2018-06-01

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

  9. A Systematic Method to Analyze Force Majeure in Construction Claims

    Directory of Open Access Journals (Sweden)

    Saud Alshammari

    2017-12-01

    Full Text Available In construction delay claims, force majeure is normally recognized as an excusable risk that entitles contractors only to time extensions, but neither of the contracting parties is entitled to monetary compensation to recover delay damages. However, there are instances where contractors are entitled to both time and cost compensations, as evidenced by some court cases relating to force majeure claims. Such instances involve attributing the occurrence of the force majeure to the effect of other prior delay events that pushed project performance into the period of the force majeure. Existing delay analysis methods are not capable of addressing this issue, as none take the impact of other delays into consideration when analyzing force majeure claims. Stimulated by this gap, this study proposes an improved and sound method for fairly analyzing the responsibility of force majeure delay claims amongst contracting parties. This method was implemented on a case project to help demonstrate its application and also ascertain its practicability. The contribution of this paper is twofold. First, it has highlighted the situation of force majeure delay that can be compensable, creating more awareness among researchers and industry practitioners. The second is a proposed systematic process to appropriately analyze its responsibility, which equitably addresses claims from such delays with little or no chance of dispute ensuing.

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

    Directory of Open Access Journals (Sweden)

    Kyle Quynn Hoffmann

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

  11. Force field refinement from NMR scalar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Huang Jing [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland); Meuwly, Markus, E-mail: m.meuwly@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

    2012-03-02

    Graphical abstract: We show that two classes of H-bonds are sufficient to quantitatively describe scalar NMR coupling constants in small proteins. Highlights: Black-Right-Pointing-Pointer We present force field refinements based on explicit MD simulations using scalar couplings across hydrogen bonds. Black-Right-Pointing-Pointer This leads to {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.03 Hz at best compared to experiment. Black-Right-Pointing-Pointer A classification of H-bonds according to secondary structure is not sufficiently robust. Black-Right-Pointing-Pointer Grouping H-bonds into two classes and reparametrization yields an RMSD of 0.07 Hz. Black-Right-Pointing-Pointer This is an improvement of 50. - Abstract: NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.

  12. Understrength Air Force Officer Career Fields. A Force Management Approach

    Science.gov (United States)

    2005-01-01

    LtCol John Crown (DPSA). In addition, we had very helpful interviews with Mr. Vaughan Blackstone (DPAPP) and Mr. Dennis Miller (DPPAO). Also at...problems in managing personnel assignments. First, there is a high " tax " for special-duty jobs that requires them to place personnel officers into...targeted year-groups populated above the ideal force- structure line (called TOPLINE), in the run up to the RIF of 1992, the desire to avoid or

  13. Massive fields as systematics for single field inflation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Hongliang; Wang, Yi, E-mail: hjiangag@connect.ust.hk, E-mail: phyw@ust.hk [Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong (China)

    2017-06-01

    During inflation, massive fields can contribute to the power spectrum of curvature perturbation via a dimension-5 operator. This contribution can be considered as a bias for the program of using n {sub s} and r to select inflation models. Even the dimension-5 operator is suppressed by Λ = M {sub p} , there is still a significant shift on the n {sub s} - r diagram if the massive fields have m ∼ H . On the other hand, if the heavy degree of freedom appears only at the same energy scale as the suppression scale of the dimension-5 operator, then significant shift on the n {sub s} - r diagram takes place at m =Λ ∼ 70 H , which is around the inflationary time-translation symmetry breaking scale. Hence, the systematics from massive fields pose a greater challenge for future high precision experiments for inflationary model selection. This result can be thought of as the impact of UV sensitivity to inflationary observables.

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

    Science.gov (United States)

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

    2018-04-10

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

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

    Science.gov (United States)

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

    2018-04-01

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  17. A systematic study of the octupole correlations in the lanthanides with realistic forces

    International Nuclear Information System (INIS)

    Egido, J.L.; Robledo, L.M.

    1992-01-01

    We have performed a systematic study of the octupole degree of freedom in the nuclei 140 Ba, 142-150 deg Ce, 144-152 Nd and 146-154 Sm. The static properties (ground state deformations, energy gaps, dipole moments, etc.) have been analyzed within the Hartree-Fock plus BCS approximation (HFBCS); for the dynamical ones (energy splittings, transition probabilities, etc.) the adiabatic time-dependent Hartree-Fock plus zero point energy in the cranking approximation (ATDHF+ZPE) has been applied. In both approximations the realistic density-dependent Gogny force has been used. In our parameter-free calculations we are able to describe very well the whole experimental systematic of energy splittings and B(E1), among others. The flatness of the whole experimental systematic of energy splittings and B(E1), among others. The flatness of the potential energy of some nuclei makes the mean field approach unreliable for such nuclei. (orig.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Krause, J [Universidad Central de Venezuela, Caracas

    1976-02-01

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

  19. Higgs effective field theories. Systematics and applications

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Claudius G.

    2016-07-28

    Researchers of the Large Hadron Collider (LHC) at the European Organization for Nuclear Research (CERN) announced on July 4th, 2012, the observation of a new particle. The properties of the particle agree, within the relatively large experimental uncertainties, with the properties of the long-sought Higgs boson. Particle physicists around the globe are now wondering, ''Is it the Standard Model Higgs that we observe; or is it another particle with similar properties?'' We employ effective field theories (EFTs) for a general, model-independent description of the particle. We use a few, minimal assumptions - Standard Model (SM) particle content and a separation of scales to the new physics - which are supported by current experimental results. By construction, effective field theories describe a physical system only at a certain energy scale, in our case at the electroweak-scale v. Effects of new physics from a higher energy-scale, Λ, are described by modified interactions of the light particles. In this thesis, ''Higgs Effective Field Theories - Systematics and Applications'', we discuss effective field theories for the Higgs particle, which is not necessarily the Higgs of the Standard Model. In particular, we focus on a systematic and consistent expansion of the EFT. The systematics depends on the dynamics of the new physics. We distinguish two different consistent expansions. EFTs that describe decoupling new-physics effects and EFTs that describe non-decoupling new-physics effects. We briefly discuss the first case, the SM-EFT. The focus of this thesis, however, is on the non-decoupling EFTs. We argue that the loop expansion is the consistent expansion in the second case. We introduce the concept of chiral dimensions, equivalent to the loop expansion. Using the chiral dimensions, we expand the electroweak chiral Lagrangian up to next-to-leading order, O(f{sup 2}/Λ{sup 2})=O(1/16π{sup 2}). Further, we discuss how different

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

    Science.gov (United States)

    Piquemal, Jean-Philip; Jordan, Kenneth D.

    2017-10-01

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

  1. Approximate photochemical dynamics of azobenzene with reactive force fields

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-04-01

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

  3. The interoperability force in the ERP field

    Science.gov (United States)

    Boza, Andrés; Cuenca, Llanos; Poler, Raúl; Michaelides, Zenon

    2015-04-01

    Enterprise resource planning (ERP) systems participate in interoperability projects and this participation sometimes leads to new proposals for the ERP field. The aim of this paper is to identify the role that interoperability plays in the evolution of ERP systems. To go about this, ERP systems have been first identified within interoperability frameworks. Second, the initiatives in the ERP field driven by interoperability requirements have been identified from two perspectives: technological and business. The ERP field is evolving from classical ERP as information system integrators to a new generation of fully interoperable ERP. Interoperability is changing the way of running business, and ERP systems are changing to adapt to the current stream of interoperability.

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

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

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

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

    Science.gov (United States)

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

    2011-01-01

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

  6. Systematic reviews in the field of nutrition

    Science.gov (United States)

    Systematic reviews are valuable tools for staying abreast of evolving nutrition and aging -related topics, formulating dietary guidelines, establishing nutrient reference intakes, formulating clinical practice guidance, evaluating health claims, and setting research agendas. Basic steps of conductin...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    1986-01-01

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

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

    Science.gov (United States)

    Kohoutek, John Michael

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

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

    International Nuclear Information System (INIS)

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

    1976-01-01

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

  11. Force-free field model of ball lightning

    International Nuclear Information System (INIS)

    Tsui, K.H.

    2001-01-01

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

  12. Systematics of higher-spin gauge fields

    International Nuclear Information System (INIS)

    de Wit, B.; Freedman, D.Z.

    1980-01-01

    Free-field theories for symmetric tensor and tensor-spinor gauge fields have recently been obtained which describe massless particles of arbitrary integer or half-integer spin. An independent discussion of these field theories is given here, based on a hierarchy of generalized Christoffel symbols with simple gauge transformation properties. The necessity of certain constraints on gauge fields and parameters is easily seen. Wave equations and Lagrangians are expressed in terms of the Christoffel symbols, and the independent modes of the system are counted in covariant gauges. Minimal-coupling inconsistency and a combined system of higher-spin boson gauge fields interacting with relativistic particles is discussed

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

    Science.gov (United States)

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

    2014-09-16

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

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

    International Nuclear Information System (INIS)

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

    1981-04-01

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

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

    Science.gov (United States)

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

    2013-12-15

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

  16. A Systematic Method to Analyze Force Majeure in Construction Claims

    OpenAIRE

    Saud Alshammari; Khalid Al-Gahtani; Ibrahim Alhammad; Nuhu Braimah

    2017-01-01

    In construction delay claims, force majeure is normally recognized as an excusable risk that entitles contractors only to time extensions, but neither of the contracting parties is entitled to monetary compensation to recover delay damages. However, there are instances where contractors are entitled to both time and cost compensations, as evidenced by some court cases relating to force majeure claims. Such instances involve attributing the occurrence of the force majeure to the effect of othe...

  17. Energy buildup in sheared force-free magnetic fields

    Science.gov (United States)

    Wolfson, Richard; Low, Boon C.

    1992-01-01

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

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

    International Nuclear Information System (INIS)

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

    1977-01-01

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

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

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  1. Various aspects of magnetic field influence on forced convection

    Directory of Open Access Journals (Sweden)

    Pleskacz Lukasz

    2016-01-01

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

  2. Fano resonance of the ultrasensitve optical force excited by Gaussian evanescent field

    International Nuclear Information System (INIS)

    Yang, Yang; Li, Jiafang; Li, Zhi-Yuan

    2015-01-01

    In this paper, we study the angle-dependent Fano-like optical force spectra of plasmonic Ag nanoparticles, which exhibit extraordinary transformation from Lorentzian resonance to Fano resonance when excited by a Gaussian evanescent wave. We systematically analyze the behavior of this asymmetric scattering induced optical force under different conditions and find that this Fano interference-induced force is ultrasensitive to the excitation wavelength, incident angle and particle size, as well as the core–shell configuration, which could be useful for wavelength- and angle-dependent size-selective optical manipulation. The origin of this Fano resonance is further identified as the interference between the two adjacent-order multipolar plasmonic modes excited in the Ag particle under the excitation of an inhomogeneously distributed evanescent field. (paper)

  3. The growth of the concept of forces and fields

    International Nuclear Information System (INIS)

    Mukherji, Visvapriya

    1979-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    Leib, Raz; Karniel, Amir; Nisky, Ilana

    2015-05-01

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

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

    Science.gov (United States)

    Mangalam, A.; Prasad, A.

    2018-01-01

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

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

    Science.gov (United States)

    Geng, Yanan; Wu, Weida

    2014-05-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  9. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  10. Tuning the Mass of Chameleon Fields in Casimir Force Experiments

    CERN Document Server

    Brax, Ph; Davis, A C; Shaw, D J; Iannuzzi, D

    2010-01-01

    We have calculated the chameleon pressure between two parallel plates in the presence of an intervening medium that affects the mass of the chameleon field. As intuitively expected, the gas in the gap weakens the chameleon interaction mechanism with a screening effect that increases with the plate separation and with the density of the intervening medium. This phenomenon might open up new directions in the search of chameleon particles with future long range Casimir force experiments.

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

    Science.gov (United States)

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

    2013-08-07

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

  12. Application of Enlisted Force Retention Levels and Career Field Stability

    Science.gov (United States)

    2017-03-23

    APPLICATION OF ENLISTED FORCE RETENTION LEVELS AND CAREER FIELD STABILITY THESIS Presented to the Faculty Department of Operational Sciences ...Fulfillment of the Requirements for the Degree of Master of Science in Operations Research Jamie T. Zimmermann, MS, BS Captain, USAF March 2017...Appendix B. The function proc lifetest is a nonparametric estimate of the survivor function using either the Kaplan-Meier method or the actuarial

  13. Implications of confining force field structures in hard hadronic processes

    International Nuclear Information System (INIS)

    Bengtsson, H.-U.

    1983-04-01

    This thesis is centered on the study of confining force field structures in hard scattering processes. Perturbative QCD provides the means of calculating any process on the parton level, but to be able accurately to describe the actual outcome of an event, one still needs a phenomenological model for how quarks and gluons transform into observable hadrons. One such model is based on the assumption that the particles are produced by the confining fields stretched between the partons. The actual particle distributions will then depend on the topology of the confining fields. We have developed a Monte Carlo program to simulate complete events in hard scattering, and we use this to study the properties of the confining field in different trigger situations. We further look at the amount of hard processes that can be expected in experiments that trigger on transverse energy sum (calorimeter experiments). Finally, we investigate charm production within our model. (author)

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

    Science.gov (United States)

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

    2016-07-28

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

  15. Field Science Ethnography: Methods For Systematic Observation on an Expedition

    Science.gov (United States)

    Clancey, William J.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    The Haughton-Mars expedition is a multidisciplinary project, exploring an impact crater in an extreme environment to determine how people might live and work on Mars. The expedition seeks to understand and field test Mars facilities, crew roles, operations, and computer tools. I combine an ethnographic approach to establish a baseline understanding of how scientists prefer to live and work when relatively unemcumbered, with a participatory design approach of experimenting with procedures and tools in the context of use. This paper focuses on field methods for systematically recording and analyzing the expedition's activities. Systematic photography and time-lapse video are combined with concept mapping to organize and present information. This hybrid approach is generally applicable to the study of modern field expeditions having a dozen or more multidisciplinary participants, spread over a large terrain during multiple field seasons.

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

    NARCIS (Netherlands)

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

    1990-01-01

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

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

    Science.gov (United States)

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

    2018-05-01

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

  18. Rigorous force field optimization principles based on statistical distance minimization

    Energy Technology Data Exchange (ETDEWEB)

    Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)

    2015-10-14

    We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.

  19. Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field

    DEFF Research Database (Denmark)

    Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena

    2013-01-01

    The phase behavior of the coarse-grained MARTINI model for three-component lipid bilayers composed of dipalmytoyl-phosphatidylcholine (DPPC), cholesterol (Chol), and an unsaturated phosphatidylcholine (PC) was systematically investigated by molecular dynamics simulations. The aim of this study...... is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field...... PCs, such as dilinoleyl-phosphatidylcholine (DUPC) and diarachidonoyl-phosphatidylcholine (DAPC). Through systematic tweaking of the interactions between the hydrophobic groups of the PC molecules, we show that the appearance of phase separation in three-component lipid bilayers, as modeled through...

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

    Science.gov (United States)

    Pound, Adam

    2012-10-01

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

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

    Science.gov (United States)

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

    2013-09-27

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

  2. On the use of quartic force fields in variational calculations

    Science.gov (United States)

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

    2013-06-01

    Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine (-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods.

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

    International Nuclear Information System (INIS)

    Nyman, E.M.

    1979-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Chung D.-Y.

    2006-07-01

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

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

    Science.gov (United States)

    Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

    2017-08-08

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  7. A Multiposture Locomotor Training Device with Force-Field Control

    Directory of Open Access Journals (Sweden)

    Jianfeng Sui

    2014-11-01

    Full Text Available This paper introduces a multiposture locomotor training device (MPLTD with a closed-loop control scheme based on joint angle feedback, which is able to overcome various difficulties resulting from mechanical vibration and the weight of trainer to achieve higher accuracy trajectory. By introducing the force-field control scheme used in the closed-loop control, the device can obtain the active-constrained mode including the passive one. The MPLTD is mainly composed of three systems: posture adjusting and weight support system, lower limb exoskeleton system, and control system, of which the lower limb exoskeleton system mainly includes the indifferent equilibrium mechanism with two degrees of freedom (DOF and the driving torque is calculated by the Lagrangian function. In addition, a series of experiments, the weight support and the trajectory accuracy experiment, demonstrate a good performance of mechanical structure and the closed-loop control.

  8. New arrangements in force in the field of transport

    CERN Multimedia

    Tom Wegelius

    2006-01-01

    Please take note of the following information concerning new arrangements in force in the field of transport: China: Regulations applying to wooden packaging materials as of 1st January 2006 As scheduled, China introduced standard ISPM No. 15 on 1st January 2006. This was officially confirmed in a letter from the Federal Minister for Consumer Protection, Food and Agriculture. Henceforth, China will apply the same conditions to the importation of wooden packaging materials as various other countries, including the United States, Mexico and Brazil. This means that items shipped to China in wooden packaging will no longer need to be accompanied by a certificate relating to the protection of plant species or other phytosanitary documents (such as heat treatment certificates). However, a guarantee that the wooden packaging complies with standard ISPM No. 15 will be required. Phase II of US regulations concerning wooden packaging material Phase II of regulations concerning the importation of wooden packaging ma...

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

    Science.gov (United States)

    Yang, Honghua

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

  10. International Acquisitons in Multinacionals: Under a Force Field

    Directory of Open Access Journals (Sweden)

    Américo da Costa Ramos Filho

    2010-12-01

    Full Text Available The purpose of this essay is to debate the performance of multinational companies concerning the management alternatives of their foreign unities, especially the ones derived from acquisitions, with consequences on the interaction between the headquarters and its subsidiaries or colligates and the managerial learning and knowledge associated to this process. First the problematic of internationalized companies by foreign direct investments – FDI’s, mainly by acquisitions and strategic alliances, is discussed. The intensity of the assimilation and interchange of values and practices within organizations in interacting process is stressed, including a set of typologies derived from the existing related literature. After this, a more specific approach about intra and interorganization aspects of the multinationals is performed, related to strategies, competences and roles of headquarters and subsidiaries, as well as their impact on the knowledge flux and its derived learning modes, evolving a established typologies set. The next step is to discuss two visions about the opposition between the universal and the particular in international management, with global and contextual aspects: a convergence-divergence opposition, like a force field, impacting on the knowledge transfer. Finally, some concluding comments are made, emphasizing, for the purpose of contribution, another type of multinationals typology relating the convergence-divergence duality to the organizational and national levels, as well the positioning of the companies in the resulted matrix.

  11. Quantum mechanical force fields for condensed phase molecular simulations

    Science.gov (United States)

    Giese, Timothy J.; York, Darrin M.

    2017-09-01

    Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

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

    Directory of Open Access Journals (Sweden)

    Anne eFocke

    2013-07-01

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

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

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-31

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

  15. The Nab Spectrometer, Precision Field Mapping, and Associated Systematic Effects

    Science.gov (United States)

    Fry, Jason; Nab Collaboration

    2017-09-01

    The Nab experiment will make precision measurements of a, the e- ν correlation parameter, and b, the Fierz interference term, in neutron beta decay, aiming to deliver an independent determination of the ratio λ =GA /GV to sensitively test CKM unitarity. Nab utilizes a novel, long asymmetric spectrometer to measure the proton TOF and electron energy. We extract a from the slope of the measured TOF distribution for different electron energies. A reliable relation of the measured proton TOF to a requires detailed knowledge of the effective proton pathlength, which in turn imposes further requirements on the precision of the magnetic fields in the Nab spectrometer. The Nab spectrometer, magnetometry, and associated systematics will be discussed.

  16. Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

    Science.gov (United States)

    Motta, Mario; Zhang, Shiwei

    2018-05-01

    We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  18. The air forces on a systematic series of biplane and triplane cellule models

    Science.gov (United States)

    Munk, Max M

    1927-01-01

    The air forces on a systematic series of biplane and triplane cellule models are the subject of this report. The test consist in the determination of the lift, drag, and moment of each individual airfoil in each cellule, mostly with the same wing section. The magnitude of the gap and of the stagger is systematically varied; not, however, the decalage, which is zero throughout the tests. Certain check tests with a second wing section make the tests more complete and conclusions more convincing. The results give evidence that the present army and navy specifications for the relative lifts of biplanes are good. They furnish material for improving such specifications for the relative lifts of triplanes. A larger number of factors can now be prescribed to take care of different cases.

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

    Science.gov (United States)

    1968-03-01

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

  20. Vibrations of a molecule in an external force field.

    Science.gov (United States)

    Okabayashi, Norio; Peronio, Angelo; Paulsson, Magnus; Arai, Toyoko; Giessibl, Franz J

    2018-05-01

    The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

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

    NARCIS (Netherlands)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    NARCIS (Netherlands)

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

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-15

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

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

    International Nuclear Information System (INIS)

    Haydock, David

    2005-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-14

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

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

    International Nuclear Information System (INIS)

    G.S. Choe; C.Z. Cheng

    2002-01-01

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

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

    International Nuclear Information System (INIS)

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

    2002-01-01

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

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

    International Nuclear Information System (INIS)

    Low, B.C.; Nakagawa, Y.

    1975-01-01

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

  11. Spatial Confinement of Ultrasonic Force Fields in Microfluidic Channels

    DEFF Research Database (Denmark)

    Manneberg, O; Hagsäter, Melker; Svennebring, J

    2009-01-01

    -PIV). The confinement of the ultrasonic fields during single-or dual-segment actuation, as well as the cross-talk between two adjacent. fields, is characterized and quantified. Our results show that the field confinement typically scales with the acoustic wavelength, and that the cross-talk is insignificant between...... adjacent. fields. The goal is to define design strategies for implementing several spatially separated ultrasonic manipulation functions in series for use in advanced particle or cell handling and processing applications. One such proof-of-concept application is demonstrated, where. flow...

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

    Science.gov (United States)

    Riniker, Sereina

    2018-03-26

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

  13. A Systematic study of modular coil characteristics for 2-field periods quasi-axisymmetric stellarator QAS-LA

    International Nuclear Information System (INIS)

    Zheng, Jinxing; Song, Yuntao; Breslau, Joshua; Neilson, George Hutch

    2014-01-01

    Highlights: • Systematic studies of modular coils characteristics for quasi-axisymmetric stellarator were carried out for the key design parameters. • We systematically analyzed the relationships between design parameters of modular coils and electromagnetic properties such as the maximum field. • The approximate formulae relating modular coil parameters to the maximum magnetic field were derived by the use of simple two coil systems. - Abstract: Modular coil characteristics of a 2-field periods quasi-axisymmetric stellarator QAS-LA configuration with an aspect ratio A p = 3, magnetic pressure ∼4% and rotational transform ι ∼ 0.15 per field period supplied by its own shaping have been detailed studied. In addition, the characteristics of modular coils for QAS-LA were compared with those of an intermediate QA configuration QAS-LAx and a tokamak based on the same center magnet field B 0 , aspect ratio and number of coils. As expected, the B max /B 0 , force F and overturning moment M, increase with the increased complexity of the coil shape. The relationships between the modular coils’ parameters (such as radius curvature ρ, distance from coil to coil Δ c–c and the cross-section of coils) and the electromagnetic characteristics have been systematically summarized. The approximate formula for the maximum magnetic field in the coil body as functions of modular coil parameters (Δ c–c , ρ) was derived for a simple two wire system which will be useful when optimizations of coil properties are called for

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

    International Nuclear Information System (INIS)

    Stroscio, M.A.

    1985-01-01

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

  15. Force Characteristics Analysis for Linear Machine with DC Field Excitations

    Directory of Open Access Journals (Sweden)

    A/L Krishna Preshant

    2018-01-01

    Full Text Available In urban regions and particularly in developing countries such as Malaysia with its ever-growing transport sector, there is the need for energy efficient systems. In urban railway systems there is a requirement of frequent braking and start/stop motion, and energy is lost during these processes. To improve the issues of the conventional braking systems, particularly in Japan, they have introduced linear induction motor techniques. The drawbacks of this method, however, is the use of permanent magnets, which not only increase the weight of the entire system but also increases magnetic cogging. Hence an alternative is required which uses the same principles as Magnetic-Levitation but using a magnet-less system. Therefore, the objective of this research is to propose an electromagnetic rail brake system and to analyze the effect of replacing permanent magnets with a magnet-less braking systems to produce a significant amount of brake thrust as compared with the permanent magnet system. The modeling and performance analysis of the model is done using Finite Element Analysis (FEA. The mechanical aspects of the model are designed on Solidworks and then imported to JMAG Software to proceed with the electro-magnetic analysis of the model. There are 3 models developed: Base Model (steel, Permanent Magnet (PM Model and DC Coil Model. The performance of the proposed 2D models developed is evaluated in terms of average force produced and motor constant square density. By comparing the values for the 3 models for the same case of 9A current supplied for a 0.1mm/s moving velocity, the base model, permanent magnet model and DC coil model produced an average force of 7.78 N, 7.55 N, and 8.34 N respectively, however, with increase in DC current supplied to the DC coil model, the average force produced is increased to 13.32 N. Thus, the advantage of the DC coil (magnet-less model, is, that the force produced can be controlled by varying the number of turns in the

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

    International Nuclear Information System (INIS)

    Maeda, N.

    1988-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-14

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

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

    Science.gov (United States)

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

    2016-03-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-06-07

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

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

    Science.gov (United States)

    Best, Robert B; Hummer, Gerhard

    2009-07-02

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

  1. Association of orthodontic force system and root resorption: A systematic review.

    Science.gov (United States)

    Roscoe, Marina G; Meira, Josete B C; Cattaneo, Paolo M

    2015-05-01

    In this systematic review, we assessed the literature to determine which evidence level supports the association of orthodontic force system and root resorption. PubMed, Cochrane, and Embase databases were searched with no restrictions on year, publication status, or language. Selection criteria included human studies conducted with fixed orthodontic appliances or aligners, with at least 10 patients and the force system well described. A total of 259 articles were retrieved in the initial search. After the review process, 21 full-text articles met the inclusion criteria. Sample sizes ranged from 10 to 73 patients. Most articles were classified as having high evidence levels and low risks of bias. Although a meta-analysis was not performed, from the available literature, it seems that positive correlations exist between increased force levels and increased root resorption, as well as between increased treatment time and increased root resorption. Moreover, a pause in tooth movement seems to be beneficial in reducing root resorption because it allows the resorbed cementum to heal. The absence of a control group, selection criteria of patients, and adequate examinations before and after treatment are the most common methodology flaws. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

  2. Brownian motion in a field of force and the diffusion theory of chemical reactions. II

    NARCIS (Netherlands)

    Brinkman, H.C.

    1956-01-01

    H. A. Kramers has studied the rate of chemical reactions in view of the Brownian forces caused by a surrounding medium in temperature equilibrium. In a previous paper 3) the author gave a solution of Kramers' diffusion equation in phase space by systematic development. In this paper the general

  3. LEPS potential for H3 from force field data

    International Nuclear Information System (INIS)

    Varandas, A.J.C.

    1979-01-01

    A new potential energy surface for H 3 of the London--Eyring--Polanyi--Sato type has been obtained which reproduces the best available estimates for the geometry, classical barrier height, and quadratic force constants of the D/sub infinityh/ saddle point. Other attributes of the surface, e.g., minimum energy profile for the exchange process, spherically averaged potential V 0 , and leading anisotropic potential V 2 , are also shown to be in good agreement with the best available estimates. The simplicity of its functional form further commends it for future dynamical studies

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  6. Occupational exposure to electromagnetic fields in the Polish Armed Forces.

    Science.gov (United States)

    Sobiech, Jaromir; Kieliszek, Jarosław; Puta, Robert; Bartczak, Dagmara; Stankiewicz, Wanda

    2017-06-19

    Standard devices used by military personnel that may pose electromagnetic hazard include: radars, missile systems, radio navigation systems and radio transceivers. The aim of this study has been to evaluate the exposure of military personnel to electromagnetic fields. Occupational exposure to electromagnetic fields was analyzed in the work environment of personnel of 204 devices divided into 5 groups (surface-to-air missile system radars, aircraft and helicopters, communication devices, surveillance and height finder radars, airport radars and radio navigation systems). Measurements were carried out at indicators, device terminals, radio panels, above vehicle seats, in vehicle hatches, by cabinets containing high power vacuum tubes and other transmitter components, by transmission lines, connectors, etc. Portable radios emit the electric field strength between 20-80 V/m close to a human head. The manpack radio operator's exposure is 60-120 V/m. Inside vehicles with high frequency/very high frequency (HF/VHF) band radios, the electric field strength is between 7-30 V/m and inside the radar cabin it ranges between 9-20 V/m. Most of the personnel on ships are not exposed to the electromagnetic field from their own radar systems but rather by accidental exposure from the radar systems of other ships. Operators of surface-to-air missile systems are exposed to the electric field strength between 7-15 V/m and the personnel of non-directional radio beacons - 100-150 V/m. In 57% of military devices Polish soldiers work in the occupational protection zones. In 35% of cases, soldiers work in intermediate and hazardous zones and in 22% - only in the intermediate zone. In 43% of devices, military personnel are not exposed to electromagnetic field. Int J Occup Med Environ Health 2017;30(4):565-577. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

  7. Occupational exposure to electromagnetic fields in the Polish Armed Forces

    Directory of Open Access Journals (Sweden)

    Jarosław Kieliszek

    2017-08-01

    Full Text Available Objectives: Standard devices used by military personnel that may pose electromagnetic hazard include: radars, missile systems, radio navigation systems and radio transceivers. The aim of this study has been to evaluate the exposure of military personnel to electromagnetic fields. Material and Methods: Occupational exposure to electromagnetic fields was analyzed in the work environment of personnel of 204 devices divided into 5 groups (surface-to-air missile system radars, aircraft and helicopters, communication devices, surveillance and height finder radars, airport radars and radio navigation systems. Measurements were carried out at indicators, device terminals, radio panels, above vehicle seats, in vehicle hatches, by cabinets containing high power vacuum tubes and other transmitter components, by transmission lines, connectors, etc. Results: Portable radios emit the electric field strength between 20–80 V/m close to a human head. The manpack radio operator’s exposure is 60–120 V/m. Inside vehicles with high frequency/very high frequency (HF/VHF band radios, the electric field strength is between 7–30 V/m and inside the radar cabin it ranges between 9–20 V/m. Most of the personnel on ships are not exposed to the electromagnetic field from their own radar systems but rather by accidental exposure from the radar systems of other ships. Operators of surface-to-air missile systems are exposed to the electric field strength between 7–15 V/m and the personnel of non-directional radio beacons – 100–150 V/m. Conclusions: In 57% of military devices Polish soldiers work in the occupational protection zones. In 35% of cases, soldiers work in intermediate and hazardous zones and in 22% – only in the intermediate zone. In 43% of devices, military personnel are not exposed to electromagnetic field. Int J Occup Med Environ Health 2017;30(4:565–577

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

    Science.gov (United States)

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

    2018-02-01

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

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

    International Nuclear Information System (INIS)

    Arriola, E.R.

    2011-01-01

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

  10. Microscopic mean field approximation and beyond with the Gogny force

    Directory of Open Access Journals (Sweden)

    Péru S.

    2014-03-01

    Full Text Available Fully consistent axially-symmetric-deformed quasiparticle random phase approximation calculations have been performed with the D1S Gogny force. A brief review on the main results obtained in this approach is presented. After a reminder on the method and on the first results concerning giant resonances in deformed Mg and Si isotopes, the multipole responses up to octupole in the deformed and heavy nucleus 238U are discussed. In order to analyse soft dipole modes in exotic nuclei, the dipole responses have been studied in Ne isotopes and in N=16 isotopes, for which results are presented. In these nuclei, the QRPA results on the low lying 2+ states are compared to the 5-Dimensional Collective Hamiltonian ones.

  11. Sigma exchange in the nuclear force and effective field theory

    International Nuclear Information System (INIS)

    Donoghue, John F.

    2006-01-01

    In the phenomenological description of the nuclear interaction an important role is traditionally played by the exchange of a scalar I=0 meson, the sigma, of mass 500-600 MeV, which however is not seen clearly in the particle spectrum and which has a very ambiguous status in QCD. I show that a remarkably simple and reasonably controlled combination of ingredients can reproduce the features of this part of the nuclear force. The use of chiral perturbation theory calculations for two pion exchange supplemented by the Omnes function for pion rescattering suffices to reproduce the magnitude and shape of the exchange of a supposed σ particle. I also attempt to relate this description to the contact interaction that enters more modern descriptions of the internucleon interaction

  12. Force Structure Matters: The US Field Artillery in Operational Art

    Science.gov (United States)

    2015-05-23

    2003 (Fort Sill, OK: US Army Field Artillery Center, 2004), 62-63. 3 Sean Bateman and Steven Hady, “King of Battle Once Again: An Organizational...To What Ends Military Power?” International Security 4, no. 4 (Spring 1980): 3- 35. Bateman , Sean and Steven Hady. “King of Battle Once Again: An

  13. Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields

    DEFF Research Database (Denmark)

    Karlsen, Jonas Tobias; Augustsson, Per; Bruus, Henrik

    2016-01-01

    , the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip....

  14. Epidemiology of Substance Use among Forced Migrants: A Global Systematic Review.

    Directory of Open Access Journals (Sweden)

    Danielle Horyniak

    Full Text Available Forced migration is occurring at unprecedented levels. Forced migrants may be at risk for substance use for reasons including coping with traumatic experiences, co-morbid mental health disorders, acculturation challenges and social and economic inequality. This paper aimed to systematically review the literature examining substance use among forced migrants, and identify priority areas for intervention and future research.Seven medical, allied health and social science databases were searched from inception to September 2015 in accordance with PRISMA guidelines to identify original peer-reviewed articles describing any findings relating to alcohol and/or illicit drug use among refugees, internally displaced people (IDPs, asylum seekers, people displaced by disasters and deportees. A descriptive synthesis of evidence from quantitative studies was conducted, focusing primarily on studies which used validated measures of substance use. Synthesis of evidence from qualitative studies focused on identifying prominent themes relating to the contexts and consequences of substance use. Critical Appraisal Skills Programme (CASP checklists were used to assess methodological quality of included studies.Forty-four quantitative (82% cross-sectional, 16 qualitative and three mixed-methods studies were included. Ten studies were rated as high methodological quality (16%, 39 as moderate quality (62% and 14 as low quality (22%. The majority of research was conducted among refugees, IDPs and asylum seekers (n = 55, 87%, predominantly in high-income settings. The highest-quality prevalence estimates of hazardous/harmful alcohol use ranged from 17%-36% in camp settings and 4%-7% in community settings. Few studies collected validated measures of illicit drug use. Seven studies compared substance use among forced migrants to other migrant or native-born samples. Among eight studies which conducted multivariable analysis, male sex, trauma exposure and symptoms of

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  16. Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

    International Nuclear Information System (INIS)

    Haydock, David

    2005-01-01

    We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important

  17. Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-04-15

    We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-08-14

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

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

    Science.gov (United States)

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Xie Baisong; Yin Xintao; Luo Xia

    2006-01-01

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

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

    Science.gov (United States)

    Radosinski, Lukasz; Labus, Karolina

    2017-10-05

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

  4. Application of systematic review methodology to the field of nutrition

    Science.gov (United States)

    Systematic reviews represent a rigorous and transparent approach of synthesizing scientific evidence that minimizes bias. They evolved within the medical community to support development of clinical and public health practice guidelines, set research agendas and formulate scientific consensus state...

  5. Matter waves from localized sources in homogeneous force fields

    OpenAIRE

    Kramer, Tobias

    2010-01-01

    We derive a scattering theory in constant potentials based on the energy-dependent Green function. This approach enables us to formulate modern experiments in terms of Green function. One application discussed is the photodetachment of electrons in external electromagnetic fields. In this case an intricate currentdensity distributions exists, that can be explained in terms of interfering classical trajectories. We also derive analytically the two-dimensional Green function in perpendicular el...

  6. The forced flow high field test facility SULTAN

    International Nuclear Information System (INIS)

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

    1984-01-01

    The construction of the 8 Tesla, 1 m bore Test Facility SULTAN - I, a common action of ENEA (I-Frascati), ECN (NL-Petten) and SIN (CH-Villigen), is completed. Results on assembly, cooldown and the first operation of the whole system are presented. The SULTAN facility provides a wide range of capability of parameter variations (field, current, cooling) for the investigation of steady state performance and stability of technical superconductors unders nominal and limiting conditions

  7. Peak Vertical Ground Reaction Force during Two-Leg Landing: A Systematic Review and Mathematical Modeling

    Directory of Open Access Journals (Sweden)

    Wenxin Niu

    2014-01-01

    Full Text Available Objectives. (1 To systematically review peak vertical ground reaction force (PvGRF during two-leg drop landing from specific drop height (DH, (2 to construct a mathematical model describing correlations between PvGRF and DH, and (3 to analyze the effects of some factors on the pooled PvGRF regardless of DH. Methods. A computerized bibliographical search was conducted to extract PvGRF data on a single foot when participants landed with both feet from various DHs. An innovative mathematical model was constructed to analyze effects of gender, landing type, shoes, ankle stabilizers, surface stiffness and sample frequency on PvGRF based on the pooled data. Results. Pooled PvGRF and DH data of 26 articles showed that the square root function fits their relationship well. An experimental validation was also done on the regression equation for the medicum frequency. The PvGRF was not significantly affected by surface stiffness, but was significantly higher in men than women, the platform than suspended landing, the barefoot than shod condition, and ankle stabilizer than control condition, and higher than lower frequencies. Conclusions. The PvGRF and root DH showed a linear relationship. The mathematical modeling method with systematic review is helpful to analyze the influence factors during landing movement without considering DH.

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

    Science.gov (United States)

    Dokur, Derya; Keskin, Seda

    2018-02-14

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

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

    OpenAIRE

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

    2005-01-01

    The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

  10. Retrofitting Forced Air Combi Systems: A Cold Climate Field Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Schoenbauer, Ben [NorthernSTAR, St. Paul, MN (United States); Bohac, Dave [NorthernSTAR, St. Paul, MN (United States); McAlpine, Jack [NorthernSTAR, St. Paul, MN (United States); Hewett, Martha [NorthernSTAR, St. Paul, MN (United States)

    2017-06-01

    This project analyzed combined condensing water heaters or boilers and hydronic air coils to provide high efficiency domestic hot water (DHW) and forced air space heating. Called "combi" systems, they provided similar space and water heating performance less expensively than installing two condensing appliances. The system's installed costs were cheaper than installing a condensing furnace and either a condensing tankless or condensing storage water heater. However, combi costs must mature and be reduced before they are competitive with a condensing furnace and power vented water heater (energy factor of 0.60). Better insulation and tighter envelopes are reducing space heating loads for new and existing homes. For many homes, decreased space heating loads make it possible for both space and domestic water heating loads to be provided with a single heating plant. These systems can also eliminate safety issues associated with natural draft appliances through the use of one common sealed combustion vent. The combined space and water heating approach was not a new idea. Past systems have used non-condensing heating plants, which limited their usefulness in climates with high heating loads. Previous laboratory work (Schoenbauer et al. 2012a) showed that proper installation was necessary to achieve condensing with high efficiency appliances. Careful consideration was paid to proper system sizing and minimizing the water temperature returning from the air handling unit to facilitate condensing operation.

  11. Retrofitting Forced Air Combi Systems: A Cold Climate Field Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Schoenbauer, Ben [Univ. of Minnesota, St. Paul, MN (United States). NorthernSTAR Building America Partnership; Bohac, Dave [Univ. of Minnesota, St. Paul, MN (United States). NorthernSTAR Building America Partnership; McAlpine, Jake [Univ. of Minnesota, St. Paul, MN (United States). NorthernSTAR Building America Partnership; Hewett, Martha [Univ. of Minnesota, St. Paul, MN (United States). NorthernSTAR Building America Partnership

    2017-06-23

    This project analyzed combined condensing water heaters or boilers and hydronic air coils to provide high efficiency domestic hot water (DHW) and forced air space heating. Called 'combi' systems, they provided similar space and water heating performance less expensively than installing two condensing appliances. The system's installed costs were cheaper than installing a condensing furnace and either a condensing tankless or condensing storage water heater. However, combi costs must mature and be reduced before they are competitive with a condensing furnace and power vented water heater (energy factor of 0.60). Better insulation and tighter envelopes are reducing space heating loads for new and existing homes. For many homes, decreased space heating loads make it possible for both space and domestic water heating loads to be provided with a single heating plant. These systems can also eliminate safety issues associated with natural draft appliances through the use of one common sealed combustion vent. The combined space and water heating approach was not a new idea. Past systems have used non-condensing heating plants, which limited their usefulness in climates with high heating loads. Previous laboratory work (Schoenbauer et al. 2012a) showed that proper installation was necessary to achieve condensing with high efficiency appliances. Careful consideration was paid to proper system sizing and minimizing the water temperature returning from the air handling unit to facilitate condensing operation.

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

    International Nuclear Information System (INIS)

    Hegna, C.C.

    1997-08-01

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

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-28

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

  15. SYSTEMATIC FIELD SURVEY ON LIMES TRANSALUTANUS. SĂPATA CASE

    Directory of Open Access Journals (Sweden)

    Eugen S. Teodor

    2017-07-01

    Full Text Available Two adjoined forts and their surroundings, elements of the 3rd century Roman frontier in Dacia – Limes Transalutanus, which were last archaeologically investigated in 1930, were recently systematic surface surveyed, resulting in the identification of the associated civilian settlement in what seemed, at first glance, as an unexpected location, more distant than other military vici the team had previously identified along the same frontier line.Not only the limits of the settlement at Săpata were established, but also the density of occupation and territory division into various functional areas, allowing further interpretations regarding the network of ancient local roads and a better understanding of the way in which the Romans adjusted their built facilities to available resources (water or exploited the strategical features of the relief.Using an efficient, quick and rather inexpensive combination of survey methods (field walking and measurements of the magnetic susceptibility of the soil applied on a 4.8 ha surface, followed by pottery typological and spatial distribution analysis, the investigation team tried to mitigate the challenging vegetation situation, adjusting likewise to the limited resources of a scheduled research project.  Data relevance was increased by applying statistical corrections and using complementary investigation methods in order to cover the various available types of land (relief, vegetation, visibility; while data integration was ensured employing a unitary spatial gridded system for fieldwork and also by relating the obtained results to the high resolution digital terrain model of the sites obtained during UAV photogrammetric aerial survey.In particular, the study takes the opportunity opened by the analysis of the Roman Age pottery found in Săpata vicus to debate on the significance of the traditional, yet not unitary perceived, scholarly division between ‘Chilia-Militari’ ware (dwelling on Dacian

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

    DEFF Research Database (Denmark)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    International Nuclear Information System (INIS)

    Veto, B

    2011-01-01

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

  19. Application of systematic review methodology to the field of nutrition.

    Science.gov (United States)

    Lichtenstein, Alice H; Yetley, Elizabeth A; Lau, Joseph

    2008-12-01

    Systematic reviews represent a rigorous and transparent approach to synthesizing scientific evidence that minimizes bias. They evolved within the medical community to support development of clinical and public health practice guidelines, set research agendas, and formulate scientific consensus statements. The use of systematic reviews for nutrition-related topics is more recent. Systematic reviews provide independently conducted comprehensive and objective assessments of available information addressing precise questions. This approach to summarizing available data is a useful tool for identifying the state of science including knowledge gaps and associated research needs, supporting development of science-based recommendations and guidelines, and serving as the foundation for updates as new data emerge. Our objective is to describe the steps for performing systematic reviews and highlight areas unique to the discipline of nutrition that are important to consider in data assessment. The steps involved in generating systematic reviews include identifying staffing and planning for outside expert input, forming a research team, developing an analytic framework, developing and refining research questions, defining eligibility criteria, identifying search terms, screening abstracts according to eligibility criteria, retrieving articles for evaluation, constructing evidence and summary tables, assessing methodological quality and applicability, and synthesizing results including performing meta-analysis, if appropriate. Unique and at times challenging, nutrition-related considerations include baseline nutrient exposure, nutrient status, bioequivalence of bioactive compounds, bioavailability, multiple and interrelated biological functions, undefined nature of some interventions, and uncertainties in intake assessment. Systematic reviews are a valuable and independent component of decision-making processes by groups responsible for developing science-based recommendations

  20. Probing Field Distributions on Waveguide Structures with an Atomic Force/Photon Scanning Tunneling Microscope

    NARCIS (Netherlands)

    Borgonjen, E.G.; Borgonjen, E.G.; Moers, M.H.P.; Moers, M.H.P.; Ruiter, A.G.T.; van Hulst, N.F.

    1995-01-01

    A 'stand-alone' Photon Scanning Tunneling Microscope combined with an Atomic force Microscope, using a micro-fabricated silicon-nitride probe, is applied to the imaging of field distribution in integrated optical ridge waveguides. The electric field on the waveguide is locally probed by coupling to

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-04-14

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

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

    Science.gov (United States)

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

    2016-04-14

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Sorin Zaharia; Cheng, C.Z.

    2002-01-01

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

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

    Science.gov (United States)

    Takagi, Hideki; Nakashima, Motomu; Ozaki, Takashi; Matsuuchi, Kazuo

    2013-07-26

    This study aims to clarify the mechanism of generating unsteady hydrodynamic forces acting on a hand during swimming in order to directly measure the forces, pressure distribution, and flow field around the hand by using a robotic arm and particle image velocimetry (PIV). The robotic arm consisted of the trunk, shoulder, upper arm, forearm, and hand, and it was independently computer controllable in five degrees of freedom. The elbow-joint angle of the robotic arm was fixed at 90°, and the arm was moved in semicircles around the shoulder joint in a plane perpendicular to the water surface. Two-component PIV was used for flow visualization around the hand. The data of the forces and pressure acting on the hand were sampled at 200Hz and stored on a PC. When the maximum resultant force acting on the hand was observed, a pair of counter-rotating vortices appeared on the dorsal surface of the hand. A vortex attached to the hand increased the flow velocity, which led to decreased surface pressure, increasing the hydrodynamic forces. This phenomenon is known as the unsteady mechanism of force generation. We found that the drag force was 72% greater and the lift force was 4.8 times greater than the values estimated under steady flow conditions. Therefore, it is presumable that swimmers receive the benefits of this unsteady hydrodynamic force. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    International Nuclear Information System (INIS)

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

    1982-01-01

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

  7. Resonance oscillations of nonreciprocal long-range van der Waals forces between atoms in electromagnetic fields

    Science.gov (United States)

    Sherkunov, Yury

    2018-03-01

    We study theoretically the van der Waals interaction between two atoms out of equilibrium with an isotropic electromagnetic field. We demonstrate that at large interatomic separations, the van der Waals forces are resonant, spatially oscillating, and nonreciprocal due to resonance absorption and emission of virtual photons. We suggest that the van der Waals forces can be controlled and manipulated by tuning the spectrum of artificially created random light.

  8. Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

    Directory of Open Access Journals (Sweden)

    Michael A Cook

    Full Text Available BACKGROUND: Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM, we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. CONCLUSIONS/SIGNIFICANCE: These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

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

    Science.gov (United States)

    Sonnleitner, Matthias; Barnett, Stephen M.

    2017-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-05-01

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

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

    Science.gov (United States)

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

    2016-03-05

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    1995-01-01

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

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

    Science.gov (United States)

    Stolworthy, L D; Shirts, R B

    1997-03-01

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

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

    Yao, Shuang; Zhang, Yang; Guan, Baiou

    2015-08-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    Vanommeslaeghe, K; MacKerell, A D

    2012-12-21

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

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

    Science.gov (United States)

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

    2010-06-03

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

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

    International Nuclear Information System (INIS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-01-01

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

  1. Steady state models for filamentary plasma structures associated with force free magnetic fields

    International Nuclear Information System (INIS)

    Marklund, G.

    1978-05-01

    This paper presents a model for filamentary plasma structures associated with force-free magnetic fields. A homogenous electric field parallel to the symmetry axis of the magnetic field is assumed. Under the influence of these fields, the plasma will drift radially inwards resulting in an accumulation of plasma in the central region. We assume recombination losses to keep the central plasma density at a finite value, and the recombined plasma i.e. the neutrals to diffuse radially outwards. Plasma density and some neutral gas density distributions for a steady state situation are calculated for various cases

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

    International Nuclear Information System (INIS)

    Guo, Y.; Ding, M. D.; Liu, Y.; Sun, X. D.; DeRosa, M. L.; Wiegelmann, T.

    2012-01-01

    We test a nonlinear force-free field (NLFFF) optimization code in spherical geometry using an analytical solution from Low and Lou. Several tests are run, ranging from idealized cases where exact vector field data are provided on all boundaries, to cases where noisy vector data are provided on only the lower boundary (approximating the solar problem). Analytical tests also show that the NLFFF code in the spherical geometry performs better than that in the Cartesian one when the field of view of the bottom boundary is large, say, 20° × 20°. Additionally, we apply the NLFFF model to an active region observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory (SDO) both before and after an M8.7 flare. For each observation time, we initialize the models using potential field source surface (PFSS) extrapolations based on either a synoptic chart or a flux-dispersal model, and compare the resulting NLFFF models. The results show that NLFFF extrapolations using the flux-dispersal model as the boundary condition have slightly lower, therefore better, force-free, and divergence-free metrics, and contain larger free magnetic energy. By comparing the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the Atmospheric Imaging Assembly on board SDO, we find that the NLFFF performs better than the PFSS not only for the core field of the flare productive region, but also for large EUV loops higher than 50 Mm.

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

    Directory of Open Access Journals (Sweden)

    Alexandru Capatina

    2017-09-01

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

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

    Science.gov (United States)

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

    1994-01-01

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

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

    Science.gov (United States)

    Pietropolli Charmet, Andrea; Cornaton, Yann

    2018-05-01

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

  6. Confinement of plasma along shaped open magnetic fields from the centrifugal force of supersonic plasma rotation.

    Science.gov (United States)

    Teodorescu, C; Young, W C; Swan, G W S; Ellis, R F; Hassam, A B; Romero-Talamas, C A

    2010-08-20

    Interferometric density measurements in plasmas rotating in shaped, open magnetic fields demonstrate strong confinement of plasma parallel to the magnetic field, with density drops of more than a factor of 10. Taken together with spectroscopic measurements of supersonic E × B rotation of sonic Mach 2, these measurements are in agreement with ideal MHD theory which predicts large parallel pressure drops balanced by centrifugal forces in supersonically rotating plasmas.

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

    Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

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

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

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

  10. Atomic force and scanning near-field optical microscopy study of carbocyanine dye J-aggregates

    Czech Academy of Sciences Publication Activity Database

    Prokhorov, V.V.; Petrova, M.G.; Kovaleva, Natalia; Demikhov, E.I.

    2014-01-01

    Roč. 10, č. 5 (2014), s. 700-704 ISSN 1573-4137 Institutional support: RVO:68378271 Keywords : carbocyanine dye * elementary fibri * high-resolution atomic force microscopy * J-aggregate * probe microscopy * scanning near-field optical microscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.096, year: 2014

  11. Three-dimensional computation of magnetic fields and Lorentz forces of an LHC dipole magnet

    International Nuclear Information System (INIS)

    Daum, C.; Avest, D. ter

    1989-07-01

    Magnetic fields and Lorentz forces of an LHC dipole magnet are calculated using the method of image currents to represent the effect of the iron shield. The calculation is performed for coils of finite length using a parametrization for coil heads of constant perimeter. A comparison with calculations based on POISSON and TOSCA is made. (author). 5 refs.; 31 figs.; 6 tabs

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

    Science.gov (United States)

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

    2017-09-05

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

  13. Adaptation of multi-joint balance coordination to whole body force fields

    NARCIS (Netherlands)

    Engelhart, Denise; Schouten, Alfred Christiaan; Pasma, Jantsje; Aarts, Ronald G.K.M.; Pasma, J.; Meskers, Carel; Maier, Andrea; van der Kooij, Herman

    2014-01-01

    Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  15. Edge effects on forces and magnetic fields produced by a conductor moving past a magnet

    Energy Technology Data Exchange (ETDEWEB)

    Mulcahy, T.M.; Hull, J.R.; Almer, J.D. (Argonne National Lab., IL (United States)); Rossing, T.D. (Northern Illinois Univ., De Kalb, IL (United States))

    1992-01-01

    Experiments have been performed to further understand the forces acting on magnets moving along and over the edge of a continuous conducting sheet and to produce a comprehensive data set for the validation of analysis methods. Mapping the magnetic field gives information about the eddy currents induced in the conductor, which agrees with numerical calculations.

  16. Edge effects on forces and magnetic fields produced by a conductor moving past a magnet

    Energy Technology Data Exchange (ETDEWEB)

    Mulcahy, T.M.; Hull, J.R.; Almer, J.D. [Argonne National Lab., IL (United States); Rossing, T.D. [Northern Illinois Univ., De Kalb, IL (United States)

    1992-04-01

    Experiments have been performed to further understand the forces acting on magnets moving along and over the edge of a continuous conducting sheet and to produce a comprehensive data set for the validation of analysis methods. Mapping the magnetic field gives information about the eddy currents induced in the conductor, which agrees with numerical calculations.

  17. An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-02-10

    A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.

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

    Science.gov (United States)

    Mason, Elisa

    1999-01-01

    Describes the evolution of refugee and forced migration studies, identifies factors that render it a challenging field to research, and highlights a variety of Internet-based and other electronic resources that can be used to locate monographs, periodicals, grey literature, and current information. Provides a bibliography of reference materials in…

  19. Recent Progress in Molecular Simulation of Aqueous Electrolytes: Force Fields, Chemical Potentials and Solubility.

    Czech Academy of Sciences Publication Activity Database

    Nezbeda, Ivo; Moučka, F.; Smith, W.R.

    2016-01-01

    Roč. 114, č. 11 (2016), s. 1665-1690 ISSN 0026-8976 R&D Projects: GA ČR GA15-19542S Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : force fields * chemical potentials * aqueous electrolytes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.870, year: 2016

  20. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

    Science.gov (United States)

    Lee, Kuo Hao; Chen, Jianhan

    2017-06-15

    Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Veto, B.

    2011-01-01

    The Machian effect of distant masses of the universe in the frame of reference of the rotating Earth is demonstrated using the gravitomagnetic approach of general relativity. This effect appears in the form of a gravitomagnetic Lorentz force acting on moving bodies on the Earth. The gravitomagnetic field of the universe--deduced from a simple…

  2. A verification of quantum field theory – measurement of Casimir force

    Indian Academy of Sciences (India)

    journal of. Feb. & Mar. 2001 physics pp. 239–243. A verification of quantum field theory ... minum coated a sphere and flat plate using an atomic force microscope. ... where R is the radius of curvature of the spherical surface. The finite .... sured by AFM) of 60% Au/40% Pd, to form a nonreactive and conductive top layer. For.

  3. Calculation of magnetic field and electromagnetic forces in MHD superconducting magnets

    International Nuclear Information System (INIS)

    Martinelli, G.; Morini, A.; Moisio, M.F.

    1992-01-01

    The realization of a superconducting prototype magnet for MHD energy conversion is under development in Italy. Electromechanical industries and University research groups are involved in the project. The paper deals with analytical methods developed at the Department of Electrical Engineering of Padova University for calculating magnetic field and electromagnetic forces in MHD superconducting magnets and utilized in the preliminary design of the prototype

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

    Science.gov (United States)

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

    2016-04-12

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

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

    Science.gov (United States)

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

    2017-10-01

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

  6. Calculation of electromagnetic fields and forces in coil systems of arbitrary geometry

    International Nuclear Information System (INIS)

    Sackett, S.J.

    1975-01-01

    A computer program, EFFI, is described which calculates the electric and magnetic fields due to an arbitrary spatial distribution of current-carrying circular loops, circular arcs, and straight lines. The electric field is assumed to arise solely from the time variation of the magnetic field, and the magnetic field due to the changing electric field is assumed to be negligible. In addition, the conductor bundle elements (loops, arcs, lines) are assumed to be absent. Electric and magnetic flux lines and magnetic forces and inductances are also calculated by the program. The algorithm used in the code, which is based on a combination of direct and numerical integration using the Biot-Savart law, is discussed. The methods used to maintain accuracy in calculating fields within the conductor bundle, in particular, are detailed. Several examples are then presented to illustrate the input and output features as well as the accuracy obtained and the running time required

  7. Ionization induced by strong electromagnetic field in low dimensional systems bound by short range forces

    Energy Technology Data Exchange (ETDEWEB)

    Eminov, P.A., E-mail: peminov@mail.ru [Moscow State University of Instrument Engineering and Computer Sciences, 20 Stromynka Street, Moscow 2107996 (Russian Federation); National Research University Higher School of Economics, 3/12 Bolshoy Trekhsvyatskiy pereulok, Moscow 109028 (Russian Federation)

    2013-10-01

    Ionization processes for a two dimensional quantum dot subjected to combined electrostatic and alternating electric fields of the same direction are studied using quantum mechanical methods. We derive analytical equations for the ionization probability in dependence on characteristic parameters of the system for both extreme cases of a constant electric field and of a linearly polarized electromagnetic wave. The ionization probabilities for a superposition of dc and low frequency ac electric fields of the same direction are calculated. The impulse distribution of ionization probability for a system bound by short range forces is found for a superposition of constant and alternating fields. The total probability for this process per unit of time is derived within exponential accuracy. For the first time the influence of alternating electric field on electron tunneling probability induced by an electrostatic field is studied taking into account the pre-exponential term.

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

    Science.gov (United States)

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

    2017-12-01

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

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

    International Nuclear Information System (INIS)

    Sonnleitner, M.

    2014-01-01

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

  10. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    International Nuclear Information System (INIS)

    Morante, S.; Rossi, G.C.

    2017-01-01

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  11. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)

    2017-02-15

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  12. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-01-01

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities

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

    International Nuclear Information System (INIS)

    Arutyunyan, S.G.

    1989-01-01

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

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

    International Nuclear Information System (INIS)

    Jiang Chaowei; Feng Xueshang; Xiang Changqing

    2012-01-01

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

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

    Science.gov (United States)

    Xu, Dong; Zhang, Yang

    2012-07-01

    Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  17. On the Shape of Force-Free Field Lines in the Solar Corona

    KAUST Repository

    Prior, C.

    2012-02-02

    This paper studies the shape parameters of looped field lines in a linear force-free magnetic field. Loop structures with a sufficient amount of kinking are generally seen to form S or inverse S (Z) shapes in the corona (as viewed in projection). For a single field line, we can ask how much the field line is kinked (as measured by the writhe), and how much neighbouring flux twists about the line (as measured by the twist number). The magnetic helicity of a flux element surrounding the field line can be decomposed into these two quantities. We find that the twist helicity contribution dominates the writhe helicity contribution, for field lines of significant aspect ratio, even when their structure is highly kinked. These calculations shed light on some popular assumptions of the field. First, we show that the writhe of field lines of significant aspect ratio (the apex height divided by the footpoint width) can sometimes be of opposite sign to the helicity. Secondly, we demonstrate the possibility of field line structures which could be interpreted as Z-shaped, but which have a helicity value sign expected of an S-shaped structure. These results suggest that caution should be exercised in using two-dimensional images to draw conclusions on the helicity value of field lines and flux tubes. © 2012 Springer Science+Business Media B.V.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-15

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

  19. Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

    International Nuclear Information System (INIS)

    Abdoli, A; Mirzaee, I; Purmahmod, N; Anvari, A

    2008-01-01

    Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s -1 at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A b and D c , have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications

  20. Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

    Energy Technology Data Exchange (ETDEWEB)

    Abdoli, A; Mirzaee, I; Purmahmod, N [Faculty of Engineering, Urmia University, Urmia (Iran, Islamic Republic of); Anvari, A [Department of Physics, Sharif University of Technology, Tehran (Iran, Islamic Republic of)], E-mail: ab.abdoli@gmail.com

    2008-09-07

    Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s{sup -1} at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A{sub b} and D{sub c}, have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications.

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

    Science.gov (United States)

    Takagi, Hideki; Shimada, Shohei; Miwa, Takahiro; Kudo, Shigetada; Sanders, Ross; Matsuuchi, Kazuo

    2014-12-01

    The goal of this research is to clarify the mechanism by which unsteady forces are generated during sculling by a skilled swimmer and thereby to contribute to improving propulsive techniques. We used particle image velocimetry (PIV) to acquire data on the kinematics of the hand during sculling, such as fluid forces and flow field. By investigating the correlations between these data, we expected to find a new propulsion mechanism. The experiment was performed in a flow-controlled water channel. The participant executed sculling motions to remain at a fixed position despite constant water flow. PIV was used to visualize the flow-field cross-section in the plane of hand motion. Moreover, the fluid forces acting on the hand were estimated from pressure distribution measurements performed on the hand and simultaneous three-dimensional motion analysis. By executing the sculling motion, a skilled swimmer produces large unsteady fluid forces when the leading-edge vortex occurs on the dorsal side of the hand and wake capture occurs on the palm side. By using a new approach, we observed interesting unsteady fluid phenomena similar to those of flying insects. The study indicates that it is essential for swimmers to fully exploit vortices. A better understanding of these phenomena might lead to an improvement in sculling techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

    Directory of Open Access Journals (Sweden)

    A. V. Sulimov

    2017-01-01

    Full Text Available Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

  3. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

    Science.gov (United States)

    Sulimov, A V; Kutov, D C; Katkova, E V; Sulimov, V B

    2017-01-01

    Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

  4. Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

    Science.gov (United States)

    Kim, Seonah; Orendt, Anita M; Ferraro, Marta B; Facelli, Julio C

    2009-10-01

    This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

  5. Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

    Science.gov (United States)

    2014-01-01

    We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

  6. Near-field Light Scattering Techniques for Measuring Nanoparticle-Surface Interaction Energies and Forces.

    Science.gov (United States)

    Schein, Perry; Ashcroft, Colby K; O'Dell, Dakota; Adam, Ian S; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David

    2015-08-15

    Nanoparticles are quickly becoming commonplace in many commercial and industrial products, ranging from cosmetics to pharmaceuticals to medical diagnostics. Predicting the stability of the engineered nanoparticles within these products a priori remains an important and difficult challenge. Here we describe our techniques for measuring the mechanical interactions between nanoparticles and surfaces using near-field light scattering. Particle-surface interfacial forces are measured by optically "pushing" a particle against a reference surface and observing its motion using scattered near-field light. Unlike atomic force microscopy, this technique is not limited by thermal noise, but instead takes advantage of it. The integrated waveguide and microfluidic architecture allow for high-throughput measurements of about 1000 particles per hour. We characterize the reproducibility of and experimental uncertainty in the measurements made using the NanoTweezer surface instrument. We report surface interaction studies on gold nanoparticles with 50 nm diameters, smaller than previously reported in the literature using similar techniques.

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  9. Zero mass field quantization and Kibble's long-range force criterion for the Goldstone theorem

    International Nuclear Information System (INIS)

    Wright, S.H.

    1981-01-01

    The central theme of the dissertation is an investigation of the long-range force criterion used by Kibble in his discussion of the Goldstone Theorem. This investigation is broken up into the following sections: I. Introduction. Spontaneous symmetry breaking, the Goldstone Theorem and the conditions under which it holds are discussed. II. Massless Wave Expansions. In order to make explicit calculations of the operator commutators used in applying Kibble's criterion, it is necessary to work out the operator expansions for a massless field. Unusual results are obtained which include operators corresponding to classical macroscopic field modes. III. The Kibble Criterion for Simple Models Exhibiting Spontaneously Broken Symmetries. The results of the previous section are applied to simple models with spontaneously broken symmetries, namely, the real scalar massless field and the Goldstone model without gauge coupling. IV. The Higgs Mechanism in Classical Field Theory. It is shown that the Higgs Mechanism has a simple interpretation in terms of classical field theory, namely, that it arises from a derivative coupling term between the Goldstone fields and the gauge fields. V. The Higgs Mechanism and Kibble's Criterion. This section draws together the material discussed in sections II to IV. Explicit calculations are made to evaluate Kibble's criterion on a Goldstone-Higgs type of model in the Coulomb gauge. It is found, as expected, that the criterion is not met, but not for reasons relating to the range of the mediating force. By referring to the findings of sections III and IV, it is concluded that the common denominator underlying both the Higgs Mechanism and the failure of Kibble's criterion is a structural aspect of the field equations: derivative coupling between fields

  10. Continuous Force Decoding from Local Field Potentials of the Primary Motor Cortex in Freely Moving Rats.

    Science.gov (United States)

    Khorasani, Abed; Heydari Beni, Nargess; Shalchyan, Vahid; Daliri, Mohammad Reza

    2016-10-21

    Local field potential (LFP) signals recorded by intracortical microelectrodes implanted in primary motor cortex can be used as a high informative input for decoding of motor functions. Recent studies show that different kinematic parameters such as position and velocity can be inferred from multiple LFP signals as precisely as spiking activities, however, continuous decoding of the force magnitude from the LFP signals in freely moving animals has remained an open problem. Here, we trained three rats to press a force sensor for getting a drop of water as a reward. A 16-channel micro-wire array was implanted in the primary motor cortex of each trained rat, and obtained LFP signals were used for decoding of the continuous values recorded by the force sensor. Average coefficient of correlation and the coefficient of determination between decoded and actual force signals were r = 0.66 and R 2  = 0.42, respectively. We found that LFP signal on gamma frequency bands (30-120 Hz) had the most contribution in the trained decoding model. This study suggests the feasibility of using low number of LFP channels for the continuous force decoding in freely moving animals resembling BMI systems in real life applications.

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

    OpenAIRE

    吉田, 欣二郎; 松田, 茂雄; 松本, 洋和

    2000-01-01

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

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

    Science.gov (United States)

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

    2002-03-01

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

  13. Force-free fields in the vicinity of a Reissner-Nordstroem black hole

    International Nuclear Information System (INIS)

    Evangelidis, E.

    1978-01-01

    The behaviour of a force-free field has been studied in a Reissner-Nordstroem metric. An expansion in tensor harmonics of even-odd parity reduced the radial equations in a differential equation of the Sturm-Liouville system which was solved asymptotically in a conveniently defined space coordinate. Further, it has been possible to regularize the singular behaviour of the Reissner-Nordstroem metric at the event horizon and the modified metric to be given explicitly. (Auth.)

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

    Directory of Open Access Journals (Sweden)

    Mustapha Carab Ahmed

    2018-06-01

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

  15. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

    DEFF Research Database (Denmark)

    Rossi, G.; Monticelli, L.; Puisto, S. R.

    2011-01-01

    We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....

  16. Relativistic equation of the orbit of a particle in a arbitrary central force field

    International Nuclear Information System (INIS)

    Aaron, Francisc D.

    2005-01-01

    The equation of the orbit of a relativistic particle moving in an arbitrary central force field is derived. Straightforward generalizations of well-known first and second order differential equations are given. It is pointed out that the relativistic equation of the orbit has the same form as in the non-relativistic case, the only changes consisting in the appearance of additional terms proportional to 1/c 2 in both potential and total energies. (author)

  17. Study of vapour phase dynamics with nitrogen boiling in the field of centrifugal forces

    International Nuclear Information System (INIS)

    Levchenko, N.M.; Kolod'ko, I.M.

    1987-01-01

    The vapour phase dynamics during film boiling of liquid nitrogen on horizontal wire in the field of centrifugal forces has been studied experimentally in a wide range of overloads(1 ≤ η ≤ 375) and heat fluxes (q kp2 ≤ q ≤ 4q kpi ). The available data confirmed and the theoretical relationships suggested make it possible to calculate the hydrodynamic film boiling parameters (wave length, bubble departure diameter and frequency) for other liquids

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

    DEFF Research Database (Denmark)

    Fileti, E. E.; Chaban, V. V.

    2014-01-01

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

  19. Baryonic forces and hyperons in nuclear matter from SU(3) chiral effective field theory

    Energy Technology Data Exchange (ETDEWEB)

    Petschauer, Stefan Karl

    2016-02-12

    In this work the baryon-baryon interaction is studied at next-to-leading order in SU(3) chiral effective field theory and applied to hyperon-nucleon scattering. The properties of hyperons in isospin-symmetric as well as asymmetric nuclear matter are calculated within the Bruecker-Hartree-Fock formalism. Moreover, the leading three-baryon interaction is derived and its low-energy constants are estimated from decuplet intermediate states. We conclude, that chiral effective field theory is a well-suited tool to describe the baryonic forces.

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

    Science.gov (United States)

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

    2018-06-01

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

  1. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

    Science.gov (United States)

    Miller, Mark S.; Lay, Wesley K.

    2016-01-01

    Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

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

    Science.gov (United States)

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-01

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

  3. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

    Science.gov (United States)

    Wu, Xiaojing; Clavaguera, Carine; Lagardère, Louis; Piquemal, Jean-Philip; de la Lande, Aurélien

    2018-04-16

    We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.

  4. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

    Science.gov (United States)

    Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke

    2015-06-25

    Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

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

    Science.gov (United States)

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

    2018-05-04

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

  6. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    Science.gov (United States)

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  7. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    Science.gov (United States)

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

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

    International Nuclear Information System (INIS)

    Weening, R. H.

    2011-01-01

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

  9. A Simple Model of Fields Including the Strong or Nuclear Force and a Cosmological Speculation

    Directory of Open Access Journals (Sweden)

    David L. Spencer

    2016-10-01

    Full Text Available Reexamining the assumptions underlying the General Theory of Relativity and calling an object's gravitational field its inertia, and acceleration simply resistance to that inertia, yields a simple field model where the potential (kinetic energy of a particle at rest is its capacity to move itself when its inertial field becomes imbalanced. The model then attributes electromagnetic and strong forces to the effects of changes in basic particle shape. Following up on the model's assumption that the relative intensity of a particle's gravitational field is always inversely related to its perceived volume and assuming that all black holes spin, may create the possibility of a cosmic rebound where a final spinning black hole ends with a new Big Bang.

  10. Do runners who suffer injuries have higher vertical ground reaction forces than those who remain injury-free? A systematic review and meta-analysis

    NARCIS (Netherlands)

    van der Worp, Henk; Vrielink, Jelte W.; Bredeweg, Steef W.

    2016-01-01

    Background Vertical ground reaction force (VGRF) parameters have been implicated as a cause of several running-related injuries. However, no systematic review has examined this relationship. Aim We systematically reviewed evidence for a relation between VGRF parameters and specific running-related

  11. Reduction of systematic biases in regional climate downscaling through ensemble forcing

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hongwei; Wang, Bin [Chinese Academy of Sciences, LASG, Institute of Atmospheric Physics, Beijing (China); Wang, Bin [University of Hawaii at Manoa, Department of Meteorology, Honolulu, Hawaii (United States); University of Hawaii at Manoa, International Pacific Research Center, Honolulu, Hawaii (United States)

    2012-02-15

    Simulations of the East Asian summer monsoon for the period of 1979-2001 were carried out using the Weather Research and Forecast (WRF) model forced by three reanalysis datasets (NCEP-R2, ERA-40, and JRA-25). The experiments forced by different reanalysis data exhibited remarkable differences, primarily caused by uncertainties in the lateral boundary (LB) moisture fluxes over the Bay of Bengal and the Philippine Sea. The climatological mean water vapor convergence into the model domain computed from ERA-40 was about 24% higher than that from the NCEP-R2 reanalysis. We demonstrate that using the ensemble mean of NCEP-R2, ERA-40, and JRA-25 as LB forcing considerably reduced the biases in the model simulation. The use of ensemble forcing improved the performance in simulated mean circulation and precipitation, inter-annual variation in seasonal precipitation, and daily precipitation. The model simulated precipitation was superior to that in the reanalysis in both climatology and year-to-year variations, indicating the added value of dynamic downscaling. The results suggest that models having better performance under one set of LB forcing might worsen when another set of reanalysis data is used as LB forcing. Use of ensemble mean LB forcing for assessing regional climate model performance is recommended. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Alessandro Vato

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

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

    Science.gov (United States)

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

    2015-02-11

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

  14. Small strain multiphase-field model accounting for configurational forces and mechanical jump conditions

    Science.gov (United States)

    Schneider, Daniel; Schoof, Ephraim; Tschukin, Oleg; Reiter, Andreas; Herrmann, Christoph; Schwab, Felix; Selzer, Michael; Nestler, Britta

    2018-03-01

    Computational models based on the phase-field method have become an essential tool in material science and physics in order to investigate materials with complex microstructures. The models typically operate on a mesoscopic length scale resolving structural changes of the material and provide valuable information about the evolution of microstructures and mechanical property relations. For many interesting and important phenomena, such as martensitic phase transformation, mechanical driving forces play an important role in the evolution of microstructures. In order to investigate such physical processes, an accurate calculation of the stresses and the strain energy in the transition region is indispensable. We recall a multiphase-field elasticity model based on the force balance and the Hadamard jump condition at the interface. We show the quantitative characteristics of the model by comparing the stresses, strains and configurational forces with theoretical predictions in two-phase cases and with results from sharp interface calculations in a multiphase case. As an application, we choose the martensitic phase transformation process in multigrain systems and demonstrate the influence of the local homogenization scheme within the transition regions on the resulting microstructures.

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

    Directory of Open Access Journals (Sweden)

    Cui Rong

    2016-10-01

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

  16. Magnetic Field Equivalent Current Analysis-Based Radial Force Control for Bearingless Permanent Magnet Synchronous Motors

    Directory of Open Access Journals (Sweden)

    Huangqiu Zhu

    2015-05-01

    Full Text Available Bearingless permanent magnet synchronous motors (BPMSMs, with all advantages of permanent magnet motors (PMSMs and magnetic bearings, have become an important research direction in the bearingless motor field. To realize a stable suspension for the BPMSM, accurate decoupling control between the electromagnetic torque and radial suspension force is indispensable. In this paper, a concise and reliable analysis method based on a magnetic field equivalent current is presented. By this analysis method, the operation principle is analyzed theoretically, and the necessary conditions to produce a stable radial suspension force are confirmed. In addition, mathematical models of the torque and radial suspension force are established which is verified by the finite element analysis (FEA software ANSYS. Finally, an experimental prototype of a 2-4 poles surface-mounted BPMSM is tested with the customized control strategy. The simulation and experimental results have shown that the motor has good rotation and suspension performance, and validated the accuracy of the proposed analysis method and the feasibility of the control strategy.

  17. Characterization of electromagnetic fields in the aSPECT spectrometer and reduction of systematic errors

    Energy Technology Data Exchange (ETDEWEB)

    Ayala Guardia, Fidel

    2011-10-15

    The aSPECT spectrometer has been designed to measure, with high precision, the recoil proton spectrum of the free neutron decay. From this spectrum, the electron antineutrino angular correlation coefficient a can be extracted with high accuracy. The goal of the experiment is to determine the coefficient a with a total relative error smaller than 0.3%, well below the current literature value of 5%. First measurements with the aSPECT spectrometer were performed in the Forschungs-Neutronenquelle Heinz Maier-Leibnitz in Munich. However, time-dependent background instabilities prevented us from reporting a new value of a. The contents of this thesis are based on the latest measurements performed with the aSPECT spectrometer at the Institut Laue-Langevin (ILL) in Grenoble, France. In these measurements, background instabilities were considerably reduced. Furthermore, diverse modifications intended to minimize systematic errors and to achieve a more reliable setup were successfully performed. Unfortunately, saturation effects of the detector electronics turned out to be too high to determine a meaningful result. However, this and other systematics were identified and decreased, or even eliminated, for future aSPECT beamtimes. The central part of this work is focused on the analysis and improvement of systematic errors related to the aSPECT electromagnetic fields. This work yielded in many improvements, particularly in the reduction of the systematic effects due to electric fields. The systematics related to the aSPECT magnetic field were also minimized and determined down to a level which permits to improve the present literature value of a. Furthermore, a custom NMR-magnetometer was developed and improved during this thesis, which will lead to reduction of magnetic field-related uncertainties down to a negligible level to determine a with a total relative error of at least 0.3%.

  18. Characterization of electromagnetic fields in the αSPECTspectrometer and reduction of systematic errors

    International Nuclear Information System (INIS)

    Ayala Guardia, Fidel

    2011-10-01

    The aSPECT spectrometer has been designed to measure, with high precision, the recoil proton spectrum of the free neutron decay. From this spectrum, the electron antineutrino angular correlation coefficient a can be extracted with high accuracy. The goal of the experiment is to determine the coefficient a with a total relative error smaller than 0.3%, well below the current literature value of 5%. First measurements with the aSPECT spectrometer were performed in the Forschungs-Neutronenquelle Heinz Maier-Leibnitz in Munich. However, time-dependent background instabilities prevented us from reporting a new value of a. The contents of this thesis are based on the latest measurements performed with the aSPECT spectrometer at the Institut Laue-Langevin (ILL) in Grenoble, France. In these measurements, background instabilities were considerably reduced. Furthermore, diverse modifications intended to minimize systematic errors and to achieve a more reliable setup were successfully performed. Unfortunately, saturation effects of the detector electronics turned out to be too high to determine a meaningful result. However, this and other systematics were identified and decreased, or even eliminated, for future aSPECT beamtimes. The central part of this work is focused on the analysis and improvement of systematic errors related to the aSPECT electromagnetic fields. This work yielded in many improvements, particularly in the reduction of the systematic effects due to electric fields. The systematics related to the aSPECT magnetic field were also minimized and determined down to a level which permits to improve the present literature value of a. Furthermore, a custom NMR-magnetometer was developed and improved during this thesis, which will lead to reduction of magnetic field-related uncertainties down to a negligible level to determine a with a total relative error of at least 0.3%.

  19. Theory and numerical calculation of the acoustic field exerted by eddy-current forces

    Energy Technology Data Exchange (ETDEWEB)

    Kawashima, K.

    1976-01-01

    The equations for calculating the acoustic field produced within a nonmagnetic metal by interaction of eddy currents with a static magnetic field were obtained on the assumptions (1) an ultrasonic wave is generated by the electromagentic force through classical and macroscopic phenomena; (2) the electric, magnetic, and elastic properties of the metal are linear, isotropic, and homogeneous throughout the metal, which occupies semi-infinite space; (3) the whole system is axially symmetric; and (4) eddy currents and elastic waves show a steady-state sinusoidal variation. The acoustic field produced by a specific electromagnetic ultrasonic transducer with axial symmetry was calculated numerically, and the results showed a well-defined ultrasonic wave beam, which was narrower than had been expected from the size of the transducer. (auth)

  20. Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

    International Nuclear Information System (INIS)

    Kim, S H; Hashi, S; Ishiyama, K

    2011-01-01

    This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and 19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

  1. Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

    Science.gov (United States)

    Kim, S. H.; Hashi, S.; Ishiyama, K.

    2011-01-01

    This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

  2. A code for calculating force and temperature of a bitter plate type toroidal field coil system

    International Nuclear Information System (INIS)

    Christensen, U.

    1989-01-01

    To assist the design effort of the TF coils for CIT, a set of programs was developed to calculate the transient spatial distribution of the current density, the temperature and the forces in the TF coil conductor region. The TF coils are of the Bitter (disk) type design and therefore have negligible variation of current density in the toroidal direction. During the TF pulse, voltages are induced which cause the field and current to diffuse in the minor radial direction. This penetration, combined with the increase of resistance due to the temperature rise determines the distribution of the current. After the current distribution has been determined, the in-plane (TF-TF) and the out-of-plane (TF-PF) forces in the conductor are computed. The predicted currents and temperatures have been independently corroborated using the SPARK code which has been modified for this type of problem. 6 figs

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

    Directory of Open Access Journals (Sweden)

    Jesús Sanz Maudes

    2012-08-01

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

  4. Effect of simulated resistance, fleeing, and use of force on standardized field sobriety testing.

    Science.gov (United States)

    Ho, Jeffrey; Dawes, Donald; Nystrom, Paul; Moore, Johanna; Steinberg, Lila; Tilton, Annemarie; Miner, James

    2015-07-01

    When a law enforcement officer (LEO) stops a suspect believed to be operating (a vehicle) while impaired (OWI), the suspect may resist or flee, and the LEO may respond with force. The suspect may then undergo a Standardized Field Sobriety Test (SFST) to gauge impairment. It is not known whether resistance, fleeing, or actions of force can create an inaccurate SFST result. We examined the effect of resistance, fleeing, and force on the SFST. Human volunteers were prospectively randomized to have a SFST before and after one of five scenarios: (1) five-second conducted electrical weapon exposure; (2) 100-yard (91.4 m) sprint; (3) 45-second physical fight; (4) police dog bite with protective gear; and (5) Oleoresin Capsicum spray to the face with eyes shielded. The SFST was administered and graded by a qualified LEO. After the SFST, the volunteer entered their scenario and was then administered another SFST. Data were analyzed using descriptive statistics. SFST performance was compared before and after using chi-square tests. Fifty-seven subjects enrolled. Three received a single-point penalty during one component of the three-component SFST pre-scenario. No subject received a penalty point in any components of the SFST post-scenario (p = 0.08). This is the first human study to examine the effects of physical resistance, flight, and use of force on the SFST result. We did not detect a difference in the performance of subjects taking the SFST before and after exposure to resistance, flight, or a simulated use of force. © Australian Council for Educational Research 2014.

  5. Mapping the global football field: a sociological model of transnational forces within the world game.

    Science.gov (United States)

    Giulianotti, Richard; Robertson, Roland

    2012-06-01

    This paper provides a sociological model of the key transnational political and economic forces that are shaping the 'global football field'. The model draws upon, and significantly extends, the theory of the 'global field' developed previously by Robertson. The model features four quadrants, each of which contains a dominant operating principle, an 'elemental reference point', and an 'elemental theme'. The quadrants contain, first, neo-liberalism, associated with the individual and elite football clubs; second, neo-mercantilism, associated with nation-states and national football systems; third, international relations, associated with international governing bodies; and fourth, global civil society, associated with diverse institutions that pursue human development and/or social justice. We examine some of the interactions and tensions between the major institutional and ideological forces across the four quadrants. We conclude by examining how the weakest quadrant, featuring global civil society, may gain greater prominence within football. In broad terms, we argue that our four-fold model may be utilized to map and to examine other substantive research fields with reference to globalization. © London School of Economics and Political Science 2012.

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

    International Nuclear Information System (INIS)

    Prajapati, R.P.

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    S. Mahdiuon-Rad

    2013-08-01

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

  8. An automated analysis workflow for optimization of force-field parameters using neutron scattering data

    Energy Technology Data Exchange (ETDEWEB)

    Lynch, Vickie E.; Borreguero, Jose M. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Bhowmik, Debsindhu [Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Ganesh, Panchapakesan; Sumpter, Bobby G. [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Proffen, Thomas E. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Goswami, Monojoy, E-mail: goswamim@ornl.gov [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)

    2017-07-01

    Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.

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

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

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

  10. Improvement of a force field to model the edges of clay particles

    International Nuclear Information System (INIS)

    Pouvreau, Maxime

    2016-01-01

    The CLAYFF force field is widely used to model the interfaces of clay minerals - and related layered materials - with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nano sized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O-H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O-H and Mg-O-H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH) 3 and brucite Mg(OH) 2 , whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O-H term was parametrized from an edge model of kaolinite Al 2 Si 2 O 5 (OH) 4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O-H term were performed. The modified force field clearly improves the description of hydroxylated surfaces: the orientation and the vibrational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality [fr

  11. The force analysis for superparamagnetic nanoparticles-based gene delivery in an oscillating magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jiajia [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Shi, Zongqian, E-mail: zqshi@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Jia, Shenli [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Zhang, Pengbo [Department of Anesthesiology, Second Affiliated Hospital of Xi’an Jiaotong University School of Medicine, No.157 West 5 Road, Xi’an, Shaanxi Province 710004 (China)

    2017-04-01

    Due to the peculiar magnetic properties and the ability to function in cell-level biological interaction, superparamagnetic nanoparticles (SMNP) have been being the attractive carrier for gene delivery. The superparamagnetic nanoparticles with surface-bound gene vector can be attracted to the surface of cells by the Kelvin force provided by external magnetic field. In this article, the influence of the oscillating magnetic field on the characteristics of magnetofection is studied in terms of the magnetophoretic velocity. The magnetic field of a cylindrical permanent magnet is calculated by equivalent current source (ECS) method, and the Kelvin force is derived by using the effective moment method. The results show that the static magnetic field accelerates the sedimentation of the particles, and drives the particles inward towards the axis of the magnet. Based on the investigation of the magnetophoretic velocity of the particle under horizontally oscillating magnetic field, an oscillating velocity within the amplitude of the magnet oscillation is observed. Furthermore, simulation results indicate that the oscillating amplitude plays an important role in regulating the active region, where the particles may present oscillating motion. The analysis of the magnetophoretic velocity gives us an insight into the physical mechanism of the magnetofection. It's also helpful to the optimal design of the magnetofection system. - Highlights: • We compare the results of the ECS method and FEA method with the commercial software, Ansys. • We analyze the physic mechanism of the oscillating motion of the particles in the presence of an oscillating magnet. • We discuss the influence of the oscillating amplitude of the magnet on the behavior of the particle.

  12. Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

    Science.gov (United States)

    1996-03-01

    differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

  13. Study of vapour phase dynamics with nitrogen boiling in the field of centrifugal forces

    Energy Technology Data Exchange (ETDEWEB)

    Levchenko, N M; Kolod' ko, I M

    1987-07-01

    The vapour phase dynamics during film boiling of liquid nitrogen on horizontal wire in the field of centrifugal forces has been studied experimentally in a wide range of overloads(1 less than or equal to eta less than or equal to 375) and heat fluxes (q/sub kp2/ less than or equal to q less than or equal to 4q/sub kpi/). The available data confirmed and the theoretical relationships suggested make it possible to calculate the hydrodynamic film boiling parameters (wave length, bubble departure diameter and frequency) for other liquids.

  14. Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes

    DEFF Research Database (Denmark)

    Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus

    2015-01-01

    The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical...

  15. Force Field Benchmark of the TraPPE_UA for Polar Liquids: Density, Heat of Vaporization, Dielectric Constant, Surface Tension, Volumetric Expansion Coefficient, and Isothermal Compressibility.

    Science.gov (United States)

    Núñez-Rojas, Edgar; Aguilar-Pineda, Jorge Alberto; Pérez de la Luz, Alexander; de Jesús González, Edith Nadir; Alejandre, José

    2018-02-08

    The transferable potential for a phase equilibria force field in its united-atom version, TraPPE_UA, is evaluated for 41 polar liquids that include alcohols, thiols, ethers, sulfides, aldehydes, ketones, and esters to determine its ability to reproduce experimental properties that were not included in the parametrization procedure. The intermolecular force field parameters for pure components were fit to reproduce experimental boiling temperature, vapor-liquid coexisting densities, and critical point (temperature, density, and pressure) using Monte Carlo simulations in different ensembles. The properties calculated in this work are liquid density, heat of vaporization, dielectric constant, surface tension, volumetric expansion coefficient, and isothermal compressibility. Molecular dynamics simulations were performed in the gas and liquid phases, and also at the liquid-vapor interface. We found that relative error between calculated and experimental data is 1.2% for density, 6% for heat of vaporization, and 6.2% for surface tension, in good agreement with the experimental data. The dielectric constant is systematically underestimated, and the relative error is 37%. Evaluating the performance of the force field to reproduce the volumetric expansion coefficient and isothermal compressibility requires more experimental data.

  16. Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

    Energy Technology Data Exchange (ETDEWEB)

    Tamma, Venkata Ananth [CaSTL Center, Department of Chemistry, University of California, Irvine, California 92697 (United States); Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu [Department of Electrical Engineering and Computer Science, 142 Engineering Tower, University of California, Irvine, California 92697 (United States); Nowak, Derek [Molecular Vista, Inc., 6840 Via Del Oro, San Jose, California 95119 (United States)

    2016-06-06

    We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol and l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.

  17. raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

    Science.gov (United States)

    Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

    2017-03-01

    We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

  18. Projection and nested force-gradient methods for quantum field theories

    Energy Technology Data Exchange (ETDEWEB)

    Shcherbakov, Dmitry

    2017-07-26

    For the Hybrid Monte Carlo algorithm (HMC), often used to study the fundamental quantum field theory of quarks and gluons, quantum chromodynamics (QCD), on the lattice, one is interested in efficient numerical time integration schemes which preserve geometric properties of the flow and are optimal in terms of computational costs per trajectory for a given acceptance rate. High order numerical methods allow the use of larger step sizes, but demand a larger computational effort per step; low order schemes do not require such large computational costs per step, but need more steps per trajectory. So there is a need to balance these opposing effects. In this work we introduce novel geometric numerical time integrators, namely, projection and nested force-gradient methods in order to improve the efficiency of the HMC algorithm in application to the problems of quantum field theories.

  19. Coupled force-balance and particle-occupation rate equations for high-field electron transport

    International Nuclear Information System (INIS)

    Lei, X. L.

    2008-01-01

    It is pointed out that in the framework of balance-equation approach, the coupled force-balance and particle-occupation rate equations can be used as a complete set of equations to determine the high-field transport of semiconductors in both strong and weak electron-electron interaction limits. We call to attention that the occupation rate equation conserves the total particle number and maintains the energy balance of the relative electron system, and there is no need to introduce any other term in it. The addition of an energy-drift term in the particle-occupation rate equation [Phys. Rev. B 71, 195205 (2005)] is physically inadequate for the violation of the total particle-number conservation and the energy balance. It may lead to a substantial unphysical increase of the total particle number by the application of a dc electric field

  20. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor.

    Science.gov (United States)

    Dennis, John Ojur; Ahmad, Farooq; Khir, M Haris Bin Md; Bin Hamid, Nor Hisham

    2015-07-27

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT.

  1. Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.

    Science.gov (United States)

    Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo

    2013-03-21

    The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

  2. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field

    National Research Council Canada - National Science Library

    Bunte, Steven

    2000-01-01

    To investigate the mechanical and other condensed phase properties of energetic materials using atomistic simulation techniques, the COMPASS force field has been expanded to include high-energy nitro functional groups...

  3. NONLINEAR FORCE-FREE MAGNETIC FIELD FITTING TO CORONAL LOOPS WITH AND WITHOUT STEREOSCOPY

    International Nuclear Information System (INIS)

    Aschwanden, Markus J.

    2013-01-01

    We developed a new nonlinear force-free magnetic field (NLFFF) forward-fitting algorithm based on an analytical approximation of force-free and divergence-free NLFFF solutions, which requires as input a line-of-sight magnetogram and traced two-dimensional (2D) loop coordinates of coronal loops only, in contrast to stereoscopically triangulated three-dimensional loop coordinates used in previous studies. Test results of simulated magnetic configurations and from four active regions observed with STEREO demonstrate that NLFFF solutions can be fitted with equal accuracy with or without stereoscopy, which relinquishes the necessity of STEREO data for magnetic modeling of active regions (on the solar disk). The 2D loop tracing method achieves a 2D misalignment of μ 2 = 2.°7 ± 1.°3 between the model field lines and observed loops, and an accuracy of ≈1.0% for the magnetic energy or free magnetic energy ratio. The three times higher spatial resolution of TRACE or SDO/AIA (compared with STEREO) also yields a proportionally smaller misalignment angle between model fit and observations. Visual/manual loop tracings are found to produce more accurate magnetic model fits than automated tracing algorithms. The computation time of the new forward-fitting code amounts to a few minutes per active region.

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

    International Nuclear Information System (INIS)

    Green, P.H.

    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

  5. Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

    Directory of Open Access Journals (Sweden)

    Kenichi Dedachi

    2013-01-01

    Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

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

    International Nuclear Information System (INIS)

    Peng Yi; Huang Heji; Pan Wenxia

    2013-01-01

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

  7. Systematic Analysis of Theses in the Field of Emergency Medicine in Turkey

    Directory of Open Access Journals (Sweden)

    Erdem CEVIK

    2015-03-01

    Full Text Available SUMMARY: Objectives: The aim of this study is to systematically evaluate the theses in the field of emergency medicine in Turkey and to determine whether they were published as a scientific paper. Methods: This is a retrospective observational study. Theses in the field of emergency medicine between 1998 and 2013 were browsed from the internet database of National Thesis Center (Council of Higher Education. Study type, both if it was in the field of emergency, or if it was published and the journal's scope of published studies were assessed and recorded in the study chart. Results: 579 theses were included in the study. 27.1% of them were published and 14.9% of them were published in SCI/SCI-E journals. Advisors of theses were emergency medicine specialists in 67.6% of theses and 493 (85.1% of them were in the field of emergency medicine. 77.4% of theses were observational and 20.9% were experimental study. Most of the experimental studies (72.7%, n=88 were animal studies. Conclusions: It was concluded that very few theses in the field of emergency medicine were published in journals that were indexed in SCI/SCI-E. Key words: Emergency medicine, systematic analysis, theses

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

    Science.gov (United States)

    Saito, Minoru; Okazaki, Isao

    2009-12-01

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

  9. Air Force Officer Accession Planning: Addressing Key Gaps in Meeting Career Field Academic Degree Requirements for Nonrated Officers

    Science.gov (United States)

    2016-06-09

    C O R P O R A T I O N Research Report Air Force Officer Accession Planning Addressing Key Gaps in Meeting Career Field Academic Degree Requirements...potential performance, and how to include these quality measures in the classification process. The research sponsor asked us to focus on academic ...Andrew P., and James K. Lowe, “Decision Support for the Career Field Selection Process at the US Air Force Academy,” European Journal of Operational

  10. Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges

    Directory of Open Access Journals (Sweden)

    Agustín Leobardo Herrera-May

    2016-08-01

    Full Text Available Microelectromechanical systems (MEMS resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases.

  11. Construction of force-free fields which have toroidal surfaces about a given surface

    International Nuclear Information System (INIS)

    Bouligand, G.

    1983-05-01

    A study of two-fields (B vector, rotB vector) of conservative flux which admits a family of toroidal surfaces of parameter phi on a domain limited by a given surface S, suggests their construction by a Cauchy-Arzela method of step by step. Taking into account the Newcomb condition this method is consistent with force-free magnetic fields and with helical equilibria with scalar pressure. The method supposes that B vector is of class C 1 . This construction makes use of the remarkable property of the field B vector to be the surface gradient of a generating multivalued function Q on a closed surface. Consequently, the initial surface will be given with its normal metric coefficient K; that is to say, B vector admits a family F of homotopic surfaces on a infinitesimal domain about S, an element of F. From this, the periodic part of Q is a solution of a Beltrami equation for the flux conservation of which numerical resolution is envisaged. The study of these fields is made in a biorthogonal system of coordinates. The coeffficients of the two fundamental metric forms of magnetic surfaces vary with phi and are interrelated by a sixth order differential system of equations which gives their variation [fr

  12. Controlling the structure of forced convective flow by means of rotating magnetic-field inductors

    International Nuclear Information System (INIS)

    Sorkin, M.Z.; Mozgirs, O.Kh.

    1993-01-01

    The forced convective flow generated by a rotating magnetic-field inductor is used in a melt as a means of controlling the transfer of mass and heat in the case of directed crystallization. An obvious advantage in using a rotating field is the generation of azimuthal twisting of the fluid, this providing for an evening out of the crystallization conditions in the azimuthal direction under nonsymmetrical boundary conditions in an actual technological process. From the standpoint of affecting the crystallization processes it would be preferable to use an inductor which would allow alteration of the intensity and of the direction of the meridional flow. Mixing in the form of velocity pulsations generated by the inductor within the melt would be if interest from the standpoint of affecting the crystallization processes, in particular to intensify the crystallization purification. The authors propose the use of a double magnetohydrodynmic rotator which consists of two rotating magnetic-field inductors, separated in altitude, with separate power supplies. The supply of power to the inductors with various current loads allows the generation of a controllable nonuniformity in field distribution and in the azimuthal velocity through the altitude and thus allows control of both the intensity and configuration of the meridional flows. The dual rotator makes it possible to purposefully control the structure of the meridional flows and the pulsation component of velocity and can be recommended for use in processes of directed crystallization as well as in crystallization purification. 4 refs., 3 figs

  13. TEMPORAL AND SPATIAL RELATIONSHIP OF FLARE SIGNATURES AND THE FORCE-FREE CORONAL MAGNETIC FIELD

    Energy Technology Data Exchange (ETDEWEB)

    Thalmann, J. K.; Veronig, A.; Su, Y., E-mail: julia.thalmann@uni-graz.at [Institute of Physics/IGAM, University of Graz, Universitätsplatz 5/II, A-8010 Graz (Austria)

    2016-08-01

    We investigate the plasma and magnetic environment of active region NOAA 11261 on 2011 August 2 around a GOES M1.4 flare/CME (SOL2011-08-02T06:19). We compare coronal emission at the (extreme) ultraviolet and X-ray wavelengths, using SDO AIA and RHESSI images, in order to identify the relative timing and locations of reconnection-related sources. We trace flare ribbon signatures at ultraviolet wavelengths in order to pin down the intersection of previously reconnected flaring loops in the lower solar atmosphere. These locations are used to calculate field lines from three-dimensional (3D) nonlinear force-free magnetic field models, established on the basis of SDO HMI photospheric vector magnetic field maps. Using this procedure, we analyze the quasi-static time evolution of the coronal model magnetic field previously involved in magnetic reconnection. This allows us, for the first time, to estimate the elevation speed of the current sheet’s lower tip during an on-disk observed flare as a few kilometers per second. A comparison to post-flare loops observed later above the limb in STEREO EUVI images supports this velocity estimate. Furthermore, we provide evidence for an implosion of parts of the flaring coronal model magnetic field, and identify the corresponding coronal sub-volumes associated with the loss of magnetic energy. Finally, we spatially relate the build up of magnetic energy in the 3D models to highly sheared fields, established due to the dynamic relative motions of polarity patches within the active region.

  14. HIV/STI interventions targeting women who experience forced sex: A systematic review of global literature.

    Science.gov (United States)

    Deming, Michelle E; Bhochhibhoya, Amir; Ingram, LaDrea; Stafford, Crystal; Li, Xiaoming

    2018-04-12

    Women are disproportionately affected by HIV in many regions of the world and they represent the fastest growing demographic in the HIV epidemic. In addition, sexual violence against women is a global public health issue which increases women's vulnerability of HIV/STI acquisition. However, the relationship between sexual violence and HIV/STI risk are complex and contribute to the growing epidemic of women infected with HIV/STIs. Our purpose for this review is to examine existing HIV/STI interventions that target women who experience forced sex. Interventions designed to address women's unique needs in HIV/STI prevention are critical in reducing women's vulnerability to HIV/STIs.

  15. Determination of the viscous acoustic field for liquid drop positioning/forcing in an acoustic levitation chamber in microgravity

    Science.gov (United States)

    Lyell, Margaret J.

    1992-01-01

    The development of acoustic levitation systems has provided a technology with which to undertake droplet studies as well as do containerless processing experiments in a microgravity environment. Acoustic levitation chambers utilize radiation pressure forces to position/manipulate the drop. Oscillations can be induced via frequency modulation of the acoustic wave, with the modulated acoustic radiation vector acting as the driving force. To account for tangential as well as radial forcing, it is necessary that the viscous effects be included in the acoustic field. The method of composite expansions is employed in the determination of the acoustic field with viscous effects.

  16. Influence of AC external magnetic field on guidance force relaxation between HTS bulk and NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Longcai [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)], E-mail: zhlcai2000@163.com; Wang Suyu; Wang Jiasu; Zheng Jun [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)

    2007-12-01

    Superconducting maglev vehicle is one of the most promising applications of HTS bulks. In such a system, the HTS bulks are always exposed to time-varying external magnetic field, which is generated by the inhomogeneous surface magnetic field of the NdFeB guideway. So it is required to study whether the guidance force of the bulks is influenced by the inhomogeneity. In this paper, we studied the characteristics of the guidance force relaxation between the HTS bulk and the NdFeB guideway by an experiment in which AC external magnetic field generated by an electromagnet was used to simulate the time-varying external magnetic field caused by the inhomogeneity of the guideway. From the experiment results, it was found that the guidance force was decreased with the application of the AC external magnetic field, and the decay increased with the amplitude and was almost independent of the frequency.

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

    Science.gov (United States)

    Marston, Philip L; Zhang, Likun

    2017-05-01

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

  18. Field Monitoring of Deformations and Internal Forces of Surrounding Rocks and Lining Structures in the Construction of the Gangkou Double-Arched Tunnel—A Case Study

    Directory of Open Access Journals (Sweden)

    Qixiang Yan

    2017-02-01

    Full Text Available Double-arched tunnel is a special and complex underground structure which needs to be monitored carefully during construction. Taking the Gangkou tunnel as the engineering background, this paper presents a case study of field monitoring of a representative double-arched tunnel. Typical cross sections were chosen in each class of surrounding rock masses in the tunnel area and different types of sensors were embedded in designed locations, and the deformations and forces of both surrounding rocks and lining structures were monitored systematically. The dynamic evolution as well as the spatial distribution characteristics of the monitoring data including the internal displacements of surrounding rocks and the contact pressures between surrounding rocks and primary linings, the axial forces in rock bolts and the internal forces in both steel arches and secondary linings were analyzed. The monitoring and analysis results show that the deformations and forces of both surrounding rocks and lining structures are directly related to the construction procedures, geological conditions and locations in the double-arched tunnel. According to the results, some reasonable suggestions were provided for the improvement of the tunnel construction. This study will provide useful reference and guidance for the design, construction and monitoring of similar engineering projects in future.

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

    Science.gov (United States)

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

    2018-07-10

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

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

    Directory of Open Access Journals (Sweden)

    Jiang Hualiang

    2010-11-01

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

  1. Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

    Science.gov (United States)

    Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

    2018-03-01

    Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

  2. Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

    Directory of Open Access Journals (Sweden)

    R. Hedayati

    2018-03-01

    Full Text Available Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of “action-at-a-distance” metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson’s ratios as a way of making “action-at-a-distance” metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable robotics and exosuits.

  3. Effects of kinesthetic and cutaneous stimulation during the learning of a viscous force field.

    Science.gov (United States)

    Rosati, Giulio; Oscari, Fabio; Pacchierotti, Claudio; Prattichizzo, Domenico

    2014-01-01

    Haptic stimulation can help humans learn perceptual motor skills, but the precise way in which it influences the learning process has not yet been clarified. This study investigates the role of the kinesthetic and cutaneous components of haptic feedback during the learning of a viscous curl field, taking also into account the influence of visual feedback. We present the results of an experiment in which 17 subjects were asked to make reaching movements while grasping a joystick and wearing a pair of cutaneous devices. Each device was able to provide cutaneous contact forces through a moving platform. The subjects received visual feedback about joystick's position. During the experiment, the system delivered a perturbation through (1) full haptic stimulation, (2) kinesthetic stimulation alone, (3) cutaneous stimulation alone, (4) altered visual feedback, or (5) altered visual feedback plus cutaneous stimulation. Conditions 1, 2, and 3 were also tested with the cancellation of the visual feedback of position error. Results indicate that kinesthetic stimuli played a primary role during motor adaptation to the viscous field, which is a fundamental premise to motor learning and rehabilitation. On the other hand, cutaneous stimulation alone appeared not to bring significant direct or adaptation effects, although it helped in reducing direct effects when used in addition to kinesthetic stimulation. The experimental conditions with visual cancellation of position error showed slower adaptation rates, indicating that visual feedback actively contributes to the formation of internal models. However, modest learning effects were detected when the visual information was used to render the viscous field.

  4. An atomistic fingerprint algorithm for learning ab initio molecular force fields

    Science.gov (United States)

    Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

    2018-01-01

    Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

  5. Pedagogical systematic derivation of Noether point symmetries in special relativistic field theories and extended gravity cosmology

    International Nuclear Information System (INIS)

    Haas, Fernando

    2016-01-01

    A didactic and systematic derivation of Noether point symmetries and conserved currents is put forward in special relativistic field theories, without a priori assumptions about the transformation laws. Given the Lagrangian density, the invariance condition develops as a set of partial differential equations determining the symmetry transformation. The solution is provided in the case of real scalar, complex scalar, free electromagnetic, and charged electromagnetic fields. Besides the usual conservation laws, a less popular symmetry is analyzed: the symmetry associated with the linear superposition of solutions, whenever applicable. The role of gauge invariance is emphasized. The case of the charged scalar particle under external electromagnetic fields is considered, and the accompanying Noether point symmetries determined. Noether point symmetries for a dynamical system in extended gravity cosmology are also deduced. (paper)

  6. Pedagogical systematic derivation of Noether point symmetries in special relativistic field theories and extended gravity cosmology

    Science.gov (United States)

    Haas, Fernando

    2016-11-01

    A didactic and systematic derivation of Noether point symmetries and conserved currents is put forward in special relativistic field theories, without a priori assumptions about the transformation laws. Given the Lagrangian density, the invariance condition develops as a set of partial differential equations determining the symmetry transformation. The solution is provided in the case of real scalar, complex scalar, free electromagnetic, and charged electromagnetic fields. Besides the usual conservation laws, a less popular symmetry is analyzed: the symmetry associated with the linear superposition of solutions, whenever applicable. The role of gauge invariance is emphasized. The case of the charged scalar particle under external electromagnetic fields is considered, and the accompanying Noether point symmetries determined. Noether point symmetries for a dynamical system in extended gravity cosmology are also deduced.

  7. Systematic observation of tunneling field-ionization in highly excited Rb Rydberg atoms

    International Nuclear Information System (INIS)

    Kishimoto, Y.; Tada, M.; Kominato, K.; Shibata, M.; Yamada, S.; Haseyama, T.; Ogawa, I.; Funahashi, H.; Yamamoto, K.; Matsuki, S.

    2002-01-01

    Pulsed field ionization of high-n (90≤n≤150) manifold states in Rb Rydberg atoms has been investigated in high slew-rate regime. Two peaks in the field ionization spectra were systematically observed for the investigated n region, where the field values at the lower peak do not almost depend on the excitation energy in the manifold, while those at the higher peak increase with increasing excitation energy. The fraction of the higher peak component to the total ionization signals increases with increasing n, exceeding 80% at n=147. Characteristic behavior of the peak component and the comparison with theoretical predictions indicate that the higher peak component is due to the tunneling process. The obtained results show that the tunneling process plays increasingly the dominant role at such highly excited nonhydrogenic Rydberg atoms

  8. Trampoline effect and the force field inside the void in complex plasma under microgravity conditions

    International Nuclear Information System (INIS)

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

    2005-01-01

    The PKE-Nefedov facility onboard the International Space Station (ISS),operational since March, 2'001, has enabled the study of complex (dusty) plasmas under microgravity conditions. A complex plasma is generated by introducing micron sized grains in a capacitively coupled rf discharge. The grains form a cloud inside the bulk of the discharge and can be easily visualized with the help of standard tools-laser illumination and video cameras. In most of the experiments under microgravity conditions the central region of the discharge is free of grains a so called void is formed. Due to recent theoretical advances, showing that the ion drag force can be more than a factor of ten larger than had traditionally been believed, void formation is now through to be a consequence of this (enhanced) interaction. The way this process works is the following: the ions drifting from the central region of a discharge to its walls and electrodes transfer their momentum to the grains pushing them out of the center. However, no direct experimental results on the origin of the void formation were reported so far. In this paper we report new results on the observation of a weak instability of the void-complex plasma interface observed at a relatively low gas pressure (p=12Pa). The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called trampoline effect), The trajectories of injected particles are analyzed providing information on the force field and potential energy distribution inside the void. For the relatively low neutral gas pressure used in the experiment a direct comparison with theory involving a model of the ion drag force in the collisionless regime is possible. Such a comparison yields good agreement, implying that we have observed the first experimental confirmation of the ion drag mechanism as being responsible for the void formation. (Author)

  9. Trampoline effect and the force field inside the void in complex plasma under microgravity conditions

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-07-01

    The PKE-Nefedov facility onboard the International Space Station (ISS),operational since March, 2'001, has enabled the study of complex (dusty) plasmas under microgravity conditions. A complex plasma is generated by introducing micron sized grains in a capacitively coupled rf discharge. The grains form a cloud inside the bulk of the discharge and can be easily visualized with the help of standard tools-laser illumination and video cameras. In most of the experiments under microgravity conditions the central region of the discharge is free of grains a so called void is formed. Due to recent theoretical advances, showing that the ion drag force can be more than a factor of ten larger than had traditionally been believed, void formation is now through to be a consequence of this (enhanced) interaction. The way this process works is the following: the ions drifting from the central region of a discharge to its walls and electrodes transfer their momentum to the grains pushing them out of the center. However, no direct experimental results on the origin of the void formation were reported so far. In this paper we report new results on the observation of a weak instability of the void-complex plasma interface observed at a relatively low gas pressure (p=12Pa). The instability leads to periodic injections of a relatively small number of particles into the void region (by analogy this effect is called trampoline effect), The trajectories of injected particles are analyzed providing information on the force field and potential energy distribution inside the void. For the relatively low neutral gas pressure used in the experiment a direct comparison with theory involving a model of the ion drag force in the collisionless regime is possible. Such a comparison yields good agreement, implying that we have observed the first experimental confirmation of the ion drag mechanism as being responsible for the void formation. (Author)

  10. Volume pinning force and upper critical field of irradiated Nb3Sn

    International Nuclear Information System (INIS)

    Maier, P.; Seibt, E.

    1981-01-01

    Irradiation by neutrons and ions in A15 superconductors (Nb 3 Sn, V 3 Ga) exerts a stronger influence on the pinning behavior than in nonordered alloys (NbTi). In this work it is shown for deuteron irradiated Nb 3 /Sn wires prepared by the bronze process that the dose curve of the volume pinning force P/sub V/ can be conveniently described by a sum of two terms, due to the grain boundary pinning and to the radiation pinning, respectively. After deduction of the contribution by the radiation-induced pinning centers, good agreement is obtained between the measured P/sub V/ values and those calculated using the upper critical field B/sub c/2 and the transition temperature T/sub c/ on the basis of the irradiation fluence. The use of a theoretical relationship between B/sub c/2 and T/sub c/ is supported by measured values. Application to multifilamentary superconductors with high current carrying capabilities simplifies the calculation of P/sub V/, since the radiation induced volume pinning force can be neglected

  11. Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

    DEFF Research Database (Denmark)

    Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

    2004-01-01

    of the (gg, gt and tg) rotamers of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol. respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error...

  12. Research on desulfurisation of fine coal under compounding the physics force field

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Y.; Fu, D.; Tao, D.; Liu, J.; Zhao, Y. [China University of Mining and Technology, Xuzhou (China)

    2005-08-15

    Desulphurization experiment carried on under compounding the physics force field was described for -0.5 mm fine particle of high sulphur coal. The experiment factorial plan of desulphurization on centrifugal gravity Falcon separator was designed and its results were analyzed by using Design-Expert 6.0 software. The 2-reactor interaction relation model between comprehensive desulphurization efficiency of pyrite sulphur and different operation variable was drawn, i.e. 2 FI model, and the 2-factor interaction on pyrite desulphurization efficiency of the operation factors differently was analyzed. The interaction on pyrite desulphurization efficiency of feed rate and feed concentration is significant. The optimization test condition for desulphurization was proposed by Design-Expert 6.0, and comprehensive desulphurization efficiency of 86.90% can be achieved. 5 refs., 3 figs., 7 tabs.

  13. Plasmonic micropillars for precision cell force measurement across a large field-of-view

    Science.gov (United States)

    Xiao, Fan; Wen, Ximiao; Tan, Xing Haw Marvin; Chiou, Pei-Yu

    2018-01-01

    A plasmonic micropillar platform with self-organized gold nanospheres is reported for the precision cell traction force measurement across a large field-of-view (FOV). Gold nanospheres were implanted into the tips of polymer micropillars by annealing gold microdisks with nanosecond laser pulses. Each gold nanosphere is physically anchored in the center of a pillar tip and serves as a strong, point-source-like light scattering center for each micropillar. This allows a micropillar to be clearly observed and precisely tracked even under a low magnification objective lens for the concurrent and precision measurement across a large FOV. A spatial resolution of 30 nm for the pillar deflection measurement has been accomplished on this platform with a 20× objective lens.

  14. Intermolecular Force Field Parameters Optimization for Computer Simulations of CH4 in ZIF-8

    Directory of Open Access Journals (Sweden)

    Phannika Kanthima

    2016-01-01

    Full Text Available The differential evolution (DE algorithm is applied for obtaining the optimized intermolecular interaction parameters between CH4 and 2-methylimidazolate ([C4N2H5]− using quantum binding energies of CH4-[C4N2H5]− complexes. The initial parameters and their upper/lower bounds are obtained from the general AMBER force field. The DE optimized and the AMBER parameters are then used in the molecular dynamics (MD simulations of CH4 molecules in the frameworks of ZIF-8. The results show that the DE parameters are better for representing the quantum interaction energies than the AMBER parameters. The dynamical and structural behaviors obtained from MD simulations with both sets of parameters are also of notable differences.

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

    Science.gov (United States)

    Lindahl, B I; Arhem, P

    1994-11-07

    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.

  16. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

    DEFF Research Database (Denmark)

    Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.

    2014-01-01

    validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule....... In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....

  17. Screening for Syphilis: Updated Evidence Report and Systematic Review for the US Preventive Services Task Force.

    Science.gov (United States)

    Cantor, Amy G; Pappas, Miranda; Daeges, Monica; Nelson, Heidi D

    2016-06-07

    Screening for syphilis infection is currently recommended for high-risk individuals, including those with previous syphilis infection, an infected sexual partner, HIV infection, or more than 4 sex partners in the preceding year. To update a 2004 systematic review of studies of syphilis screening effectiveness, test accuracy, and screening harms in nonpregnant adults and adolescents. Cochrane Central Register of Controlled Trials and Cochrane Database of Systematic Reviews through October 2015 and Ovid MEDLINE (January 2004 to October 2015), with updated search through March 2016. English-language trials and observational studies of screening effectiveness, test accuracy, and screening harms in nonpregnant adults and adolescents. One investigator abstracted data, a second checked data for accuracy, and 2 investigators independently assessed study quality using predefined criteria. Transmission of disease, including HIV; complications of syphilis; diagnostic accuracy; and harms of screening. No evidence was identified regarding the effectiveness of screening on clinical outcomes or the effectiveness of risk assessment instruments; the harms of screening; or the effectiveness of screening in average-risk, nonpregnant adolescents or adults or high-risk individuals other than men who have sex with men (MSM) or men who are HIV positive. Four non-US studies indicated higher rates of syphilis detection with screening every 3 months vs 6 or 12 months for early syphilis in HIV-positive men or MSM. For example, there was an increased proportion of asymptomatic, higher-risk MSM in Australia (n = 6789 consultations) receiving a diagnosis of early syphilis when tested every 3 months vs annually (53% vs 16%, P = .001), but no difference among low-risk MSM. Treponemal and nontreponemal tests were accurate in asymptomatic individuals (sensitivity >85%, specificity >91%) in 3 studies but required confirmatory testing. Reverse sequence testing with an initial automated

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

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  19. The outflows accelerated by the magnetic fields and radiation force of accretion disks

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Xinwu, E-mail: cxw@shao.ac.cn [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, Shanghai, 200030 (China)

    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, Θ=c{sub s}{sup 2}/r{sup 2}Ω{sub K}{sup 2}≪(H/r){sup 2}, which is significantly lower than that of a gas-pressure-dominated disk, Θ ∼ (H/r){sup 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.

  20. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  1. Correlation Between Orthodontic Forces and Root Resorption – a Systematic Review of the Literature

    Directory of Open Access Journals (Sweden)

    Vlasa Alexandru

    2016-09-01

    Full Text Available Orthodontically induced external apical root resorption (OIEARR is a major concern regarding periodontal status after nonsurgical orthodontic treatment. The aim of this study was to assess this sequel by a systematic review of published data. For assessment, we performed an electronic search of one database for comprehensive data, using keywords in different combinations: “root resorption”, “periodontics” and “nonsurgical orthodontic treatment”. We supplemented the results searching by hand in published journals and we cross-referenced with the accessed articles. Patients included in the results presented a good general health status, with no previous history of OIEARR and no other associated pathologies. Finally, twenty-three studies were selected and included in this review. A high prevalence (69–98% and moderate severity of OIEARR (<5 mm and <1/3 from original root length were reported. No difference in root resorption was found regarding the sex of the patients. A moderate positive correlation between treatment duration and root resorption was found. Also, a mild correlation regarding antero-posterior apical displacement and root resorption was found.

  2. Effects of Anisotropic Thermal Conductivity and Lorentz Force on the Flow and Heat Transfer of a Ferro-Nanofluid in a Magnetic Field

    Directory of Open Access Journals (Sweden)

    Yubai Li

    2017-07-01

    Full Text Available In this paper, we study the effects of the Lorentz force and the induced anisotropic thermal conductivity due to a magnetic field on the flow and the heat transfer of a ferro-nanofluid. The ferro-nanofluid is modeled as a single-phase fluid, where the viscosity depends on the concentration of nanoparticles; the thermal conductivity shows anisotropy due to the presence of the nanoparticles and the external magnetic field. The anisotropic thermal conductivity tensor, which depends on the angle of the applied magnetic field, is suggested considering the principle of material frame indifference according to Continuum Mechanics. We study two benchmark problems: the heat conduction between two concentric cylinders as well as the unsteady flow and heat transfer in a rectangular channel with three heated inner cylinders. The governing equations are made dimensionless, and the flow and the heat transfer characteristics of the ferro-nanofluid with different angles of the magnetic field, Hartmann number, Reynolds number and nanoparticles concentration are investigated systematically. The results indicate that the temperature field is strongly influenced by the anisotropic behavior of the nanofluids. In addition, the magnetic field may enhance or deteriorate the heat transfer performance (i.e., the time-spatially averaged Nusselt number in the rectangular channel depending on the situations.

  3. MAGNETO-FRICTIONAL MODELING OF CORONAL NONLINEAR FORCE-FREE FIELDS. I. TESTING WITH ANALYTIC SOLUTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Y.; Keppens, R. [School of Astronomy and Space Science, Nanjing University, Nanjing 210023 (China); Xia, C. [Centre for mathematical Plasma-Astrophysics, Department of Mathematics, KU Leuven, B-3001 Leuven (Belgium); Valori, G., E-mail: guoyang@nju.edu.cn [University College London, Mullard Space Science Laboratory, Holmbury St. Mary, Dorking, Surrey RH5 6NT (United Kingdom)

    2016-09-10

    We report our implementation of the magneto-frictional method in the Message Passing Interface Adaptive Mesh Refinement Versatile Advection Code (MPI-AMRVAC). The method aims at applications where local adaptive mesh refinement (AMR) is essential to make follow-up dynamical modeling affordable. We quantify its performance in both domain-decomposed uniform grids and block-adaptive AMR computations, using all frequently employed force-free, divergence-free, and other vector comparison metrics. As test cases, we revisit the semi-analytic solution of Low and Lou in both Cartesian and spherical geometries, along with the topologically challenging Titov–Démoulin model. We compare different combinations of spatial and temporal discretizations, and find that the fourth-order central difference with a local Lax–Friedrichs dissipation term in a single-step marching scheme is an optimal combination. The initial condition is provided by the potential field, which is the potential field source surface model in spherical geometry. Various boundary conditions are adopted, ranging from fully prescribed cases where all boundaries are assigned with the semi-analytic models, to solar-like cases where only the magnetic field at the bottom is known. Our results demonstrate that all the metrics compare favorably to previous works in both Cartesian and spherical coordinates. Cases with several AMR levels perform in accordance with their effective resolutions. The magneto-frictional method in MPI-AMRVAC allows us to model a region of interest with high spatial resolution and large field of view simultaneously, as required by observation-constrained extrapolations using vector data provided with modern instruments. The applications of the magneto-frictional method to observations are shown in an accompanying paper.

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

    International Nuclear Information System (INIS)

    Vega, Ian; Detweiler, Steven

    2008-01-01

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

  5. From Thin Films to Monolayer, A Systematic Approach for BTBT Based Organic Field Effect Transistors

    OpenAIRE

    Yousefi Amin, Atefeh

    2013-01-01

    This work focuses on theoretical and experimental understanding of how low-voltage organic field effect transistors based on BTBT ([1] benzothieno[3,2-b][1]benzothiophene) operate. The focus is in deducing the electrical and interfacial landscape in the device, while using ultra-thin hybrid layers of AlOx/SAM (Self-Assembled Monolayer) as a dielectric. This thesis proposes a systematic study on an optimum solution for facing challenges in molecular and device properties. It first focuses on d...

  6. Compatibility of the Chameleon-Field Model with Fifth-Force Experiments, Cosmology, and PVLAS and CAST Results

    International Nuclear Information System (INIS)

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

    2007-01-01

    We analyze the PVLAS results using a chameleon field whose properties depend on the environment. We find that, assuming a runaway bare potential V(φ) and a universal coupling to matter, the chameleon potential is such that the scalar field can act as dark energy. Moreover, the chameleon-field model is compatible with the CERN Axion Solar Telescope results, fifth-force experiments, and cosmology

  7. Electric field metrology for SI traceability: Systematic measurement uncertainties in electromagnetically induced transparency in atomic vapor

    Science.gov (United States)

    Holloway, Christopher L.; Simons, Matt T.; Gordon, Joshua A.; Dienstfrey, Andrew; Anderson, David A.; Raithel, Georg

    2017-06-01

    We investigate the relationship between the Rabi frequency (ΩRF, related to the applied electric field) and Autler-Townes (AT) splitting, when performing atom-based radio-frequency (RF) electric (E) field strength measurements using Rydberg states and electromagnetically induced transparency (EIT) in an atomic vapor. The AT splitting satisfies, under certain conditions, a well-defined linear relationship with the applied RF field amplitude. The EIT/AT-based E-field measurement approach derived from these principles is currently being investigated by several groups around the world as a means to develop a new SI-traceable RF E-field measurement technique. We establish conditions under which the measured AT-splitting is an approximately linear function of the RF electric field. A quantitative description of systematic deviations from the linear relationship is key to exploiting EIT/AT-based atomic-vapor spectroscopy for SI-traceable field measurement. We show that the linear relationship is valid and can be used to determine the E-field strength, with minimal error, as long as the EIT linewidth is small compared to the AT-splitting. We also discuss interesting aspects of the thermal dependence (i.e., hot- versus cold-atom) of this EIT-AT technique. An analysis of the transition from cold- to hot-atom EIT in a Doppler-mismatched cascade system reveals a significant change of the dependence of the EIT linewidth on the optical Rabi frequencies and of the AT-splitting on ΩRF.

  8. Systematic Analysis of Theses in the Field of Emergency Medicine in Turkey.

    Science.gov (United States)

    Cevik, Erdem; Karakus Yilmaz, Banu; Acar, Yahya Ayhan; Dokur, Mehmet

    2015-03-01

    The aim of this study is to systematically evaluate the theses in the field of emergency medicine in Turkey and to determine whether they were published as a scientific paper. This is a retrospective observational study. Theses in the field of emergency medicine between 1998 and 2013 were browsed from the internet database of National Thesis Center (Council of Higher Education). Study type, both if it was in the field of emergency, or if it was published and the journal's scope of published studies were assessed and recorded in the study chart. 579 theses were included in the study. 27.1% of them were published and 14.9% of them were published in SCI/SCI-E journals. Advisors of theses were emergency medicine specialists in 67.6% of theses and 493 (85.1%) of them were in the field of emergency medicine. 77.4% of theses were observational and 20.9% were experimental study. Most of the experimental studies (72.7%, n=88) were animal studies. It was concluded that very few theses in the field of emergency medicine were published in journals that were indexed in SCI/SCI-E.

  9. Bioethics teaching in the field of health sciences in Brazil: study of systematic review

    Directory of Open Access Journals (Sweden)

    Antônio Macena Figueiredo

    2009-01-01

    Full Text Available The objective of this work is to know the scientific productions about the bioethics teaching in the field of Sciences of Health in Brazil. Exploratory and descriptive study used the systematic revision technique to collect data. Survey carried through in periodic scientific in the following databases: LILACS, SciELO, BDENF, BBO, and the database of thesis of CAPES and BDTD/IBICT. 18 articles and 12 post-graduation stricto sensu works were identified. The articles were classified in original articles, of revision and reflection. The dissertations and thesis were included in the categories: studies with or without empirical evidences. It was concluded that, after two decades of teaching and research, the works related to the Bioethics teaching in the field of the health are still few. Keywords: Bioethics; Teaching; Higher Education; Health Sciences; Brazil.

  10. Supersymmetric gauged double field theory: systematic derivation by virtue of twist

    International Nuclear Information System (INIS)

    Cho, Wonyoung; Fernández-Melgarejo, J.J.; Jeon, Imtak; Park, Jeong-Hyuck

    2015-01-01

    In a completely systematic and geometric way, we derive maximal and half-maximal supersymmetric gauged double field theories in lower than ten dimensions. To this end, we apply a simple twisting ansatz to the D=10 ungauged maximal and half-maximal supersymmetric double field theories constructed previously within the so-called semi-covariant formalism. The twisting ansatz may not satisfy the section condition. Nonetheless, all the features of the semi-covariant formalism, including its complete covariantizability, are still valid after the twist under alternative consistency conditions. The twist allows gaugings as supersymmetry preserving deformations of the D=10 untwisted theories after Scherk-Schwarz-type dimensional reductions. The maximal supersymmetric twist requires an extra condition to ensure both the Ramond-Ramond gauge symmetry and the 32 supersymmetries unbroken.

  11. An inverse method for determining the interaction force between the probe and sample using scanning near-field optical microscopy

    International Nuclear Information System (INIS)

    Chang, Win-Jin; Fang, Te-Hua

    2006-01-01

    This study proposes a means for calculating the interaction force during the scanning process using a scanning near-field optical microscope (SNOM) probe. The determination of the interaction force in the scanning system is regarded as an inverse vibration problem. The conjugate gradient method is applied to treat the inverse problem using available displacement measurements. The results show that the conjugate gradient method is less sensitive to measurement errors and prior information on the functional form of quality was not required. Furthermore, the initial guesses for the interaction force can be arbitrarily chosen for the iteration process

  12. Energy expenditure and intake during Special Operations Forces field training in a jungle and glacial environment.

    Science.gov (United States)

    Johnson, Caleb D; Simonson, Andrew J; Darnell, Matthew E; DeLany, James P; Wohleber, Meleesa F; Connaboy, Christopher

    2018-04-01

    The purpose of this study was to identify and compare energy requirements specific to Special Operations Forces in field training, in both cool and hot environments. Three separate training sessions were evaluated, 2 in a hot environment (n = 21) and 1 in a cool environment (n = 8). Total energy expenditure was calculated using doubly labeled water. Dietary intake was assessed via self-report at the end of each training mission day, and macronutrient intakes were calculated. Across the 3 missions, mean energy expenditure (4618 ± 1350 kcal/day) exceeded mean energy intake (2429 ± 838 kcal/day) by an average of 2200 kcal/day. Macronutrient intakes (carbohydrates (g/(kg·day body weight (bw)) -1 ) = 3.2 ± 1.2; protein (g/(kg·day bw) -1 ) = 1.3 ± 0.7; fat (g/(kg·day bw) -1 ) = 1.2 ± 0.7) showed inadequate carbohydrate and possibly protein intake across the study period, compared with common recommendations. Total energy expenditures were found to be similar between hot (4664 ± 1399 kcal/day) and cool (4549 ± 1221 kcal/day) environments. However, energy intake was found to be higher in the cool (3001 ± 900 kcal/day) compared with hot (2200 ± 711 kcal/day) environments. Based on the identified energy deficit, high variation in energy expenditures, and poor macronutrient intake, a greater attention to feeding practices during similar training scenarios for Special Operations Forces is needed to help maintain performance and health. The differences in environmental heat stress between the 2 climates/environments had no observed effect on energy expenditures, but may have influenced intakes.

  13. Trace Contraband Detection Field-Test by the South Texas Specialized Crimes and Narcotics Task Force

    Energy Technology Data Exchange (ETDEWEB)

    Hannum, David W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Contraband Detection Dept.; Shannon, Gary W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Contraband Detection Dept.

    2006-04-01

    This report describes the collaboration between the South Texas Specialized Crimes and Narcotics Task Force (STSCNTF) and Sandia National Laboratories (SNL) in a field test that provided prototype hand-held trace detection technology for use in counter-drug operations. The National Institute of Justice (NIJ)/National Law Enforcement and Corrections Technology Center (NLECTC)/Border Research and Technology Center (BRTC) was contacted by STSCNTF for assistance in obtaining cutting-edge technology. The BRTC created a pilot project for Sandia National Laboratories (SNL) and the STSCNTF for the use of SNL’s Hound, a hand-held sample collection and preconcentration system that, when combined with a commercial chemical detector, can be used for the trace detection of illicit drugs and explosives. The STSCNTF operates in an area of high narcotics trafficking where methods of concealment make the detection of narcotics challenging. Sandia National Laboratories’ (SNL) Contraband Detection Department personnel provided the Hound system hardware and operational training. The Hound system combines the GE VaporTracer2, a hand-held commercial chemical detector, with an SNL-developed sample collection and preconcentration system. The South Texas Task force reported a variety of successes, including identification of a major shipment of methamphetamines, the discovery of hidden compartments in vehicles that contained illegal drugs and currency used in drug deals, and the identification of a suspect in a nightclub shooting. The main advantage of the hand-held trace detection unit is its ability to quickly identify the type of chemical (drugs or explosives) without a long lag time for laboratory analysis, which is the most common analysis method for current law enforcement procedures.

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

    Science.gov (United States)

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

    2009-12-01

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

  15. Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

    Science.gov (United States)

    Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

    2018-04-05

    Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

  16. Recent advances toward a general purpose linear-scaling quantum force field.

    Science.gov (United States)

    Giese, Timothy J; Huang, Ming; Chen, Haoyuan; York, Darrin M

    2014-09-16

    Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to

  17. A systematic review of health promotion intervention studies in the police force: study characteristics, intervention design and impacts on health.

    Science.gov (United States)

    MacMillan, Freya; Karamacoska, Diana; El Masri, Aymen; McBride, Kate A; Steiner, Genevieve Z; Cook, Amelia; Kolt, Gregory S; Klupp, Nerida; George, Emma S

    2017-12-01

    To systematically review studies of health promotion intervention in the police force. Four databases were searched for articles reporting on prepost single and multigroup studies in police officers and trainees. Data were extracted and bias assessed to evaluate study characteristics, intervention design and the impact of interventions on health. Database searching identified 25 articles reporting on 21 studies relevant to the aims of this review. Few studies (n=3) were of long duration (≥6 months). Nine of 21 studies evaluated structured physical activity and/or diet programmes only, 5 studies used education and behaviour change support-only interventions, 5 combined structured programmes with education and behaviour change support, and 2 studies used computer prompts to minimise sedentary behaviour. A wide array of lifestyle behaviour and health outcomes was measured, with 11/13 multigroup and 8/8 single-group studies reporting beneficial impacts on outcomes. High risk of bias was evident across most studies. In those with the lowest risk of bias (n=2), a large effect on blood pressure and small effects on diet, sleep quality, stress and tobacco use, were reported. Health promotion interventions can impact beneficially on health of the police force, particularly blood pressure, diet, sleep, stress and tobacco use. Limited reporting made comparison of findings challenging. Combined structured programmes with education and behaviour change support and programmes including peer support resulted in the most impact on health-related outcomes. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. Constraining Carbonaceous Aerosol Climate Forcing by Bridging Laboratory, Field and Modeling Studies

    Science.gov (United States)

    Dubey, M. K.; Aiken, A. C.; Liu, S.; Saleh, R.; Cappa, C. D.; Williams, L. R.; Donahue, N. M.; Gorkowski, K.; Ng, N. L.; Mazzoleni, C.; China, S.; Sharma, N.; Yokelson, R. J.; Allan, J. D.; Liu, D.

    2014-12-01

    Biomass and fossil fuel combustion emits black (BC) and brown carbon (BrC) aerosols that absorb sunlight to warm climate and organic carbon (OC) aerosols that scatter sunlight to cool climate. The net forcing depends strongly on the composition, mixing state and transformations of these carbonaceous aerosols. Complexities from large variability of fuel types, combustion conditions and aging processes have confounded their treatment in models. We analyse recent laboratory and field measurements to uncover fundamental mechanism that control the chemical, optical and microphysical properties of carbonaceous aerosols that are elaborated below: Wavelength dependence of absorption and the single scattering albedo (ω) of fresh biomass burning aerosols produced from many fuels during FLAME-4 was analysed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCEFI)—higher MCEFI results in lower ω values and greater spectral dependence of ω (Liu et al GRL 2014). A parameterization of ω as a function of MCEFI for fresh BB aerosols is derived from the laboratory data and is evaluated by field data, including BBOP. Our laboratory studies also demonstrate that BrC production correlates with BC indicating that that they are produced by a common mechanism that is driven by MCEFI (Saleh et al NGeo 2014). We show that BrC absorption is concentrated in the extremely low volatility component that favours long-range transport. We observe substantial absorption enhancement for internally mixed BC from diesel and wood combustion near London during ClearFlo. While the absorption enhancement is due to BC particles coated by co-emitted OC in urban regions, it increases with photochemical age in rural areas and is simulated by core-shell models. We measure BrC absorption that is concentrated in the extremely low volatility components and attribute it to wood burning. Our results support

  19. The effect of visual training for patients with visual field defects due to brain damage : a systematic review

    NARCIS (Netherlands)

    Bouwmeester, Lies; Heutink, Joost; Lucas, Cees

    The objective of this review was to evaluate whether systematic visual training leads to ( 1) a restitution of the visual field ( restoration), ( 2) an increase in the visual search field size or an improvement in scanning strategies (compensation) and ( 3) a transfer of training-related

  20. The effect of visual training for patients with visual field defects due to brain damage: a systematic review

    NARCIS (Netherlands)

    Bouwmeester, Lies; Heutink, Joost; Lucas, Cees

    2007-01-01

    The objective of this review was to evaluate whether systematic visual training leads to (1) a restitution of the visual field (restoration), (2) an increase in the visual search field size or an improvement in scanning strategies (compensation) and (3) a transfer of training-related improvements in

  1. Systematic study of hyperfine fields in Rh2 Y Z type Heusler alloys with 119 Sn impurity using Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Ramos, S.M.M.

    1985-01-01

    The magnetic hyperfine fields in the Heusler alloys Rh 2 Mn .98 Ge Sn 02 , Rh 2 Mn Ge .98 Sn .02 , Rh 2 Mn Pb .98 Sn .02 and Rh 2 Mn Sn has been studied by 119 Sn Moessbauer spectroscopy at 293 K, 77 K, 4.2 K and 293 K with applied external magnetic field. The results show that when one compare the magnetic hyperfine fields systematic with the Heusler alloys X 2 Mn Z (X = Co, Ni, Cu, Pd, and Z = s p metal), this systematic is similar to the Co alloys, although can not explained by the currents models for the Heusler alloys. (author)

  2. Systematic review of biological effects of exposure to static electric fields. Part II: Invertebrates and plants.

    Science.gov (United States)

    Schmiedchen, Kristina; Petri, Anne-Kathrin; Driessen, Sarah; Bailey, William H

    2018-01-01

    The construction of high-voltage direct current (HVDC) lines for the long-distance transport of energy is becoming increasingly popular. This has raised public concern about potential environmental impacts of the static electric fields (EF) produced under and near HVDC power lines. As the second part of a comprehensive literature analysis, the aim of this systematic review was to assess the effects of static EF exposure on biological functions in invertebrates and plants and to provide the basis for an environmental impact assessment of such exposures. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) was used to guide the methodological conduct and reporting. Thirty-three studies - 14 invertebrate and 19 plant studies - met the eligibility criteria and were included in this review. The reported behavioral responses of insects and planarians upon exposure strongly suggest that invertebrates are able to perceive the presence of a static EF. Many other studies reported effects on physiological functions that were expressed as, for example, altered metabolic activity or delayed reproductive and developmental stages in invertebrates. In plants, leaf damage, alterations in germination rates, growth and yield, or variations in the concentration of essential elements, for example, have been reported. However, these physiological responses and changes in plant morphology appear to be secondary to surface stimulation by the static EF or caused by concomitant parameters of the electrostatic environment. Furthermore, all of the included studies suffered from methodological flaws, which lowered credibility in the results. At field levels encountered from natural sources or HVDC lines (plants. At far higher field levels (> 35kV/m), adverse effects on physiology and morphology, presumably caused by corona-action, appear to be more likely. Higher quality studies are needed to unravel the role of air ions, ozone, nitric oxide and corona current on

  3. The impact of previous knee injury on force plate and field-based measures of balance.

    Science.gov (United States)

    Baltich, Jennifer; Whittaker, Jackie; Von Tscharner, Vinzenz; Nettel-Aguirre, Alberto; Nigg, Benno M; Emery, Carolyn

    2015-10-01

    Individuals with post-traumatic osteoarthritis demonstrate increased sway during quiet stance. The prospective association between balance and disease onset is unknown. Improved understanding of balance in the period between joint injury and disease onset could inform secondary prevention strategies to prevent or delay the disease. This study examines the association between youth sport-related knee injury and balance, 3-10years post-injury. Participants included 50 individuals (ages 15-26years) with a sport-related intra-articular knee injury sustained 3-10years previously and 50 uninjured age-, sex- and sport-matched controls. Force-plate measures during single-limb stance (center-of-pressure 95% ellipse-area, path length, excursion, entropic half-life) and field-based balance scores (triple single-leg hop, star-excursion, unipedal dynamic balance) were collected. Descriptive statistics (mean within-pair difference; 95% confidence intervals) were used to compare groups. Linear regression (adjusted for injury history) was used to assess the relationship between ellipse-area and field-based scores. Injured participants on average demonstrated greater medio-lateral excursion [mean within-pair difference (95% confidence interval); 2.8mm (1.0, 4.5)], more regular medio-lateral position [10ms (2, 18)], and shorter triple single-leg hop distances [-30.9% (-8.1, -53.7)] than controls, while no between group differences existed for the remaining outcomes. After taking into consideration injury history, triple single leg hop scores demonstrated a linear association with ellipse area (β=0.52, 95% confidence interval 0.01, 1.01). On average the injured participants adjusted their position less frequently and demonstrated a larger magnitude of movement during single-limb stance compared to controls. These findings support the evaluation of balance outcomes in the period between knee injury and post-traumatic osteoarthritis onset. Copyright © 2015 Elsevier Ltd. All rights

  4. Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

    International Nuclear Information System (INIS)

    Zhang Longcai; Wang Suyu; Wang Jiasu

    2009-01-01

    Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

  5. Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Longcai, E-mail: zhlcai2000@163.co [College of Air Traffic Management, Civil Aviation Flight University of China, Guanghan, Sichuan 618307 (China); Wang Suyu; Wang Jiasu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)

    2009-07-01

    Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

  6. Screening for Dyslipidemia in Younger Adults: A Systematic Review for the U.S. Preventive Services Task Force.

    Science.gov (United States)

    Chou, Roger; Dana, Tracy; Blazina, Ian; Daeges, Monica; Bougatsos, Christina; Jeanne, Thomas L

    2016-10-18

    Dyslipidemia may occur in younger adults (defined as persons aged 21 to 39 years) and is an important risk factor for cardiovascular disease. Screening might identify younger adults with asymptomatic dyslipidemia who may benefit from lipid-lowering therapies. To update the 2008 U.S. Preventive Services Task Force review on dyslipidemia screening in younger adults. The Cochrane Central Register of Controlled Trials, the Cochrane Database of Systematic Reviews, and MEDLINE through May 2016, and reference lists. Randomized, controlled trials; cohort studies; and case-control studies on screening for or treatment of asymptomatic dyslipidemia in adults aged 21 to 39 years. The plan was for 1 investigator to abstract data and a second to check their accuracy, and for 2 investigators to independently assess study quality; however, no studies met the inclusion criteria. No study evaluated the effects of lipid screening versus no screening, treatment versus no treatment, or delayed versus earlier treatment on clinical outcomes in younger adults. In addition, no study evaluated the diagnostic yield of alternative screening strategies (such as targeted screening of persons with a family history of hyperlipidemia vs. general screening) in younger adults. No direct relevant evidence. Direct evidence on the benefits and harms of screening for or treatment of dyslipidemia in younger adults remains unavailable. Estimating the potential effects of screening for dyslipidemia in this population requires extrapolation from studies performed in older adults. Agency for Healthcare Research and Quality.

  7. Combination Rules for Morse-Based van der Waals Force Fields.

    Science.gov (United States)

    Yang, Li; Sun, Lei; Deng, Wei-Qiao

    2018-02-15

    In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.

  8. Determination of a silane intermolecular force field potential model from an ab initio calculation

    International Nuclear Information System (INIS)

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-01-01

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  9. Comparison of force fields and calculation methods for vibration intervals of isotopic H+3 molecules

    International Nuclear Information System (INIS)

    Carney, G.D.; Adler-Golden, S.M.; Lesseski, D.C.

    1986-01-01

    This paper reports (a) improved values for low-lying vibration intervals of H + 3 , H 2 D + , D 2 H + , and D + 3 calculated using the variational method and Simons--Parr--Finlan representations of the Carney--Porter and Dykstra--Swope ab initio H + 3 potential energy surfaces, (b) quartic normal coordinate force fields for isotopic H + 3 molecules, (c) comparisons of variational and second-order perturbation theory, and (d) convergence properties of the Lai--Hagstrom internal coordinate vibrational Hamiltonian. Standard deviations between experimental and ab initio fundamental vibration intervals of H + 3 , H 2 D + , D 2 H + , and D + 3 for these potential surfaces are 6.9 (Carney--Porter) and 1.2 cm -1 (Dykstra--Swope). The standard deviations between perturbation theory and exact variational fundamentals are 5 and 10 cm -1 for the respective surfaces. The internal coordinate Hamiltonian is found to be less efficient than the previously employed ''t'' coordinate Hamiltonian for these molecules, except in the case of H 2 D +

  10. Relation of twist of magnetic force tube and flare magnetic field

    International Nuclear Information System (INIS)

    Tanaka, H.

    1978-01-01

    The configuration of magnetic field and its development in the regions of big flare were investigated to study the features of magnetic force tubes. The photographs of delta type solar spots taken at Mt. Wilson Observatory were selected. 94 percent of the delta type spots belong to the class B activity or more active class. The features of delta type spots are the reverse configuration and the shear motion. The reverse configuration is divided into the p/f configuration and the f/p configuration. The shear motion is divided into the normal motion, the reverse motion, and the indefinite motion. Vortex structures appeared around the solar spots of reverse configuration showing normal motion. The relation among the direction of twist, reverse configuration and the direction of shear motion was deduced. In the region of normal motion, the p/f configuration corresponds to the reverse S type vortices and the f/p configuration to S type. In the region of reverse motion, the p/f configuration corresponds to the S type vortices and the f/p corresponds to the reverse S type vortices. The mechanism of development of delta type solar spots is discussed. (Kato, T.)

  11. The ELBA force field for coarse-grain modeling of lipid membranes.

    Directory of Open Access Journals (Sweden)

    Mario Orsi

    Full Text Available 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 (ε(r = 1. 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.

  12. Ligandbook: an online repository for small and drug-like molecule force field parameters.

    Science.gov (United States)

    Domanski, Jan; Beckstein, Oliver; Iorga, Bogdan I

    2017-06-01

    Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Ligandbook is available online at https://ligandbook.org and supports all modern browsers. Parameters can be searched and downloaded without registration, including access through a programmatic RESTful API. Deposition of files requires free user registration. Ligandbook is implemented in the PHP Symfony2 framework with TCL scripts using the CACTVS toolkit. oliver.beckstein@asu.edu or bogdan.iorga@cnrs.fr ; contact@ligandbook.org . Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

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

    Science.gov (United States)

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-05

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-21

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

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

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

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

  16. Systems science and systems thinking for public health: a systematic review of the field.

    Science.gov (United States)

    Carey, Gemma; Malbon, Eleanor; Carey, Nicole; Joyce, Andrew; Crammond, Brad; Carey, Alan

    2015-12-30

    This paper reports on findings from a systematic review designed to investigate the state of systems science research in public health. The objectives were to: (1) explore how systems methodologies are being applied within public health and (2) identify fruitful areas of activity. A systematic review was conducted from existing literature that draws on or uses systems science (in its various forms) and relates to key public health areas of action and concern, including tobacco, alcohol, obesity and the social determinants of health. 117 articles were included in the review. An inductive qualitative content analysis was used for data extraction. The following were systematically extracted from the articles: approach, methodology, transparency, strengths and weaknesses. These were then organised according to theme (ie, commonalities between studies within each category), in order to provide an overview of the state of the field as a whole. The assessment of data quality was intrinsic to the goals of the review itself, and therefore, was carried out as part of the analysis. 4 categories of research were identified from the review, ranging from editorial and commentary pieces to complex system dynamic modelling. Our analysis of each of these categories of research highlighted areas of potential for systems science to strengthen public health efforts, while also revealing a number of limitations in the dynamic systems modelling being carried out in public health. There is a great deal of interest in how the application of systems concepts and approach might aid public health. Our analysis suggests that soft systems modelling techniques are likely to be the most useful addition to public health, and align well with current debate around knowledge transfer and policy. However, the full range of systems methodologies is yet to be engaged with by public health researchers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under

  17. Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

    International Nuclear Information System (INIS)

    Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

    2011-01-01

    In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

  18. Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas

    International Nuclear Information System (INIS)

    Ebihara, Ken-ichi; Watanabe, Tadashi

    2000-10-01

    The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)

  19. Influence of Complete Coriolis Force on the Dispersion Relation of Ocean Internal-wave in a Background Currents Field

    Directory of Open Access Journals (Sweden)

    Liu Yongjun

    2015-01-01

    Full Text Available In this thesis, the influence of complete Coriolis force (the model includes both the vertical and horizontal components of Coriolis force on the dispersion relation of ocean internal-wave under background currents field are studied, it is important to the study of ocean internal waves in density-stratified ocean. We start from the control equation of sea water movement in the background of the non-traditional approximation, and the vertical velocity solution is derived where buoyancy frequency N(z gradually varies with the ocean depth z. The results show that the influence of complete Coriolis force on the dispersion relation of ocean internal-wave under background currents field is obvious, and these results provide strong evidence for the understanding of dynamic process of density stratified ocean internal waves.

  20. Moessbauer study of the fast magnetization reversal forced in permalloy and invar by an external rf magnetic field

    International Nuclear Information System (INIS)

    Kopcewicz, M.

    1978-01-01

    The effect of fast magnetization reversal leading to fast relaxation of the hyperfine field (collapse effect) forced by an external rf magnetic field is studied using the Moessbauer technique for permalloy and invar. The rf collapse and sideband effects are investigated as a function of external rf field, frequency, and intensity. The collapse of the hfs spectrum through unresolved hfs spectrum, triangular shape to a single line, as well as the formation of sidebands is observed. The rf collapse effect is attributed to the rf forced uniform rotation of internal magnetization which causes fast magnetization reversal leading to fast relaxation of the hyperfine field as a result of which the average field at the Moessbauer nuclei is reduced to zero. The difference of the magnetization reversal process in permalloy and invar are discussed. It is shown that the origin of collapse and sideband effects is totaly different: the collapse effect being of purely magnetic origin while the formation of sidebands is due to the rf induced mechanical vibrations of iron atoms within the sample. It is possible to damp sidebands without affecting the collapse effect. The results obtained show that the application of the rf field to ferromagnetic materials gives a unique possibility to force, simulate, and control the relaxation effects in ferromagnetic materials. (author)

  1. Analysis of the magnetic field, force, and torque for two-dimensional Halbach cylinders

    DEFF Research Database (Denmark)

    Bjørk, Rasmus; Smith, Anders; Bahl, Christian Robert Haffenden

    2010-01-01

    for a two dimensional Halbach cylinder are derived. The remanent flux density of a Halbach magnet is characterized by the integer p. For a number of applications the force and torque between two concentric Halbach cylinders are important. These quantities are calculated and the force is shown to be zero...... except for the case where p for the inner magnet is one minus p for the outer magnet. Also the force is shown never to be balancing. The torque is shown to be zero unless the inner magnet p is equal to minus the outer magnet p. Thus there can never be a force and a torque in the same system....

  2. Operation of a scanning near field optical microscope in reflection in combination with a scanning force microscope

    NARCIS (Netherlands)

    van Hulst, N.F.; Moers, M.H.P.; Moers, M.H.P.; Noordman, O.F.J.; Noordman, O.F.J.; Faulkner, T.; Segerink, Franciscus B.; van der Werf, Kees; de Grooth, B.G.; Bölger, B.; Bölger, B.

    1992-01-01

    Images obtained with a scanning near field optical microscope (SNOM) operating in reflection are presented. We have obtained the first results with a SiN tip as optical probe. The instrument is simultaneously operated as a scanning force microscope (SFM). Moreover, the instrument incorporates an

  3. Multiscale modeling of interaction of alane clusters on Al(111) surfaces : a reactive force field and infrared absorbtion spectroscopy approach

    NARCIS (Netherlands)

    Ojwang, J.G.O.; Chaudhuri, S.; Duin, van A.C.T.; Chabal, Y.J.; Veyan, J.-F.; Santen, van R.A.; Kramer, G.J.; Goddard III, W.A.

    2010-01-01

    We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to

  4. Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

    DEFF Research Database (Denmark)

    Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter

    2013-01-01

    In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously rep...

  5. Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

    NARCIS (Netherlands)

    Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

    Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

  6. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Ye [Sanford-Burnham-Prebys Medical Discovery Institute (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham-Prebys Medical Discovery Institute (United States)

    2017-01-15

    Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

  7. Radiofrequency electromagnetic field exposure and non-specific symptoms of ill health: a systematic review.

    Science.gov (United States)

    Röösli, Martin

    2008-06-01

    This article is a systematic review of whether everyday exposure to radiofrequency electromagnetic field (RF-EMF) causes symptoms, and whether some individuals are able to detect low-level RF-EMF (below the ICNIRP [International Commission on Non-Ionizing Radiation Protection] guidelines). Peer-reviewed articles published before August 2007 were identified by means of a systematic literature search. Meta-analytic techniques were used to pool the results from studies investigating the ability to discriminate active from sham RF-EMF exposure. RF-EMF discrimination was investigated in seven studies including a total of 182 self-declared electromagnetic hypersensitive (EHS) individuals and 332 non-EHS individuals. The pooled correct field detection rate was 4.2% better than expected by chance (95% CI: -2.1 to 10.5). There was no evidence that EHS individuals could detect presence or absence of RF-EMF better than other persons. There was little evidence that short-term exposure to a mobile phone or base station causes symptoms based on the results of eight randomized trials investigating 194 EHS and 346 non-EHS individuals in a laboratory. Some of the trials provided evidence for the occurrence of nocebo effects. In population based studies an association between symptoms and exposure to RF-EMF in the everyday environment was repeatedly observed. This review showed that the large majority of individuals who claims to be able to detect low level RF-EMF are not able to do so under double-blind conditions. If such individuals exist, they represent a small minority and have not been identified yet. The available observational studies do not allow differentiating between biophysical from EMF and nocebo effects.

  8. Radiofrequency electromagnetic field exposure and non-specific symptoms of ill health: A systematic review

    International Nuclear Information System (INIS)

    Roeoesli, Martin

    2008-01-01

    This article is a systematic review of whether everyday exposure to radiofrequency electromagnetic field (RF-EMF) causes symptoms, and whether some individuals are able to detect low-level RF-EMF (below the ICNIRP [International Commission on Non-Ionizing Radiation Protection] guidelines). Peer-reviewed articles published before August 2007 were identified by means of a systematic literature search. Meta-analytic techniques were used to pool the results from studies investigating the ability to discriminate active from sham RF-EMF exposure. RF-EMF discrimination was investigated in seven studies including a total of 182 self-declared electromagnetic hypersensitive (EHS) individuals and 332 non-EHS individuals. The pooled correct field detection rate was 4.2% better than expected by chance (95% CI: -2.1 to 10.5). There was no evidence that EHS individuals could detect presence or absence of RF-EMF better than other persons. There was little evidence that short-term exposure to a mobile phone or base station causes symptoms based on the results of eight randomized trials investigating 194 EHS and 346 non-EHS individuals in a laboratory. Some of the trials provided evidence for the occurrence of nocebo effects. In population based studies an association between symptoms and exposure to RF-EMF in the everyday environment was repeatedly observed. This review showed that the large majority of individuals who claims to be able to detect low level RF-EMF are not able to do so under double-blind conditions. If such individuals exist, they represent a small minority and have not been identified yet. The available observational studies do not allow differentiating between biophysical from EMF and nocebo effects

  9. Fulfilling the promise of personalized medicine? Systematic review and field synopsis of pharmacogenetic studies.

    Directory of Open Access Journals (Sweden)

    Michael V Holmes

    2009-12-01

    Full Text Available Studies of the genetic basis of drug response could help clarify mechanisms of drug action/metabolism, and facilitate development of genotype-based predictive tests of efficacy or toxicity (pharmacogenetics.We conducted a systematic review and field synopsis of pharmacogenetic studies to quantify the scope and quality of available evidence in this field in order to inform future research.Original research articles were identified in Medline, reference lists from 24 meta-analyses/systematic reviews/review articles and U.S. Food and Drug Administration website of approved pharmacogenetic tests. STUDY ELIGIBILITY CRITERIA, PARTICIPANTS, AND INTERVENTION CRITERIA: We included any study in which either intended or adverse response to drug therapy was examined in relation to genetic variation in the germline or cancer cells in humans.Study characteristics and data reported in abstracts were recorded. We further analysed full text from a random 10% subset of articles spanning the different subclasses of study.From 102,264 Medline hits and 1,641 articles from other sources, we identified 1,668 primary research articles (1987 to 2007, inclusive. A high proportion of remaining articles were reviews/commentaries (ratio of reviews to primary research approximately 25 ratio 1. The majority of studies (81.8% were set in Europe and North America focussing on cancer, cardiovascular disease and neurology/psychiatry. There was predominantly a candidate gene approach using common alleles, which despite small sample sizes (median 93 [IQR 40-222] with no trend to an increase over time, generated a high proportion (74.5% of nominally significant (por=4 studies, only 31 meta-analyses were identified. The majority (69.4% of end-points were continuous and likely surrogate rather than hard (binary clinical end-points.The high expectation but limited translation of pharmacogenetic research thus far may be explained by the preponderance of reviews over primary research

  10. New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking.

    Science.gov (United States)

    Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B

    2017-11-01

    Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

    Science.gov (United States)

    Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

    2010-07-28

    Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

  12. An ionic force-field study of monomers, dimers and higher polymers in pentafluoride vapors

    Energy Technology Data Exchange (ETDEWEB)

    Cicek Onem, Z. [Department of Physics, Istanbul University, Istanbul (Turkey); Akdeniz, Z. [Department of Physics, Istanbul University, Istanbul (Turkey); Classe di Scienze, Scuola Normale Superiore, I-56126 Pisa (Italy)], E-mail: zakdeniz@istanbul.edu.tr; Tosi, M.P. [Classe di Scienze, Scuola Normale Superiore, I-56126 Pisa (Italy)], E-mail: tosim@sns.it

    2008-08-01

    Pentafluoride compounds such as NbF{sub 5} and TaF{sub 5} have been reported in the literature to admit various states of polymerization coexisting with monomers in their vapor phase, in relative concentrations that vary with temperature and pressure. We construct a microscopic interionic force-field model for the molecular monomer of these compounds (including VF{sub 5}, SbF{sub 5} and MoF{sub 5} in addition to NbF{sub 5} and TaF{sub 5}), the stable form of the monomer being in the shape of a D{sub 3h} trigonal bipyramid in all cases. The model emulates chemical bonds by allowing for electrical and short-range overlap polarizabilities of the fluorines, and is used to evaluate the structure and the stability of (MF{sub 5}){sub n} molecules with n running from 2 to 6. The dimer is formed by two distorted edge-sharing octahedral, while the trimer and the higher polymers can form rings of distorted corner-sharing octahedra. A chain-like configuration is also found for the trimer of NbF{sub 5}, which consists of a seven-fold coordinated Nb bonded to two distorted octahedra via edge sharing. Comparison of calculated vibrational frequencies and bond lengths with experimental data is made whenever possible. We find that there is a small net gain of energy in the formation of a dimer, while otherwise the static energy of the n-mer is very close to that of n separated monomers. High sensitivity of the state of molecular aggregation to the thermodynamic conditions of the vapor is clearly indicated by our calculations.

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

    Science.gov (United States)

    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. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Field Measurements of Heating Efficiency of Electric Forced-Air Furnaces in Six Manufactured Homes.

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Bob; Palmiter, Larry S.; Siegel, Jeff

    1994-07-26

    This report presents the results of field measurements of heating efficiency for six manufactured homes in the Pacific Northwest heated with electric forced-air systems. This is the first in a series of regional and national efforts to measure in detail the heating efficiency of manufactured homes. Only six homes were included in this study because of budgetary constraints; therefore this is not a representative sample. These investigations do provide some useful information on the heating efficiency of these homes. Useful comparisons can be drawn between these study homes and site-built heating efficiencies measured with a similar protocol. The protocol used to test these homes is very similar to another Ecotope protocol used in the study conducted in 1992 and 1993 for the Bonneville Power Administration to test the heating efficiency of 24 homes. This protocol combined real-time power measurements of furnace energy usage with energy usage during co-heat periods. Accessory data such as house and duct tightness measurements and tracer gas measurements were used to describe these homes and their heating system efficiency. Ensuring that manufactured housing is constructed in an energy and resource efficient manner is of increasing concern to manufactured home builders and consumers. No comparable work has been done to measure the heating system efficiency of MCS manufactured homes, although some co-heat tests have been performed on manufactured homes heated with natural gas to validate HUD thermal standards. It is expected that later in 1994 more research of this kind will be conducted, and perhaps a less costly and less time-consuming method for testing efficiencies will be develops.

  15. Modeling the sorption dynamics of NaH using a reactive force field

    International Nuclear Information System (INIS)

    Ojwang, J. G. O.; Santen, Rutger van; Kramer, Gert Jan; Duin, Adri C. T. van; Goddard, William A. III

    2008-01-01

    We have parametrized a reactive force field for NaH, ReaxFF NaH , against a training set of ab initio derived data. To ascertain that ReaxFF NaH is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF NaH was done. The results and trend of ReaxFF NaH are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF NaH . There is a good match between the two results, showing that ReaxFF NaH is correctly parametrized by the ab initio training set. ReaxFF NaH has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF NaH properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments

  16. Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

    Science.gov (United States)

    Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

    2005-06-01

    We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

  17. Task-space separation principle: a force-field approach to motion planning for redundant manipulators.

    Science.gov (United States)

    Tommasino, Paolo; Campolo, Domenico

    2017-02-03

    In this work, we address human-like motor planning in redundant manipulators. Specifically, we want to capture postural synergies such as Donders' law, experimentally observed in humans during kinematically redundant tasks, and infer a minimal set of parameters to implement similar postural synergies in a kinematic model. For the model itself, although the focus of this paper is to solve redundancy by implementing postural strategies derived from experimental data, we also want to ensure that such postural control strategies do not interfere with other possible forms of motion control (in the task-space), i.e. solving the posture/movement problem. The redundancy problem is framed as a constrained optimization problem, traditionally solved via the method of Lagrange multipliers. The posture/movement problem can be tackled via the separation principle which, derived from experimental evidence, posits that the brain processes static torques (i.e. posture-dependent, such as gravitational torques) separately from dynamic torques (i.e. velocity-dependent). The separation principle has traditionally been applied at a joint torque level. Our main contribution is to apply the separation principle to Lagrange multipliers, which act as task-space force fields, leading to a task-space separation principle. In this way, we can separate postural control (implementing Donders' law) from various types of tasks-space movement planners. As an example, the proposed framework is applied to the (redundant) task of pointing with the human wrist. Nonlinear inverse optimization (NIO) is used to fit the model parameters and to capture motor strategies displayed by six human subjects during pointing tasks. The novelty of our NIO approach is that (i) the fitted motor strategy, rather than raw data, is used to filter and down-sample human behaviours; (ii) our framework is used to efficiently simulate model behaviour iteratively, until it converges towards the experimental human strategies.

  18. Simulating the physicochemical properties of borosilicate and lanthanum borosilicate glasses using a polarizable force field

    International Nuclear Information System (INIS)

    Pacaud, Fabien

    2016-01-01

    as result of the nuclear waste vitrification, the knowledge and understanding of the dynamic and structural properties of glasses, including the behavior of radionuclides, is important (in liquid and solid phases). It can influence the glass waste properties, the lifetime of the vitrification process and the amount of radionuclides introduced in the glass matrix. Molecular dynamic simulations have been done to study the influence of the glass matrix composition into the structural and dynamic properties of the glass. a simplified glass, with 3 major oxides of the R7T7 glass such as SiO_2, B_2O_3 and Na_2O, have been used to simulate the R7T7 industrial nuclear glass (a 30 oxides glass). The inclusion of La_2O_3 allows us to simulate the impact of fission products and minor actinides into the properties of the glass matrix. Both systems, the SiO_2-B_2O_3-Na_2O and SiO_2-B_2O_3-Na_2O-La_2O_3, allow us to study the sodium and lanthanum effect on the properties of the glass. During this work, a polarizable force field has been developed to do these simulations. The results obtained at room temperature let us reproduce the experimental results of the structure, the distribution of BIII/BIV and the density. a study has been done on the viscosity and electrical conductivity of the liquid. The distribution BIV/BIII and the influence of the structural changes on the density along with the temperature have also been observed with thermal quenching. The current limits of this approach are also described. (author) [fr

  19. Stem breakage of salt marsh vegetation under wave forcing: A field and model study

    Science.gov (United States)

    Vuik, Vincent; Suh Heo, Hannah Y.; Zhu, Zhenchang; Borsje, Bas W.; Jonkman, Sebastiaan N.

    2018-01-01

    One of the services provided by coastal ecosystems is wave attenuation by vegetation, and subsequent reduction of wave loads on flood defense structures. Therefore, stability of vegetation under wave forcing is an important factor to consider. This paper presents a model which determines the wave load that plant stems can withstand before they break or fold. This occurs when wave-induced bending stresses exceed the flexural strength of stems. Flexural strength was determined by means of three-point-bending tests, which were carried out for two common salt marsh species: Spartina anglica (common cord-grass) and Scirpus maritimus (sea club-rush), at different stages in the seasonal cycle. Plant stability is expressed in terms of a critical orbital velocity, which combines factors that contribute to stability: high flexural strength, large stem diameter, low vegetation height, high flexibility and a low drag coefficient. In order to include stem breakage in the computation of wave attenuation by vegetation, the stem breakage model was implemented in a wave energy balance. A model parameter was calibrated so that the predicted stem breakage corresponded with the wave-induced loss of biomass that occurred in the field. The stability of Spartina is significantly higher than that of Scirpus, because of its higher strength, shorter stems, and greater flexibility. The model is validated by applying wave flume tests of Elymus athericus (sea couch), which produced reasonable results with regards to the threshold of folding and overall stem breakage percentage, despite the high flexibility of this species. Application of the stem breakage model will lead to a more realistic assessment of the role of vegetation for coastal protection.

  20. Limited interlimb transfer of locomotor adaptations to a velocity-dependent force field during unipedal walking.

    Science.gov (United States)

    Houldin, Adina; Chua, Romeo; Carpenter, Mark G; Lam, Tania

    2012-08-01

    Several studies have demonstrated that motor adaptations to a novel task environment can be transferred between limbs. Such interlimb transfer of motor commands is consistent with the notion of centrally driven strategies that can be generalized across different frames of reference. So far, studies of interlimb transfer of locomotor adaptations have yielded disparate results. Here we sought to determine whether locomotor adaptations in one (trained) leg show transfer to the other (test) leg during a unipedal walking task. We hypothesized that adaptation in the test leg to a velocity-dependent force field previously experienced by the trained leg will be faster, as revealed by faster recovery of kinematic errors and earlier onset of aftereffects. Twenty able-bodied adults walked unipedally in the Lokomat robotic gait orthosis, which applied velocity-dependent resistance to the legs. The amount of resistance was scaled to 10% of each individual's maximum voluntary contraction of the hip flexors. Electromyography and kinematics of the lower limb were recorded. All subjects were right-leg dominant and were tested for transfer of motor adaptations from the right leg to the left leg. Catch trials, consisting of unexpected removal of resistance, were presented after the first step with resistance and after a period of adaptation to test for aftereffects. We found no significant differences in the sizes of the aftereffects between the two legs, except for peak hip flexion during swing, or in the rate at which peak hip flexion adapted during steps against resistance between the two legs. Our results indicate that interlimb transfer of these types of locomotor adaptation is not a robust phenomenon. These findings add to our current understanding of motor adaptations and provide further evidence that generalization of adaptations may be dependent on the movement task.

  1. Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

    Science.gov (United States)

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

    2012-12-01

    Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

  2. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  3. Grip Force Adjustments Reflect Prediction of Dynamic Consequences in Varying Gravitoinertial Fields

    Directory of Open Access Journals (Sweden)

    Olivier White

    2018-02-01

    Full Text Available Humans have a remarkable ability to adjust the way they manipulate tools through a genuine regulation of grip force according to the task. However, rapid changes in the dynamical context may challenge this skill, as shown in many experimental approaches. Most experiments adopt perturbation paradigms that affect only one sensory modality. We hypothesize that very fast adaptation can occur if coherent information from multiple sensory modalities is provided to the central nervous system. Here, we test whether participants can switch between different and never experienced dynamical environments induced by centrifugation of the body. Seven participants lifted an object four times in a row successively in 1, 1.5, 2, 2.5, 2, 1.5, and 1 g. We continuously measured grip force, load force and the gravitoinertial acceleration that was aligned with body axis (perceived gravity. Participants adopted stereotyped grasping movements immediately upon entry in a new environment and needed only one trial to adapt grip forces to a stable performance in each new gravity environment. This result was underlined by good correlations between grip and load forces in the first trial. Participants predictively applied larger grip forces when they expected increasing gravity steps. They also decreased grip force when they expected decreasing gravity steps, but not as much as they could, indicating imperfect anticipation in that condition. The participants' performance could rather be explained by a combination of successful scaling of grip force according to gravity changes and a separate safety factor. The data suggest that in highly unfamiliar dynamic environments, grip force regulation is characterized by a combination of a successful anticipation of the experienced environmental condition, a safety factor reflecting strategic response to uncertainties about the environment and rapid feedback mechanisms to optimize performance under constant conditions.

  4. Feedforward compensation for novel dynamics depends on force field orientation but is similar for the left and right arms.

    Science.gov (United States)

    Reuter, Eva-Maria; Cunnington, Ross; Mattingley, Jason B; Riek, Stephan; Carroll, Timothy J

    2016-11-01

    There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153-167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. Copyright © 2016 the American Physiological Society.

  5. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  7. Effects of ponderomotive forces and space-charge field on laser plasma hydrodynamics

    International Nuclear Information System (INIS)

    Cang Yu; Lu Xin; Wu Huichun; Zhang Jie

    2005-01-01

    Using a two-fluid two-temperature hydrodynamic code, authors studied the hydrodynamics in the interaction of intense (10 15 W/cm 2 ) ultrashort (150 fs) laser pulses and linear density plasmas. The simulation results show the ponderomotive force effect on the formation of the electron density ripples in under-dense region, such ripples increase the reflection of the laser pulse, and on the separation of the plasma in critical surface. Quasi-electroneutrality is not suitable in this case because of the different ponderomotive force and the gradient of thermal-pressure for ions and electrons. Ions are moved by the electrostatic force. Comparing with the simulation results from one-fluid two-temperature code, authors find that under strong ponderomotive force and gradient of thermo-pressure, two-fluid code is more suitable to simulate the hydrodynamics of plasmas. (authors)

  8. Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

    Energy Technology Data Exchange (ETDEWEB)

    Treweek, Benjamin C., E-mail: btreweek@utexas.edu; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F. [Applied Research Laboratories, The University of Texas at Austin, P.O. Box 8029, Austin, TX 78713-8029 (United States)

    2015-10-28

    Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.

  9. The influence of inhomogeneous magnetic field over a NdFeB guideway on levitation force of the HTS bulk maglev system

    Science.gov (United States)

    Zhao, Lifeng; Deng, Jiangtao; Li, Linbo; Feng, Ning; Wei, Pu; Lei, Wei; Jiang, Jing; Wang, Xiqin; Zhang, Yong; Zhao, Yong

    2018-04-01

    Dynamic responses of high temperature superconducting bulk to inhomogeneous magnetic field distribution of permanent magnet guideway, as well as enlarged amplitude of magnetic field obtained by partially covering the permanent magnet guideway (PMG) with iron sheets in different thickness, are investigated. Experiments show that the instantaneous levitation force increases with the increase of the variation rate of magnetic field (dB/dt). Meanwhile, inhomogeneous magnetic field from PMG causes the decay of levitation force. The decay of levitation force almost increases linearly with the increase of alternating magnetic field amplitude. It should be very important for the application of high-speed maglev system.

  10. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  11. Construction of an accurate quartic force field by using generalised least-squares fitting and experimental design

    International Nuclear Information System (INIS)

    Carbonniere, Philippe; Begue, Didier; Dargelos, Alain; Pouchan, Claude

    2004-01-01

    In this work we present an attractive least-squares fitting procedure which allows for the calculation of a quartic force field by jointly using energy, gradient, and Hessian data, obtained from electronic wave function calculations on a suitably chosen grid of points. We use the experimental design to select the grid points: a 'simplex-sum' of Box and Behnken grid was chosen for its efficiency and accuracy. We illustrate the numerical implementations of the method by using the energy and gradient data for H 2 O and H 2 CO. The B3LYP/cc-pVTZ quartic force field performed from 11 and 44 simplex-sum configurations shows excellent agreement in comparison to the classical 44 and 168 energy calculations

  12. Non-uniform current distribution in a force-cooled superconductor under changing magnetic field

    International Nuclear Information System (INIS)

    Koizumi, Norikiyo

    2000-02-01

    Strands in a large current force-cooled superconductor, referred to a CICC (cable-in-conduit conductor) hereafter, are coated with formvar (insulated layer) or chrome plating (high resistive layer) to reduce coupling current loss due to magnetic field variation. The author first carried out an experiment of the large superconducting coil consisting of such CICCs for demonstration of their applicability to a large superconducting coil. These CICCs exhibited instability, i.e. the normal zone propagation with thermal runaway (quench), at 1/20 and 1/5 of the expected conductor critical currents, respectively. The author constructed the database of this instability and studies its reason through experimental and theoretical investigations and then finds such instability is caused as a result of non-uniform current distribution in the conductor. Joule heating loss at electrical connections at the ends of the conductor should be small. Therefore, the strands in the CICC are electrically connected from each other with low resistance there. Circulation current is induced in the loop composed of the strands electrically connected at the ends of the conductor if its leakage magnetic flux is not completely vanished. The non-uniform current distribution is caused as a result of superimposition of the circulation and transport currents. The strand carrying large current becomes the normal state when it reaches or approaches to its critical current. Thus, the strands are twisted in order to vanish the leakage magnetic flux. The instability due to the current imbalance was not observed in the middle-scale coil (an element coil, such as a single double-pancake, of a large superconducting coil) consisting of the conductor in which the formvar-coated strands were twisted as above-mentioned. Consequently, it was believed that the leakage magnetic flux could be vanished by the normal twisting. However, the magnetic field increases in a large coil as a result of piling element coils

  13. The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

    2017-01-01

    of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...

  14. Harms of Breast Cancer Screening: Systematic Review to Update the 2009 U.S. Preventive Services Task Force Recommendation.

    Science.gov (United States)

    Nelson, Heidi D; Pappas, Miranda; Cantor, Amy; Griffin, Jessica; Daeges, Monica; Humphrey, Linda

    2016-02-16

    In 2009, the U.S. Preventive Services Task Force recommended biennial mammography screening for women aged 50 to 74 years and selective screening for those aged 40 to 49 years. To review studies of screening in average-risk women with mammography, magnetic resonance imaging, or ultrasonography that reported on false-positive results, overdiagnosis, anxiety, pain, and radiation exposure. MEDLINE and Cochrane databases through December 2014. English-language systematic reviews, randomized trials, and observational studies of screening. Investigators extracted and confirmed data from studies and dual-rated study quality. Discrepancies were resolved through consensus. Based on 2 studies of U.S. data, 10-year cumulative rates of false-positive mammography results and biopsies were higher with annual than biennial screening (61% vs. 42% and 7% vs. 5%, respectively) and for women aged 40 to 49 years, those with dense breasts, and those using combination hormone therapy. Twenty-nine studies using different methods reported overdiagnosis rates of 0% to 54%; rates from randomized trials were 11% to 22%. Women with false-positive results reported more anxiety, distress, and breast cancer-specific worry, although results varied across 80 observational studies. Thirty-nine observational studies indicated that some women reported pain during mammography (1% to 77%); of these, 11% to 46% declined future screening. Models estimated 2 to 11 screening-related deaths from radiation-induced cancer per 100,000 women using digital mammography, depending on age and screening interval. Five observational studies of tomosynthesis and mammography indicated increased biopsies but reduced recalls compared with mammography alone. Studies of overdiagnosis were highly heterogeneous, and estimates varied depending on the analytic approach. Studies of anxiety and pain used different outcome measures. Radiation exposure was based on models. False-positive results are common and are higher for

  15. Forces acting on a small particle in an acoustical field in a thermoviscous fluid

    DEFF Research Database (Denmark)

    Karlsen, Jonas Tobias; Bruus, Henrik

    2015-01-01

    We present a theoretical analysis of the acoustic radiation force on a single small spherical particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Within the perturbation assumptions, our analysis places no rest...... as to handling of nanoparticles in lab-on-a-chip systems.......We present a theoretical analysis of the acoustic radiation force on a single small spherical particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Within the perturbation assumptions, our analysis places...... of materials, we also find a sign change in the acoustic radiation force on different-sized but otherwise identical particles. These findings lead to the concept of a particle-size-dependent acoustophoretic contrast factor, highly relevant to acoustic separation of microparticles in gases, as well...

  16. Optical force on a discrete invisibility cloak in time-dependent fields

    International Nuclear Information System (INIS)

    Chaumet, Patrick C.; Zolla, Frederic; Nicolet, Andre; Belkebir, Kamal; Rahmani, Adel

    2011-01-01

    We study, in time domain, the exchange of momentum between an electromagnetic pulse and a three-dimensional, discrete, spherical invisibility cloak. We find that a discrete cloak, initially at rest, would experience an electromagnetic force due to the pulse but would acquire zero net momentum and net displacement. On the other hand, we find that while the cloak may manage to conceal an object and shroud it from the electromagnetic forces associated with the pulse, the cloak itself can experience optomechanical stress on a scale much larger than the object would in the absence of the cloak. We also consider the effects of material dispersion and losses on the electromagnetic forces experienced by the cloak and show that they lead to a transfer of momentum from the pulse to the cloak.

  17. ALOAD - a code to determine the concentrated forces equivalent with a distributed pressure field for a FEM analysis

    Directory of Open Access Journals (Sweden)

    Nicolae APOSTOLESCU

    2010-12-01

    Full Text Available The main objective of this paper is to describe a code for calculating an equivalent systemof concentrate loads for a FEM analysis. The tables from the Aerodynamic Department containpressure field for a whole bearing surface, and integrated quantities both for the whole surface andfor fixed and mobile part. Usually in a FEM analysis the external loads as concentrated loadsequivalent to the distributed pressure field are introduced. These concentrated forces can also be usedin static tests. Commercial codes provide solutions for this problem, but what we intend to develop isa code adapted to the user’s specific needs.

  18. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

    Science.gov (United States)

    Pavlova, Anna; Parks, Jerry M; Gumbart, James C

    2018-02-13

    Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

  19. On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters.

    Science.gov (United States)

    Bachmann, Stephan J; Lin, Zhixiong; Stafforst, Thorsten; van Gunsteren, Wilfred F; Dolenc, Jožica

    2014-01-14

    The technique of one-step perturbation to explore the relation between particular force-field parameters on the one hand and particular properties of a biomolecular system on the other hand from one or a few molecular dynamics simulations is applied to investigate the dependence of the free enthalpy of dimer formation and of crystal dissolution of a self-complementary fragment (H-CGTACG-NH2) of peptide nucleic acid, PNA, a mimic of DNA. The simulations show that PNA dimer formation in aqueous solution is favored by a decrease in the base charges with respect to values of the GROMOS 45A4 force field, while it is disfavored by a decrease in the backbone charges. In contrast, crystal dissolution of the PNA dimer is favored by a decrease in base charges, while a variation of backbone charges has a minor effect on this free enthalpy change. These opposite effects in a crystalline versus aqueous solution environment can be understood from the different water contents for these systems and have consequences for biomolecular force-field development.

  20. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    Energy Technology Data Exchange (ETDEWEB)

    MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  1. Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

    Science.gov (United States)

    Müller, Erich A; Jackson, George

    2014-01-01

    A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

  2. Systematic Mapping on Research Methodology in the Field of E-commerce

    Directory of Open Access Journals (Sweden)

    elham asadamraji

    2016-10-01

    Full Text Available The importance of Methodology Researches in the field of e-commerce is related to the science generation practices and to understand the logic of problem solving in this area. In every scientific discipline, this type of research is critical for the scientific community.The aim of this paper was to review articles that have been published in three Journals of Electronic Commerce from 2009 to 2013 using systematic mapping study. As a result of this study, 337 articles were extracted from a total of 422 articles to investigate different dimensions such as type, goal, scope and method of researches along with philosophical paradigm and unit of analysis, in qualitative and quantitative manner. The results showed that quantitative researches based on positivism paradigm with practical purposes on issues dealing with the development of new products and services and survey research methods in the society unit of analysis had the highest frequency. Finally, we also analyzed the relations between some results, using the Clementine software.

  3. The flow field acting on the fluttering profile, kinematics, forces and total moment

    Czech Academy of Sciences Publication Activity Database

    Kozánek, Jan; Vlček, Václav; Zolotarev, Igor

    2013-01-01

    Roč. 13, č. 7 (2013), s. 1-7 ISSN 0219-4554 R&D Projects: GA ČR GA101/09/1522 Institutional support: RVO:61388998 Keywords : fluttering profile * interferometry visualization * acting forces and moment Subject RIV: JU - Aeronautics, Aerodynamics, Aircrafts Impact factor: 1.059, year: 2013

  4. Forces acting on a small particle in an acoustical field in a thermoviscous fluid.

    Science.gov (United States)

    Karlsen, Jonas T; Bruus, Henrik

    2015-10-01

    We present a theoretical analysis of the acoustic radiation force on a single small spherical particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Within the perturbation assumptions, our analysis places no restrictions on the length scales of the viscous and thermal boundary-layer thicknesses δ(s) and δ(t) relative to the particle radius a, but it assumes the particle to be small in comparison to the acoustic wavelength λ. This is the limit relevant to scattering of ultrasound waves from nanometer- and micrometer-sized particles. For particles of size comparable to or smaller than the boundary layers, the thermoviscous theory leads to profound consequences for the acoustic radiation force. Not only do we predict forces orders of magnitude larger than expected from ideal-fluid theory, but for certain relevant choices of materials, we also find a sign change in the acoustic radiation force on different-sized but otherwise identical particles. These findings lead to the concept of a particle-size-dependent acoustophoretic contrast factor, highly relevant to acoustic separation of microparticles in gases, as well as to handling of nanoparticles in lab-on-a-chip systems.

  5. Mapping the absolute magnetic field and evaluating the quadratic Zeeman-effect-induced systematic error in an atom interferometer gravimeter

    Science.gov (United States)

    Hu, Qing-Qing; Freier, Christian; Leykauf, Bastian; Schkolnik, Vladimir; Yang, Jun; Krutzik, Markus; Peters, Achim

    2017-09-01

    Precisely evaluating the systematic error induced by the quadratic Zeeman effect is important for developing atom interferometer gravimeters aiming at an accuracy in the μ Gal regime (1 μ Gal =10-8m /s2 ≈10-9g ). This paper reports on the experimental investigation of Raman spectroscopy-based magnetic field measurements and the evaluation of the systematic error in the gravimetric atom interferometer (GAIN) due to quadratic Zeeman effect. We discuss Raman duration and frequency step-size-dependent magnetic field measurement uncertainty, present vector light shift and tensor light shift induced magnetic field measurement offset, and map the absolute magnetic field inside the interferometer chamber of GAIN with an uncertainty of 0.72 nT and a spatial resolution of 12.8 mm. We evaluate the quadratic Zeeman-effect-induced gravity measurement error in GAIN as 2.04 μ Gal . The methods shown in this paper are important for precisely mapping the absolute magnetic field in vacuum and reducing the quadratic Zeeman-effect-induced systematic error in Raman transition-based precision measurements, such as atomic interferometer gravimeters.

  6. Radiofrequency electromagnetic field exposure in everyday microenvironments in Europe: A systematic literature review.

    Science.gov (United States)

    Sagar, Sanjay; Dongus, Stefan; Schoeni, Anna; Roser, Katharina; Eeftens, Marloes; Struchen, Benjamin; Foerster, Milena; Meier, Noëmi; Adem, Seid; Röösli, Martin

    2018-03-01

    The impact of the introduction and advancement in communication technology in recent years on exposure level of the population is largely unknown. The main aim of this study is to systematically review literature on the distribution of radiofrequency electromagnetic field (RF-EMF) exposure in the everyday environment in Europe and summarize key characteristics of various types of RF-EMF studies conducted in the European countries. We systematically searched the ISI Web of Science for relevant literature published between 1 January 2000 and 30 April 2015, which assessed RF-EMF exposure levels by any of the methods: spot measurements, personal measurement with trained researchers and personal measurement with volunteers. Twenty-one published studies met our eligibility criteria of which 10 were spot measurements studies, 5 were personal measurement studies with trained researchers (microenvironmental), 5 were personal measurement studies with volunteers and 1 was a mixed methods study combining data collected by volunteers and trained researchers. RF-EMF data included in the studies were collected between 2005 and 2013. The mean total RF-EMF exposure for spot measurements in European "Homes" and "Outdoor" microenvironments was 0.29 and 0.54 V/m, respectively. In the personal measurements studies with trained researchers, the mean total RF-EMF exposure was 0.24 V/m in "Home" and 0.76 V/m in "Outdoor". In the personal measurement studies with volunteers, the population weighted mean total RF-EMF exposure was 0.16 V/m in "Homes" and 0.20 V/m in "Outdoor". Among all European microenvironments in "Transportation", the highest mean total RF-EMF 1.96 V/m was found in trains of Belgium during 2007 where more than 95% of exposure was contributed by uplink. Typical RF-EMF exposure levels are substantially below regulatory limits. We found considerable differences between studies according to the type of measurements procedures, which precludes cross

  7. Measurement of time series variation of thermal diffusivity of magnetic fluid under magnetic field by forced Rayleigh scattering method

    Energy Technology Data Exchange (ETDEWEB)

    Motozawa, Masaaki, E-mail: motozawa.masaaki@shizuoka.ac.jp [Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu-shi, Shizuoka 432-8561 (Japan); Muraoka, Takashi [Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu-shi, Shizuoka 432-8561 (Japan); Motosuke, Masahiro, E-mail: mot@rs.tus.ac.jp [Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585 (Japan); Fukuta, Mitsuhiro, E-mail: fukuta.mitsuhiro@shizuoka.ac.jp [Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu-shi, Shizuoka 432-8561 (Japan)

    2017-04-15

    It can be expected that the thermal diffusivity of a magnetic fluid varies from time to time after applying a magnetic field because of the growth of the inner structure of a magnetic fluid such as chain-like clusters. In this study, time series variation of the thermal diffusivity of a magnetic fluid caused by applying a magnetic field was investigated experimentally. For the measurement of time series variation of thermal diffusivity, we attempted to apply the forced Rayleigh scattering method (FRSM), which has high temporal and high spatial resolution. We set up an optical system for the FRSM and measured the thermal diffusivity. A magnetic field was applied to a magnetic fluid in parallel and perpendicular to the heat flux direction, and the magnetic field intensity was 70 mT. The FRSM was successfully applied to measurement of the time series variation of the magnetic fluid from applying a magnetic field. The results show that a characteristic configuration in the time series variation of the thermal diffusivity of magnetic fluid was obtained in the case of applying a magnetic field parallel to the heat flux direction. In contrast, in the case of applying a magnetic field perpendicular to the heat flux, the thermal diffusivity of the magnetic fluid hardly changed during measurement. - Highlights: • Thermal diffusivity was measured by forced Rayleigh scattering method (FRSM). • FRSM has high temporal and high spatial resolutions for measurement. • We attempted to apply FRSM to magnetic fluid (MF). • Time series variation of thermal diffusivity of MF was successfully measured by FRSM. • Anisotropic thermal diffusivity of magnetic fluid was also successfully confirmed.

  8. Stigma-related barriers and facilitators to help seeking for mental health issues in the armed forces: a systematic review and thematic synthesis of qualitative literature.

    Science.gov (United States)

    Coleman, S J; Stevelink, S A M; Hatch, S L; Denny, J A; Greenberg, N

    2017-08-01

    A recent quantitative review in the area of stigma and help seeking in the armed forces has questioned the association between these factors (Sharp et al. 2015). To date, the contribution of qualitative literature in this area has largely been ignored, despite the value this research brings to the understanding of complex social constructs such as stigma. The aim of the current systematic review of qualitative studies was to identify appropriate literature, assess the quality and synthesize findings across studies regarding evidence of stigma-related barriers and facilitators to help seeking for mental health issues within the armed forces. A multi-database text word search incorporating searches of PsycINFO, MEDLINE, Social Policy and Practice, Social Work Abstracts, EMBASE, ERIC and EBM Review databases between 1980 and April 2015 was conducted. Literature was quality assessed using the Critical Appraisal Skills Programme tool. Thematic synthesis was conducted across the literature. The review identified eight studies with 1012 participants meeting the inclusion criteria. Five overarching themes were identified across the literature: (1) non-disclosure; (2) individual beliefs about mental health; (3) anticipated and personal experience of stigma; (4) career concerns; and (5) factors influencing stigma. The findings from the current systematic review found that unlike inconsistent findings in the quantitative literature, there was substantial evidence of a negative relationship between stigma and help seeking for mental health difficulties within the armed forces. The study advocates for refinement of measures to accurately capture the complexity of stigma and help seeking in future quantitative studies.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-21

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

  10. Investigation into the Effect of Acoustic Radiation Force and Acoustic Streaming on Particle Patterning in Acoustic Standing Wave Fields

    Directory of Open Access Journals (Sweden)

    Shilei Liu

    2017-07-01

    Full Text Available Acoustic standing waves have been widely used in trapping, patterning, and manipulating particles, whereas one barrier remains: the lack of understanding of force conditions on particles which mainly include acoustic radiation force (ARF and acoustic streaming (AS. In this paper, force conditions on micrometer size polystyrene microspheres in acoustic standing wave fields were investigated. The COMSOL® Mutiphysics particle tracing module was used to numerically simulate force conditions on various particles as a function of time. The velocity of particle movement was experimentally measured using particle imaging velocimetry (PIV. Through experimental and numerical simulation, the functions of ARF and AS in trapping and patterning were analyzed. It is shown that ARF is dominant in trapping and patterning large particles while the impact of AS increases rapidly with decreasing particle size. The combination of using both ARF and AS for medium size particles can obtain different patterns with only using ARF. Findings of the present study will aid the design of acoustic-driven microfluidic devices to increase the diversity of particle patterning.

  11. Investigation into the Effect of Acoustic Radiation Force and Acoustic Streaming on Particle Patterning in Acoustic Standing Wave Fields

    Science.gov (United States)

    Yang, Yanye; Ni, Zhengyang; Guo, Xiasheng; Luo, Linjiao; Tu, Juan; Zhang, Dong

    2017-01-01

    Acoustic standing waves have been widely used in trapping, patterning, and manipulating particles, whereas one barrier remains: the lack of understanding of force conditions on particles which mainly include acoustic radiation force (ARF) and acoustic streaming (AS). In this paper, force conditions on micrometer size polystyrene microspheres in acoustic standing wave fields were investigated. The COMSOL® Mutiphysics particle tracing module was used to numerically simulate force conditions on various particles as a function of time. The velocity of particle movement was experimentally measured using particle imaging velocimetry (PIV). Through experimental and numerical simulation, the functions of ARF and AS in trapping and patterning were analyzed. It is shown that ARF is dominant in trapping and patterning large particles while the impact of AS increases rapidly with decreasing particle size. The combination of using both ARF and AS for medium size particles can obtain different patterns with only using ARF. Findings of the present study will aid the design of acoustic-driven microfluidic devices to increase the diversity of particle patterning. PMID:28753955

  12. Magnetic field and force analysis of high Tc superconductor with flux flow and creep

    International Nuclear Information System (INIS)

    Yoshida, Yoshikatsu; Uesaka, Mitsuru; Miya, Kenzo

    1994-01-01

    This paper describes a new method for the magnetic force analysis of high T c superconductor based on the flux flow and creep model. The introduction of the artificial conductivity, which is used in the conventional method, is not needed. The CPU time requirement of the calculations is considerably lower than that in the case of the conventional method. Thereby the vibration of a levitated permanent magnet was numerically analyzed by taking into account the flux flow and creep

  13. Analysis of force characteristics of a superconducting ball in a given magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Liu Jianhua, E-mail: liujianhua@mail.iee.ac.c [Institute of Electrical Engineering, Chinese Academy of Sciences, No. 6 Beiertiao, Zhongguancun, Beijing 100190 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Wang Qiuliang; Yan Luguang [Institute of Electrical Engineering, Chinese Academy of Sciences, No. 6 Beiertiao, Zhongguancun, Beijing 100190 (China)

    2009-07-01

    The electromagnetic force characteristics along Z direction of a superconducting ball levitated by spherical coils with shaping blocks are calculated based on a semi-analytical method. The calculating results from the semi-analytical method are compared with the finite element analysis (FEA) method through a calculation example. The method can be applied to further analysis of dynamic characteristics and parameter optimization in the suspension system.

  14. Robot-assisted adaptive training: custom force fields for teaching movement patterns.

    Science.gov (United States)

    Patton, James L; Mussa-Ivaldi, Ferdinando A

    2004-04-01

    Based on recent studies of neuro-adaptive control, we tested a new iterative algorithm to generate custom training forces to "trick" subjects into altering their target-directed reaching movements to a prechosen movement as an after-effect of adaptation. The prechosen movement goal, a sinusoidal-shaped path from start to end point, was never explicitly conveyed to the subject. We hypothesized that the adaptation would cause an alteration in the feedforward command that would result in the prechosen movement. Our results showed that when forces were suddenly removed after a training period of 330 movements, trajectories were significantly shifted toward the prechosen movement. However, de-adaptation occurred (i.e., the after-effect "washed out") in the 50-75 movements that followed the removal of the training forces. A second experiment suppressed vision of hand location and found a detectable reduction in the washout of after-effects, suggesting that visual feedback of error critically influences learning. A final experiment demonstrated that after-effects were also present in the neighborhood of training--44% of original directional shift was seen in adjacent, unpracticed movement directions to targets that were 60 degrees different from the targets used for training. These results demonstrate the potential for these methods for teaching motor skills and for neuro-rehabilitation of brain-injured patients. This is a form of "implicit learning," because unlike explicit training methods, subjects learn movements with minimal instructions, no knowledge of, and little attention to the trajectory.

  15. The inertial effect of acceleration fields on a self-decoupled wheel force transducer

    Directory of Open Access Journals (Sweden)

    Lihang Feng

    Full Text Available AbstractWheel force transducer (WFT is a tool which can measure the three-axis forces and three-axis torques applied to the wheel in vehicle testing applications. However, the transducer is generally mounted on the wheel of a moving vehicle, when abruptly accelerating or braking, the mass/inertia of the transducer itself has extra effects on the sensor response so that inertia/mass loads will be detected and coupled into the signal outputs. This is the inertia coupling effect that decreases the sensor accuracy and should be avoided. In this paper, the inertia coupling problem induced by six dimensional accelerations is investigated for a universal WFT. Inertia load distribution of the WFT is solved based on the principle of equivalent mass and rotary inertia firstly, thus then its impact can be identified with the theoretical derivation. FEM simulation and experimental verification are performed as well. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear respectively. The relative errors are acceptable within less than 5% and the maximum impact of inertia loads on the signal output is about 1.5% in the measuring range.

  16. Acoustic radiation force on a multilayered sphere in a Gaussian standing field

    Science.gov (United States)

    Wang, Haibin; Liu, Xiaozhou; Gao, Sha; Cui, Jun; Liu, Jiehui; He, Aijun; Zhang, Gutian

    2018-03-01

    We develop a model for calculating the radiation force on spherically symmetric multilayered particles based on the acoustic scattering approach. An expression is derived for the radiation force on a multilayered sphere centered on the axis of a Gaussian standing wave propagating in an ideal fluid. The effects of the sound absorption of the materials and sound wave on acoustic radiation force of a multilayered sphere immersed in water are analyzed, with particular emphasis on the shell thickness of every layer, and the width of the Gaussian beam. The results reveal that the existence of particle trapping behavior depends on the choice of the non-dimensional frequency ka, as well as the shell thickness of each layer. This study provides a theoretical basis for the development of acoustical tweezers in a Gaussian standing wave, which may benefit the improvement and development of acoustic control technology, such as trapping, sorting, and assembling a cell, and drug delivery applications. Project supported by National Key R&D Program (Grant No. 2016YFF0203000), the National Natural Science Foundation of China (Grant Nos. 11774167 and 61571222), the Fundamental Research Funds for the Central Universities of China (Grant No. 020414380001), the Key Laboratory of Underwater Acoustic Environment, Institute of Acoustics, Chinese Academy of Sciences (Grant No. SSHJ-KFKT-1701), and the AQSIQ Technology R&D Program of China (Grant No. 2017QK125).

  17. New exact solutions of Einstein's field equations: gravitational force can also be repulsive!

    International Nuclear Information System (INIS)

    Dietz, W.

    1988-01-01

    This article has not been written for specialists of exact solutions of Einstein's field equations but for physicists who are interested in nontrivial information on this topic. We recall the history and some basic properties of exact solutions of Einstein's vacuum equations. We show that the field equations for stationary axisymmetric vacuum gravitational fields can be expressed by only one nonlinear differential equation for a complex function. This compact form of the field equations allows the generation of almost all stationary axisymmetric vacuum gravitational fields. We present a new stationary two-body solution of Einstein's equations as an application of this generation technique. This new solution proves the existence of a macroscopic, repulsive spin-spin interaction in general relativity. Some estimates that are related to this new two-body solution are given

  18. A comparison between highly resolved S-component observations and model calculations using force-free magnetic field extrapolations

    International Nuclear Information System (INIS)

    Seehafer, N.; Hildebrandt, J.; Krueger, A.; Akhmedov, Sh.; Gel'frejkh, G.B.

    1983-01-01

    Extensive model calculations of solar radio emission features were presented for the complex of solar active regions Hale No 16862, 16863, and 16864 on May 27, 1980 using force-free extrapolated magnetic fields with constant α and a treatment of radiative transfer of S-component emission. The photospheric magnetic field data were taken from magnetographic measurements whereas the required height distribution of temperature and electron density have been adopted from semi-empirical sunspot models based on recent X-, EUV-, optical, and radio observations. In contrast to the simpler magnetic field structure used in other studies, the complex source structure of the S-component emission is clearly represented by other characteristics. The results of the calculations are compared with the observations of the WRST (6 cm) and RATAN-600 (3.2 cm). (author)

  19. Screening for speech and language delay in preschool children: systematic evidence review for the US Preventive Services Task Force.

    Science.gov (United States)

    Nelson, Heidi D; Nygren, Peggy; Walker, Miranda; Panoscha, Rita

    2006-02-01

    PEDIATRICS (ISSN Numbers: Print, 0031-4005; Online, 1098-4275). Published in the public domain by the American Academy of Pediatrics. Speech and language development is a useful indicator of a child's overall development and cognitive ability and is related to school success. Identification of children at risk for developmental delay or related problems may lead to intervention services and family assistance at a young age, when the chances for improvement are best. However, optimal methods for screening for speech and language delay have not been identified, and screening is practiced inconsistently in primary care. We sought to evaluate the strengths and limits of evidence about the effectiveness of screening and interventions for speech and language delay in preschool-aged children to determine the balance of benefits and adverse effects of routine screening in primary care for the development of guidelines by the US Preventive Services Task Force. The target population includes all children up to 5 years old without previously known conditions associated with speech and language delay, such as hearing and neurologic impairments. Studies were identified from Medline, PsycINFO, and CINAHL databases (1966 to November 19, 2004), systematic reviews, reference lists, and experts. The evidence review included only English-language, published articles that are available through libraries. Only randomized, controlled trials were considered for examining the effectiveness of interventions. Outcome measures were considered if they were obtained at any time or age after screening and/or intervention as long as the initial assessment occurred while the child was birth order, and family size. The performance characteristics of evaluation techniques that take or =2 screening techniques in 1 population, and comparisons of a single screening technique across different populations are lacking. Fourteen good- and fair-quality randomized, controlled trials of interventions

  20. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

    Science.gov (United States)

    Lemkul, Justin A; MacKerell, Alexander D

    2017-05-09

    Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

  1. Systematic optimization of exterior measurement locations for the determination of interior magnetic field vector components in inaccessible regions

    Energy Technology Data Exchange (ETDEWEB)

    Nouri, N.; Plaster, B.

    2014-12-11

    An experiment may face the challenge of real-time determination of the magnetic field vector components present within some interior region of the experimental apparatus over which it is impossible to directly measure the field components during the operation of the experiment. As a solution to this problem, we propose a general concept which provides for a unique determination of the field components within such an interior region solely from exterior measurements at fixed discrete locations. The method is general and does not require the field to possess any type of symmetry. We describe our systematic approach for optimizing the locations of these exterior measurements which maximizes their sensitivity to successive terms in a multipole expansion of the field.

  2. Numerical analyses of magnetic field and force in toroidal superconducting magnetic energy storage using unit coils (abstract)

    International Nuclear Information System (INIS)

    Kanamaru, Y.; Nakayama, T.; Amemiya, Y.

    1997-01-01

    Superconducting magnetic energy storage (SMES) is more useful than other systems of electric energy storage because of its larger amounts of stored energy and its higher efficiency. There are two types of SMES. One is the solenoid type and the other is the toroidal type. Some models of solenoid-type SMES are designed in the U.S. and in Japan. But the large scale SMES causes a high magnetic field in the living environment, and causes the erroneous operation of electronic equipment. The authors studied some suitable designs of magnetic shielding for the solenoidal-type SMES to reduce the magnetic field in the living environment. The toiroidal type SMES is studied in this article. The magnetic leakage flux of the toiroidal-type SMES is generally lower than that of the solenoid-type SMES. The toroidal-type SMES is constructed of unit coils, which are convenient for construction. The magnetic leakage flux occurs between unit coils. The electromagnetic force of the coils is very strong. Therefore analyses of the leakage flux and electromagnetic force are important to the design of SMES. The authors studied the number, radius, and length of unit coils. The storage energy is 5 G Wh. The numerical analyses of magnetic fields in the toroidal type SMES are obtained by analytical solutions. copyright 1997 American Institute of Physics

  3. Identification and characterization of outcome measures reported in animal models of epilepsy: Protocol for a systematic review of the literature-A TASK2 report of the AES/ILAE Translational Task Force of the ILAE.

    Science.gov (United States)

    Simonato, Michele; Iyengar, Sloka; Brooks-Kayal, Amy; Collins, Stephen; Depaulis, Antoine; Howells, David W; Jensen, Frances; Liao, Jing; Macleod, Malcolm R; Patel, Manisha; Potschka, Heidrun; Walker, Matthew; Whittemore, Vicky; Sena, Emily S

    2017-11-01

    Current antiseizure therapy is ineffective in approximately one third of people with epilepsy and is often associated with substantial side effects. In addition, most current therapeutic paradigms offer treatment, but not cure, and no therapies are able to modify the underlying disease, that is, can prevent or halt the process of epileptogenesis or alleviate the cognitive and psychiatric comorbidities. Preclinical research in the field of epilepsy has been extensive, but unfortunately, not all the animal models being used have been validated for their predictive value. The overall goal of TASK2 of the AES/ILAE Translational Task Force is to organize and coordinate systematic reviews on selected topics regarding animal research in epilepsy. Herein we describe our strategy. In the first part of the paper we provide an overview of the usefulness of systematic reviews and meta-analysis for preclinical research and explain the essentials for their conduct. Then we describe in detail the protocol for a first systematic review, which will focus on the identification and characterization of outcome measures reported in animal models of epilepsy. The specific goals of this study are to define systematically the phenotypic characteristics of the most commonly used animal models, and to effectively compare these with the manifestations of human epilepsy. This will provide epilepsy researchers with detailed information on the strengths and weaknesses of epilepsy models, facilitating their refinement and future research. Ultimately, this could lead to a refined use of relevant models for understanding the mechanism(s) of the epilepsies and developing novel therapies. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

  4. Impact of online visual feedback on motor acquisition and retention when learning to reach in a force field.

    Science.gov (United States)

    Batcho, C S; Gagné, M; Bouyer, L J; Roy, J S; Mercier, C

    2016-11-19

    When subjects learn a novel motor task, several sources of feedback (proprioceptive, visual or auditory) contribute to the performance. Over the past few years, several studies have investigated the role of visual feedback in motor learning, yet evidence remains conflicting. The aim of this study was therefore to investigate the role of online visual feedback (VFb) on the acquisition and retention stages of motor learning associated with training in a reaching task. Thirty healthy subjects made ballistic reaching movements with their dominant arm toward two targets, on 2 consecutive days using a robotized exoskeleton (KINARM). They were randomly assigned to a group with (VFb) or without (NoVFb) VFb of index position during movement. On day 1, the task was performed before (baseline) and during the application of a velocity-dependent resistive force field (adaptation). To assess retention, participants repeated the task with the force field on day 2. Motor learning was characterized by: (1) the final endpoint error (movement accuracy) and (2) the initial angle (iANG) of deviation (motor planning). Even though both groups showed motor adaptation, the NoVFb-group exhibited slower learning and higher final endpoint error than the VFb-group. In some condition, subjects trained without visual feedback used more curved initial trajectories to anticipate for the perturbation. This observation suggests that learning to reach targets in a velocity-dependent resistive force field is possible even when feedback is limited. However, the absence of VFb leads to different strategies that were only apparent when reaching toward the most challenging target. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Simultaneous fitting of a potential-energy surface and its corresponding force fields using feedforward neural networks

    Science.gov (United States)

    Pukrittayakamee, A.; Malshe, M.; Hagan, M.; Raff, L. M.; Narulkar, R.; Bukkapatnum, S.; Komanduri, R.

    2009-04-01

    An improved neural network (NN) approach is presented for the simultaneous development of accurate potential-energy hypersurfaces and corresponding force fields that can be utilized to conduct ab initio molecular dynamics and Monte Carlo studies on gas-phase chemical reactions. The method is termed as combined function derivative approximation (CFDA). The novelty of the CFDA method lies in the fact that although the NN has only a single output neuron that represents potential energy, the network is trained in such a way that the derivatives of the NN output match the gradient of the potential-energy hypersurface. Accurate force fields can therefore be computed simply by differentiating the network. Both the computed energies and the gradients are then accurately interpolated using the NN. This approach is superior to having the gradients appear in the output layer of the NN because it greatly simplifies the required architecture of the network. The CFDA permits weighting of function fitting relative to gradient fitting. In every test that we have run on six different systems, CFDA training (without a validation set) has produced smaller out-of-sample testing error than early stopping (with a validation set) or Bayesian regularization (without a validation set). This indicates that CFDA training does a better job of preventing overfitting than the standard methods currently in use. The training data can be obtained using an empirical potential surface or any ab initio method. The accuracy and interpolation power of the method have been tested for the reaction dynamics of H+HBr using an analytical potential. The results show that the present NN training technique produces more accurate fits to both the potential-energy surface as well as the corresponding force fields than the previous methods. The fitting and interpolation accuracy is so high (rms error=1.2 cm-1) that trajectories computed on the NN potential exhibit point-by-point agreement with corresponding

  6. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    International Nuclear Information System (INIS)

    Liu Minxian; Wang Yan

    2012-01-01

    The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

  7. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Liu Minxian, E-mail: liukey_sjtu@263.net [School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Wang Yan [Luoyang Institute of Science and Technology, Luoyang, Henan 471023 (China)

    2012-01-15

    The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

  8. Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding.

    Science.gov (United States)

    Cole, Daniel J; Payne, Mike C; Csányi, Gábor; Spearing, S Mark; Colombi Ciacchi, Lucio

    2007-11-28

    We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidized Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO(2) polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress, and interactions with single water molecules of a natively oxidized Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidized and amorphous silica surfaces of 97 and 90 mJm(2), respectively, at a water adsorption coverage of approximately 1 ML. The difference arises from the stronger interaction of the natively oxidized surface with liquid water, resulting in a higher heat of immersion (203 vs 166 mJm(2)), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller densities with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.

  9. Observation of self-assembled fluorescent beads by scanning near-field optical microscopy and atomic force microscopy

    International Nuclear Information System (INIS)

    Oh, Y.J.; Jo, W.; Kim, Min-Gon; Kyu Park, Hyun; Hyun Chung, Bong

    2006-01-01

    Optical response and topography of fluorescent latex beads both on flat self-assembled monolayer and on a micron-patterned surface with poly(dimethylsiloxane) are studied. Scanning near-field optical microscopy and atomic force microscopy were utilized together for detecting fluorescence and imaging topography of the patterned latex beads, respectively. As a result, the micro-patterned latex beads where a specific chemical binding occurred show a strong signal, whereas no signals are observed in the case of nonspecific binding. With fluorescein isothiocyanate (FITC), it is convenient to measure fluorescence signal from the patterned beads allowing us to monitor the small balls of fluorescent latex

  10. Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration

    Czech Academy of Sciences Publication Activity Database

    Beššeová, Ivana; Banáš, Pavel; Kührová, P.; Košinová, P.; Otyepka, Michal; Šponer, Jiří

    Roč. 116, č. 33 ( 2012 ), s. 9899-9916 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034; GA ČR(CZ) GAP208/12/1878; GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476 Grant - others:GA AV ČR(CZ) GPP301/11/P558 Program:GP Institutional research plan: CEZ:AV0Z50040702 Keywords : A-RNA * molecular dynamics * force field Subject RIV: BO - Biophysics Impact factor: 3.607, year: 2012

  11. Application of the nuclear field theory to monopole interactions which include all the vertices of a general force

    International Nuclear Information System (INIS)

    Bes, D.R.; Dussel, G.G.; Liotta, R.J.; Sofia, H.M.; Broglia, R.A.

    1976-01-01

    The field treatment is applied to the monopole pairing and monopole particle-hole interactions in a two-level model. All the vertices of realistic interactions appear, and the problems treated here have most of the complexities of real nuclei. Yet, the model remains sufficiently simple, so that a close comparison with the results of a (conventional) treatment in which only the fermion degrees of freedom are considered is possible. The applicability to actual physical situations appears to be feasible, both for schematic or realistic forces. The advantage of including the exchange components of the interaction in the construction of the phonon is discussed. (Auth.)

  12. Near-field multiple traps of paraxial acoustic vortices with strengthened gradient force generated by sector transducer array

    Science.gov (United States)

    Wang, Qingdong; Li, Yuzhi; Ma, Qingyu; Guo, Gepu; Tu, Juan; Zhang, Dong

    2018-01-01

    In order to improve the capability of particle trapping close to the source plane, theoretical and experimental studies on near-field multiple traps of paraxial acoustic vortices (AVs) with a strengthened acoustic gradient force (AGF) generated by a sector transducer array were conducted. By applying the integration of point source radiation, numerical simulations for the acoustic fields generated by the sector transducer array were conducted and compared with those produced by the circular transducer array. It was proved that strengthened AGFs of near-field multiple AVs with higher peak pressures and smaller vortex radii could be produced by the sector transducer array with a small topological charge. The axial distributions of the equivalent potential gradient indicated that the AGFs of paraxial AVs in the near field were much higher than those in the far field, and the distances at the near-field vortex antinodes were also proved to be the ideal trapping positions with relatively higher AGFs. With the established 8-channel AV generation system, theoretical studies were also verified by the experimental measurements of pressure and phase for AVs with various topological charges. The formation of near-field multiple paraxial AVs was verified by the cross-sectional circular pressure distributions with perfect phase spirals around central pressure nulls, and was also proved by the vortex nodes and antinodes along the center axis. The favorable results demonstrated the feasibility of generating near-field multiple traps of paraxial AVs with strengthened AGF using the sector transducer array, and suggested the potential applications of close-range particle trapping in biomedical engineering.

  13. Numerical study of magnetic field effect on nano-fluid forced convection in a channel

    Energy Technology Data Exchange (ETDEWEB)

    Heidary, H., E-mail: Heidary_ha@aut.ac.ir [Department of Mechanical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran (Iran, Islamic Republic of); Hosseini, R. [Department of Mechanical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran (Iran, Islamic Republic of); Pirmohammadi, M., E-mail: Pirmohamadi@pardisiau.ac.ir [Department of Mechanical Engineering, Pardis Branch, Islamic Azad University, Pardis New City, Tehran (Iran, Islamic Republic of); Kermani, M.J. [Department of Mechanical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran (Iran, Islamic Republic of)

    2015-01-15

    In this study heat transfer and fluid flow analysis in a straight channel utilizing nano-fluid is numerically studied, while flow field is under magnetic field. Usage of nano-particles in base fluid and also applying magnetic field transverse to fluid velocity are two ways recommended in this paper to enhance heat exchange in straight duct. The fluid temperature at the channel inlet (T{sub in}) is taken less than that of the walls (T{sub w}). With assuming thermal equilibrium state of both the fluid phase and nano-particles and ignoring the slip velocity between the phases, single phase approach is used for modeling of nano-fluid. The governing equations are numerically solved in the domain by the control volume approach based on the SIMPLE technique. Numerical studies are performed over a range of Reynolds number, nano-fluid volume fraction and Hartmann number. The influence of these parameters is investigated on the local and average Nusselt numbers. Computations show excellent agreement with the literature. From this study, it is concluded that heat transfer in channels can enhance up to 75% due to the presence of nano-particles and magnetic field in channels. In industrial applications for cooling or heating purposes, the recommended ways in this paper, can provide helpful guidelines to the manufacturers to enhance efficiencies without heat exchanger area increase. - Highlights: • Addition of 10% nano-particles (copper here) can enhance the heat exchange by 26%. • Presence of magnetic field with Ha=30 in pure fluid can enhance the heat exchange by 50%. • Presence of magnetic field and nanofluid with Ha=30 and ϕ=0.1, can enhance the heat exchange by 76%. • Increasing Re{sub H} from 50 to 1000, the average Nu number can increase by a factor of ≈3.

  14. Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

    KAUST Repository

    Lacoste, Deanna; Xiong, Yuan; Moeck, Jonas P.; Chung, Suk-Ho; Roberts, William L.; Cha, Min

    2016-01-01

    The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

  15. Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

    KAUST Repository

    Lacoste, Deanna

    2016-06-23

    The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

  16. Isokinetic force of under-twenties soccer players: comparison of players in different field positions

    Directory of Open Access Journals (Sweden)

    Raphael Mendes Ritti Dias

    2007-06-01

    Full Text Available During a soccer match, countless movements involving muscular force are performed. While some studies have analyzed the force exerted by soccer players, their results have been divergent, particularly when force has been analyzed with respect to fi eld positions. The objective of this study was to compare peak torque, total muscular work, maximum power and isokinetic fatigue index of the knee fl exor and extensor muscles of soccer players in a variety of fi eld positions. Seventy-eight under-twenty soccer players were classifi ed according to the position they play: goalkeepers (n=7, full backs (n=14, wingers (n=16, defensive midfi elders (n=11, center midfi elders (n=14 and forwards (n=16. The concentric isokinetic force of knee fl exor and extensor muscles was evaluated using an isokinetic dynamometer, Cybex® brand Norm™ 6000 model (CSMI, USA. Data was analyzed in terms of non-parametric statistics and results expressed in medians and semi-interquartile range. The Kruskal-Wallis test was applied and when results were signifi cant to pRESUMO Durante uma partida de futebol são realizados inúmeros movimentos que envolvem a força muscular. Embora alguns estudos tenham analisado a força de jogadores de futebol, os resultados encontrados têm sido controversos, principalmente quando analisada a força em função da posição de jogo. O objetivo deste estudo foi comparar o pico de torque, trabalho muscular total, potência máxima e índice de fadiga isocinético dos músculos fl exores e extensores de joelho de jogadores de futebol que atuam em diferentes posições de jogo. Foram incluídos 78 atletas de futebol, pertencentes à categoria Sub-20, foram agrupados de acordo com a posição em campo de jogo: goleiros (n=7, zagueiros (n=14, laterais (n=16, volantes (n=11, meio campo (n=14 e atacantes (n=16. Foi realizada avaliação da força isocinética concêntrica dos músculos fl exores e extensores de joelho em dinamômetro isocin

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

    Czech Academy of Sciences Publication Activity Database

    Beššeová, Ivana; Otyepka, Michal; Réblová, Kamila; Šponer, Jiří

    2009-01-01

    Roč. 11, č. 45 (2009), s. 10701-10711 ISSN 1463-9076 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GD203/09/H046 Grant - others:GA MŠk(CZ) LC512; GA ČR(CZ) GA203/09/1476 Program:LC; GA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : force fileds * RNA * A-form Subject RIV: BO - Biophysics Impact factor: 4.116, year: 2009

  18. Coulomb Force Correction to the Decay b→ccs in the Threshold(Particles and Fields)

    OpenAIRE

    Kouhei, HASEGAWA; Department of Physics, University of Alberta

    2007-01-01

    We study the physical origins of the O(α_s) and O(α^2_s) corrections to the c-s current in the decay b→ccs in the threshold region δ=(M_b-2m_c)/2M_b ≪1. We obtain the corrections which are produced by the Coulomb force between the anti-charm and strange quarks. The Coulomb corrections C_Fπ^2 at O(α_s) and -C^2_Fπ^2ln δ at O(α^2_s) account for 300% and 120% of the corresponding terms in the Abelian-type perturbative corrections respectively. The differences between the Coulomb and perturbative...

  19. On the Shape of Force-Free Field Lines in the Solar Corona

    KAUST Repository

    Prior, C.; Berger, M. A.

    2012-01-01

    of field line structures which could be interpreted as Z-shaped, but which have a helicity value sign expected of an S-shaped structure. These results suggest that caution should be exercised in using two-dimensional images to draw conclusions

  20. EFFECT OF POLARIMETRIC NOISE ON THE ESTIMATION OF TWIST AND MAGNETIC ENERGY OF FORCE-FREE FIELDS

    International Nuclear Information System (INIS)

    Tiwari, Sanjiv Kumar; Venkatakrishnan, P.; Gosain, Sanjay; Joshi, Jayant

    2009-01-01

    The force-free parameter α, also known as helicity parameter or twist parameter, bears the same sign as the magnetic helicity under some restrictive conditions. The single global value of α for a whole active region gives the degree of twist per unit axial length. We investigate the effect of polarimetric noise on the calculation of global α value and magnetic energy of an analytical bipole. The analytical bipole has been generated using the force-free field approximation with a known value of constant α and magnetic energy. The magnetic parameters obtained from the analytical bipole are used to generate Stokes profiles from the Unno-Rachkovsky solutions for polarized radiative transfer equations. Then we add random noise of the order of 10 -3 of the continuum intensity (I c ) in these profiles to simulate the real profiles obtained by modern spectropolarimeters such as Hinode (SOT/SP), SVM (USO), ASP, DLSP, POLIS, and SOLIS etc. These noisy profiles are then inverted using a Milne-Eddington inversion code to retrieve the magnetic parameters. Hundred realizations of this process of adding random noise and polarimetric inversion is repeated to study the distribution of error in global α and magnetic energy values. The results show that (1) the sign of α is not influenced by polarimetric noise and very accurate values of global twist can be calculated, and (2) accurate estimation of magnetic energy with uncertainty as low as 0.5% is possible under the force-free condition.

  1. Improved tests of extra-dimensional physics and thermal quantum field theory from new Casimir force measurements

    International Nuclear Information System (INIS)

    Decca, R.S.; Fischbach, E.; Klimchitskaya, G.L.; Mostepanenko, V.M.; Krause, D.E.; Lopez, D.

    2003-01-01

    We report new constraints on extra-dimensional models and other physics beyond the standard model based on measurements of the Casimir force between two dissimilar metals for separations in the range 0.2-1.2 μm. The Casimir force between a Au-coated sphere and a Cu-coated plate of a microelectromechanical torsional oscillator was measured statically with an absolute error of 0.3 pN. In addition, the Casimir pressure between two parallel plates was determined dynamically with an absolute error of ≅0.6 mPa. Within the limits of experimental and theoretical errors, the results are in agreement with a theory that takes into account the finite conductivity and roughness of the two metals. The level of agreement between experiment and theory was then used to set limits on the predictions of extra-dimensional physics and thermal quantum field theory. It is shown that two theoretical approaches to the thermal Casimir force which predict effects linear in temperature are ruled out by these experiments. Finally, constraints on Yukawa corrections to Newton's law of gravity are strengthened by more than an order of magnitude in the range 56-330 nm

  2. Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

    Directory of Open Access Journals (Sweden)

    Lihang Feng

    Full Text Available Wheel force transducer (WFT, which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range.

  3. Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

    Science.gov (United States)

    Feng, Lihang; Lin, Guoyu; Zhang, Weigong; Dai, Dong

    2015-01-01

    Wheel force transducer (WFT), which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range.

  4. A Pilot Study of Individual Muscle Force Prediction during Elbow Flexion and Extension in the Neurorehabilitation Field

    Directory of Open Access Journals (Sweden)

    Jiateng Hou

    2016-11-01

    Full Text Available This paper proposes a neuromusculoskeletal (NMS model to predict individual muscle force during elbow flexion and extension. Four male subjects were asked to do voluntary elbow flexion and extension. An inertial sensor and surface electromyography (sEMG sensors were attached to subject's forearm. Joint angle calculated by fusion of acceleration and angular rate using an extended Kalman filter (EKF and muscle activations obtained from the sEMG signals were taken as the inputs of the proposed NMS model to determine individual muscle force. The result shows that our NMS model can predict individual muscle force accurately, with the ability to reflect subject-specific joint dynamics and neural control solutions. Our method incorporates sEMG and motion data, making it possible to get a deeper understanding of neurological, physiological, and anatomical characteristics of human dynamic movement. We demonstrate the potential of the proposed NMS model for evaluating the function of upper limb movements in the field of neurorehabilitation.

  5. The GeoFlow experiment-spherical Rayleigh-Benard convection under the influence of an artificial central force field

    International Nuclear Information System (INIS)

    Gellert, M; Beltrame, P; Egbers, C

    2005-01-01

    Spherical Rayleigh-Benard convection under the influence of an artificial central force field produced by the so-called dielectrophoretic effect is studied as a simplified model of the flow in the outer earth core. The fluid motion there is most probably driving the earth's dynamo and the energy source for the earth's magnetic field. Studying convective flows in earth-like geometry could lead to a deeper understanding of the basics of these processes. This research is a preparatory study for the experiments on the International Space Station (ISS). A bifurcation-theoretical approach shows the existence of heteroclinic cycles between spherical modes (l, l + 1) for the non-rotating system. This behavior depends strong on the radius ratio of the spheres and will be hard to detect in the experiment. For slow rotations interactions of the azimuthal modes (m, m + 1) found in numerical simulations for supercritical states are supposed to be experimentally observable

  6. Development of a shear-force scanning near-field cathodoluminescence microscope for characterization of nanostructures' optical properties.

    Science.gov (United States)

    Bercu, N B; Troyon, M; Molinari, M

    2016-09-01

    An original scanning near-field cathodoluminescence microscope for nanostructure characterization has been developed and successfully tested. By using a bimorph piezoelectric stack both as actuator and detector, the developed setup constitutes a real improvement compared to previously reported SEM-based solutions. The technique combines a scanning probe and a scanning electron microscope in order to simultaneously offer near-field cathodoluminescence and topographic images of the sample. Share-force topography and cathodoluminescence measurements on GaN, SiC and ZnO nanostructures using the developed setup are presented showing a nanometric resolution in both topography and cathodoluminescence images with increased sensitivity compared to classical luminescence techniques. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  7. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

    Directory of Open Access Journals (Sweden)

    Raiker Witter

    2015-01-01

    Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

  8. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

    Directory of Open Access Journals (Sweden)

    Longhua Yang

    2016-09-01

    Full Text Available Cytochrome c oxidase (CcO is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F, we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.

  9. Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring

    DEFF Research Database (Denmark)

    Lanzarotti, Esteban; Marcatili, Paolo; Nielsen, Morten

    2018-01-01

    Interactions of T cell receptors (TCR) to peptides in complex with MHC (p:MHC) are key features that mediate cellular immune responses. While MHC binding is required for a peptide to be presented to T cells, not all MHC binders are immunogenic. The interaction of a TCR to the p:MHC complex holds...... terms. Building a benchmark of TCR:p:MHC complexes where epitopes and non-epitopes are modelled using state-of-the-art molecular modelling tools, scoring p:MHC to a given TCR using force-fields, optimized in a cross-validation setup to evaluate TCR inter atomic interactions involved with each p:MHC, we...... and model the TCR:p:MHC complex structure. In summary, we conclude that it is possible to identify the TCR cognate target among different candidate peptides by using a force-field based model, and believe this works could lay the foundation for future work within prediction of TCR:p:MHC interactions....

  10. Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

    Science.gov (United States)

    Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

    2017-03-28

    Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

  11. Mean field based calculations with the Gogny force: Some theoretical tools to explore the nuclear structure

    Energy Technology Data Exchange (ETDEWEB)

    Peru, S. [CEA, DAM, DIF, Arpajon (France); Martini, M. [Ghent University, Department of Physics and Astronomy, Gent (Belgium); CEA, DAM, DIF, Arpajon (France); Universite Libre de Bruxelles, Institut d' Astronomie et d' Astrophysique, CP-226, Brussels (Belgium)

    2014-05-15

    We present a review of several works using the finite-range Gogny interaction in mean field approaches and beyond to explore the most striking nuclear structure features. Shell evolution along the N = 16, 20, 28, 40 isotopic chains is investigated. The static deformation obtained in the mean field description are shown to be often in disagreement with the one experimentally determined. Dynamics is addressed in a GCM-like method, including rotational degrees of freedom, namely the five-dimension collective Hamiltonian (5DCH). This framework allows the description of the low-energy collective excitations. Nevertheless, some data cannot be reproduced with the collective Hamiltonian approach. Thus the QRPA formalism is introduced and used to simultaneously describe high- and low-energy spectroscopy as well as collective and individual excitations. After the description of giant resonances in doubly magic exotic nuclei, the role of the intrinsic deformation in giant resonances is presented. The appearance of low-energy dipole resonances in light nuclei is also discussed. In particular the isoscalar or isovector nature of Pygmy states is debated. Then, the first microscopic fully coherent description of the multipole spectrum of heavy deformed nucleus {sup 238}U is presented. Finally, a comparison of the low-energy spectrum obtained within the two extensions of the static mean field, namely QRPA and 5DCH, is performed for 2{sup +} states in N = 16 isotones, nickel and tin isotopes. For the first time the different static and dynamic factors involved in the generation of the 2{sup +} states in the nickel isotopic chain, from drip line to drip line, can be analysed in only one set of coherent approaches, free of adjustable parameters, using the same two-body interaction D1S and the resulting HFB mean field. (orig.)

  12. Psychological interventions for the treatment of depression, anxiety, alcohol misuse or anger in armed forces veterans and their families: systematic review and meta-analysis protocol.

    Science.gov (United States)

    O'Shea, Luke; Watkins, Ed; Farrand, Paul

    2017-06-15

    Evidence highlights a high prevalence of common mental health disorders in armed forces veterans and their families, with depression, anxiety, alcohol misuse and anger being more common than PTSD. This paper presents a protocol for a systematic review and meta-analysis to identify existing randomised controlled trial (RCT) research testing the effectiveness of psychological interventions for these difficulties in armed forces veterans and their family members. Electronic databases (CENTRAL, PsycInfo, MEDLINE, CINAHL, The Cochrane Register of Clinical Trials, EMBASE and ASSIA) will be searched to identify suitable studies for inclusion in the review supplemented by forward and backward reference checking, grey literature searches and contact with subject authors. Research including armed forces veterans and their family members will be included in the review with research including serving personnel or individuals under the age of 18 being excluded. Few RCTs examining the treatment of depression, anxiety, alcohol misuse or anger exist in armed forces veterans to date. The primary outcome will be symptomatic change following intervention for these difficulties. The secondary outcomes will include methodological aspects of interest such as discharge type and recruitment setting if data permits. In the event that the number of studies identified is too low to undertake a meta-analysis, a narrative review will be conducted. Quality assessment will be undertaken using the Cochrane Collaboration Tool and Cochran's Q statistic calculated to test for heterogeneity as suggested by the Cochrane handbook. The review will examine the findings of existing intervention research for depression, anxiety, alcohol misuse or anger in armed forces veterans and their families, along with any effect sizes that may exist. PROSPERO CRD42016036676.

  13. Correlation of the vapor pressure isotope effect with molecular force fields in the liquid state

    International Nuclear Information System (INIS)

    Pollin, J.S.; Ishida, T.

    1976-07-01

    The present work is concerned with the development and application of a new model for condensed phase interactions with which the vapor pressure isotope effect (vpie) may be related to molecular forces and structure. The model considers the condensed phase as being represented by a cluster of regularly arranged molecules consisting of a central molecule and a variable number of molecules in the first coordination shell. The methods of normal coordinate analysis are used to determine the modes of vibration of the condensed phase cluster from which, in turn, the isotopic reduced partition function can be calculated. Using the medium cluster model, the observed vpie for a series of methane isotopes has been successfully reproduced with better agreement with experiment than has been possible using the simple cell model. We conclude, however, that insofar as the medium cluster model provides a reasonable picture of the liquid state, the vpie is not sufficiently sensitive to molecular orientation to permit an experimental determination of intermolecular configuration in the condensed phase through measurement of isotopic pressure ratios. The virtual independence of vapor pressure isotope effects on molecular orientation at large cluster sizes is a demonstration of the general acceptability of the cell model assumptions for vpie calculations

  14. Dispersion Forces

    CERN Document Server

    Buhmann, Stefan Yoshi

    2012-01-01

    In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

  15. Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

    Science.gov (United States)

    Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

    2015-10-08

    Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

  16. Some aspects of forces and fields in atomic models of crack tips

    International Nuclear Information System (INIS)

    Hoagland, R.G.; Daw, M.S.; Hirth, J.P.

    1991-01-01

    This paper examines the stresses and displacement gradients in atomistic models of cracks based on an EAM potential devised for aluminum. Methods for computing these quantities are described. Results are presented for two models differing in terms of the orientations of the crack relative to the crystal, a [100](010) orientation that behaves in a brittle fashion and a [111](110) orientation which emits partial dislocations prior to extending. Both models display lattice trapping. The stresses in the brittle crack model are compared with the linear elastic prediction and found to be in remarkably good agreement to within distances of about one lattice parameter of the crack tip and at the free surface where contributions from sources other than strain energy (e.g., surface tension) influence the results. Similar results are observed for the ductile model until dislocation emission occurs. The largest stresses that develop just prior to crack extension or dislocation emission are used to estimate the ratio of theoretical tensile strength to shear strength in this material. Eshelby's conservation integrals, F and M, are also computed. F is found to be essentially contour independent and in agreement with the linear elastic prediction in both models until dislocation emission occurs, at which point a large screening contribution arises from the emitted partials. The contour size dependence of M reveals some interesting features of the crack tip including a slight wobble of the crack tip inside its potential well with changing applied K and the existence of forces acting to move the crack faces apart as blunting occurs

  17. GeoFORCE Alaska: Four-Year Field Program Brings Rural Alaskan High School Students into the STEM Pipeline

    Science.gov (United States)

    Fowell, S. J.; Rittgers, A.; Stephens, L.; Hutchinson, S.; Peters, H.; Snow, E.; Wartes, D.

    2016-12-01

    GeoFORCE Alaska is a four-year, field-based, summer geoscience program designed to raise graduation rates in rural Alaskan high schools, encourage participants to pursue college degrees, and increase the diversity of Alaska's technical workforce. Residents of predominantly Alaska Native villages holding degrees in science, technology, engineering, or math (STEM) bring valuable perspectives to decisions regarding management of cultural and natural resources. However, between 2010 and 2015 the average dropout rate for students in grades 7-12 was 8.5% per year in the North Slope School District and 7% per year in the Northwest Arctic School District. 2015 graduation rates were 70% and 75%, respectively. Statewide statistics highlight the challenge for Alaska Native students. During the 2014-2015 school year alone 37.6% of Alaska Native students dropped out of Alaskan public schools. At the college level, Alaska Native students are underrepresented in University of Alaska Fairbanks (UAF) science departments. Launched in 2012 by UAF in partnership with the longstanding University of Texas at Austin program, GeoFORCE applies the cohort model, leading the same group of high school students on geological field academies during four consecutive summers. Through a combination of active learning, teamwork, and hands-on projects at spectacular geological locations, students gain academic skills and confidence that facilitate high school and college success. To date, GeoFORCE Alaska has recruited two cohorts. 78% of these students identify as Alaska Native, reflecting community demographics. The inaugural cohort of 18 students from the North Slope Borough completed the Fourth-Year Academy in summer 2015. 94% of these students graduated from high school, at least 72% plan to attend college, and 33% will major in geoscience. A second cohort of 34 rising 9th and 10th graders entered the program in 2016. At the request of corporate sponsors, this cohort was recruited from both the

  18. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance.

    Science.gov (United States)

    Noel, Martin; Fortin, Karine; Bouyer, Laurent J

    2009-06-03

    Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during

  19. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

    Directory of Open Access Journals (Sweden)

    Bouyer Laurent J

    2009-06-01

    Full Text Available Abstract Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min, during (5 min and after (5 min exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion. To evaluate modifications in feedforward control, strides with no force field ('catch strides' were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%, subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99. Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%, plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive

  20. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

    Science.gov (United States)

    Noel, Martin; Fortin, Karine; Bouyer, Laurent J

    2009-01-01

    Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle

  1. Critical heat flux of forced convection boiling in an oscilating acceleration field. Pt. 1

    International Nuclear Information System (INIS)

    Otsuji, T.; Kurosawa, A.

    1982-01-01

    The influence of periodically varying acceleration on critical heat flux (CHF) of Freon-113 flowing upward in a uniformly heated vertical annular channel has been studied experimentally. The freon loop was oscillated vertically to determine the ratio of CHF in the oscillating acceleration field to the corresponding stationary value. The amplitude of inlet flow oscillation induced by variation of acceleration, which causes early CHF, is proportional to the acceleration amplitude. The dependence of inlet flow rate on the oscillating acceleration decreases with increasing inlet subcooling, and no oscillation of inlet flow is observed in the case of negative exit quality (subcooled boiling). Nevertheless the degradation of CHF is more remarkable in the low quality region. This result suggests the necessity to introduce an other mechanism of early CHF than flow oscillation. (orig.)

  2. The selected models of the mesostructure of composites percolation, clusters, and force fields

    CERN Document Server

    Herega, Alexander

    2018-01-01

    This book presents the role of mesostructure on the properties of composite materials. A complex percolation model is developed for the material structure containing percolation clusters of phases and interior boundaries. Modeling of technological cracks and the percolation in the Sierpinski carpet are described. The interaction of mesoscopic interior boundaries of the material, including the fractal nature of interior boundaries, the oscillatory nature of it interaction and also the stochastic model of the interior boundaries’ interaction, the genesis, structure, and properties are discussed. One of part of the book introduces the percolation model of the long-range effect which is based on the notion on the multifractal clusters with transforming elements, and the theorem on the field interaction of multifractals is described. In addition small clusters, their characteristic properties and the criterion of stability are presented.

  3. Systematic study of even-even nuclei with Hartree-Fock+BCS method using Skyrme SIII force

    Energy Technology Data Exchange (ETDEWEB)

    Tajima, Naoki; Takahara, Satoshi; Onishi, Naoki [Tokyo Univ. (Japan). Coll. of Arts and Sciences

    1997-03-01

    We have applied the Hartree-Fock+BCS method with Skyrme SIII force formulated in a three-dimensional Cartesian-mesh representation to even-even nuclei with 2 {<=} Z {<=} 114. We discuss the results concerning the atomic masses, the quadrupole (m=0, 2) and hexadecapole (m=0, 2, 4) deformations, the skin thicknesses, and the halo radii. We also discuss the energy difference between oblate and prolate solutions and the shape difference between protons and neutrons. (author)

  4. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

    2018-03-01

    The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

  5. A systematic search for new X-ray pulsators in ROSAT fields

    Science.gov (United States)

    Israel, G. L.

    1996-10-01

    powered neutron stars, some of which were observed in the X-ray band, can show highly coherent signals as well. Photospheric oscillations due to opacity instability in a layer close to the surface of an isolated hot white dwarf or pre-white dwarf star can be also observed in the very soft X-ray band. Light curves with increased statistical quality, time resolution and duration have become available in recent years for a variety of astronomical objects and over different bands of the electromagnetic spectrum. Power spectrum analysis is probably the single most important technique that is applied to time series, in order to detect periodicities and quasi-periodicities by the presence of significant power spectrum peaks. Applications to time series of high energy astronomical data have been especially numerous and successful over the last decade, as a consequence of the pronounced variability (often both periodic and non-periodic in character) detected in many sources. ROSAT, an acronym for the German word Rontgensatellit, is an X-ray satellite launched in June 1990. Its X-ray telescope covers the soft X-ray band from 0.05 keV to 2.4 keV. The main aim of the mission was to perform the first all-sky survey (RASS) with imaging telescopes, possessing an X-ray sensitivity of about a factor 1000 higher than that of UHURU. The survey took the first 6 months of the operations of ROSAT. After that the satellite has been used to carry out pointed observations of selected targets. These observations cover a much smaller portion of the sky than the RASS, but afford a factor 10-1000 higher sensitivity. A systematic exploitation of the public domain ROSAT pointed observations with the Position Sensitive Proportional Counter (PSPC; about 10% of the sky and about 5300 fields until May 1996) was carried out by several groups. NASA-HEASARC and MPE have produced catalogues containing about 60000 serendipitous sources (WGA by White, Giommi & Angelini 1994; ROSATSRC by Zimmermann 1994). This

  6. High-Stakes Systematic Reviews: A Case Study From the Field of Teen Pregnancy Prevention.

    Science.gov (United States)

    Goesling, Brian; Oberlander, Sarah; Trivits, Lisa

    2016-08-19

    Systematic reviews help policy makers and practitioners make sense of research findings in a particular program, policy, or practice area by synthesizing evidence across multiple studies. However, the link between review findings and practical decision-making is rarely one-to-one. Policy makers and practitioners may use systematic review findings to help guide their decisions, but they may also rely on other information sources or personal judgment. To describe a recent effort by the U.S. federal government to narrow the gap between review findings and practical decision-making. The Teen Pregnancy Prevention (TPP) Evidence Review was launched by the U.S. Department of Health and Human Services (HHS) in 2009 as a systematic review of the TPP literature. HHS has used the review findings to determine eligibility for federal funding for TPP programs, marking one of the first attempts to directly link systematic review findings with federal funding decisions. The high stakes attached to the review findings required special considerations in designing and conducting the review. To provide a sound basis for federal funding decisions, the review had to meet accepted methodological standards. However, the review team also had to account for practical constraints of the funding legislation and needs of the federal agencies responsible for administering the grant programs. The review team also had to develop a transparent process for both releasing the review findings and updating them over time. Prospective review authors and sponsors must recognize both the strengths and limitations of this approach before applying it in other areas. © The Author(s) 2016.

  7. Estimation of Prestress Force Distribution in Multi-Strand System of Prestressed Concrete Structures Using Field Data Measured by Electromagnetic Sensor.

    Science.gov (United States)

    Cho, Keunhee; Cho, Jeong-Rae; Kim, Sung Tae; Park, Sung Yong; Kim, Young-Jin; Park, Young-Hwan

    2016-08-18

    The recently developed smart strand can be used to measure the prestress force in the prestressed concrete (PSC) structure from the construction stage to the in-service stage. The higher cost of the smart strand compared to the conventional strand renders it unaffordable to replace all the strands by smart strands, and results in the application of only a limited number of smart strands in the PSC structure. However, the prestress forces developed in the strands of the multi-strand system frequently adopted in PSC structures differ from each other, which means that the prestress force in the multi-strand system cannot be obtained by simple proportional scaling using the measurement of the smart strand. Therefore, this study examines the prestress force distribution in the multi-strand system to find the correlation between the prestress force measured by the smart strand and the prestress force distribution in the multi-strand system. To that goal, the prestress force distribution was measured using electromagnetic sensors for various factors of the multi-strand system adopted on site in the fabrication of actual PSC girders. The results verified the possibility to assume normal distribution for the prestress force distribution per anchor head, and a method computing the mean and standard deviation defining the normal distribution is proposed. This paper presents a meaningful finding by proposing an estimation method of the prestress force based upon field-measured data of the prestress force distribution in the multi-strand system of actual PSC structures.

  8. Measurement of physical performance by field tests in programs of cardiac rehabilitation: a systematic review and meta-analysis.

    Science.gov (United States)

    Travensolo, Cristiane; Goessler, Karla; Poton, Roberto; Pinto, Roberta Ramos; Polito, Marcos Doederlein

    2018-04-13

    The literature concerning the effects of cardiac rehabilitation (CR) on field tests results is inconsistent. To perform a systematic review with meta-analysis on field tests results after programs of CR. Studies published in PubMed and Web of Science databases until May 2016 were analyzed. The standard difference in means correct by bias (Hedges' g) was used as effect size (g) to measure que amount of modifications in performance of field tests after CR period. Potential differences between subgroups were analyzed by Q-test based on ANOVA. Fifteen studies published between 1996 e 2016 were included in the review, 932 patients and age ranged 54,4 - 75,3 years old. Fourteen studies used the six-minutes walking test to evaluate the exercise capacity and one study used the Shuttle Walk Test. The random Hedges's g was 0.617 (P<0.001), representing a drop of 20% in the performance of field test after CR. The meta-regression showed significantly association (P=0.01) to aerobic exercise duration, i.e., for each 1-min increase in aerobic exercise duration, there is a 0.02 increase in effect size for performance in the field test. Field tests can detect physical modification after CR, and the large duration of aerobic exercise during CR was associated with a better result. Copyright © 2018 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

  9. Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

    Science.gov (United States)

    Georgieva, Miglena K.

    2004-03-01

    The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

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

    Science.gov (United States)

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

    2014-02-27

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

  11. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

    Science.gov (United States)

    Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

    2014-12-23

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

  12. On a role of the Bsub(z) component of interplanetary magnetic field in a force balance in the day time magnetopause

    International Nuclear Information System (INIS)

    Kuznetsova, T.V.

    1980-01-01

    The role of interplanetary magnetic field (IMF) in the force balance in the day time magnetopause is discussed. The effect of the circular DR-current on the balance of pressures in the magnetopause is taken into account in the calculations. It is shown that IMF plays a significant role in the balance of forces in the day time magnetopause. The ratio of magnetic pressure to the thermal pressure of solar wind in subsolar point is k=0.5. The field observed in magnetosphere near the neutral line is lower by the value of transition region field. All the conclusions are obtained for Bsub(z) [ru

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

    Science.gov (United States)

    Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

    2012-01-10

    The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats

  14. Systematic Interviewing Microskills and Neuroscience: Developing Bridges between the Fields of Communication and Counseling Psychology

    Science.gov (United States)

    Ivey, Allen E.; Daniels, Thomas

    2016-01-01

    Originating in 1966-68, Microcounseling was the first video-based listening program and its purposes and methods overlap with the communications field. This article presents history, research, and present applications in multiple fields nationally and internationally. Recent neuroscience and neurobiology research is presented with the important…

  15. Searching for non-genetic molecular and imaging PTSD risk and resilience markers: Systematic review of literature and design of the German Armed Forces PTSD biomarker study.

    Science.gov (United States)

    Schmidt, Ulrike; Willmund, Gerd-Dieter; Holsboer, Florian; Wotjak, Carsten T; Gallinat, Jürgen; Kowalski, Jens T; Zimmermann, Peter

    2015-01-01

    Biomarkers allowing the identification of individuals with an above average vulnerability or resilience for posttraumatic stress disorder (PTSD) would especially serve populations at high risk for trauma exposure like firefighters, police officers and combat soldiers. Aiming to identify the most promising putative PTSD vulnerability markers, we conducted the first systematic review on potential imaging and non-genetic molecular markers for PTSD risk and resilience. Following the PRISMA guidelines, we systematically screened the PubMed database for prospective longitudinal clinical studies and twin studies reporting on pre-trauma and post-trauma PTSD risk and resilience biomarkers. Using 25 different combinations of search terms, we retrieved 8151 articles of which we finally included and evaluated 9 imaging and 27 molecular studies. In addition, we briefly illustrate the design of the ongoing prospective German Armed Forces (Bundeswehr) PTSD biomarker study (Bw-BioPTSD) which not only aims to validate these previous findings but also to identify novel and clinically applicable molecular, psychological and imaging risk, resilience and disease markers for deployment-related psychopathology in a cohort of German soldiers who served in Afghanistan. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Does remnant gastric cancer really differ from primary gastric cancer? A systematic review of the literature by the Task Force of Japanese Gastric Cancer Association.

    Science.gov (United States)

    Shimada, Hideaki; Fukagawa, Takeo; Haga, Yoshio; Oba, Koji

    2016-04-01

    Remnant gastric cancer, most frequently defined as cancer detected in the remnant stomach after distal gastrectomy for benign disease and those cases after surgery of gastric cancer at least 5 years after the primary surgery, is often reported as a tumor with poor prognosis. The Task Force of Japanese Gastric Cancer Association for Research Promotion evaluated the clinical impact of remnant gastric cancer by systematically reviewing publications focusing on molecular carcinogenesis, lymph node status, patient survival, and surgical complications. A systematic literature search was performed using PubMed/MEDLINE with the keywords "remnant," "stomach," and "cancer," revealing 1154 relevant reports published up to the end of December 2014. The mean interval between the initial surgery and the diagnosis of remnant gastric cancer ranged from 10 to 30 years. The incidence of lymph node metastases at the splenic hilum for remnant gastric cancer is not significantly higher than that for primary proximal gastric cancer. Lymph node involvement in the jejunal mesentery is a phenomenon peculiar to remnant gastric cancer after Billroth II reconstruction. Prognosis and postoperative morbidity and mortality rates seem to be comparable to those for primary proximal gastric cancer. The crude 5-year mortality for remnant gastric cancer was 1.08 times higher than that for primary proximal gastric cancer, but this difference was not statistically significant. In conclusion, although no prospective cohort study has yet evaluated the clinical significance of remnant gastric cancer, our literature review suggests that remnant gastric cancer does not adversely affect patient prognosis and postoperative course.

  17. Different forces

    CERN Multimedia

    1982-01-01

    The different forces, together with a pictorial analogy of how the exchange of particles works. The table lists the relative strength of the couplings, the quanta associated with the force fields and the bodies or phenomena in which they have a dominant role.

  18. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

    Science.gov (United States)

    2016-01-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  19. An analysis of the energetic reward offered by field bean (Vicia faba) flowers: Nectar, pollen, and operative force.

    Science.gov (United States)

    Bailes, Emily J; Pattrick, Jonathan G; Glover, Beverley J

    2018-03-01

    Global consumption of crops with a yield that is dependent on animal pollinators is growing, with greater areas planted each year. However, the floral traits that influence pollinator visitation are not usually the focus of breeding programmes, and therefore, it is likely that yield improvements may be made by optimizing floral traits to enhance pollinator visitation rates. We investigated the variation present in the floral reward of the bee-pollinated crop Vicia faba (field bean). We examined the genetic potential for breeding flowers with a greater reward into current commercial varieties and used bee behavioral experiments to gain insight into the optimal nectar concentration to maximize bee preference. There was a large range of variation in the amount of pollen and nectar reward of flowers in the genotypes investigated. Bee behavioral experiments using nectar sugar concentrations found in V. faba lines suggest that Bombus terrestris prefers 55% w/w sugar solution over 40% w/w, but has no preference between 55% w/w and 68% w/w sugar solution. We provide a first indication of the force required to open V. faba flowers. Our results provide a valuable starting point toward breeding for varieties with optimized floral reward. Field studies are now needed to verify whether the genetic potential for breeding more rewarding flowers can translate into higher yield and yield stability.

  20. [Environmental investigation of ground water contamination at Wright-Patterson Air Force Base, Ohio]. Volume 5, Field Investigation report

    Energy Technology Data Exchange (ETDEWEB)

    1992-03-01

    An environmental investigation of ground water conditions has been undertaken at Wright-Patterson Air Force Base (WPAFB), Ohio to obtain data to assist in the evaluation of a potential removal action to prevent, to the extent practicable, migration of the contaminated ground water across Base boundaries. Field investigations were limited to the central section of the southwestern boundary of Area C and the Springfield Pike boundary of Area B. Further, the study was limited to a maximum depth of 150 feet below grade. Three primary activities of the field investigation were: (1) installation of 22 monitoring wells, (2) collection and analysis of ground water from 71 locations, (3) measurement of ground water elevations at 69 locations. Volatile organic compounds including trichloroethylene, perchloroethylene, and/or vinyl chloride were detected in concentrations exceeding Maximum Contaminant Levels (MCL) at three locations within the Area C investigation area. Ground water at the Springfield Pike boundary of Area B occurs in two primary units, separated by a thicker-than-expected clay layers. One well within Area B was determined to exceed the MCL for trichloroethylene.

  1. In their own words: a synthesis of the qualitative research on the experiences of adults seeking asylum. A systematic review of qualitative findings in forced migration.

    Science.gov (United States)

    Hoare, Thomas; Vidgen, Andrew; Roberts, Neil

    2017-12-01

    Quantitative research indicates that some forced migrants have mental health needs. Asylum seekers are a group of forced migrants applying for asylum status in a host country, and are often subject to rights restrictions and threat of deportation, though little is known about subjective experiences of the asylum journey and process of claiming asylum. The current paper therefore describes a systematic review of the qualitative literature, examining asylum seekers experiences of asylum journey, from country of origin, to arrival and adaptation to host countries. A search of four databases yielded 122 studies. Inclusion/exclusion criteria were applied and 15 studies were retained and critically appraised. The country where research was conducted, study aims, sample characteristics and methodological approaches were all critically reviewed for included studies. Study aims fell into four themes; 'an aspect of the asylum seeker journey'; 'psychological distress and wellbeing'; 'cultural identity and adaptation to new environment' and 'social welfare, employment and housing'. Studies were generally high quality and indicate issues around choice of asylum destination, distress created by uncertainty around asylum decision and hostile reactions of host communities. However, few studies have examined the experiences of asylum seekers specifically, which is important given the unique circumstances of this population.

  2. Systematic measurements of transient fields for W, Os and Pt ions traversing Fe

    International Nuclear Information System (INIS)

    Stuchbery, A.E.; Heseltine, T.H.; Anderssen, S.S.; Bolotin, H.H.; Byrne, A.P.; Fabricius, B.; Kibedi, T.

    1994-01-01

    Transient magnetic fields were measured for W, Os and Pt ions traversing iron hosts with average velocities in the range from approximately 1.6 v 0 to 4.8 v 0 (v 0 = c/137, Bohr velocity). Transient fields for W and Os in Fe are consistent with behaviour found for lighter rare-earth ions and are about 20% stronger than those for Pt in Fe over the majority of the velocity range examined. A measurement was made to confirm that possible heavy-ion beam induced attenuations of the transient field are negligible for low-velocity Pt ions excited by Ni beams. Results are discussed in terms of both empirical and model-based parameterizations of the transient field strength. (orig.)

  3. Spatiotemporal, kinematic, force and muscle activation outcomes during gait and functional exercise in water compared to on land: A systematic review.

    Science.gov (United States)

    Heywood, Sophie; McClelland, Jodie; Geigle, Paula; Rahmann, Ann; Clark, Ross

    2016-07-01

    Exercises replicating functional activities are commonly used in aquatic rehabilitation although it is not clear how the movement characteristics differ between the two environments. A systematic review was completed in order to compare the biomechanics of gait, closed kinetic chain and plyometric exercise when performed in water and on land. Databases including MEDLINE, CINAHL, SPORTDiscus, Embase and the Cochrane library were searched. Studies were included where a functional lower limb activity was performed in water and on land with the same instructions. Standardized mean differences (SMD) and 95% confidence intervals were calculated for spatiotemporal, kinematic, force and muscle activation outcomes. 28 studies included walking or running (19 studies), stationary running (three), closed kinetic chain exercise (two), plyometric exercise (three) and timed-up and go (one). Very large effect sizes showed self-selected speed of walking (SMD >4.66) and vertical ground reaction forces (VGRF) (SMD >1.91) in water were less than on land, however, lower limb range of movement and muscle activity were similar. VGRF in plyometric exercise was lower in water when landing but more similar between the two environments in propulsion. Maximal speed of movement for walking and stationary running was lower in water compared to on land (SMD>3.05), however was similar in propulsion in plyometric exercise. Drag forces may contribute to lower self-selected speed of walking. Monitoring speed of movement in water assists in determining the potential advantages or limitations of aquatic exercise and the task specificity to land-based function. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Effect of resistance training on muscle strength and rate of force development in healthy older adults: A systematic review and meta-analysis.

    Science.gov (United States)

    Guizelini, Pedrode Camargo; de Aguiar, Rafael Alves; Denadai, Benedito Sérgio; Caputo, Fabrizio; Greco, Camila Coelho

    2018-02-01

    Rapid force capacity, identified by rate of rise in contractile force at the onset of contraction, i.e., the rate of force development (RFD), has been considered an important neuromuscular parameter of physical fitness in elderly individuals. Randomized control studies conducted in adults have found that resistance training may elicit different outcomes in terms of RFD and muscle strength. Thus, the main purpose of this study was to review systematically the literature for studies regarding the influence of resistance training on muscle strength and RFD in elderly persons. A literature search was performed in major electronic databases from inception to March 2017. Studies including health individuals with a mean age≥60years, describing the effect of resistance training on RFD and muscle strength were found eligible. The outcomes were calculated as the difference in percentage change between control and experimental groups (% change) and data were presented as mean±95% confidence limits. Meta-analyses were performed using a random-effects model and, in addition, simple and multiple meta-regression analyses were used to identify effects of age, training type, sessions per week and training duration on % change in RFD and muscle strength. Thirteen training effects were collected from 10 studies included in the meta-analysis. The resistance training program had a moderate beneficial effect on both muscle strength (% change=18.40%, 95% CL 13.69-23.30, pchange=26.68, 95% CL 14.41-35.52, pchanges in muscle strength and RFD. It can be concluded that explosive training and heavy strength training are effective resistance training methods aiming to improve both muscle strength and RFD after short-to-medium training period. However, muscle strength and RFD seem to adapt differently to resistance training programs, suggesting caution for their interchangeable use in clinical assessments of the elderly. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. International veterinary epilepsy task force recommendations for systematic sampling and processing of brains from epileptic dogs and cats.

    Science.gov (United States)

    Matiasek, Kaspar; Pumarola I Batlle, Martí; Rosati, Marco; Fernández-Flores, Francisco; Fischer, Andrea; Wagner, Eva; Berendt, Mette; Bhatti, Sofie F M; De Risio, Luisa; Farquhar, Robyn G; Long, Sam; Muñana, Karen; Patterson, Edward E; Pakozdy, Akos; Penderis, Jacques; Platt, Simon; Podell, Michael; Potschka, Heidrun; Rusbridge, Clare; Stein, Veronika M; Tipold, Andrea; Volk, Holger A

    2015-08-28

    Traditionally, histological investigations of the epileptic brain are required to identify epileptogenic brain lesions, to evaluate the impact of seizure activity, to search for mechanisms of drug-resistance and to look for comorbidities. For many instances, however, neuropathological studies fail to add substantial data on patients with complete clinical work-up. This may be due to sparse training in epilepsy pathology and or due to lack of neuropathological guidelines for companion animals.The protocols introduced herein shall facilitate systematic sampling and processing of epileptic brains and therefore increase the efficacy, reliability and reproducibility of morphological studies in animals suffering from seizures.Brain dissection protocols of two neuropathological centres with research focus in epilepsy have been optimised with regards to their diagnostic yield and accuracy, their practicability and their feasibility concerning clinical research requirements.The recommended guidelines allow for easy, standardised and ubiquitous collection of brain regions, relevant for seizure generation. Tissues harvested the prescribed way will increase the diagnostic efficacy and provide reliable material for scientific investigations.

  6. Influence of grain size and upper critical magnetic field on global pinning force of bronze-processed Nb/sub 3/Sn compound

    International Nuclear Information System (INIS)

    Ochiai, S.; Osamura, K.

    1986-01-01

    In order to know the dependency of global pinning force of Nb/sub 3/Sn compound on grain size and upper critical magnetic field, the global pinning force was measured at 3-15 T using bronze-processed multifilamentary composites. The grain size and upper critical magnetic field were varied by two types of annealing treatment: one is the isothermal annealing at 873, 973 and 1073 K up to 1730 ks and another is the two-stage annealing (low temperature annealing to form fine grains at 873 K for 1730 ks + high temperature annealing to raise upper critical magnetic field at 1073 K up to 18 ks). In the case of isothermal annealing treatment, both of grain size and upper critical magnetic field increased with increasing annealing temperature and time except for the annealing treatments at high temperature for prolonged times. In the case of two-stage annealing, both of them increased with second stage annealing time. The increase in grain size led to decrease in the pinning force but the increase in upper critical magnetic field to increase in it. From the analysis of the present data based on the Suenaga's speculation concerning with the density of pinning site and the Kramer's equation, it was suggested that the pinning force is, to a first approximation, proportional to the product of inverse grain size and (1-h)/sup 2/h/sup 1/2/ where h is the reduced magnetic field

  7. Systematic Analysis and Synthesis of Integral Estimations of Bachelors’ Training in the Field of Financial Monitoring

    Directory of Open Access Journals (Sweden)

    Alena Gaibatova

    2016-05-01

    Full Text Available The following article describes methods and algorithms of improving the quality of students’ training in NRNU MEPHI on the profile activities in the sphere of financial monitoring. In this work, we have investigated a new subject field: application of the principal component analysis method to examine students’ performance in different profiles of their training.

  8. Systematic Field Study of NO(x) Emission Control Methods for Utility Boilers.

    Science.gov (United States)

    Bartok, William; And Others

    A utility boiler field test program was conducted. The objectives were to determine new or improved NO (x) emission factors by fossil fuel type and boiler design, and to assess the scope of applicability of combustion modification techniques for controlling NO (x) emissions from such installations. A statistically designed test program was…

  9. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    Science.gov (United States)

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  10. Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions.

    Science.gov (United States)

    Vymětal, Jiří; Vondrášek, Jiří

    2014-09-04

    We present a novel force field model of 2,2,2-trifluoroethanol (TFE) based on the generalized AMBER force field. The model was exhaustively parametrized to reproduce liquid-state properties of pure TFE, namely, density, enthalpy of vaporization, self-diffusion coefficient, and population of trans and gauche conformers. The model predicts excellently other liquid-state properties such as shear viscosity, thermal expansion coefficient, and isotropic compressibility. The resulting model describes unexpectedly well the state equation of the liquid region in the range of 100 K and 10 MPa. More importantly, the proposed TFE model was optimized for use in combination with the TIP4P/Ew and TIP4P/2005 water models. It does not manifest excessive aggregation, which is known for other models, and therefore, it is supposed to more realistically describe the behavior of TFE/water mixtures. This was demonstrated by means of the Kirkwood-Buff theory of solutions and reasonable agreement with experimental data. We explored a considerable part of the parameter space and systematically tested individual combinations of parameters for performance in combination with the TIP4P/Ew and TIP4P/2005 water models. We observed ambiguity in parameters describing pure liquid TFE; however, most of them failed for TFE/water mixtures. We clearly demonstrated the necessity for balanced TFE-TFE, TFE-water, and water-water interactions which can be acquired only by employing implicit polarization correction in the course of parametrization.

  11. Reactive force field simulation of proton diffusion in BaZrO{sub 3} using an empirical valence bond approach

    Energy Technology Data Exchange (ETDEWEB)

    Raiteri, Paolo; Gale, Julian D [Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box 1987, Perth, WA 6845 (Australia); Bussi, Giovanni, E-mail: paolo@ivec.org, E-mail: julian@ivec.org [Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste (Italy)

    2011-08-24

    A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO{sub 3} 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 BaZrO{sub 3} 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 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.

  12. Augmentation of forced-convection heat transfer by applying electric fields to disturb flow near a wall

    International Nuclear Information System (INIS)

    Nariai, H.; Ishiguro, H.; Nagata, S.; Yabe, A.

    1991-01-01

    This paper reports on the augmentation effect of electrohydrodynamically (EHD) induced flow disturbance on forced-convection heat transfer in a channel that was experimentally investigated in order to determine the applicability of the enhanced heat transfer into a low- pressure drop heat exchanger, such as a high-performance oil cooler. The investigation is mainly based on the study carried out on the unique point where the flow is disturbed actively and controllably by applying electric fields between the wall and array of wire electrodes installed near the wall along the main stream. The liquid mixture of refrigerant R113 (96 wt %) and ethanol (4 wt %), called Fronsorubu AE, was selected as a working fluid. Heat transfer was found to be promoted intensely in the turbulent flow as well as in the laminar flow, up to a factor of about twenty-three in the case of laminar flow. It is noteworthy that the rate of increase in heat transfer coefficient is larger compared to that in the pressure drop. From a measurement of velocities by a laser Doppler velocimeter, it was made clear that the electrohydrodynamically induced flow disturbance brings about large heat transfer coefficients

  13. Gas adsorption in Mg-porphyrin-based porous organic frameworks: A computational simulation by first-principles derived force field.

    Science.gov (United States)

    Pang, Yujia; Li, Wenliang; Zhang, Jingping

    2017-09-15

    A novel type of porous organic frameworks, based on Mg-porphyrin, with diamond-like topology, named POF-Mgs is computationally designed, and the gas uptakes of CO 2 , H 2 , N 2 , and H 2 O in POF-Mgs are investigated by Grand canonical Monte Carlo simulations based on first-principles derived force fields (FF). The FF, which describes the interactions between POF-Mgs and gases, are fitted by dispersion corrected double-hybrid density functional theory, B2PLYP-D3. The good agreement between the obtained FF and the first-principle energies data confirms the reliability of the FF. Furthermore our simulation shows the presence of a small amount of H 2 O (≤ 0.01 kPa) does not much affect the adsorption quantity of CO 2 , but the presence of higher partial pressure of H 2 O (≥ 0.1 kPa) results in the CO 2 adsorption decrease significantly. The good performance of POF-Mgs in the simulation inspires us to design novel porous materials experimentally for gas adsorption and purification. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Development of the ReaxFFCBN reactive force field for the improved design of liquid CBN hydrogen storage materials.

    Science.gov (United States)

    Pai, Sung Jin; Yeo, Byung Chul; Han, Sang Soo

    2016-01-21

    Liquid CBN (carbon-boron-nitrogen) hydrogen-storage materials such as 3-methyl-1,2-BN-cyclopentane have the advantage of being easily accessible for use in current liquid-fuel infrastructure. To develop practical liquid CBN hydrogen-storage materials, it is of great importance to understand the reaction pathways of hydrogenation/dehydrogenation in the liquid phase, which are difficult to discover by experimental methods. Herein, we developed a reactive force field (ReaxFFCBN) from quantum mechanical (QM) calculations based on density functional theory for the storage of hydrogen in BN-substituted cyclic hydrocarbon materials. The developed ReaxFFCBN provides similar dehydrogenation pathways and energetics to those predicted by QM calculations. Moreover, molecular dynamics (MD) simulations with the developed ReaxFFCBN can predict the stability and dehydrogenation behavior of various liquid CBN hydrogen-storage materials. Our simulations reveal that a unimolecular dehydrogenation mechanism is preferred in liquid CBN hydrogen-storage materials. However, as the temperature in the simulation increases, the contribution of a bimolecular dehydrogenation mechanism also increases. Moreover, our ReaxFF MD simulations show that in terms of thermal stability and dehydrogenation kinetics, liquid CBN materials with a hexagonal structure are more suitable materials than those with a pentagonal structure. We expect that the developed ReaxFFCBN could be a useful protocol in developing novel liquid CBN hydrogen-storage materials.

  15. Effect of Magnetic Field on Entropy Generation Due to Laminar Forced Convection Past a Horizontal Flat Plate

    Directory of Open Access Journals (Sweden)

    Moh'd A. Al-Nimr

    2004-06-01

    Full Text Available Magnetic field effect on local entropy generation due to steady two-dimensional laminar forced convection flow past a horizontal plate was numerically investigated. This study was focused on the entropy generation characteristics and its dependency on various dimensionless parameters. The effect of various dimensionless parameters, such as Hartmann number (Ha, Eckert number (Ec, Prandtl number (Pr, Joule heating parameter (R and the free stream temperature parameter (θ∞ on the entropy generation characteristics is analyzed. The dimensionless governing equations in Cartesian coordinate were solved by an implicit finite difference technique. The solutions were carried out for Ha2=0.5-3, Ec=0.01-0.05, Pr=1-5 and θ∞=1.1-2.5. It was found that, the entropy generation increased with increasing Ha, Ec and R. While, increasing the free stream temperature parameter, and Prandtl number tend to decrease the local entropy generation.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-22

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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  18. A molecular dynamic simulation study of mechanical properties of graphene–polythiophene composite with Reax force field

    International Nuclear Information System (INIS)

    Nayebi, Payman; Zaminpayma, Esmaeil

    2016-01-01

    In this paper, we performed molecular dynamic simulations by Reax force field to study the mechanical properties of graphene–polythiophene nanocomposite. By computing elastic constant, breaking stress, breaking strain and Young's modulus from the stress–strain curve for the nanocomposites, we investigated effects of tension orientation, graphene loading to the polymer, temperature of nanocomposite and defect of graphene on these mechanical characters. It is found that mechanical characters of tension along the zigzag orientation are higher than other directions. Also, by increasing the weight concentration of graphene in composite, the Young's modulus and breaking