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Sample records for amber force field

  1. 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.

  2. Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

    DEFF Research Database (Denmark)

    Reichert, David E.; Norrby, Per-Ola; Welch, Michael J.

    2001-01-01

    In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER* force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new pa...

  3. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

    Science.gov (United States)

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

    2007-01-01

    We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the α/γ concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the α/γ = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 μs of state-of-the-art molecular dynamics simulations in aqueous solution. PMID:17351000

  4. Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Otyepka, M.; Šponer, Jiří; Hobza, P.; Jurečka, P.

    2010-01-01

    Roč. 12, č. 35 (2010), s. 10476-10493 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA203/09/1476 Grant - others:GA MŠk(CZ) LC512; GA MŠk(CZ) GD203/09/H046 Program:LC; GD Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : amber empirical potential * DFT-SAPT * compensation of errors Subject RIV: BO - Biophysics Impact factor: 3.454, year: 2010

  5. Reference simulations of noncanonical nucleic acids with different chí variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Zgarbová, M.; Stadlbauer, Petr; Otyepka, M.; Banáš, P.; Koča, J.; Cheatham III, T.E.; Jurečka, P.; Šponer, Jiří

    2012-01-01

    Roč. 8, č. 7 (2012), s. 2506-2520 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GD203/09/H046; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GAP208/11/1822; GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : refinement of empirical force fields * DNA * Z-DNA backbone Subject RIV: BO - Biophysics Impact factor: 5.389, year: 2012

  6. African Meridian B-Field Education and Research (AMBER) Array

    Science.gov (United States)

    Yizengaw, E.; Moldwin, M. B.

    2009-04-01

    The AMBER array contains four magnetometers and spans across the geomagnetic equator from L of 1 to an L of 1.4. In addition to filling the largest land-based gap in global magnetometer coverage, the AMBER array will address two fundamental areas of space physics: (1) the processes governing electrodynamics of the equatorial ionosphere as a function of latitude (or L-shell), local time, longitude, magnetic activity, and season, and (2) ULF pulsation strength and its connection with equatorial electrojet strength at low/mid-latitude regions. Satellite observations show unique equatorial ionospheric structures in the African sector, though these have not been confirmed by observation from the ground due to lack of ground-based instruments in the region. In order to have a complete global understanding of equatorial ionosphere motions, deployment of ground-based magnetometers in Africa is essential. One focus of IHY is the deployment of networks of small instruments, including the development of research infrastructure in developing nations through the United Nations Basic Space Science (UNBSS) Small Instrument Array. Therefore, AMBER magnetometer array in partnership with parallel US funded GPS receivers in Africa will allow us to understand the electrodynamics that governs equatorial ionosphere motions. While AMBER routinely observes the F region plasma drift mechanism ( E × B drift), the GPS stations will monitor the structure of plasma at low/mid-latitudes in the African sectors. In addition to new scientific discoveries and advancing the space science research into Africa by establishing scientific collaborations between scientists in the developing and developed nations, the AMBER project also contributes to developing the basic science of heliophysics through cross-disciplinary studies of universal process. This includes the creation of sustainable research/training infrastructure within the developing nations (Africa).

  7. 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

    -generation carbohydrate force fields. No single force field is consistently better than the others for all the test cases. A statistical assessment of the performance of the force fields indicates that CHEAT(95), CFF, certain versions of Amber and of MM3 have the best overall performance, for these gas phase...

  8. light amber and dark amber

    African Journals Online (AJOL)

    Both samples showed high amount of carbohydrate, that of light amber being higher. The antioxidant vitamins (vitamins A, C and E) content of the two honeys are 4.08± 0.21, 2.22± 0.10and 0.28± 0.03(mg/dl), (for light amber), and 4.42± 0.06, 2.61± 0.11,and 0.26± 0.02 (mg/dl), (for dark amber) respectively. Both samples

  9. 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...

  10. 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...

  11. Assessing the Current State of Amber Force Field Modifications for DNA

    Czech Academy of Sciences Publication Activity Database

    Galindo-Murillo, R.; Robertson, J.; Zgarbová, M.; Šponer, Jiří; Otyepka, M.; Jurečka, P.; Cheatham III, T. E.

    2016-01-01

    Roč. 12, č. 8 (2016), s. 4114-4127 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * particle mesh ewald * pair opening kinetics Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016

  12. 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....

  13. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.

    Science.gov (United States)

    Heinz, Hendrik; Lin, Tzu-Jen; Mishra, Ratan Kishore; Emami, Fateme S

    2013-02-12

    The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and

  14. 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.

  15. 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.

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

    Science.gov (United States)

    Leontyev, Igor; Stuchebrukhov, Alexei

    2011-02-21

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole μ∼ 3D reported in recent ab initio and experimental studies with the value μ(eff)∼ 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value μ(eff) = μ/√ε(el), where ε(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes.

  17. 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

  18. 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

  19. 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...

  20. 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...

  1. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  2. Static and dynamical Meissner force fields

    Science.gov (United States)

    Weinberger, B. R.; Lynds, L.; Hull, J. R.; Mulcahy, T. M.

    1991-01-01

    The coupling between copper-based high temperature superconductors (HTS) and magnets is represented by a force field. Zero-field cooled experiments were performed with several forms of superconductors: 1) cold-pressed sintered cylindrical disks; 2) small particles fixed in epoxy polymers; and 3) small particles suspended in hydrocarbon waxes. Using magnets with axial field symmetries, direct spatial force measurements in the range of 0.1 to 10(exp 4) dynes were performed with an analytical balance and force constants were obtained from mechanical vibrational resonances. Force constants increase dramatically with decreasing spatial displacement. The force field displays a strong temperature dependence between 20 and 90 K and decreases exponentially with increasing distance of separation. Distinct slope changes suggest the presence of B-field and temperature-activated processes that define the forces. Hysteresis measurements indicated that the magnitude of force scales roughly with the volume fraction of HTS in composite structures. Thus, the net force resulting from the field interaction appears to arise from regions as small or smaller than the grain size and does not depend on contiguous electron transport over large areas. Results of these experiments are discussed.

  3. Validation of molecular force field parameters for peptides including isomerized amino acids.

    Science.gov (United States)

    Oda, Akifumi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Yamaotsu, Noriyuki; Hirono, Shuichi; Takahashi, Ohgi

    2018-04-01

    Recently, stereoinversions and isomerizations of amino acid residues in the proteins of living beings have been observed. Because isomerized amino acids cause structural changes and denaturation of proteins, isomerizations of amino acid residues are suspected to cause age-related diseases. In this study, AMBER molecular force field parameters were tested by using computationally generated nonapeptides and tripeptides including stereoinverted and/or isomerized amino acid residues. Energy calculations by using density functional theory were also performed for comparison. Although the force field parameters were developed by parameter fitting for l-α-amino acids, the accuracy of the computational results for d-amino acids and β-amino acids was comparable to those for l-α-amino acids. The conformational energies for tripeptides calculated by using density functional theory were reproduced more accurately than those for nonapeptides calculated by using the molecular mechanical force field. The evaluations were performed for the ff99SB, ff03, ff12SB, and the latest ff14SB force field parameters. © 2018 Wiley Periodicals, Inc.

  4. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ONAB INITIOTARGET DATA.

    Science.gov (United States)

    Huang, Lei; Roux, Benoît

    2013-08-13

    Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.

  5. Solar Force-free Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Thomas Wiegelmann

    2012-09-01

    Full Text Available The structure and dynamics of the solar corona is dominated by the magnetic field. In most areas in the corona magnetic forces are so dominant that all non-magnetic forces like plasma pressure gradient and gravity can be neglected in the lowest order. This model assumption is called the force-free field assumption, as the Lorentz force vanishes. This can be obtained by either vanishing electric currents (leading to potential fields or the currents are co-aligned with the magnetic field lines. First we discuss a mathematically simpler approach that the magnetic field and currents are proportional with one global constant, the so-called linear force-free field approximation. In the generic case, however, the relation between magnetic fields and electric currents is nonlinear and analytic solutions have been only found for special cases, like 1D or 2D configurations. For constructing realistic nonlinear force-free coronal magnetic field models in 3D, sophisticated numerical computations are required and boundary conditions must be obtained from measurements of the magnetic field vector in the solar photosphere. This approach is currently of large interests, as accurate measurements of the photospheric field become available from ground-based (for example SOLIS and space-born (for example Hinode and SDO instruments. If we can obtain accurate force-free coronal magnetic field models we can calculate the free magnetic energy in the corona, a quantity which is important for the prediction of flares and coronal mass ejections. Knowledge of the 3D structure of magnetic field lines also help us to interpret other coronal observations, e.g., EUV images of the radiating coronal plasma.

  6. 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 ...

  7. Organic geochemistry of Czech amber

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Sýkorová, Ivana; Mach, K.; Dvořák, Z.

    2015-01-01

    Roč. 11, č. 1 (2015), s. 146 ISSN 1336-7242. [Zjazd chemikov /67./. 07.09.2015-11.09.2015, Horný Smokovec] R&D Projects: GA ČR(CZ) GA13-18482S Institutional research plan: CEZ:AV0Z30460519 Keywords : fossil resin * amber * resinite Subject RIV: DD - Geochemistry

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

    Science.gov (United States)

    Durmaz, Vedat

    2015-03-01

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

  9. A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

    Directory of Open Access Journals (Sweden)

    Giuliano Malloci

    2015-08-01

    Full Text Available We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors. For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

  10. Provenance studies of amber by PIXE

    Energy Technology Data Exchange (ETDEWEB)

    Lowe, L.; Ruvalcaba S, J.L. [Centro de Estudios Mayas, Instituto de Investigaciones Filologicas, UNAM C.P. 04510 Mexico D.F. (Mexico)

    1999-07-01

    Analyses by Infrared Spectroscopy and {sup 13} C Nuclear Magnetic Resonance are suitable to determine the paleobotanic source of amber, but cannot differentiate between beds of the same paleobotanic source. Particle Induced X-ray Emission (PIXE) using an external set-up is presented as a new and non-destructive semiquantitative method for provenance studies of amber. PIXE analysis is focused at inorganic contents of amber, considering that the composition of microscopic inclusions depends on the sedimentation environment and it can be used to determine similarities and differences between amber samples and correlate them with amber beds. Results of analyses on amber samples from several world regions and a group of archaeological samples from Chiapas, Mexico, are presented. Amber from different regions have specific inorganic elemental contents; archaeological samples can be associated with beds, even if they have the same paleobotanic origin. (Author)

  11. Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Jurečka, P.; Banáš, P.; Havrila, Marek; Šponer, Jiří; Otyepka, M.

    2017-01-01

    Roč. 121, č. 11 (2017), s. 2420-2433 ISSN 1520-6106 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * sugar-phosphate backbone * free-energy landscape * ribosomal-rna Subject RIV: BO - Biophysics OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

  12. 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)

  13. Amber Gemstones Sorting By Colour

    OpenAIRE

    Sinkevicius, Saulius; Lipnickas, Arunas; Rimkus, Kestas

    2017-01-01

    The objective of this study is to create computer vision algorithms for autonomous multiclass identification of amber nuggets by their colour. By applying the proposed methods an automated production sorting system has been developed. This system can be used, for example in combination with conveyor systems, and in any other case that requires distinguishing objects of many classes in a high-rate flow of objects. In order to achieve this, the proposed system operates with colour features sele...

  14. 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).

  15. Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models.

    Science.gov (United States)

    Zhang, Haiyang; Yin, Chunhua; Jiang, Yang; van der Spoel, David

    2018-04-18

    Thermodynamic and kinetic properties are of critical importance for the applicability of computational models to biomolecules such as proteins. Here we present an extensive evaluation of the Amber ff99SB-ILDN force field for modeling of hydration and diffusion of amino acids with three-site (SPC, SPC/E, SPC/E b , and TIP3P), four-site (TIP4P, TIP4P-Ew, and TIP4P/2005), and five-site (TIP5P and TIP5P-Ew) water models. Hydration free energies (HFEs) of neutral amino acid side chain analogues have little dependence on the water model, with a root-mean-square error (RMSE) of ∼1 kcal/mol from experimental observations. On the basis of the number of interacting sites in the water model, HFEs of charged side chains can be putatively classified into three groups, of which the group of three-site models lies between those of four- and five-site water models; for each group, the water model dependence is greatly eliminated when the solvent Galvani potential is considered. Some discrepancies in the location of the first hydration peak ( R RDF ) in the ion-water radial distribution function between experimental and calculated observations were detected, such as a systematic underestimation of the acetate (Asp side chain) ion. The RMSE of calculated diffusion coefficients of amino acids from experiment increases linearly with the increasing diffusion coefficients of the solvent water models at infinite dilution. TIP3P has the fastest diffusivity, in line with literature findings, while the "FB" and "OPC" water model families as well as TIP4P/2005 perform well, within a relative error of 5%, and TIP4P/2005 yields the most accurate estimate for the water diffusion coefficient. All of the tested water models overestimate amino acid diffusion coefficients by approximately 40% (TIP4P/2005) to 200% (TIP3P). Scaling of protein-water interactions with TIP4P/2005 in the Amber ff99SBws and ff03ws force fields leads to more negative HFEs but has little influence on the diffusion of

  16. Potassium bromide, KBr/ ε: New Force Field

    Science.gov (United States)

    Fuentes-Azcatl, Raúl; Barbosa, Marcia C.

    2018-02-01

    We propose a new force field for the Potassium Bromide, the KBr/ ε. The crystal density and structure, as well as, the density, the viscosity and the dielectric constant of the solution in water were computed and compared with the experiments and other atomistic models. Next, the transferability of the KBr/ ε and of the NaCl/ ε models is verified by creating the KCl/ ε and the NaBr/ ε models. The strategy was to employ the same parameters obtained for the NaCl/ ε and for the KBr/ ε force fields for the building up of the KCl/ ε and the NaBr/ ε models . The thermodynamic and dynamic properties of these two new models were compared with the experimental

  17. Thermally stimulated properties of amber

    International Nuclear Information System (INIS)

    Bowlt, C.

    1983-01-01

    Thermoelectrets yielded thermally stimulated currents but radioelectrets could not be produced even following exposures of 16000 R of ionising radiation. It is concluded that the thermally stimulated currents are due to the depolarisation of dipoles, with activation energy of 1.4 +- 0.1 eV, rather than to discharge of trapped charge carriers. Amber exhibits thermal luminescence following exposure to light of lambda < 500 nm but not to ionising radiation after exposures up to 5500 R, indicating localised impurity/trap/recombination complexes in the specimen surface, with a trap depth of 1.5 +- 0.1 eV. (author)

  18. RNA force field with accuracy comparable to state-of-the-art protein force fields.

    Science.gov (United States)

    Tan, Dazhi; Piana, Stefano; Dirks, Robert M; Shaw, David E

    2018-02-13

    Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models ("force fields") available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluate these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields, thus significantly advancing the utility of MD simulation as a tool for elucidating the structural dynamics and function of RNA molecules and RNA-containing biological assemblies. Copyright © 2018 the Author(s). Published by PNAS.

  19. Implementation of project Safe in Amber. Verification study for SFR 1 SAR-08

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Gavin; Herben, Martin; Lloyd, Pam; Rose, Danny; Smith, Chris; Barraclough, Ian (Enviros Consulting Ltd (GB))

    2008-03-15

    This report documents an exercise in which AMBER has been used to represent the models used in Project SAFE, a safety assessment undertaken on SFR 1. (AMBER is a flexible, graphical-user-interface based tool that allows users to build their own dynamic compartmental models to represent the migration, degradation and fate of contaminants in an environmental system. AMBER allows the user to assess routine, accidental and long-term contaminant release.) AMBER has been used to undertake assessment calculations on all of the disposal system, including all disposal tunnels and the Silo, the geosphere and several biosphere modules. The near-field conceptual models were implemented with minimal changes to the approach undertaken previously in Project SAFE. Model complexity varied significantly between individual disposal facilities increasing significantly from the BLA to the BTF and BMA tunnels and Silo. Radionuclide transport through the fractured granite geosphere was approximated using a compartment model approach in AMBER. Several biosphere models were implemented in AMBER including reasonable biosphere development, which considered the evolution of the Forsmark area from coastal to lacustrine to agricultural environments in response to land uplift. Parameters were sampled from distributions and simulations were run for 1,000 realisations. In undertaking the comparison of AMBER with the various codes and calculation tools used in Project SAFE it was necessary to undertake a detailed analysis of the modelling approach previously adopted, with particular focus given to the near-field models. As a result some discrepancies in the implementation of the models and documentation were noted. The exercise demonstrates that AMBER is fully capable of representing the features of the SFR 1 disposal system in a safety assessment suitable for SAR-08

  20. 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.

  1. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA.

    Science.gov (United States)

    Karakas, Esra; Taveneau, Cyntia; Bressanelli, Stéphane; Marchi, Massimo; Robert, Bruno; Abel, Stéphane

    2017-01-01

    In this paper, we describe the derivation and the validation of original RESP atomic partial charges for the N, N-dimethyl-dodecylamine oxide (LDAO) surfactant. These charges, designed to be fully compatible with all the AMBER force fields, are at first tested against molecular dynamics simulations of pure LDAO micelles and with a fragment of the lipid kinase PIK4A (DI) modeled with the QUARK molecular modeling server. To model the micelle, we used two distinct AMBER force fields (i.e. Amber99SB and Lipid14) and a variety of starting conditions. We find that the micelle structural properties (such as the shape, size, the LDAO headgroup hydration, and alkyl chain conformation) slightly depend on the force field but not on the starting conditions and more importantly are in good agreement with experiments and previous simulations. We also show that the Lipid14 force field should be used instead of the Amber99SB one to better reproduce the C(sp3)C(sp3)C(sp3)C(sp3) conformation in the surfactant alkyl chain. Concerning the simulations with LDAO-DI protein, we carried out different runs at two NaCl concentrations (i.e. 0 and 300 mM) to mimic, in the latter case, the experimental conditions. We notice a small dependence of the simulation results with the LDAO parameters and the salt concentration. However, we find that in the simulations, three out of four tryptophans of the DI protein are not accessible to water in agreement with our fluorescence spectroscopy experiments reported in the paper.

  2. The critical role of force-fields in property prediction

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Welsh, William J.; Rasmussen, Kjeld

    1999-01-01

    of conformational energydifferences and interaction energies vary significantly from one force-field to another. As a test for the reliability of the non-bonded interactions, vapor-liquid equilibrium (VLE) data have been calculated for a small number of systems using three different force-fields. The force...

  3. Reactive Force Fields via Explicit Valency

    Science.gov (United States)

    Kale, Seyit

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

  4. The Amber Industry: Development Сhallenges and Combating Amber Trafficking in the Baltic Region

    Directory of Open Access Journals (Sweden)

    Volchetskaya Т. S.

    2017-12-01

    Full Text Available This article considers the current state and prospective development of the amber industry in the Baltic Sea region. The authors identify the main obstacles to the industry’s development in Russia — poor pricing mechanisms for raw amber, an imbalance between supply and demand, a slow pace of technological modernisation, and a delayed introduction of new technologies and processing techniques. The authors identify gaps in the regulatory framework and highlight problems of legal regulation and law enforcement as regards the amber industry. Combating illegal amber extraction and trafficking is a pressing problem in the Kaliningrad region (Russia and other Baltic region states. The article explores theoretical aspects of the legislative policy on combating illegal amber extraction and trafficking. The authors focus on the relevant law enforcement practices and hold that administrative sanctions for unauthorised amber extraction and trade are not fully effective in Russia. The authors stress the need for introducing criminal liability for a repeated offence and outline opportunities for using forensic gemological examination of amber and amber products.

  5. Carnivorous leaves from Baltic amber.

    Science.gov (United States)

    Sadowski, Eva-Maria; Seyfullah, Leyla J; Sadowski, Friederike; Fleischmann, Andreas; Behling, Hermann; Schmidt, Alexander R

    2015-01-06

    The fossil record of carnivorous plants is very scarce and macrofossil evidence has been restricted to seeds of the extant aquatic genus Aldrovanda of the Droseraceae family. No case of carnivorous plant traps has so far been reported from the fossil record. Here, we present two angiosperm leaves enclosed in a piece of Eocene Baltic amber that share relevant morphological features with extant Roridulaceae, a carnivorous plant family that is today endemic to the Cape flora of South Africa. Modern Roridula species are unique among carnivorous plants as they digest prey in a complex mutualistic association in which the prey-derived nutrient uptake depends on heteropteran insects. As in extant Roridula, the fossil leaves possess two types of plant trichomes, including unicellular hairs and five size classes of multicellular stalked glands (or tentacles) with an apical pore. The apices of the narrow and perfectly tapered fossil leaves end in a single tentacle, as in both modern Roridula species. The glandular hairs of the fossils are restricted to the leaf margins and to the abaxial lamina, as in extant Roridula gorgonias. Our discovery supports current molecular age estimates for Roridulaceae and suggests a wide Eocene distribution of roridulid plants.

  6. Investigation of fossil resins and amber

    Directory of Open Access Journals (Sweden)

    E.Yu. Makarova

    2017-05-01

    Full Text Available Fossil resins and amber are a product of lithogenesis of resinous substances of higher plants – resinite. These components of plants, like other lipoid ingredients (suberins, coutines, sporinins, natural rubbers are resistant to microbial action, so they are well preserved in bacterial processing of organic matter in the stages of sedimento- and diagenesis, and are well diagnosed in microscopic studies. They occur in a rather wide age range of sedimentary rocks. The amber of the Baltic region of the Eocene age is most fully studied. The article presents the results of a study of the collection of fossil resins and amber from various regions of the world. Samples were studied microscopically; carbon isotope analysis, infrared spectroscopy (IR spectroscopy were performed. The most informative analysis of high-molecular polymeric compounds is IR spectroscopy. It was found that in the analyzed samples of fossil resins of different ages, aromatic compounds are not observed, most of which are first volatilized in fossilization processes. The possibility of influencing the group composition of amber and amber-like resins for sedimentation, diagenesis and catagenesis is discussed. The IR spectra of fossil and modern resin conifers are compared. Using the IR spectroscopy method, an attempt was made to identify the botanical origin of fossil resins.

  7. Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

    Science.gov (United States)

    Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

    2016-02-21

    Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.

  8. An opilioacarid mite in Cretaceous Burmese amber

    Science.gov (United States)

    Dunlop, Jason A.; de Oliveira Bernardi, Leopoldo Ferreira

    2014-09-01

    A fossil opilioacarid mite (Parasitiformes: Opilioacarida) in Burmese amber is described as ? Opilioacarus groehni sp. nov. This ca. 99 Ma record (Upper Cretaceous: Cenomanian) represents only the third fossil example of this putatively basal mite lineage, the others originating from Eocene Baltic amber (ca. 44-49 Ma). Our new record is not only the oldest record of Opilioacarida, but it is also one of the oldest examples of the entire Parasitiformes clade. The presence of Opilioacarida—potentially Opiloacarus—in the Cretaceous of SE Asia suggests that some modern genus groups were formerly more widely distributed across the northern hemisphere, raising questions about previously suggested Gondwanan origins for these mites.

  9. Evidence concerning oxidation as a surface reaction in Baltic amber

    DEFF Research Database (Denmark)

    Shashoua, Yvonne

    2012-01-01

    The aim of this study was to provide evidence about oxidation as a surface reaction during degradation of Baltic amber. A clear understanding of the amber-oxygen interaction modalities is essential to develop conservation techniques for museum collections of amber objects. Pellet-shaped samples...

  10. 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).

  11. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator.

    Science.gov (United States)

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T; Singh, Hukam; Hammel, Jörg U; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-10-04

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

  12. A fossil biting midge (Diptera: Ceratopogonidae) from early Eocene Indian amber with a complex pheromone evaporator

    Science.gov (United States)

    Stebner, Frauke; Szadziewski, Ryszard; Rühr, Peter T.; Singh, Hukam; Hammel, Jörg U.; Kvifte, Gunnar Mikalsen; Rust, Jes

    2016-10-01

    The life-like fidelity of organisms captured in amber is unique among all kinds of fossilization and represents an invaluable source for different fields of palaeontological and biological research. One of the most challenging aspects in amber research is the study of traits related to behaviour. Here, indirect evidence for pheromone-mediated mating behaviour is recorded from a biting midge (Ceratopogonidae) in 54 million-year-old Indian amber. Camptopterohelea odora n. sp. exhibits a complex, pocket shaped structure on the wings, which resembles the wing folds of certain moth flies (Diptera: Psychodidae) and scent organs that are only known from butterflies and moths (Lepidoptera) so far. Our studies suggests that pheromone releasing structures on the wings have evolved independently in biting midges and might be much more widespread in fossil as well as modern insects than known so far.

  13. 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.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems...

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

    Science.gov (United States)

    El-Kaddah, N.; Szekely, J.

    1982-01-01

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

  16. 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

  17. Mitigated-force carriage for high magnetic field environments

    Science.gov (United States)

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

    2015-05-19

    A carriage for high magnetic field environments includes a plurality of work-piece separators disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla for supporting and separating a plurality of work-pieces by a preselected, essentially equal spacing, so that, as a first work-piece is inserted into the magnetic field, a second work-piece is simultaneously withdrawn from the magnetic field, so that an attractive magnetic force imparted on the first work-piece offsets a resistive magnetic force imparted on the second work-piece.

  18. 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.

  19. 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.

  20. Penis morphology in a Burmese amber harvestman

    Science.gov (United States)

    Dunlop, Jason A.; Selden, Paul A.; Giribet, Gonzalo

    2016-02-01

    A unique specimen of the fossil harvestman Halitherses grimaldii Giribet and Dunlop, 2005 (Arachnida: Opiliones) from the Cretaceous (ca. 99 Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in H. grimaldii appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which H. grimaldii was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that H. grimaldii represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.

  1. A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution.

    Science.gov (United States)

    Mishra, Ratan K; Fernández-Carrasco, Lucia; Flatt, Robert J; Heinz, Hendrik

    2014-07-21

    Tricalcium aluminate (C3A) is a major phase of Portland cement clinker and some dental root filling cements. An accurate all-atom force field is introduced to examine structural, surface, and hydration properties as well as organic interfaces to overcome challenges using current laboratory instrumentation. Molecular dynamics simulation demonstrates excellent agreement of computed structural, thermal, mechanical, and surface properties with available experimental data. The parameters are integrated into multiple potential energy expressions, including the PCFF, CVFF, CHARMM, AMBER, OPLS, and INTERFACE force fields. This choice enables the simulation of a wide range of inorganic-organic interfaces at the 1 to 100 nm scale at a million times lower computational cost than DFT methods. Molecular models of dry and partially hydrated surfaces are introduced to examine cleavage, agglomeration, and the role of adsorbed organic molecules. Cleavage of crystalline tricalcium aluminate requires approximately 1300 mJ m(-2) and superficial hydration introduces an amorphous calcium hydroxide surface layer that reduces the agglomeration energy from approximately 850 mJ m(-2) to 500 mJ m(-2), as well as to lower values upon surface displacement. The adsorption of several alcohols and amines was examined to understand their role as grinding aids and as hydration modifiers in cement. The molecules mitigate local electric fields through complexation of calcium ions, hydrogen bonds, and introduction of hydrophobicity upon binding. Molecularly thin layers of about 0.5 nm thickness reduce agglomeration energies to between 100 and 30 mJ m(-2). Molecule-specific trends were found to be similar for tricalcium aluminate and tricalcium silicate. The models allow quantitative predictions and are a starting point to provide fundamental understanding of the role of C3A and organic additives in cement. Extensions to impure phases and advanced hydration stages are feasible.

  2. Ohmic dissipation and relaxation of force-free magnetic fields

    International Nuclear Information System (INIS)

    Solov'ev, A.A.

    1985-01-01

    A study is made of the process of passive ohmic dissipation of a force-free magnetic field in a low-pressure plasma with inhomogeneous conductivity. It is shown that the force-free field (curl →H = α→H) preserves its geometrical shape in the process of the dissipation if the ratio α 2 /σ does not depend on the coordinates. The process of topological resistive relaxation of a force-free field in a twisted magnetic loop to the state with least magnetic energy is investigated. It is found that for fixed external pressure and given moment of the forces at the ends of the magnetic loop a uniformly twisted magnetic filament corresponds to this state. Taylor's relaxation model is analyzed critically. It is shown that a force-free field of variable sign with α = const corresponds to a minimum of only the ratio ε/K, where K is the spirality of the field, and not to a minimum of the total magnetic energy ε /sub m/ of the system

  3. 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

  4. Force-free field model of ball lightning

    Science.gov (United States)

    Tsui, K. H.

    2001-03-01

    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.

  5. 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.

  6. Machine Learning Force Field Parameters from Ab Initio Data

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying [Argonne; Li, Hui [Department; Pickard, Frank C. [Laboratory; Narayanan, Badri [Center; Sen, Fatih G. [Center; Chan, Maria K. Y. [Center; Computational; Sankaranarayanan, Subramanian K. R. S. [Center; Computational; Brooks, Bernard R. [Laboratory; Roux, Benoît [Department; Center; Computational

    2017-08-11

    Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

  7. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

    Czech Academy of Sciences Publication Activity Database

    Zgarbová, M.; Šponer, Jiří; Otyepka, M.; Cheatham III, T. E.; Galindo-Murillo, R.; Jurečka, P.

    2015-01-01

    Roč. 11, č. 12 (2015), s. 5723-5736 ISSN 1549-9618 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * NUCLEIC-ACID STRUCTURES * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 5.301, year: 2015

  8. 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...... 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...

  9. 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

  10. 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

  11. Mitigated-force carriage for high magnetic field environments

    Science.gov (United States)

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

    2014-05-20

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

  12. 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.

  13. AMBER: Uma linguagem para o desenvolvimento de sistemas distribuidos

    NARCIS (Netherlands)

    Ferreira Pires, Luis; Farines, J-M.; Westphall, C.; Guareis de farias, Cléver

    2001-01-01

    This paper presents the architectural model AMBER for the design of distributed systems developed at the University of Twente. This model allows the specification of distributed systems in terms of structures of functional entities and their corresponding behaviour. AMBER was originally developed to

  14. Raman microspectroscopic studies of amber resins with insect inclusions

    Science.gov (United States)

    Edwards, Howell G. M.; Farwell, Dennis W.; Villar, Susana E. Jorge

    2007-12-01

    Raman microscope spectra of specimens of Baltic and Mexican amber resins containing insect inclusions have been analysed using near-infrared excitation to assess the potential for discrimination between the keratotic remains of the insects and the terpenoid matrix. For the Mexican amber specimen the insect spectra exhibit evidence of significant protein degradation compared with the insect remains in the Baltic amber specimen. In both cases the Raman spectra of the insect remains are still distinguishable from the amber resins. Despite its better preservation, however, no spectra could be obtained from the inside of the larger insect preserved in the Baltic amber in agreement with the observation that most insect inclusions in amber are hollow. It is noted that the Mexican amber insect is located adjacent to a large gas bubble in the amber matrix, to which the observed degradation of the insect and its poor state of preservation are attributed. It is concluded that Raman spectra of insect inclusions can provide useful information about the chemical composition of the remains and that confocal microscopy is particularly advantageous in this respect.

  15. 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

  16. 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.

  17. 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

    2017-05-01

    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.

  18. Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea in early Eocene Cambay amber

    Directory of Open Access Journals (Sweden)

    Frauke Stebner

    2017-05-01

    Full Text Available One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.

  19. Spatial Confinement of Ultrasonic Force Fields in Microfluidic Channels

    DEFF Research Database (Denmark)

    Manneberg, O; Hagsäter, Melker; Svennebring, J

    2009-01-01

    of the microfluidic channel. The channel segments are remotely actuated by the use of frequency-specific external transducers with refracting wedges placed on top of the chips. The force field in each channel segment is characterized by the use of micrometer-resolution particle image velocimetry ( micro......-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...

  20. Force fields and scoring functions for carbohydrate simulation.

    Science.gov (United States)

    Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

    2015-01-12

    Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. 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

  2. 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

  3. 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

  4. Force Fields and Point Charges for Crystal Structure Modeling

    OpenAIRE

    Svärd, Michael; Rasmuson, Åke C.

    2009-01-01

    Molecular simulation is increasingly used by chemical engineers and industrial chemists in process and product development. In particular, the possibility to predict the structure and stability of potential polymorphs of a substance is of tremendous interest to the pharmaceutical and specialty chemicals industry. Molecular mechanics modeling relies on the use of parametrized force fields and methods of assigning point charges to the atoms in the molecules. In commercial molecular simulation s...

  5. 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.

  6. 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)

  7. Molecular mechanics force-field development for amino acid zwitterions.

    Science.gov (United States)

    Kirschner, K N; Lewin, A H; Bowen, J P

    2003-01-15

    Understanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas-phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. Møller-Plesset second-order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 111-128, 2003

  8. 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.

  9. Aquatic organisms as amber inclusions and examples from a modern swamp forest

    OpenAIRE

    Schmidt, Alexander R.; Dilcher, David L.

    2007-01-01

    To find aquatic organisms in tree resin may seem to be highly unlikely, but the fossil record provides numerous amber-preserved limnetic arthropods (e.g., water beetles, water striders, and crustaceans) and microorganisms (e.g., bacteria, algae, ciliates, testate amoebae, and rotifers). Here we explain the frequently discussed process of embedding aquatic organisms in tree resin based on field studies in a Florida swamp forest. Different aquatic arthropods and all major groups of limnetic mic...

  10. Casimir force for a scalar field in warped brane worlds

    International Nuclear Information System (INIS)

    Linares, Roman; Morales-Tecotl, Hugo A.; Pedraza, Omar

    2008-01-01

    In looking for imprints of extra dimensions in braneworld models one usually builds these so that they are compatible with known low energy physics and thus focuses on high energy effects. Nevertheless, just as submillimeter Newton's law tests probe the mode structure of gravity other low energy tests might apply to matter. As a model example, in this work we determine the 4D Casimir force corresponding to a scalar field subject to Dirichlet boundary conditions on two parallel planes lying within the single brane of a Randall-Sundrum scenario extended by one compact extra dimension. Using the Green's function method such a force picks the contribution of each field mode as if it acted individually but with a weight given by the square of the mode wave functions on the brane. In the low energy regime one regains the standard 4D Casimir force that is associated to a zero mode in the massless case or to a quasilocalized or resonant mode in the massive one while the effect of the extra dimensions gets encoded as an additional term.

  11. Applications of diamond crystal ATR FTIR spectroscopy to the characterization of ambers.

    Science.gov (United States)

    Guiliano, Michel; Asia, Laurence; Onoratini, Gérard; Mille, Gilbert

    2007-08-01

    Diamond crystal ATR FTIR spectroscopy is a rapid technique with virtually no sample preparation which requires small sample amounts and showed potential in the study of ambers. FTIR spectra of ambers present discriminating patterns and can be used to distinguish amber from immature resins as copal, to determine local or Baltic origin of archaeological ambers and to detect most of the falsifications encountered in the amber commercialisation.

  12. 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.

  13. Parametrization of a reactive force field for aluminum hydride

    OpenAIRE

    Ojwang, J. G. O.; van Santen, Rutger A.; Kramer, Gert Jan; van Duin, Adri C. T.; Goddard, William A., III

    2009-01-01

    A reactive force field, REAXFF, for aluminum hydride has been developed based on density functional theory (DFT) derived data. REAXFF_(AlH_3) is used to study the dynamics governing hydrogen desorption in AlH_3. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by REAXFF_(AlH_3). Results on heat of desorption versus cluster size show that there is a strong dependence of the heat of desorption on the particle size, which implies that nan...

  14. 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.

  15. The first fossil cyphophthalmid harvestman from Baltic amber

    Directory of Open Access Journals (Sweden)

    Dunlop, Jason A.

    2011-01-01

    Full Text Available The first fossil cyphophthalmid harvestman (Opiliones: Cyphophthalmi from Palaeogene (Eocene Baltic amber is described. This is only the third fossil example of this basal harvestman lineage; the others being from the probably slightly younger Bitterfeld amber and the much older, early Cretaceous, Myanmar (Burmese amber. Although incomplete and lacking most of the appendages, the new Baltic amber fossil can be identified as a female. The somatic characters preserved, especially spiracle morphology and the coxo-genital region, allow it to be assigned with some confidence to the extant genus Siro Latreille, 1796 (Sironidae. This fossil is formally described here as Siro balticus sp. nov. It resembles modern North American Siro species more than modern European ones, and can be distinguished principally on its relatively large size and the outline form of the body.

  16. Response of Magnetic Force Microscopy Probes under AC Magnetic Field

    Science.gov (United States)

    Sungthong, A.; Ruksasakchai, P.; Saengkaew, K.; Cheowanish, I.; Damrongsak, B.

    2017-09-01

    In this paper, magnetic force microscopy (MFM) probes with different coating materials were characterized under AC magnetic field. A perpendicular magnetic write head similar to those used in hard disk drives was employed as the AC magnetic field generator. In order to measure a response of MFM probes to AC magnetic field, a MFM probe under test was scanned, at a scan height of 10 nm, across the surface of the magnetic write head. During MFM imaging, the write head was biased by a sufficient magnitude of AC current, approximately 30 mA. A spectral analysis for a frequency sweep from 1 kHz to 100 MHz was extracted from post-processing MFM images. As expected, a MFM probe coated with hard magnetic alloys, i.e. FePt, has the lowest response to AC magnetic fields. MFM probes coated with soft magnetic alloys, i.e. NiFe and NiCoCr, have a relatively high and flat response across the frequency range. Ni coated MFM probe has the highest response to AC magnetic fields. In addition, CoCr and NiCo coated MFM probes show lower response than NiFe and NiCoCr probes at low frequencies; however, theirs response to AC magnetic field increase for the AC magnetic field with a frequency above 50 kHz. This can be implied that those MFM probes are a good candidate for being used to study the high-frequency performance of perpendicular magnetic write heads. Noting that response of all MFM probes significantly decreased when driven frequencies above 1 MHz due to the limitation of the hardware, i.e. response of quadrant photodiode and op-amp in a pre-amplifier.

  17. 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.

  18. 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.)

  19. Links between the charge model and bonded parameter force constants in biomolecular force fields

    Science.gov (United States)

    Cerutti, David S.; Debiec, Karl T.; Case, David A.; Chong, Lillian T.

    2017-10-01

    The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5-19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α -helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA3 by 50% or more, forming long-lived α -helices in simulations of a β -hairpin, and increasing the likelihood that the disordered p53 N-terminal peptide will also form a helix. This may indicate a systematic bias imparted by the ff15ipq-Qsolv parameter development strategy, which has the hallmarks of strategies used to develop

  20. Measuring Single-Bond Rupture Forces Using High Electric Fields in Microfluidic Channels and DNA Oligomers as Force Tags

    OpenAIRE

    Breisch, Stefanie; Gonska, Julian; Deissler, Helmut; Stelzle, Martin

    2005-01-01

    The disruption force of specific biotin-streptavidin bonds was determined using DNA oligomers as force tags. Forces were generated by an electric field acting on a biotinylated fluorescently labeled DNA oligomer. DNA oligomers were immobilized via biotin-streptavidin bonds on the walls of microfluidic channels. Channel layout and fluid-based deposition process were designed to enable well-defined localized deposition of the oligomers in a narrow gap of the microchannel. Electric fields of up ...

  1. Advanced multiple beam equalization radiography (AMBER)

    International Nuclear Information System (INIS)

    Ravin, C.E.

    1988-01-01

    Radiographic imaging of the thorax remains one of the most challenging and technically difficult areas in all of diagnostic imaging. Plain chest radiography, because it is so commonly utilized, is often considered to be a simple radiographic procedure. However, the inherent configuration of the thorax presents many technical challenges to obtaining good chest radiographs. The ability to visualize both lung parenchyma and mediastinal structures on a single film is technically very difficult as the attenuation of the x-ray beam in the lungs is markedly less than that which occurs in the mediastinum. Therefore it is very difficult to apply the x-ray beam to the thorax in a manner such that relatively similar numbers of photons exit the chest over both the lungs and mediastinum and expose the receptor film. In the past several years interest has turned to exposure techniques which automatically compensate for differences in attenuation between the lungs and mediastinum. These techniques result in a more balanced exposure which in turn is more easily recorded and displayed on film. The author supplied with an AMBER system for initial clinical evaluation. The results of this evaluation are discussed

  2. Evaluating Force Fields for the Computational Prediction of Ionized Arginine and Lysine Side-Chains Partitioning into Lipid Bilayers and Octanol.

    Science.gov (United States)

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-04-14

    Abundant peptides and proteins containing arginine (Arg) and lysine (Lys) amino acids can apparently permeate cell membranes with ease. However, the mechanisms by which these peptides and proteins succeed in traversing the free energy barrier imposed by cell membranes remain largely unestablished. Precise thermodynamic studies (both theoretical and experimental) on the interactions of Arg and Lys residues with model lipid bilayers can provide valuable clues to the efficacy of these cationic peptides and proteins. We have carried out molecular dynamics simulations to calculate the interactions of ionized Arg and Lys side-chains with the zwitterionic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid bilayer for 10 widely used lipid/protein force fields: CHARMM36/CHARMM36, SLIPID/AMBER99SB-ILDN, OPLS-AA/OPLS-AA, Berger/OPLS-AA, Berger/GROMOS87, Berger/GROMOS53A6, GROMOS53A6/GROMOS53A6, nonpolarizable MARTINI, polarizable MARTINI, and BMW MARTINI. We performed umbrella sampling simulations to obtain the potential of mean force for Arg and Lys side-chains partitioning from water to the bilayer interior. We found significant differences between the force fields, both for the interactions between side-chains and bilayer surface, as well as the free energy cost for placing the side-chain at the center of the bilayer. These simulation results were compared with the Wimley-White interfacial scale. We also calculated the free energy cost for transferring ionized Arg and Lys side-chains from water to both dry and wet octanol. Our simulations reveal rapid diffusion of water molecules into octanol whereby the equilibrium mole fraction of water in the wet octanol phase was ∼25%. Surprisingly, our free energy calculations found that the high water content in wet octanol lowered the water-to-octanol partitioning free energies for cationic residues by only 0.6 to 0.7 kcal/mol.

  3. Parametrization of a reactive force field for aluminum hydride.

    Science.gov (United States)

    Ojwang, J G O; van Santen, Rutger A; Kramer, Gert Jan; van Duin, Adri C T; Goddard, William A

    2009-07-28

    A reactive force field, REAXFF, for aluminum hydride has been developed based on density functional theory (DFT) derived data. REAXFF(AlH(3)) is used to study the dynamics governing hydrogen desorption in AlH(3). During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by REAXFF(AlH(3)). Results on heat of desorption versus cluster size show that there is a strong dependence of the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. In the gas phase, it was observed that small alane clusters agglomerated into a bigger cluster. After agglomeration molecular hydrogen was desorbed from the structure. This thermodynamically driven spontaneous agglomeration followed by desorption of molecular hydrogen provides a mechanism on how mobile alane clusters can facilitate the mass transport of aluminum atoms during the thermal decomposition of NaAlH(4).

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

    Science.gov (United States)

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

    2008-11-15

    The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids. 2008 Wiley Periodicals, Inc.

  5. 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...

  6. 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.

  7. Identification of rumanite (Romanian amber) as thermally altered succinite (Baltic amber)

    Science.gov (United States)

    Stout, E. C.; Beck, C. W.; Anderson, K. B.

    Romanian amber (rumanite) has been considered to be a separate species of fossil resin for more than a century. While earlier investigators held it to be very similar to succinite (Baltic amber), modern scholars have assigned it a distinctly different botanical origin. We have found that almost all of the constituents of the ether-soluble fractions of 13 specimens of authentic rumanite identified by gas chromatography-mass spectrometry have previously been reported in the soluble fraction of succinite, including succinic acid and its monoterpene esters. Additionally and significantly, the soluble fraction of rumanite contains a number defunctionalized compounds that do not preexist in succinite, but that are produced by pyrolysis of whole succinite or of its insoluble polymeric fraction. Simultaneous methylation pyrolysis-gas chromatography-mass spectrometry of the polymeric fraction of seven of the rumanite specimens yielded further copious amounts of dimethyl succinate, a number of diterpene resin acid methyl esters, and additional defunctionalized compounds known to be pyrolysis products of succinite. The evidence shows conclusively that the botanical origin of rumanite is not distinct from that of succinite. Rather, rumanite is a succinite that has suffered partial thermal degradation in the course of the folding of the Oligocene Kliwa sandstone formation in which it is most commonly found.

  8. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber.

    Science.gov (United States)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan C; Alonso, Jesús; Ascaso, Carmen

    2009-05-01

    Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.

  9. Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber

    Science.gov (United States)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan C.; Alonso, Jesús; Ascaso, Carmen

    2009-05-01

    Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  11. Two new fossil species of Cryptocephalus Geoffroy (Coleoptera: Chrysomelidae) from Baltic and Dominican Amber

    Science.gov (United States)

    Two new species of Cryptocephalus Geoffroy (Coleoptera: Chrysomelidae) are described and illustrated from fossil resin: Cryptocephalus groehni sp. nov (Baltic amber) and Cryptocephalus kheelorum sp. nov. (Dominican amber). These are the first described species of Cryptocephalinae from fossil resin. ...

  12. A new soldier beetle from Eocene Baltic amber

    Directory of Open Access Journals (Sweden)

    Fabrizio Fanti

    2017-11-01

    Full Text Available The family Cantharidae is a worldwide distributed group of flattened and soft-bodied beetles displaying aposematic colouration. These beetles, commonly known as soldier beetles, have an extensive fossil record dating back to the Lower Cretaceous. The majority of fossil material, referred to Cantharidae, is known from amber inclusions. In this paper we describe and illustrate a new soldier beetle Kuskaella macroptera gen. et sp. nov. from the Baltic amber. It is characterised by pronotum of the male parallel-sided in basal third and abruptly narrowed towards apex, and of the female gradually and steadily narrowing from the basal margin to the apex; globular head; unequal maxillary palpomeres with the last segment elongated-globular and pointed; long elytra slightly surpassing the last abdominal segment. This finding is the first described species of both sexes preserved in a single amber piece.

  13. IOT Overview: Calibrations of the VLTI Instruments (MIDI and AMBER)

    Science.gov (United States)

    Morel, S.; Rantakyrö, F.; Rivinius, T.; Stefl, S.; Hummel, C.; Brillant, S.; Schöller, M.; Percheron, I.; Wittkowski, M.; Richichi, A.; Ballester, P.

    We present here a short review of the calibration processes that are currently applied to the instruments AMBER and MIDI of the VLTI (Very Large Telescope Interferometer) at Paranal. We first introduce the general principles to calibrate the raw data (the "visibilities") that have been measured by long-baseline optical interferometry. Then, we focus on the specific case of the scientific operation of the VLTI instruments. We explain the criteria that have been used to select calibrator stars for the observations with the VLTI instruments, as well as the routine internal calibration techniques. Among these techniques, the "P2VM" (Pixel-to-Visibility Matrix) in the case of AMBER is explained. Also, the daily monitoring of AMBER and MIDI, that has recently been implemented, is shortly introduced.

  14. In the intimacy of stars with AMBER at the VLTI

    Science.gov (United States)

    Malbet, F.; Petrov, R.; Weigelt, G.; Chesneau, O.; Domiciano de Souza, A.; Meilland, A.; Millour, F.; Tatulli, E.; Amber Consortium

    2007-07-01

    The AMBER instrument installed at the Very Large Telescope (VLT) combines the beams from three telescopes to produce spectrally dispersed interference fringes with milli-arcsecond angular scales in the near infrared. Three years after installation, first scientific observations have been carried out mostly during the Science Demonstration Time and the Guaranteed Time. The first science has mainly focused on the environment of various types of stars. Because AMBER has dramatically increased the number of measures per baseline, this instrument brings strong constraints on morphology and models.

  15. Amber Trust on ostmas Tallinna Külmhoone emafirmat / Liis Kängsepp

    Index Scriptorium Estoniae

    Kängsepp, Liis, 1981-

    2005-01-01

    Skandinaavia-USA investeerimisfond Amber Trust loodab enne aasta lõppu allkirjastada Tallinna Külmhoone emafirma Kauno Pieno Centras ostulepingu. Diagramm: Tallinna Külmhoone majandusnäitajad. Vt. samas: Amber Trust tahab investeerida üle 2 miljardi krooni; Amber laiendas tegevust Vetteli kaudu Soome

  16. Isolation and genetic analysis of amber uvrA and uvrB mutants

    International Nuclear Information System (INIS)

    Morimyo, M.; Shimazu, Y.; Ishii, N.

    1976-01-01

    Genetic properties of amber uvrA and uvrB mutants of Escherichia coli K-12 are described. The isolation of three amber uvrA and two amber uvrB mutants indicates that the products of these genes are proteins

  17. Scalar self-force on a static particle in Schwarzschild using the massive field approach

    OpenAIRE

    Rosenthal, Eran

    2004-01-01

    We use the recently developed massive field approach to calculate the scalar self-force on a static particle in a Schwarzschild spacetime. In this approach the scalar self-force is obtained from the difference between the (massless) scalar field, and an auxiliary massive scalar field combined with a certain limiting process. By applying this approach to a static particle in Schwarzschild we show that the scalar self-force vanishes in this case. This result conforms with a previous analysis by...

  18. 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

  19. New fossil ants in French Cretaceous amber (Hymenoptera: Formicidae)

    Science.gov (United States)

    Perrichot, Vincent; Nel, André; Néraudeau, Didier; Lacau, Sébastien; Guyot, Thierry

    2008-02-01

    Recent studies on the ant phylogeny are mainly based on the molecular analyses of extant subfamilies and do not include the extinct, only Cretaceous subfamily Sphecomyrminae. However, the latter is of major importance for ant relationships, as it is considered the most basal subfamily. Therefore, each new discovery of a Mesozoic ant is of high interest for improving our understanding of their early history and basal relationships. In this paper, a new sphecomyrmine ant, allied to the Burmese amber genus Haidomyrmex, is described from mid-Cretaceous amber of France as Haidomyrmodes mammuthus gen. and sp. n. The diagnosis of the tribe Haidomyrmecini is emended based on the new type material, which includes a gyne (alate female) and two incomplete workers. The genus Sphecomyrmodes, hitherto known by a single species from Burmese amber, is also reported and a new species described as S. occidentalis sp. n. after two workers remarkably preserved in a single piece of Early Cenomanian French amber. The new fossils provide additional information on early ant diversity and relationships and demonstrate that the monophyly of the Sphecomyrminae, as currently defined, is still weakly supported.

  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. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field

    NARCIS (Netherlands)

    García-Pérez, E.; Serra-Crespo, P.; Hamad, S.; Kapteijn, F.; Gascon, J.

    2014-01-01

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations

  2. 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

  3. Forces in a 3D magnetic field of conducting current contours

    Directory of Open Access Journals (Sweden)

    Stancheva Rumena

    2008-01-01

    Full Text Available The present paper deals with 3D magnetic field analysis of conducting current contours. The magnetic field and forces were calculated analytically and by FEM applying the Comsol Multiphysics package. Forces were calculated by the Maxwell stress tensor and by volume force density. Numerical results for real and ideal contours with the same linear dimensions are discussed. Comparison between analytical and numerical data shows satisfactory agreement.

  4. 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

    Force field adaptation of locomotor muscle activity is one way of studying the ability of the motor control networks in the brain and spinal cord to adapt in a flexible way to changes in the environment. Here, we investigate whether the corticospinal tract is involved in this adaptation. We...... 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...

  5. 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

  6. Axial acoustic radiation force on a sphere in Gaussian field

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Rongrong; Liu, Xiaozhou, E-mail: xzliu@nju.edu.cn; Gong, Xiufen [Key Laboratory of Modern Acoustics, Institute of Acoustics and School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China)

    2015-10-28

    Based on the finite series method, the acoustical radiation force resulting from a Gaussian beam incident on a spherical object is investigated analytically. When the position of the particles deviating from the center of the beam, the Gaussian beam is expanded as a spherical function at the center of the particles and the expanded coefficients of the Gaussian beam is calculated. The analytical expression of the acoustic radiation force on spherical particles deviating from the Gaussian beam center is deduced. The acoustic radiation force affected by the acoustic frequency and the offset distance from the Gaussian beam center is investigated. Results have been presented for Gaussian beams with different wavelengths and it has been shown that the interaction of a Gaussian beam with a sphere can result in attractive axial force under specific operational conditions. Results indicate the capability of manipulating and separating spherical spheres based on their mechanical and acoustical properties, the results provided here may provide a theoretical basis for development of single-beam acoustical tweezers.

  7. Optical forces acting on Rayleigh particle placed into interference field

    Czech Academy of Sciences Publication Activity Database

    Zemánek, Pavel; Karásek, Vítězslav; Sasso, A.

    2004-01-01

    Roč. 240, 4-6 (2004), s. 401-415 ISSN 0030-4018 R&D Projects: GA AV ČR KSK2067107 Keywords : optical force * Rayleigh particle * colloidal particle Subject RIV: BH - Optics, Masers, Lasers Impact factor: 1.581, year: 2004

  8. 40Ar/39Ar systematics and argon diffusion in amber: implications for ancient earth atmospheres

    Science.gov (United States)

    Landis, G.P.; Snee, L.W.

    1991-01-01

    Argon isotope data indicate retained argon in bulk amber (matrix gas) is radiogenic [40Ar/39Ar ???32o] than the much more abundant surface absorbed argon [40Ar/39Ar ???295.5]. Neutron-induced 39Ar is retained in amber during heating experiments to 150?? -250??C, with no evidence of recoiled 39Ar found after irradiation. A maximum permissible volume diffusion coefficient of argon in amber (at ambient temperature) D???1.5 x 10-17 cm2S-1 is calculated from 39Ar retention. 40Ar/39Ar age calculations indicate Dominican Republic amber is ??? 45 Ma and North Dakota amber is ??? 89 Ma, both at least reasonable ages for the amber based upon stratigraphic and paleontological constraints and upon the small amount of radiogenic 40Ar. To date, over 300 gas analyses of ambers and resins of Cretaceous to Recent age that are geographically distributed among fifteen noted world locations identify mixtures of gases in different sites within amber (Berner and Landis, 1988). The presence of multiple mixing trends between compositionally distinct end-members gases within the same sample and evidence for retained radiogenic argon within the amber argue persuasivley against rapid exchange by diffusion of amber-contained gases with moder air. Only gas in primary bubbles entrapped between successive flows of tree resin has been interpreted as original "ancient air", which is an O2-rich end-member gas with air-like N2/Ar ratios. Gas analyses of these primary bubbles indicate atmospheric O2 levels in the Late Cretaceous of ??? 35%, and that atmospheric O2 dropped by early Tertiary time to near a present atmospheric level of 21% O2. A very low argon diffusion coefficient in amber persuasively argues for a gas in primary bubbles trapped in amber being ancient air (possibly modified only by O2 reaction with amber). ?? 1991.

  9. GEOFLOW: simulation of convection in a spherical shell under central force field

    Directory of Open Access Journals (Sweden)

    P. Beltrame

    2006-01-01

    Full Text Available Time-dependent dynamical simulations related to convective motion in a spherical gap under a central force field due to the dielectrophoretic effect are discussed. This work is part of the preparation of the GEOFLOW-experiment which is planned to run in a microgravity environment. The goal of this experiment is the simulation of large-scale convective motion in a geophysical or astrophysical framework. This problem is new because of, on the one hand, the nature of the force field (dielectrophoretic effect and, on another hand, the high degree of symmetries of the system, e.g. the top-bottom reflection. Thus, the validation of this simulation with well-known results is not possible. The questions concerning the influence of the dielectrophoretic force and the possibility to reproduce the theoretically expected motions in the astrophysical framework, are open. In the first part, we study the system in terrestrial conditions: the unidirectional Earth's force is superimposed on the central dielectrophoretic force field to compare with the laboratory experiments during the development of the equipment. In the second part, the GEOFLOW-experiment simulations in weightless conditions are compared with theoretical studies in the astrophysical framework's, in the first instance a fluid under a self-gravitating force field. We present complex time-dependent dynamics, where the dielectrophoretic force field causes significant differences in the flow compared to the case that does not involve this force field.

  10. Identitas Kultur dalam Relasi Etnik Komin-Amber di Papua

    Directory of Open Access Journals (Sweden)

    Syarif Syarifuddin

    2017-07-01

    Full Text Available Identitas bukan sekedar persoalan nama, tetapi apa makna di balik nama tersebut. Setidaknya nama merupakan tanda pengenal dan identitas yang dapat menunjukkan ciri-ciri serta karakternya. Jika ciri khas itu melekat pada suatu etnik, maka hal itu menjadi penanda jati diri pada etnik tersebut. Penelitian ini bertujuan untuk menganalisis dan mendeskripsikan identitas kultur etnik Komin sebagai masyarakat pribumi dan etnik Amber sebagai masyarakat pendatang dalam perspektif komunikasi antarbudaya. Metode penelitian dirancang dalam skema penelitian kombinasi (mixed method yang menggabungkan metode kualitatif dan kuantitatif dengan strategi eksploratoris sekuensial. Penelitian dilaksanakan di Kota Jayapura Provinsi Papua dengan sampel 200 responden dan 8 (delapan partisipan. Hasil penelitian menunjukkan bahwa identititas kultur pada etnik Komin dan Amber berbeda nyata dalam hal: 1 Konteks komunikasi (high context vs low context communication, 2 Orientasi budaya (individualist vs collectivist, dan 3 Self construal (Independent vs Interdependent.

  11. Aquatic organisms as amber inclusions and examples from a modern swamp forest

    Science.gov (United States)

    Schmidt, Alexander R.; Dilcher, David L.

    2007-01-01

    To find aquatic organisms in tree resin may seem to be highly unlikely, but the fossil record provides numerous amber-preserved limnetic arthropods (e.g., water beetles, water striders, and crustaceans) and microorganisms (e.g., bacteria, algae, ciliates, testate amoebae, and rotifers). Here we explain the frequently discussed process of embedding aquatic organisms in tree resin based on field studies in a Florida swamp forest. Different aquatic arthropods and all major groups of limnetic microorganisms were found embedded in resin that had contact with swamp water. The taphonomy of aquatic organisms differs from that of terrestrial plants and animals that get stuck on resin surfaces and are enclosed by successive resin outflows. Large and highly motile arthropods are predestined for embedding. The number of microbial inclusions is increased when tiny drops of water with aquatic organisms become enclosed in resin while it is flowing in an aquatic environment. Bacteria and fungi may grow inside the resin as long as it has not solidified and therefore become secondarily accumulated. In contact with air, even resin that had initially been flowing into water may solidify and potentially form amber. PMID:17940051

  12. 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

  13. The first araripeneurine antlion in Burmese amber (Neuroptera: Myrmeleontidae)

    OpenAIRE

    Huang, Diying; Azar, Dany; Engel, Michael S.; Garrouste, Romain; Cai, Chenyang; Nel, André

    2016-01-01

    International audience; Burmaneura minuta gen. et sp. nov., the first araripeneurine antlion in amber, is characterized, described and compared with the modern and Mesozoic Myrmeleontidae. The precise position of the fossil within this group is debatable. Interestingly, despite a rather rich fossil record, all Mesozoic Myrmeleontidae belong to subfamilies that are not recorded in the Cenozoic, although this might merely reflect the artificiality of the classification as the extinct groups may...

  14. Structural changes in amber due to uranium mineralization

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Machovič, Vladimír; Mizera, Jiří; Sýkorová, Ivana; René, Miloš; Borecká, Lenka; Lapčák, L.; Bičáková, Olga; Janeček, O.; Dvořák, Z.

    158-159, JUL (2016), s. 89-101 ISSN 0265-931X R&D Projects: GA ČR(CZ) GA13-18482S Grant - others:OPPK(XE) CZ.2.16/3.1.00/21538 Program:OPPK Institutional support: RVO:67985891 Keywords : fossil resin * amber * uranium * radiolytic alteration * micro-FTIR * mapping * SEM/EDX Subject RIV: DD - Geochemistry Impact factor: 2.310, year: 2016

  15. Structural changes in amber due to uranium mineralization

    Czech Academy of Sciences Publication Activity Database

    Havelcová, M.; Machovič, V.; Mizera, Jiří; Sýkorová, I.; Rene, M.; Borecká, L.; Lapčák, L.; Bičáková, O.; Janeček, O.; Dvořák, Z.

    2016-01-01

    Roč. 158, JUL (2016), s. 89-101 ISSN 0265-931X R&D Projects: GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LM2011019 Institutional support: RVO:61389005 Keywords : fossil resin * amber * Uranium * radiolytic alteration * micro-FTIR * mapping * SEM/EDX Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.310, year: 2016

  16. Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber.

    Science.gov (United States)

    Martín-González, Ana; Wierzchos, Jacek; Gutiérrez, Juan-Carlos; Alonso, Jesús; Ascaso, Carmen

    2009-02-20

    Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Pyritization is the most important and extensive mode of preservation of animals and especially of plants. Entrapping in amber, a fossilized resin, is considered an alternative mode of biological preservation. For the first time, the internal organization of 114-million-year-old microfossils entrapped in Lower Cretaceous amber is described and analyzed, using adapted scanning electron microscopy in backscattered electron mode in association with energy dispersive X-ray spectroscopy microanalysis. Double fossilization of several protists included in diverse taxonomical groups and some vegetal debris is described and analyzed. In protists without an exoskeleton or shell (ciliates, naked amoebae, flagellates), determinate structures, including the nuclei, surface envelopes (cortex or cytoplasmic membrane) and hyaloplasm are the main sites of pyritization. In protists with a biomineralized skeleton (diatoms), silicon was replaced by pyrite. Permineralization was the main mode of pyritization. Framboidal, subhedral and microcrystalline are the predominant pyrite textures detected in the cells. Abundant pyritized vegetal debris have also been found inside the amber nuggets and the surrounding sediments. This vegetal debris usually contained numerous pyrite framboids and very densely packed polycrystalline pyrite formations infilled with different elements of the secondary xylem. Embedding in amber and pyritization are not always alternative modes of biological preservation during geological times, but double fossilization is possible under certain environmental conditions. Pyritization in protists shows a quite different pattern with regard to plants, due to the different composition and cellular architecture in these microorganisms and organisms. Anaerobic sulphate-reducing bacteria could play a crucial role in this microbial

  17. Double fossilization in eukaryotic microorganisms from Lower Cretaceous amber

    Directory of Open Access Journals (Sweden)

    Alonso Jesús

    2009-02-01

    Full Text Available Abstract Background Microfossils are not only useful for elucidating biological macro- and microevolution but also the biogeochemical history of our planet. Pyritization is the most important and extensive mode of preservation of animals and especially of plants. Entrapping in amber, a fossilized resin, is considered an alternative mode of biological preservation. For the first time, the internal organization of 114-million-year-old microfossils entrapped in Lower Cretaceous amber is described and analyzed, using adapted scanning electron microscopy in backscattered electron mode in association with energy dispersive X-ray spectroscopy microanalysis. Double fossilization of several protists included in diverse taxonomical groups and some vegetal debris is described and analyzed. Results In protists without an exoskeleton or shell (ciliates, naked amoebae, flagellates, determinate structures, including the nuclei, surface envelopes (cortex or cytoplasmic membrane and hyaloplasm are the main sites of pyritization. In protists with a biomineralized skeleton (diatoms, silicon was replaced by pyrite. Permineralization was the main mode of pyritization. Framboidal, subhedral and microcrystalline are the predominant pyrite textures detected in the cells. Abundant pyritized vegetal debris have also been found inside the amber nuggets and the surrounding sediments. This vegetal debris usually contained numerous pyrite framboids and very densely packed polycrystalline pyrite formations infilled with different elements of the secondary xylem. Conclusion Embedding in amber and pyritization are not always alternative modes of biological preservation during geological times, but double fossilization is possible under certain environmental conditions. Pyritization in protists shows a quite different pattern with regard to plants, due to the different composition and cellular architecture in these microorganisms and organisms. Anaerobic sulphate

  18. 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.

  19. 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.

  20. Seeking carotenoid pigments in amber-preserved fossil feathers

    Science.gov (United States)

    Thomas, Daniel B.; Nascimbene, Paul C.; Dove, Carla J.; Grimaldi, David A.; James, Helen F.

    2014-06-01

    Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

  1. Seeking carotenoid pigments in amber-preserved fossil feathers.

    Science.gov (United States)

    Thomas, Daniel B; Nascimbene, Paul C; Dove, Carla J; Grimaldi, David A; James, Helen F

    2014-06-09

    Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

  2. Diversity of Scydmaeninae (Coleoptera: Staphylinidae) in Upper Eocene Rovno amber.

    Science.gov (United States)

    Jałoszyński, Paweł; Perkovsky, Evgeny

    2016-08-25

    Among nearly 1270 inclusions of Coleoptera found in Upper Eocene Rovno amber, 69 were identified as ant-like stone beetles (Scydmaeninae); 34 were possible to unambiguously determine to the tribal level and were studied in detail. Rovnoleptochromus ableptonoides gen. & sp. n. (Mastigitae: Clidicini), Vertheia quadrisetosa gen. & sp. n. (Cephenniitae: Eutheiini), Cephennomicrus giganteus sp. n. (Cephenniitae: Cephenniini), Glaesoconnus unicus gen. & sp. n. (Scydmaenitae: Glandulariini), Rovnoscydmus frontalis gen. & sp. n. (Scydmaenitae: Glandulariini; type species of Rovnoscydmus), Rovnoscydmus microscopicus sp. n., Euconnus (incertae sedis, near Cladoconnus) palaeogenus sp. n. (Scydmaenitae: Glandulariini), and Stenichnus (s. str.) proavus sp. n. (Scydmaenitae: Glandulariini) are described. Additionally, specimens representing one undescribed species of Vertheia, one of Cephennodes, five of Cephennomicrus, one of Euconnus, one of Microscydmus are recorded, and nine specimens representing an unknown number of species of Rovnoscydmus (and two putative Rovnoscydmus), one Euconnus (and one putative Euconnus), two putative Microscydmus and one putative Scydmoraphes were found in the studied material. The composition of Scydmaeninae fauna in Rovno amber is discussed in the context of ecological preferences and distribution of extant taxa. It is concluded that subtropical and tropical taxa were present in the region where Rovno amber has formed, most notably the second genus and species of the extant tribe Clidicini known from the Eocene of Europe, and six species of the extant genus Cephennomicrus, for the first time found in the fossil record. An annotated catalog of nominal species of Scydmaeninae known in the fossil record is given.

  3. On averaged force acting on a particle in H.F electromagnetic field

    International Nuclear Information System (INIS)

    Ogunniyi, J.F.; Tskhakaya, D.D.

    1989-06-01

    A general expression is obtained for the time averaged force acting on a particle immersed in a magnetic field in the presence of H.F quasiplanar, quasimonochromatic electromagnetic wave. Here, averaging is done over the period of the H.F wave. It is shown that this averaged force is proportional to the time derivative of the squared H.F wave amplitude. The force also includes a term proportional to the gradient of the time constant magnetic field and is connected with the induced magnetic moment in the H.F field. (author). 7 refs

  4. 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.

  5. 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

  6. 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.

  7. Predator Force Structure Changes at Indian Springs Air Force Auxiliary Field, Nevada Environmental Assessment

    Science.gov (United States)

    2003-07-01

    inventory of Cold War era structures at ISAFAF was conducted in 1994 ( Mariah and Associates 1994); no Cold War era significant structures were identified...1996-0001. June. Mariah and Associates, Inc. 1994. Systematic Study of Air Combat Command Cold War Material Culture. MAI Project 735-15...November. Moulton, Carey L. 1990. Air Force Procedure for Predicting Aircraft Noise Around Airbases: Noise Exposure Model (NOISEMAP) User’s Manual

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

    International Nuclear Information System (INIS)

    Peru, S.; Martini, M.

    2014-01-01

    We review the main results of several works using the finite range Gogny interaction within mean field-based approaches. Starting from static mean field description, a GCM-like method including rotational degrees of freedom, namely the five-dimension collective Hamiltonian, is applied. The theoretical results are used to interpret the shell evolution along the N = 16 isotonic chain. The quasiparticle random-phase-approximation formalism is introduced and used to simultaneously describe high- and low-energy spectroscopy as well as collective and individual excitations. After a discussion on the role of the intrinsic deformation in giant resonances, the appearance of low-energy dipole resonances in light nuclei is analysed. Finally, a comparison of the low-energy spectroscopy obtained with these two extensions of static mean field is performed for 2 + states of N = 16 isotopes. (authors)

  9. Study of Geomagnetic Field Response to Solar Wind Forcing

    Science.gov (United States)

    Kim, S.; Li, X.; Damas, M. C.; Ngwira, C.

    2017-12-01

    The solar wind is an integral component of space weather that has a huge impact on the near-Earth space conditions, which can in turn adversely impact technological infrastructure. By analyzing solar wind data, we can investigate the response of the Earth's magnetic field to changes in solar wind conditions, such as dynamic pressure, speed, and interplanetary magnetic fields (IMF). When a coronal mass ejection (CME) hits the Earth's magnetosphere, it compresses the dayside magnetosphere, which leads to SSC (Sudden Storm Commencement) seen in Dst or SYM-H index. Dst and SYM-H index are a measure of geomagnetic storm intensity that represents the magnetic field perturbations in the equatorial region originating from ring current. In this study, we focused on SSC intervals with sudden density increase, density, greater than 10 n/cc from 2000 to 2015 using data obtained from the NASA CDAWEB service. A total of 1,049 events were picked for this project. Then using INTERMAGNET service, corresponding horizontal component of magnetic field data were collected from several stations located in equatorial region, mid-latitude region, high-latitude region on the day-side and night-side of Earth. Using MATLAB, we calculated the rate of change of magnetic fields (dB/dt) for each station and each event. We found that in most cases, the sudden increase in proton density is associated with large changes in magnetic fields, dB/dt. The largest magnetic field changes were observed on the day-side than night-side at high latitudes. Interestingly, some exceptions were found such that greater dB/dt was found on night-side than day-side during some events, particularly at high latitudes. We suspect these are driven by magnetospheric substorms, which are manifested by an explosive release of energy in the local midnight sector. The next step will be creating the statistical form to see the correlation between proton density changes and magnetic field changes.

  10. Subfamily Limoniinae Speiser, 1909 (Diptera, Limoniidae) from Baltic amber (Eocene): the genus Helius Lepeletier & Serville, 1828.

    Science.gov (United States)

    Kania, Iwona

    2014-06-10

    A revision of the genus Helius Lepeletier & Serville, 1828 (Diptera: Limoniidae) from Baltic amber (Eocene) is presented. Redescriptions of 5 species, Helius formosus Krzemiński, 1993, Helius linus Podenas, 2002, Helius minutus (Loew, 1850), Helius mutus Podenas, 2002, Helius pulcher (Loew, 1850) of this genus from Baltic amber are given and documented by photographs and drawings. Four new species of the genus Helius from Baltic amber are described: Helius gedanicus sp. nov., Helius hoffeinsorum sp. nov., Helius similis sp. nov., Helius fossilis sp. nov. A key to species of Helius from Baltic amber is provided. Patterns morphological evolution and the aspects evolutionary history of Helius are discussed.

  11. 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.

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Villegas, A.; Diez, F. J.

    2014-04-01

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

  15. 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

  16. Linear force-free field of a toroidal symmetry

    Czech Academy of Sciences Publication Activity Database

    Romashets, E. P.; Vandas, Marek

    2009-01-01

    Roč. 499, č. 1 (2009), s. 17-20 ISSN 0004-6361 R&D Projects: GA AV ČR(CZ) 1QS300120506; GA MŠk(CZ) ME09032; GA ČR GA205/09/0170 Institutional research plan: CEZ:AV0Z10030501 Keywords : magnetic fields * solar wind * magnetic clouds Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 4.179, year: 2009

  17. 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

  18. Force field and a surface model database for silica to simulate interfacial properties in atomic resolution

    OpenAIRE

    Emami, FS; Puddu, V; Berry, RJ; Varshney, V; Patwardhan, SV; Perry, CC; Heinz, H

    2014-01-01

    Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last thirty years and reduces uncertainties in computed interfacial properties relative to experiment from several 100% to less than 5%. I...

  19. Anharmonic force field and vibrational frequencies of tetrafluoromethane (CF$_4$) and tetrafluorosilane (SiF$_4$)

    OpenAIRE

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

    1999-01-01

    Accurate quartic anharmonic force fields for CF$_4$ and SiF$_4$ have been calculated using the CCSD(T) method and basis sets of $spdf$ quality. Based on the {\\it ab initio} force field with a minor empirical adjustment, the vibrational energy levels of these two molecules and their isotopomers are calculated by means of high order Canonical Van Vleck Perturbation Theory(CVPT) based on curvilinear coordinates. The calculated energies agree very well with the experimental data. The full quadrat...

  20. 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

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

    International Nuclear Information System (INIS)

    Makarov, V. P.; Rukhadze, A. A.

    2010-01-01

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

  2. 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.

  3. 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.

  4. Force

    CERN Document Server

    Graybill, George

    2007-01-01

    Forces are at work all around us. Discover what a force is, and different kinds of forces that work on contact and at a distance. We use simple language and vocabulary to make this invisible world easy for students to ""see"" and understand. Examine how forces ""add up"" to create the total force on an object, and reinforce concepts and extend learning with sample problems.

  5. New records and species of Crepidodera Chevrolat (Coleoptera: Chrysomelidae) in Eocene European amber, with a brief review of described fossil beetles from Bitterfeld amber.

    Science.gov (United States)

    Bukejs, Andris; Biondi, Maurizio; Alekseev, Vitalii I

    2016-11-15

    Based on six relatively well-preserved specimens from Eocene Baltic amber, Crepidodera tertiotertiaria sp. nov. is described. The new species is illustrated and compared with morphologically similar extant and fossil relatives. It is the third described fossil species of Crepidodera Chevrolat. In addition to the new taxon, new fossil records of C. decolorata Nadein & Perkovsky from Baltic and Bitterfeld amber are presented. A key to species of Crepidodera described from fossil resins is provided, and a checklist of Coleoptera described from Bitterfeld amber is compiled.

  6. Mie scattering and optical forces from evanescent fields: a complex-angle approach.

    Science.gov (United States)

    Bekshaev, Aleksandr Y; Bliokh, Konstantin Y; Nori, Franco

    2013-03-25

    Mie theory is one of the main tools describing scattering of propagating electromagnetic waves by spherical particles. Evanescent optical fields are also scattered by particles and exert radiation forces which can be used for optical near-field manipulations. We show that the Mie theory can be naturally adopted for the scattering of evanescent waves via rotation of its standard solutions by a complex angle. This offers a simple and powerful tool for calculations of the scattered fields and radiation forces. Comparison with other, more cumbersome, approaches shows perfect agreement, thereby validating our theory. As examples of its application, we calculate angular distributions of the scattered far-field irradiance and radiation forces acting on dielectric and conducting particles immersed in an evanescent field.

  7. 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.

  8. 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.

  9. Anti-allergy activities of Kuji amber extract and kujigamberol.

    Science.gov (United States)

    Maruyama, Miku; Kobayashi, Miki; Uchida, Takeshi; Shimizu, Eisaku; Higashio, Hironori; Ohno, Misa; Uesugi, Shota; Kimura, Ken-Ichi

    2018-03-05

    Amber is fossilized tree resin and several biologically active compounds were isolated from ambers using the growth-restoring activity of the mutant yeast [Saccharomyces cerevisiae (zds1∆ erg3∆ pdr1∆ pdr3∆)] involving Ca 2+ -signal transduction. The aim of this study is to investigate the anti-allergic effect of both the methanol extract of Kuji amber (MEKA) and its main biologically active constituent, kujigamberol (15,20-dinor-5,7,9-labdatrien-18-ol) having activity against the mutant yeast. Both MEKA and kujigamberol inhibited the degranulation of RBL-2H3 cells by stimulation of thapsigargin (Tg) (IC 50  = 15.0 μg/ml and 29.1 μM) and A23187 (IC 50  = 19.6 μg/ml and 24.9 μM) without cytotoxicity, but not by stimulation of IgE + DNP-BSA (Ag) (IC 50  > 50.0 μg/ml and 50.0 μM). However, both inhibited Ca 2+ -influx in RBL-2H3 cells by all three stimulations in a dose dependent manner. Leukotriene C 4 production in RBL-2H3 cells stimulated by A23187 was also inhibited by both through the inhibition of ERK1/2 phosphorylation. In an ovalbumin-induced rhinitis model of guinea pigs, nasal administration of MEKA and kujigamberol inhibited nasal blockade in a dose-dependent manner and the effect was about 5 times potent than that of a steroid clinical drug, mometasone furoate. The growth-restoring activity of MEKA and kujigamberol against the mutant yeast is involved in the anti-allergic activities against cells and animals, and both are expected to be candidates for the development new anti-allergy agents. Copyright © 2018. Published by Elsevier B.V.

  10. Study of the leakage field of magnetic force microscopy thin-film tips using electron holography

    NARCIS (Netherlands)

    Frost, B.G.; van Hulst, N.F.; Lunedei, E.; Matteucci, G.; Rikkers, E.

    1996-01-01

    Electron holography is applied for the study of the leakage field of thin-film ferromagnetic tips used as probes in magnetic force microscopy. We used commercially available pyramidal tips covered o­n o­ne face with a thin NiCo film, which were then placed in a high external magnetic field directed

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

    Science.gov (United States)

    Aly, J. J.

    1985-01-01

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

  12. A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

    Science.gov (United States)

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

    2017-12-31

    In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.

  13. 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.

  14. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

    Science.gov (United States)

    Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

    2017-06-20

    With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. 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.

  16. A new fossil cricket of the genus Proanaxipha in Miocene amber from the Dominican Republic (Orthoptera, Gryllidae, Pentacentrinae).

    Science.gov (United States)

    Heads, Sam W; Penney, David; Green, David I

    2012-01-01

    A new species of the cricket genus Proanaxipha Vickery & Poinar (Orthoptera: Gryllidae: Pentacentrinae) from Early Miocene Dominican amber is described and illustrated. Proanaxipha madgesuttonaesp. n. is distinguished from congeners by: (1) head capsule bearing a distinctive posteriorly bilobed colour spot on the vertex; (2) presence of crossveins in the proximal part of the mediocubital area; (3) apical field of tegmen entirely dark; and (4) median process of epiphallus short. The poorly known Proanaxipha bicolorata Vickery & Poinar, of questionable affinity and status, is herein regarded as a nomen inquirendum.

  17. 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.

  18. Drag force in strongly coupled { N }=4 supersymmetric Yang–Mills plasma in a magnetic field

    Science.gov (United States)

    Zhang, Zi-qiang; Ma, Ke; Hou, De-fu

    2018-02-01

    Applying AdS/CFT correspondence, we study the effect of a constant magnetic field { B } on the drag force associated with a heavy quark moving through a strongly-coupled { N }=4 supersymmetric Yang–Mills plasma. The quark is considered moving transverse and parallel to { B }. It is shown that for transverse case, the drag force is linearly dependent on { B } in all regions, while for parallel case, the drag force increases monotonously with increasing { B } and also reveals a linear behavior in the regions of strong { B }. In addition, we find that { B } has a more important effect in the transverse case than for the parallel.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study.

    Science.gov (United States)

    Tzanov, Alexandar T; Cuendet, Michel A; Tuckerman, Mark E

    2014-06-19

    The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR-UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase.

  4. 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).

  5. 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

  6. 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.

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

    Science.gov (United States)

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

    2000-01-01

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

  8. The 'Arm Force Field' method to predict manual arm strength based on only hand location and force direction.

    Science.gov (United States)

    La Delfa, Nicholas J; Potvin, Jim R

    2017-03-01

    This paper describes the development of a novel method (termed the 'Arm Force Field' or 'AFF') to predict manual arm strength (MAS) for a wide range of body orientations, hand locations and any force direction. This method used an artificial neural network (ANN) to predict the effects of hand location and force direction on MAS, and included a method to estimate the contribution of the arm's weight to the predicted strength. The AFF method predicted the MAS values very well (r 2  = 0.97, RMSD = 5.2 N, n = 456) and maintained good generalizability with external test data (r 2  = 0.842, RMSD = 13.1 N, n = 80). The AFF can be readily integrated within any DHM ergonomics software, and appears to be a more robust, reliable and valid method of estimating the strength capabilities of the arm, when compared to current approaches. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

    Science.gov (United States)

    Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

    2017-12-12

    London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the

  10. 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/ .

  11. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří

    2015-01-01

    Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  12. 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

    Czech Academy of Sciences Publication Activity Database

    Vymětal, Jiří; Vondrášek, Jiří

    2014-01-01

    Roč. 118, č. 35 (2014), s. 10390-10404 ISSN 1520-6106 R&D Projects: GA MŠk(CZ) LH11020 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * alpha-helical structure * der Waals interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

  13. 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

    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...... the MARTINI force field, is primarily due to the interactions between the coarse-grained molecules, i.e., the beads, rather than due to the differences between the conformations of saturated and unsaturated lipid acyl chains, namely entropy driven....

  14. Parallel alignment of bacteria using near-field optical force array for cell sorting

    Science.gov (United States)

    Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

    2017-08-01

    This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

  15. 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

  16. 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.

  17. 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.

  18. Evaluation of Sulfide Control by Air-Injection in Sewer Force Mains: Field and Laboratory Study

    Directory of Open Access Journals (Sweden)

    Juan T. García

    2017-03-01

    Full Text Available Chemical and biological processes consume dissolved oxygen (DO in urban wastewater during transportation along sewer systems. Anaerobic conditions (DO < 0.2 mg/L are easily reached, leading to sulfide (S2− generation. Release of free sulfide, hydrogen sulfide gas (H2S, from the liquid to the gaseous phase, causes odor, corrosion of pipes and supposes a risk for health of people working in sewers. These issues get worse in force mains, due to inability to take oxygen from the gaseous phase of pipe. Air injection is a suggested practice to control H2S emission in force mains. That technique aims to keep aerobic conditions in wastewater in order to avoid sulfide generation and favor a decrease of Biochemical Organic Demand (BOD. However, several force mains with air injection are not achieving their goals due to a limited oxygen transfer. Field measurements of dissolved oxygen in urban wastewater are presented in an existing force main with air injection during the summer of 2014 in the southeast of Spain. A laboratory scale model is constructed to quantify two-phase flow conditions in pipe due to air injection for different incoming flows rates of water and air. Particularly, for the case of plug flow, also known as elongated bubble flow. Velocity field measurement of water phase in laboratory allows estimating turbulent diffusivity of oxygen in the water, Em, and inter-phase mass transfer coefficient KL(T. In the laboratory, flow and air depth, bubble length, water velocity field, pressure inside force main and water and airflow rates are determined experimentally. These variables are used to assess DO in water phase of force main by comparison with those obtained from field measurements. This work allows assessing air injection efficiency in wastewater, and, therefore, to predict DO in wastewater in force mains.

  19. 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.

  20. 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.

  1. 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.

  2. Evolutionary and paleobiological implications of Coleoptera (Insecta from Tethyan-influenced Cretaceous ambers

    Directory of Open Access Journals (Sweden)

    David Peris

    2016-07-01

    Full Text Available The intense study of coleopteran inclusions from Spanish (Albian in age and French (Albian–Santonian in age Cretaceous ambers, both of Laurasian origin, has revealed that the majority of samples belong to the Polyphaga suborder and, in contrast to the case of the compression fossils, only one family of Archostemata, one of Adephaga, and no Myxophaga suborders are represented. A total of 30 families from Spain and 16 families from France have been identified (with almost twice bioinclusions identified in Spain than in France; 13 of these families have their most ancient representatives within these ambers. A similar study had previously only been performed on Lebanese ambers (Barremian in age and Gondwanan in origin, recording 36 coleopteran families. Few lists of taxa were available for Myanmar (Burmese amber (early Cenomanian in age and Laurasian in origin. Coleopteran families found in Cretaceous ambers share with their modern relatives mainly saproxylic and detritivorous habits in the larval or adult stages, rather than wood-boring behavior. Fifteen of the coleopteran families occur in both the Lebanese and Spanish ambers; while only five are present in both Spanish and French. Considering the paleogeographic proximity and similarity of age of the Spanish and French ambers, the small number of taxa found in common at both areas is surprising. The ancient origin for the Lebanese and Spanish ambers, the paleogeography (including some barriers for terrestrial biota and the local paleohabitats are factors that may explain the dissimilarity with the French specimens. Wildfires are believed to be a more likely cause of resin production during the Cretaceous than infestation by beetles. Current knowledge of the beetle species found in the Cretaceous ambers is introduced.

  3. 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...

  4. A valence force field-Monte Carlo algorithm for quantum dot growth modeling

    DEFF Research Database (Denmark)

    Barettin, Daniele; Kadkhodazadeh, Shima; Pecchia, Alessandro

    2017-01-01

    We present a novel kinetic Monte Carlo version for the atomistic valence force fields algorithm in order to model a self-assembled quantum dot growth process. We show our atomistic model is both computationally favorable and capture more details compared to traditional kinetic Monte Carlo models...

  5. 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

  6. Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

    Science.gov (United States)

    Lin, Fang-Yu; MacKerell, Alexander D

    2018-02-13

    The quality of the force field is crucial to ensure the accuracy of simulations used in molecular modeling, including computer-aided drug design (CADD). To perform more accurate modeling and simulations of halogenated molecules, in this study the polarizable force field based on the classical Drude oscillator model was extended to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds for the halogens F, Cl, Br, and I. The force field parameters were optimized targeting quantum mechanical dipole moments, water interactions, and molecular polarizabilities as well as experimental observables, including enthalpies of vaporization, molecular volumes, hydration free energies, and dielectric constants. The developed halogenated polarizable force field is capable of reproducing QM relative energies and geometries of both halogen bonds and halogen-hydrogen bond donor interactions at an unprecedented level due to the inclusion of a virtual particle and anisotropic atomic polarizability on the halogen and, notably, the inclusion of Lennard-Jones parameters on the halogen Drude particle. The model was validated on the basis of its ability to accurately reproduce pure solvent properties for halogenated naphthalenes and alkanes, including species analogous to those used as refrigerants. Accordingly, it is anticipated that the model will be applicable for the study of halogenated derivatives in CADD as well as in other chemical and biophysical studies.

  7. 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.

  8. 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

  9. 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…

  10. 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.

  11. Effects of sleep deprivation on event-related fields and alpha activity during rhythmic force production

    NARCIS (Netherlands)

    Boonstra, T.W.; Daffertshofer, A.; Beek, P.J.

    2005-01-01

    The influence of sleep deprivation (SD) on event-related fields and the distribution of power over the scalp of MEG imaged brain activity was studied during acoustically paced rhythmic force production. At the behavioral level, SD resulted in a reduction of the lag (negative asynchrony) between

  12. A molecular mechanics valence force field for sulfonamides derived by ab initio methods

    Energy Technology Data Exchange (ETDEWEB)

    Nicholas, J.B.; Burke, B.J.; Hopfinger, A.J. (Univ. of Illinois, Chicago (United States)); Vance, R.; Martin, E. (DowElanco, Walnut Creek, CA (United States))

    1991-11-28

    Molecular mechanics valence force field parameters for the sulfonamide group, SO[sub 2]NH, have been derived from ab initio calculations at the RHF/6-31G* level of theory. The force field parameters were designed to be used in conjunction with existing parameters from the MM2/MMP2 force field. The new parameters are demonstrated to accurately reproduce the ab initio optimized geometries of four molecules that contain the sulfonamide group. The strategy used in force field parametrization is discussed. The conformational flexibility of the sulfonamide group has been investigated. Calculations at the RHF/6-31G* level reveal the existence of two stable conformers and that interconversion is achieved by nitrogen inversion rather than rotation about the S-N bond. The energetic effects of expanding the basis set to 6-31G** and of including MP2 and MP3 corrections for electron correlation are discussed. The geometries and Mulliken charges for the ab initio optimized structures are also reported.

  13. 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.

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

    NARCIS (Netherlands)

    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.

    2014-01-01

    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

  15. parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages.

    Science.gov (United States)

    Peñalver, Enrique; Arillo, Antonio; Delclòs, Xavier; Peris, David; Grimaldi, David A; Anderson, Scott R; Nascimbene, Paul C; Pérez-de la Fuente, Ricardo

    2017-12-12

    Ticks are currently among the most prevalent blood-feeding ectoparasites, but their feeding habits and hosts in deep time have long remained speculative. Here, we report direct and indirect evidence in 99 million-year-old Cretaceous amber showing that hard ticks and ticks of the extinct new family Deinocrotonidae fed on blood from feathered dinosaurs, non-avialan or avialan excluding crown-group birds. A †Cornupalpatum burmanicum hard tick is entangled in a pennaceous feather. Two deinocrotonids described as †Deinocroton draculi gen. et sp. nov. have specialised setae from dermestid beetle larvae (hastisetae) attached to their bodies, likely indicating cohabitation in a feathered dinosaur nest. A third conspecific specimen is blood-engorged, its anatomical features suggesting that deinocrotonids fed rapidly to engorgement and had multiple gonotrophic cycles. These findings provide insight into early tick evolution and ecology, and shed light on poorly known arthropod-vertebrate interactions and potential disease transmission during the Mesozoic.

  16. Entrapment Bias of Arthropods in Miocene Amber Revealed by Trapping Experiments in a Tropical Forest in Chiapas, Mexico

    Science.gov (United States)

    Solórzano Kraemer, Mónica M.; Kraemer, Atahualpa S.; Stebner, Frauke; Bickel, Daniel J.; Rust, Jes

    2015-01-01

    All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measurements of the trapped arthropods, and guild distribution, that the amber trap is a complex entomological trap not comparable with a single artificial trap. At the order level, the most similar trap to amber is the sticky trap. However, in the case of Diptera, at the family level, the Malaise trap is also very similar to amber. Amber captured a higher diversity of arthropods than each of the artificial traps, based on our study of Mexican amber from the Middle Miocene, a time of climate optimum, where temperature and humidity were probably higher than in modern Central America. We conclude that the size bias is qualitatively independent of the kind of trap for non–extreme values. We suggest that frequent specimens in amber were not necessarily the most frequent arthropods in the former amber forest. Selected taxa with higher numbers of specimens appear in amber because of their ecology and behavior, usually closely related with a tree–inhabiting life. Finally, changes of diversity from the Middle Miocene to Recent time in Central and South America can be analyzed by comparing the rich amber faunas from Mexico and the Dominican Republic with the fauna trapped using sticky and Malaise traps in Central America. PMID:25785584

  17. Entrapment bias of arthropods in Miocene amber revealed by trapping experiments in a tropical forest in Chiapas, Mexico.

    Science.gov (United States)

    Solórzano Kraemer, Mónica M; Kraemer, Mónica M Solórzano; Kraemer, Atahualpa S; Stebner, Frauke; Bickel, Daniel J; Rust, Jes

    2015-01-01

    All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measurements of the trapped arthropods, and guild distribution, that the amber trap is a complex entomological trap not comparable with a single artificial trap. At the order level, the most similar trap to amber is the sticky trap. However, in the case of Diptera, at the family level, the Malaise trap is also very similar to amber. Amber captured a higher diversity of arthropods than each of the artificial traps, based on our study of Mexican amber from the Middle Miocene, a time of climate optimum, where temperature and humidity were probably higher than in modern Central America. We conclude that the size bias is qualitatively independent of the kind of trap for non-extreme values. We suggest that frequent specimens in amber were not necessarily the most frequent arthropods in the former amber forest. Selected taxa with higher numbers of specimens appear in amber because of their ecology and behavior, usually closely related with a tree-inhabiting life. Finally, changes of diversity from the Middle Miocene to Recent time in Central and South America can be analyzed by comparing the rich amber faunas from Mexico and the Dominican Republic with the fauna trapped using sticky and Malaise traps in Central America.

  18. 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.

  19. A Force Field for Water over Pt(111): Development, Assessment and Comparison.

    Science.gov (United States)

    Steinmann, Stephan N; Ferreira de Morais, Rodrigo; Götz, Andreas W; Fleurat-Lessard, Paul; Iannuzzi, Marcella; Sautet, Philippe; Michel, Carine

    2018-04-16

    Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water; (ii) a Gaussian term to improve the surface corrugation and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches, that have not been validated against extensive first principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from ice-like layers and an MD simulation of an interface between a c(4x6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.

  20. 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

  1. Orthodontic magnets. A study of force and field pattern, biocompatibility and clinical effects.

    Science.gov (United States)

    Bondemark, L

    1994-01-01

    Magnetic forces have been incorporated into orthodontic mechanics during recent years. However, the biocompatibility of magnet alloys and the possible risk of harmful or unusual reactions in tissues exposed to static magnetic fields have been characterized as inconsistent and often contradictory. It has also been questioned whether magnetic forces have significant advantages over traditional mechanics. The present series of studies aimed to analyse the force and field properties, the biocompatibility and the clinical effects of rare earth magnets as well as to compare the efficiency of tooth movement between magnets and another force system. Samarium-cobalt magnets for molar distalization were tested in experimental models for force and field properties. The cytotoxicity of different magnet alloys (rare earth types) as well as of clinically used and recycled magnets was assessed by two in vitro methods, the millipore filter method and an extraction method. The effect of static magnetic fields on human gingival tissue and dental pulp was examined histologically for alterations in cell pattern and cell morphology. The effects of using repelling samarium-cobalt magnets for simultaneous distalization of maxillary first and second molars were analysed in individuals with Class II malocclusion. The efficiency of molar distalization was also intra-individually compared between repelling magnets and superelastic NiTi-coils in individuals with Class II malocclusion and deep bite. The magnet forces decreased approximately with the reciprocal square of the separation distance between the magnets. No fatigue of force over time could be seen. The static magnetic fields were weak and had a limited extent and the flux density dropped exponentially in all directions with increased distance from the magnets, implying a small exposure area when the magnets are used clinically. Rare earth magnets showed good biocompatibility, particularly coated magnets. However, uncoated samarium

  2. 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

  3. Unsteady flow field around a human hand and propulsive force in swimming.

    Science.gov (United States)

    Matsuuchi, K; Miwa, T; Nomura, T; Sakakibara, J; Shintani, H; Ungerechts, B E

    2009-01-05

    Much effort has been undertaken for the estimation of propulsive force of swimmers in the front crawl. Estimation is typically based on steady flow theory: the so-called quasi-steady analysis. Flow fields around a swimmer, however, are extremely unsteady because the change direction of hand produces unsteady vortex motions. To evaluate the force correctly, it is necessary to know the unsteady properties determined from the vortex dynamics because that unsteadiness is known to make the force greater. Unsteady flow measurements were made for this study using a sophisticated technique called particle image velocimetry (PIV) in several horizontal planes for subjects swimming in a flume. Using that method, a 100 time-sequential flow fields are obtainable simultaneously. Each flow field was calculated from two particle images using the cross-correlation method. The intensity of vortices and their locations were identified. A strong vortex was generated near the hand and then shed by directional change of the hand in the transition phase from in-sweep to out-sweep. When the vortex was shed, a new vortex rotating in the opposite direction around the hand was created. The pair of vortices induced the velocity component in the direction opposite to the swimming. Results of this study show that the momentum change attributable to the increase in this velocity component is the origin of thrust force by the hand.

  4. 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.

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

    Science.gov (United States)

    Morante, S.; Rossi, G. C.

    2017-02-01

    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.

  6. 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

  7. The first known fossil Masoninae (Hymenoptera: Braconidae) from Miocene Dominican amber

    NARCIS (Netherlands)

    Achterberg, van C.

    2001-01-01

    The first fossil species of the genus Masona van Achterberg, 1995, of the subfamily Masoninae (Hymenoptera: Braconidae) is described and illustrated. It originates from approximately 15-20 millions years old (= Miocene) Dominican amber.

  8. Natural amber, copal resin and colophony investigated by UV-VIS, infrared and Raman spectrum

    Science.gov (United States)

    Rao, ZhiFan; Dong, Kun; Yang, XiaoYun; Lin, JinChang; Cui, XiaoYing; Zhou, RongFeng; Deng, Qing

    2013-08-01

    Natural amber, copal resin and colophony are have investigated by UV-VIS, infrared and Raman spectrum. In order to distinguish the natural amber, copal resin and colophony, we have successfully used the nondestructive examination (NDE) technology. The results show that UV-VIS could not distinguish these compositions. The infrared spectra can distinguish them, but the technology may destroy the specimen. The Raman spectra show three characteristic peaks of vibration near position 932 cm-1 and position 1179 cm-1 of copal resin, which confirm the existence of terpenes compounds in it. In the Raman spectra of colophony, the vibration characteristic peak at position 1589 cm-1, caused by the conjugate double bond of internal unsaturated resin acid, is the basis of the characteristic difference between colophony and natural amber. The advantages of the distinguished technology by Raman spectroscopy are convenient and nondestructive examination for natural amber, copal resin and colophony.

  9. 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

  10. 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.

  11. Protein-DNA docking with a coarse-grained force field

    Directory of Open Access Journals (Sweden)

    Setny Piotr

    2012-09-01

    Full Text Available Abstract Background Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the prediction of complex architecture given detailed structures of its constituents. They are becoming an increasingly important tool in the field of macromolecular assemblies, complementing particularly demanding protein-nucleic acids X ray crystallography and providing means for the refinement and integration of low resolution data coming from rapidly advancing methods such as cryoelectron microscopy. Results We present a new coarse-grained force field suitable for protein-DNA docking. The force field is an extension of previously developed parameter sets for protein-RNA and protein-protein interactions. The docking is based on potential energy minimization in translational and orientational degrees of freedom of the binding partners. It allows for fast and efficient systematic search for native-like complex geometry without any prior knowledge regarding binding site location. Conclusions We find that the force field gives very good results for bound docking. The quality of predictions in the case of unbound docking varies, depending on the level of structural deviation from bound geometries. We analyze the role of specific protein-DNA interactions on force field performance, both with respect to complex structure prediction, and the reproduction of experimental binding affinities. We find that such direct, specific interactions only partially contribute to protein-DNA recognition, indicating an important role of shape complementarity and sequence-dependent DNA internal energy, in line with the concept of indirect protein-DNA readout mechanism.

  12. Aerodynamic Characterization of ‘DelFly Micro’ in Forward Flight Configuration by Force Measurements and Flow Field Visualization

    OpenAIRE

    Deng, Shuanghou; Percin, Mustafa; van Oudheusden, Bas

    2015-01-01

    This study explores the flow structures and unsteady force generation mechanisms of a flapping-wing micro air vehicle ‘DelFly Micro’ in forward flight configuration. Stereoscopic Particle Image Velocimetry (Stereo-PIV) measurements were performed to acquire three dimensional flow fields in the wake. Six components of forces and moments were captured simultaneously by use of a miniature force sensor.

  13. Vibrational spectroscopy with chromatographic methods in molecular analyses of Moravian amber samples (Czech Republic)

    Czech Academy of Sciences Publication Activity Database

    Havelcová, Martina; Machovič, Vladimír; Linhartová, M.; Lapčák, L.; Přichystal, A.; Dvořák, Z.

    2016-01-01

    Roč. 128, SEP (2016), 153-160 ISSN 0026-265X R&D Projects: GA ČR(CZ) GA13-18482S Grant - others:OPPK(XE) CZ.2.16/3.1.00/21538 Program:OPPK Institutional support: RVO:67985891 Keywords : studlovite * valchovite * amber * fossil resin * Baltic amber Subject RIV: DD - Geochemistry Impact factor: 3.034, year: 2016

  14. A gilled mushroom, Gerontomyces lepidotus gen. et sp. nov. (Basidiomycota: Agaricales), in Baltic amber.

    Science.gov (United States)

    Poinar, George

    2016-09-01

    A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  15. Polyhedra Formation and Transient Cone Ejection of a Resonant Microdrop Forced by an ac Electric Field

    Science.gov (United States)

    Wang, Ping; Maheshwari, Siddharth; Chang, Hsueh-Chia

    2006-06-01

    New deformation or fission phenomena are reported for microdrops driven by an ac electric field at their resonant frequencies. The Maxwell forces that pull out the vertices from a drop can be enhanced when the ac frequency is comparable to both the drop resonant frequency and the inverse charge relaxation time of the diffuse layer. The selected polyhedra possess symmetries that ensure a global force balance of the Maxwell forces and a linear dimension consistent with a sphere whose nth harmonic (n is up to six in the observation) coincides with the applied ac frequency. At high voltages, the resonant focusing of charges by the vibration modes produces evenly distributed and transient Taylor cones that can eject charged nanodrops.

  16. Statistical field theory with constraints: Application to critical Casimir forces in the canonical ensemble.

    Science.gov (United States)

    Gross, Markus; Gambassi, Andrea; Dietrich, S

    2017-08-01

    The effect of imposing a constraint on a fluctuating scalar order parameter field in a system of finite volume is studied within statistical field theory. The canonical ensemble, corresponding to a fixed total integrated order parameter (e.g., the total number of particles), is obtained as a special case of the theory. A perturbative expansion is developed which allows one to systematically determine the constraint-induced finite-volume corrections to the free energy and to correlation functions. In particular, we focus on the Landau-Ginzburg model in a film geometry (i.e., in a rectangular parallelepiped with a small aspect ratio) with periodic, Dirichlet, or Neumann boundary conditions in the transverse direction and periodic boundary conditions in the remaining, lateral directions. Within the expansion in terms of ε=4-d, where d is the spatial dimension of the bulk, the finite-size contribution to the free energy of the confined system and the associated critical Casimir force are calculated to leading order in ε and are compared to the corresponding expressions for an unconstrained (grand canonical) system. The constraint restricts the fluctuations within the system and it accordingly modifies the residual finite-size free energy. The resulting critical Casimir force is shown to depend on whether it is defined by assuming a fixed transverse area or a fixed total volume. In the former case, the constraint is typically found to significantly enhance the attractive character of the force as compared to the grand canonical case. In contrast to the grand canonical Casimir force, which, for supercritical temperatures, vanishes in the limit of thick films, in the canonical case with fixed transverse area the critical Casimir force attains for thick films a negative value for all boundary conditions studied here. Typically, the dependence of the critical Casimir force both on the temperaturelike and on the fieldlike scaling variables is different in the two ensembles.

  17. Game Theory Model of Traffic Participants within Amber Time at Signalized Intersection

    Directory of Open Access Journals (Sweden)

    Weiwei Qi

    2014-01-01

    Full Text Available The traffic light scheme is composed of red, green, and amber lights, and it has been defined clearly for the traffic access of red and green lights; however, the definition of that for the amber light is indistinct, which leads to the appearance of uncertainty factors and serious traffic conflicts during the amber light. At present, the traffic administrations are faced with the decision of whether to forbid passing or not during the amber light in the cities of China. On one hand, it will go against the purpose of setting amber lights if forbidding passing; on the other hand, it may lead to a mess of traffic flow running if not. And meanwhile the drivers are faced with the decision of passing the intersection or stopping during the amber light as well. So the decision-making behavior of traffic administrations and drivers can be converted into a double game model. And through quantification of their earnings in different choice conditions, the optimum decision-making plan under specific conditions could be solved via the Nash equilibrium solution concept. Thus the results will provide a basis for the formulation of the traffic management strategy.

  18. Terpenoid Compositions and Botanical Origins of Late Cretaceous and Miocene Amber from China

    Science.gov (United States)

    Shi, Gongle; Dutta, Suryendu; Paul, Swagata; Wang, Bo; Jacques, Frédéric M. B.

    2014-01-01

    The terpenoid compositions of the Late Cretaceous Xixia amber from Central China and the middle Miocene Zhangpu amber from Southeast China were analyzed by gas chromatography-mass spectrometry (GC-MS) to elucidate their botanical origins. The Xixia amber is characterized by sesquiterpenoids, abietane and phyllocladane type diterpenoids, but lacks phenolic abietanes and labdane derivatives. The molecular compositions indicate that the Xixia amber is most likely contributed by the conifer family Araucariaceae, which is today distributed primarily in the Southern Hemisphere, but widely occurred in the Northern Hemisphere during the Mesozoic according to paleobotanical evidence. The middle Miocene Zhangpu amber is characterized by amyrin and amyrone-based triterpenoids and cadalene-based sesquiterpenoids. It is considered derived from the tropical angiosperm family Dipterocarpaceae based on these compounds and the co-occurring fossil winged fruits of the family in Zhangpu. This provides new evidence for the occurrence of a dipterocarp forest in the middle Miocene of Southeast China. It is the first detailed biomarker study for amber from East Asia. PMID:25354364

  19. Insect outbreaks produce distinctive carbon isotope signatures in defensive resins and fossiliferous ambers.

    Science.gov (United States)

    McKellar, Ryan C; Wolfe, Alexander P; Muehlenbachs, Karlis; Tappert, Ralf; Engel, Michael S; Cheng, Tao; Sánchez-Azofeifa, G Arturo

    2011-11-07

    Despite centuries of research addressing amber and its various inclusions, relatively little is known about the specific events having stimulated the production of geologically relevant volumes of plant resin, ultimately yielding amber deposits. Although numerous hypotheses have invoked the role of insects, to date these have proven difficult to test. Here, we use the current mountain pine beetle outbreak in western Canada as an analogy for the effects of infestation on the stable isotopic composition of carbon in resins. We show that infestation results in a rapid (approx. 1 year) (13)C enrichment of fresh lodgepole pine resins, in a pattern directly comparable with that observed in resins collected from uninfested trees subjected to water stress. Furthermore, resin isotopic values are shown to track both the progression of infestation and instances of recovery. These findings can be extended to fossil resins, including Miocene amber from the Dominican Republic and Late Cretaceous New Jersey amber, revealing similar carbon-isotopic patterns between visually clean ambers and those associated with the attack of wood-boring insects. Plant exudate δ(13)C values constitute a sensitive monitor of ecological stress in both modern and ancient forest ecosystems, and provide considerable insight concerning the genesis of amber in the geological record.

  20. A method to study precision grip control in viscoelastic force fields using a robotic gripper.

    Science.gov (United States)

    Lambercy, Olivier; Metzger, Jean-Claude; Santello, Marco; Gassert, Roger

    2015-01-01

    Instrumented objects and multipurpose haptic displays have commonly been used to investigate sensorimotor control of grasping and manipulation. A major limitation of these devices, however, is the extent to which the experimenter can vary the interaction dynamics to fully probe sensorimotor control mechanisms. We propose a novel method to study precision grip control using a grounded robotic gripper with two moving, mechanically coupled finger pads instrumented with force sensors. The device is capable of stably rendering virtual mechanical properties with a wide dynamic range of achievable impedances. Eight viscoelastic force fields with different combinations of stiffness and damping parameters were implemented, and tested on eight healthy subjects performing 30 consecutive repetitions of a grasp, hold, and release task with time and position constraints. Rates of thumb and finger force were found to be highly correlated (r>0.9) during grasping, revealing that, despite the mechanical coupling of the two finger pads, subjects performed grasping movements in a physiological fashion. Subjects quickly adapted to the virtual dynamics (within seven trials), but, depending on the presented force field condition, used different control strategies to correctly perform the task. The proof of principle presented in this paper underscores the potential of such a one-degree-of-freedom robotic gripper to study neural control of grasping, and to provide novel insights on sensorimotor control mechanisms.

  1. All-Optical Chirality-Sensitive Sorting via Reversible Lateral Forces in Interference Fields.

    Science.gov (United States)

    Zhang, Tianhang; Mahdy, Mahdy Rahman Chowdhury; Liu, Yongmin; Teng, Jing Hua; Lim, Chwee Teck; Wang, Zheng; Qiu, Cheng-Wei

    2017-04-25

    Separating substances by their chirality faces great challenges as well as opportunities in chemistry and biology. In this study, we propose an all-optical solution for passive sorting of chiral objects using chirality-dependent lateral optical forces induced by judiciously interfered fields. First, we investigate the optical forces when the chiral objects are situated in the interference field formed by two plane waves with arbitrary polarization states. When the plane waves are either linearly or circularly polarized, nonzero lateral forces are found at the particle's trapping positions, making such sideways motions observable. Although the lateral forces have different magnitudes on particles with different chirality, their directions are the same for opposite handedness particles, rendering it difficult to separate the chiral particles. We further solve the sorting problem by investigating more complicated polarization states. Finally, we achieve the chiral-selective separation by illuminating only one beam toward the chiral substance situated at an interface between two media, taking advantage of the native interference between the incident and reflective beams at the interface. Our study provides a robust and insightful approach to sort chiral substances and biomolecules with plausible optical setups.

  2. 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.

  3. 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

  4. 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

    in the parameterization. We refine the MARTINI procedure by including one additional target property related to the structure of the polymer, namely the radius of gyration. The force-field optimization is mainly based on experimental data. We test our procedure on polystyrene, a standard benchmark for coarse-grained (CG...... 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.......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...

  5. Acoustics forces on a solid sphere in focused sound fields and their use for acoustical traps

    DEFF Research Database (Denmark)

    Cutanda Henriquez, Vicente; Juhl, Peter Møller; Kristensen, Søren H.

    2009-01-01

    It is known that stationary sound fields can be used to levitate small objects in air; this phenomenon has potential applications in containerless processing of materials. Recently the use of acoustic forces have been considered for the manipulation of small samples, which offers several advantages...... in the cases of hazardous substances, processing of materials under pure conditions, handling of fragile or sticky objects, for instance. Several theoretical investigations on the use of focused Gaussian and Bessel acoustic beams have been reported in literature. In those papers, water has been assumed...... of the work. A theoretical investigation based on the boundary element method (BEM) is first described, where the acoustical forces on a rigid sphere are analyzed. It is assumed that the focused sound field is generated by means of a piezoelectric transducer with a shape of a section of a sphere, which...

  6. 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...... that three parameters per interaction site (atom diameter, depth of potential well, point electrostatic charge) provide a sufficient basis to predict thermodynamics (heat of vaporization, density), structure (radial distributions), and transport (diffusion, viscosity, conductivity) of ILs at room conditions...

  7. The force-field derivation and application of explosive/additive interfaces

    Science.gov (United States)

    Long, Yao; Chen, Jun

    2016-10-01

    The inter-molecular force-field across RDX/(paraffin, fluoropolymer) interfaces are derived from first-principles calculated energies under the GGA+vdW functional. Based on the force-field, the polycrystal structures of mixture explosives are obtained, and a set of thermodynamic properties are calculated, including the elastic constants, thermal expansion coefficient, heat capacity, isothermal curve and the Hugoniot curve. The results are in good agreement with the available experiments, and provide a reasonable prediction about the properties of plastic bonded explosives. We find that the thermal expansion coefficient of a multi-component explosive is not only determined by the properties of the components, but is also affected by the thermal stress at the explosive/additive interfaces.

  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. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  10. Surface Tension of Organic Liquids Using the OPLS/AA Force Field.

    Science.gov (United States)

    Zubillaga, Rafael A; Labastida, Ariana; Cruz, Bibiana; Martínez, Juan Carlos; Sánchez, Enrique; Alejandre, José

    2013-03-12

    Molecular dynamics simulations are performed to obtain the surface tension of 61 organic liquids using the OPLS/AA (all-atom optimized potential for liquid simulations). The force field parameters are the same as those recently used (Caleman et al. J. Chem. Theory Comput.2012, 8, 61) to determine several thermodynamic properties of 146 organic liquids. The correct evaluation of surface tension using slab simulations of liquids requires one to properly take into account the long-range interactions (Trukhymchuk and Alejandre J. Chem. Phys.1999, 111, 8510). In addition, the liquid density from slab simulations has to be the same as that obtained in liquid simulations at constant temperature and pressure. The new results of surface tensions from this work improve those reported by Caleman et al. The OPLS/AA force field gives good surface tensions compared with experimental data for most of the systems studied in this work, although it was developed to simulate liquids.

  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. Determining force field parameters using a physically based equation of state.

    Science.gov (United States)

    van Westen, Thijs; Vlugt, Thijs J H; Gross, Joachim

    2011-06-23

    Force field parameters used in classical molecular simulations can be estimated from quantum mechanical calculations or spectroscopic measurements. This especially applies to bonded interactions such as bond-stretching, bond-bending, and torsional interactions. However, it is difficult and computational expensive to obtain accurate parameters describing the nonbonded van der Waals interactions from quantum mechanics. In many studies, these parameters are adjusted to reproduce experimental data, such as vapor-liquid equilibria (VLE) data. Adjusting these force field parameters to VLE data is currently a cumbersome and computationally expensive task. The reason is that the result of a calculation of the vapor-liquid equilibria depends on the van der Waals interactions of all atom types in the system, therefore requiring many time-consuming iterations. In this work, we use an analytical equation of state, the perturbed chain statistical associating fluid theory (PC-SAFT), to predict the results of molecular simulations for VLE. The analytical PC-SAFT equation of state is used to approximate the objective function f(p) as a function of the array of force field parameters p. The objective function is here for example defined as the deviations of vapor pressure, enthalpy of vaporization and liquid density data, with respect to experimental data. The parameters are optimized using the analytical PC-SAFT equation of state, which is orders of magnitude quicker to calculate than molecular simulation. The solution is an excellent approximation of the real objective function, so that the resulting method requires only very few molecular simulation runs to converge. The method is here illustrated by optimizing transferable Lennard-Jones parameters for the n-alkane series. Optimizing four force field parameters p = (ε(CH(2))(CH(2)), ε(CH(3))(CH(3)), σ(CH(2))(CH(2)), σ(CH(3))(CH(3))) we obtain excellent agreement of coexisting densities, vapor pressure and caloric properties

  13. A force field for 3,3,3-fluoro-1-propenes, including HFO-1234yf.

    Science.gov (United States)

    Raabe, Gabriele; Maginn, Edward J

    2010-08-12

    The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field.

  14. Polarizable water model for the coarse-grained MARTINI force field.

    Directory of Open Access Journals (Sweden)

    Semen O Yesylevskyy

    2010-06-01

    Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.

  15. Solvation structure and dynamics of Ni{sup 2+}(aq) from a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Mareš, Jiří, E-mail: jiri.mares@oulu.fi; Vaara, Juha

    2014-10-31

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

  16. 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.

  17. 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...

  18. 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.

  19. Molecular dynamics simulations of AP/HMX composite with a modified force field.

    Science.gov (United States)

    Zhu, Wei; Wang, Xijun; Xiao, Jijun; Zhu, Weihua; Sun, Huai; Xiao, Heming

    2009-08-15

    An all-atom force field for ammonium perchlorate (AP) is developed with the framework of pcff force field. The structural parameters of AP obtained with the modified force field are in good agreement with experimental values. Molecular dynamics (MD) simulations have been performed to investigate AP/HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane) composite at different temperatures. The binding energies, thermal expansion coefficient, and the trigger bond lengths of HMX in the AP/HMX composite have been obtained. The binding energies of the system increase slightly with temperature increasing, peak at 245K, and then gradually decrease. The volume thermal expansion coefficient of the AP/HMX composite has been derived from the volume variation with temperature. As the temperature rises, the maximal lengths of the trigger bond N-NO(2) of HMX increase gradually. The simulated results indicate that the maximal length of trigger bond can be used as a criterion for judging the sensitivity of energetic composite.

  20. 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.

  1. 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.

  2. A new Acartophthalmites Hennig from Eocene Baltic amber (Diptera, Acalyptratae

    Directory of Open Access Journals (Sweden)

    Ricardo Pérez-de la Fuente

    2018-02-01

    Full Text Available A new fossil fly species, Acartophthalmites willii sp. n. (Diptera: Acalyptratae: Opomyzoidea from Baltic amber (Eocene, 56−33.9 Ma, is described based on a male originally assigned by Hennig (1969 to A. tertiaria Hennig, 1965, who erroneously also referred to it in the same work as “A. electrica Hennig” (unavailable name. The new species, representing the third named species of the extinct genus with unclear familial relationships Acartophthalmites Hennig, 1965, is herein described and illustrated in detail, and its systematic implications and relationships are discussed. From the morphological standpoint, the new species represents an intermediate form between the two formerly described species within the genus, therefore expanding the character combination diversity in this lineage of acalyptrate flies. The genus Acartophthalmites is considered to be most closely related to Clusiidae and, therefore, it is herein tentatively classified within the superfamily Opomyzoidea. The current work takes part of an effort to review the Acartophthalmites diversity in order to gain knowledge on the morphological data from the specimens described within the genus and ultimately enable a reliable analysis of its phylogenetic relationships with other acalyptrates.

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

    Science.gov (United States)

    Vato, Alessandro; Szymanski, Francois D; Semprini, Marianna; Mussa-Ivaldi, Ferdinando A; Panzeri, Stefano

    2014-01-01

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

  4. 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.

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

    Science.gov (United States)

    Semprini, Marianna; Mussa-Ivaldi, Ferdinando A.; Panzeri, Stefano

    2014-01-01

    We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field) applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop. PMID:24626393

  6. A force field and phonon dispersion curves. I: Application to Cs2 MX6 type systems

    International Nuclear Information System (INIS)

    Cortes, E.; Acevedo, R.

    1998-01-01

    A physical symmetry adapted formalism of general applicability is put forward to gain understanding of both the short and the long range interactions included in the dynamic matrix in solid state Physics. This formalism is carried out with reference to the Cs 2 U Br 6 which belongs to the Fm 3m(O 5 h ) space group. This system has been chosen since many theoretical and experimental studies have been already reported. This research article represents a new effort to gain understanding with reference to the N- body problem in lattice dynamics. based upon new and non published experimental data we have developed an strategy to work out convergence tests so that to carry out through studies of the lattice sums on both, the direct and the reciprocal spaces. This article reports updated information of the phonon dispersion curves along different polarizations directions, with explicit applications to the Cs 2 U Br 6 crystal. The lattice dynamic of this crystal has been worked out, utilising a model which includes a total of 13 force constants, which are derived when a mixed force field: general valence force field (GVFF)-Urey-Bradley force field (UBFF) is employed and a total of three effective charges on the Cesium, Uranium and Bromide ions. It is shown that our model is suitable to describe both the short and the long range interactions. Furthermore and for reasons of completeness, we have included interactions among atoms belonging to different unit cells. This is indeed a rather important breakthrough of the model reported in the literature previously. The advantages and disadvantages of the current formalism are discussed in the text, though we many anticipate a fair degree of success in the description in the description of several important physical observable and in particular in the description of the LO-TO energy gap. (author)

  7. Development of complex classical force fields through force matching to ab initio data: application to a room-temperature ionic liquid.

    Science.gov (United States)

    Youngs, Tristan G A; Del Pópolo, Mario G; Kohanoff, Jorge

    2006-03-23

    Recent experimental neutron diffraction data and ab initio molecular dynamics simulation of the ionic liquid dimethylimidazolium chloride ([dmim]Cl) have provided a structural description of the system at the molecular level. However, partial radial distribution functions calculated from the latter, when compared to previous classical simulation results, highlight some limitations in the structural description offered by force field-based simulations. With the availability of ab initio data it is possible to improve the classical description of [dmim]Cl by using the force matching approach, and the strategy for fitting complex force fields in their original functional form is discussed. A self-consistent optimization method for the generation of classical potentials of general functional form is presented and applied, and a force field that better reproduces the observed first principles forces is obtained. When used in simulation, it predicts structural data which reproduces more faithfully that observed in the ab initio studies. Some possible refinements to the technique, its application, and the general suitability of common potential energy functions used within many ionic liquid force fields are discussed.

  8. 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.

  9. Muscle co-contraction patterns in robot-mediated force field learning to guide specific muscle group training.

    Science.gov (United States)

    Pizzamiglio, Sara; Desowska, Adela; Shojaii, Pegah; Taga, Myriam; Turner, Duncan L

    2017-01-01

    Muscle co-contraction is a strategy of increasing movement accuracy and stability employed in dealing with force perturbation of movement. It is often seen in neuropathological populations. The direction of movement influences the pattern of co-contraction, but not all movements are easily achievable for populations with motor deficits. Manipulating the direction of the force instead, may be a promising rehabilitation protocol to train movement with use of a co-contraction reduction strategy. Force field learning paradigms provide a well described procedure to evoke and test muscle co-contraction. The aim of this study was to test the muscle co-contraction pattern in a wide range of arm muscles in different force-field directions utilising a robot-mediated force field learning paradigm of motor adaptation. Forty-two participants volunteered to participate in a study utilising robot-mediated force field motor adaptation paradigm with a clockwise or counter-clockwise force field. Kinematics and surface electromyography (EMG) of eight arm muscles were measured. Both muscle activation and co-contraction was earlier and stronger in flexors in the clockwise condition and in extensors in the counter-clockwise condition. Manipulating the force field direction leads to changes in the pattern of muscle co-contraction.

  10. 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

    2017-08-01

    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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. Influence of the temperature-dependent viscosity on convective flow in the radial force field.

    Science.gov (United States)

    Travnikov, Vadim; Zaussinger, Florian; Beltrame, Philippe; Egbers, Christoph

    2017-08-01

    The numerical investigation of convective flows in the radial force field caused by an oscillating electric field between spherical surfaces has been performed. A temperature difference (T_{1}>T_{2}) as well as a radial force field triggers a fluid flow similar to the Rayleigh-Bénard convection. The onset of convective flow has been studied by means of the linear stability analysis as a function of the radius ratio η=R_{1}/R_{2}. The influence of the temperature-dependent viscosity has been investigated in detail. We found that a varying viscosity contrast β=ν(T_{2})/ν(T_{1}) between β=1 (constant viscosity) and β=50 decreases the critical Rayleigh number by a factor of 6. Additionally, we perform a bifurcation analysis based on numerical simulations which have been calculated using a modified pseudospectral code. Numerical results have been compared with the GeoFlow experiment which is located on the International Space Station (ISS). Nonturbulent three-dimensional structures are found in the numerically predicted parameter regime. Furthermore, we observed multiple stable solutions in both experiments and numerical simulations, respectively.

  18. 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.

  19. 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.

  20. 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

  1. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-04-01

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

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

    International Nuclear Information System (INIS)

    Sun, Jiajia; Shi, Zongqian; Jia, Shenli; Zhang, Pengbo

    2017-01-01

    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.

  4. Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Weimin; Niu, Haitao; Lin, Tong; Wang, Xungai; Kong, Lingxue [Institute for Frontier Materials, Deakin University, Waurn Ponds VIC 3216 (Australia)

    2014-01-28

    The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

  5. Fossil mesostigmatid mites (Mesostigmata: Gamasina, Microgyniina, Uropodina), associated with longhorn beetles (Coleoptera: Cerambycidae) in Baltic amber

    Science.gov (United States)

    Dunlop, Jason A.; Kontschán, Jenő; Zwanzig, Michael

    2013-04-01

    Fossil mesostigmatid mites are extremely rare. Inclusions assignable to the tortoise mites (Mesostigmata, Uropodina) are described here for the first time from Eocene (ca. 44-49 Ma) Baltic amber. This is the oldest record of Uropodina and documents the first unequivocal amber examples potentially assignable to the extant genus Uroobovella Berlese, 1903 (Uropodoidea: Urodinychidae). Further mites in the same amber pieces are tentatively assigned to Microgynioidea (Microgyniina) and Ascidae (Gamasina), both potentially representing the oldest records of their respective superfamily and family groups. This new material also preserves behavioural ecology in the form of phoretic deutonymphs attached to their carriers via a characteristic anal pedicel. These deutonymphs in amber are intimately associated with longhorn beetles (Coleoptera: Cerambycidae), probably belonging to the extinct species Nothorhina granulicollis Zang, 1905. Modern uropodines have been recorded phoretic on species belonging to several beetle families, including records of living Uroobovella spp. occurring on longhorn beetles. Through these amber inclusions, a uropodine-cerambycid association can now be dated back to at least the Eocene.

  6. Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields

    Czech Academy of Sciences Publication Activity Database

    Fadrná, E.; Špačková, Naďa; Sarzynska, J.; Koča, J.; Orozco, M.; Cheatham III, T.E.; Kulinski, T.; Šponer, Jiří

    2009-01-01

    Roč. 5, č. 9 (2009), s. 2514-2530 ISSN 1549-9618 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802 Grant - others:GA ČR(CZ) GA203/09/1476 Program:GA Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA quadruplex * MD simulation * force fields Subject RIV: BO - Biophysics Impact factor: 4.804, year: 2009

  7. Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins

    Czech Academy of Sciences Publication Activity Database

    Banáš, P.; Hollas, D.; Zgarbová, M.; Jurečka, P.; Orozco, M.; Cheatham III, T.E.; Šponer, Jiří; Otyepka, M.

    2010-01-01

    Roč. 6, č. 12 (2010), s. 3836-3849 ISSN 1549-9618 R&D Projects: GA MŠk(CZ) LC06030; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802 Grant - others:GA MŠk(CZ) LC512 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : molecular dynamics * force fields * RNA * tetraloops Subject RIV: BO - Biophysics Impact factor: 5.138, year: 2010

  8. Fibre-top atomic force microscope probe with optical near-field detection capabilities.

    Science.gov (United States)

    Tiribilli, B; Margheri, G; Baschieri, P; Menozzi, C; Chavan, D; Iannuzzi, D

    2011-04-01

    We present a fibre-top probe fabricated by carving a tipped cantilever on an optical fibre, with the tip machined in correspondence of the fibre core. When approached to an optical prism illuminated under total internal reflection conditions, the tip of the cantilever detects the optical tunnelling signal, while the light coupled from the opposite end of the fibre measures the deflection of the cantilever. Our results suggest that fibre-top technology can be used for the development of a new generation of hybrid probes that can combine atomic force microscopy with scanning near field optical microscopy. © 2010 The Authors Journal of Microscopy © 2010 Royal Microscopical Society.

  9. Field investigation source area ST58 old Quartermaster service station, Eielson Air Force Base, Alaska

    Energy Technology Data Exchange (ETDEWEB)

    Liikala, T.L.; Evans, J.C.

    1995-01-01

    Source area ST58 is the site of the old Quartermaster service station at Eielson Air Force Base, Alaska. The source area is one of several Source Evaluation Report sites being investigated by Pacific Northwest Laboratory for the US Air Force as candidates for no further remedial action, interim removal action, or a remedial investigation/feasibility study under a Federal Facilities Agreement. The purpose of this work was to characterize source area ST58 and excavate the most contaminated soils for use in composting treatability studies. A field investigation was conducted to determine the nature and extent of soil contamination. The field investigation entailed a records search; grid node location, surface geophysical, and soil gas surveys; and test pit soil sampling. Soil excavation followed based on the results of the field investigation. The site was backfilled with clean soil. Results from this work indicate close spatial correlation between screening instruments, used during the field investigation and soil excavation, and laboratory analyses. Gasoline was identified as the main subsurface contaminant based on the soil gas surveys and test pit soil sampling. A center of contamination was located near the northcentral portion of the source area, and a center was located in the northwestern comer. The contamination typically occurred near or below a former soil horizon probably as a result of surface spills and leaks from discontinuities and/or breaks in the underground piping. Piping locations were delineated during the surface geophysical surveys and corresponded very well to unscaled drawings of the site. The high subsurface concentrations of gasoline detected in the northwestern comer of the source area probably reflect ground-water contamination and/or possibly floating product.

  10. 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.

  11. Some interesting consequences from Newton's modified expression of gravitational force in the vector model for gravitational field

    International Nuclear Information System (INIS)

    Vo Van On

    2009-01-01

    In this paper, based on the Vector model for gravitational field we show some interesting consequence from Newton's modified expression of gravitational force: dividing the space into regions around galaxies, maximal sire of stable galaxies. (author)

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

    International Nuclear Information System (INIS)

    Peng Yi; Huang Heji; Pan Wenxia

    2013-01-01

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

  13. Influence of the vortex shedding on the time evolution of instantaneous pressure fields and forces in rotating airfoils

    Science.gov (United States)

    Villegas, Arturo; Diez, Francisco J.

    2013-11-01

    Time-resolved measurements of instantaneous pressure fields and aerodynamic loads are obtained for rotating airfoils. These allowed evaluating temporal variations in the flow field and were able to capture the evolution of vortex shedding in the wake of the rotating blade. The results show the influence of vortex shedding in the instantaneous loads. These measurements involve obtaining first the velocity field from TR-PIV. This is used to calculate the pressure field from the Poisson pressure equation, and later the forces from the integral momentum equation. The robustness of the measurements is analyzed by calculating the PIV uncertainty, and the independence of the calculated forces. Experimental mean aerodynamic forces are compared to theoretical predictions from the Blade Element Momentum theory (BEM) showing good agreement. The instantaneous pressure varied with time only in the wake due to vortex shedding. This is the first time the evolution of the instantaneous pressure field has been resolved for a rotating airfoil. The contribution to the instantaneous forces from each term in the integral momentum equation is evaluated. The analysis shows that the larger contributions to the normal force coefficient are from the unsteady and the pressure terms while the larger contribution to the tangential force coefficient is from the convective term. The method can be used to measure unsteady forces in rotating airfoils, providing useful information not just for computational studies, but also for aerodynamics, material and structural optimization and safety purposes.

  14. Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

    Science.gov (United States)

    Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

    2017-10-01

    Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

  15. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    Science.gov (United States)

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model 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 Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only 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).

  16. [Analysis on instantaneous spatial pattern of thermal force field in Harbin].

    Science.gov (United States)

    Zhu, Ning; Wang, Cheng; Zhou, Hongze; Li, Min

    2003-11-01

    The spatial pattern of urban thermal force field is not only the dominant content in assessing city ecological environment, but also an important base for city green system planning. The status of spatial pattern of thermal force field in Harbin was analyzed with RS and GIS techniques. Based on the instantaneous radiation temperature of the land surfaces in the city when the TM image was sensed remotely, all the patches were divided into 3 levels, i.e., low radiation temperature ( 28 degrees C) were uneven in their areas. The biggest area in these patches was 1489 hm2, and the smallest one was 0.72 hm2. The proportion of the patches with an area less than 1 hm2, between 1-5 hm2, and more than 5 hm2 was 95.02%, 3.46%, and 1.58%, respectively. There were 3 types of spatial patterns of the super-thermal radiation patches, i.e., round form (the average radiation temperature was 30.8 degrees C), ring form (the average radiation temperature was 27 degrees C), and pieces form (the average radiation temperature was 24.7 degrees C). Daowai District and Daoli District were round form, districts along the ring routes of railway in the city were ring form, and Nangang District and Dongli District were pieces form. Some advices to resolve the problem of 'heat island effect' influenced by the factors including greenland covering rate, greenland area and building dimension were discussed.

  17. Vibrational Study and Force Field of the Citric Acid Dimer Based on the SQM Methodology

    Directory of Open Access Journals (Sweden)

    Laura Cecilia Bichara

    2011-01-01

    Full Text Available We have carried out a structural and vibrational theoretical study for the citric acid dimer. The Density Functional Theory (DFT method with the B3LYP/6-31G∗ and B3LYP/6-311++G∗∗ methods have been used to study its structure and vibrational properties. Then, in order to get a good assignment of the IR and Raman spectra in solid phase of dimer, the best fit possible between the calculated and recorded frequencies was carry out and the force fields were scaled using the Scaled Quantum Mechanic Force Field (SQMFF methodology. An assignment of the observed spectral features is proposed. A band of medium intensity at 1242 cm−1 together with a group of weak bands, previously not assigned to the monomer, was in this case assigned to the dimer. Furthermore, the analysis of the Natural Bond Orbitals (NBOs and the topological properties of electronic charge density by employing Bader's Atoms in Molecules theory (AIM for the dimer were carried out to study the charge transference interactions of the compound.

  18. New Force Field Model for Propylene Glycol: Insight to Local Structure and Dynamics.

    Science.gov (United States)

    Ferreira, Elisabete S C; Voroshylova, Iuliia V; Koverga, Volodymyr A; Pereira, Carlos M; Cordeiro, M Natália D S

    2017-12-07

    In this work we developed a new force field model (FFM) for propylene glycol (PG) based on the OPLS all-atom potential. The OPLS potential was refined using quantum chemical calculations, taking into account the densities and self-diffusion coefficients. The validation of this new FFM was carried out based on a wide range of physicochemical properties, such as density, enthalpy of vaporization, self-diffusion coefficients, isothermal compressibility, surface tension, and shear viscosity. The molecular dynamics (MD) simulations were performed over a large range of temperatures (293.15-373.15 K). The comparison with other force field models, such as OPLS, CHARMM27, and GAFF, revealed a large improvement of the results, allowing a better agreement with experimental data. Specific structural properties (radial distribution functions, hydrogen bonding and spatial distribution functions) were then analyzed in order to support the adequacy of the proposed FFM. Pure propylene glycol forms a continuous phase, displaying no microstructures. It is shown that the developed FFM gives rise to suitable results not only for pure propylene glycol but also for mixtures by testing its behavior for a 50 mol % aqueous propylene glycol solution. Furthermore, it is demonstrated that the addition of water to the PG phase produces a homogeneous solution and that the hydration interactions prevail over the propylene glycol self-association interactions.

  19. 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

  20. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    Science.gov (United States)

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-09

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.

  1. Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development.

    Science.gov (United States)

    Verstraelen, Toon; Vandenbrande, Steven; Heidar-Zadeh, Farnaz; Vanduyfhuys, Louis; Van Speybroeck, Veronique; Waroquier, Michel; Ayers, Paul W

    2016-08-09

    Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g., obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method, but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Scheffler scheme for dispersion interactions.

  2. 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.

  3. Modelling of Ion Transport in Solids with a General Bond Valence Based Force-Field

    Directory of Open Access Journals (Sweden)

    S. Adams

    2010-12-01

    Full Text Available Empirical bond length - bond valence relations provide insight into the link between structure of and ion transport in solid electrolytes. Building on our earlier systematic adjustment of bond valence (BV parameters to the bond softness, here we discuss how the squared BV mismatch can be linked to the absolute energy scale and used as a general Morse-type interaction potential for analyzing low-energy pathways in ion conducting solid or mixed conductors either by an energy landscape approach or by molecular dynamics (MD simulations. For a wide range of Lithium oxides we could thus model ion transport revealing significant differences to an earlier geometric approach. Our novel BV-based force-field has also been applied to investigate a range of mixed conductors, focusing on cathode materials for lithium ion battery (LIB applications to promote a systematic design of LIB cathodes that combine high energy density with high power density. To demonstrate the versatility of the new BV-based force-field it is applied in exploring various strategies to enhance the power performance of safe low cost LIB materials (LiFePO4, LiVPO4F, LiFeSO4F, etc..

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

    Science.gov (United States)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical

  5. 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.

  6. 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

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

    Science.gov (United States)

    Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

    2016-08-24

    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).

  8. Electric field and force modeling for electrostatic levitation of lossy dielectric plates

    Science.gov (United States)

    Woo, S. J.; Higuchi, T.

    2010-11-01

    Electrostatic levitation holds great promise for the semiconductor, solar panel, and flat-panel display industry where the handling of dielectrics in a contact-free manner can bring many advantages and solve long-standing contamination and particulate control problems. In this work an analytical model is developed for the electrostatic levitation field between a lossy dielectric plate and a generic stator electrode structure consisting of a regular planar array of parallel bar electrodes. Time-varying voltages of differing polarities are alternatingly applied to the bar electrodes. Atmospheric humidity-related surface conduction on the plate is explicitly taken into account in the model since it has a profound effect on the field dynamics. Based on this model, the electrostatic levitation force is calculated using the Maxwell stress tensor formulation. The levitation force dynamics are investigated by evaluating the transient response of the field under a step in the applied voltages. In this context, the rate of electric charge build up on the plate is characterized by the suspension initiation time (TSI), which is defined as the time elapsed between applying step voltages to the stator electrodes and start of lift-off of the dielectric plate from its initial position. TSI is theoretically predicted for 0.7 mm thick soda-lime glass substrates, typically used in the manufacturing of liquid crystal displays (LCDs), as a function of electrode geometry, air gap separation, ambient humidity, and step voltage magnitudes. The predicted results are shown to be in good agreement with previously published experimental data for soda-lime glass substrates.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Accurate force field for molybdenum by machine learning large materials data

    Science.gov (United States)

    Chen, Chi; Deng, Zhi; Tran, Richard; Tang, Hanmei; Chu, Iek-Heng; Ong, Shyue Ping

    2017-09-01

    In this work, we present a highly accurate spectral neighbor analysis potential (SNAP) model for molybdenum (Mo) developed through the rigorous application of machine learning techniques on large materials data sets. Despite Mo's importance as a structural metal, existing force fields for Mo based on the embedded atom and modified embedded atom methods do not provide satisfactory accuracy on many properties. We will show that by fitting to the energies, forces, and stress tensors of a large density functional theory (DFT)-computed dataset on a diverse set of Mo structures, a Mo SNAP model can be developed that achieves close to DFT accuracy in the prediction of a broad range of properties, including elastic constants, melting point, phonon spectra, surface energies, grain boundary energies, etc. We will outline a systematic model development process, which includes a rigorous approach to structural selection based on principal component analysis, as well as a differential evolution algorithm for optimizing the hyperparameters in the model fitting so that both the model error and the property prediction error can be simultaneously lowered. We expect that this newly developed Mo SNAP model will find broad applications in large and long-time scale simulations.

  14. 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

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

    DEFF Research Database (Denmark)

    Pøhlsgaard, Jacob; Harpsøe, Kasper; Jørgensen, Flemming Steen

    2012-01-01

    The binding affinity of a drug like molecule depends among other things on the availability of the bioactive conformation. If the bioactive conformation has a significantly higher energy than the global minimum energy conformation, the molecule is unlikely to bind to its target. Determination...... of the global minimum energy conformation and calculation of conformational penalties of binding are prerequisites for prediction of reliable binding affinities. Here, we present a simple and computationally efficient procedure to estimate the global energy minimum for a wide variety of structurally diverse...... molecules, including polar and charged compounds. Identifying global energy minimum conformations of such compounds with force-field methods is problematic due to the exaggeration of intramolecular electrostatic interactions. We demonstrate that the global energy minimum conformations of zwitterionic...

  16. Shape Design of Unsteady Forced Heat-convection Fields to Control Temperature Distribution History

    Science.gov (United States)

    Katamine, Eiji; Okada, Naoya

    2017-11-01

    This paper presents a numerical solution to shape design of unsteady forced heat-convection fields to control temperature to a prescribed distribution. The square error integral between the actual temperature distributions and the prescribed temperature distributions on the prescribed sub-domains during the specified period of time is used as the objective functional. Shape gradient of the shape design problem is derived theoretically using the Lagrange multiplier method, adjoint variable method, and the formulae of the material derivative. Reshaping is carried out by the traction method proposed as an approach to solving shape optimization problems. Numerical analyses program for the shape design is developed based on FreeFem++, and the validity of proposed method is confirmed by results of 2D numerical analyses.

  17. 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

  18. Quasi-static evolution of force-free magnetic fields and a model for two-ribbon solar flares

    Science.gov (United States)

    Aly, J. J.

    1985-01-01

    It is shown that a two-dimensional force-free field in the solar corona can evolve in a quasi-static manner toward an open configuration, assuming the coronal field is invariant with respect to translations parallel to the x-axis. The theoretical result is applied to the quantitative theory of the evolution of two-ribbon solar flares of Kopp and Pneuman (1976), and the results are discussed. It is concluded that the two-dimensional force is the principal mechanism for the opening of the coronal magnetic field prior to reconnection during a solar flare.

  19. Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atom-centered charge, extra-point and polarizable force fields.

    Science.gov (United States)

    Baucom, Jason; Transue, Thomas; Fuentes-Cabrera, Miguel; Krahn, Joseph; Darden, Thomas; Sagui, Celeste

    2004-03-01

    Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)2 were used to study the relationship between DNA sequence and structure. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field and an ``extra-point" force field (with additional charges on extra-nuclear sites). It is found that in crystal environment all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force fields, however, outperforms the other two, pointing out to the need of the inclusion of polarization for accurate descriptions of DNA.

  20. A swarm of whiteflies—the first record of gregarious behavior from Eocene Baltic amber

    Science.gov (United States)

    Szwedo, Jacek; Drohojowska, Jowita

    2016-04-01

    A new whitefly Snotra christelae gen. et sp. n. is characterized, illustrated, and described from the Baltic amber. It represents the first record of gregarious behavior of Aleyrodinae (Aleyrodidae) whiteflies in fossil state. Implications of this finding on interpretation of whiteflies and their host-plant relationships and evolutionary traits of the group are discussed.

  1. Biogeographic and evolutionary implications of a diverse paleobiota in amber from the early Eocene of India

    Science.gov (United States)

    Rust, Jes; Singh, Hukam; Rana, Rajendra S.; McCann, Tom; Singh, Lacham; Anderson, Ken; Sarkar, Nivedita; Nascimbene, Paul C.; Stebner, Frauke; Thomas, Jennifer C.; Solórzano Kraemer, Monica; Williams, Christopher J.; Engel, Michael S.; Sahni, Ashok; Grimaldi, David

    2010-01-01

    For nearly 100 million years, the India subcontinent drifted from Gondwana until its collision with Asia some 50 Ma, during which time the landmass presumably evolved a highly endemic biota. Recent excavations of rich outcrops of 50–52-million-year-old amber with diverse inclusions from the Cambay Shale of Gujarat, western India address this issue. Cambay amber occurs in lignitic and muddy sediments concentrated by near-shore chenier systems; its chemistry and the anatomy of associated fossil wood indicates a definitive source of Dipterocarpaceae. The amber is very partially polymerized and readily dissolves in organic solvents, thus allowing extraction of whole insects whose cuticle retains microscopic fidelity. Fourteen orders and more than 55 families and 100 species of arthropod inclusions have been discovered thus far, which have affinities to taxa from the Eocene of northern Europe, to the Recent of Australasia, and the Miocene to Recent of tropical America. Thus, India just prior to or immediately following contact shows little biological insularity. A significant diversity of eusocial insects are fossilized, including corbiculate bees, rhinotermitid termites, and modern subfamilies of ants (Formicidae), groups that apparently radiated during the contemporaneous Early Eocene Climatic Optimum or just prior to it during the Paleocene-Eocene Thermal Maximum. Cambay amber preserves a uniquely diverse and early biota of a modern-type of broad-leaf tropical forest, revealing 50 Ma of stasis and change in biological communities of the dipterocarp primary forests that dominate southeastern Asia today. PMID:20974929

  2. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package.

    Science.gov (United States)

    Mermelstein, Daniel J; Lin, Charles; Nelson, Gard; Kretsch, Rachael; McCammon, J Andrew; Walker, Ross C

    2018-03-12

    Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  3. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    DEFF Research Database (Denmark)

    Ou, Yiyu; Iida, Daisuke; Liu, Jin

    2018-01-01

    We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW) samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light...

  4. A new genus of highly specialized ants in Cretaceous Burmese amber (Hymenoptera: Formicidae).

    Science.gov (United States)

    Barden, Phillip; Grimaldi, David

    2013-01-01

    A new genus of ants, Zigrasimecia Barden and Grimaldi, is described for a new and uniquely specialized species, Z. tonsora Barden and Grimaldi n.sp., preserved in Cretaceous amber from Myanmar. The amber is radiometrically dated at 99 myo. Zigrasimecia is closely related to another basal genus of ants known only in Burmese and French Cretaceous amber, Sphecomyrmodes Engel and Grimaldi, based in part on the shared possession of a comb of pegs on the clypeal margin, as well as mandible structure. Highly specialized features of Zigrasimecia include extensive development of the clypeal comb, a thick brush of setae on the oral surface of the mandibles and on the labrum, and a head that is broad, flattened, and which bears a crown of blackened, rugose cuticle. Mouthparts are hypothesized to have functioned in a unique manner, showing no clear signs of dentition representative of "chewing" or otherwise processing solid food. Although all ants in Burmese amber are basal, stem-group taxa, there is an unexpected diversity of mouthpart morphologies and probable feeding modes.

  5. New predatory cockroaches (Insecta: Blattaria: Manipulatoridae fam.n.) from the Upper Cretaceous Myanmar amber

    Science.gov (United States)

    Vršanský, Peter; Bechly, Günter

    2015-04-01

    We describe a new extinct lineage Manipulatoridae (new family) of cockroaches from the Upper Cretaceous (Cenomanian) amber of Myanmar. Manipulator modificaputis gen. et sp. n. is a morphologically unique extinct cockroach that represents the first (of a total of 29 known worldwide) cockroach family reported exclusively from the Myanmar amber. This family represents an early side branch of the stem group of Mantodea (most probably a sister group of Eadiidae within Blattaria/Corydioidea) because it has some synapomorphies with the Mantodea (including the stem group and Eadiidae). This family also retains symplesiomorphies that exclude a position in the crown group, and furthermore has unique autapomorphies that exclude a position as a direct ancestor of Mantodea. The unique adaptations such as strongly elongated extremities and freely movable head on a long neck suggest that these animals were pursuit predators. Five additional specimens (including two immatures) reported from the Myanmar amber suggest that this group was relatively rare but belonged to the indigenous and autochthonous inhabitants of the ancient amber forest of the Myanmar region.

  6. A new fossil species of the genus Coptodera Dejean, 1825 (Coleoptera: Carabidae: Lebiinae) from Baltic amber.

    Science.gov (United States)

    Gamboa, Sara; Ortuño, Vicente M

    2015-07-07

    In this paper a new species of fossil ground-beetle, Coptodera elektra n. sp. (Coleoptera: Carabidae) preserved in a piece of Baltic amber (Eocene) is described and the paleobiology of the species is studied. This new species represents the first known fossil record for the genus, as well as the first record of its presence in Europe.

  7. 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

  8. Current sheet formation in a sheared force-free-magnetic field. [in sun

    Science.gov (United States)

    Wolfson, Richard

    1989-01-01

    This paper presents the results of a study showing how continuous shearing motion of magnetic footpoints in a tenuous, infinitely conducting plasma can lead to the development of current sheets, despite the absence of such sheets or even of neutral points in the initial state. The calculations discussed here verify the earlier suggestion by Low and Wolfson (1988) that extended current sheets should form due to the shearing of a force-free quadrupolar magnetic field. More generally, this work augments earlier studies suggesting that the appearance of discontinuities - current sheets - may be a necessary consequence of the topological invariance imposed on the magnetic field geometry of an ideal MHD system by virtue of its infinite conductivity. In the context of solar physics, the work shows how the gradual and continuous motion of magnetic footpoints at the solar photosphere may lead to the buildup of magnetic energy that can then be released explosively when finite conductivity effects become important and lead to the rapid dissipation of current sheets. Such energy release may be important in solar flares, coronal mass ejections, and other eruptive events.

  9. 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.

  10. Magnetic displacement force and torque on dental keepers in the static magnetic field of an MR scanner.

    Science.gov (United States)

    Omatsu, Mika; Obata, Takayuki; Minowa, Kazuyuki; Yokosawa, Koichi; Inagaki, Eri; Ishizaka, Kinya; Shibayama, Koichi; Yamamoto, Toru

    2014-12-01

    To evaluate the effect of the static magnetic field of magnetic resonance (MR) scanners on keepers (ie, ferromagnetic stainless steel plate adhered to the abutment tooth of dental magnetic attachments). Magnetically induced displacement force and torque on keepers were measured using 1.5 Tesla (T) and 3.0 T MR scanners and a method outlined by American Society for Testing and Materials (ASTM). Changes in magnetic flux density before and after exposure to scanner static magnetic field were examined. The maximum magnetically induced displacement forces were calculated to be 10.3 × 10(-2) N at 1.5 T and 13.9 × 10(-2) N at 3.0 T on the cover surface. The maximum torques exerted on the keeper (4 mm in diameter) were 0.83 N × 4 mm at 1.5 T and 0.85 N × 4 mm at 3.0 T. These forces were considerably higher than the gravitational force (7.7 × 10(-4) N) of the keeper but considerably lower than the keeper-root cap proper adhesive force. The keepers' magnetic flux density remained less than that of the Earth. Magnetically induced displacement force and torque on the keeper in the MR scanner do not influence the keeper-root cap proper adhesive force. © 2013 Wiley Periodicals, Inc.

  11. 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.

  12. 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.

  13. 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.

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

    Indian Academy of Sciences (India)

    : F = &z where & is the force constant and z is the cantilever deflection. The cantilever is calibrated and the residual potential difference between the grounded sphere and plate is measured using the electrostatic force between them. The detail ...

  15. 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

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

    Indian Academy of Sciences (India)

    Abstract. Here we review our work on measurement of the Casimir force between a large alu- minum coated a sphere and flat plate using an atomic force microscope. The average statistical pre- cision is 1% of the force measured at the closest separation. We have also shown nontrival boundary dependence of the Casimir ...

  17. 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

  18. Extension of the ReaxFF Combustion Force Field toward Syngas Combustion and Initial Oxidation Kinetics.

    Science.gov (United States)

    Ashraf, Chowdhury; van Duin, Adri C T

    2017-02-09

    A detailed insight of key reactive events related to oxidation and pyrolysis of hydrocarbon fuels further enhances our understanding of combustion chemistry. Though comprehensive kinetic models are available for smaller hydrocarbons (typically C 3 or lower), developing and validating reaction mechanisms for larger hydrocarbons is a daunting task, due to the complexity of their reaction networks. The ReaxFF method provides an attractive computational method to obtain reaction kinetics for complex fuel and fuel mixtures, providing an accuracy approaching ab-initio-based methods but with a significantly lower computational expense. The development of the first ReaxFF combustion force field by Chenoweth et al. (CHO-2008 parameter set) in 2008 has opened new avenues for researchers to investigate combustion chemistry from the atomistic level. In this article, we seek to address two issues with the CHO-2008 ReaxFF description. While the CHO-2008 description has achieved significant popularity for studying large hydrocarbon combustion, it fails to accurately describe the chemistry of small hydrocarbon oxidation, especially conversion of CO 2 from CO, which is highly relevant to syngas combustion. Additionally, the CHO-2008 description was obtained faster than expected H abstraction by O 2 from hydrocarbons, thus underestimating the oxidation initiation temperature. In this study, we seek to systemically improve the CHO-2008 description and validate it for these cases. Additionally, our aim was to retain the accuracy of the 2008 description for larger hydrocarbons and provide similar quality results. Thus, we expanded the ReaxFF CHO-2008 DFT-based training set by including reactions and transition state structures relevant to the syngas and oxidation initiation pathways and retrained the parameters. To validate the quality of our force field, we performed high-temperature NVT-MD simulations to study oxidation and pyrolysis of four different hydrocarbon fuels, namely

  19. 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...... force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector....... A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained....

  20. 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

  1. 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.

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

    Science.gov (United States)

    Agrawalla, Satyam; van Duin, Adri C T

    2011-02-17

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

  3. 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.

  4. 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.

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

    International Nuclear Information System (INIS)

    Ramakrishnan, Raghunathan; Rauhut, Guntram

    2015-01-01

    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

  6. Surface field of forces and protein adsorption behavior of poly(hydroxyethylmethacrylate) films deposited from plasma.

    Science.gov (United States)

    Morra, M; Cassinelli, C

    1995-01-01

    Polymeric films were deposited from hydroxyethylmethacrylate (HEMA) plasma on non-woven poly(butyleneterephtalate) (PBT) filter materials. To test the effect of deposition conditions on surface properties, film were deposited using a constant monomer flow rate and a discharge power ranging from 40-100 W. Surface composition and surface energetics were evaluated by Electron Spectroscopy for Chemical Analysis (ESCA) and contact angle measurement, respectively. Albumin (Alb) and fibrinogen (Fg) adsorption from single protein solutions to the plasma-coated filters was measured. Results illustrate the marked effects of the deposition condition on the surface composition, the surface field of forces, and the protein adsorption behavior. The latter is modeled by the application of the Good-van Oss-Chaudhury theory of Lewis acid-base contribution to interfacial energetics. Materials endowed with widely different properties are obtained from the same monomer and different deposition conditions, a result that must be taken into account both in the production step, to assure constant quality, and in the development of specifically tailored materials.

  7. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    Science.gov (United States)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-04-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars ( d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  8. 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 +

  9. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field

    Science.gov (United States)

    Nielsen, Jakob T.; Eghbalnia, Hamid R.; Nielsen, Niels Chr.

    2011-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field. PMID:22293396

  10. 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.

  11. 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.

  12. 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

    a key, but currently poorly comprehended, component for our understanding of this variation in the immunogenicity of MHC binding peptides. Here, we demonstrate that identification of the cognate target of a TCR from a set of p:MHC complexes to a high degree is achievable using simple force-field energy...

  13. New Parameterization of the Cornell et al Empirical Force Field Covering Amino Group Nonplanarity in Nucleic Acid Bases

    Czech Academy of Sciences Publication Activity Database

    Ryjáček, Filip; Kubař, Tomáš; Hobza, Pavel

    2003-01-01

    Roč. 24, - (2003), s. 1891-1901 ISSN 0192-8651 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : Cornell et al. potential * nonplanar amino group * force field parameterization Subject RIV: CF - Physical ; Theoretical Chem istry Impact factor: 3.186, year: 2003

  14. 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

  15. Molecular dynamic study of Shock wave response of bulk amorphous polyvinyl chloride: effect of chain length and force field

    Science.gov (United States)

    Neogi, Anupam; Mitra, Nilanjan

    2015-06-01

    Atomistic molecular dynamics in conjunction with multi-scale shock technique is utilized to investigate shock wave response of bulk amorphous polyvinyl chloride. Dependence of chain length on physical and mechanical behaviour of polymeric material at ambient condition of temperature and pressure are well known but unknown for extreme conditions. Non-reactive force fields PCFF, COMPASS and PCFF+ were used to determine applicability of the force field for the study of the material subjected to shock loads. Several samples of PVC with various chain lengths were subjected to a range of shock compression from 1.5-10.0 km/s. Even though dependence of chain length was observed for lower shock strengths but was not for intense shock loads. The principle Hugoniot points, calculated by applying hydrostatic Rankine-Hugoniot equations and as well as multi-scale shock technique, were compared against LASL experimental shock data, demonstrating superior performance of PCFF+ force-field over PCFF and COMPASS. Shock induced melting characteristic and vibrational spectroscopic study were conducted and compared with experimental data to observe differences in response with relation to different force fields, chain length of the material for different shock intensities.

  16. Aerodynamic Characterization of ‘DelFly Micro’ in Forward Flight Configuration by Force Measurements and Flow Field Visualization

    NARCIS (Netherlands)

    Deng, S.; Percin, M.; Van Oudheusden, B.

    2015-01-01

    This study explores the flow structures and unsteady force generation mechanisms of a flapping-wing micro air vehicle ‘DelFly Micro’ in forward flight configuration. Stereoscopic Particle Image Velocimetry (Stereo-PIV) measurements were performed to acquire three dimensional flow fields in the wake.

  17. Host and adsorbate dynamics in silicates with flexible frameworks: Empirical force field simulation of water in silicalite

    Science.gov (United States)

    Bordat, Patrice; Cazade, Pierre-André; Baraille, Isabelle; Brown, Ross

    2010-03-01

    Molecular dynamics simulations are performed on the pure silica zeolite silicalite (MFI framework code), maintaining via a new force field both framework flexibility and realistic account of electrostatic interactions with adsorbed water. The force field is similar to the well-known "BKS" model [B. W. H. van Beest et al., Phys. Rev. Lett. 64, 1955 (1990)], but with reduced partial atomic charges and reoptimized covalent bond potential wells. The present force field reproduces the monoclinic to orthorhombic transition of silicalite. The force field correctly represents the hydrophobicity of pure silica silicalite, both the adsorption energy, and the molecular diffusion constants of water. Two types of adsorption, specific and weak unspecific, are predicted on the channel walls and at the channel intersection. We discuss molecular diffusion of water in silicalite, deducing a barrier to crossing between the straight and the zigzag channels. Analysis of the thermal motion shows that at room temperature, framework oxygen atoms incurring into the zeolite channels significantly influence the dynamics of adsorbed water.

  18. 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

  19. Development of ACBIO: A Biosphere Template Using AMBER for a Potential Radioactive Waste Repository

    International Nuclear Information System (INIS)

    Lee, Youn Myoung; Hwang, Yong Soo; Kang, Chul Hyung; Hahn, Pil Soo

    2005-01-01

    Nuclides in radioactive wastes are assumed to be transported in the geosphere by groundwater and probably discharged into the biosphere. Quantitative evaluation of doses to human beings due to nuclide transport in the geosphere and through the various pathways in the biosphere is the final step of safety assessment of the radioactive waste repository. To calculate the flux to dose conversion factors (DCFs) for nuclides appearing at GBIs with their decay chains, a template ACBIO which is an AMBER case file based on mathematical model for the mass transfer coefficients between the compartments has been developed considering material balance among the compartments in biosphere and then implementing to AMBER, a general and flexible software tool that allows to build dynamic compartment models. An illustrative calculation with ACBIO is shown.

  20. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    Directory of Open Access Journals (Sweden)

    Ou Yiyu

    2018-01-01

    Full Text Available We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extraction efficiency. The size-dependent strain relaxation effect was characterized by photoluminescence, Raman spectroscopy and time-resolved photoluminescence measurements. In addition, the light extraction efficiency of different MQW samples was studied by finite-different time-domain simulations. Compared to the as-grown sample, the nanopillar amber MQW sample with a diameter of 300 nm has demonstrated an emission enhancement by a factor of 23.8.

  1. Efficiency enhancement of InGaN amber MQWs using nanopillar structures

    KAUST Repository

    Ou, Yiyu

    2017-09-09

    We have investigated the use of nanopillar structures on high indium content InGaN amber multiple quantum well (MQW) samples to enhance the emission efficiency. A significant emission enhancement was observed which can be attributed to the enhancement of internal quantum efficiency and light extraction efficiency. The size-dependent strain relaxation effect was characterized by photoluminescence, Raman spectroscopy and time-resolved photoluminescence measurements. In addition, the light extraction efficiency of different MQW samples was studied by finite-different time-domain simulations. Compared to the as-grown sample, the nanopillar amber MQW sample with a diameter of 300 nm has demonstrated an emission enhancement by a factor of 23.8.

  2. 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.

  3. 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 2 O 3 and Na 2 O, have been used to simulate the R7T7 industrial nuclear glass (a 30 oxides glass). The inclusion of La 2 O 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 2 O 3 -Na 2 O and SiO 2 -B 2 O 3 -Na 2 O-La 2 O 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

  4. 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.

  5. 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.

  6. 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

    distributions, we show that the electrons are subject to both magnetic and electric forces, whereas the ionic lattice of the metal is dragged by an electric force. Furthermore, an analysis of the orders of magnitude involved in the problem gives counterintuitive results with valuable educational potential. We...

  7. 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...

  8. Exploring the water and carbon monoxide shell around Betelgeuse with VLTI/AMBER

    OpenAIRE

    Montargès, Miguel; Kervella, Pierre; Perrin, Guy; Ohnaka, Keiichi

    2013-01-01

    Betelgeuse Workshop, November 2012, Paris. To be published in the European Astronomical Society Publications Series, 2013, Editors: Pierre Kervella, Thibaut Le Bertre & Guy Perrin; International audience; We present the results of the analysis of our recent interferometric observations of Betelgeuse, using the AMBER instrument of the VLTI. Using the medium spectral resolution mode ($R \\sim 1500$) we detected the presence of the water vapour and carbon monoxide (CO) molecules in the H and K ba...

  9. Advantages of Study of Amber Fossils with lonization Detector in Variable Pressure SEM

    Czech Academy of Sciences Publication Activity Database

    Neděla, Vilém; Weyda, František; Černoch, P.

    2007-01-01

    Roč. 13, Suppl. 3 (2007), s. 250-251 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA102/05/0886; GA AV ČR KJB200650602 Institutional research plan: CEZ:AV0Z20650511; CEZ:AV0Z50070508 Keywords : VP-SEM * amber * morphology Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.941, year: 2007

  10. Amber light-emitting diode comprising a group III-nitride nanowire active region

    Science.gov (United States)

    Wang, George T.; Li, Qiming; Wierer, Jr., Jonathan J.; Koleske, Daniel

    2014-07-22

    A temperature stable (color and efficiency) III-nitride based amber (585 nm) light-emitting diode is based on a novel hybrid nanowire-planar structure. The arrays of GaN nanowires enable radial InGaN/GaN quantum well LED structures with high indium content and high material quality. The high efficiency and temperature stable direct yellow and red phosphor-free emitters enable high efficiency white LEDs based on the RGYB color-mixing approach.

  11. The oldest micropepline beetle from Cretaceous Burmese amber and its phylogenetic implications (Coleoptera: Staphylinidae)

    Science.gov (United States)

    Cai, Chen-Yang; Huang, Di-Ying

    2014-10-01

    The staphylinid subfamily Micropeplinae includes small strongly sclerotized beetles with truncate elytra leaving the most part of abdomen exposed. Fossil micropeplines are rare and confined to Cenozoic representatives of extant genera. Here, we describe the oldest micropepline, Protopeplus cretaceus gen. and sp. n., from the Upper Cretaceous Burmese amber. Fluorescence microscope and confocal laser scanning microscopy (CLSM) were both used to reveal diagnostic features of Micropeplinae and some primitive traits that place Protopeplus very basally within Micropeplinae.

  12. Axisymmetric force-free magnetosphere in the exterior of a neutron star - II. Maximum storage and open field energies

    Science.gov (United States)

    Kojima, Yasufumi; Okamoto, Satoki

    2018-04-01

    A magnetar's magnetosphere gradually evolves by the injection of energy and helicity from the interior. Axisymmetric static solutions for a relativistic force-free magnetosphere with a power-law current model are numerically obtained. They provide information about the configurations in which the stored energy is large. The energy along a sequence of equilibria increases and becomes sufficient to open the magnetic field. A magnetic flux rope, in which a large amount of toroidal field is confined, is formed in the vicinity of the star, for states exceeding the open field energy. These states are energetically metastable, and the excess energy may be ejected as a magnetar outburst.

  13. Contributions to the palaeofauna of Ptinidae (Coleptera) known from Baltic amber.

    Science.gov (United States)

    Bukejs, Andris; Alekseev, Vitalii I; Cooper, David M L; King, Gavin A; McKellar, Ryan C

    2017-11-06

    Hemicoelus favonii sp. nov. is described and illustrated from Eocene Baltic amber. This new fossil species differs from extant congeners in having 11-segmented antennae; a metathoracic ventrite with large impression in its anterior portion; a pronotum distinctly narrower than the elytral base region; the posterior suture of abdominal ventrite 1 weakly arcuate medially; sharp lateral pronotal margins that are incomplete and distinct in their basal half only; elytral striae that are not grouped in pairs; posterior pronotal angles that are rounded; elytral intestriae 3, 5, 7 and 9 that are distinctly convex; and a comparatively small total body size. The presence of Hemicoelus in Baltic amber suggests that moist, rotting wood was available as a microhabitat in the ancient forest. Beyond the new species description, the systematic placement of Anobium jacquelinae Hawkeswood, Makhan & Turner is discussed. A new fossil record for Microbregma waldwico Bukejs & Alekseev, and the first report of the genus Trichodesma LeConte from Eocene Baltic amber are also presented.

  14. Quantum mechanics based force field for carbon (QMFF-Cx) validated to reproduce the mechanical and thermodynamics properties of graphite

    Science.gov (United States)

    Pascal, Tod A.; Karasawa, Naoki; Goddard, William A.

    2010-10-01

    As assemblies of graphene sheets, carbon nanotubes, and fullerenes become components of new nanotechnologies, it is important to be able to predict the structures and properties of these systems. A problem has been that the level of quantum mechanics practical for such systems (density functional theory at the PBE level) cannot describe the London dispersion forces responsible for interaction of the graphene planes (thus graphite falls apart into graphene sheets). To provide a basis for describing these London interactions, we derive the quantum mechanics based force field for carbon (QMFF-Cx) by fitting to results from density functional theory calculations at the M06-2X level, which demonstrates accuracies for a broad class of molecules at short and medium range intermolecular distances. We carried out calculations on the dehydrogenated coronene (C24) dimer, emphasizing two geometries: parallel-displaced X (close to the observed structure in graphite crystal) and PD-Y (the lowest energy transition state for sliding graphene sheets with respect to each other). A third, eclipsed geometry is calculated to be much higher in energy. The QMFF-Cx force field leads to accurate predictions of available experimental mechanical and thermodynamics data of graphite (lattice vibrations, elastic constants, Poisson ratios, lattice modes, phonon dispersion curves, specific heat, and thermal expansion). This validates the use of M06-2X as a practical method for development of new first principles based generations of QMFF force fields.

  15. The SPASIBA force field of aldehydes. Part II: structure and vibrational wavenumbers of ethandial, propenal and 2-methylpropenal

    Science.gov (United States)

    Durier, V.; Zanoun a, A.; Belaidi, A.; Vergoten, G.

    1999-02-01

    The SPASIBA potential energy function has been extended to conjugated aldehydes. Molecular structures, conformational energies, moments of inertia, dipole moments and vibrational wavenumbers have all been examined. The tested molecules are ethandial (glyoxal), propenal (acrolein), 2-methylpropenal (methacrolein) and some of their deuterated analogs. The parameters of the force field were developed in order to reproduce experimental values: structures, conformational energies and vibrational wavenumbers (minimization of the standard deviation between observed and calculated vibrational wavenumbers). A set of 30 independent force constants was found to be sufficient to describe correctly the structure and vibrational wavenumbers. The average r.m.s errors is 15.25 cm -1.

  16. DFT calculations for anharmonic force field and spectroscopic constants of YC2 and its 13C isotopologues

    Science.gov (United States)

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Li, Jing

    2018-02-01

    The construction of the complete third and the semi-diagonal quartic force fields including the anharmonicity of the ground state (X˜2A1) for yttrium dicarbide (YC2) is carried out employing the vibrational second-order perturbation theory (VPT2) in combination with the density functional theory (DFT). The equilibrium geometries optimization, anharmonic force field and vibrational spectroscopic constants of YC2 are calculated by B3LYP, B3PW91 and B3P86 methods. Aug-cc-pVnZ (n = D, T, Q) and cc-pVnZ-PP (n = D, T, Q) basis sets are chosen for C and Y atoms, respectively. The calculated geometry parameters of YC2 agree well with the corresponding experimental and previous theoretical results. The bonding characters of Ysbnd C2 or Csbnd C are discussed. Based on the optimized equilibrium geometries, the spectroscopic constants and anharmonic force field of YC2 are calculated. Comparing with the spectroscopic constants of YC2 derived from the experiment, the calculated results show that the B3PW91 and B3P86 methods are superior to B3LYP for YC2. The Coriolis coupling constants, cubic and quartic force constants of YC2 are reasonably predicted. Besides, the spectroscopic constants and anharmonic force field of Y13C2 (X˜2A1) and Y13CC (X˜2A‧) are calculated for the first time, which are expected to guide the high resolution experimental work for YC2 and its 13C isotopologues.

  17. 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.

  18. DFT calculations for anharmonic force field and spectroscopic constants of YC2and its13C isotopologues.

    Science.gov (United States)

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Li, Jing

    2018-02-15

    The construction of the complete third and the semi-diagonal quartic force fields including the anharmonicity of the ground state (X˜ 2 A 1 ) for yttrium dicarbide (YC 2 ) is carried out employing the vibrational second-order perturbation theory (VPT2) in combination with the density functional theory (DFT). The equilibrium geometries optimization, anharmonic force field and vibrational spectroscopic constants of YC 2 are calculated by B3LYP, B3PW91 and B3P86 methods. Aug-cc-pVnZ (n=D, T, Q) and cc-pVnZ-PP (n=D, T, Q) basis sets are chosen for C and Y atoms, respectively. The calculated geometry parameters of YC 2 agree well with the corresponding experimental and previous theoretical results. The bonding characters of YC 2 or CC are discussed. Based on the optimized equilibrium geometries, the spectroscopic constants and anharmonic force field of YC 2 are calculated. Comparing with the spectroscopic constants of YC 2 derived from the experiment, the calculated results show that the B3PW91 and B3P86 methods are superior to B3LYP for YC 2 . The Coriolis coupling constants, cubic and quartic force constants of YC 2 are reasonably predicted. Besides, the spectroscopic constants and anharmonic force field of Y 13 C 2 (X˜ 2 A 1 ) and Y 13 CC (X˜ 2 A ' ) are calculated for the first time, which are expected to guide the high resolution experimental work for YC 2 and its 13 C isotopologues. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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.

  20. 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)

  1. Forcing of a photochemical air quality model with atmospheric fields simulated by a regional climate model

    CSIR Research Space (South Africa)

    Naidoo, M

    2010-10-01

    Full Text Available Within the context of climate change over southern Africa, little is understood about the potential local response of air quality to changes in the larger scale environment. Under future climate forcing, there may be significant changes...

  2. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.

    Energy Technology Data Exchange (ETDEWEB)

    De Hatten, Xavier [University of Bordeaux; Cournia, Zoe [Yale University; Smith, Jeremy C [ORNL; Metzler-Nolte, Nils [University of Bochum, Germany

    2007-08-01

    The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

  3. Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

    Energy Technology Data Exchange (ETDEWEB)

    de Hatten, Xavier; Cournia, Zoe; Huc, Ivan; Smith, Jeremy C.; Metzler-Nolte, Nils

    2007-10-05

    The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

  4. 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.

  5. Unsteady hydrodynamic forces acting on a robotic arm and its flow field: application to the crawl stroke.

    Science.gov (United States)

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

    2014-04-11

    This study aims to clarify the mechanisms by which unsteady hydrodynamic forces act on the hand of a swimmer during a crawl stroke. Measurements were performed for a hand attached to a robotic arm with five degrees of freedom independently controlled by a computer. The computer was programmed so the hand and arm mimicked a human performing the stroke. We directly measured forces on the hand and pressure distributions around it at 200 Hz; flow fields underwater near the hand were obtained via 2D particle image velocimetry (PIV). The data revealed two mechanisms that generate unsteady forces during a crawl stroke. One is the unsteady lift force generated when hand movement changes direction during the stroke, leading to vortex shedding and bound vortex created around it. This bound vortex circulation results in a lift that contributes to the thrust. The other occurs when the hand moves linearly with a large angle of attack, creating a Kármán vortex street. This street alternatively sheds clockwise and counterclockwise vortices, resulting in a quasi-steady drag contributing to the thrust. We presume that professional swimmers benefit from both mechanisms. Further studies are necessary in which 3D flow fields are measured using a 3D PIV system and a human swimmer. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: a systematic study of several common force fields.

    Science.gov (United States)

    Trinh, Thuat T; Vlugt, Thijs J H; Kjelstrup, Signe

    2014-10-07

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  7. 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

  8. Non-empirical calculations of force field and vibrational spectrum of LiBH3+ complex ion using the MO lcao sct method

    International Nuclear Information System (INIS)

    Ozerova, V.M.; Solomonik, V.G.

    1983-01-01

    Non-empiric calculations of the force field, frequencies of normal oscillations and intensities of oscillations in JR spectrum of LiBH 3 + complex ions are performed using the MO lcao SCF method. The alteration of the force field and vibrational spectrum of BH 3 molecule is analyzed in the case of its coordination with Li + cation

  9. Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring.

    Science.gov (United States)

    Lanzarotti, Esteban; Marcatili, Paolo; Nielsen, Morten

    2018-02-01

    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 a key, but currently poorly comprehended, component for our understanding of this variation in the immunogenicity of MHC binding peptides. Here, we demonstrate that identification of the cognate target of a TCR from a set of p:MHC complexes to a high degree is achievable using simple force-field energy 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 demonstrate that this approach can successfully be used to distinguish between epitopes and non-epitopes. A detailed analysis of the performance of this force-field-based approach demonstrate that its predictive performance depend on the ability to both accurately predict the binding of the peptide to the MHC 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. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. A Force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution

    OpenAIRE

    Mishra, Ratan K.; Fernández Carrasco, Lucía; Flatt, Robert J.; Heinz, Hendrik

    2014-01-01

    Tricalcium aluminate (C3A) is a major phase of Portland cement clinker and some dental root filling cements. An accurate all-atom force field is introduced to examine structural, surface, and hydration properties as well as organic interfaces to overcome challenges using current laboratory instrumentation. Molecular dynamics simulation demonstrates excellent agreement of computed structural, thermal, mechanical, and surface properties with available experimental data. The parameters are integ...

  11. Molecular Dynamics Simulation of Cross-Linked Epoxy Polymers: the Effect of Force Field on the Estimation of Properties

    OpenAIRE

    B. Arab; A. Shokuhfar

    2013-01-01

    In this paper, the molecular dynamics method was used to calculate the physical and mechanical properties of the cross-linked epoxy polymer composed of diglycidyl ether of bisphenol-A (DGEBA) as resin and diethylenetriamine (DETA) as curing agent. Calculation of the properties was performed using the constant-strain (static) approach. A series of independent simulations were carried out based on four widely used force fields; COMPASS, PCFF, UFF and Dreiding. Proper comparisons between the res...

  12. [Analysis of the use of field medical units in the armies of NATO and Russian Armed Forces].

    Science.gov (United States)

    Korniushko, I G; Iakovlev, S V; Murashev, I V; Sidorov, V A; Medvedev, V R; Matveev, A G

    2011-12-01

    An analysis of medical services of NATO and the Medical Service of the Armed Forces of the Russian Federation of modern technology deployment stages of medical evacuation (tents, inflatable structures, shelters, containers, medical armored vehicles, cars, etc.) is presented. Examples of their usage in isolated employment, usage in the group as a mobile medical stations and field hospitals in various conditions, the prospects and directions of development of technical means deployment of medical service are given.

  13. 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.

  14. Optical force on a discrete invisibility cloak in time-dependent fields

    Energy Technology Data Exchange (ETDEWEB)

    Chaumet, Patrick C.; Zolla, Frederic; Nicolet, Andre; Belkebir, Kamal [Institut Fresnel, CNRS, Aix-Marseille Universite, Campus de St-Jerome 13013 Marseille (France); Rahmani, Adel [Department of Mathematical Sciences, University of Technology, Sydney, Broadway NSW 2007 (Australia)

    2011-09-15

    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.

  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 restrictions on the length scales of the viscous and thermal boundary-layer thicknesses δs and δt 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...

  16. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties

    Science.gov (United States)

    Mamatkulov, Shavkat; Schwierz, Nadine

    2018-02-01

    Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg2+. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups.

  17. Electro-hydrodynamic force field and flow patterns generated by a DC corona discharge in the air

    Science.gov (United States)

    Monrolin, Nicolas; Plouraboue, Franck; Praud, Olivier

    2016-11-01

    Ionic wind refers to the electro-convection of ionised air between high voltage electrodes. Microscopic ion-neutral collisions are responsible for momentum transfer from accelerated ions, subjected to the electric field, to the neutral gas molecules resulting in a macroscopic airflow acceleration. In the past decades it has been investigated for various purposes from food drying through aerodynamic flow control and eventually laptop cooling. One consequence of air acceleration between the electrodes is thrust generation, often referred to as the Biefeld-Brown effect or electro-hydrodynamic thrust. In this experimental study, the ionic wind velocity field is measured with the PIV method. From computing the acceleration of the air we work out the electrostatic force field for various electrodes configurations. This enables an original direct evaluation of the force distribution as well as the influence of electrodes shape and position. Thrust computation based on the flow acceleration are compared with digital scale measurements. Complex flow features are highlighted such as vortex shedding, indicating that aerodynamic effects may play a significant role. Furthermore, the aerodynamic drag force exerted on the electrodes is quantified by choosing an appropriate control volume. Authors thank Region Midi-Pyrenee and CNES Launcher Directorate for financial support.

  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. 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.

  20. Maxwell-Faraday stresses in electromagnetic fields and the self-force on a uniformly accelerating point charge

    International Nuclear Information System (INIS)

    Rowland, D R

    2007-01-01

    The physical analysis of a uniformly accelerating point charge provides a rich problem to explore in advanced courses in electrodynamics and relativity since it brings together fundamental concepts in relation to electromagnetic radiation, Einstein's equivalence principle and the inertial mass of field energy in ways that reveal subtleties in each of these concepts. By first exploring the heuristic value of Maxwell's and Faraday's idea that the electromagnetic field is like a stressed material medium, it is shown in this paper that the problem also provides an interesting application of the electromagnetic stress-energy-momentum tensor and that an analysis using this tensor provides clear physical insight into this highly subtle and contentious problem and the so-called '4/3 problem' of classical electromagnetic theory. In particular, it is shown that the stress force on a uniformly accelerating, uniformly charged spherical shell due to its own field is simply the (relativistic) inertial mass of the charge's electrostatic field times the acceleration. Since the inertial mass of the electromagnetic field forms part of the observed rest mass of a charged particle, it is argued that the results are therefore consistent with the Lorentz-Abraham-Dirac equation of motion for an accelerating point charge, which implies that for uniform acceleration, the work done by the force acting on the charge only goes into increasing the kinetic energy of the charge, none goes into the creation of radiation

  1. 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

  2. Forces acting on a small particle in an acoustical field in a viscous fluid

    DEFF Research Database (Denmark)

    Settnes, Mikkel; Bruus, Henrik

    2012-01-01

    We calculate the acoustic radiation force from an ultrasound wave on a compressible, spherical particle suspended in a viscous fluid. Using Prandtl-Schlichting boundary-layer theory, we include the kinematic viscosity of the solvent and derive an analytical expression for the resulting radiation...

  3. The value of advanced multiple beam equalization radiography (AMBER) and storage phosphor radiography in chest X-rays

    International Nuclear Information System (INIS)

    Richter, C.S.; Richter, K.; Stein, R.; Busch, H.P.

    1993-01-01

    The study compared the quality of roentgenologic criteria in the evaluation of the heart and pulmonary vessels on chest X-rays obtained with different imaging systems. Fifty patients had four different chest radiographs, i.e. conventional chest X-rays, AMBER images, digital storage phosphor images, and digital storage radiographs that were obtained with the AMBER system. Comparison of techniques was based on 12 well-defined quality criteria of chest X-rays. Four radiologists with expertise reviewed the films according to these criteria. The AMBER technique was found to be superior to the remaining imaging modalities in visualization of the central pulmonary vessels, the descending aorta, and the left atrium. Peripheral pulmonary vessels were best appreciated with AMBER technique combined with storage phosphor technique. The same technique was superior in the assessment of all cardiovascular criteria. The superiority of this technique versus conventional chest X-rays can be explained on the basis of the linear slope of the gradation curve of AMBER and digital techniques. (orig.) [de

  4. Measurement of time-varying displacement fields in cell culture for traction force optical coherence microscopy (Conference Presentation)

    Science.gov (United States)

    Mulligan, Jeffrey A.; Adie, Steven G.

    2017-02-01

    Mechanobiology is an emerging field which seeks to link mechanical forces and properties to the behaviors of cells and tissues in cancer, stem cell growth, and other processes. Traction force microscopy (TFM) is an imaging technique that enables the study of traction forces exerted by cells on their environment to migrate as well as sense and manipulate their surroundings. To date, TFM research has been performed using incoherent imaging modalities and, until recently, has been largely confined to the study of cell-induced tractions within two-dimensions using highly artificial and controlled environments. As the field of mechanobiology advances, and demand grows for research in physiologically relevant 3D culture and in vivo models, TFM will require imaging modalities that support such settings. Optical coherence microscopy (OCM) is an interferometric imaging modality which enables 3D cellular resolution imaging in highly scattering environments. Moreover, optical coherence elastography (OCE) enables the measurement of tissue mechanical properties. OCE relies on the principle of measuring material deformations in response to artificially applied stress. By extension, similar techniques can enable the measurement of cell-induced deformations, imaged with OCM. We propose traction force optical coherence microscopy (TF-OCM) as a natural extension and partner to existing OCM and OCE methods. We report the first use of OCM data and digital image correlation to track temporally varying displacement fields exhibited within a 3D culture setting. These results mark the first steps toward the realization of TF-OCM in 2D and 3D settings, bolstering OCM as a platform for advancing research in mechanobiology.

  5. Generation of fast electrons in reversed field pinches by the equilibrium grad |B| force

    International Nuclear Information System (INIS)

    Fiksel, G.

    1994-10-01

    It is shown that a decreasing magnetic field profile in reversed-field pinch plasmas leads to formation of an anisotropic electron distribution function at the plasma edge. The mechanism is the conservation of the magnetic moment and the energy of electrons that collisionlessly travel outward in a stochastic magnetic field. As a result, the electrons have high parallel energies and low perpendicular energies at the edge. The details of the distribution function correspond well to experimental results

  6. Effect of boundary heat flux on solidification in a forced liquid metal flow: a phase-field simulation

    Science.gov (United States)

    Du, Lifei; Zhang, Rong

    2014-12-01

    A phase-field model coupling with velocity field is employed to study the effect of boundary heat flux on the microstructure formation of a Ni-40.8%Cu alloy with liquid flow during the solidification, and an anti-trapping current is introduced to suppress the solute trapping due to the larger interface width used in simulations than a real solidifying material. The effect of the flow field coupling with boundary heat extractions on the microstructure formation as well as distributions of concentration and temperature fields are analyzed and discussed. The forced liquid flow can significantly affect the heat and solute diffusions, thus influencing morphology formation, concentration and temperature distributions during the solidification. The solute segregation and concentration diffusion are changed by boundary heat extractions, and the morphology, concentration and temperature distributions are significantly influenced by increasing the heat extraction, which relatively makes the effect of liquid flow constrained. By increasing the initial velocity of liquid flow, the lopsided rate of the primary dendrite arm is enlarged and the growth manner of dendrite arms gets changed, and the transition of the microstructure from dendrite to cellular moves to the large heat extraction direction. Therefore, there exists the competition between the heat flux, temperature gradient and forced liquid flow that finally determines the microstructure formation during directional solidification.

  7. Tuning the instability in static mode atomic force spectroscopy as obtained in an AFM by applying an electric field between the tip and the substrate.

    Science.gov (United States)

    Biswas, Soma; Raychaudhuri, A K; Sreeram, P A; Dietzel, Dirk

    2012-11-01

    We have investigated experimentally the role of cantilever instabilities in determination of the static mode force-distance curves in presence of a dc electric field. The electric field has been applied between the tip and the sample in an atomic force microscope working in ultra-high vacuum. We have shown how an electric field modifies the observed force (or cantilever deflection)-vs-distance curves, commonly referred to as the static mode force spectroscopy curves, taken using an atomic force microscope. The electric field induced instabilities shift the jump-into-contact and jump-off-contact points and also the deflection at these instability points. We explained the experimental results using a model of the tip-sample interaction and quantitatively established a relation between the observed static mode force spectroscopy curves and the applied electric field which modifies the effective tip-sample interaction in a controlled manner. The investigation establishes a way to quantitatively evaluate the electrostatic force in an atomic force microscope using the static mode force spectroscopy curves. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. 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.

  9. 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.

  10. Amber from western Amazonia reveals Neotropical diversity during the middle Miocene

    Science.gov (United States)

    Antoine, Pierre-Olivier; De Franceschi, Dario; Flynn, John J.; Nel, André; Baby, Patrice; Benammi, Mouloud; Calderón, Ysabel; Espurt, Nicolas; Goswami, Anjali; Salas-Gismondi, Rodolfo

    2006-01-01

    Tertiary insects and arachnids have been virtually unknown from the vast western Amazonian basin. We report here the discovery of amber from this region containing a diverse fossil arthropod fauna (13 hexapod families and 3 arachnid species) and abundant microfossil inclusions (pollen, spores, algae, and cyanophyceae). This unique fossil assemblage, recovered from middle Miocene deposits of northeastern Peru, greatly increases the known diversity of Cenozoic tropical–equatorial arthropods and microorganisms and provides insights into the biogeography and evolutionary history of modern Neotropical biota. It also strengthens evidence for the presence of more modern, high-diversity tropical rainforest ecosystems during the middle Miocene in western Amazonia. PMID:16950875

  11. Multiple infection of amber Succinea putris snails with sporocysts of Leucochloridium spp. (Trematoda).

    Science.gov (United States)

    Ataev, G L; Zhukova, A A; Tokmakova, А S; Prokhorova, Е E

    2016-08-01

    Amber Succinea putris snails were collected in the Leningrad Region (Russia). Some of them were infected with trematodes Leucochloridium paradoxum, Leucochloridium perturbatum and Leucochloridium vogtianum. One snail had triple infection with all these species. Genotyping of sporocysts by ITS1-5.8S-ITS2 nucleotide sequences of ribosomal DNA (rDNA) and phylogenetic analysis were performed. The results confirmed the species identification of sporocysts of Leucochloridium based on the shape and colour of mature broodsacs. Sporocyst broodsacs could leave the host snail on their own, remaining viable in the environment for up to an hour. This ability of sporocysts may prevent the excessive infection of the molluscan host.

  12. An early and mysterious histerid inquiline from Cretaceous Burmese amber (Coleoptera, Histeridae).

    Science.gov (United States)

    Caterino, Michael S; Maddison, David R

    2018-01-01

    We describe a new genus and species of Histeridae from Upper Cretaceous Burmese amber, Amplectister tenax Caterino & Maddison, gen. & sp. n. This species represents the third known Cretaceous histerid, which, like the others, is highly distinct and cannot easily be placed to subfamily. It exhibits prosternal characters in common with Saprininae, but other characters appear inconsistent with this possibility. The abdominal venter is strongly concave, and the hind legs are enlarged and modified for grasping. We hypothesize that this represents the earliest example in Histeridae of modifications for phoresy on social insects.

  13. Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.

    Science.gov (United States)

    Knight, Chris; Maupin, C Mark; Izvekov, Sergei; Voth, Gregory A

    2010-10-12

    In this report, a general methodology is presented for the parametrization of a reactive force field using data from a condensed phase ab initio molecular dynamics (AIMD) simulation. This algorithm allows for the creation of an empirical reactive force field that accurately reproduces the underlying ab initio reactive surface while providing the ability to achieve long-time statistical sampling for large systems not possible with AIMD alone. In this work, a model for the hydrated excess proton is constructed where the hydronium cation and proton hopping portions of the model are statistically force-matched to the results of Car-Parrinello Molecular Dynamics (CPMD) simulations. The flexible nature of the algorithm also allows for the use of the more accurate classical simple point-charge flexible water (SPC/Fw) model to describe the water-water interactions while utilizing the ab initio data to create an overall multistate molecular dynamics (MS-MD) reactive model of the hydrated excess proton in water. The resulting empirical model for the system qualitatively reproduces thermodynamic and dynamic properties calculated from the ab initio simulation while being in good agreement with experimental results and previously developed multistate empirical valence bond (MS-EVB) models. The present methodology, therefore, bridges the AIMD technique with the MS-MD modeling of reactive events, while incorporating key strengths of both.

  14. 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.

  15. Live cell near-field optical imaging and voltage sensing with ultrasensitive force control.

    Science.gov (United States)

    Brahami, Aaron; Levy, Hadas; Zlotkin-Rivkin, Efrat; Melamed-Book, Naomi; Tal, Nataly; Lev, Dmitry; Yeshua, Talia; Fedosyeyev, Oleg; Aroeti, Benjamin; Lewis, Aaron

    2017-05-29

    Force controlled optical imaging of membranes of living cells is demonstrated. Such imaging has been extended to image membrane potential changes to demonstrate that live cell imaging has been achieved. To accomplish this advance, limitations inherent in atomic force microscopy (AFM) since its inception in 1986 [G. Binnig, C. F. Quate, and C. Gerber, "Atomic Force Microscope," Phys. Rev. Lett. 56, 930-933 (1986).] had to be overcome. The advances allow for live cell imaging of a whole genre of functional biological imaging with stiff (1-10N/m) scanned probe imaging cantilevers. Even topographic imaging of fine cell protrusions, such as microvilli, has been accomplished with such cantilevers. Similar topographic imaging has only recently been demonstrated with the standard soft (0.05N/m) cantilevers that are generally required for live cell imaging. The progress reported here demonstrates both ultrasensitive AFM (~100pN), capable of topographic imaging of even microvilli protruding from cell membranes and new functional applications that should have a significant impact on optical and other approaches in biological imaging of living systems and ultrasoft materials.

  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. 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.

  18. Linear evolution of current sheets in sheared force-free magnetic fields with discontinuous connectivity

    Science.gov (United States)

    Wolfson, Richard

    1990-01-01

    Thin current sheets arising in tenuous, magnetized solar coronal plasmas may constitute an important mechanism for energy buildups and subsequent energy releases; they could arise from the continuous-and-random motion of magnetic footprints associated with photospheric velocity fields. A model is presented for study of the quasi-static evolution of current sheets due to shearing of the footpoints, in a highly idealized geometry that incorporates an abrupt jump in field-line connectivity. The model highlights that formation of thin current layers and allows large shearing motions prior to violation of the linear approximation. Excess energy comparable to that released by solar flares can be stored in a sheared field.

  19. First record of Microscapha LeConte from Baltic amber with description of a new species and list of fossil Melandryidae (Coleoptera: Tenebrionoidea).

    Science.gov (United States)

    Bukejs, Andris; Alekseev, Vitalii I

    2015-09-03

    Microscapha andrzeji sp. nov., the first fossil representative of the genus is described from Eocene Baltic amber. An updated list of fossil Melandryidae (Coleoptera: Tenebrionoidea) is provided. The presence of Microscapha within Baltic amber suggests some potential for palaeoenvironmental inferences based on the melandryid assemblage within the deposit.

  20. Three-dimensional morphologies of inclined equiaxed dendrites growing under forced convection by phase-field-lattice Boltzmann method

    Science.gov (United States)

    Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi; Shimokawabe, Takashi; Aoki, Takayuki

    2018-02-01

    Three-dimensional growth morphologies of equiaxed dendrites growing under forced convection, with their preferred growth direction inclined from the flow direction, were investigated by performing large-scale phase-field lattice Boltzmann simulations on a graphical-processing-unit supercomputer. The tip velocities of the dendrite arms with their preferred growth directions inclined toward the upstream and downstream directions increased and decreased, respectively, as a result of forced convection. In addition, the tip velocities decreased monotonically as the angle between the preferred growth direction and the upstream direction increased. Here, the degree of acceleration of the upstream tips was larger than the degree of deceleration of the downstream tips. The angles between the actual tip growth directions and the preferred growth direction of the dendrite arms exhibited a characteristic change with two local maxima and two local minima.

  1. π -Stacking interactions in YFP, quantum mechanics and force field evaluations in the S0 and S1 states

    Science.gov (United States)

    Merabti, Karim Elhadj; Azizi, Sihem; Ridard, Jacqueline; Lévy, Bernard; Demachy, Isabelle

    2017-08-01

    We study the π -stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the isolated Chromophore-Tyrosine complex (Eint) to the 26 nm red shift observed from GFP to YFP, (ii) compare the effects of Eint and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S0 and S1 states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12-19 nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.

  2. A comparative Study between GoldSim and AMBER Based Biosphere Assessment Models for an HLW Repository

    International Nuclear Information System (INIS)

    Lee, Youn-Myoung; Hwang, Yong-Soo

    2007-01-01

    To demonstrate the performance of a repository, the dose exposure rate to human being due to long-term nuclide releases from a high-level waste repository (HLW) should be evaluated and the results compared to the dose limit presented by the regulatory bodies. To evaluate such a dose rate to an individual, biosphere assessment models have been developed and implemented for a practical calculation with the aid of such commercial tools as AMBER and GoldSim, both of which are capable of probabilistic and deterministic calculation. AMBER is a general purpose compartment modeling tool and GoldSim is another multipurpose simulation tool for dynamically modeling complex systems, supporting a higher graphical user interface than AMBER and a postprocessing feature. And also unlike AMBER, any kind of compartment scheme can be rather simply constructed with an appropriate transition rate between compartments, GoldSim is designed to facilitate the object-oriented modules to address any specialized programs, similar to solving jig saw puzzles. During the last couple of years a compartment modeling approach for a biosphere has been mainly carried out with AMBER in KAERI in order to conservatively or rather roughly provide dose conversion factors to get the final exposure rate due to a nuclide flux into biosphere over various geosphere-biosphere interfaces (GBIs) calculated through nuclide transport modules. This caused a necessity for a newly devised biosphere model that could be coupled to a nuclide transport model with less conservatism in the frame of the development of a total system performance assessment modeling tool, which could be successfully done with the aid of GoldSim. Therefore, through the current study, some comparison results of the AMBER and the GoldSim approaches for the same case of a biosphere modeling without any consideration of geosphere transport are introduced by extending a previous study

  3. Direction Change of the Force Action upon Conductor under Frequency Variation of the Acting Magnetic Field

    OpenAIRE

    Batygin, Yu.; Khimenko, l.; Lavinsky, V.

    2004-01-01

    The present work is dedicated to the description of the thin-walled conductor attraction effect by the pulse magnetic field. This phenomenon was displayed experimentally. The effect pointed out relates to the direction of the pulse magnetic fields energy practical usage for the different technologies in manufacture. In the scientific literature this direction is known as the magnetic pulse metal forming. A hypothesis about the physical essence of the displayed phenomenon is suggested.

  4. An Empirical Evaluation of Air Force Field Feeding with Recommendations for a New System

    Science.gov (United States)

    1984-06-01

    Refrigerator 1 Hobart HS-l 1585.00 Hot Holding Cabinets 2 Crescent Metal H-138-COD- 1834 930.00 Vegetable Slicer, Grater, Shredder 1 Qualheim 440...the main complaint of 75% of the cooks concerned the breakdowns in the provision of steam. -o ., 0_ 󈨑T --v7 T. 4. APPENDIX D 1. THE HARVEST BARE FOOD...food service operations. The Air Force allows for further breakdown based on operational requirements. The URN kits are arranged so that support pack

  5. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

    Liu Minxian, E-mail: liukey_sjtu@263.net [School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Wang Yan [Luoyang Institute of Science and Technology, Luoyang, Henan 471023 (China)

    2012-01-15

    The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

  6. 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. Combining displacement field and grip force information to determine mechanical properties of planar tissue with complicated geometry.

    Science.gov (United States)

    Nagel, Tina M; Hadi, Mohammad F; Claeson, Amy A; Nuckley, David J; Barocas, Victor H

    2014-11-01

    Performing planar biaxial testing and using nominal stress-strain curves for soft-tissue characterization is most suitable when (1) the test produces homogeneous strain fields, (2) fibers are aligned with the coordinate axes, and (3) strains are measured far from boundaries. Some tissue types [such as lamellae of the annulus fibrosus (AF)] may not allow for these conditions to be met due to their natural geometry and constitution. The objective of this work was to develop and test a method utilizing a surface displacement field, grip force-stretch data, and finite-element (FE) modeling to facilitate analysis of such complex samples. We evaluated the method by regressing a simple structural model to simulated and experimental data. Three different tissues with different characteristics were used: Superficial pectoralis major (SPM) (anisotropic, aligned with axes), facet capsular ligament (FCL) (anisotropic, aligned with axes, bone attached), and a lamella from the AF (anisotropic, aligned off-axis, bone attached). We found that the surface displacement field or the grip force-stretch data information alone is insufficient to determine a unique parameter set. Utilizing both data types provided tight confidence regions (CRs) of the regressed parameters and low parameter sensitivity to initial guess. This combined fitting approach provided robust characterization of tissues with varying fiber orientations and boundaries and is applicable to tissues that are poorly suited to standard biaxial testing. The structural model, a set of C++ finite-element routines, and a Matlab routine to do the fitting based on a set of force/displacement data is provided in the on-line supplementary material.

  8. 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

  9. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field

    Science.gov (United States)

    Jing, Zhifeng; Qi, Rui; Liu, Chengwen; Ren, Pengyu

    2017-10-01

    The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

  10. 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.

  11. Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

    Science.gov (United States)

    Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

    2017-10-01

    We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

  12. 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

  13. Te inclusion-induced electrical field perturbation in CdZnTe single crystals revealed by Kelvin probe force microscopy.

    Science.gov (United States)

    Gu, Yaxu; Jie, Wanqi; Li, Linglong; Xu, Yadong; Yang, Yaodong; Ren, Jie; Zha, Gangqiang; Wang, Tao; Xu, Lingyan; He, Yihui; Xi, Shouzhi

    2016-09-01

    To understand the effects of tellurium (Te) inclusions on the device performance of CdZnTe radiation detectors, the perturbation of the electrical field in and around Te inclusions was studied in CdZnTe single crystals via Kelvin probe force microscopy (KPFM). Te inclusions were proved to act as lower potential centers with respect to surrounding CdZnTe matrix. Based on the KPFM results, the energy band diagram at the Te/CdZnTe interface was established, and the bias-dependent effects of Te inclusion on carrier transportation is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 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.)

  15. Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian Indian Amber.

    Directory of Open Access Journals (Sweden)

    Jochen Heinrichs

    Full Text Available Cambay amber originates from the warmest period of the Eocene, which is also well known for the appearance of early angiosperm-dominated megathermal forests. The humid climate of these forests may have triggered the evolution of epiphytic lineages of bryophytes; however, early Eocene fossils of bryophytes are rare. Here, we present evidence for lejeuneoid liverworts and pleurocarpous mosses in Cambay amber. The preserved morphology of the moss fossil is inconclusive for a detailed taxonomic treatment. The liverwort fossil is, however, distinctive; its zig-zagged stems, suberect complicate-bilobed leaves, large leaf lobules, and small, deeply bifid underleaves suggest a member of Lejeuneaceae subtribe Lejeuneinae (Harpalejeunea, Lejeunea, Microlejeunea. We tested alternative classification possibilities by conducting divergence time estimates based on DNA sequence variation of Lejeuneinae using the age of the fossil for corresponding age constraints. Consideration of the fossil as a stem group member of Microlejeunea or Lejeunea resulted in an Eocene to Late Cretaceous age of the Lejeuneinae crown group. This reconstruction is in good accordance with published divergence time estimates generated without the newly presented fossil evidence. Balancing available evidence, we describe the liverwort fossil as the extinct species Microlejeunea nyiahae, representing the oldest crown group fossil of Lejeuneaceae.

  16. 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.

  17. 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.

  18. Environmental Assessment for BRAC Facilities and Remote Field Training Site, Wright-Patterson Air Force Base

    Science.gov (United States)

    2008-03-01

    of 1930’s Art Deco Printed Ont’ Recycled Paper •ti’ Appendix F Page 13 style architecture. The building housed the Wright Field Technical Data...stairway is consistent with Art Deco details throughout the building and, we believe, constitutes a character-defining feature of the property. Every

  19. 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

  20. Bidimensional nano-optomechanics and topological backaction in a non-conservative radiation force field.

    Science.gov (United States)

    Gloppe, A; Verlot, P; Dupont-Ferrier, E; Siria, A; Poncharal, P; Bachelier, G; Vincent, P; Arcizet, O

    2014-11-01

    Optomechanics, which explores the fundamental coupling between light and mechanical motion, has made important advances in manipulating macroscopic mechanical oscillators down to the quantum level. However, dynamical effects related to the vectorial nature of the optomechanical interaction remain to be investigated. Here we study a nanowire with subwavelength dimensions coupled strongly to a tightly focused beam of light, enabling an ultrasensitive readout of the nanoresonator dynamics. We determine experimentally the vectorial structure of the optomechanical interaction and demonstrate that a bidimensional dynamical backaction governs the nanowire dynamics. Moreover, the spatial topology of the optomechanical interaction is responsible for novel canonical signatures of strong coupling between mechanical modes, which leads to a topological instability that underlies the non-conservative nature of the optomechanical interaction. These results have a universal character and illustrate the increased sensitivity of nanomechanical devices towards spatially varying interactions, opening fundamental perspectives in nanomechanics, optomechanics, ultrasensitive scanning force microscopy and nano-optics.

  1. 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.

  2. Thermal analysis of the forced cooled conductor for the TF [toroidal field] superconducting coils in the TIBER II ETR design

    International Nuclear Information System (INIS)

    Kerns, J.A.; Slack, D.S.; Miller, J.R.

    1987-01-01

    The Tokamak Ignition/Burn Experimental Reactor (TIBER) is being designed to provide nuclear testing capabilities for first wall and blanket design concepts. The baseline design for TIBER II is to provide steady-state nuclear burn capabilities. These objectives must be met using reactor relevant components, such as state-of-the-art current drive schemes coupled with superconducting toroidal field (TF) and poloidal field (PF) coils. The design is also constrained to be cost effective, which forces the machine to be as small as possible. This last constraint limits the nuclear shielding in TIBER. Therefore, the TF coils will have a high nuclear heat load of up to 4.5 kW per coil. The cooling scheme and the thermal analysis for this design are presented

  3. 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

  4. 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.

  5. Vibrational spectra of trimethyl gallium species in relation to the force field and methyl group internal rotation

    Science.gov (United States)

    McKean, D. C.; McQuillan, G. P.; Duncan, J. L.; Shephard, N.; Munro, B.; Fawcett, V.; Edwards, H. G. M.

    Infrared and Raman spectra are reported for Ga(CH 3) 3, Ga(CD 3) 3 and Ga(CHD 2) 3 in the gas phase. These were also examined in the i.r. spectrum in the solid phase at 78 K. The new Raman spectra of the CHD 2 species strongly support earlier i.r. evidence for CH force constant variation during free internal rotation of the methyl groups, from the presence of two bands at 2940 (vs) and 2922 cm -1 (w) identified as due to ν avis and ν †is respectively. The observed a' and e' frequencies of the d0 and d9 species are used to obtain a force field in which three interaction constants are well defined. The best value of the Ga-C stretching force constant is 2.356(28) mdyn Å -1. In the crystal phase at 78 K, the e' modes due to δ s Me and ν as GaC 3 are split, indicating a site group symmetry lower than C3. Gallium and carbon isotope frequency shifts are predicted.

  6. 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.

  7. Development of a reactive force field for the Fe-C interaction to investigate the carburization of iron.

    Science.gov (United States)

    Lu, Kuan; Huo, Chun-Fang; Guo, Wen-Ping; Liu, Xing-Wu; Zhou, Yuwei; Peng, Qing; Yang, Yong; Li, Yong-Wang; Wen, Xiao-Dong

    2018-01-03

    The approach of molecular dynamics with Reactive Force Field (ReaxFF) is a promising way to investigate the carburization of iron which is pivotal in the preparation of desired iron-based materials and catalysts. However, it is a challenge to develop a reliable ReaxFF to describe the Fe-C interaction, especially when it involves bond rearrangement. In this work, we develop an exclusive set of Reactive Force Field (ReaxFF) parameters, denoted RPOIC-2017, to describe the diffusion behavior of carbon atoms in the α-Fe system. It inherited some partial parameters in 2012 (ReaxFF-2012) which are suitable for hydrogen adsorption and dissociation. This set of parameters is trained against data from first-principles calculations, including the equations of state of α-Fe, the crystal constant of Fe 3 C and Fe 4 C, a variety of periodic surface structures with varying carbon coverages, as well as the barriers of carbon diffusion in the α-Fe bulk and on diverse surfaces. The success in predicting the carbon diffusion coefficient and the diffusion barrier using the developed RPOIC-2017 potential demonstrates that the performance is superior to that of the traditional MEAM potential. The new ReaxFF for the Fe-C interaction developed in this work is not only essential for the design of novel iron based materials, but could also help understand atomic arrangements and the interfacial structure of iron carbides.

  8. Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide.

    Science.gov (United States)

    Cao, Fenglei; Deetz, Joshua D; Sun, Huai

    2017-01-23

    The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.

  9. Molecular simulation of caloric properties of fluids modelled by force fields with intramolecular contributions: Application to heat capacities

    Science.gov (United States)

    Smith, William R.; Jirsák, Jan; Nezbeda, Ivo; Qi, Weikai

    2017-07-01

    The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. We describe the correct methodology required to perform such calculations and illustrate it in this paper for the case of the internal energy and the enthalpy and their corresponding molar heat capacities. We provide numerical results for cP, one of the most important caloric properties. We also consider approximations to the correct calculation procedure previously used in the literature and illustrate their consequences for the examples of the relatively simple molecule 2-propanol, CH3CH(OH)CH3, and for the more complex molecule monoethanolamine, HO(CH2)2NH2, an important fluid used in carbon capture.

  10. Multi-Field Analysis and Experimental Verification on Piezoelectric Valve-Less Pumps Actuated by Centrifugal Force

    Science.gov (United States)

    Ma, Yu-Ting; Pei, Zhi-Guo; Chen, Zhong-Xiang

    2017-07-01

    A piezoelectric centrifugal pump was developed previously to overcome the low frequency responses of piezoelectric pumps with check valves and liquid reflux of conventional valveless piezoelectric pumps. However, the electro-mechanical-fluidic analysis on this pump has not been done. Therefore, multi-field analysis and experimental verification on piezoelectrically actuated centrifugal valveless pumps are conducted for liquid transport applications. The valveless pump consists of two piezoelectric sheets and a metal tube with piezoelectric elements pushing the metal tube to swing at the first bending resonant frequency. The centrifugal force generated by the swinging motion will force the liquid out of the metal tube. The governing equations for the solid and fluid domains are established, and the coupling relations of the mechanical, electrical and fluid fields are described. The bending resonant frequency and bending mode in solid domain are discussed, and the liquid flow rate, velocity profile, and gauge pressure are investigated in fluid domain. The working frequency and flow rate concerning different components sizes are analyzed and verified through experiments to guide the pump design. A fabricated prototype with an outer diameter of 2.2 mm and a length of 80 mm produced the largest flow rate of 13.8 mL/min at backpressure of 0.8 kPa with driving voltage of 80 Vpp. By solving the electro-mechanical-fluidic coupling problem, the model developed can provide theoretical guidance on the optimization of centrifugal valveless pump characters.

  11. Correlation of the vapor pressure isotope effect with molecular force fields in the liquid state

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. The effects of aircraft noise at Williams Air Force Base Auxiliary Field on residential property values

    Energy Technology Data Exchange (ETDEWEB)

    Morey, M.J.

    1990-11-01

    This report considers the environmental consequences of moving the flight training operations of the US Air Force's 82nd Flying Training Wing from the auxiliary airfield, Coolidge-Florence Municipal Airport (CFMA), to a more remote location in Pinal County, Arizona. It examines how actual noise from touch-and-go flights of T-37 aircraft and perceived (anticipated) noise affect the market value of residential property near CFMA. Noise, measured by a noise index, is correlated with market values through a regression analysis applied to a hedonic price model of the Coolidge-Florence housing market. Prices and characteristics of 42 residential properties sold in 1987 and 1988 were used to estimate a perceived noise effect. The report finds that the coefficient on the measure of perceived noise, based on the noise exposure forecast (NEF) index, is statistically insignificant, even though the sign and value are consistent with those estimated in other studies. It concludes that current flights do not have a significant effect on residential property values, partially because there is no housing near CFMA. This and larger studies indicate that flight operations at a new auxiliary airfield would not affect property values if runways were at least 12,000 feet away from housing. 12 refs., 2 tabs.

  13. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods.

    Science.gov (United States)

    Broo, Anders; Nilsson Lill, Sten O

    2016-08-01

    A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.

  14. Description of Pintomyia (Pifanomyia falcaorum sp. n. (Diptera: Psychodidae: Phlebotominae, a Fossil Sand Fly from Dominican Amber

    Directory of Open Access Journals (Sweden)

    Reginaldo Peçanha Brazil

    2002-06-01

    Full Text Available A new species of sand fly, Pintomyia (Pifanomyia falcaorum is described from an amber originated from the northern mountain range of Dominican Republic. The male sand fly specimen is well preserved and most features used in Phlebotominae taxonomy are seen with remarkable clarity.

  15. First fossil Lamprosomatinae leaf beetles (Coleoptera: Chrysomelidae) with descriptions of new genera and species from Baltic amber.

    Science.gov (United States)

    Bukejs, Andris; Nadein, Konstantin

    2015-03-11

    In the current paper the first fossil representatives of leaf-beetles from the subfamily Lamprosomatinae (Coleoptera: Chrysomelidae) are described and illustrated from Upper Eocene Baltic amber: Succinoomorphus warchalowskii gen. et sp. nov., Archelamprosomius balticus gen. et sp. nov., and Archelamprosomius kirejtshuki sp. nov. A key to fossil Lamprosomatinae is provided.

  16. Dispersion Forces

    CERN Document Server

    Buhmann, Stefan Yoshi

    2012-01-01

    In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

  17. 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

  18. 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

  19. Exploring the water and carbon monoxide shell around Betelgeuse with VLTI/AMBER

    Science.gov (United States)

    Montargès, M.; Kervella, P.; Perrin, G.; Ohnaka, K.

    2013-05-01

    We present the results of the analysis of our recent interferometric observations of Betelgeuse, using the AMBER instrument of the VLTI. Using the medium spectral resolution mode (R ~ 1500) we detected the presence of the water vapour and carbon monoxide (CO) molecules in the H and K bands. We also derived the photospheric angular diameter in the continuum. By analysing the depth of the molecular lines and the interferometric visibilities, we derived the column densities of the molecules, as well as the temperature and the size of the corresponding regions in the atmosphere of Betelgeuse (the MOLsphere) using a single shell model around the photosphere. Our results confirm the findings by Perrin et al. (2004) and Ohnaka et al. (2011) that the H2O and CO molecules are distributed around Betelgeuse in a MOLsphere extending to approximately 1.3 times the star's photospheric radius.

  20. New earwigs in mid-Cretaceous amber from Myanmar (Dermaptera, Neodermaptera).

    Science.gov (United States)

    Engel, Michael S

    2011-01-01

    Two new earwigs (Dermaptera) recently discovered in mid-Cretaceous (latest Albian) amber from Myanmar are described and figured. Astreptolabis ethirosomatiagen. et sp. n. is represented by a peculiar pygidicranoid female, assigned to a new subfamily, Astreptolabidinaesubfam. n., and differs from other protodermapterans in the structure of the head, pronotum, tegmina, and cercal forceps. Tytthodiplatys mecynocercusgen. et sp. n. is a distinctive form of first-instar nymph of the Diplatyidae, the earliest record for this basal earwig family. The taxon can be distinguished from other Early Cretaceous nymphs by the structure of the head, antennae, legs, and most notably its filamentous and annulate cerci. The character affinities of these taxa among Neodermaptera are generally discussed as is the identity of an enigmatic 'earwig-like' species from the Jurassic of China.

  1. New earwigs in mid-Cretaceous amber from Myanmar (Dermaptera, Neodermaptera

    Directory of Open Access Journals (Sweden)

    Michael Engel

    2011-09-01

    Full Text Available Two new earwigs (Dermaptera recently discovered in mid-Cretaceous (latest Albian amber from Myanmar are described and figured. Astreptolabis ethirosomatia gen. et sp. n. is represented by a peculiar pygidicranoid female, assigned to a new subfamily, Astreptolabidinae subfam. n., and differs from other protodermapterans in the structure of the head, pronotum, tegmina, and cercal forceps. Tytthodiplatys mecynocercus gen. et sp. n. is a distinctive form of first-instar nymph of the Diplatyidae, the earliest record for this basal earwig family. The taxon can be distinguished from other Early Cretaceous nymphs by the structure of the head, antennae, legs, and most notably its filamentous and annulate cerci. The character affinities of these taxa among Neodermaptera are generally discussed as is the identity of an enigmatic ‘earwig-like’ species from the Jurassic of China.

  2. Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards.

    Science.gov (United States)

    Daza, Juan D; Stanley, Edward L; Wagner, Philipp; Bauer, Aaron M; Grimaldi, David A

    2016-03-01

    Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.

  3. Rovno Amber Ant Assamblage: Bias toward Arboreal Strata or Sampling Effect?

    Directory of Open Access Journals (Sweden)

    Perkovsky E. E.

    2016-06-01

    Full Text Available In 2015 B. Guenard with co-authors indicated that the Rovno amber ant assemblage, as described by G. Dlussky and A. Rasnitsyn (2009, showed modest support for a bias towards arboreal origin comparing the Baltic and Bitterfeld assemblages, although it is not clear whether this reflects a sampling error or a signal of real deviation. Since 2009, the Rovno ant collection has now grown more than twice in volume which makes possible to check if the above inference about the essentially arboreal character of the assemblage is real or due to a sampling error. The comparison provided suggests in favour of the latter reason for the bias revealed by B. Guenard and co-authors. The new and larger data on the Rovno assemblage show that the share of non-arboreal ants is now well comparable with those concerning the Baltic and Bitterfeld assemblages. This holds true for the both total assemblages and subassemblages of worker ants only.

  4. A wide field of view force protection system for ground vehicles

    Science.gov (United States)

    Way, Scott; Archer, Cynthia; Jolivet, Noel; Cannon, Bruce; Hansen, Joel; Holt, Jordon; Olsen, Steven; Sarao, Jeremy

    2009-05-01

    The latest generation of heavily armored vehicles and the proliferation of IEDs in urban combat environments dictate that electro-optical systems play a greater role in situational awareness for ground vehicles. FLIR systems has been addressing the needs of the ground vehicle community by developing unique sensor systems combining thermal imaging and electro-optical sensors, advanced image processing, and networking capabilities into compact, cost effective packages. This paper will discuss one of those new products, the WideEye II. The WideEye II combines long wave infrared and electro-optical sensors in a 180 degree field of view, single integrated package to meet the critical needs of the warfighter. It includes seamless electronic stitching of the 180 degree image, and state of the art networking capability to allow it to be operated standalone or to be fully integrated with modern combat vehicle systems. The paper will discuss system tradeoffs and capabilities of this new product and show potential applications for its use.

  5. Stability of diclofenac sodium oral suspensions packaged in amber polyvinyl chloride bottles.

    Science.gov (United States)

    Donnelly, Ronald F; Pascuet, Elena; Ma, Carmen; Vaillancourt, Régis

    2010-01-01

    Prescribing of diclofenac for children usually involves a dose different from commercially available strengths. This drug is available only as tablets, which can be divided only so many times before the dose obtained becomes inaccurate. In addition, children may have difficulty swallowing tablets. For these reasons, a compounding formula for a liquid dosage form is essential to ensure effective delivery of the drug to pediatric patients. To develop a compounding formula for diclofenac sodium and to determine the extended physical and chemical stability of this compound when stored in amber polyvinyl chloride (PVC) prescription bottles under refrigeration and at room temperature. A suspension of diclofenac sodium (10 mg/mL) was prepared from commercially available diclofenac sodium tablets, with Ora-Blend as the suspending and flavouring agent. The suspension was packaged in 60-mL amber PVC prescription bottles and stored at either room temperature (23°C) or under refrigeration (5°C). Samples were collected on days 0, 7, 14, 21, 27, 56, and 93. Chemical stability was determined using a validated stability-indicating high-performance liquid chromatography method. At each sampling time, the suspensions were checked for changes in appearance (i.e., colour, layering, caking, ease of resuspension), odour, and pH. The diclofenac sodium suspensions were very stable, retaining at least 99.5% of the original concentration for up to 93 days, regardless of storage temperature. There were no apparent changes in the physical appearance of the suspensions, nor were there any substantial changes in odour or pH. Suspensions of diclofenac sodium (10 mg/mL) were quantitatively stable but difficult to prepare because of the enteric coating of the tablets. Therefore, it is recommended that diclofenac powder be used for the preparation of suspensions. For pediatric use, palatability is a consideration, and a masking agent should be added before administration. An expiry date of up to

  6. 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.

  7. Effects of pulsed electromagnetic field vibration on tooth movement induced by magnetic and mechanical forces: a preliminary study.

    Science.gov (United States)

    Darendeliler, M Ali; Zea, A; Shen, G; Zoellner, H

    2007-12-01

    This study was designed to determine whether or not high-frequency and low-magnitude vibration affects orthodontic tooth movement caused by magnetic or/and mechanical forces. Forty-four 7-week-old Wistar rats were randomly divided into four groups, with each group further divided into experimental and control subgroups. Neodymium-Iron-Boron (Nd-Fe-B) magnets and Sentalloy closed coil springs were placed between maxillary or mandibular first molars and incisors to activate tooth movement. The animals of experimental subgroups were exposed to the vibration induced by pulsed electromagnetic fields (PEMF) whilst the control subgroups were under normal atmosphere. The experiment lasted for 14 days and all of the animals were sacrificed for examination. The changes in the space between the molar and incisor were measured to indicate the amount of tooth movement. The coil springs, either with sham or active magnets, move molar much more than magnets alone, regardless of absence or presence of PEMF (p < 0.001). Under PEMF, the coil spring moved significantly more amount of tooth movement than that of coil-magnet combination (p < 0.01), as did the magnets compared to sham magnets (p < 0.019). Under a non-PEMF scenario, there was no significant difference in tooth movement between coil spring and coil-magnets combination, nor was there difference between magnets and sham magnets. It is suggested that the PEMF-induced vibration may enhance the effect of mechanical and magnetic forces on tooth movement.

  8. Force, torque, and absorbed energy for a body of arbitrary shape and constitution in an electromagnetic radiation field

    Science.gov (United States)

    Farsund, Ø.; Felderhof, B. U.

    1996-02-01

    The force and torque exerted on a body of arbitrary shape and constitution by a stationary radiation field are in principle given by integrals of Minkowski's stress tensor over a surface surrounding the body. Similarly the absorbed energy is given by an integral of the Poynting vector. These integrals are notoriously difficult to evaluate, and so far only spherical bodies have been considered. It is shown here that the integrals may be cast into a simpler form by use of Debye potentials. General expressions for the integrals are derived as sums of bilinear expressions in the coefficients of the expansion of the incident and scattered waves in terms of vector spherical waves. The expressions are simplified for small particles, such as atoms, for which the electric dipole approximation may be used. It is shown that the calculation is also relevant for bodies with nonlinear electromagnetic response.

  9. Vibrational Analysis of Brucite Surfaces and the Development of an Improved Force Field for Molecular Simulation of Interfaces.

    Science.gov (United States)

    Zeitler, Todd R; Greathouse, Jeffery A; Gale, Julian D; Cygan, Randall T

    2014-04-17

    We introduce a nonbonded three-body harmonic potential energy term for Mg-O-H interactions for improved edge surface stability in molecular simulations. The new potential term is compatible with the Clayff force field and is applied here to brucite, a layered magnesium hydroxide mineral. Comparisons of normal mode frequencies from classical and density functional theory calculations are used to verify a suitable spring constant ( k parameter) for the Mg-O-H bending motion. Vibrational analysis of hydroxyl librations at two brucite surfaces indicates that surface Mg-O-H modes are shifted to frequencies lower than the corresponding bulk modes. A comparison of DFT and classical normal modes validates this new potential term. The methodology for parameter development can be applied to other clay mineral components (e.g., Al, Si) to improve the modeling of edge surface stability, resulting in expanded applicability to clay mineral applications.

  10. Infrared and Raman spectra of bicyclic molecules using scaled noncorrelated and correlated {ital ab initio} force fields

    Energy Technology Data Exchange (ETDEWEB)

    Collier, W.B. [Department of Chemistry, Oral Roberts University, Tulsa, Oklahoma 74171 (United States); Magdo, I. [Gedeon Richter Ltd., Molecular Design Unit, P.O. Box 27, H-1475, Budapest (Hungary); Klots, T.D. [Bartlesville Thermodynamic Group, BDM Petroleum Technologies, P.O. Box 2543, Bartlesville, Oklahoma 74005 (United States)

    1999-03-01

    This paper reports the application of a scaled {ital ab initio} calculated harmonic force field to predict the frequencies, infrared intensities, Raman intensities, and depolarization ratios of benzofuran, benzothiophene, indole, benzothiazole, and benzoxazole. The theoretical calculations were made using the Hartree{endash}Fock HF/3-21G{sup {asterisk}} and HF/6-31G{sup {asterisk}} basis sets and density-functional theory (DFT)B3-LYP/6-31G{sup {asterisk}} levels. The equilibrium calculated force constants are scaled according to the method of Pulay and compared with the experimentally determined frequencies, intensities, and depolarization ratios to assess the accuracy and fit of the theoretical calculation. Methods for quantitative comparison of intensities were developed. The double numerical differentiation algorithm of Komornicki and McIver was analyzed and used to calculate the Raman intensities for the (DFT)B3-LYP/6-31G{sup {asterisk}} model. The (DFT)B3-LYP/6-31G{sup {asterisk}} model is approaching the harmonic limit in the planar and nonplanar refinement of these bicyclics with wave number fits of 5 and 4 cm{sup {minus}1}, respectively. It reduces the need for scale factors and increases their transfer accuracy, largely because the scale factors values cluster near unity. The Komornicki and McIver algorithm is still a viable method for calculating Raman intensity information for methods that do not have analytic routines programmed. The main shortcoming to this method may lie in the tighter self-consistent field (SCF) convergence criterion possibly needed to calculate Raman intensities for the totally symmetric modes of large molecules. The (DFT)B3-LYP/6-31G{sup {asterisk}} model was superior for calculating the planar intensities, but equal to the HF methods for predicting the nonplanar intensities. {copyright} {ital 1999 American Institute of Physics.}

  11. Modulation of the band structure in bilayer zigzag graphene nanoribbons on hexagonal boron nitride using the force and electric fields

    International Nuclear Information System (INIS)

    Ilyasov, V.V.; Nguyen, Chuong V.; Ershov, I.V.; Nguyen, Chien D.; Hieu, Nguyen N.

    2015-01-01

    Modulation of semiconductor–halfmetal–metal transition in the antiferromagnetic (AF) ordering of bilayer zigzag graphene nanoribbons (BZGNRs) on hexagonal boron nitride (h-BN) heterostructure using the external force field F ext and transverse electric fields E ext (in the presence of interaction with the substrate) was performed within the framework of the density functional theory (DFT). We established critical values of E ext and interlayer distance in the bilayer providing for semiconductor–halfmetal–metal transition in one of electron spin configurations. Our calculations also show that the energy gap E g in the AF-BZGNR/h-BN(0001) heterostructure can be controlled in a wide range of the F ext and E ext . This makes the AF-8-ZGNR/h-BN(0001) heterostructure being potentially promising for application in spintronic devices. - Highlights: • We used DFT to examine the opportunities for modulation of the band structure in AF-8-BZGNR/h-BN(0001). • We estimated the critical values of the F ext and E ext providing for SC-HM-M transition. • The energy gap in the AF-BZGNR/h-BN(0001) can be monitored in a wide range of the F ext and E ext

  12. [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.

  13. SpaGrOW—A Derivative-Free Optimization Scheme for Intermolecular Force Field Parameters Based on Sparse Grid Methods

    Directory of Open Access Journals (Sweden)

    Dirk Reith

    2013-09-01

    Full Text Available Molecular modeling is an important subdomain in the field of computational modeling, regarding both scientific and industrial applications. This is because computer simulations on a molecular level are a virtuous instrument to study the impact of microscopic on macroscopic phenomena. Accurate molecular models are indispensable for such simulations in order to predict physical target observables, like density, pressure, diffusion coefficients or energetic properties, quantitatively over a wide range of temperatures. Thereby, molecular interactions are described mathematically by force fields. The mathematical description includes parameters for both intramolecular and intermolecular interactions. While intramolecular force field parameters can be determined by quantum mechanics, the parameterization of the intermolecular part is often tedious. Recently, an empirical procedure, based on the minimization of a loss function between simulated and experimental physical properties, was published by the authors. Thereby, efficient gradient-based numerical optimization algorithms were used. However, empirical force field optimization is inhibited by the two following central issues appearing in molecular simulations: firstly, they are extremely time-consuming, even on modern and high-performance computer clusters, and secondly, simulation data is affected by statistical noise. The latter provokes the fact that an accurate computation of gradients or Hessians is nearly impossible close to a local or global minimum, mainly because the loss function is flat. Therefore, the question arises of whether to apply a derivative-free method approximating the loss function by an appropriate model function. In this paper, a new Sparse Grid-based Optimization Workflow (SpaGrOW is presented, which accomplishes this task robustly and, at the same time, keeps the number of time-consuming simulations relatively small. This is achieved by an efficient sampling procedure

  14. [Measurements of the flux densities of static magnetic fields generated by two types of dental magnetic attachments and their retentive forces].

    Science.gov (United States)

    Xu, Chun; Chao, Yong-lie; Du, Li; Yang, Ling

    2004-05-01

    To measure and analyze the flux densities of static magnetic fields generated by two types of commonly used dental magnetic attachments and their retentive forces, and to provide guidance for the clinical application of magnetic attachments. A digital Gaussmeter was used to measure the flux densities of static magnetic fields generated by two types of magnetic attachments, under four circumstances: open-field circuit; closed-field circuit; keeper and magnet slid laterally for a certain distance; and existence of air gap between keeper and magnet. The retentive forces of the magnetic attachments in standard closed-field circuit, with the keeper and magnet sliding laterally for a certain distance or with a certain air gap between keeper and magnet were measured by a tensile testing machine. There were flux leakages under both the open-field circuit and closed-field circuit of the two types of magnetic attachments. The flux densities on the surfaces of MAGNEDISC 800 (MD800) and MAGFIT EX600W (EX600) magnetic attachments under open-field circuit were 275.0 mT and 147.0 mT respectively. The flux leakages under closed-field circuit were smaller than those under open-field circuit. The respective flux densities on the surfaces of MD800 and EX600 magnetic attachments decreased to 11.4 mT and 4.5 mT under closed-field circuit. The flux density around the magnetic attachment decreased as the distance from the surface of the attachment increased. When keeper and magnet slid laterally for a certain distance or when air gap existed between keeper and magnet, the flux leakage increased in comparison with that under closed-field circuit. Under the standard closed-field circuit, the two types of magnetic attachments achieved the largest retentive forces. The retentive forces of MD800 and EX600 magnetic attachments under the standard closed-field circuit were 6.20 N and 4.80 N respectively. The retentive forces decreased with the sliding distance or with the increase of air gap

  15. 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.

  16. The riffle beetles (Coleoptera: Elmidae) of the Eocene Baltic amber: Heterelmis groehni sp. nov. and Heterlimnius samlandicus (Bollow, 1940) comb. nov.

    Science.gov (United States)

    Bukejs, Andris; Alekseev, Vitalii I; Jäch, Manfred A

    2015-07-20

    The Eocene elmid beetles known from Baltic amber so far are reviewed, and their natural environment is discussed. Palaeoriohelmis samlandica Bollow, 1940 is re-described based on examination of the holotype. The genus Palaeoriohelmis Bollow, 1940 is synonymized with Heterlimnius Hinton, 1935, and Palaeoriohelmis samlandica is transferred to Heterlimnius (H. samlandicus comb. nov.). Heterelmis groehni sp. nov. is described and illustrated. Elmadulescens rugosus Peris, Maier & Sánchez-García, 2015 from Cretaceous Spanish amber is removed from Elmidae.

  17. Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus

    Energy Technology Data Exchange (ETDEWEB)

    Dunlop, Jason A.; Apanaskevich, Dmitry A.; Lehmann, Jens; Hoffmann, René; Fusseis, Florian; Ehlke, Moritz; Zachow, Stefan; Xiao, Xianghui

    2016-10-10

    Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44–49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil’s referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner’s amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases.

  18. Static force fields simulations of reduced CeO2 (110) surface: Structure and adsorption of H2O molecule

    Science.gov (United States)

    Vives, Serge; Meunier, Cathy

    2018-02-01

    The CeO2(110) surface properties are largely involved in the catalysis, energy and biological phenomenon. The Static Force Fields simulations are able to describe large atomic systems surface even if no information on the electronic structure can be obtained. We employ those simulations to study the formation of the neutral 2 CeCe‧ VO•• cluster. We focus on seven different cluster configurations and find that the defect formation energy is the lower for the 1N-2N configurations. Two geometries are possible, as it is the case for the ab initio studies, the in plane and the more stable bridging one. We evidence the modifications of the surface energy and the Potential Energy Surface due to the presence of the 2 CeCe‧ VO•• defect. The physical adsorption of a water molecule is calculated and the geometry described for all the cluster configurations. The H2O molecule physisorption stabilizes the Ce(110) surface and the presence of the 2 CeCe‧ VO•• defect increases this effect.

  19. 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.

  20. Phase-field simulation on dendritic to semi-circular morphology transition induced by forced liquid flow

    Science.gov (United States)

    Du, Lifei; Zhang, Peng; Yang, Shaomei; Gao, Zhongtang; Chen, Jie; Du, Huiling

    2018-02-01

    A 2-D phase-field model coupling with convection is implemented to investigate the dendritic morphology evolution of the Ni-40.8%Cu alloy during solidification with forced liquid flow. Simulation results indicate that liquid flow can significantly affect the distributions of temperature and concentration near the liquid-solid interface, leading to asymmetric formation of the dendritic microstructure. Increasing the liquid flow will enhance the asymmetry of dendrite morphology with much more suppressed growth in the downstream and intensified morphology development in the upstream, leading to a dendritic to semi-circular morphology transition in the microstructure formation. Based on the simulations, it can be concluded that the morphology changes with increasing flow velocity in this study is attributed to the difference of the constitutional supercooling near the solid-liquid interfaces, which is the result of the asymmetric solute diffusion induced by the liquid flow. Therefore, controlling the liquid flow during the solidification might lead to the microstructure optimization to achieve materials with excellent properties.

  1. 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

  2. Simulation studies of structure and edge tension of lipid bilayer edges: effects of tail structure and force-field.

    Science.gov (United States)

    West, Ana; Ma, Kevin; Chung, Jonathan L; Kindt, James T

    2013-08-15

    Molecular dynamics simulations of lipid bilayer ribbons have been performed to investigate the structures and line tensions associated with free bilayer edges. Simulations carried out for dioleoyl phosphatidylcholine with three different force-field parameter sets yielded edge line tensions of 45 ± 2 pN, over 50% greater than the most recently reported experimentally determined value for this lipid. Edge tensions obtained from simulations of a series of phosphatidylcholine lipid bilayer ribbons with saturated acyl tails of length 12-16 carbons and with monounsaturated acyl tails of length 14-18 carbons could be correlated with the excess area associated with forming the edge, through a two-parameter fit. Saturated-tail lipids underwent local thickening near the edge, producing denser packing that correlated with lower line tensions, while unsaturated-tail lipids showed little or no local thickening. In a dipalmitoyl phosphatidylcholine ribbon initiated in a tilted gel-phase structure, lipid headgroups tended to tilt toward the nearer edge producing a herringbone pattern, an accommodation that may account for the reported edge-induced stabilization of an ordered structure at temperatures near a lipid gel-fluid phase transition.

  3. From lime to silica and alumina: systematic modeling of cement clinkers using a general force-field.

    Science.gov (United States)

    Freitas, A A; Santos, R L; Colaço, R; Bayão Horta, R; Canongia Lopes, J N

    2015-07-28

    Thirteen different cement-clinker crystalline phases present in the lime-silica-alumina system have been systematically modeled using a simple and general force field. This constitutes a new type of approach towards the study of lime-silica-alumina systems, where the simpler and more transferable Lennard-Jones potential was used instead of the more traditional Buckingham potential. The results were validated using experimental density and structural data. The elastic properties were also considered. Six amorphous phases (corresponding to calcium/silicon ratios corresponding to belite, rankinite, wollastonite and alumina-doped amorphous wollastonite with 5%, 10% and 15% alumina content) were also studied using molecular dynamics simulations. The obtained MD trajectories were used to characterize the different crystalline and amorphous phases in terms of the corresponding radial distribution functions, aggregate analyses and connectivity among silica groups. These studies allowed a direct comparison between the crystalline and amorphous phases and revealed how the structure of the silica network was modified in the amorphous materials or by the inclusion of other structural units such as alumina. The knowledge at an atomistic level of such modifications is paramount for the formulation of new cement-clinker phases.

  4. The infrared spectra and structure of acetylsalicylic acid (aspirin) and its oxyanion: an ab initio force field treatment

    Science.gov (United States)

    Binev, I. G.; Stamboliyska, B. A.; Binev, Y. I.

    1996-05-01

    The structures of acetylsalicylic acid (aspirin) (I) and its oxyanion (II) have been studied by means of infrared spectra and ab initio 3-21 G force field calculations. The 3100-1100 cm -1 region bands of both the aspirin molecule and its oxyanion have been assigned. The theoretical infrared data for the free aspirin anion are in good agreement with the experimental data for aspirin alkali-metal salts in dimethyl sulfoxide- d6. The theoretical geometrical parameters for the isolated aspirin molecule are close to the literature X-ray diffraction data for its dimer in the solid state, except for those of the carboxy group, which participates directly in hydrogen bond formation. The changes in both the spectral and geometrical parameters, caused by the conversion of the aspirin molecule into the anion, are essential, but they are localized mainly within the carboxy group and the adjacent C-Ph bond. This is also true for the changes in the corresponding bond indices and electronic charges.

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

    Science.gov (United States)

    Fortenberry, Ryan

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

  6. Atomic force and optical near-field microscopic investigations of polarization holographic gratings in a liquid crystalline azobenzene side-chain polyester

    DEFF Research Database (Denmark)

    Ramanujam, P.S.; Holme, N.C.R.; Hvilsted, S.

    1996-01-01

    Atomic force and scanning near-field optical microscopic investigations have been carried out on a polarization holographic grating recorded in an azobenzene side-chain Liquid crystalline polyester. It has been found that immediately following laser irradiation, a topographic surface grating......-field optical microscopic scanning of the grating reveals, however, that the bulk of the film remains optically anisotropic. (C) 1996 American Institute of Physics....

  7. Exact Green's function method of solar force-free magnetic-field computations with constant alpha. I - Theory and basic test cases

    Science.gov (United States)

    Chiu, Y. T.; Hilton, H. H.

    1977-01-01

    Exact closed-form solutions to the solar force-free magnetic-field boundary-value problem are obtained for constant alpha in Cartesian geometry by a Green's function approach. The uniqueness of the physical problem is discussed. Application of the exact results to practical solar magnetic-field calculations is free of series truncation errors and is at least as economical as the approximate methods currently in use. Results of some test cases are presented.

  8. Bridging the gap between chewing and sucking in the hemipteroid insects: new insights from Cretaceous amber.

    Science.gov (United States)

    Yoshizawa, Kazunori; Lienhard, Charles

    2016-02-11

    The diversity of feeding apparatuses in insects far exceeds that observed in any other animal group. Consequently, tracking mouthpart innovation in insects is one of the keys toward understanding their diversification. In hemipteroid insects (clade Paraneoptera or Acercaria: lice, thrips, aphids, cicadas, bugs, etc.), the transition from chewing to piercing-and-sucking mouthparts is widely regarded as the turning point that enabled hyperdiversification of the Hemiptera, the fifth largest insect order. However, the transitional process from chewing to piercing-and-sucking in the Paraneoptera was hitherto completely unknown. In this paper, we report a well preserved mid Cretaceous amber fossil of the paraneopteran insect family Archipsyllidae and describe it as Mydiognathus eviohlhoffae gen. et sp. n. This species has elongate mandibles and styliform laciniae similar to Hemiptera but retains functional chewing mouthparts. A number of morphological characters place the Archipsyllidae as the sister group of the thrips plus hemipterans, which strongly suggests that the mouthparts of M. eviohlhoffae represent a transitional condition from primitive chewing to derived piercing-and-sucking mouthparts. The clade composed of Archipsyllidae, thrips, and hemipterans is here named Pancondylognatha, a new supra-ordinal taxon. Based on newly obtained information, we also assess the monophyly of the Paraneoptera, which was called into question by recent phylogenomic analyses. A phylogenetic analysis that includes Mydiognathus strongly supports the monophyly of the Paraneoptera.

  9. Afro-Asian cockroach from Chiapas amber and the lost Tertiary American entomofauna

    Science.gov (United States)

    Vršanský, Peter; Cifuentes-Ruiz, Paulina; Vidlička, Ľubomír; Čiampor, Fedor; Vega, Francisco J.

    2011-10-01

    Cockroach genera with synanthropic species (Blattella, Ectobius, Supella, Periplaneta, Diploptera and ?Blatta), as well as other insects such as honeybees, although natively limited to certain continents nowadays, had circumtropic distribution in the past. The ease of their reintroduction into their former range suggests a post-Early Miocene environmental stress which led to the extinction of cosmopolitan Tertiary entomofauna in the Americas, whilst in Eurasia, Africa and Australia this fauna survived. This phenomenon is demonstrated here on a low diversity (10 spp.) living cockroach genus Supella, which is peculiar for the circumtropical synanthropic brownbanded cockroach S. longipalpa and also for its exclusively free-living cavicolous species restricted to Africa. S. (Nemosupella) miocenica sp. nov. from the Miocene amber of Chiapas in Mexico is a sister species to the living S. mirabilis from the Lower Guinea forests and adjacent savannas. The difference is restricted to the shape of the central macula on the pronotum, and size, which may indicate the around-Miocene origin of the living, extremely polymorphic Supella species and possibly also the isochronic invasion into the Americas. The species also has a number of characteristics of the Asian (and possibly also Australian) uniform genus Allacta (falling within the generic variability of Supella) suggesting Supella is a direct ancestor of the former. The present species is the first significant evidence for incomplete hiati between well defined cockroach genera — a result of the extensive fossil record of the group. The reported specimen is covered by a mycelium of a parasitic fungus Cordyceps or Entomophthora.

  10. Amber fossils demonstrate deep-time stability of Caribbean lizard communities.

    Science.gov (United States)

    Sherratt, Emma; del Rosario Castañeda, María; Garwood, Russell J; Mahler, D Luke; Sanger, Thomas J; Herrel, Anthony; de Queiroz, Kevin; Losos, Jonathan B

    2015-08-11

    Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils--only three have been described to date--has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15-20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.

  11. Seryl-tRNA Synthetases from Methanogenic Archaea: Suppression of Bacterial Amber Mutation and Heterologous Toxicity

    Directory of Open Access Journals (Sweden)

    Drasko Boko

    2010-01-01

    Full Text Available Methanogenic archaea possess unusual seryl-tRNA synthetases (SerRS, evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. Our recent X-ray structural analysis of Methanosarcina barkeri SerRS revealed an idiosyncratic N-terminal domain and catalytic zinc ion in the active site. To shed further light on substrate discrimination by methanogenic-type SerRS, we set up to explore in vivo the interaction of methanogenic-type SerRSs with their cognate tRNAs in Escherichia coli or Saccharomyces cerevisiae. The expression of various methanogenic-type SerRSs was toxic for E. coli, resulting in the synthesis of erroneous proteins, as revealed by β-galactosidase stability assay. Although SerRSs from methanogenic archaea recognize tRNAsSer from all three domains of life in vitro, the toxicity presumably precluded the complementation of endogenous SerRS function in both, E. coli and S. cerevisiae. However, despite the observed toxicity, coexpression of methanogenic-type SerRS with its cognate tRNA suppressed bacterial amber mutation.

  12. Numerical evaluation of guidance force decay of HTS bulk exposed to AC magnetic field over a NdFeB guideway

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-12-01

    The guidance force of the YBCO bulk over a NdFeB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In our previous work, we explained that the decay was due to the temperature rise of the HTS bulk caused by AC losses. In this paper, we adopted an analytic model to evaluate the decay of the critical current density of the bulk. And based on the analytic results and the Bean critical-state model, we calculated the guidance force as a function of times. Compared with the experimental results, the calculation results have almost the same trend and can qualitatively reveal the characteristics of guidance force of HTS bulk in this situation. Therefore, the guidance force decay of HTS bulk in the maglev vehicle system can be evaluated simply by this numerical method.

  13. Research on a novel axial-flux magnetic-field-modulated brushless double-rotor machine with low axial force and high efficiency

    Directory of Open Access Journals (Sweden)

    Chengde Tong

    2017-05-01

    Full Text Available The axial-flux magnetic-field-modulated brushless double-rotor machine (MFM-BDRM is a possible alternative as a power-split device for hybrid electric vehicles (HEVs. However, the existence of large axial force may lead to assembly problems and rich inner air-gap harmonics could result in high PM loss and low efficiency. This paper proposes a novel axial-flux MFM-BDRM with improved PM rotor structure. 2-D analytical method to predict the magnetic-field distribution of the proposed MFM-BDRM is developed and the design procedure of the proposed machine is illustrated. The impact of key geometrical parameters on axial force and torque is investigated. To evaluate the advantage of the proposed machine, a comparison is made with a conventional one with respect to electromagnetic performances. Results show that the proposed machine is effective in reducing PM eddy loss and axial force by 60% and 35%, respectively.

  14. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  15. Quantification of Force and Torque Applied by a High-Field Magnetic Resonance Imaging System on an Ultrasonic Motor for MRI-Guided Robot-Assisted Interventions

    Directory of Open Access Journals (Sweden)

    Peyman Shokrollahi

    2017-09-01

    Full Text Available The risk of accidental dislodgement of robot-operated surgical mechanisms can lead to morbidity or mortality. The force and torque applied by a 3.0-tesla scanner on an ultrasonic motor are not fully known. The force and torque may displace the motor, which is not fully magnetic resonance imaging (MRI-compatible but can be safely used in MR environments. A suspension apparatus was designed to measure the angles of deflection and rotation applied to the motor by MR magnetic fields. Three orientations and two power states of the motor were assessed inside the MR bore. The displacement force and torque were measured at eight locations with respect to the bore. The displacement force on the motor from 10 cm outside the magnet bore to 20 cm inside the bore ranged from 3 to 7 gF. The experimental measurements are in agreement with the theoretical values. Running the motor altered the force by 1 gF. The force does not significantly change when the MRI scanner is on. Considerable displacement force is applied to the motor, and no deflection torque is observed. Quantified values can be used to solve dynamic equations for robotic mechanisms intended for MRI-guided operations.

  16. Shear force distance control in a scanning near-field optical microscope: in resonance excitation of the fiber probe versus out of resonance excitation

    International Nuclear Information System (INIS)

    Lapshin, D.A.; Letokhov, V.S.; Shubeita, G.T.; Sekatskii, S.K.; Dietler, G.

    2004-01-01

    The experimental results of the direct measurement of the absolute value of interaction force between the fiber probe of a scanning near-field optical microscope (SNOM) operated in shear force mode and a sample, which were performed using combined SNOM-atomic force microscope setup, are discussed for the out-of-resonance fiber probe excitation mode. We demonstrate that the value of the tapping component of the total force for this mode at typical dither amplitudes is of the order of 10 nN and thus is quite comparable with the value of this force for in resonance fiber probe excitation mode. It is also shown that for all modes this force component is essentially smaller than the usually neglected static attraction force, which is of the order of 200 nN. The true contact nature of the tip-sample interaction during the out of resonance mode is proven. From this, we conclude that such a detection mode is very promising for operation in liquids, where other modes encounter great difficulties

  17. 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

    cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more...

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

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Chenyu; van Duin, Adri C.T.; Sorescu, Dan C.

    2012-06-01

    We have developed a ReaxFF reactive force field to describe hydrogen adsorption and dissociation on iron and iron carbide surfaces relevant for simulation of Fischer–Tropsch (FT) synthesis on iron catalysts. This force field enables large system (>>1000 atoms) simulations of hydrogen related reactions with iron. The ReaxFF force field parameters are trained against a substantial amount of structural and energetic data including the equations of state and heats of formation of iron and iron carbide related materials, as well as hydrogen interaction with iron surfaces and different phases of bulk iron. We have validated the accuracy and applicability of ReaxFF force field by carrying out molecular dynamics simulations of hydrogen adsorption, dissociation and recombination on iron and iron carbide surfaces. The barriers and reaction energies for molecular dissociation on these two types of surfaces have been compared and the effect of subsurface carbon on hydrogen interaction with iron surface is evaluated. We found that existence of carbon atoms at subsurface iron sites tends to increase the hydrogen dissociation energy barrier on the surface, and also makes the corresponding hydrogen dissociative state relatively more stable compared to that on bare iron. These properties of iron carbide will affect the dissociation rate of H{sub 2} and will retain more surface hydride species, thus influencing the dynamics of the FT synthesis process.

  19. The effect of electric field geometry on the performance of electromembrane extraction systems: Footprints of a third driving force along with migration and diffusion

    International Nuclear Information System (INIS)

    Moazami, Hamid Reza; Hosseiny Davarani, Saied Saeed; Mohammadi, Jamil; Nojavan, Saeed; Abrari, Masoud

    2015-01-01

    The distribution of electric field vectors was first calculated for electromembrane extraction (EME) systems in classical and cylindrical electrode geometries. The results showed that supported liquid membrane (SLM) has a general field amplifying effect due to its lower dielectric constant in comparison with aqueous donor/acceptor solutions. The calculated norms of the electric field vector showed that a DC voltage of 50 V can create huge electric field strengths up to 64 kV m −1 and 111 kV m −1 in classical and cylindrical geometries respectively. In both cases, the electric field strength reached its peak value on the inner wall of the SLM. In the case of classical geometry, the field strength was a function of the polar position of the SLM whereas the field strength in cylindrical geometry was angularly uniform. In order to investigate the effect of the electrode geometry on the performance of real EME systems, the analysis was carried out in three different geometries including classical, helical and cylindrical arrangements using naproxen and sodium diclofenac as the model analytes. Despite higher field strength and extended cross sectional area, the helical and cylindrical geometries gave lower recoveries with respect to the classical EME. The observed decline of the signal was proved to be against the relations governing migration and diffusion processes, which means that a third driving force is involved in EME. The third driving force is the interaction between the radially inhomogeneous electric field and the analyte in its neutral form. - Highlights: • Electric field vectors have been calculated in EME systems. • A new driving force has been proposed in EME systems. • EME can be theoretically applied to nonionic polarizable analytes.

  20. The effect of electric field geometry on the performance of electromembrane extraction systems: Footprints of a third driving force along with migration and diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Moazami, Hamid Reza [School of Physics and Accelerators, NSTRI, P. O. Box, 11365-8486, Tehran (Iran, Islamic Republic of); Hosseiny Davarani, Saied Saeed, E-mail: ss-hosseiny@sbu.ac.ir [Faculty of Chemistry, Shahid Beheshti University, G. C., 1983963113, Evin, Tehran (Iran, Islamic Republic of); Mohammadi, Jamil; Nojavan, Saeed [Faculty of Chemistry, Shahid Beheshti University, G. C., 1983963113, Evin, Tehran (Iran, Islamic Republic of); Abrari, Masoud [Laser and Plasma Research Institute, Shahid Beheshti University, G. C., 1983963113, Evin, Tehran (Iran, Islamic Republic of)

    2015-09-03

    The distribution of electric field vectors was first calculated for electromembrane extraction (EME) systems in classical and cylindrical electrode geometries. The results showed that supported liquid membrane (SLM) has a general field amplifying effect due to its lower dielectric constant in comparison with aqueous donor/acceptor solutions. The calculated norms of the electric field vector showed that a DC voltage of 50 V can create huge electric field strengths up to 64 kV m{sup −1} and 111 kV m{sup −1} in classical and cylindrical geometries respectively. In both cases, the electric field strength reached its peak value on the inner wall of the SLM. In the case of classical geometry, the field strength was a function of the polar position of the SLM whereas the field strength in cylindrical geometry was angularly uniform. In order to investigate the effect of the electrode geometry on the performance of real EME systems, the analysis was carried out in three different geometries including classical, helical and cylindrical arrangements using naproxen and sodium diclofenac as the model analytes. Despite higher field strength and extended cross sectional area, the helical and cylindrical geometries gave lower recoveries with respect to the classical EME. The observed decline of the signal was proved to be against the relations governing migration and diffusion processes, which means that a third driving force is involved in EME. The third driving force is the interaction between the radially inhomogeneous electric field and the analyte in its neutral form. - Highlights: • Electric field vectors have been calculated in EME systems. • A new driving force has been proposed in EME systems. • EME can be theoretically applied to nonionic polarizable analytes.