Monitoring of Qualifications and Employment in Austria: An Empirical Approach Based on the Labour Force Survey

ERIC Educational Resources Information Center

Lassnigg, Lorenz; Vogtenhuber, Stefan

2011-01-01

The empirical approach referred to in this article describes the relationship between education and training (ET) supply and employment in Austria; the use of the new ISCED (International Standard Classification of Education) fields of study variable makes this approach applicable abroad. The purpose is to explore a system that produces timely…

Perspectives on the simulation of protein–surface interactions using empirical force field methods

PubMed Central

Latour, Robert A.

2014-01-01

Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents.

PubMed

Borodin, Oleg; Smith, Grant D

2006-03-30

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.

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

NASA Astrophysics Data System (ADS)

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soules, T F; Gilmer, G H; Matthews, M J

2010-10-21

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

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

PubMed

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.

A theoretical method for the analysis and design of axisymmetric bodies. [flow distribution and incompressible fluids

NASA Technical Reports Server (NTRS)

Beatty, T. D.

1975-01-01

A theoretical method is presented for the computation of the flow field about an axisymmetric body operating in a viscous, incompressible fluid. A potential flow method was used to determine the inviscid flow field and to yield the boundary conditions for the boundary layer solutions. Boundary layer effects in the forces of displacement thickness and empirically modeled separation streamlines are accounted for in subsequent potential flow solutions. This procedure is repeated until the solutions converge. An empirical method was used to determine base drag allowing configuration drag to be computed.

Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

PubMed

Kundu, Sangeeta

2018-02-01

The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Driving reconnection in sheared magnetic configurations with forced fluctuations

NASA Astrophysics Data System (ADS)

Pongkitiwanichakul, Peera; Makwana, Kirit D.; Ruffolo, David

2018-02-01

We investigate reconnection of magnetic field lines in sheared magnetic field configurations due to fluctuations driven by random forcing by means of numerical simulations. The simulations are performed with an incompressible, pseudo-spectral magnetohydrodynamics code in 2D where we take thick, resistively decaying, current-sheet like sheared magnetic configurations which do not reconnect spontaneously. We describe and test the forcing that is introduced in the momentum equation to drive fluctuations. It is found that the forcing does not change the rate of decay; however, it adds and removes energy faster in the presence of the magnetic shear structure compared to when it has decayed away. We observe that such a forcing can induce magnetic reconnection due to field line wandering leading to the formation of magnetic islands and O-points. These reconnecting field lines spread out as the current sheet decays with time. A semi-empirical formula is derived which reasonably explains the formation and spread of O-points. We find that reconnection spreads faster with stronger forcing and longer correlation time of forcing, while the wavenumber of forcing does not have a significant effect. When the field line wandering becomes large enough, the neighboring current sheets with opposite polarity start interacting, and then the magnetic field is rapidly annihilated. This work is useful to understand how forced fluctuations can drive reconnection in large scale current structures in space and astrophysical plasmas that are not susceptible to reconnection.

Organic Crystal Engineering of Thermosetting Cyanate Ester Monomers: Influence of Structure on Melting Point

DTIC Science & Technology

2016-05-27

often discussed in the field of thermosetting materials, crystal engineering1-4 plays a key role in facilitating the successful utilization of these...not to alter the desirable properties of the polymerized networks. Fortunately, the field of crystal engineering provides examples where even very...Chickos and Acree.26 For molecular modeling, methods ranging from atomistic simulations with semi-empirical force fields to density functional

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Predictions of the physicochemical properties of amino acid side chain analogs using molecular simulation.

PubMed

Ahmed, Alauddin; Sandler, Stanley I

2016-03-07

A candidate drug compound is released for clinical trails (in vivo activity) only if its physicochemical properties meet desirable bioavailability and partitioning criteria. Amino acid side chain analogs play vital role in the functionalities of protein and peptides and as such are important in drug discovery. We demonstrate here that the predictions of solvation free energies in water, in 1-octanol, and self-solvation free energies computed using force field-based expanded ensemble molecular dynamics simulation provide good accuracy compared to existing empirical and semi-empirical methods. These solvation free energies are then, as shown here, used for the prediction of a wide range of physicochemical properties important in the assessment of bioavailability and partitioning of compounds. In particular, we consider here the vapor pressure, the solubility in both water and 1-octanol, and the air-water, air-octanol, and octanol-water partition coefficients of amino acid side chain analogs computed from the solvation free energies. The calculated solvation free energies using different force fields are compared against each other and with available experimental data. The protocol here can also be used for a newly designed drug and other molecules where force field parameters and charges are obtained from density functional theory.

Very empirical treatment of solvation and entropy: a force field derived from Log Po/w

NASA Astrophysics Data System (ADS)

Kellogg, Glen Eugene; Burnett, James C.; Abraham, Donald J.

2001-04-01

A non-covalent interaction force field model derived from the partition coefficient of 1-octanol/water solubility is described. This model, HINT for Hydropathic INTeractions, is shown to include, in very empirical and approximate terms, all components of biomolecular associations, including hydrogen bonding, Coulombic interactions, hydrophobic interactions, entropy and solvation/desolvation. Particular emphasis is placed on: (1) demonstrating the relationship between the total empirical HINT score and free energy of association, ΔG interaction; (2) showing that the HINT hydrophobic-polar interaction sub-score represents the energy cost of desolvation upon binding for interacting biomolecules; and (3) a new methodology for treating constrained water molecules as discrete independent small ligands. An example calculation is reported for dihydrofolate reductase (DHFR) bound with methotrexate (MTX). In that case the observed very tight binding, ΔG interaction≤-13.6 kcal mol-1, is largely due to ten hydrogen bonds between the ligand and enzyme with estimated strength ranging between -0.4 and -2.3 kcal mol-1. Four water molecules bridging between DHFR and MTX contribute an additional -1.7 kcal mol-1 stability to the complex. The HINT estimate of the cost of desolvation is +13.9 kcal mol-1.

GPS-Based Reduced Dynamic Orbit Determination Using Accelerometer Data

NASA Technical Reports Server (NTRS)

VanHelleputte, Tom; Visser, Pieter

2007-01-01

Currently two gravity field satellite missions, CHAMP and GRACE, are equipped with high sensitivity electrostatic accelerometers, measuring the non-conservative forces acting on the spacecraft in three orthogonal directions. During the gravity field recovery these measurements help to separate gravitational and non-gravitational contributions in the observed orbit perturbations. For precise orbit determination purposes all these missions have a dual-frequency GPS receiver on board. The reduced dynamic technique combines the dense and accurate GPS observations with physical models of the forces acting on the spacecraft, complemented by empirical accelerations, which are stochastic parameters adjusted in the orbit determination process. When the spacecraft carries an accelerometer, these measured accelerations can be used to replace the models of the non-conservative forces, such as air drag and solar radiation pressure. This approach is implemented in a batch least-squares estimator of the GPS High Precision Orbit Determination Software Tools (GHOST), developed at DLR/GSOC and DEOS. It is extensively tested with data of the CHAMP and GRACE satellites. As accelerometer observations typically can be affected by an unknown scale factor and bias in each measurement direction, they require calibration during processing. Therefore the estimated state vector is augmented with six parameters: a scale and bias factor for the three axes. In order to converge efficiently to a good solution, reasonable a priori values for the bias factor are necessary. These are calculated by combining the mean value of the accelerometer observations with the mean value of the non-conservative force models and empirical accelerations, estimated when using these models. When replacing the non-conservative force models with accelerometer observations and still estimating empirical accelerations, a good orbit precision is achieved. 100 days of GRACE B data processing results in a mean orbit fit of a few centimeters with respect to high-quality JPL reference orbits. This shows a slightly better consistency compared to the case when using force models. A purely dynamic orbit, without estimating empirical accelerations thus only adjusting six state parameters and the bias and scale factors, gives an orbit fit for the GRACE B test case below the decimeter level. The in orbit calibrated accelerometer observations can be used to validate the modelled accelerations and estimated empirical accelerations computed with the GHOST tools. In along track direction they show the best resemblance, with a mean correlation coefficient of 93% for the same period. In radial and normal direction the correlation is smaller. During days of high solar activity the benefit of using accelerometer observations is clearly visible. The observations during these days show fluctuations which the modelled and empirical accelerations can not follow.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

The ReaxFF reactive force-field: Development, applications, and future directions

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

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.

Machine Learning Force Field Parameters from Ab Initio Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ying; Li, Hui; Pickard, Frank C.

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 duringmore » 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.« less

Effect of microfibril twisting in theoretical powder diffraction studies of cellulose Iß

USDA-ARS?s Scientific Manuscript database

Previous studies of calculated diffraction patterns for cellulose crystallites have suggested that the distortions arising once models have been subjected to MD simulation are likely the result of dimensional changes induced by the empirical force field, but have been unable to determine to what ext...

Information driving force and its application in agent-based modeling

NASA Astrophysics Data System (ADS)

Chen, Ting-Ting; Zheng, Bo; Li, Yan; Jiang, Xiong-Fei

2018-04-01

Exploring the scientific impact of online big-data has attracted much attention of researchers from different fields in recent years. Complex financial systems are typical open systems profoundly influenced by the external information. Based on the large-scale data in the public media and stock markets, we first define an information driving force, and analyze how it affects the complex financial system. The information driving force is observed to be asymmetric in the bull and bear market states. As an application, we then propose an agent-based model driven by the information driving force. Especially, all the key parameters are determined from the empirical analysis rather than from statistical fitting of the simulation results. With our model, both the stationary properties and non-stationary dynamic behaviors are simulated. Considering the mean-field effect of the external information, we also propose a few-body model to simulate the financial market in the laboratory.

Prediction of destabilizing blade tip forces for shrouded and unshrouded turbines

NASA Technical Reports Server (NTRS)

Qiu, Y. J.; Martinezsanchez, M.

1985-01-01

The effect of a nonuniform flow field on the Alford force calculation is investigated. The ideas used here are based on those developed by Horlock and Greitzer. It is shown that the nonuniformity of the flow field does contribute to the Alford force calculation. An attempt is also made to include the effect of whirl speed. The values predicted by the model are compared with those obtained experimentally by Urlicks and Wohlrab. The possibility of using existing turbine tip loss correlations to predict beta is also exploited. The nonuniform flow field induced by the tip clearnance variation tends to increase the resultant destabilizing force over and above what would be predicted on the basis of the local variation of efficiency. On the one hand, the pressure force due to the nonuniform inlet and exit pressure also plays a part even for unshrouded blades, and this counteracts the flow field effects, so that the simple Alford prediction remains a reasonable approximation. Once the efficiency variation with clearance is known, the presented model gives a slightly overpredicted, but reasonably accurate destabilizing force. In the absence of efficiency vs. clearance data, an empirical tip loss coefficient can be used to give a reasonable prediction of destabilizing force. To a first approximation, the whirl does have a damping effect, but only of small magnitude, and thus it can be ignored for some purposes.

Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics

USDA-ARS?s Scientific Manuscript database

Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...

Adapting to the Pedagogy of Technology in Educational Administration

ERIC Educational Resources Information Center

Berry, James E.; Marx, Gary

2010-01-01

The field of educational administration is in a pedagogical transition. Though empirical evidence may be lacking about the efficacy of online teaching and learning, programs in educational administration are part of the greater movement to Internet delivery by virtue of market forces and advances in software and hardware tools for teaching in a…

The Educational Afterlife of Greater Britain, 1903-1914

ERIC Educational Resources Information Center

Gardner, Philip

2012-01-01

Following its late nineteenth-century emergence as an important element within federalist thinking across the British Empire, the idea of Greater Britain lost much of its political force in the years following the Boer War. The concept however continued to retain considerable residual currency in other fields of Imperial debate, including those…

Structural study of Na2O-B2O3-SiO2 glasses from molecular simulations using a polarizable force field.

PubMed

Pacaud, Fabien; Delaye, Jean-Marc; Charpentier, Thibault; Cormier, Laurent; Salanne, Mathieu

2017-10-28

Sodium borosilicate glasses Na 2 O-B 2 O 3 -SiO 2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO 4 and BO 4 (B IV ) and triangular BO 3 (B III ). One of the salient features of these compounds is the change of the B III /B IV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of B III /B IV with respect to the composition and the temperature.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

NASA Astrophysics Data System (ADS)

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/˜knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores.

PubMed

Law, Y K; Hassanali, A A

2018-03-14

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

NASA Astrophysics Data System (ADS)

Law, Y. K.; Hassanali, A. A.

2018-03-01

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface

PubMed Central

Choudhary, Kamal; Congo, Faical Yannick P.; Liang, Tao; Becker, Chandler; Hennig, Richard G.; Tavazza, Francesca

2017-01-01

Classical empirical potentials/force-fields (FF) provide atomistic insights into material phenomena through molecular dynamics and Monte Carlo simulations. Despite their wide applicability, a systematic evaluation of materials properties using such potentials and, especially, an easy-to-use user-interface for their comparison is still lacking. To address this deficiency, we computed energetics and elastic properties of variety of materials such as metals and ceramics using a wide range of empirical potentials and compared them to density functional theory (DFT) as well as to experimental data, where available. The database currently consists of 3248 entries including energetics and elastic property calculations, and it is still increasing. We also include computational tools for convex-hull plots for DFT and FF calculations. The data covers 1471 materials and 116 force-fields. In addition, both the complete database and the software coding used in the process have been released for public use online (presently at http://www.ctcms.nist.gov/∼knc6/periodic.html) in a user-friendly way designed to enable further material design and discovery. PMID:28140407

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

PubMed

Trnka, Tomáš; Tvaroška, Igor; Koča, Jaroslav

2018-01-09

Computational studies of the reaction mechanisms of various enzymes are nowadays based almost exclusively on hybrid QM/MM models. Unfortunately, the success of this approach strongly depends on the selection of the QM region, and computational cost is a crucial limiting factor. An interesting alternative is offered by empirical reactive molecular force fields, especially the ReaxFF potential developed by van Duin and co-workers. However, even though an initial parametrization of ReaxFF for biomolecules already exists, it does not provide the desired level of accuracy. We have conducted a thorough refitting of the ReaxFF force field to improve the description of reaction energetics. To minimize the human effort required, we propose a fully automated approach to generate an extensive training set comprised of thousands of different geometries and molecular fragments starting from a few model molecules. Electrostatic parameters were optimized with QM electrostatic potentials as the main target quantity, avoiding excessive dependence on the choice of reference atomic charges and improving robustness and transferability. The remaining force field parameters were optimized using the VD-CMA-ES variant of the CMA-ES optimization algorithm. This method is able to optimize hundreds of parameters simultaneously with unprecedented speed and reliability. The resulting force field was validated on a real enzymatic system, ppGalNAcT2 glycosyltransferase. The new force field offers excellent qualitative agreement with the reference QM/MM reaction energy profile, matches the relative energies of intermediate and product minima almost exactly, and reduces the overestimation of transition state energies by 27-48% compared with the previous parametrization.

Binding preference of carbon nanotube over proline-rich motif ligand on SH3-domain: a comparison with different force fields.

PubMed

Shi, Biyun; Zuo, Guanghong; Xiu, Peng; Zhou, Ruhong

2013-04-04

With the widespread applications of nanomaterials such as carbon nanotubes, there is a growing concern on the biosafety of these engineered nanoparticles, in particular their interactions with proteins. In molecular simulations of nanoparticle-protein interactions, the choice of empirical parameters (force fields) plays a decisive role, and thus is of great importance and should be examined carefully before wider applications. Here we compare three commonly used force fields, CHARMM, OPLSAA, and AMBER in study of the competitive binding of a single wall carbon nanotube (SWCNT) with a native proline-rich motif (PRM) ligand on its target protein SH3 domain, a ubiquitous protein-protein interaction mediator involved in signaling and regulatory pathways. We find that the SWCNT displays a general preference over the PRM in binding with SH3 domain in all the three force fields examined, although the degree of preference can be somewhat different, with the AMBER force field showing the highest preference. The SWCNT prevents the ligand from reaching its native binding pocket by (i) occupying the binding pocket directly, and (ii) binding with the ligand itself and then being trapped together onto some off-sites. The π-π stacking interactions between the SWCNT and aromatic residues are found to play a significant role in its binding to the SH3 domain in all the three force fields. Further analyses show that even the SWCNT-ligand binding can also be relatively more stable than the native ligand-protein binding, indicating a serious potential disruption to the protein SH3 function.

Anti-gravity with present technology - Implementation and theoretical foundation

NASA Astrophysics Data System (ADS)

Alzofon, F. E.

1981-07-01

This paper proposes a semi-empirical model of the processes leading to the gravitational field based on accepted features of subatomic processes. Through an analogy with methods of cryogenics, a method of decreasing (or increasing) the gravitational force on a vehicle, using presently-known technology, is suggested. Various ways of ultilizing this effect in vehicle propulsion are described. A unified field theory is then detailed which provides a more formal foundation for the gravitational field model first introduced. In distinction to the general theory of relativity, it features physical processes which generate the gravitational field.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

Sedimentation Coefficient, Frictional Coefficient, and Molecular Weight: A Preparative Ultracentrifuge Experiment for the Advanced Undergraduate Laboratory.

ERIC Educational Resources Information Center

Halsall, H. B.; Wermeling, J. R.

1982-01-01

Describes an experiment using a high-speed preparative centrifuge and calculator to demonstrate effects of the frictional coefficient of a macromolecule on its rate of transport in a force field and to estimate molecular weight of the macromolecule using an empirical relationship. Background information, procedures, and discussion of results are…

High Reynolds number turbulence model of rotating shear flows

NASA Astrophysics Data System (ADS)

Masuda, S.; Ariga, I.; Koyama, H. S.

1983-09-01

A Reynolds stress closure model for rotating turbulent shear flows is developed. Special attention is paid to keeping the model constants independent of rotation. First, general forms of the model of a Reynolds stress equation and a dissipation rate equation are derived, the only restrictions of which are high Reynolds number and incompressibility. The model equations are then applied to two-dimensional equilibrium boundary layers and the effects of Coriolis acceleration on turbulence structures are discussed. Comparisons with the experimental data and with previous results in other external force fields show that there exists a very close analogy between centrifugal, buoyancy and Coriolis force fields. Finally, the model is applied to predict the two-dimensional boundary layers on rotating plane walls. Comparisons with existing data confirmed its capability of predicting mean and turbulent quantities without employing any empirical relations in rotating fields.

Retrieving both phase and amplitude information of Green's functions by ambient seismic wave field cross-correlation: A case study with a limestone mine induced seismic event

NASA Astrophysics Data System (ADS)

Kwak, S.; Song, S. G.; Kim, G.; Shin, J. S.

2015-12-01

Recently many seismologists have paid attention to ambient seismic field, which is no more referred as noise and called as Earth's hum, but as useful signal to understand subsurface seismic velocity structure. It has also been demonstrated that empirical Green's functions can be constructed by retrieving both phase and amplitude information from ambient seismic field (Prieto and Beroza 2008). The constructed empirical Green's functions can be used to predict strong ground motions after focal depth and double-couple mechanism corrections (Denolle et al. 2013). They do not require detailed subsurface velocity model and intensive computation for ground motion simulation. In this study, we investigate the capability of predicting long period surface waves by the ambient seismic wave field with a seismic event of Mw 4.0, which occurred with a limestone mine collapse in South Korea on January 31, 2015. This limestone-mine event provides an excellent opportunity to test the efficiency of the ambient seismic wave field in retrieving both phase and amplitude information of Green's functions due to the single force mechanism of the collapse event. In other words, both focal depth and double-couple mechanism corrections are not required for this event. A broadband seismic station, which is about 5.4 km away from the mine event, is selected as a source station. Then surface waves retrieved from the ambient seismic wave field cross-correlation are compared with those generated by the event. Our preliminary results show some potential of the ambient seismic wave field in retrieving both phase and amplitude of Green's functions from a single force impulse source at the Earth's surface. More comprehensive analysis by increasing the time length of stacking may improve the results in further studies. We also aim to investigate the efficiency of retrieving the full empirical Green's functions with the 2007 Mw 4.6 Odaesan earthquake, which is one of the strongest earthquakes occurred in South Korea in the last decade.

Utilization of Women in Industrial Career Fields. Final Report for Period 14 March 1977-28 April 1978.

ERIC Educational Resources Information Center

Polit, Denise; And Others

To expand the use of women in nontraditional industrial careers, the U.S. Air Force examined the questions of recruiting, selecting, and training women for traditionally male blue collar work. An extensive review of the literature revealed that little empirical data on the effectiveness of various administrative policies had been collected. The…

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

PubMed

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 computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.

Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

PubMed Central

Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

2013-01-01

One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

Pillars of Power: Silver and Steel of the Ottoman Empire.

NASA Astrophysics Data System (ADS)

Nerantzis, N.

The Ottoman Empire was forged over disintegrating Byzantium, stretching across Anatolia and the Balkans and ruled for almost five centuries. One crucial parameter that allowed for its quick expansion has been a combination of economic wealth and superiority of armed forces. The Ottomans succeeded in both sectors by promoting innovative technology in the field of silver and steel production for supplying their monetary system and weapons industry. Rich mines and smelting workshops provided increased output in metals, allowing for quick expansion and economic growth. Some of the major centres for silver and steel production are being discussed in this paper in conjunction with analytical data from smelting residues.

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

PubMed Central

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

2013-01-01

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

New Method to Calculate the Time Variation of the Force Field Parameter

NASA Astrophysics Data System (ADS)

Santiago, A.; Lara, A.; Enríquez-Rivera, O.; Caballero-Lopez, R. A.

2018-03-01

Galactic cosmic rays (CRs) entering the heliosphere are affected by interplanetary magnetic fields and solar wind disturbances resulting in the modulation of the CR total flux observed in the inner heliosphere. The so-called force field model is often used to compute the galactic CR spectrum modulated by the solar activity due to the fact that it characterizes this process by only one parameter (the modulation potential, ϕ). In this work, we present two types of an empirical simplification (ES) method used to reconstruct the time variation of the modulation potential (Δϕ). Our ES offers a simple and fast alternative to compute the Δϕ at any desired time. The first ES type is based on the empirical fact that the dependence between Δϕ and neutron monitor (NM) count rates can be parameterized by a second-degree polynomial. The second ES type is based on the assumption that there is a inverse relation between Δϕ and NM count rates. We report the parameters found for the two types, which may be used to compute Δϕ for some NMs in a very fast and efficient way. In order to test the validity of the proposed ES, we compare our results with Δϕ obtained from literature. Finally, we apply our method to obtain the proton and helium spectra of primary CRs near the Earth at four randomly selected times.

Forest impact estimated with NOAA AVHRR and landsat TM data related to an empirical hurricane wind-field distribution

USGS Publications Warehouse

Ramsey, Elijah W.; Hodgson, M.E.; Sapkota, S.K.; Nelson, G.A.

2001-01-01

An empirical model was used to relate forest type and hurricane-impact distribution with wind speed and duration to explain the variation of hurricane damage among forest types along the Atchafalaya River basin of coastal Louisiana. Forest-type distribution was derived from Landsat Thematic Mapper image data, hurricane-impact distribution from a suite of transformed advanced very high resolution radiometer images, and wind speed and duration from a wind-field model. The empirical model explained 73%, 84%, and 87% of the impact variances for open, hardwood, and cypress-tupelo forests, respectively. These results showed that the estimated impact for each forest type was highly related to the duration and speed of extreme winds associated with Hurricane Andrew in 1992. The wind-field model projected that the highest wind speeds were in the southern basin, dominated by cypress-tupelo and open forests, while lower wind speeds were in the northern basin, dominated by hardwood forests. This evidence could explain why, on average, the impact to cypress-tupelos was more severe than to hardwoods, even though cypress-tupelos are less susceptible to wind damage. Further, examination of the relative importance of wind speed in explaining the impact severity to each forest type showed that the impact to hardwood forests was mainly related to tropical-depression to tropical-storm force wind speeds. Impacts to cypress-tupelo and open forests (a mixture of willows and cypress-tupelo) were broadly related to tropical-storm force wind speeds and by wind speeds near and somewhat in excess of hurricane force. Decoupling the importance of duration from speed in explaining the impact severity to the forests could not be fully realized. Most evidence, however, hinted that impact severity was positively related to higher durations at critical wind speeds. Wind-speed intervals, which were important in explaining the impact severity on hardwoods, showed that higher durations, but not the highest wind speeds, were concentrated in the northern basin, dominated by hardwoods. The extreme impacts associated with the cypress-tupelo forests in the southeast corner of the basin intersected the highest durations as well as the highest wind speeds. ?? 2001 Published by Elsevier Science Inc.

Understanding Friction Stir Welding

NASA Technical Reports Server (NTRS)

Nunes, A. C., Jr.

2018-01-01

This Technical Memorandum explains the friction stir welding process in terms of two basic concepts: the concentration of deformation in a shear surface enveloping the tool and the composition of the overall plastic flow field around the tool from simple flow field components. It is demonstrated how weld structure may be understood and torque, drag, and lateral tool forces may be estimated using these concepts. Some discrepancies between computations and accompanying empirical data are discussed in the text. This work is intended to be helpful to engineers in diagnosing problems and advancing technology.

Statistical parameters of thermally driven turbulent anabatic flow

NASA Astrophysics Data System (ADS)

Hilel, Roni; Liberzon, Dan

2016-11-01

Field measurements of thermally driven turbulent anabatic flow over a moderate slope are reported. A collocated hot-films-sonic anemometer (Combo) obtained the finer scales of the flow by implementing a Neural Networks based in-situ calibration technique. Eight days of continuous measurements of the wind and temperature fluctuations reviled a diurnal pattern of unstable stratification that forced development of highly turbulent unidirectional up slope flow. Empirical fits of important turbulence statistics were obtained from velocity fluctuations' time series alongside fully resolved spectra of velocity field components and characteristic length scales. TKE and TI showed linear dependence on Re, while velocity derivative skewness and dissipation rates indicated the anisotropic nature of the flow. Empirical fits of normalized velocity fluctuations power density spectra were derived as spectral shapes exhibited high level of similarity. Bursting phenomenon was detected at 15% of the total time. Frequency of occurrence, spectral characteristics and possible generation mechanism are discussed. BSF Grant #2014075.

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

PubMed

Shim, Jihyun; Mackerell, Alexander D

2011-05-01

A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more detailed presentation of issues and limitations associated with empirical energy functions and conformational sampling methods.

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

PubMed

Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

2012-11-01

One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

Application of the Semi-Empirical Force-Limiting Approach for the CoNNeCT SCAN Testbed

NASA Technical Reports Server (NTRS)

Staab, Lucas D.; McNelis, Mark E.; Akers, James C.; Suarez, Vicente J.; Jones, Trevor M.

2012-01-01

The semi-empirical force-limiting vibration method was developed and implemented for payload testing to limit the structural impedance mismatch (high force) that occurs during shaker vibration testing. The method has since been extended for use in analytical models. The Space Communications and Navigation Testbed (SCAN Testbed), known at NASA as, the Communications, Navigation, and Networking re-Configurable Testbed (CoNNeCT), project utilized force-limiting testing and analysis following the semi-empirical approach. This paper presents the steps in performing a force-limiting analysis and then compares the results to test data recovered during the CoNNeCT force-limiting random vibration qualification test that took place at NASA Glenn Research Center (GRC) in the Structural Dynamics Laboratory (SDL) December 19, 2010 to January 7, 2011. A compilation of lessons learned and considerations for future force-limiting tests is also included.

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

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

2013-08-07

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 biological ion channels through membranes.

Swimming in a granular frictional fluid

NASA Astrophysics Data System (ADS)

Goldman, Daniel

2012-02-01

X-ray imaging reveals that the sandfish lizard swims within granular media (sand) using axial body undulations to propel itself without the use of limbs. To model the locomotion of the sandfish, we previously developed an empirical resistive force theory (RFT), a numerical sandfish model coupled to an experimentally validated Discrete Element Method (DEM) model of the granular medium, and a physical robot model. The models reveal that only grains close to the swimmer are fluidized, and that the thrust and drag forces are dominated by frictional interactions among grains and the intruder. In this talk I will use these models to discuss principles of swimming within these granular ``frictional fluids". The empirical drag force laws are measured as the steady-state forces on a small cylinder oriented at different angles relative to the displacement direction. Unlike in Newtonian fluids, resistive forces are independent of speed. Drag forces resemble those in viscous fluids while the ratio of thrust to drag forces is always larger in the granular media than in viscous fluids. Using the force laws as inputs, the RFT overestimates swimming speed by approximately 20%. The simulation reveals that this is related to the non-instantaneous increase in force during reversals of body segments. Despite the inaccuracy of the steady-state assumption, we use the force laws and a recently developed geometric mechanics theory to predict optimal gaits for a model system that has been well-studied in Newtonian fluids, the three-link swimmer. The combination of the geometric theory and the force laws allows us to generate a kinematic relationship between the swimmer's shape and position velocities and to construct connection vector field and constraint curvature function visualizations of the system dynamics. From these we predict optimal gaits for forward, lateral and rotational motion. Experiment and simulation are in accord with the theoretical prediction, and demonstrate that swimming in sand can be viewed as movement in a localized frictional fluid.

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

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

PubMed

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

2014-09-16

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

High-Frequency Orographically Forced Variability in a Single-Layer Model of the Martian Atmosphere

NASA Technical Reports Server (NTRS)

Keppenne, C. L.; Ingersoll, A. P.

1993-01-01

A shallow water model with realistic topography and idealized zonal wind forcing is used toinvestigate orographically forced modes in the Martian atmosphere. Locally, the model reproduceswell the climatology at the sites of Viking Lander I and II (VL1 and VL2) as inferred from theViking Lander fall and spring observations. Its variability at those sites is dominated by a 3-sol(Martian solar day) oscillation in the region of VL1 and by a 6-sol oscillation in that of VL2. Theseoscillations are forced by the zonal asymmetries of the Martian mountain field. It is suggested thatthey contribute to the observed variability by reinforcing the baroclinic oscillations with nearbyperiods identified in observational studies. The spatial variability associated with the orographicallyforced oscillations is studied by means of extended empirical orthogonal function analysis. The 3-solVL1 oscillation corresponds to a tropical, eastward-traveling, zonal-wavenumber one pattern...

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Perspectives on empirical approaches for ocean color remote sensing of chlorophyll in a changing climate.

PubMed

Dierssen, Heidi M

2010-10-05

Phytoplankton biomass and productivity have been continuously monitored from ocean color satellites for over a decade. Yet, the most widely used empirical approach for estimating chlorophyll a (Chl) from satellites can be in error by a factor of 5 or more. Such variability is due to differences in absorption and backscattering properties of phytoplankton and related concentrations of colored-dissolved organic matter (CDOM) and minerals. The empirical algorithms have built-in assumptions that follow the basic precept of biological oceanography--namely, oligotrophic regions with low phytoplankton biomass are populated with small phytoplankton, whereas more productive regions contain larger bloom-forming phytoplankton. With a changing world ocean, phytoplankton composition may shift in response to altered environmental forcing, and CDOM and mineral concentrations may become uncoupled from phytoplankton stocks, creating further uncertainty and error in the empirical approaches. Hence, caution is warranted when using empirically derived Chl to infer climate-related changes in ocean biology. The Southern Ocean is already experiencing climatic shifts and shows substantial errors in satellite-derived Chl for different phytoplankton assemblages. Accurate global assessments of phytoplankton will require improved technology and modeling, enhanced field observations, and ongoing validation of our "eyes in space."

The Costs of the Soviet Empire.

DTIC Science & Technology

1983-09-01

Soviet Union is a multi -national state consisting of 15 distinct national repub- lics and over 60 nationalities, 23 of which have populations greater...think of the annual costs of attaining and maintaining an empire as following an oscillating pattern like a somewhat uneven sine -curve. First, costs...and time-on-station of Soviet naval and other forces. In this sense, the empire acts to multi - ply the effectiveness of Soviet forces. Alternatively

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides

PubMed Central

Jana, Madhurima; MacKerell, Alexander D.

2015-01-01

An empirical all-atom CHARMM polarizable force filed for aldopentofuranoses and methyl-aldopentofuranosides based on the classical Drude oscillator is presented. A single electrostatic model is developed for eight different diastereoisomers of aldopentofuranoses by optimizing the existing electrostatic and bonded parameters as transferred from ethers, alcohols and hexopyranoses to reproduce quantum mechanical (QM) dipole moments, furanose-water interaction energies and conformational energies. Optimization of selected electrostatic and dihedral parameters was performed to generate a model for methyl-aldopentofuranosides. Accuracy of the model was tested by reproducing experimental data for crystal intramolecular geometries and lattice unit cell parameters, aqueous phase densities, and ring pucker and exocyclic rotamer populations as obtained from NMR experiments. In most cases the model is found to reproduce both QM data and experimental observables in an excellent manner, while for the remainder the level of agreement is in the satisfactory regimen. In aqueous phase simulations the monosaccharides have significantly enhanced dipoles as compared to the gas phase. The final model from this study is transferrable for future studies on carbohydrates and can be used with the existing CHARMM Drude polarizable force field for biomolecules. PMID:26018564

Mixing and unmixedness in plasma jets 1: Near-field analysis

NASA Technical Reports Server (NTRS)

Ilegbusi, Olusegun J.

1993-01-01

The flow characteristics in the near-field of a plasma jet are simulated with a two-fluid model. This model accounts for both gradient-diffusion mixing and uni-directional sifting motion resulting from pressure-gradient-body-force imbalance. This latter mechanism is believed to be responsible for the umixedness observed in plasma jets. The unmixedness is considered to be essentially a Rayleigh-Taylor kind instability. Transport equations are solved for the individual plasma and ambient gas velocities, temperatures and volume fractions. Empirical relations are employed for the interface transfers of mass, momentum and heat. The empirical coefficients are first established by comparison of predictions with available experimental data for shear flows. The model is then applied to an Argon plasma jet ejecting into stagnant air. The predicted results show the significant build-up of unmixed air within the plasma gas, even relatively far downstream of the torch. By adjusting the inlet condition, the model adequately reproduces the experimental data.

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

DTIC Science & Technology

1984-06-01

however, lack of temperature control results in generally poor quality. Cooking eggs to order is difficult, if not impossible; browning meats is...from or Short Order Menu Two Juices Two Entrees -Hot and Cold Cereal Two Potatoes or Substitutes Eggs to Order Two Vegetables *One Breakfast Meat Three...designed to meet the requirement. 6. The menu to be served must be considered. A complete breakfast with eggs to order including omelets requires specific

Alternative to particle dark matter

NASA Astrophysics Data System (ADS)

Khoury, Justin

2015-01-01

We propose an alternative to particle dark matter that borrows ingredients of modified Newtonian dynamics (MOND) while adding new key components. The first new feature is a dark matter fluid, in the form of a scalar field with small equation of state and sound speed. This component is critical in reproducing the success of cold dark matter for the expansion history and the growth of linear perturbations, but does not cluster significantly on nonlinear scales. Instead, the missing mass problem on nonlinear scales is addressed by a modification of the gravitational force law. The force law approximates MOND at large and intermediate accelerations, and therefore reproduces the empirical success of MOND at fitting galactic rotation curves. At ultralow accelerations, the force law reverts to an inverse-square law, albeit with a larger Newton's constant. This latter regime is important in galaxy clusters and is consistent with their observed isothermal profiles, provided the characteristic acceleration scale of MOND is mildly varying with scale or mass, such that it is 12 times higher in clusters than in galaxies. We present an explicit relativistic theory in terms of two scalar fields. The first scalar field is governed by a Dirac-Born-Infeld action and behaves as a dark matter fluid on large scales. The second scalar field also has single-derivative interactions and mediates a fifth force that modifies gravity on nonlinear scales. Both scalars are coupled to matter via an effective metric that depends locally on the fields. The form of this effective metric implies the equality of the two scalar gravitational potentials, which ensures that lensing and dynamical mass estimates agree. Further work is needed in order to make both the acceleration scale of MOND and the fraction at which gravity reverts to an inverse-square law explicitly dynamical quantities, varying with scale or mass.

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

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

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

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

PubMed

Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

2011-01-01

To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

A Time-dependent Heliospheric Model Driven by Empirical Boundary Conditions

NASA Astrophysics Data System (ADS)

Kim, T. K.; Arge, C. N.; Pogorelov, N. V.

2017-12-01

Consisting of charged particles originating from the Sun, the solar wind carries the Sun's energy and magnetic field outward through interplanetary space. The solar wind is the predominant source of space weather events, and modeling the solar wind propagation to Earth is a critical component of space weather research. Solar wind models are typically separated into coronal and heliospheric parts to account for the different physical processes and scales characterizing each region. Coronal models are often coupled with heliospheric models to propagate the solar wind out to Earth's orbit and beyond. The Wang-Sheeley-Arge (WSA) model is a semi-empirical coronal model consisting of a potential field source surface model and a current sheet model that takes synoptic magnetograms as input to estimate the magnetic field and solar wind speed at any distance above the coronal region. The current version of the WSA model takes the Air Force Data Assimilative Photospheric Flux Transport (ADAPT) model as input to provide improved time-varying solutions for the ambient solar wind structure. When heliospheric MHD models are coupled with the WSA model, density and temperature at the inner boundary are treated as free parameters that are tuned to optimal values. For example, the WSA-ENLIL model prescribes density and temperature assuming momentum flux and thermal pressure balance across the inner boundary of the ENLIL heliospheric MHD model. We consider an alternative approach of prescribing density and temperature using empirical correlations derived from Ulysses and OMNI data. We use our own modeling software (Multi-scale Fluid-kinetic Simulation Suite) to drive a heliospheric MHD model with ADAPT-WSA input. The modeling results using the two different approaches of density and temperature prescription suggest that the use of empirical correlations may be a more straightforward, consistent method.

Investigation of the relationship between hurricane waves and extreme runup

NASA Astrophysics Data System (ADS)

Thompson, D. M.; Stockdon, H. F.

2006-12-01

In addition to storm surge, the elevation of wave-induced runup plays a significant role in forcing geomorphic change during extreme storms. Empirical formulations for extreme runup, defined as the 2% exceedence level, are dependent on some measure of significant offshore wave height. Accurate prediction of extreme runup, particularly during hurricanes when wave heights are large, depends on selecting the most appropriate measure of wave height that provides energy to the nearshore system. Using measurements from deep-water wave buoys results in an overprediction of runup elevation. Under storm forcing these large waves dissipate across the shelf through friction, whitecapping and depth-limited breaking before reaching the beach and forcing swash processes. The use of a local, shallow water wave height has been shown to provide a more accurate estimate of extreme runup elevation (Stockdon, et. al. 2006); however, a specific definition of this local wave height has yet to be defined. Using observations of nearshore waves from the U.S. Army Corps of Engineers' Field Research Facility (FRF) in Duck, NC during Hurricane Isabel, the most relevant measure of wave height for use in empirical runup parameterizations was examined. Spatial and temporal variability of the hurricane wave field, which made landfall on September 18, 2003, were modeled using SWAN. Comparisons with wave data from FRF gages and deep-water buoys operated by NOAA's National Data Buoy Center were used for model calibration. Various measures of local wave height (breaking, dissipation-based, etc.) were extracted from the model domain and used as input to the runup parameterizations. Video based observations of runup collected at the FRF during the storm were used to ground truth modeled values. Assessment of the most appropriate measure of wave height can be extended over a large area through comparisons to observations of storm- induced geomorphic change.

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

NASA Astrophysics Data System (ADS)

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 energy surface. QFFs can regularly predict the fundamental vibrational frequencies to within 5 cm-1 of experimentally measured values. This level of accuracy represents a reduction in discrepancies by an order of magnitude compared with harmonic frequencies calculated with density functional theory (DFT). The major limitation of the QFF strategy is that the level of electronic-structure theory required to develop a predictive force field is prohibitively time consuming for molecular systems larger than 5 atoms. Recent advances in QFF techniques utilizing informed DFT approaches have pushed the size of the systems studied up to 24 heavy atoms, but relevant PAHs can have up to hundreds of atoms. We have developed alternative electronic-structure methods that maintain the accuracy of the coupled-cluster calculations extrapolated to the complete basis set limit with relativistic and core correlation corrections applied: the CcCR QFF. These alternative methods are based on simplifications of Hartree—Fock theory in which the computationally intensive two-electron integrals are approximated using empirical parameters. These methods reduce computational time to orders of magnitude less than the CcCR calculations. We have derived a set of optimized empirical parameters to minimize the difference molecular ions of astrochemical significance. We have shown that it is possible to derive a set of empirical parameters that will produce RMS energy differences of less than 2 cm- 1 for our test systems. We are proposing to adopt this reparameterization strategy and some of the lessons learned from the informed DFT studies to create a semi-empirical method whose tremendous speed will allow us to study the rovibrational structure of large PAHs with up to 100s of carbon atoms.

Empirical potential for molecular simulation of graphene nanoplatelets

NASA Astrophysics Data System (ADS)

Bourque, Alexander J.; Rutledge, Gregory C.

2018-04-01

A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

The application of the electrodynamic separator in minerals beneficiation

NASA Astrophysics Data System (ADS)

Skowron, M.; Syrek, P.; Surowiak, A.

2017-05-01

The aim of presented paper is elaboration of methodology of upgrading natural minerals in example of chalcocite and bornite sample. The results were obtained by means of laboratory drum separator. This device operates in accordance to properties of materials, which in this case was electrical conductivity. The study contains the analysis of the forces occurring inside of electrodynamic separator chamber, that act on the particles of various electrical properties. Both, the potential and electric field strength distributions were calculated, with set of separators setpoints. Theoretical analysis influenced on separator parameters, and hence impacted the empirical results too. Next, the authors conducted empirical research on chalcocite and bornite beneficiation by means of electrodynamic separation. The results of this process were shown graphically in form of upgrading curves of chalcocite considering elementary copper and lead.

Was Newton right? A search for non-Newtonian behavior of weak-field gravity

NASA Astrophysics Data System (ADS)

Boynton, Paul; Moore, Michael; Newman, Riley; Berg, Eric; Bonicalzi, Ricco; McKenney, Keven

2014-06-01

Empirical tests of Einstein's metric theory of gravitation, even in the non-relativistic, weak-field limit, could play an important role in judging theory-driven extensions of the current Standard Model of fundamental interactions. Guided by Galileo's work and his own experiments, Newton formulated a theory of gravity in which the force of attraction between two bodies is independent of composition and proportional to the inertia of each, thereby transparently satisfying Galileo's empirically informed conjecture regarding the Universality of Free Fall. Similarly, Einstein honored the manifest success of Newton's theory by assuring that the linearized equations of GTR matched the Newtonian formalism under "classical" conditions. Each of these steps, however, was explicitly an approximation raised to the status of principle. Perhaps, at some level, Newtonian gravity does not accurately describe the physical interaction between uncharged, unmagnetized, macroscopic bits of ordinary matter. What if Newton were wrong? Detecting any significant deviation from Newtonian behavior, no matter how small, could provide new insights and possibly reveal new physics. In the context of physics as an empirical science, for us this yet unanswered question constitutes sufficient motivation to attempt precision measurements of the kind described here. In this paper we report the current status of a project to search for violation of the Newtonian inverse square law of gravity.

Cholesterol orientation and tilt modulus in DMPC bilayers

PubMed Central

Khelashvili, George; Pabst, Georg; Harries, Daniel

2010-01-01

We performed molecular dynamics (MD) simulations of hydrated bilayers containing mixtures of dimyristoylphosphatidylcholine (DMPC) and Cholesterol at various ratios, to study the effect of cholesterol concentration on its orientation, and to characterize the link between cholesterol tilt and overall phospholipid membrane organization. The simulations show a substantial probability for cholesterol molecules to transiently orient perpendicular to the bilayer normal, and suggest that cholesterol tilt may be an important factor for inducing membrane ordering. In particular, we find that as cholesterol concentration increases (1%–40% cholesterol) the average cholesterol orientation changes in a manner strongly (anti)correlated with the variation in membrane thickness. Furthermore, cholesterol orientation is found to be determined by the aligning force exerted by other cholesterol molecules. To quantify this aligning field, we analyzed cholesterol orientation using, to our knowledge, the first estimates of the cholesterol tilt modulus χ from MD simulations. Our calculations suggest that the aligning field that determines χ is indeed strongly linked to sterol composition. This empirical parameter (χ) should therefore become a useful quantitative measure to describe cholesterol interaction with other lipids in bilayers, particularly in various coarse-grained force fields. PMID:20518573

Friction and Wear on the Atomic Scale

NASA Astrophysics Data System (ADS)

Gnecco, Enrico; Bennewitz, Roland; Pfeiffer, Oliver; Socoliuc, Anisoara; Meyer, Ernst

Friction has long been the subject of research: the empirical da Vinci-Amontons friction laws have been common knowledge for centuries. Macroscopic experiments performed by the school of Bowden and Tabor revealed that macroscopic friction can be related to the collective action of small asperities. Over the last 15 years, experiments performed with the atomic force microscope have provided new insights into the physics of single asperities sliding over surfaces. This development, together with the results from complementary experiments using surface force apparatus and the quartz microbalance, have led to the new field of nanotribology. At the same time, increasing computing power has permitted the simulation of processes that occur during sliding contact involving several hundreds of atoms. It has become clear that atomic processes cannot be neglected when interpreting nanotribology experiments. Even on well-defined surfaces, experiments have revealed that atomic structure is directly linked to friction force. This chapter will describe friction force microscopy experiments that reveal, more or less directly, atomic processes during sliding contact.

Non-invasive measurement of instantaneous forces during aquatic locomotion: a case study of the bluegill sunfish pectoral fin.

PubMed

Peng, Jifeng; Dabiri, John O; Madden, Peter G; Lauder, George V

2007-02-01

Swimming and flying animals generate unsteady locomotive forces by delivering net momentum into the fluid wake. Hence, swimming and flying forces can be quantified by measuring the momentum of animal wakes. A recently developed model provides an approach to empirically deduce swimming and flying forces based on the measurement of velocity and vortex added-mass in the animal wake. The model is contingent on the identification of the vortex boundary in the wake. This paper demonstrates the application of that method to a case study quantifying the instantaneous locomotive forces generated by the pectoral fins of the bluegill sunfish (Lepomis macrochirus Rafinesque), measured using digital particle image velocimetry (DPIV). The finite-time Lyapunov exponent (FTLE) field calculated from the DPIV data was used to determine the wake vortex boundary, according to recently developed fluid dynamics theory. Momentum of the vortex wake and its added-mass were determined and the corresponding instantaneous locomotive forces were quantified at discrete time points during the fin stroke. The instantaneous forces estimated in this study agree in magnitude with the time-averaged forces quantified for the pectoral fin of the same species swimming in similar conditions and are consistent with the observed global motion of the animals. A key result of this study is its suggestion that the dynamical effect of the vortex wake on locomotion is to replace the real animal fin with an ;effective appendage', whose geometry is dictated by the FTLE field and whose interaction with the surrounding fluid is wholly dictated by inviscid concepts from potential flow theory. Benefits and limitations of this new framework for non-invasive instantaneous force measurement are discussed, and its application to comparative biomechanics and engineering studies is suggested.

Comparing the model-simulated global warming signal to observations using empirical estimates of unforced noise.

PubMed

Brown, Patrick T; Li, Wenhong; Cordero, Eugene C; Mauget, Steven A

2015-04-21

The comparison of observed global mean surface air temperature (GMT) change to the mean change simulated by climate models has received much public and scientific attention. For a given global warming signal produced by a climate model ensemble, there exists an envelope of GMT values representing the range of possible unforced states of the climate system (the Envelope of Unforced Noise; EUN). Typically, the EUN is derived from climate models themselves, but climate models might not accurately simulate the correct characteristics of unforced GMT variability. Here, we simulate a new, empirical, EUN that is based on instrumental and reconstructed surface temperature records. We compare the forced GMT signal produced by climate models to observations while noting the range of GMT values provided by the empirical EUN. We find that the empirical EUN is wide enough so that the interdecadal variability in the rate of global warming over the 20(th) century does not necessarily require corresponding variability in the rate-of-increase of the forced signal. The empirical EUN also indicates that the reduced GMT warming over the past decade or so is still consistent with a middle emission scenario's forced signal, but is likely inconsistent with the steepest emission scenario's forced signal.

Comparing the model-simulated global warming signal to observations using empirical estimates of unforced noise

PubMed Central

Brown, Patrick T.; Li, Wenhong; Cordero, Eugene C.; Mauget, Steven A.

2015-01-01

The comparison of observed global mean surface air temperature (GMT) change to the mean change simulated by climate models has received much public and scientific attention. For a given global warming signal produced by a climate model ensemble, there exists an envelope of GMT values representing the range of possible unforced states of the climate system (the Envelope of Unforced Noise; EUN). Typically, the EUN is derived from climate models themselves, but climate models might not accurately simulate the correct characteristics of unforced GMT variability. Here, we simulate a new, empirical, EUN that is based on instrumental and reconstructed surface temperature records. We compare the forced GMT signal produced by climate models to observations while noting the range of GMT values provided by the empirical EUN. We find that the empirical EUN is wide enough so that the interdecadal variability in the rate of global warming over the 20th century does not necessarily require corresponding variability in the rate-of-increase of the forced signal. The empirical EUN also indicates that the reduced GMT warming over the past decade or so is still consistent with a middle emission scenario's forced signal, but is likely inconsistent with the steepest emission scenario's forced signal. PMID:25898351

Single-particle potential of the Λ hyperon in nuclear matter with chiral effective field theory NLO interactions including effects of Y N N three-baryon interactions

NASA Astrophysics Data System (ADS)

Kohno, M.

2018-03-01

Adopting hyperon-nucleon and hyperon-nucleon-nucleon interactions parametrized in chiral effective field theory, single-particle potentials of the Λ and Σ hyperons are evaluated in symmetric nuclear matter and in pure neutron matter within the framework of lowest-order Bruckner theory. The chiral NLO interaction bears strong Λ N -Σ N coupling. Although the Λ potential is repulsive if the coupling is switched off, the Λ N -Σ N correlation brings about the attraction consistent with empirical data. The Σ potential is repulsive, which is also consistent with empirical information. The interesting result is that the Λ potential becomes shallower beyond normal density. This provides the possibility of solving the hyperon puzzle without introducing ad hoc assumptions. The effects of the Λ N N -Λ N N and Λ N N -Σ N N three-baryon forces are considered. These three-baryon forces are first reduced to normal-ordered effective two-baryon interactions in nuclear matter and then incorporated in the G -matrix equation. The repulsion from the Λ N N -Λ N N interaction is of the order of 5 MeV at normal density and becomes larger with increasing density. The effects of the Λ N N -Σ N N coupling compensate the repulsion at normal density. The net effect of the three-baryon interactions on the Λ single-particle potential is repulsive at higher densities.

The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison.

PubMed

Verstraelen, Toon; Van Speybroeck, Veronique; Waroquier, Michel

2009-07-28

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500,000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

Force Limited Random Vibration Test of TESS Camera Mass Model

NASA Technical Reports Server (NTRS)

Karlicek, Alexandra; Hwang, James Ho-Jin; Rey, Justin J.

2015-01-01

The Transiting Exoplanet Survey Satellite (TESS) is a spaceborne instrument consisting of four wide field-of-view-CCD cameras dedicated to the discovery of exoplanets around the brightest stars. As part of the environmental testing campaign, force limiting was used to simulate a realistic random vibration launch environment. While the force limit vibration test method is a standard approach used at multiple institutions including Jet Propulsion Laboratory (JPL), NASA Goddard Space Flight Center (GSFC), European Space Research and Technology Center (ESTEC), and Japan Aerospace Exploration Agency (JAXA), it is still difficult to find an actual implementation process in the literature. This paper describes the step-by-step process on how the force limit method was developed and applied on the TESS camera mass model. The process description includes the design of special fixtures to mount the test article for properly installing force transducers, development of the force spectral density using the semi-empirical method, estimation of the fuzzy factor (C2) based on the mass ratio between the supporting structure and the test article, subsequent validating of the C2 factor during the vibration test, and calculation of the C.G. accelerations using the Root Mean Square (RMS) reaction force in the spectral domain and the peak reaction force in the time domain.

[Productivity and academic assessment in the Brazilian public health field: challenges for Human and Social Sciences research].

PubMed

Bosi, Maria Lúcia Magalhães

2012-12-01

This article analyzes some challenges for knowledge output in the human and social sciences in the public health field, under the current academic assessment model in Brazil. The article focuses on the qualitative research approach in human and social sciences, analyzing its status in comparison to the other traditions vying for hegemony in the public health field, conjugating the dialogue with the literature, especially the propositions pertaining to the social fields present in the work of Pierre Bourdieu, with elements concerning the field's dynamics, including some empirical data. Challenges identified in the article include hurdles to interdisciplinary dialogue and equity in the production of knowledge, based on recognition of the founding place of human and social sciences in the public health field. The article discusses strategies to reshape the current correlation of forces among centers of knowledge in public health, especially those capable of impacting the committees and agendas that define the accumulation of symbolic and economic capital in the field.

An Empirical Non-TNT Approach to Launch Vehicle Explosion Modeling

NASA Technical Reports Server (NTRS)

Blackwood, James M.; Skinner, Troy; Richardson, Erin H.; Bangham, Michal E.

2015-01-01

In an effort to increase crew survivability from catastrophic explosions of Launch Vehicles (LV), a study was conducted to determine the best method for predicting LV explosion environments in the near field. After reviewing such methods as TNT equivalence, Vapor Cloud Explosion (VCE) theory, and Computational Fluid Dynamics (CFD), it was determined that the best approach for this study was to assemble all available empirical data from full scale launch vehicle explosion tests and accidents. Approximately 25 accidents or full-scale tests were found that had some amount of measured blast wave, thermal, or fragment explosion environment characteristics. Blast wave overpressure was found to be much lower in the near field than predicted by most TNT equivalence methods. Additionally, fragments tended to be larger, fewer, and slower than expected if the driving force was from a high explosive type event. In light of these discoveries, a simple model for cryogenic rocket explosions is presented. Predictions from this model encompass all known applicable full scale launch vehicle explosion data. Finally, a brief description of on-going analysis and testing to further refine the launch vehicle explosion environment is discussed.

Monte Carlo simulations of mixtures involving ketones and aldehydes by a direct bubble pressure calculation.

PubMed

Ferrando, Nicolas; Lachet, Véronique; Boutin, Anne

2010-07-08

Ketone and aldehyde molecules are involved in a large variety of industrial applications. Because they are mainly present mixed with other compounds, the prediction of phase equilibrium of mixtures involving these classes of molecules is of first interest particularly to design and optimize separation processes. The main goal of this work is to propose a transferable force field for ketones and aldehydes that allows accurate molecular simulations of not only pure compounds but also complex mixtures. The proposed force field is based on the anisotropic united-atoms AUA4 potential developed for hydrocarbons, and it introduces only one new atom, the carbonyl oxygen. The Lennard-Jones parameters of this oxygen atom have been adjusted on saturated thermodynamic properties of both acetone and acetaldehyde. To simulate mixtures, Monte Carlo simulations are carried out in a specific pseudoensemble which allows a direct calculation of the bubble pressure. For polar mixtures involved in this study, we show that this approach is an interesting alternative to classical calculations in the isothermal-isobaric Gibbs ensemble. The pressure-composition diagrams of polar + polar and polar + nonpolar binary mixtures are well reproduced. Mutual solubilities as well as azeotrope location, if present, are accurately predicted without any empirical binary interaction parameters or readjustment. Such result highlights the transferability of the proposed force field, which is an essential feature toward the simulation of complex oxygenated mixtures of industrial interest.

A controllable tactile device for human-like tissue realization using smart magneto-rheological fluids: fabrication and modeling

NASA Astrophysics Data System (ADS)

Cha, Seung-Woo; Kang, Seok-Rae; Hwang, Yong-Hoon; Oh, Jong-Seok; Choi, Seung-Bok

2018-06-01

This paper proposes a new tactile device to realize the force of human-like organs using the viscoelastic property by combing a smart magneto-rheological (MR) fluid with a sponge (MR sponge in short). The effectiveness of the sensor is validated through the comparison of the force obtained through measurement and the proposed prediction model. As the first step, a conventional standard linear solid model is adopted to independently investigate the force characteristics of MR fluid and sponge. Force is measured using a 3-axis robot with a force sensor to obtain certain properties of MR fluid and sponge. In addition, to show that the proposed MR sponge can realize the force of human-like tissues, experiments are performed using three specimens, i.e., porcine heart, lung, and liver. Subsequently, a quasi-static model for predicting the field-dependent force of the MR sponge is formulated using empirical values. It is demonstrated through comparison that the proposed force model can accurately predict the force of the specimens without significant error. In addition, a psychophysical test is carried out by ordinary subjects to validate the effectiveness of the proposed tactile device. Results show that the MR sponge tactile device can easily produce various levels of the force of human-like tissues, such as the liver and lung of the porcine, by controlling input current.

It's Rather like Learning a Language: Development of talk and conceptual understanding in mechanics lessons

NASA Astrophysics Data System (ADS)

Rincke, Karsten

2011-01-01

Although a broad literature exists concerning the development of conceptual understanding of force and other topics within mechanics, little is known about the role and development of students' talk about the subject. The paper presents an in-depth investigation of students' talk whilst being introduced to the concept of force. The main research goal was to investigate and understand how students develop an understanding of the concept of force and how they use and understand the term 'force'. Therefore, we make relation to the research field of students' preconceptions and the field of second language learning. Two classes of students (N = 47) were videotaped during a time period of nine lessons, each transcribed and analysed using a category system. Additional data were obtained via written tasks, logs kept by the students, and tests. The detailed analysis of the talk and the results of the tests indicate that students face difficulties in using the term 'force' scientifically similar to those in a foreign language instruction. Vygotsky already recognised a relationship between learning in science and learning a language. In this paper, important aspects of this relationship are discussed based upon empirical data. We conclude that in some respects it might be useful to make reference to the research related to language learning when thinking about improving science education. In particular, according to Selinker's concept of interlanguage describing language-learning processes within language instruction, the language used by the students during physics lessons can be viewed as a 'scientific interlanguage'.

Space, Time, Ether, and Kant

NASA Astrophysics Data System (ADS)

Wong, Wing-Chun Godwin

This dissertation focused on Kant's conception of physical matter in the Opus postumum. In this work, Kant postulates the existence of an ether which fills the whole of space and time with its moving forces. Kant's arguments for the existence of an ether in the so-called Ubergang have been acutely criticized by commentators. Guyer, for instance, thinks that Kant pushes the technique of transcendental deduction too far in trying to deduce the empirical ether. In defense of Kant, I held that it is not the actual existence of the empirical ether, but the concept of the ether as a space-time filler that is subject to a transcendental deduction. I suggested that Kant is doing three things in the Ubergang: First, he deduces the pure concept of a space-time filler as a conceptual hybrid of the transcendental object and permanent substance to replace the category of substance in the Critique. Then he tries to prove the existence of such a space-time filler as a reworking of the First Analogy. Finally, he takes into consideration the empirical determinations of the ether by adding the concept of moving forces to the space -time filler. In reconstructing Kant's proofs, I pointed out that Kant is absolutely committed to the impossibility of action-at-a-distance. If we add this new principle of no-action-at-a-distance to the Third Analogy, the existence of a space-time filler follows. I argued with textual evidence that Kant's conception of ether satisfies the basic structure of a field: (1) the ether is a material continuum; (2) a physical quantity is definable on each point in the continuum; and (3) the ether provides a medium to support the continuous transmission of action. The thrust of Kant's conception of ether is to provide a holistic ontology for the transition to physics, which can best be understood from a field-theoretical point of view. This is the main thesis I attempted to establish in this dissertation.

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

NASA Astrophysics Data System (ADS)

Liwo, Adam; Czaplewski, Cezary; Pillardy, Jarosław; Scheraga, Harold A.

2001-08-01

A general method to derive site-site or united-residue potentials is presented. The basic principle of the method is the separation of the degrees of freedom of a system into the primary and secondary ones. The primary degrees of freedom describe the basic features of the system, while the secondary ones are averaged over when calculating the potential of mean force, which is hereafter referred to as the restricted free energy (RFE) function. The RFE can be factored into one-, two-, and multibody terms, using the cluster-cumulant expansion of Kubo. These factors can be assigned the functional forms of the corresponding lowest-order nonzero generalized cumulants, which can, in most cases, be evaluated analytically, after making some simplifying assumptions. This procedure to derive coarse-grain force fields is very valuable when applied to multibody terms, whose functional forms are hard to deduce in another way (e.g., from structural databases). After the functional forms have been derived, they can be parametrized based on the RFE surfaces of model systems obtained from all-atom models or on the statistics derived from structural databases. The approach has been applied to our united-residue force field for proteins. Analytical expressions were derived for the multibody terms pertaining to the correlation between local and electrostatic interactions within the polypeptide backbone; these expressions correspond to up to sixth-order terms in the cumulant expansion of the RFE. These expressions were subsequently parametrized by fitting to the RFEs of selected peptide fragments, calculated with the empirical conformational energy program for peptides force field. The new multibody terms enable not only the heretofore predictable α-helical segments, but also regular β-sheets, to form as the lowest-energy structures, as assessed by test calculations on a model helical protein A, as well as a model 20-residue polypeptide (betanova); the latter was not possible without introducing these new terms.

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

PubMed

Das, A K; Meuwly, M

2016-01-01

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed. © 2016 Elsevier Inc. All rights reserved.

Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos.

PubMed

Yuwen, Tairan; Xue, Yi; Skrynnikov, Nikolai R

2016-03-29

In the first part of this work (paper 1, Xue, Y. et al. Biochemistry 2014 , 53 , 6473 ), we have studied the complex between the 10-residue peptide Sos and N-terminal SH3 domain from adaptor protein c-Crk. In the second part (this paper), we designed the double mutant of the c-Crk N-SH3 domain, W169F/Y186L, with the intention to eliminate the interactions responsible for tight peptide-protein binding, while retaining the interactions that create the initial electrostatic encounter complex. The resulting system was characterized experimentally by measuring the backbone and side-chain (15)N relaxation rates, as well as binding shifts and (1)H(N) temperature coefficients. In addition, it was also modeled via a series of ∼5 μs molecular dynamics (MD) simulations recorded in a large water box under an Amber ff99SB*-ILDN force field. Similar to paper 1, we have found that the strength of arginine-aspartate and arginine-glutamate salt bridges is overestimated in the original force field. To address this problem we have applied the empirical force-field correction described in paper 1. Specifically, the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across Arg-to-Asp/Glu salt bridges has been increased by 3%. This modification led to MD models in good agreement with the experimental data. The emerging picture is that of a fuzzy complex, where the peptide "dances" over the surface of the protein, making transient contacts via salt-bridge interactions. Every once in a while the peptide assumes a certain more stable binding pose, assisted by a number of adventitious polar and nonpolar contacts. On the other hand, occasionally Sos flies off the protein surface; it is then guided by electrostatic steering to quickly reconnect with the protein. The dynamic interaction between Sos and the double mutant of c-Crk N-SH3 gives rise to only small binding shifts. The peptide retains a high degree of conformational mobility, although it is appreciably slowed down due to its (loose) association with the protein. Note that spin relaxation data are indispensable in determining the dynamic status of the peptide. Such data can be properly modeled only on a basis of bona fide MD simulations, as shown in our study. We anticipate that in future the field will move away from the ensemble view of protein disorder and toward more sophisticated MD models. This will require further optimization of force fields, aimed specifically at disordered systems. Efforts in this direction have been recently initiated by several research groups; the empirical salt-bridge correction proposed in our work falls in the same category. MD models obtained with the help of suitably refined force fields and guided by experimental NMR data will provide a powerful insight into an intricate world of disordered biomolecules.

Reflections on discrimination and health in India.

PubMed

Srivatsan, R

2015-01-01

This is a speculative paper on the structure of caste-based discrimination in India. It sketches the field by a) proposing four empirical and historical examples of discrimination in different medical situations; b) suggesting an analytical framework composed of domain, register, temporality and intensity of discrimination; c) proposing that in the Indian historical context, discrimination masks itself, hiding its character behind the veneer of secular ideas; d) arguing that discrimination is not some unfortunate residue of backwardness in modern society that will go away, but is the force of social hierarchy transforming itself into a fully modern capitalist culture. The paper then arrives at the understanding that discrimination is pandemic across India. The conclusion suggests that in India today, we need proposals, hypotheses and arguments that help us establish the ethical framework for meaningful empirical research that sociological studies of medical ethics and the epidemiology of discrimination can pursue. Its method is that of logical and speculative argument based on experience, with examples of different forms of discrimination to clarify the point being made. No specific research was undertaken for this purpose since the paper is not empirically based.

Forced convection heat transfer to air/water vapor mixtures

NASA Technical Reports Server (NTRS)

Richards, D. R.; Florschuetz, L. W.

1984-01-01

Heat transfer coefficients were measured using both dry and humid air in the same forced convection cooling scheme and were compared using appropriate nondimensional parameters (Nusselt, Prandtl and Reynolds numbers). A forced convection scheme with a complex flow field, two dimensional arrays of circular jets with crossflow, was utilized with humidity ratios (mass ratio of water vapor to air) up to 0.23. The dynamic viscosity, thermal conductivity and specific heat of air, steam and air/steam mixtures are examined. Methods for determining gaseous mixture properties from the properties of their pure components are reviewed as well as methods for determining these properties with good confidence. The need for more experimentally determined property data for humid air is discussed. It is concluded that dimensionless forms of forced convection heat transfer data and empirical correlations based on measurements with dry air may be applied to conditions involving humid air with the same confidence as for the dry air case itself, provided that the thermophysical properties of the humid air mixtures are known with the same confidence as their dry air counterparts.

An operational search and rescue model for the Norwegian Sea and the North Sea

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Allen, Arthur A.

A new operational, ensemble-based search and rescue model for the Norwegian Sea and the North Sea is presented. The stochastic trajectory model computes the net motion of a range of search and rescue objects. A new, robust formulation for the relation between the wind and the motion of the drifting object (termed the leeway of the object) is employed. Empirically derived coefficients for 63 categories of search objects compiled by the US Coast Guard are ingested to estimate the leeway of the drifting objects. A Monte Carlo technique is employed to generate an ensemble that accounts for the uncertainties in forcing fields (wind and current), leeway drift properties, and the initial position of the search object. The ensemble yields an estimate of the time-evolving probability density function of the location of the search object, and its envelope defines the search area. Forcing fields from the operational oceanic and atmospheric forecast system of The Norwegian Meteorological Institute are used as input to the trajectory model. This allows for the first time high-resolution wind and current fields to be used to forecast search areas up to 60 h into the future. A limited set of field exercises show good agreement between model trajectories, search areas, and observed trajectories for life rafts and other search objects. Comparison with older methods shows that search areas expand much more slowly using the new ensemble method with high resolution forcing fields and the new leeway formulation. It is found that going to higher-order stochastic trajectory models will not significantly improve the forecast skill and the rate of expansion of search areas.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

Unified description of ^{6}Li structure and deuterium-^{4}He dynamics with chiral two- and three-nucleon forces.

PubMed

Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr

2015-05-29

We provide a unified ab initio description of the ^{6}Li ground state and elastic scattering of deuterium (d) on ^{4}He (α) using two- and three-nucleon forces from chiral effective field theory. We analyze the influence of the three-nucleon force and reveal the role of continuum degrees of freedom in shaping the low-lying spectrum of ^{6}Li. The calculation reproduces the empirical binding energy of ^{6}Li, yielding an asymptotic D- to S-state ratio of the ^{6}Li wave function in the d+α configuration of -0.027, in agreement with a determination from ^{6}Li-^{4}He elastic scattering, but overestimates the excitation energy of the 3^{+} state by 350 keV. The bulk of the computed differential cross section is in good agreement with data. These results endorse the application of the present approach to the evaluation of the ^{2}H(α,γ)^{6}Li radiative capture, responsible for the big-bang nucleosynthesis of ^{6}Li.

Inlet Guide Vane Wakes Including Rotor Effects

NASA Astrophysics Data System (ADS)

Johnston, R. T.; Fleeter, S.

2001-02-01

Fundamental experiments are described directed at the investigation of forcing functions generated by an inlet guide vane (IGV) row, including interactions with the downstream rotor, for application to turbomachine forced response design systems. The experiments are performed in a high-speed research fan facility comprised of an IGV row upstream of a rotor. IGV-rotor axial spacing is variable, with the IGV row able to be indexed circumferentially, thereby allowing measurements to be made across several IGV wakes. With an IGV relative Mach number of 0.29, measurements include the IGV wake pressure and velocity fields for three IGV-rotor axial spacings. The decay characteristics of the IGV wakes are compared to the Majjigi and Gliebe empirical correlations. After Fourier decomposition, a vortical-potential gust splitting analysis is implemented to determine the vortical and potential harmonic wake gust forcing functions both upstream and downstream of the rotor. Higher harmonics of the vortical gust component of the IGV wakes are found to decay at a uniform rate due to viscous diffusion.

Numerical study on the hydrodynamic characteristics of biofouled full-scale net cage

NASA Astrophysics Data System (ADS)

Bi, Chun-wei; Zhao, Yun-peng; Dong, Guo-hai

2015-06-01

The effect of biofouling on the hydrodynamic characteristics of the net cage is of particular interest as biofouled nettings can significantly reduce flow of well-oxygenated water reaching the stocked fish. For computational efficiency, the porous-media fluid model is proposed to simulate flow through the biofouled plane net and full-scale net cage. The porous coefficients of the porous-media fluid model can be determined from the quadratic-function relationship between the hydrodynamic forces on a plane net and the flow velocity using the least squares method. In this study, drag forces on and flow fields around five plane nets with different levels of biofouling are calculated by use of the proposed model. The numerical results are compared with the experimental data of Swift et al. (2006) and the effectiveness of the numerical model is presented. On that basis, flow through full-scale net cages with the same level of biofouling as the tested plane nets are modeled. The flow fields inside and around biofouled net cages are analyzed and the drag force acting on a net cage is estimated by a control volume analysis method. According to the numerical results, empirical formulas of reduction in flow velocity and load on a net cage are derived as function of drag coefficient of the corresponding biofouled netting.

Numerical Simulations of Flow Separation Control in Low-Pressure Turbines using Plasma Actuators

NASA Technical Reports Server (NTRS)

Suzen, Y. B.; Huang, P. G.; Ashpis, D. E.

2007-01-01

A recently introduced phenomenological model to simulate flow control applications using plasma actuators has been further developed and improved in order to expand its use to complicated actuator geometries. The new modeling approach eliminates the requirement of an empirical charge density distribution shape by using the embedded electrode as a source for the charge density. The resulting model is validated against a flat plate experiment with quiescent environment. The modeling approach incorporates the effect of the plasma actuators on the external flow into Navier Stokes computations as a body force vector which is obtained as a product of the net charge density and the electric field. The model solves the Maxwell equation to obtain the electric field due to the applied AC voltage at the electrodes and an additional equation for the charge density distribution representing the plasma density. The new modeling approach solves the charge density equation in the computational domain assuming the embedded electrode as a source therefore automatically generating a charge density distribution on the surface exposed to the flow similar to that observed in the experiments without explicitly specifying an empirical distribution. The model is validated against a flat plate experiment with quiescent environment.

Force limits measured on a space shuttle flight

NASA Technical Reports Server (NTRS)

Scharton, T.

2000-01-01

The random vibration forces between a payload and the sidewall of the space shuttle have been measured in flight and compared with the force specifications used in ground vibration tests. The flight data are in agreement with a semi-empirical method, which is widely used to predict vibration test force limits.

The Rise and Fall of Andean Empires: El Nino History Lessons.

ERIC Educational Resources Information Center

Wright, Kenneth R.

2000-01-01

Provides information on El Nino and the methods for investigating ancient climate record. Traces the rise and fall of the Andean empires focusing on the climatic forces that each empire (Tiwanaku, Wari, Moche, and Inca) endured. States that modern societies should learn from the experiences of these ancient civilizations. (CMK)

Landslide caracteristics determination using bayesian inversion and seismic recording

NASA Astrophysics Data System (ADS)

Mangeney, A.; Moretti, L.; Capdeville, Y.; Stutzmann, E.; Bodin, T.; Bouchut, F.

2014-12-01

Gravitational instabilities, such as landslides, avalanches, or debris flows, play a key role in erosional processes and represent one of the major natural hazards in mountainous, coastal, and volcanic regions. Despite the great amount of field, experimental and numerical work devoted to this problem, the understanding of the physical processes at work in gravitational flows is still an open issue, in particular due to the lack of observations relevant to their dynamics. In this context, the seismic signal generated by gravitational flows is a unique opportunity to obtain information on their dynamics and characteristics. Here we present the study of the 1997 Boxing Day landslide that occurred in Montserrat. We accessed the force applied by the landslide to the ground surface responsible of the seismic waves by inverting the seismic waveform recorded (force-time function). This force was then used as a constraint in a bayesian inversion problem where the forward problem is the force-time function calculation obtained by simulating the landslide with the SHALTOP model (mangeney et al., 2007). With this method, we are able to give an estimate of the rheology (friction coefficient) and the initial shape of the collapsing mass. The volume retrieved is very similar to that obtained by field observations. The friction coefficient determined is also similar to that constrained by former studies or to that predicted by empirical laws (Lucas et al., 2014). Furthermore the method permits to give an estimate of the error made on these parameters.

Semi-empirical model for prediction of unsteady forces on an airfoil with application to flutter

NASA Technical Reports Server (NTRS)

Mahajan, Aparajit J.; Kaza, Krishna Rao V.

1992-01-01

A semi-empirical model is described for predicting unsteady aerodynamic forces on arbitrary airfoils under mildly stalled and unstalled conditions. Aerodynamic forces are modeled using second order ordinary differential equations for lift and moment with airfoil motion as the input. This model is simultaneously integrated with structural dynamics equations to determine flutter characteristics for a two degrees-of-freedom system. Results for a number of cases are presented to demonstrate the suitability of this model to predict flutter. Comparison is made to the flutter characteristics determined by a Navier-Stokes solver and also the classical incompressible potential flow theory.

Semi-empirical model for prediction of unsteady forces on an airfoil with application to flutter

NASA Technical Reports Server (NTRS)

Mahajan, A. J.; Kaza, K. R. V.; Dowell, E. H.

1993-01-01

A semi-empirical model is described for predicting unsteady aerodynamic forces on arbitrary airfoils under mildly stalled and unstalled conditions. Aerodynamic forces are modeled using second order ordinary differential equations for lift and moment with airfoil motion as the input. This model is simultaneously integrated with structural dynamics equations to determine flutter characteristics for a two degrees-of-freedom system. Results for a number of cases are presented to demonstrate the suitability of this model to predict flutter. Comparison is made to the flutter characteristics determined by a Navier-Stokes solver and also the classical incompressible potential flow theory.

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

NASA Astrophysics Data System (ADS)

Sagui, Celeste; Pedersen, Lee G.; Darden, Thomas A.

2004-01-01

The accurate simulation of biologically active macromolecules faces serious limitations that originate in the treatment of electrostatics in the empirical force fields. The current use of "partial charges" is a significant source of errors, since these vary widely with different conformations. By contrast, the molecular electrostatic potential (MEP) obtained through the use of a distributed multipole moment description, has been shown to converge to the quantum MEP outside the van der Waals surface, when higher order multipoles are used. However, in spite of the considerable improvement to the representation of the electronic cloud, higher order multipoles are not part of current classical biomolecular force fields due to the excessive computational cost. In this paper we present an efficient formalism for the treatment of higher order multipoles in Cartesian tensor formalism. The Ewald "direct sum" is evaluated through a McMurchie-Davidson formalism [L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978)]. The "reciprocal sum" has been implemented in three different ways: using an Ewald scheme, a particle mesh Ewald (PME) method, and a multigrid-based approach. We find that even though the use of the McMurchie-Davidson formalism considerably reduces the cost of the calculation with respect to the standard matrix implementation of multipole interactions, the calculation in direct space remains expensive. When most of the calculation is moved to reciprocal space via the PME method, the cost of a calculation where all multipolar interactions (up to hexadecapole-hexadecapole) are included is only about 8.5 times more expensive than a regular AMBER 7 [D. A. Pearlman et al., Comput. Phys. Commun. 91, 1 (1995)] implementation with only charge-charge interactions. The multigrid implementation is slower but shows very promising results for parallelization. It provides a natural way to interface with continuous, Gaussian-based electrostatics in the future. It is hoped that this new formalism will facilitate the systematic implementation of higher order multipoles in classical biomolecular force fields.

Dynamic equilibrium behaviour observed on two contrasting tidal flats from daily monitoring of bed-level changes

NASA Astrophysics Data System (ADS)

Hu, Zhan; van der Wal, Daphne; Cai, Huayang; van Belzen, Jim; Bouma, Tjeerd J.

2018-06-01

Dynamic equilibrium theory (DET) has been applied to tidal flats to systematically explain intertidal morphological responses to various distributions of bed shear stress (BSS). However, it is difficult to verify this theory with field observations because of the discrepancy between the idealized conceptions of theory and the complex reality of intertidal dynamics. The core relation between intertidal morphodynamics and BSS distribution can be easily masked by noise in complex datasets, leading to conclusions of insufficient field evidence to support DET. In the current study, hydrodynamic and morphodynamic data were monitored daily for one year on two tidal flats with contrasting wave exposures. BSS distribution was obtained by validated numerical models. Tidal flat dynamic equilibrium behaviour and BSS were linked via Empirical Orthogonal Function (EOF) analysis. We show that the principal morphodynamic modes corresponded well with the respective modes of BSS found at both sites. Tide-induced BSS was the dominant force at both sites, regardless of the level of wave exposure. The overall erosional and steepening trend found at the two flats can be attributed to the prevailing action of tidal forcing and reduced sediment supply. Hence, EOF analysis confirmed that tidal flat morphodynamics are consistent with DET, providing both field and model evidence to support this theory.

Effects of Deformation on Drag and Lift Forces Acting on a Droplet in a Shear Flow

NASA Astrophysics Data System (ADS)

Suh, Youngho; Lee, Changhoon

2010-11-01

The droplet behavior in a linear shear flow is studied numerically to investigate the effect of deformation on the drag and lift acting on droplet. The droplet shape is calculated by a level set method which is improved by incorporating a sharp-interface modeling technique for accurately enforcing the matching conditions at the liquid- gas interface. By adopting the feedback forces which can maintain the droplet at a fixed position, we determine the acting force on a droplet in shear flow field with efficient handling of deformation. Based on the numerical results, drag and lift forces acting on a droplet are observed to depend strongly on the deformation. Droplet shapes are observed to be spherical, deformed, and oscillating depending on the Reynolds number. Also, the present method is proven to be applicable to a three- dimensional deformation of droplet in the shear flow, which cannot be properly analyzed by the previous studies. Comparisons of the calculated results by the current method with those obtained from body-fitted methods [Dandy and Leal, J. Fluid Mech. 208, 161 (1989)] and empirical models [Feng and Beard, J. Atmos. Sci. 48, 1856 (1991)] show good agreement.

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

PubMed Central

Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

2012-01-01

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

PubMed

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO 2 , without fitting to experimental data.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Relative performance of empirical and physical models in assessing the seasonal and annual glacier surface mass balance of Saint-Sorlin Glacier (French Alps)

NASA Astrophysics Data System (ADS)

Réveillet, Marion; Six, Delphine; Vincent, Christian; Rabatel, Antoine; Dumont, Marie; Lafaysse, Matthieu; Morin, Samuel; Vionnet, Vincent; Litt, Maxime

2018-04-01

This study focuses on simulations of the seasonal and annual surface mass balance (SMB) of Saint-Sorlin Glacier (French Alps) for the period 1996-2015 using the detailed SURFEX/ISBA-Crocus snowpack model. The model is forced by SAFRAN meteorological reanalysis data, adjusted with automatic weather station (AWS) measurements to ensure that simulations of all the energy balance components, in particular turbulent fluxes, are accurately represented with respect to the measured energy balance. Results indicate good model performance for the simulation of summer SMB when using meteorological forcing adjusted with in situ measurements. Model performance however strongly decreases without in situ meteorological measurements. The sensitivity of the model to meteorological forcing indicates a strong sensitivity to wind speed, higher than the sensitivity to ice albedo. Compared to an empirical approach, the model exhibited better performance for simulations of snow and firn melting in the accumulation area and similar performance in the ablation area when forced with meteorological data adjusted with nearby AWS measurements. When such measurements were not available close to the glacier, the empirical model performed better. Our results suggest that simulations of the evolution of future mass balance using an energy balance model require very accurate meteorological data. Given the uncertainties in the temporal evolution of the relevant meteorological variables and glacier surface properties in the future, empirical approaches based on temperature and precipitation could be more appropriate for simulations of glaciers in the future.

Unified description of 6Li structure and deuterium- 4He dynamics with chiral two- and three-nucleon forces

DOE PAGES

Hupin, Guillaume; Quaglioni, Sofia; Navratil, Petr

2015-05-29

Here, we provide a unified ab initio description of the 6Li ground state and elastic scattering of deuterium (d) on 4He (α) using two- and three-nucleon forces from chiral effective field theory. We analyze the influence of the three-nucleon force and reveal the role of continuum degrees of freedom in shaping the low-lying spectrum of 6Li. The calculation reproduces the empirical binding energy of 6Li, yielding an asymptotic D- to S-state ratio of the 6Li wave function in the d+α configuration of –0.027, in agreement with a determination from 6Li– 4He elastic scattering, but overestimates the excitation energy of themore » 3 + state by 350 keV. The bulk of the computed differential cross section is in good agreement with data. These results endorse the application of the present approach to the evaluation of the 2H(α,γ) 6Li radiative capture, responsible for the big-bang nucleosynthesis of 6Li.« less

Fast time-resolved electrostatic force microscopy: Achieving sub-cycle time resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karatay, Durmus U.; Harrison, Jeffrey S.; Glaz, Micah S.

The ability to measure microsecond- and nanosecond-scale local dynamics below the diffraction limit with widely available atomic force microscopy hardware would enable new scientific studies in fields ranging from biology to semiconductor physics. However, commercially available scanning-probe instruments typically offer the ability to measure dynamics only on time scales of milliseconds to seconds. Here, we describe in detail the implementation of fast time-resolved electrostatic force microscopy using an oscillating cantilever as a means to measure fast local dynamics following a perturbation to a sample. We show how the phase of the oscillating cantilever relative to the perturbation event is criticalmore » to achieving reliable sub-cycle time resolution. We explore how noise affects the achievable time resolution and present empirical guidelines for reducing noise and optimizing experimental parameters. Specifically, we show that reducing the noise on the cantilever by using photothermal excitation instead of piezoacoustic excitation further improves time resolution. We demonstrate the discrimination of signal rise times with time constants as fast as 10 ns, and simultaneous data acquisition and analysis for dramatically improved image acquisition times.« less

Evaluation of an urban vegetative canopy scheme and impact on plume dispersion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Matthew A; Williams, Michael D; Zajic, Dragan

2009-01-01

The Quick Urban and Industrial Complex (QUIC) atmospheric dispersion modeling system attempts to fill an important gap between the fast, but nonbuilding-aware Gaussian plume models and the building-aware but slow computational fluid dynamics (CFD) models. While Gaussian models have the ability to give answers quickly to emergency responders, they are unlikely to be able to adequately account for the effects of the building-induced complex flow patterns on the near-source dispersion of contaminants. QUIC uses a diagnostic massconsistent empirical wind model called QUIC-URB that is based on the methodology of Rockle (1990), (see also Kaplan and Dinar 1996). In this approach,more » the recirculation zones that form around and between buildings are inserted into the flow using empirical parameterizations and then the wind field is forced to be mass consistent. Although not as accurate as CFD codes, this approach is several orders of magnitude faster and accounts for the bulk effects of buildings.« less

A Simplified Model of Local Structure in Aqueous Proline Amino Acid Revealed by First-Principles Molecular Dynamics Simulations

PubMed Central

Troitzsch, Raphael Z.; Tulip, Paul R.; Crain, Jason; Martyna, Glenn J.

2008-01-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data. PMID:18790850

A simplified model of local structure in aqueous proline amino acid revealed by first-principles molecular dynamics simulations.

PubMed

Troitzsch, Raphael Z; Tulip, Paul R; Crain, Jason; Martyna, Glenn J

2008-12-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.

Analytical and Empirical Modeling of Wear and Forces of CBN Tool in Hard Turning - A Review

NASA Astrophysics Data System (ADS)

Patel, Vallabh Dahyabhai; Gandhi, Anishkumar Hasmukhlal

2017-08-01

Machining of steel material having hardness above 45 HRC (Hardness-Rockwell C) is referred as a hard turning. There are numerous models which should be scrutinized and implemented to gain optimum performance of hard turning. Various models in hard turning by cubic boron nitride tool have been reviewed, in attempt to utilize appropriate empirical and analytical models. Validation of steady state flank and crater wear model, Usui's wear model, forces due to oblique cutting theory, extended Lee and Shaffer's force model, chip formation and progressive flank wear have been depicted in this review paper. Effort has been made to understand the relationship between tool wear and tool force based on the different cutting conditions and tool geometries so that appropriate model can be used according to user requirement in hard turning.

Walking Ahead: The Headed Social Force Model.

PubMed

Farina, Francesco; Fontanelli, Daniele; Garulli, Andrea; Giannitrapani, Antonio; Prattichizzo, Domenico

2017-01-01

Human motion models are finding an increasing number of novel applications in many different fields, such as building design, computer graphics and robot motion planning. The Social Force Model is one of the most popular alternatives to describe the motion of pedestrians. By resorting to a physical analogy, individuals are assimilated to point-wise particles subject to social forces which drive their dynamics. Such a model implicitly assumes that humans move isotropically. On the contrary, empirical evidence shows that people do have a preferred direction of motion, walking forward most of the time. Lateral motions are observed only in specific circumstances, such as when navigating in overcrowded environments or avoiding unexpected obstacles. In this paper, the Headed Social Force Model is introduced in order to improve the realism of the trajectories generated by the classical Social Force Model. The key feature of the proposed approach is the inclusion of the pedestrians' heading into the dynamic model used to describe the motion of each individual. The force and torque representing the model inputs are computed as suitable functions of the force terms resulting from the traditional Social Force Model. Moreover, a new force contribution is introduced in order to model the behavior of people walking together as a single group. The proposed model features high versatility, being able to reproduce both the unicycle-like trajectories typical of people moving in open spaces and the point-wise motion patterns occurring in high density scenarios. Extensive numerical simulations show an increased regularity of the resulting trajectories and confirm a general improvement of the model realism.

Enantiomeric Recognition of Organic Ammonium Salts by Chiral Dialkyl-, Dialkenyl-, and Tetramethyl-Substituted Pyridino-18-Crown-6 and Tetramethyl- Substituted Bis-Pyridino-18-Crown-6 Ligands: Comparison of Temperature-Dependent 1H NMR and Empirical Force Field Techniques

DTIC Science & Technology

1990-04-18

COVERED 14, DATE OF REPORT (Year. Month, Day) 15. PAGE COUNT Interim FROM _ _ TO April 18, 1990 16. SUPPLEMENTARY NOTATION 17 , COSATI CODES 18. SUBJECT...to epoxide 17 was carried out ,o by using the method of Koppenhoefer and Schurig.241-2 Our epoxides 17 where R was isopropyl, isobutyl, and Scheme i... 17 with diethylene glycol and a catalytic amount of sodium was carried out as reported for the preparation of the chiral dimethyl- tetraethylene glycol

Improvements in GRACE Gravity Field Determination through Stochastic Observation Modeling

NASA Astrophysics Data System (ADS)

McCullough, C.; Bettadpur, S. V.

2016-12-01

Current unconstrained Release 05 GRACE gravity field solutions from the Center for Space Research (CSR RL05) assume random observation errors following an independent multivariate Gaussian distribution. This modeling of observations, a simplifying assumption, fails to account for long period, correlated errors arising from inadequacies in the background force models. Fully modeling the errors inherent in the observation equations, through the use of a full observation covariance (modeling colored noise), enables optimal combination of GPS and inter-satellite range-rate data and obviates the need for estimating kinematic empirical parameters during the solution process. Most importantly, fully modeling the observation errors drastically improves formal error estimates of the spherical harmonic coefficients, potentially enabling improved uncertainty quantification of scientific results derived from GRACE and optimizing combinations of GRACE with independent data sets and a priori constraints.

Wind tunnel seeding particles for laser velocimeter

NASA Technical Reports Server (NTRS)

Ghorieshi, Anthony

1992-01-01

The design of an optimal air foil has been a major challenge for aerospace industries. The main objective is to reduce the drag force while increasing the lift force in various environmental air conditions. Experimental verification of theoretical and computational results is a crucial part of the analysis because of errors buried in the solutions, due to the assumptions made in theoretical work. Experimental studies are an integral part of a good design procedure; however, empirical data are not always error free due to environmental obstacles or poor execution, etc. The reduction of errors in empirical data is a major challenge in wind tunnel testing. One of the recent advances of particular interest is the use of a non-intrusive measurement technique known as laser velocimetry (LV) which allows for obtaining quantitative flow data without introducing flow disturbing probes. The laser velocimeter technique is based on measurement of scattered light by the particles present in the flow but not the velocity of the flow. Therefore, for an accurate flow velocity measurement with laser velocimeters, two criterion are investigated: (1) how well the particles track the local flow field, and (2) the requirement of light scattering efficiency to obtain signals with the LV. In order to demonstrate the concept of predicting the flow velocity by velocity measurement of particle seeding, the theoretical velocity of the gas flow is computed and compared with experimentally obtained velocity of particle seeding.

Evidencing `Tight Bound States' in the Hydrogen Atom:. Empirical Manipulation of Large-Scale XD in Violation of QED

NASA Astrophysics Data System (ADS)

Amoroso, Richard L.; Vigier, Jean-Pierre

2013-09-01

In this work we extend Vigier's recent theory of `tight bound state' (TBS) physics and propose empirical protocols to test not only for their putative existence, but also that their existence if demonstrated provides the 1st empirical evidence of string theory because it occurs in the context of large-scale extra dimensionality (LSXD) cast in a unique M-Theoretic vacuum corresponding to the new Holographic Anthropic Multiverse (HAM) cosmological paradigm. Physicists generally consider spacetime as a stochastic foam containing a zero-point field (ZPF) from which virtual particles restricted by the quantum uncertainty principle (to the Planck time) wink in and out of existence. According to the extended de Broglie-Bohm-Vigier causal stochastic interpretation of quantum theory spacetime and the matter embedded within it is created annihilated and recreated as a virtual locus of reality with a continuous quantum evolution (de Broglie matter waves) governed by a pilot wave - a `super quantum potential' extended in HAM cosmology to be synonymous with the a `force of coherence' inherent in the Unified Field, UF. We consider this backcloth to be a covariant polarized vacuum of the (generally ignored by contemporary physicists) Dirac type. We discuss open questions of the physics of point particles (fermionic nilpotent singularities). We propose a new set of experiments to test for TBS in a Dirac covariant polarized vacuum LSXD hyperspace suggestive of a recently tested special case of the Lorentz Transformation put forth by Kowalski and Vigier. These protocols reach far beyond the recent battery of atomic spectral violations of QED performed through NIST.

Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.

PubMed

Stroet, Martin; Koziara, Katarzyna B; Malde, Alpeshkumar K; Mark, Alan E

2017-12-12

A general method for parametrizing atomic interaction functions is presented. The method is based on an analysis of surfaces corresponding to the difference between calculated and target data as a function of alternative combinations of parameters (parameter space mapping). The consideration of surfaces in parameter space as opposed to local values or gradients leads to a better understanding of the relationships between the parameters being optimized and a given set of target data. This in turn enables for a range of target data from multiple molecules to be combined in a robust manner and for the optimal region of parameter space to be trivially identified. The effectiveness of the approach is illustrated by using the method to refine the chlorine 6-12 Lennard-Jones parameters against experimental solvation free enthalpies in water and hexane as well as the density and heat of vaporization of the liquid at atmospheric pressure for a set of 10 aromatic-chloro compounds simultaneously. Single-step perturbation is used to efficiently calculate solvation free enthalpies for a wide range of parameter combinations. The capacity of this approach to parametrize accurate and transferrable force fields is discussed.

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

The Impact of Human Capital on the Cost of Air Force Acquisition Programs

DTIC Science & Technology

2007-03-01

inspection as well as an empirical test of the data. To empirically test for heteroskedasticty, the Breusch - Pagan /Cook-Weisberg test was used. With a p...19 Pre-Specification Tests ......................................................................................................20 Post...Specification Tests .....................................................................................................22 Regression Results

Small field detector correction factors kQclin,Qmsr (fclin,fmsr) for silicon-diode and diamond detectors with circular 6 MV fields derived using both empirical and numerical methods.

PubMed

O'Brien, D J; León-Vintró, L; McClean, B

2016-01-01

The use of radiotherapy fields smaller than 3 cm in diameter has resulted in the need for accurate detector correction factors for small field dosimetry. However, published factors do not always agree and errors introduced by biased reference detectors, inaccurate Monte Carlo models, or experimental errors can be difficult to distinguish. The aim of this study was to provide a robust set of detector-correction factors for a range of detectors using numerical, empirical, and semiempirical techniques under the same conditions and to examine the consistency of these factors between techniques. Empirical detector correction factors were derived based on small field output factor measurements for circular field sizes from 3.1 to 0.3 cm in diameter performed with a 6 MV beam. A PTW 60019 microDiamond detector was used as the reference dosimeter. Numerical detector correction factors for the same fields were derived based on calculations from a geant4 Monte Carlo model of the detectors and the Linac treatment head. Semiempirical detector correction factors were derived from the empirical output factors and the numerical dose-to-water calculations. The PTW 60019 microDiamond was found to over-respond at small field sizes resulting in a bias in the empirical detector correction factors. The over-response was similar in magnitude to that of the unshielded diode. Good agreement was generally found between semiempirical and numerical detector correction factors except for the PTW 60016 Diode P, where the numerical values showed a greater over-response than the semiempirical values by a factor of 3.7% for a 1.1 cm diameter field and higher for smaller fields. Detector correction factors based solely on empirical measurement or numerical calculation are subject to potential bias. A semiempirical approach, combining both empirical and numerical data, provided the most reliable results.

Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villarreal, Oscar D.; Yu, Lili; Department of Laboratory Medicine, Yancheng Vocational Institute of Health Sciences, Yancheng, Jiangsu 224006

Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanicsmore » of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity- -pulling out the ligand- -closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature.« less

Forced sound transmission through a finite-sized single leaf panel subject to a point source excitation.

PubMed

Wang, Chong

2018-03-01

In the case of a point source in front of a panel, the wavefront of the incident wave is spherical. This paper discusses spherical sound waves transmitting through a finite sized panel. The forced sound transmission performance that predominates in the frequency range below the coincidence frequency is the focus. Given the point source located along the centerline of the panel, forced sound transmission coefficient is derived through introducing the sound radiation impedance for spherical incident waves. It is found that in addition to the panel mass, forced sound transmission loss also depends on the distance from the source to the panel as determined by the radiation impedance. Unlike the case of plane incident waves, sound transmission performance of a finite sized panel does not necessarily converge to that of an infinite panel, especially when the source is away from the panel. For practical applications, the normal incidence sound transmission loss expression of plane incident waves can be used if the distance between the source and panel d and the panel surface area S satisfy d/S>0.5. When d/S ≈0.1, the diffuse field sound transmission loss expression may be a good approximation. An empirical expression for d/S=0  is also given.

Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

PubMed Central

Xue, Yi; Skrynnikov, Nikolai R

2014-01-01

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

Identifying Empirically Supported Treatments for Phobic Avoidance in Individuals with Intellectual Disabilities

ERIC Educational Resources Information Center

Jennett, Heather K.; Hagopian, Louis P.

2008-01-01

This paper reviews the literature regarding the treatment of phobic avoidance in individuals with intellectual disabilities. Criteria for classifying interventions as empirically supported, developed by the American Psychological Association (APA) Division 12 Task Force on Promotion and Dissemination of Psychological Procedures, were used. For…

Adiabatic model and design of a translating field reversed configuration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Intrator, T. P.; Siemon, R. E.; Sieck, P. E.

We apply an adiabatic evolution model to predict the behavior of a field reversed configuration (FRC) during decompression and translation, as well as during boundary compression. Semi-empirical scaling laws, which were developed and benchmarked primarily for collisionless FRCs, are expected to remain valid even for the collisional regime of FRX-L experiment. We use this approach to outline the design implications for FRX-L, the high density translated FRC experiment at Los Alamos National Laboratory. A conical theta coil is used to accelerate the FRC to the largest practical velocity so it can enter a mirror bounded compression region, where it mustmore » be a suitable target for a magnetized target fusion (MTF) implosion. FRX-L provides the physics basis for the integrated MTF plasma compression experiment at the Shiva-Star pulsed power facility at Kirtland Air Force Research Laboratory, where the FRC will be compressed inside a flux conserving cylindrical shell.« less

Empirical Agility

DTIC Science & Technology

2014-06-01

in World War II. One of its most effective applications is recorded in a very interesting little book entitled Patton’s Air Force ( Spires , 2002...Publishing Company, Amsterdam. 1973. Spires , David N, Patton’s Air Force: Forging a Legendary Air-Ground Team. Smithsonian Institution Press, Washington

Public health approaches to family maltreatment prevention: resetting family psychology's sights from the home to the community.

PubMed

Slep, Amy M Smith; Heyman, Richard E

2008-08-01

The authors review recent trends within the family maltreatment research field toward a public health approach, discuss the rationale for community-level interventions for family maltreatment, and sketch the history and development of community-level prevention approaches. Next, to illustrate the both the logistic and the scientific challenges of such work, the authors discuss the development and testing of an empirically guided, research-community partnership for the prevention of family maltreatment, the United States Air Force's NORTH STAR initiative (New Orientation to Reduce Threats to Health From Secretive Problems That Affect Readiness). Finally, recommendations are made for effective and disseminable family maltreatment prevention interventions.

Automated Optimization of Potential Parameters

PubMed Central

Michele, Di Pierro; Ron, Elber

2013-01-01

An algorithm and software to refine parameters of empirical energy functions according to condensed phase experimental measurements are discussed. The algorithm is based on sensitivity analysis and local minimization of the differences between experiment and simulation as a function of potential parameters. It is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field. PMID:24015115

Determination of errors in derived magnetic field directions in geosynchronous orbit: results from a statistical approach

NASA Astrophysics Data System (ADS)

Chen, Yue; Cunningham, Gregory; Henderson, Michael

2016-09-01

This study aims to statistically estimate the errors in local magnetic field directions that are derived from electron directional distributions measured by Los Alamos National Laboratory geosynchronous (LANL GEO) satellites. First, by comparing derived and measured magnetic field directions along the GEO orbit to those calculated from three selected empirical global magnetic field models (including a static Olson and Pfitzer 1977 quiet magnetic field model, a simple dynamic Tsyganenko 1989 model, and a sophisticated dynamic Tsyganenko 2001 storm model), it is shown that the errors in both derived and modeled directions are at least comparable. Second, using a newly developed proxy method as well as comparing results from empirical models, we are able to provide for the first time circumstantial evidence showing that derived magnetic field directions should statistically match the real magnetic directions better, with averaged errors < ˜ 2°, than those from the three empirical models with averaged errors > ˜ 5°. In addition, our results suggest that the errors in derived magnetic field directions do not depend much on magnetospheric activity, in contrast to the empirical field models. Finally, as applications of the above conclusions, we show examples of electron pitch angle distributions observed by LANL GEO and also take the derived magnetic field directions as the real ones so as to test the performance of empirical field models along the GEO orbits, with results suggesting dependence on solar cycles as well as satellite locations. This study demonstrates the validity and value of the method that infers local magnetic field directions from particle spin-resolved distributions.

Determination of errors in derived magnetic field directions in geosynchronous orbit: results from a statistical approach

DOE PAGES

Chen, Yue; Cunningham, Gregory; Henderson, Michael

2016-09-21

Our study aims to statistically estimate the errors in local magnetic field directions that are derived from electron directional distributions measured by Los Alamos National Laboratory geosynchronous (LANL GEO) satellites. First, by comparing derived and measured magnetic field directions along the GEO orbit to those calculated from three selected empirical global magnetic field models (including a static Olson and Pfitzer 1977 quiet magnetic field model, a simple dynamic Tsyganenko 1989 model, and a sophisticated dynamic Tsyganenko 2001 storm model), it is shown that the errors in both derived and modeled directions are at least comparable. Furthermore, using a newly developedmore » proxy method as well as comparing results from empirical models, we are able to provide for the first time circumstantial evidence showing that derived magnetic field directions should statistically match the real magnetic directions better, with averaged errors < ~2°, than those from the three empirical models with averaged errors > ~5°. In addition, our results suggest that the errors in derived magnetic field directions do not depend much on magnetospheric activity, in contrast to the empirical field models. Finally, as applications of the above conclusions, we show examples of electron pitch angle distributions observed by LANL GEO and also take the derived magnetic field directions as the real ones so as to test the performance of empirical field models along the GEO orbits, with results suggesting dependence on solar cycles as well as satellite locations. Finally, this study demonstrates the validity and value of the method that infers local magnetic field directions from particle spin-resolved distributions.« less

Determination of errors in derived magnetic field directions in geosynchronous orbit: results from a statistical approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yue; Cunningham, Gregory; Henderson, Michael

Our study aims to statistically estimate the errors in local magnetic field directions that are derived from electron directional distributions measured by Los Alamos National Laboratory geosynchronous (LANL GEO) satellites. First, by comparing derived and measured magnetic field directions along the GEO orbit to those calculated from three selected empirical global magnetic field models (including a static Olson and Pfitzer 1977 quiet magnetic field model, a simple dynamic Tsyganenko 1989 model, and a sophisticated dynamic Tsyganenko 2001 storm model), it is shown that the errors in both derived and modeled directions are at least comparable. Furthermore, using a newly developedmore » proxy method as well as comparing results from empirical models, we are able to provide for the first time circumstantial evidence showing that derived magnetic field directions should statistically match the real magnetic directions better, with averaged errors < ~2°, than those from the three empirical models with averaged errors > ~5°. In addition, our results suggest that the errors in derived magnetic field directions do not depend much on magnetospheric activity, in contrast to the empirical field models. Finally, as applications of the above conclusions, we show examples of electron pitch angle distributions observed by LANL GEO and also take the derived magnetic field directions as the real ones so as to test the performance of empirical field models along the GEO orbits, with results suggesting dependence on solar cycles as well as satellite locations. Finally, this study demonstrates the validity and value of the method that infers local magnetic field directions from particle spin-resolved distributions.« less

Market forces influence helping behaviour in cooperatively breeding paper wasps

PubMed Central

Grinsted, Lena; Field, Jeremy

2017-01-01

Biological market theory is potentially useful for understanding helping behaviour in animal societies. It predicts that competition for trading partners will affect the value of commodities exchanged. It has gained empirical support in cooperative breeders, where subordinates help dominant breeders in exchange for group membership, but so far without considering one crucial aspect: outside options. We find support for a biological market in paper wasps, Polistes dominula. We first show that females have a choice of cooperative partners. Second, by manipulating entire subpopulations in the field, we increase the supply of outside options for subordinates, freeing up suitable nesting spots and providing additional nesting partners. We predicted that by intensifying competition for help, our manipulation would force dominants to accept a lower price for group membership. As expected, subordinates reduce their foraging effort following our treatments. We conclude that to accurately predict the amount of help provided, social units cannot be viewed in isolation: the surrounding market must also be considered. PMID:28117836

On the unification of nuclear-structure theory: A response to Bortignon and Broglia

NASA Astrophysics Data System (ADS)

Cook, Norman D.

2016-09-01

Nuclear-structure theory is unusual among the diverse fields of quantum physics. Although it provides a coherent description of all known isotopes on the basis of a quantum-mechanical understanding of nucleon states, nevertheless, in the absence of a fundamental theory of the nuclear force acting between nucleons, the prediction of all ground-state and excited-state nuclear binding energies is inherently semi-empirical. I suggest that progress can be made by returning to the foundational work of Eugene Wigner from 1937, where the mathematical symmetries of nucleon states were first defined. Those symmetries were later successfully exploited in the development of the independent-particle model ( IPM ˜ shell model , but the geometrical implications noted by Wigner were neglected. Here I review how the quantum-mechanical, but remarkably easy-to-understand geometrical interpretation of the IPM provides constraints on the parametrization of the nuclear force. The proposed "geometrical IPM" indicates a way forward toward the unification of nuclear-structure theory that Bortignon and Broglia have called for.

Understanding social forces involved in diabetes outcomes: a systems science approach to quality-of-life research.

PubMed

Lounsbury, David W; Hirsch, Gary B; Vega, Chawntel; Schwartz, Carolyn E

2014-04-01

The field of quality-of-life (QOL) research would benefit from learning about and integrating systems science approaches that model how social forces interact dynamically with health and affect the course of chronic illnesses. Our purpose is to describe the systems science mindset and to illustrate the utility of a system dynamics approach to promoting QOL research in chronic disease, using diabetes as an example. We build a series of causal loop diagrams incrementally, introducing new variables and their dynamic relationships at each stage. These causal loop diagrams demonstrate how a common set of relationships among these variables can generate different disease and QOL trajectories for people with diabetes and also lead to a consideration of non-clinical (psychosocial and behavioral) factors that can have implications for program design and policy formulation. The policy implications of the causal loop diagrams are discussed, and empirical next steps to validate the diagrams and quantify the relationships are described.

Updates on Force Limiting Improvements

NASA Technical Reports Server (NTRS)

Kolaini, Ali R.; Scharton, Terry

2013-01-01

The following conventional force limiting methods currently practiced in deriving force limiting specifications assume one-dimensional translation source and load apparent masses: Simple TDOF model; Semi-empirical force limits; Apparent mass, etc.; Impedance method. Uncorrelated motion of the mounting points for components mounted on panels and correlated, but out-of-phase, motions of the support structures are important and should be considered in deriving force limiting specifications. In this presentation "rock-n-roll" motions of the components supported by panels, which leads to a more realistic force limiting specifications are discussed.

Climate data induced uncertainty in model based estimations of terrestrial primary productivity

NASA Astrophysics Data System (ADS)

Wu, Z.; Ahlström, A.; Smith, B.; Ardö, J.; Eklundh, L.; Fensholt, R.; Lehsten, V.

2016-12-01

Models used to project global vegetation and carbon cycle differ in their estimates of historical fluxes and pools. These differences arise not only from differences between models but also from differences in the environmental and climatic data that forces the models. Here we investigate the role of uncertainties in historical climate data, encapsulated by a set of six historical climate datasets. We focus on terrestrial gross primary productivity (GPP) and analyze the results from a dynamic process-based vegetation model (LPJ-GUESS) forced by six different climate datasets and two empirical datasets of GPP (derived from flux towers and remote sensing). We find that the climate induced uncertainty, defined as the difference among historical simulations in GPP when forcing the model with the different climate datasets, can be as high as 33 Pg C yr-1 globally (19% of mean GPP). The uncertainty is partitioned into the three main climatic drivers, temperature, precipitation, and shortwave radiation. Additionally, we illustrate how the uncertainty due to a given climate driver depends both on the magnitude of the forcing data uncertainty (the data range) and the sensitivity of the modeled GPP to the driver (the ecosystem sensitivity). The analysis is performed globally and stratified into five land cover classes. We find that the dynamic vegetation model overestimates GPP, compared to empirically based GPP data over most areas, except for the tropical region. Both the simulations and empirical estimates agree that the tropical region is a disproportionate source of uncertainty in GPP estimation. This is mainly caused by uncertainties in shortwave radiation forcing, of which climate data range contributes slightly higher uncertainty than ecosystem sensitivity to shortwave radiation. We also find that precipitation dominated the climate induced uncertainty over nearly half of terrestrial vegetated surfaces, which is mainly due to large ecosystem sensitivity to precipitation. Overall, climate data ranges are found to contribute more to the climate induced uncertainty than ecosystem sensitivity. Our study highlights the need to better constrain tropical climate and demonstrate that uncertainty caused by climatic forcing data must be considered when comparing and evaluating model results and empirical datasets.

General Khalid Bin Waleed: Understanding the 7th Century Campaign against Sassanid Persian Empire from the Perspective of Operational Art

DTIC Science & Technology

2012-12-06

ABSTRACT This monograph investigates Khalid Bin Waleed’s seventh century (AD 633-634) campaign against the Sassanid Persian Empire in Mesopotamia to...Khalid Bin Waleed’s seventh century (AD 633-634) campaign against the Sassanid Persian Empire in Mesopotamia to trace the evidence that substantiates...Bin Waleed employed characteristics and elements of operational art to defeat the Persian forces in Mesopotamia . He established operational objectives

Mapping Diffuse Seismicity Using Empirical Matched Field Processing Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, J; Templeton, D C; Harris, D B

The objective of this project is to detect and locate more microearthquakes using the empirical matched field processing (MFP) method than can be detected using only conventional earthquake detection techniques. We propose that empirical MFP can complement existing catalogs and techniques. We test our method on continuous seismic data collected at the Salton Sea Geothermal Field during November 2009 and January 2010. In the Southern California Earthquake Data Center (SCEDC) earthquake catalog, 619 events were identified in our study area during this time frame and our MFP technique identified 1094 events. Therefore, we believe that the empirical MFP method combinedmore » with conventional methods significantly improves the network detection ability in an efficient matter.« less

Discovering new events beyond the catalogue—application of empirical matched field processing to Salton Sea geothermal field seismicity

DOE PAGES

Wang, Jingbo; Templeton, Dennise C.; Harris, David B.

2015-07-30

Using empirical matched field processing (MFP), we compare 4 yr of continuous seismic data to a set of 195 master templates from within an active geothermal field and identify over 140 per cent more events than were identified using traditional detection and location techniques alone. In managed underground reservoirs, a substantial fraction of seismic events can be excluded from the official catalogue due to an inability to clearly identify seismic-phase onsets. Empirical MFP can improve the effectiveness of current seismic detection and location methodologies by using conventionally located events with higher signal-to-noise ratios as master events to define wavefield templatesmore » that could then be used to map normally discarded indistinct seismicity. Since MFP does not require picking, it can be carried out automatically and rapidly once suitable templates are defined. In this application, we extend MFP by constructing local-distance empirical master templates using Southern California Earthquake Data Center archived waveform data of events originating within the Salton Sea Geothermal Field. We compare the empirical templates to continuous seismic data collected between 1 January 2008 and 31 December 2011. The empirical MFP method successfully identifies 6249 additional events, while the original catalogue reported 4352 events. The majority of these new events are lower-magnitude events with magnitudes between M0.2–M0.8. Here, the increased spatial-temporal resolution of the microseismicity map within the geothermal field illustrates how empirical MFP, when combined with conventional methods, can significantly improve seismic network detection capabilities, which can aid in long-term sustainability and monitoring of managed underground reservoirs.« less

The Role of Empirical Evidence in Modeling Speech Segmentation

ERIC Educational Resources Information Center

Phillips, Lawrence

2015-01-01

Choosing specific implementational details is one of the most important aspects of creating and evaluating a model. In order to properly model cognitive processes, choices for these details must be made based on empirical research. Unfortunately, modelers are often forced to make decisions in the absence of relevant data. My work investigates the…

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

Testing Transitivity of Preferences on Two-Alternative Forced Choice Data

PubMed Central

Regenwetter, Michel; Dana, Jason; Davis-Stober, Clintin P.

2010-01-01

As Duncan Luce and other prominent scholars have pointed out on several occasions, testing algebraic models against empirical data raises difficult conceptual, mathematical, and statistical challenges. Empirical data often result from statistical sampling processes, whereas algebraic theories are nonprobabilistic. Many probabilistic specifications lead to statistical boundary problems and are subject to nontrivial order constrained statistical inference. The present paper discusses Luce's challenge for a particularly prominent axiom: Transitivity. The axiom of transitivity is a central component in many algebraic theories of preference and choice. We offer the currently most complete solution to the challenge in the case of transitivity of binary preference on the theory side and two-alternative forced choice on the empirical side, explicitly for up to five, and implicitly for up to seven, choice alternatives. We also discuss the relationship between our proposed solution and weak stochastic transitivity. We recommend to abandon the latter as a model of transitive individual preferences. PMID:21833217

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

PubMed

Korb, Oliver; Stützle, Thomas; Exner, Thomas E

2009-01-01

In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

Hindcast of extreme sea states in North Atlantic extratropical storms

NASA Astrophysics Data System (ADS)

Ponce de León, Sonia; Guedes Soares, Carlos

2015-02-01

This study examines the variability of freak wave parameters around the eye of northern hemisphere extratropical cyclones. The data was obtained from a hindcast performed with the WAve Model (WAM) model forced by the wind fields of the Climate Forecast System Reanalysis (CFSR). The hindcast results were validated against the wave buoys and satellite altimetry data showing a good correlation. The variability of different wave parameters was assessed by applying the empirical orthogonal functions (EOF) technique on the hindcast data. From the EOF analysis, it can be concluded that the first empirical orthogonal function (V1) accounts for greater share of variability of significant wave height (Hs), peak period (Tp), directional spreading (SPR) and Benjamin-Feir index (BFI). The share of variance in V1 varies for cyclone and variable: for the 2nd storm and Hs V1 contains 96 % of variance while for the 3rd storm and BFI V1 accounts only for 26 % of variance. The spatial patterns of V1 show that the variables are distributed around the cyclones centres mainly in a lobular fashion.

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

NASA Astrophysics Data System (ADS)

Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M.

1999-06-01

We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

Designing Free Energy Surfaces That Match Experimental Data with Metadynamics

DOE PAGES

White, Andrew D.; Dama, James F.; Voth, Gregory A.

2015-04-30

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. Previously we introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. We also introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psimore » angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. Finally, the example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.« less

Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation

PubMed Central

Burkoff, Nikolas S.; Várnai, Csilla; Wells, Stephen A.; Wild, David L.

2012-01-01

Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used. PMID:22385859

Designing free energy surfaces that match experimental data with metadynamics.

PubMed

White, Andrew D; Dama, James F; Voth, Gregory A

2015-06-09

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. We previously introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. In this work, we introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psi angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. The example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.

Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide

PubMed Central

MacKerell, Alexander D.; Shim, Ji Hyun; Anisimov, Victor M.

2010-01-01

The accuracy of empirical force fields is inherently related to the quality of the target data used for optimization of the model. With the heat of vaporization (ΔHvap) of N-methylacetamide (NMA), a range of values have been reported as target data for optimization of the nonbond parameters associated with the peptide bond in proteins. In the present work, the original experimental data and Antoine constants used for the determination of the ΔHvap of NMA are reanalyzed. Based on this analysis, the wide range of ΔHvap values reported in the literature are shown to be due to incorrect reporting of the temperatures at which the original values were extracted and limitations in the quality of experimental vapor pressure-temperature data over a wide range of temperatures. Taking these problems into account, a consistent ΔHvap value is extracted from three studies for which experimental data are available. This analysis suggests that the most reliable value for ΔHvap is 13.0±0.1 at 410 K for use in force field optimization studies. The present results also indicate that similar analyses, including analysis of Antoine constants alone, may be of utility when reported ΔHvap values are not consistent for a given neat liquid. PMID:20445813

Exploring the energy landscapes of protein folding simulations with Bayesian computation.

PubMed

Burkoff, Nikolas S; Várnai, Csilla; Wells, Stephen A; Wild, David L

2012-02-22

Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Force Field Model of Periodic Trends in Biomolecular Halogen Bonds

PubMed Central

Scholfield, Matthew R.; Ford, Melissa Coates; Vander Zanden, Crystal M.; Billman, M. Marie; Ho, P. Shing; Rappé, Anthony K.

2016-01-01

The study of the noncovalent interaction now defined as a halogen bond (X-bond) has become one of the fastest growing areas in experimental and theoretical chemistry—its applications as a design tool are highly extensive. The significance of the interaction in biology has only recently been recognized, but has now become important in medicinal chemistry. We had previously derived a set of empirical potential energy functions to model the structure-energy relationships for bromines in biomolecular X-bonds (BXBs). Here, we have extended this force field for BXBs (ffBXB) to the halogens (Cl, Br, and I) that are commonly seen to form stable X-bonds. The ffBXB calculated energies show a remarkable one-to-one linear relationship to explicit BXB energies determined from an experimental DNA junction system, thereby validating the approach and the model. The resulting parameters allow us to interpret the stabilizing effects of BXBs in terms of well-defined physical properties of the halogen atoms, including their size, shape, and charge, showing periodic trends that are predictable along the Group VII column of elements. Consequently, we have established the ffBXB as accurate computational tool that can be applied to, for example, for the design of new therapeutic compounds against clinically important targets and new biomolecular based materials. PMID:25338128

"Next Time, Just Remember the Story": Unlearning Empire in Silko's "Ceremony"

ERIC Educational Resources Information Center

Akins, Adrienne

2012-01-01

In this article, the author discusses the unlearning empire in Leslie Marmon Silko's novel titled "Ceremony." "Ceremony' has received a wealth of critical attention. A number of scholars have identified the novel's treatment of education as a colonizing force used by the white American power structure to coerce assimilation of American Indians.…

Syndemics: A theory in search of data or data in search of a theory?

PubMed

Tsai, Alexander C

2018-06-01

The concept of a syndemic was proposed more than two decades ago to explain how large-scale social forces might give rise to co-occurring epidemics that synergistically interact to undermine health in vulnerable populations. This conceptual instrument has the potential to help policymakers and program implementers in their endeavors to improve population health. Accordingly, it has become an increasingly popular heuristic for advocacy, most notably in the field of HIV treatment and prevention. However, most empirical studies purporting to validate the theory of syndemics actually do no such thing. Tomori et al. (2018) provide a novel case study from India illustrating how the dominant empirical approach fails to promote deeper understanding about how hazardous alcohol use, illicit drug use, depression, childhood sexual abuse, and intimate partner violence interact to worsen HIV risk among men who have sex with men. In this commentary, I relate the theory of syndemics to other established social science and public health theories of disease distribution, identify possible sources of conceptual and empirical confusion, and provide concrete suggestions for how to validate the theory using a mixed-methods approach. The hope is that more evidence can be mobilized -- whether informed by the theory of syndemics or not -- to improve health and psychosocial wellbeing among vulnerable populations worldwide. Copyright © 2018 Elsevier Ltd. All rights reserved.

Levitation forces of a bulk YBCO superconductor in gradient varying magnetic fields

NASA Astrophysics Data System (ADS)

Jiang, J.; Gong, Y. M.; Wang, G.; Zhou, D. J.; Zhao, L. F.; Zhang, Y.; Zhao, Y.

2015-09-01

The levitation forces of a bulk YBCO superconductor in gradient varying high and low magnetic fields generated from a superconducting magnet were investigated. The magnetic field intensity of the superconducting magnet was measured when the exciting current was 90 A. The magnetic field gradient and magnetic force field were both calculated. The YBCO bulk was cooled by liquid nitrogen in field-cooling (FC) and zero-field-cooling (ZFC) condition. The results showed that the levitation forces increased with increasing the magnetic field intensity. Moreover, the levitation forces were more dependent on magnetic field gradient and magnetic force field than magnetic field intensity.

Predicting the Performance of Chain Saw Machines Based on Shore Scleroscope Hardness

NASA Astrophysics Data System (ADS)

Tumac, Deniz

2014-03-01

Shore hardness has been used to estimate several physical and mechanical properties of rocks over the last few decades. However, the number of researches correlating Shore hardness with rock cutting performance is quite limited. Also, rather limited researches have been carried out on predicting the performance of chain saw machines. This study differs from the previous investigations in the way that Shore hardness values (SH1, SH2, and deformation coefficient) are used to determine the field performance of chain saw machines. The measured Shore hardness values are correlated with the physical and mechanical properties of natural stone samples, cutting parameters (normal force, cutting force, and specific energy) obtained from linear cutting tests in unrelieved cutting mode, and areal net cutting rate of chain saw machines. Two empirical models developed previously are improved for the prediction of the areal net cutting rate of chain saw machines. The first model is based on a revised chain saw penetration index, which uses SH1, machine weight, and useful arm cutting depth as predictors. The second model is based on the power consumed for only cutting the stone, arm thickness, and specific energy as a function of the deformation coefficient. While cutting force has a strong relationship with Shore hardness values, the normal force has a weak or moderate correlation. Uniaxial compressive strength, Cerchar abrasivity index, and density can also be predicted by Shore hardness values.

Modeling of Thermospheric Neutral Density Variations in Response to Geomagnetic Forcing using GRACE Accelerometer Data

NASA Astrophysics Data System (ADS)

Calabia, A.; Matsuo, T.; Jin, S.

2017-12-01

The upper atmospheric expansion refers to an increase in the temperature and density of Earth's thermosphere due to increased geomagnetic and space weather activities, producing anomalous atmospheric drag on LEO spacecraft. Increased drag decelerates satellites, moving their orbit closer to Earth, decreasing the lifespan of satellites, and making satellite orbit determination difficult. In this study, thermospheric neutral density variations due to geomagnetic forcing are investigated from 10 years (2003-2013) of GRACE's accelerometer-based estimates. In order to isolate the variations produced by geomagnetic forcing, 99.8% of the total variability has been modeled and removed through the parameterization of annual, LST, and solar-flux variations included in the primary Empirical Orthogonal Functions. The residual disturbances of neutral density variations have been investigated further in order to unravel their relationship to several geomagnetic indices and space weather activity indicators. Stronger fluctuations have been found in the southern polar cap, following the dipole-tilt angle variations. While the parameterization of the residual disturbances in terms of Dst index results in the best fit to training data, the use of merging electric field as a predictor leads to the best forecasting performance. An important finding is that modeling of neutral density variations in response geomagnetic forcing can be improved by accounting for the latitude-dependent delay. Our data-driven modeling results are further compared to modeling with TIEGCM.

Functions of Research in Radical Behaviorism for the Further Development of Behavior Analysis

ERIC Educational Resources Information Center

Leigland, Sam

2010-01-01

The experimental analysis of behavior began as an inductively oriented, empirically based scientific field. As the field grew, its distinctive system of science--radical behaviorism--grew with it. The continuing growth of the empirical base of the field has been accompanied by the growth of the literature on radical behaviorism and its…

Theoretical study of short pile effect in tunnel excavation

NASA Astrophysics Data System (ADS)

Tian, Xiao-yan; Liu, Jing; Gao, Xiao-mei; Li, Yuan

2017-09-01

The Misaki Sato Go ideal elastoplastic model is adopted and the two stage analysis theory is used to study the effect of tunnel excavation on short pile effect in this paper. In the first stage, the free field vertical displacement of the soil at the corresponding pile location is obtained by using empirical formula. In the second stage, the displacement is applied to the corresponding pile location. The equilibrium condition of micro physical differential equation settlement of piles. Then through logical deduction and the boundary condition expressions of the settlement calculation, obtain the pile side friction resistance and axial force of the week. Finally, an engineering example is used to analyze the influence of the change of main parameters on their effects.

Transition from order to chaos, and density limit, in magnetized plasmas.

PubMed

Carati, A; Zuin, M; Maiocchi, A; Marino, M; Martines, E; Galgani, L

2012-09-01

It is known that a plasma in a magnetic field, conceived microscopically as a system of point charges, can exist in a magnetized state, and thus remain confined, inasmuch as it is in an ordered state of motion, with the charged particles performing gyrational motions transverse to the field. Here, we give an estimate of a threshold, beyond which transverse motions become chaotic, the electrons being unable to perform even one gyration, so that a breakdown should occur, with complete loss of confinement. The estimate is obtained by the methods of perturbation theory, taking as perturbing force acting on each electron that due to the so-called microfield, i.e., the electric field produced by all the other charges. We first obtain a general relation for the threshold, which involves the fluctuations of the microfield. Then, taking for such fluctuations, the formula given by Iglesias, Lebowitz, and MacGowan for the model of a one component plasma with neutralizing background, we obtain a definite formula for the threshold, which corresponds to a density limit increasing as the square of the imposed magnetic field. Such a theoretical density limit is found to fit pretty well the empirical data for collapses of fusion machines.

Evaluating the Validity of the U.S. Military’s Global Empire

DTIC Science & Technology

2015-03-26

With this status came an unchecked and impressive global force posture . While the United States dramatically cut the number of personnel in Western...evaluates the currant pre-positioned equipment concepts, and evaluates Operation Enduring Freedom (Afghanistan) as a case study for Force Posture . The...conclusion offers five recommendations for the future of United States global force posture and actions that support access. 15. SUBJECT TERMS 16

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such asmore » limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.« less

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

An Analysis of Functional Communication Training as an Empirically Supported Treatment for Problem Behavior Displayed by Individuals with Intellectual Disabilities

ERIC Educational Resources Information Center

Kurtz, Patricia F.; Boelter, Eric W.; Jarmolowicz, David P.; Chin, Michelle D.; Hagopian, Louis P.

2011-01-01

This paper examines the literature on the use of functional communication training (FCT) as a treatment for problem behavior displayed by individuals with intellectual disabilities (ID). Criteria for empirically supported treatments developed by Divisions 12 and 16 of the American Psychological Association (Kratochwill & Stoiber, 2002; Task Force,…

Theoretical Foundation of Zisman's Empirical Equation for Wetting of Liquids on Solid Surfaces

ERIC Educational Resources Information Center

Zhu, Ruzeng; Cui, Shuwen; Wang, Xiaosong

2010-01-01

Theories of wetting of liquids on solid surfaces under the condition that van der Waals force is dominant are briefly reviewed. We show theoretically that Zisman's empirical equation for wetting of liquids on solid surfaces is a linear approximation of the Young-van der Waals equation in the wetting region, and we express the two parameters in…

Fight the power: the limits of empiricism and the costs of positivistic rigor.

PubMed

Indick, William

2002-01-01

A summary of the influence of positivistic philosophy and empiricism on the field of psychology is followed by a critique of the empirical method. The dialectic process is advocated as an alternative method of inquiry. The main advantage of the dialectic method is that it is open to any logical argument, including empirical hypotheses, but unlike empiricism, it does not automatically reject arguments that are not based on observable data. Evolutionary and moral psychology are discussed as examples of important fields of study that could benefit from types of arguments that frequently do not conform to the empirical standards of systematic observation and falsifiability of hypotheses. A dialectic method is shown to be a suitable perspective for those fields of research, because it allows for logical arguments that are not empirical and because it fosters a functionalist perspective, which is indispensable for both evolutionary and moral theories. It is suggested that all psychologists may gain from adopting a dialectic approach, rather than restricting themselves to empirical arguments alone.

Simulating the interplay between plasma transport, electric field, and magnetic field in the near-earth nightside magnetosphere

NASA Astrophysics Data System (ADS)

Gkioulidou, Malamati

The convection electric field resulting from the coupling of the Earth's magnetosphere with the solar wind and interplanetary magnetic field (IMF) drives plasma in the tail plasma sheet earthward. This transport and the resulting energy storage in the near Earth plasma sheet are important for setting up the conditions that lead to major space weather disturbances, such as storms and substorms. Penetration of plasma sheet particles into the near-Earth magnetosphere in response to enhanced convection is crucial to the development of the Region 2 field-aligned current system and large-scale magnetosphere-ionosphere (M-I) coupling, which results in the shielding of the convection electric field. In addition to the electric field, plasma transport is also strongly affected by the magnetic field, which is distinctly different from dipole field in the inner plasma sheet and changes with plasma pressure in maintaining force balance. The goal of this dissertation is to investigate how the plasma transport into the inner magnetosphere is affected by the interplay between plasma, electric field and magnetic field. For this purpose, we conduct simulations using the Rice Convection Model (RCM), which self-consistently calculates the electric field resulting from M-I coupling. In order to quantitatively evaluate the interplay, we improved the RCM simulations by establishing realistic plasma sheet particle sources, by incorporating it with a modified Dungey force balance magnetic field solver (RCM-Dungey runs), and by adopting more realistic electron loss rates. We found that plasma sheet particle sources strongly affect the shielding of the convection electric field, with a hotter and more tenuous plasma sheet resulting in less shielding than a colder and denser one and thus in more earthward penetration of the plasma sheet. The Harang reversal, which is closely associated with the shielding of the convection electric field and the earthward penetration of low-energy protons, is found to be located at lower latitudes and extend more dawnward for a hotter and more tenuous plasma sheet. In comparison with simulation runs under an empirical but not force balance magnetic field from the Tsyganenko 96 model, the simulation results show that transport under force-balanced magnetic field results in weaker pressure gradients and thus weaker R2 FAC in the near-earth region, weaker shielding of the penetration electric field and, as a result, more earthward penetration of plasma sheet protons and electrons with their inner edges being closer together and more azimuthally symmetric. To evaluate the effect of electron loss rate on ionospheric conductivity, a major contributing factor to M-I coupling, we run RCM-Dungey with a more realistic, MLT dependent electron loss rate established from observed wave activity. Comparing our results with those using a strong diffusion everywhere rate, we found that under the MLT dependent loss rate, the dawn-dusk asymmetry in the precipitating electron energy fluxes agrees better with statistical DMSP observations. The more realistic loss rate is much weaker than the strong diffusion limit in the inner magnetosphere. This allows high-energy electrons in the inner magnetosphere to remain much longer and produce substantial conductivity at lower latitudes. The higher conductivity at lower latitudes under the MLT dependent loss rate results in less efficient shielding in response to an enhanced convection electric field, and thus to deeper penetration of the ion plasma sheet into the inner magnetosphere than under the strong diffusion everywhere rate.

Advancing Empirical Scholarship to Further Develop Evaluation Theory and Practice

ERIC Educational Resources Information Center

Christie, Christina A.

2011-01-01

Good theory development is grounded in empirical inquiry. In the context of educational evaluation, the development of empirically grounded theory has important benefits for the field and the practitioner. In particular, a shift to empirically derived theory will assist in advancing more systematic and contextually relevant evaluation practice, as…

Influence of Context on Item Parameters in Forced-Choice Personality Assessments

ERIC Educational Resources Information Center

Lin, Yin; Brown, Anna

2017-01-01

A fundamental assumption in computerized adaptive testing is that item parameters are invariant with respect to context--items surrounding the administered item. This assumption, however, may not hold in forced-choice (FC) assessments, where explicit comparisons are made between items included in the same block. We empirically examined the…

The Role of Market Forces in the Delivery of Health Care: Issues for Research.

ERIC Educational Resources Information Center

National Center for Health Services Research and Health Care Technology Assessment (DHHS/PHS), Rockville, MD.

This edition of the Role of Market Forces program note suggests empirical and descriptive analyses required to complement new areas of health policy emphasis and direction. Eight areas and related questions involving health economics are outlined: (1) rural health care; (2) medical malpractice and insurance; (3) supply, productivity, and…

Experimental Study of Dry Granular Flow and Impact Behavior Against a Rigid Retaining Wall

NASA Astrophysics Data System (ADS)

Jiang, Yuan-Jun; Towhata, Ikuo

2013-07-01

Shallow slope failure in mountainous regions is a common and emergent hazard in terms of its damage to important traffic routes and local communities. The impact of dry granular flows consisting of rock fragments and other particles resulting from shallow slope failures on retaining structures has yet to be systematically researched and is not covered by current design codes. As a preliminary study of the impact caused by dry granular flows, a series of dry granular impact experiments were carried out for one model of a retaining wall. It was indirectly verified that the total normal force exerted on a retaining wall consists of a drag force ( F d), a gravitational and frictional force ( F gf), and a passive earth force ( F p), and that the calculation of F d can be based on the empirical formula defined in NF EN Eurocode 1990 ( Eurocode structuraux. Base de calcul des structures, AFNOR La plaine Saint Denis, 2003). It was also indirectly verified that, for flow with Froude number from 6 to 11, the drag coefficient ( C d) can be estimated using the previously proposed empirical parameters.

Empirical resistive-force theory for slender biological filaments in shear-thinning fluids

NASA Astrophysics Data System (ADS)

Riley, Emily E.; Lauga, Eric

2017-06-01

Many cells exploit the bending or rotation of flagellar filaments in order to self-propel in viscous fluids. While appropriate theoretical modeling is available to capture flagella locomotion in simple, Newtonian fluids, formidable computations are required to address theoretically their locomotion in complex, nonlinear fluids, e.g., mucus. Based on experimental measurements for the motion of rigid rods in non-Newtonian fluids and on the classical Carreau fluid model, we propose empirical extensions of the classical Newtonian resistive-force theory to model the waving of slender filaments in non-Newtonian fluids. By assuming the flow near the flagellum to be locally Newtonian, we propose a self-consistent way to estimate the typical shear rate in the fluid, which we then use to construct correction factors to the Newtonian local drag coefficients. The resulting non-Newtonian resistive-force theory, while empirical, is consistent with the Newtonian limit, and with the experiments. We then use our models to address waving locomotion in non-Newtonian fluids and show that the resulting swimming speeds are systematically lowered, a result which we are able to capture asymptotically and to interpret physically. An application of the models to recent experimental results on the locomotion of Caenorhabditis elegans in polymeric solutions shows reasonable agreement and thus captures the main physics of swimming in shear-thinning fluids.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Thermal and wind-driven water motions in vegetated waters and their role in greenhouse gas fluxes

NASA Astrophysics Data System (ADS)

Poindexter, C.; Variano, E. A.

2016-12-01

The relative importance of different methane transport pathways in wetlands can impact total wetland methane fluxes. The transport of methane and other gases through the water column is affected by a variety of forces. We investigate the role of wind- and thermally-driven water motions in greenhouse gas fluxes in a freshwater marsh and a rice field using in situ velocity measurements in combination with gas transfer velocity models. We measure velocity using an Acoustic Doppler velocimeter, correcting for instrument generated velocities, and a Volumetric Particle Imager. These measurements indicate the presence of wind-driven motions in the wetland water column located below a dense 3-m emergent vegetation canopy. In the rice field's water column, velocity data suggest the occurrence of thermal convection. Results from these in-situ velocity measurements correspond with the non-negligible gas transfer velocities we predict via semi-empirical models. This underscores the importance of hydrodynamics to greenhouse gas fluxes even in shallow, vegetated inland waters.

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

[Management committees in health services: an empirical study].

PubMed

Cecilio, Luiz Carlos de Oliveira

2010-03-01

The aim of the article, based on field data collected from a continuing education program for primary health clinic administrators, was to analyze the functioning of a health service management strategy called "management committees". Different meanings and operational modalities emerged in the committees. Various antimonies appeared in the way the committees operate (autonomy versus heteronomy, reproduction of "instituted" versus "instituting" processes, and communicative versus instrumental reasoning), thus reflecting the level of complexity in this management mechanism. Healthcare provision per se by the clinics only appeared occasionally on the committees' agenda, which mainly focused on administrative issues. The article suggests that further research is needed on the coordinator's involvement in the field of forces constituting the management committee, besides developing pedagogical strategies to support the clinic coordinators and health teams in building the committees. The primary data were submitted to an epistemological discussion anchored in the idea of double hermeneutics, multiple validation of research results, and the relationship between theory and practice.

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

NASA Astrophysics Data System (ADS)

Cisneros, G. Andrés; Piquemal, Jean-Philip; Darden, Thomas A.

2006-11-01

The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H2O)n, n =64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs.

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

PubMed Central

Cisneros, G. Andrés; Piquemal, Jean-Philip; Darden, Thomas A.

2007-01-01

The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15 kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H2O)n, n=64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs. PMID:17115732

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane.

PubMed

Das, Arya; Ali, Sk Musharaf

2018-02-21

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology.

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane

NASA Astrophysics Data System (ADS)

Das, Arya; Ali, Sk. Musharaf

2018-02-01

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology.

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

NASA Astrophysics Data System (ADS)

Harrop, Bryce E.; Ma, Po-Lun; Rasch, Philip J.; Neale, Richard B.; Hannay, Cecile

2018-04-01

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation can be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrop, Bryce E.; Ma, Po -Lun; Rasch, Philip J.

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation canmore » be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.« less

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

DOE PAGES

Harrop, Bryce E.; Ma, Po -Lun; Rasch, Philip J.; ...

2018-03-12

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation canmore » be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.« less

Empirical Analysis of Human Capital, Learning Culture, and Knowledge Management as Antecedents to Organizational Performance: Theoretical and Practical Implications for Logistics Readiness Officer Force Development

DTIC Science & Technology

2014-03-27

Much of the DoD’s force shaping problems in the active duty military stem from the way in which it chose to absorb the force reductions at the end...indicated the need for more joint oriented education and training to help them in the performance of their primary duties. CLL 016 (Joint Logistics... CLL 054 (Joint Task Force Port Opening) and CLL 055 (Joint Deployment and Distribution Performance Metrics Framework) all received high potential

Contact force history and dynamic response due to the impact of a soft projectile

NASA Technical Reports Server (NTRS)

Grady, J. E.

1988-01-01

A series of ballistic impact tests on several different instrumented targets was performed to characterize the dynamic contact force history resulting from the impact of a compliant projectile. The results show that the variation of contact force history with impact velocity does not follow the trends predicted by classical impact models. An empirical model was therefore developed to describe this behavior. This model was then used in a finite-element analysis to estimate the force history and calculate the resulting dynamic strain response in a transversely impacted composite laminate.

Compensation for loads during arm movements using equilibrium-point control.

PubMed

Gribble, P L; Ostry, D J

2000-12-01

A significant problem in motor control is how information about movement error is used to modify control signals to achieve desired performance. A potential source of movement error and one that is readily controllable experimentally relates to limb dynamics and associated movement-dependent loads. In this paper, we have used a position control model to examine changes to control signals for arm movements in the context of movement-dependent loads. In the model, based on the equilibrium-point hypothesis, equilibrium shifts are adjusted directly in proportion to the positional error between desired and actual movements. The model is used to simulate multi-joint movements in the presence of both "internal" loads due to joint interaction torques, and externally applied loads resulting from velocity-dependent force fields. In both cases it is shown that the model can achieve close correspondence to empirical data using a simple linear adaptation procedure. An important feature of the model is that it achieves compensation for loads during movement without the need for either coordinate transformations between positional error and associated corrective forces, or inverse dynamics calculations.

Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

DOE PAGES

Borreguero Calvo, Jose M.; Lynch, Vickie E.

2015-11-23

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

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

PubMed Central

Karniel, Amir; Nisky, Ilana

2015-01-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. PMID:25717155

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

PubMed

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

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

Lexical Link Analysis Application: Improving Web Service to Acquisition Visibility Portal

DTIC Science & Technology

2013-09-30

during the Empire Challenge 2008 and 2009 (EC08/09) field experiments and for numerous other field experiments of new technologies during Trident Warrior...Empirical Methods in Natural Language Processing and Very Large Corpora (EMNLP/ VLC -2000) (pp. 63–70). Retrieved from http://nlp.stanford.edu/manning

Using DFT methodology for more reliable predictive models: Design of inhibitors of Golgi α-Mannosidase II.

PubMed

Bobovská, Adela; Tvaroška, Igor; Kóňa, Juraj

2016-05-01

Human Golgi α-mannosidase II (GMII), a zinc ion co-factor dependent glycoside hydrolase (E.C.3.2.1.114), is a pharmaceutical target for the design of inhibitors with anti-cancer activity. The discovery of an effective inhibitor is complicated by the fact that all known potent inhibitors of GMII are involved in unwanted co-inhibition with lysosomal α-mannosidase (LMan, E.C.3.2.1.24), a relative to GMII. Routine empirical QSAR models for both GMII and LMan did not work with a required accuracy. Therefore, we have developed a fast computational protocol to build predictive models combining interaction energy descriptors from an empirical docking scoring function (Glide-Schrödinger), Linear Interaction Energy (LIE) method, and quantum mechanical density functional theory (QM-DFT) calculations. The QSAR models were built and validated with a library of structurally diverse GMII and LMan inhibitors and non-active compounds. A critical role of QM-DFT descriptors for the more accurate prediction abilities of the models is demonstrated. The predictive ability of the models was significantly improved when going from the empirical docking scoring function to mixed empirical-QM-DFT QSAR models (Q(2)=0.78-0.86 when cross-validation procedures were carried out; and R(2)=0.81-0.83 for a testing set). The average error for the predicted ΔGbind decreased to 0.8-1.1kcalmol(-1). Also, 76-80% of non-active compounds were successfully filtered out from GMII and LMan inhibitors. The QSAR models with the fragmented QM-DFT descriptors may find a useful application in structure-based drug design where pure empirical and force field methods reached their limits and where quantum mechanics effects are critical for ligand-receptor interactions. The optimized models will apply in lead optimization processes for GMII drug developments. Copyright © 2016 Elsevier Inc. All rights reserved.

Dispersion interactions in room-temperature ionic liquids: Results from a non-empirical density functional

NASA Astrophysics Data System (ADS)

Kohanoff, Jorge; Pinilla, Carlos; Youngs, Tristan G. A.; Artacho, Emilio; Soler, José M.

2011-10-01

The role of dispersion or van de Waals (VDW) interactions in imidazolium-based room-temperature ionic liquids is studied within the framework of density functional theory, using a recently developed non-empirical functional [M. Dion, H. Rydberg, E. Schröder, D. C. Langreth, and B. I. Lundqvist, Phys. Rev. Lett. 92, 246401 (2004), 10.1103/PhysRevLett.92.246401], as efficiently implemented in the SIESTA code [G. Román-Pérez and J. M. Soler, Phys. Rev. Lett. 103, 096102 (2009), 10.1103/PhysRevLett.103.096102]. We present results for the equilibrium structure and lattice parameters of several crystalline phases, finding a general improvement with respect to both the local density (LDA) and the generalized gradient approximations (GGA). Similar to other systems characterized by VDW bonding, such as rare gas and benzene dimers as well as solid argon, equilibrium distances and volumes are consistently overestimated by ≈7%, compared to -11% within LDA and 11% within GGA. The intramolecular geometries are retained, while the intermolecular distances and orientations are significantly improved relative to LDA and GGA. The quality is superior to that achieved with tailor-made empirical VDW corrections ad hoc [M. G. Del Pópolo, C. Pinilla, and P. Ballone, J. Chem. Phys. 126, 144705 (2007), 10.1063/1.2715571]. We also analyse the performance of an optimized version of this non-empirical functional, where the screening properties of the exchange have been tuned to reproduce high-level quantum chemical calculations [J. Klimes, D. Bowler, and A. Michaelides, J. Phys.: Condens. Matter 22, 074203 (2010), 10.1088/0953-8984/22/7/074203]. The results for solids are even better with volumes and geometries reproduced within 2% of experimental data. We provide some insight into the issue of polymorphism of [bmim][Cl] crystals, and we present results for the geometry and energetics of [bmim][Tf] and [mmim][Cl] neutral and charged clusters, which validate the use of empirical force fields.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Determination of rotor harmonic blade loads from acoustic measurements

NASA Technical Reports Server (NTRS)

Kasper, P. K.

1975-01-01

The magnitude of discrete frequency sound radiated by a rotating blade is strongly influenced by the presence of a nonuniform distribution of aerodynamic forces over the rotor disk. An analytical development and experimental results are provided for a technique by which harmonic blade loads are derived from acoustic measurements. The technique relates, on a one-to-one basis, the discrete frequency sound harmonic amplitudes measured at a point on the axis of rotation to the blade-load harmonic amplitudes. This technique was applied to acoustic data from two helicopter types and from a series of test results using the NASA-Langley Research Center rotor test facility. The inferred blade-load harmonics for the cases considered tended to follow an inverse power law relationship with harmonic blade-load number. Empirical curve fits to the data showed the harmonic fall-off rate to be in the range of 6 to 9 db per octave of harmonic order. These empirical relationships were subsequently used as input data in a compatible far field rotational noise prediction model. A comparison between predicted and measured off-axis sound harmonic levels is provided for the experimental cases considered.

What Supports an Aeroplane? Force, Momentum, Energy and Power in Flight

ERIC Educational Resources Information Center

Robertson, David

2014-01-01

Some apparently confusing aspects of Newton's laws as applied to an aircraft in normal horizontal flight are neatly resolved by a careful analysis of force, momentum, energy and power. A number of related phenomena are explained at the same time, including the lift and induced drag coefficients, used empirically in the aviation industry.

The Influence of Market Force Culture on British and German Academics

ERIC Educational Resources Information Center

Pritchard, Rosalind

2005-01-01

Higher education (HE) in Germany and the United Kingdom is being continually subjected to the discipline of market forces. An empirical study was conducted using questionnaires with academic staff in 12 institutions in each country to discover the extent to which their values and attitudes were converging and were in keeping with what might be…

An Empirical System for Assessing the Impact of Aptitude Requirement Adjustments on Air Force Initial Skills Training.

ERIC Educational Resources Information Center

Mumford, Michael D.; And Others

A multivariate modeling approach was developed to assess the impact of changes in aptitude requirement minimums on U.S. Air Force technical training outcomes. Initially, interviews were conducted with technical training personnel to identify significant student inputs, course content, and training outcome variables. Measures of these variables…

Comments on John Willinsky's Learning to Divide the World: Education at Empire's End

ERIC Educational Resources Information Center

Wang, Tsung Juang

2006-01-01

John Willinsky's view that imperialism and its legacy remain the driving force that divides the world into "superior" and "inferior" cultures fails to take into account other forces that also encourage peoples of different cultures to emphasize the differences between themselves. He is correct in noting that imperialism led to much injustice and…

Enhanced Thermal Diffusion of Li in Graphite by Alternating Vertical Electric Field: A Hybrid Quantum-Classical Simulation Study

NASA Astrophysics Data System (ADS)

Ohba, Nobuko; Ogata, Shuji; Tamura, Tomoyuki; Kobayashi, Ryo; Yamakawa, Shunsuke; Asahi, Ryoji

2012-02-01

Enhancing the diffusivity of the Li ion in a Li-graphite intercalation compound that has been used as a negative electrode in the Li-ion rechargeable battery, is important in improving both the recharging speed and power of the battery. In the compound, the Li ion creates a long-range stress field around itself by expanding the interlayer spacing of graphite. We advance the hybrid quantum-classical simulation code to include the external electric field in addition to the long-range stress field by first-principles simulation. In the hybrid code, the quantum region selected adaptively around the Li ion is treated using the real-space density-functional theory for electrons. The rest of the system is described with an empirical interatomic potential that includes the term relating to the dispersion force between the C atoms in different layers. Hybrid simulation runs for Li dynamics in graphite are performed at 423 K under various settings of the amplitude and frequency of alternating electric fields perpendicular to C-layers. We find that the in-plane diffusivity of the Li ion is enhanced significantly by the electric field if the amplitude is larger than 0.2 V/Å within its order and the frequency is as high as 1.7 THz. The microscopic mechanisms of the enhancement are explained.

Synchronization of motor unit firings: an epiphenomenon of firing rate characteristics not common inputs

PubMed Central

Kline, Joshua C.

2015-01-01

Synchronous motor unit firing instances have been attributed to anatomical inputs shared by motoneurons. Yet, there is a lack of empirical evidence confirming the notion that common inputs elicit synchronization under voluntary conditions. We tested this notion by measuring synchronization between motor unit action potential trains (MUAPTs) as their firing rates progressed within a contraction from a relatively low force level to a higher one. On average, the degree of synchronization decreased as the force increased. The common input notion provides no empirically supported explanation for the observed synchronization behavior. Therefore, we investigated a more probable explanation for synchronization. Our data set of 17,546 paired MUAPTs revealed that the degree of synchronization varies as a function of two characteristics of the motor unit firing rate: the similarity and the slope as a function of force. Both are measures of the excitation of the motoneurons. As the force generated by the muscle increases, the firing rate slope decreases, and the synchronization correspondingly decreases. Different muscles have motor units with different firing rate characteristics and display different amounts of synchronization. Although this association is not proof of causality, it consistently explains our observations and strongly suggests further investigation. So viewed, synchronization is likely an epiphenomenon, subject to countless unknown neural interactions. As such, synchronous firing instances may not be the product of a specific design and may not serve a specific physiological purpose. Our explanation for synchronization has the advantage of being supported by empirical evidence, whereas the common input does not. PMID:26490288

Synchronization of motor unit firings: an epiphenomenon of firing rate characteristics not common inputs.

PubMed

Kline, Joshua C; De Luca, Carlo J

2016-01-01

Synchronous motor unit firing instances have been attributed to anatomical inputs shared by motoneurons. Yet, there is a lack of empirical evidence confirming the notion that common inputs elicit synchronization under voluntary conditions. We tested this notion by measuring synchronization between motor unit action potential trains (MUAPTs) as their firing rates progressed within a contraction from a relatively low force level to a higher one. On average, the degree of synchronization decreased as the force increased. The common input notion provides no empirically supported explanation for the observed synchronization behavior. Therefore, we investigated a more probable explanation for synchronization. Our data set of 17,546 paired MUAPTs revealed that the degree of synchronization varies as a function of two characteristics of the motor unit firing rate: the similarity and the slope as a function of force. Both are measures of the excitation of the motoneurons. As the force generated by the muscle increases, the firing rate slope decreases, and the synchronization correspondingly decreases. Different muscles have motor units with different firing rate characteristics and display different amounts of synchronization. Although this association is not proof of causality, it consistently explains our observations and strongly suggests further investigation. So viewed, synchronization is likely an epiphenomenon, subject to countless unknown neural interactions. As such, synchronous firing instances may not be the product of a specific design and may not serve a specific physiological purpose. Our explanation for synchronization has the advantage of being supported by empirical evidence, whereas the common input does not. Copyright © 2016 the American Physiological Society.

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

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Leading change: a concept analysis.

PubMed

Nelson-Brantley, Heather V; Ford, Debra J

2017-04-01

To report an analysis of the concept of leading change. Nurses have been called to lead change to advance the health of individuals, populations, and systems. Conceptual clarity about leading change in the context of nursing and healthcare systems provides an empirical direction for future research and theory development that can advance the science of leadership studies in nursing. Concept analysis. CINAHL, PubMed, PsycINFO, Psychology and Behavioral Sciences Collection, Health Business Elite and Business Source Premier databases were searched using the terms: leading change, transformation, reform, leadership and change. Literature published in English from 2001 - 2015 in the fields of nursing, medicine, organizational studies, business, education, psychology or sociology were included. Walker and Avant's method was used to identify descriptions, antecedents, consequences and empirical referents of the concept. Model, related and contrary cases were developed. Five defining attributes of leading change were identified: (a) individual and collective leadership; (b) operational support; (c) fostering relationships; (d) organizational learning; and (e) balance. Antecedents were external or internal driving forces and organizational readiness. The consequences of leading change included improved organizational performance and outcomes and new organizational culture and values. A theoretical definition and conceptual model of leading change were developed. Future studies that use and test the model may contribute to the refinement of a middle-range theory to advance nursing leadership research and education. From this, empirically derived interventions that prepare and enable nurses to lead change to advance health may be realized. © 2016 John Wiley & Sons Ltd.

A Haptic-Enhanced System for Molecular Sensing

NASA Astrophysics Data System (ADS)

Comai, Sara; Mazza, Davide

The science of haptics has received an enormous attention in the last decade. One of the major application trends of haptics technology is data visualization and training. In this paper, we present a haptically-enhanced system for manipulation and tactile exploration of molecules.The geometrical models of molecules is extracted either from theoretical or empirical data using file formats widely adopted in chemical and biological fields. The addition of information computed with computational chemistry tools, allows users to feel the interaction forces between an explored molecule and a charge associated to the haptic device, and to visualize a huge amount of numerical data in a more comprehensible way. The developed tool can be used either for teaching or research purposes due to its high reliance on both theoretical and experimental data.

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

PubMed

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.

The Elegance of Disordered Granular Packings: A Validation of Edwards' Hypothesis

NASA Technical Reports Server (NTRS)

Metzger, Philip T.; Donahue, Carly M.

2004-01-01

We have found a way to analyze Edwards' density of states for static granular packings in the special case of round, rigid, frictionless grains assuming constant coordination number. It obtains the most entropic density of single grain states, which predicts several observables including the distribution of contact forces. We compare these results against empirical data obtained in dynamic simulations of granular packings. The agreement between theory and the empirics is quite good, helping validate the use of statistical mechanics methods in granular physics. The differences between theory and empirics are mainly due to the variable coordination number, and when the empirical data are sorted by that number we obtain several insights that suggest an underlying elegance in the density of states

A force field for dynamic Cu-BTC metal-organic framework.

PubMed

Zhao, Lei; Yang, Qingyuan; Ma, Qintian; Zhong, Chongli; Mi, Jianguo; Liu, Dahuan

2011-02-01

A new force field that can describe the flexibility of Cu-BTC metal-organic framework (MOF) was developed in this work. Part of the parameters were obtained using density functional theory calculations, and the others were taken from other force fields. The new force field could reproduce well the experimental crystal structure, negative thermal expansion, vibrational properties as well as adsorption behavior in Cu-BTC. In addition, the bulk modulus of Cu-BTC was predicted using the new force field. We believe the new force field is useful in understanding the structure-property relationships for MOFs, and the approach can be extended to other MOFs.

SMART (Sports Medicine and Rehabilitation Team) Centers: An Empirical Analysis

DTIC Science & Technology

2007-04-01

completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection ofinformation ...of finite health care resources, increased military operational tempo, and smaller expeditionary fighting forces, the US Navy has developed SMART...through their sacrifices due I owe my success. SMART Centers: An Empirical Analysis 5 Abstract In an era of finite health care resources, increased military

Competences in Romanian Higher Education--An Empirical Investigation for the Business Sector

ERIC Educational Resources Information Center

Deaconu, Adela; Nistor, Cristina Silvia

2017-01-01

This research study particularizes the general descriptions of the European Qualifications Framework for Lifelong Learning, as compiled and developed within the Romanian qualification framework, to the business and economics field in general and to the property economic analysis and valuation field in particular. By means of an empirical analysis,…

Functional Measurement in the Field of Empirical Bioethics

ERIC Educational Resources Information Center

Mullet, Etienne; Sorum, Paul C.; Teysseire, Nathalie; Nann, Stephanie; Martinez, Guadalupe Elizabeth Morales; Ahmed, Ramadan; Kamble, Shanmukh; Olivari, Cecilia; Sastre, Maria Teresa Munoz

2012-01-01

We present, in a synthetic way, some of the main findings from five studies that were conducted in the field of empirical bioethics, using the Functional Measurement framework. These studies were about (a) the rationing of rare treatments, (b) adolescents' abortions, (c) end-of-life decision-making regarding damaged neonates, (d) end-of-life…

Student Discipline: Legal, Empirical, and Educational Perspectives.

ERIC Educational Resources Information Center

Harris, J. John, III, Ed.; Bennett, Christine, Ed.

This book presents four perspectives on student discipline: legal and historical, empirical, educational, and futuristic. Part I examines the legal history of student discipline in papers by J. John Harris III, Richard E. Fields, and A. Reynaldo Contreras (Chapter 1); Richard E. Fields (Chapter 2); and David G. Carter, Sr. and Cynthia L. Jackson…

Accuracy Analysis of a Box-wing Theoretical SRP Model

NASA Astrophysics Data System (ADS)

Wang, Xiaoya; Hu, Xiaogong; Zhao, Qunhe; Guo, Rui

2016-07-01

For Beidou satellite navigation system (BDS) a high accuracy SRP model is necessary for high precise applications especially with Global BDS establishment in future. The BDS accuracy for broadcast ephemeris need be improved. So, a box-wing theoretical SRP model with fine structure and adding conical shadow factor of earth and moon were established. We verified this SRP model by the GPS Block IIF satellites. The calculation was done with the data of PRN 1, 24, 25, 27 satellites. The results show that the physical SRP model for POD and forecast for GPS IIF satellite has higher accuracy with respect to Bern empirical model. The 3D-RMS of orbit is about 20 centimeters. The POD accuracy for both models is similar but the prediction accuracy with the physical SRP model is more than doubled. We tested 1-day 3-day and 7-day orbit prediction. The longer is the prediction arc length, the more significant is the improvement. The orbit prediction accuracy with the physical SRP model for 1-day, 3-day and 7-day arc length are 0.4m, 2.0m, 10.0m respectively. But they are 0.9m, 5.5m and 30m with Bern empirical model respectively. We apply this means to the BDS and give out a SRP model for Beidou satellites. Then we test and verify the model with Beidou data of one month only for test. Initial results show the model is good but needs more data for verification and improvement. The orbit residual RMS is similar to that with our empirical force model which only estimate the force for along track, across track direction and y-bias. But the orbit overlap and SLR observation evaluation show some improvement. The remaining empirical force is reduced significantly for present Beidou constellation.

Influence of the Reynolds number on normal forces of slender bodies of revolution

NASA Technical Reports Server (NTRS)

Hartmann, K.

1982-01-01

Comprehensive force, moment, and pressure distribution measurements as well as flow visualization experiments were carried out to determine the influence of the Reynolds number on nonlinear normal forces of slender bodies of revolution. Experiments were performed in transonic wind tunnels at angles of attack up to 90 deg in the Mach number range 0.5 to 2.2 at variable Reynolds numbers. The results were analysed theoretically and an empirical theory was developed which describes the test results satisfactory.

Retaining U.S. Air Force Pilots When the Civilian Demand for Pilots Is Growing

DTIC Science & Technology

2016-01-01

pilot retention and determine the changes in ARP and AP that could offset those effects. It also simulates the effects of eliminating AP for pilots...array of compensation policies for pilots, thereby providing the USAF with an empirically based analytical platform to determine the special and...greatly from the input and support of our project monitor, Maj Ryan Theiss, Chief, Rated Force Policy-Mobility Forces (HQ USAF/A1PPR), as well as Lt

SU-F-T-158: Experimental Characterization of Field Size Dependence of Dose and Lateral Beam Profiles of Scanning Proton and Carbon Ion Beams for Empirical Model in Air

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y; Hsi, W; Zhao, J

2016-06-15

Purpose: The Gaussian model for the lateral profiles in air is crucial for an accurate treatment planning system. The field size dependence of dose and the lateral beam profiles of scanning proton and carbon ion beams are due mainly to particles undergoing multiple Coulomb scattering in the beam line components and secondary particles produced by nuclear interactions in the target, both of which depend upon the energy and species of the beam. In this work, lateral profile shape parameters were fitted to measurements of field size dependence dose at the center of field size in air. Methods: Previous studies havemore » employed empirical fits to measured profile data to significantly reduce the QA time required for measurements. From this approach to derive the weight and sigma of lateral profiles in air, empirical model formulations were simulated for three selected energies for both proton and carbon beams. Results: The 20%–80% lateral penumbras predicted by the double model for proton and single model for carbon with the error functions agreed with the measurements within 1 mm. The standard deviation between measured and fitted field size dependence of dose for empirical model in air has a maximum accuracy of 0.74% for proton with double Gaussian, and of 0.57% for carbon with single Gaussian. Conclusion: We have demonstrated that the double Gaussian model of lateral beam profiles is significantly better than the single Gaussian model for proton while a single Gaussian model is sufficient for carbon. The empirical equation may be used to double check the separately obtained model that is currently used by the planning system. The empirical model in air for dose of spot scanning proton and carbon ion beams cannot be directly used for irregular shaped patient fields, but can be to provide reference values for clinical use and quality assurance.« less

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

PubMed Central

Lange, Oliver F.; van der Spoel, David; de Groot, Bert L.

2010-01-01

Abstract Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data. PMID:20643085

Identification of potential compensatory muscle strategies in a breast cancer survivor population: A combined computational and experimental approach.

PubMed

Chopp-Hurley, Jaclyn N; Brookham, Rebecca L; Dickerson, Clark R

2016-12-01

Biomechanical models are often used to estimate the muscular demands of various activities. However, specific muscle dysfunctions typical of unique clinical populations are rarely considered. Due to iatrogenic tissue damage, pectoralis major capability is markedly reduced in breast cancer population survivors, which could influence arm internal and external rotation muscular strategies. Accordingly, an optimization-based muscle force prediction model was systematically modified to emulate breast cancer population survivors through adjusting pectoralis capability and enforcing an empirical muscular co-activation relationship. Model permutations were evaluated through comparisons between predicted muscle forces and empirically measured muscle activations in survivors. Similarities between empirical data and model outputs were influenced by muscle type, hand force, pectoralis major capability and co-activation constraints. Differences in magnitude were lower when the co-activation constraint was enforced (-18.4% [31.9]) than unenforced (-23.5% [27.6]) (p<0.0001). This research demonstrates that muscle dysfunction in breast cancer population survivors can be reflected through including a capability constraint for pectoralis major. Further refinement of the co-activation constraint for survivors could improve its generalizability across this population and activities. Improving biomechanical models to more accurately represent clinical populations can provide novel information that can help in the development of optimal treatment programs for breast cancer population survivors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact detection and analysis/health monitoring system for composites

NASA Astrophysics Data System (ADS)

Child, James E.; Kumar, Amrita; Beard, Shawn; Qing, Peter; Paslay, Don G.

2006-05-01

This manuscript includes information from test evaluations and development of a smart event detection system for use in monitoring composite rocket motor cases for damaging impacts. The primary purpose of the system as a sentry for case impact event logging is accomplished through; implementation of a passive network of miniaturized piezoelectric sensors, logger with pre-determined force threshold levels, and analysis software. Empirical approaches to structural characterizations and network calibrations along with implementation techniques were successfully evaluated, testing was performed on both unloaded (less propellants) as well as loaded rocket motors with the cylindrical areas being of primary focus. The logged test impact data with known physical network parameters provided for impact location as well as force determination, typically within 3 inches of actual impact location using a 4 foot network grid and force accuracy within 25%of an actual impact force. The simplistic empirical characterization approach along with the robust / flexible sensor grids and battery operated portable logger show promise of a system that can increase confidence in composite integrity for both new assets progressing through manufacturing processes as well as existing assets that may be in storage or transportation.

Design and investigations of the superconducting magnet system for the multipurpose superconducting electron cyclotron resonance ion source.

PubMed

Tinschert, K; Lang, R; Mäder, J; Rossbach, J; Spädtke, P; Komorowski, P; Meyer-Reumers, M; Krischel, D; Fischer, B; Ciavola, G; Gammino, S; Celona, L

2012-02-01

The production of intense beams of heavy ions with electron cyclotron resonance ion sources (ECRIS) is an important request at many accelerators. According to the ECR condition and considering semi-empirical scaling laws, it is essential to increase the microwave frequency together with the magnetic flux density of the ECRIS magnet system. A useful frequency of 28 GHz, therefore, requires magnetic flux densities above 2.2 T implying the use of superconducting magnets. A cooperation of European institutions initiated a project to build a multipurpose superconducting ECRIS (MS-ECRIS) in order to achieve an increase of the performances in the order of a factor of ten. After a first design of the superconducting magnet system for the MS-ECRIS, the respective cold testing of the built magnet system reveals a lack of mechanical performance due to the strong interaction of the magnetic field of the three solenoids with the sextupole field and the magnetization of the magnetic iron collar. Comprehensive structural analysis, magnetic field calculations, and calculations of the force pattern confirm thereafter these strong interactions, especially of the iron collar with the solenoidal fields. The investigations on the structural analysis as well as suggestions for a possible mechanical design solution are given.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PubMed Central

Patmanidis, Ilias

2018-01-01

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation. PMID:29688238

Analytical model of a corona discharge from a conical electrode under saturation

NASA Astrophysics Data System (ADS)

Boltachev, G. Sh.; Zubarev, N. M.

2012-11-01

Exact partial solutions are found for the electric field distribution in the outer region of a stationary unipolar corona discharge from an ideal conical needle in the space-charge-limited current mode with allowance for the electric field dependence of the ion mobility. It is assumed that only the very tip of the cone is responsible for the discharge, i.e., that the ionization zone is a point. The solutions are obtained by joining the spherically symmetric potential distribution in the drift space and the self-similar potential distribution in the space-charge-free region. Such solutions are outside the framework of the conventional Deutsch approximation, according to which the space charge insignificantly influences the shape of equipotential surfaces and electric lines of force. The dependence is derived of the corona discharge saturation current on the apex angle of the conical electrode and applied potential difference. A simple analytical model is suggested that describes drift in the point-plane electrode geometry under saturation as a superposition of two exact solutions for the field potential. In terms of this model, the angular distribution of the current density over the massive plane electrode is derived, which agrees well with Warburg's empirical law.

Prediction of Mechanical Properties of Polymers With Various Force Fields

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

Force Field for Water Based on Neural Network.

PubMed

Wang, Hao; Yang, Weitao

2018-05-18

We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: non-polarizable and polarizable force fields. Simulation results show that the non-polarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build the next generation force fields at high accuracy and low computational costs, especially for large systems.

Equilibrium stable-isotope fractionation of thallium and mercury

NASA Astrophysics Data System (ADS)

Schauble, E. A.

2005-12-01

In this study first-principles quantum mechanical and empirical force-field models are used to estimate equilibrium mass-dependent isotopic fractionations among a variety of thallium and mercury compounds. High-precision MC-ICP-MS measurements have recently uncovered evidence of stable isotope fractionation for many elements, including 2-4‰ variability in the isotopic compositions of thallium[1] (atomic no. 81) and mercury[2] (atomic no. 80). The observed thallium- and mercury-isotope fractionations are remarkable, given that the magnitude of isotopic fractionation typically decreases as atomic number increases[3]. Stable isotope measurements could improve our understanding of geochemical and biogeochemical cycling of both elements, but little is known about the mechanisms driving these fractionations. A better understanding of the chemical processes controlling stable isotope compositions could help maximize the utility of these new geochemical tracers. Standard equilibrium stable isotope fractionation theory holds that the energy driving fractionation comes from isotopic effects on vibrational frequencies, which have generally not been measured. In the present study both quantum-mechanical and empirical force fields are used to estimate unknown frequencies. Results suggest that thallium and mercury fractionations of ≥ 0.5‰ are likely during the relevant redox reactions Tl+ ↔ Tl3+ and HgO ↔ Hg2+. Methyl-mercury and mercury-halide compounds like CH3HgCl will have ~ 1‰ higher 202Hg/198Hg than atomic vapor at room temperature. Fractionations between coexisting Hg2+ species appear to be much smaller, however. 205Tl/203Tl in Tl(H2O)_63+ is predicted to be ~0.5‰ higher than in coexisting Tl+-bearing substances. This result is in qualitative agreement with data from ferromanganese crusts [1], suggesting that Tl3+ in manganese-oxides will have higher 205Tl/203Tl than aqueous Tl+. Equilibrium fractionations for both elements are much smaller than the observed range of isotopic fractionations, however, which could point to a major role for kinetic-fractionation or Rayleigh-like distillation processes. Refs.: [1] Rehämper et al. (2002) EPSL 197:65. [2] Xie et al. (2005) J. Anal. Atomic Spectrom. 20:515. [3] Bigeleisen and Mayer (1947) J. Chem. Phys. 15:261.

Sustainability Education in Early Childhood: An Updated Review of Research in the Field

ERIC Educational Resources Information Center

Somerville, Margaret; Williams, Carolyn

2015-01-01

Sustainability education is increasingly practiced in early childhood, but a previous review of the literature suggests that there is little empirical research to provide the necessary foundation and critique. The current paper addresses the question of whether there has been an increase in empirical research in the field since this review, and if…

Different elution modes and field programming in gravitational field-flow fractionation. III. Field programming by flow-rate gradient generated by a programmable pump.

PubMed

Plocková, J; Chmelík, J

2001-05-25

Gravitational field-flow fractionation (GFFF) utilizes the Earth's gravitational field as an external force that causes the settlement of particles towards the channel accumulation wall. Hydrodynamic lift forces oppose this action by elevating particles away from the channel accumulation wall. These two counteracting forces enable modulation of the resulting force field acting on particles in GFFF. In this work, force-field programming based on modulating the magnitude of hydrodynamic lift forces was implemented via changes of flow-rate, which was accomplished by a programmable pump. Several flow-rate gradients (step gradients, linear gradients, parabolic, and combined gradients) were tested and evaluated as tools for optimization of the separation of a silica gel particle mixture. The influence of increasing amount of sample injected on the peak resolution under flow-rate gradient conditions was also investigated. This is the first time that flow-rate gradients have been implemented for programming of the resulting force field acting on particles in GFFF.

GPS-Derived Precipitable Water Compared with the Air Force Weather Agency’s MM5 Model Output

DTIC Science & Technology

2002-03-26

and less then 100 sensors are available throughout Europe . While the receiver density is currently comparable to the upper-air sounding network...profiles from 38 upper air sites throughout Europe . Based on these empirical formulae and simplifications, Bevis (1992) has determined that the error...Alaska using Bevis’ (1992) empirical correlation based on 8718 radiosonde calculations over 2 years. Other studies have been conducted in Europe and

Mustafa Kemal at Gallipoli: A Leadership Analysis and Terrain Walk

DTIC Science & Technology

2016-03-01

1 AU/ACSC/PICCIRILLI, S/AY16 AIR COMMAND AND STAFF COLLEGE AIR UNIVERSITY Mustafa Kemal at Gallipoli: A Leadership Analysis and...Requirements for the Degree of MASTER OF OPERATIONAL ARTS AND SCIENCES Advisor: Mr. Patrick D. Ellis Maxwell Air Force Base, Alabama March 2016...bloody stalemate on the Western Front, knock the Ottoman Empire out of the war, and open a sea line of communication to the Russian Empire. The

Using Strong Magnetic Fields to Control Solutal Convection

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2003-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity , we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagnetic salts and solutions in magnetic fields and compare them to analytical predictions.

Experimental determination of forces applied by liquid water drops at high drop velocities impacting a glass plate with and without a shallow water layer using wavelet deconvolution

NASA Astrophysics Data System (ADS)

Yu, Y.; Hopkins, C.

2018-05-01

Time-dependent forces applied by 2 and 4.5 mm diameter drops of water (with velocities up to terminal velocity) impacting upon a glass plate with or without a water layer (up to 10 mm depth) have been measured using two different approaches, force transduction and wavelet deconvolution. Both approaches are in close agreement for drops falling on dry glass. However, only the wavelet approach is able to measure natural features of the splash on shallow water layers that impart forces to the plate after the initial impact. At relatively high velocities (including terminal velocity) the measured peak force from the initial impact is significantly higher than that predicted by idealised drop shape models and models from Roisman et al. and Marengo et al. Hence empirical formulae are developed for the initial time-dependent impact force from drops falling at (a) different velocities up to and including terminal velocity onto a dry glass surface, (b) terminal velocity onto dry glass or glass with a water layer and (c) different velocities below terminal velocity onto dry glass or glass with a water layer. For drops on dry glass, the empirical formulae are applicable to a glass plate or a composite layered plate with a glass surface, although they apply to other plate thicknesses and are applicable to any plate material with a similar surface roughness and wettability. The measurements also indicate that after the initial impact there can be high level forces when bubbles are entrained in the water layer.

Suspended sediment diffusion mechanisms in the Yangtze Estuary influenced by wind fields

NASA Astrophysics Data System (ADS)

Wang, Lihua; Zhou, Yunxuan; Shen, Fang

2018-01-01

The complexity of suspended sediment concentration (SSC) distribution and diffusion has been widely recognized because it is influenced by sediment supply and various hydrodynamic forcing conditions that vary over space and over time. Sediment suspended by waves and transported by currents are the dominant sediment transport mechanisms in estuarine and coastal areas. However, it is unclear to what extent the SSC distribution is impacted by each hydrodynamic factor. Research on the quantitative influence of wind fields on the SSC diffusion range will contribute to a better understanding of the characteristics of sediment transport change and sedimentary geomorphic evolution. This study determined SSC from three Envisat Medium-Resolution Imaging Spectrometer acquisitions, covering the Yangtze Estuary and adjacent water area under the same season and tidal conditions but with varying wind conditions. SSC was examined based on the Semi-Empirical Radiative Transfer model, which has been well validated with the observation data. Integrating the corresponding wind field information from European Centre for Medium-Range Weather Forecasts further facilitated the discussion of wind fields affecting SSC, and in turn the influence of water and suspended sediment transportation and diffusion in the Yangtze estuarine and coastal area. The results demonstrated that the SSC present much more distinctive fluvial features in the inner estuary and wind fields are one of the major factors controlling the range of turbid water diffusion.

Force field development with GOMC, a fast new Monte Carlo molecular simulation code

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.

Solar forcing - implications for the volatile inventory on Mars and Venus. (Invited)

NASA Astrophysics Data System (ADS)

Lundin, Rickard

2015-04-01

Planets in the solar system are exposed to a persistent solar forcing by solar irradiation and the solar wind. The forcing, most pronounced for the inner Earth-like planets, ionizes, heats, modifies chemically, and gradually erodes the upper atmosphere throughout the lifetime of the planets. Of the four inner planets, the Earth is at present the only one habitable. Our kin Venus and Mars have taken different evolutionary paths, the present lack of a hydrosphere being the most significant difference. However, there are ample evidence for that an early Noachian, water rich period existed on Mars. Similarly, arguments have been presented for an early water-rich period on Venus. The question is, what made Mars and Venus evolve in such a different way compared to the Earth? Under the assumption of similar initial conditions, the planets may have experienced different externally driven episodes (e.g. impacts) with time. Conversely, internal factors on Mars and Venus made them less resilient, unable to sustain solar forcing on an evolutionary time-scale. The latter has been quantified from simulations, combining atmospheric and ionospheric modeling and empiric data from solar-like stars (Sun in time). In a similar way, semi-empirical models based on experimental data were used to determine the mass-loss of volatiles back in time from Mars and Venus. This presentation will review further aspects of semi-empirical modeling based on ion and energetic neutral atom (ENA) escape data from Mars and Venus - on short term (days), mid-term (solar cycle proxies), long-term (Heliospheric flux proxies, 10 000 year), and on time scales corresponding to the solar evolution.

AN EVALUATION OF THREE EMPIRICAL AIR-TO-LEAF MODELS FOR POLYCHLORINATED DIBENZO-P-DIOXINS AND DIBENZOFURANS

EPA Science Inventory

Three empirical air-to-leaf models for estimating grass concentrations of polychlorinated dibenzo-p-dioxins and dibenzofurans (abbreviated dioxins and furans) from air concentrations of these compounds are described and tested against two field data sets. All are empirical in th...

Observational determination of surface radiative forcing by CO2 from 2000 to 2010

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feldman, Daniel R.; Collins, William D.; Gero, P. Johnathan

2015-02-25

The climatic impact of CO2 and other greenhouse gases is usually quantified in terms of radiative forcing1, calculated as the difference between estimates of the Earth’s radiation field from pre-industrial and present-day concentrations of these gases. Radiative transfer models calculate that the increase in CO2 since 1750 corresponds to a global annual-mean radiative forcing at the tropopause of 1.82 ± 0.19 W m -2 (ref. 2). However, despite widespread scientific discussion and modelling of the climate impacts of well-mixed greenhouse gases, there is little direct observational evidence of the radiative impact of increasing atmospheric CO2. Here we present observationally basedmore » evidence of clear-sky CO2 surface radiative forcing that is directly attributable to the increase, between 2000 and 2010, of 22 parts per million atmospheric CO2. The time series of this forcing at the two locations—the Southern Great Plains and the North Slope of Alaska—are derived from Atmospheric Emitted Radiance Interferometer spectra3 together with ancillary measurements and thoroughly corroborated radiative transfer calculations4. The time series both show statistically significant trends of 0.2 W m -2 per decade (with respective uncertainties of ±0.06 W m -2 per decade and ±0.07 W m-2 per decade) and have seasonal ranges of 0.1–0.2 W m -2. This is approximately ten per cent of the trend in downwelling longwave radiation5, 6, 7. These results confirm theoretical predictions of the atmospheric greenhouse effect due to anthropogenic emissions, and provide empirical evidence of how rising CO2 levels, mediated by temporal variations due to photosynthesis and respiration, are affecting the surface energy balance.« less

A semi-empirical method for calculating the pitching moment of bodies of revolution at low Mach numbers

NASA Technical Reports Server (NTRS)

Hopkins, Edward J

1951-01-01

A semiempirical method, in which potential theory is arbitrarily combined with an approximate viscous theory, for calculating the aerodynamic pitching moments for bodies of revolution is presented. The method can also be used for calculating the lift and drag forces. The calculated and experimental force and moment characteristics of 15 bodies of revolution are compared.

Collective European Security Forces: An Idea Whose Time Has Come

DTIC Science & Technology

1990-04-01

undergoing equipment conversion ( Nike ) - units to relocate under new air defense concept (CRCs, Patriot and IHawk units) - units converting by personnel...34Eastern Europe is traditionally one of the most volatile parts of the world. It has remained a volatile region under the Soviet empire. Gorba...levels of general purpose forces with offense-oriented capabilities, namely tanks, artillery, armoured troop carriers (ATCs), strike aircraft and

Energy distributions of an ion in a radio-frequency trap immersed in a buffer gas under the influence of additional external forces

NASA Astrophysics Data System (ADS)

Rouse, I.; Willitsch, S.

2018-04-01

An ion held in a radio-frequency trap interacting with a uniform buffer gas of neutral atoms develops a steady-state energy distribution characterized by a power-law tail at high energies instead of the exponential decay characteristic of thermal equilibrium. We have previously shown that the Tsallis statistics frequently used as an empirical model for this distribution is a good approximation when the ion is heated due to a combination of micromotion interruption and exchange of kinetic energy with the buffer gas [Rouse and Willitsch, Phys. Rev. Lett. 118, 143401 (2017), 10.1103/PhysRevLett.118.143401]. Here, we extend our treatment to include the heating due to additional motion of the ion caused by external forces, including the "excess micromotion" induced by uniform electric fields and rf phase offsets. We show that this also leads to a Tsallis distribution with a potentially different power-law exponent from that observed in the absence of this additional forced motion, with the difference increasing as the ratio of the mass of the neutral atoms to that of the ion decreases. Our results indicate that unless the excess micromotion is minimized to a very high degree, then even a system with very light neutrals and a heavy ion does not exhibit a thermal distribution.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

PubMed

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

2012-02-14

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

Intercomparison of Meteorological Forcing Data from Empirical and Mesoscale Model Sources in the N.F. American River Basin in northern California

NASA Astrophysics Data System (ADS)

Wayand, N. E.; Hamlet, A. F.; Hughes, M. R.; Feld, S.; Lundquist, J. D.

2012-12-01

The data required to drive distributed hydrological models is significantly limited within mountainous terrain due to a scarcity of observations. This study evaluated three common configurations of forcing data: a) one low-elevation station, combined with empirical techniques, b) gridded output from the Weather Research and Forecasting (WRF) model, and c) a combination of the two. Each configuration was evaluated within the heavily-instrumented North Fork American River Basin in northern California, during October-June 2000-2010. Simulations of streamflow and snowpack using the Distributed Hydrology Soil and Vegetation Model (DHSVM) highlighted precipitation and radiation as variables whose sources resulted in significant differences. The best source of precipitation data varied between years. On average, the performance of WRF and the single station distributed using the Parameter Regression on Independent Slopes Model (PRISM), were not significantly different. The average percent biases in simulated streamflow were 3.4% and 0.9%, for configurations a) and b) respectively, even though precipitation compared directly with gauge measurements was biased high by 6% and 17%, suggesting that gauge undercatch may explain part of the bias. Simulations of snowpack using empirically-estimated long-wave irradiance resulted in melt rates lower than those observed at high-elevation sites, while at lower-elevations the same forcing caused significant mid-winter melt that was not observed (Figure 1). These results highlight the complexity of how forcing data sources impact hydrology over different areas (high vs. low elevation snow) and different time-periods. Overall, results support the use of output from the WRF model over empirical techniques in regions with limited station data. FIG. 1. (a,b) Simulated SWE from DHSVM compared to observations at the Sierra Snow Lab (2100m) and Blue Canyon (1609m) during 2008 - 2009. Modeled (c,d) internal pack temperature, (e,f) downward short-wave irradiance, (g,h) downward long-wave irradiance, and (i,k) net-irradiance. Note that the timeperiod of plots e,g,i focus on the melt season (March-May), and plots f,h,j focus on the erroneous mid-winter melt event during January - time-periods marked with vertical dashed lines in (a) and (b).

Three Dimensional Distribution of Sensitive Field and Stress Field Inversion of Force Sensitive Materials under Constant Current Excitation.

PubMed

Zhao, Shuanfeng; Liu, Min; Guo, Wei; Zhang, Chuanwei

2018-02-28

Force sensitive conductive composite materials are functional materials which can be used as the sensitive material of force sensors. However, the existing sensors only use one-dimensional electrical properties of force sensitive conductive materials. Even in tactile sensors, the measurement of contact pressure is achieved by large-scale arrays and the units of a large-scale array are also based on the one-dimensional electrical properties of force sensitive materials. The main contribution of this work is to study the three-dimensional electrical properties and the inversion method of three-dimensional stress field of a force sensitive material (conductive rubber), which pushes the application of force sensitive material from one dimensional to three-dimensional. First, the mathematical model of the conductive rubber current field distribution under a constant force is established by the effective medium theory, and the current field distribution model of conductive rubber with different geometry, conductive rubber content and conductive rubber relaxation parameters is deduced. Secondly, the inversion method of the three-dimensional stress field of conductive rubber is established, which provides a theoretical basis for the design of a new tactile sensor, three-dimensional stress field and space force based on force sensitive materials.

Empirical Psycho-Aesthetics and Her Sisters: Substantive and Methodological Issues--Part I

ERIC Educational Resources Information Center

Konecni, Vladimir J.

2012-01-01

Empirical psycho-aesthetics--an interdisciplinary field with a long tradition--is approached in this two-part article from two directions, in each case with several objectives. Part I, in this issue of "JAE", is devoted to the first direction, which is mainly definitional and organizational: the objectives are to present an outline of the field's…

Sorting the Wheat from the Chaff: What Makes for Good Evidence of Effectiveness in the Literature in Gifted Education?

ERIC Educational Resources Information Center

Callahan, Carolyn M.; Moon, Tonya R.

2007-01-01

To provide an overview of the specific components that must be considered when making decisions about research in the field of gifted education, the authors describe and evaluate the three types of evidence--speculative or anecdotal, theoretical, and empirical--commonly offered in the literature of the field. Empirical, or evidence-based, research…

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

PubMed

Best, Robert B; Hummer, Gerhard

2009-07-02

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

Using Mason number to predict MR damper performance from limited test data

NASA Astrophysics Data System (ADS)

Becnel, Andrew C.; Wereley, Norman M.

2017-05-01

The Mason number can be used to produce a single master curve which relates MR fluid stress versus strain rate behavior across a wide range of shear rates, temperatures, and applied magnetic fields. As applications of MR fluid energy absorbers expand to a variety of industries and operating environments, Mason number analysis offers a path to designing devices with desired performance from a minimal set of preliminary test data. Temperature strongly affects the off-state viscosity of the fluid, as the passive viscous force drops considerably at higher temperatures. Yield stress is not similarly affected, and stays relatively constant with changing temperature. In this study, a small model-scale MR fluid rotary energy absorber is used to measure the temperature correction factor of a commercially-available MR fluid from LORD Corporation. This temperature correction factor is identified from shear stress vs. shear rate data collected at four different temperatures. Measurements of the MR fluid yield stress are also obtained and related to a standard empirical formula. From these two MR fluid properties - temperature-dependent viscosity and yield stress - the temperature-corrected Mason number is shown to predict the force vs. velocity performance of a full-scale rotary MR fluid energy absorber. This analysis technique expands the design space of MR devices to high shear rates and allows for comprehensive predictions of overall performance across a wide range of operating conditions from knowledge only of the yield stress vs. applied magnetic field and a temperature-dependent viscosity correction factor.

Molecular simulation study on Hofmeister cations and the aqueous solubility of benzene.

PubMed

Ganguly, Pritam; Hajari, Timir; van der Vegt, Nico F A

2014-05-22

We study the ion-specific salting-out process of benzene in aqueous alkali chloride solutions using Kirkwood-Buff (KB) theory of solutions and molecular dynamics simulations with different empirical force field models for the ions and benzene. Despite inaccuracies in the force fields, the simulations indicate that the decrease of the Setchenow salting-out coefficient for the series NaCl > KCl > RbCl > CsCl is determined by direct benzene-cation correlations, with the larger cations showing weak interactions with benzene. Although ion-specific aqueous solubilities of benzene may be affected by indirect ion-ion, ion-water, and water-water correlations, too, these correlations are found to be unimportant, with little to no effect on the Setchenow salting-out coefficients of the various salts. We further considered LiCl, which is experimentally known to be a weaker salting-out agent than NaCl and KCl and, therefore, ranks at an unusual position within the Hofmeister cation series. The simulations indicate that hydrated Li(+) ions can take part of the benzene hydration shell while the other cations are repelled by it. This causes weaker Li(+) exclusion around the solute and a resulting, weaker salting-out propensity of LiCl compared to that of the other salts. Removing benzene-water and benzene-salt electrostatic interactions in the simulations does not affect this mechanism, which may therefore also explain the smaller effect of LiCl, as compared to that of NaCl or KCl, on aqueous solvation and hydrophobic interaction of nonpolar molecules.

An Empirical Modification of the Force Field Approach to Describe the Modulation of Galactic Cosmic Rays Close to Earth in a Broad Range of Rigidities

NASA Astrophysics Data System (ADS)

Gieseler, J.; Heber, B.; Herbst, K.

2017-11-01

On their way through the heliosphere, galactic cosmic rays (GCRs) are modulated by various effects before they can be detected at Earth. This process can be described by the Parker equation, which calculates the phase space distribution of GCRs depending on the main modulation processes: convection, drifts, diffusion, and adiabatic energy changes. A first-order approximation of this equation is the force field approach, reducing it to a one-parameter dependency, the solar modulation potential ϕ. Utilizing this approach, it is possible to reconstruct ϕ from ground-based and spacecraft measurements. However, it has been shown previously that ϕ depends not only on the local interstellar spectrum (LIS) but also on the energy range of interest. We have investigated this energy dependence further, using published proton intensity spectra obtained by PAMELA and heavier nuclei measurements from IMP-8 and ACE/CRIS. Our results show severe limitations at lower energies including a strong dependence on the solar magnetic epoch. Based on these findings, we will outline a new tool to describe GCR proton spectra in the energy range from a few hundred MeV to tens of GeV over the last solar cycles. In order to show the importance of our modification, we calculate the global production rates of the cosmogenic radionuclide 10Be which is a proxy for the solar activity ranging back thousands of years.

Trust between patients and health websites: a review of the literature and derived outcomes from empirical studies

PubMed Central

Vega, Laurian C.; Montague, Enid; DeHart, Tom

2012-01-01

With the exploding growth of the web, health websites have become a dominant force in the realm of health care. Technically savvy patients have been using the web not only to self inform but to self diagnose. In this paper we examine the trust relationship between humans and health websites by outlining the existing literature on trust in health websites. A total of forty-nine papers were examined using a meta-analytical framework. Using this framework, each paper was coded for the antecedents and facets that comprise user trust in health websites. Our findings show that there is little consensus regarding the defining characteristics of the construct of trust in health websites. Further research in this field should focus on collaboratively defining trust and what factors affect trust in health web sites. PMID:22288026

New perspectives on evolutionary medicine: the relevance of microevolution for human health and disease.

PubMed

Rühli, Frank Jakobus; Henneberg, Maciej

2013-04-29

Evolutionary medicine (EM) is a growing field focusing on the evolutionary basis of human diseases and their changes through time. To date, the majority of EM studies have used pure theories of hominin macroevolution to explain the present-day state of human health. Here, we propose a different approach by addressing more empirical and health-oriented research concerning past, current and future microevolutionary changes of human structure, functions and pathologies. Studying generation-to-generation changes of human morphology that occurred in historical times, and still occur in present-day populations under the forces of evolution, helps to explain medical conditions and warns clinicians that their current practices may influence future humans. Also, analyzing historic tissue specimens such as mummies is crucial in order to address the molecular evolution of pathogens, of the human genome, and their coadaptations.

The contribution of organization theory to nursing health services research.

PubMed

Mick, Stephen S; Mark, Barbara A

2005-01-01

We review nursing and health services research on health care organizations over the period 1950 through 2004 to reveal the contribution of nursing to this field. Notwithstanding this rich tradition and the unique perspective of nursing researchers grounded in patient care production processes, the following gaps in nursing research remain: (1) the lack of theoretical frameworks about organizational factors relating to internal work processes; (2) the need for sophisticated methodologies to guide empirical investigations; (3) the difficulty in understanding how organizations adapt models for patient care delivery in response to market forces; (4) the paucity of attention to the impact of new technologies on the organization of patient care work processes. Given nurses' deep understanding of the inner workings of health care facilities, we hope to see an increasing number of research programs that tackle these deficiencies.

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

Trust between patients and health websites: a review of the literature and derived outcomes from empirical studies.

PubMed

Vega, Laurian C; Montague, Enid; Dehart, Tom

2011-11-18

With the exploding growth of the web, health websites have become a dominant force in the realm of health care. Technically savvy patients have been using the web not only to self inform but to self diagnose. In this paper we examine the trust relationship between humans and health websites by outlining the existing literature on trust in health websites. A total of forty-nine papers were examined using a meta-analytical framework. Using this framework, each paper was coded for the antecedents and facets that comprise user trust in health websites. Our findings show that there is little consensus regarding the defining characteristics of the construct of trust in health websites. Further research in this field should focus on collaboratively defining trust and what factors affect trust in health web sites.

An empirical polytrope law for solar wind thermal electrons between 0.45 and 4.76 AU - Voyager 2 and Mariner 10

NASA Technical Reports Server (NTRS)

Sittler, E. C., Jr.; Scudder, J. D.

1980-01-01

In this paper empirical evidence is presented that between 0.4 and 5 AU the thermal portion (but not all) of the solar wind electron population obeys a polytrope relation. It is also shown that this functional relationship is a member of a broader class of possible laws required of a steady state, fully ionized plasma whose proper frame electric field is dominated by the polarization electric field. The empirically determined, thermodynamically interesting value of the polytrope index (1.175) is virtually that predicted (1.16) by the theoretical considerations of Scudder and Olbert (1979). Strong, direct, empirical evidence for the nearly isothermal behavior of solar wind electrons as has been indirectly argued in the literature for some time is provided.

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

The Factor Content of Bilateral Trade: An Empirical Test.

ERIC Educational Resources Information Center

Choi, Yong-Seok; Krishna, Pravin

2004-01-01

The factor proportions model of international trade is one of the most influential theories in international economics. Its central standing in this field has appropriately prompted, particularly recently, intense empirical scrutiny. A substantial and growing body of empirical work has tested the predictions of the theory on the net factor content…

Climate data induced uncertainty in model-based estimations of terrestrial primary productivity

NASA Astrophysics Data System (ADS)

Wu, Zhendong; Ahlström, Anders; Smith, Benjamin; Ardö, Jonas; Eklundh, Lars; Fensholt, Rasmus; Lehsten, Veiko

2017-06-01

Model-based estimations of historical fluxes and pools of the terrestrial biosphere differ substantially. These differences arise not only from differences between models but also from differences in the environmental and climatic data used as input to the models. Here we investigate the role of uncertainties in historical climate data by performing simulations of terrestrial gross primary productivity (GPP) using a process-based dynamic vegetation model (LPJ-GUESS) forced by six different climate datasets. We find that the climate induced uncertainty, defined as the range among historical simulations in GPP when forcing the model with the different climate datasets, can be as high as 11 Pg C yr-1 globally (9% of mean GPP). We also assessed a hypothetical maximum climate data induced uncertainty by combining climate variables from different datasets, which resulted in significantly larger uncertainties of 41 Pg C yr-1 globally or 32% of mean GPP. The uncertainty is partitioned into components associated to the three main climatic drivers, temperature, precipitation, and shortwave radiation. Additionally, we illustrate how the uncertainty due to a given climate driver depends both on the magnitude of the forcing data uncertainty (climate data range) and the apparent sensitivity of the modeled GPP to the driver (apparent model sensitivity). We find that LPJ-GUESS overestimates GPP compared to empirically based GPP data product in all land cover classes except for tropical forests. Tropical forests emerge as a disproportionate source of uncertainty in GPP estimation both in the simulations and empirical data products. The tropical forest uncertainty is most strongly associated with shortwave radiation and precipitation forcing, of which climate data range contributes higher to overall uncertainty than apparent model sensitivity to forcing. Globally, precipitation dominates the climate induced uncertainty over nearly half of the vegetated land area, which is mainly due to climate data range and less so due to the apparent model sensitivity. Overall, climate data ranges are found to contribute more to the climate induced uncertainty than apparent model sensitivity to forcing. Our study highlights the need to better constrain tropical climate, and demonstrates that uncertainty caused by climatic forcing data must be considered when comparing and evaluating carbon cycle model results and empirical datasets.

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

PubMed

Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

2018-03-01

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

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

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

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

Mathematical modeling of PDC bit drilling process based on a single-cutter mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wojtanowicz, A.K.; Kuru, E.

1993-12-01

An analytical development of a new mechanistic drilling model for polycrystalline diamond compact (PDC) bits is presented. The derivation accounts for static balance of forces acting on a single PDC cutter and is based on assumed similarity between bit and cutter. The model is fully explicit with physical meanings given to all constants and functions. Three equations constitute the mathematical model: torque, drilling rate, and bit life. The equations comprise cutter`s geometry, rock properties drilling parameters, and four empirical constants. The constants are used to match the model to a PDC drilling process. Also presented are qualitative and predictive verificationsmore » of the model. Qualitative verification shows that the model`s response to drilling process variables is similar to the behavior of full-size PDC bits. However, accuracy of the model`s predictions of PDC bit performance is limited primarily by imprecision of bit-dull evaluation. The verification study is based upon the reported laboratory drilling and field drilling tests as well as field data collected by the authors.« less

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

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

PubMed

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

2015-05-15

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

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

PubMed

Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

2016-11-09

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol -1 . For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol -1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol -1 ) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol -1 ). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

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

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

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

Surface wave effects in the NEMO ocean model: Forced and coupled experiments

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Mogensen, Kristian; Bidlot, Jean-Raymond; Balmaseda, Magdalena Alonso; Janssen, Peter A. E. M.

2015-04-01

The NEMO general circulation ocean model is extended to incorporate three physical processes related to ocean surface waves, namely the surface stress (modified by growth and dissipation of the oceanic wavefield), the turbulent kinetic energy flux from breaking waves, and the Stokes-Coriolis force. Experiments are done with NEMO in ocean-only (forced) mode and coupled to the ECMWF atmospheric and wave models. Ocean-only integrations are forced with fields from the ERA-Interim reanalysis. All three effects are noticeable in the extratropics, but the sea-state-dependent turbulent kinetic energy flux yields by far the largest difference. This is partly because the control run has too vigorous deep mixing due to an empirical mixing term in NEMO. We investigate the relation between this ad hoc mixing and Langmuir turbulence and find that it is much more effective than the Langmuir parameterization used in NEMO. The biases in sea surface temperature as well as subsurface temperature are reduced, and the total ocean heat content exhibits a trend closer to that observed in a recent ocean reanalysis (ORAS4) when wave effects are included. Seasonal integrations of the coupled atmosphere-wave-ocean model consisting of NEMO, the wave model ECWAM, and the atmospheric model of ECMWF similarly show that the sea surface temperature biases are greatly reduced when the mixing is controlled by the sea state and properly weighted by the thickness of the uppermost level of the ocean model. These wave-related physical processes were recently implemented in the operational coupled ensemble forecast system of ECMWF.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

Optical tracking of acoustic radiation force impulse-induced dynamics in a tissue-mimicking phantom

PubMed Central

Bouchard, Richard R.; Palmeri, Mark L.; Pinton, Gianmarco F.; Trahey, Gregg E.; Streeter, Jason E.; Dayton, Paul A.

2009-01-01

Optical tracking was utilized to investigate the acoustic radiation force impulse (ARFI)-induced response, generated by a 5-MHz piston transducer, in a translucent tissue-mimicking phantom. Suspended 10-μm microspheres were tracked axially and laterally at multiple locations throughout the field of view of an optical microscope with 0.5-μm displacement resolution, in both dimensions, and at frame rates of up to 36 kHz. Induced dynamics were successfully captured before, during, and after the ARFI excitation at depths of up to 4.8 mm from the phantom’s proximal boundary. Results are presented for tracked axial and lateral displacements resulting from on-axis and off-axis (i.e., shear wave) acquisitions; these results are compared to matched finite element method modeling and independent ultrasonically based empirical results and yielded reasonable agreement in most cases. A shear wave reflection, generated by the proximal boundary, consistently produced an artifact in tracked displacement data later in time (i.e., after the initial ARFI-induced displacement peak). This tracking method provides high-frame-rate, two-dimensional tracking data and thus could prove useful in the investigation of complex ARFI-induced dynamics in controlled experimental settings. PMID:19894849

Study of Solid Particle Behavior in High Temperature Gas Flows

NASA Astrophysics Data System (ADS)

Majid, A.; Bauder, U.; Stindl, T.; Fertig, M.; Herdrich, G.; Röser, H.-P.

2009-01-01

The Euler-Lagrangian approach is used for the simulation of solid particles in hypersonic entry flows. For flow field simulation, the program SINA (Sequential Iterative Non-equilibrium Algorithm) developed at the Institut für Raumfahrtsysteme is used. The model for the effect of the carrier gas on a particle includes drag force and particle heating only. Other parameters like lift Magnus force or damping torque are not taken into account so far. The reverse effect of the particle phase on the gaseous phase is currently neglected. Parametric analysis is done regarding the impact of variation in the physical input conditions like position, velocity, size and material of the particle. Convective heat fluxes onto the surface of the particle and its radiative cooling are discussed. The variation of particle temperature under different conditions is presented. The influence of various input conditions on the trajectory is explained. A semi empirical model for the particle wall interaction is also discussed and the influence of the wall on the particle trajectory with different particle conditions is presented. The heat fluxes onto the wall due to impingement of particles are also computed and compared with the heat fluxes from the gas.

Experimental studies illuminate the cultural transmission of percussive technologies in Homo and Pan

PubMed Central

Whiten, Andrew

2015-01-01

The complexity of Stone Age tool-making is assumed to have relied upon cultural transmission, but direct evidence is lacking. This paper reviews evidence bearing on this question provided through five related empirical perspectives. Controlled experimental studies offer special power in identifying and dissecting social learning into its diverse component forms, such as imitation and emulation. The first approach focuses on experimental studies that have discriminated social learning processes in nut-cracking by chimpanzees. Second come experiments that have identified and dissected the processes of cultural transmission involved in a variety of other force-based forms of chimpanzee tool use. A third perspective is provided by field studies that have revealed a range of forms of forceful, targeted tool use by chimpanzees, that set percussion in its broader cognitive context. Fourth are experimental studies of the development of flint knapping to make functional sharp flakes by bonobos, implicating and defining the social learning and innovation involved. Finally, new and substantial experiments compare what different social learning processes, from observational learning to teaching, afford good quality human flake and biface manufacture. Together these complementary approaches begin to delineate the social learning processes necessary to percussive technologies within the Pan–Homo clade. PMID:26483537

Reducing numerical costs for core wide nuclear reactor CFD simulations by the Coarse-Grid-CFD

NASA Astrophysics Data System (ADS)

Viellieber, Mathias; Class, Andreas G.

2013-11-01

Traditionally complete nuclear reactor core simulations are performed with subchannel analysis codes, that rely on experimental and empirical input. The Coarse-Grid-CFD (CGCFD) intends to replace the experimental or empirical input with CFD data. The reactor core consists of repetitive flow patterns, allowing the general approach of creating a parametrized model for one segment and composing many of those to obtain the entire reactor simulation. The method is based on a detailed and well-resolved CFD simulation of one representative segment. From this simulation we extract so-called parametrized volumetric forces which close, an otherwise strongly under resolved, coarsely-meshed model of a complete reactor setup. While the formulation so far accounts for forces created internally in the fluid others e.g. obstruction and flow deviation through spacers and wire wraps, still need to be accounted for if the geometric details are not represented in the coarse mesh. These are modelled with an Anisotropic Porosity Formulation (APF). This work focuses on the application of the CGCFD to a complete reactor core setup and the accomplishment of the parametrization of the volumetric forces.

Integration of the radiation belt environment model into the space weather modeling framework

NASA Astrophysics Data System (ADS)

Glocer, A.; Toth, G.; Fok, M.; Gombosi, T.; Liemohn, M.

2009-11-01

We have integrated the Fok radiation belt environment (RBE) model into the space weather modeling framework (SWMF). RBE is coupled to the global magnetohydrodynamics component (represented by the Block-Adaptive-Tree Solar-wind Roe-type Upwind Scheme, BATS-R-US, code) and the Ionosphere Electrodynamics component of the SWMF, following initial results using the Weimer empirical model for the ionospheric potential. The radiation belt (RB) model solves the convection-diffusion equation of the plasma in the energy range of 10 keV to a few MeV. In stand-alone mode RBE uses Tsyganenko's empirical models for the magnetic field, and Weimer's empirical model for the ionospheric potential. In the SWMF the BATS-R-US model provides the time dependent magnetic field by efficiently tracing the closed magnetic field-lines and passing the geometrical and field strength information to RBE at a regular cadence. The ionosphere electrodynamics component uses a two-dimensional vertical potential solver to provide new potential maps to the RBE model at regular intervals. We discuss the coupling algorithm and show some preliminary results with the coupled code. We run our newly coupled model for periods of steady solar wind conditions and compare our results to the RB model using an empirical magnetic field and potential model. We also simulate the RB for an active time period and find that there are substantial differences in the RB model results when changing either the magnetic field or the electric field, including the creation of an outer belt enhancement via rapid inward transport on the time scale of tens of minutes.

Extracting the potential-well of a near-field optical trap using the Helmholtz-Hodge decomposition

NASA Astrophysics Data System (ADS)

Zaman, Mohammad Asif; Padhy, Punnag; Hansen, Paul C.; Hesselink, Lambertus

2018-02-01

The non-conservative nature of the force field generated by a near-field optical trap is analyzed. A plasmonic C-shaped engraving on a gold film is considered as the trap. The force field is calculated using the Maxwell stress tensor method. The Helmholtz-Hodge decomposition is used to extract the conservative and the non-conservative component of the force. Due to the non-negligible non-conservative component, it is found that the conventional approach of extracting the potential by direct integration of the force is not accurate. Despite the non-conservative nature of the force field, it is found that the statistical properties of a trapped nanoparticle can be estimated from the conservative component of the force field alone. Experimental and numerical results are presented to support the claims.

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

PubMed

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.

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

The application of flow competence evaluations to the assessment of flood-flow velocities and stresses

NASA Technical Reports Server (NTRS)

Komar, Paul D.

1987-01-01

The concept of flow competence is generally employed to evaluate the velocities, discharges, and bottom stresses of river floods inferred from the size of the largest sediment particles transported. Flow competence has become an important tool for evaluating the hydraulics of exceptional floods on Earth, including those which eroded the Channeled Scabland of eastern Washington, and has potential for similar evaluations of the floods which carved the outflow channels on Mars. For the most part, flow-competence evaluations were empirical, based on data compiled from a variety of sources including major terrestrial floods caused by natural processes or dam failures. Such flow-competence relationships would appear to provide a straight-forward assessment of flood-flow stresses and velocities based on the maximum size of gravel and boulders transported. However, a re-examination of the data base and comparisons with measurements of selective entrainment and transport of gravel in rivers open to question such evaluations. Analyses of the forces acting on the grain during entrainment by pivoting, rolling, or sliding, an approach which focuses more on the physical processes than the purely empirical relationships can be demonstrated. These derived equations require further testing by flume and field measurements before being applied to flow-competence evaluations. Such tests are now underway.

The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan

PubMed Central

Lipatov, Mikhail; Brown, Melissa J.; Feldman, Marcus W.

2011-01-01

With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction. PMID:21320903

The influence of social niche on cultural niche construction: modelling changes in belief about marriage form in Taiwan.

PubMed

Lipatov, Mikhail; Brown, Melissa J; Feldman, Marcus W

2011-03-27

With introduction of social niche effects into a model of cultural change, the frequency of a practice cannot predict the frequency of its underlying belief. The combination of a general model with empirical data from a specific case illustrates the importance of collaboration between modellers and field researchers, and identifies the type of quantitative data necessary for analysing case studies. Demographic data from colonial-period household registers in Taiwan document a shift in marriage form within 40 years, from a mixture of uxorilocal marriages and virilocal marriages to the latter's dominance. Ethnographic data indicate marriage-related beliefs, costs, ethnic effects and colonial policies as well as the importance of horizontal cultural transmission. We present a formal model for the effects of moral beliefs about marriage and a population economic index on the decline of uxorilocal marriage. We integrate empirical marriage rates and an estimated economic index to produce five projections of the historical frequencies of one belief. These projections demonstrate how economic development may affect a cultural niche. They also indicate the need for future research on the relationship between wealth and cultural variability, the motivational force of cultural versus social factors, and the process of cultural niche construction.

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

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.

Security Force Assistance in Afghanistan: Identifying Lessons for Future Efforts

DTIC Science & Technology

2011-01-01

Reports & Bookstore Make a charitable contribution Limited Electronic Distribution Rights This document and trademark(s) contained herein are protected by...waged by U.S. and coalition forces in Afghani- stan. The outcome of the campaign hinges, in large measure, on the effectiveness of the assistance... effectiveness of SFA in Afghanistan, and few empirically rigorous assessments exist to help answer these questions. This monograph analyzes SFA efforts in

A Physics Based Vehicle Terrain Interaction Model for Soft Soil off-Road Vehicle Simulations

DTIC Science & Technology

2012-01-01

assumed terrain deformation, use of empirical relationships for the deformation, or finite/discrete element approaches for the terrain. A real-time...vertical columns of soil, and the deformation of each is modeled using visco-elasto-plastic compressibility relationships that relate subsoil pressures to...produced by tractive and turning forces will also be incorporated into the model. Both the vertical and horizontal force/displacement relationships

Numerical simulation of a flow past a triangular sail-type blade of a wind generator using the ANSYS FLUENT software package

NASA Astrophysics Data System (ADS)

Kusaiynov, K.; Tanasheva, N. K.; Min'kov, L. L.; Nusupbekov, B. R.; Stepanova, Yu. O.; Rozhkova, A. V.

2016-02-01

An air flow past a single triangular sail-type blade of a wind turbine is analyzed by numerical simulation for low velocities of the incoming flow. The results of numerical simulation indicate a monotonic increase in the drag force and the lift force as functions of the incoming flow; empirical dependences of these quantities are obtained.

Countering Solutal Buoyant Convection with High Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemist, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitant, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity, we have been able to dramatically effect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the current status of the investigation and discuss results from the experimental and modeling efforts.

A method to integrate descriptive and experimental field studies at the level of data and empirical concepts1

PubMed Central

Bijou, Sidney W.; Peterson, Robert F.; Ault, Marion H.

1968-01-01

It is the thesis of this paper that data from descriptive and experimental field studies can be interrelated at the level of data and empirical concepts if both sets are derived from frequency-of-occurrence measures. The methodology proposed for a descriptive field study is predicated on three assumptions: (1) The primary data of psychology are the observable interactions of a biological organism and environmental events, past and present. (2) Theoretical concepts and laws are derived from empirical concepts and laws, which in turn are derived from the raw data. (3) Descriptive field studies describe interactions between behavioral and environmental events; experimental field studies provide information on their functional relationships. The ingredients of a descriptive field investigation using frequency measures consist of: (1) specifying in objective terms the situation in which the study is conducted, (2) defining and recording behavioral and environmental events in observable terms, and (3) measuring observer reliability. Field descriptive studies following the procedures suggested here would reveal interesting new relationships in the usual ecological settings and would also provide provocative cues for experimental studies. On the other hand, field-experimental studies using frequency measures would probably yield findings that would suggest the need for describing new interactions in specific natural situations. PMID:16795175

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

DTIC Science & Technology

1968-03-01

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

Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

PubMed Central

2017-01-01

We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol). PAC-MAC shows a RMSE of 0.151 kBT with a calculation speed being potentially 1.0 × 104 times greater than TI. OPLS-AA force field parameters are optimized using PAC-MAC based on vapor–liquid equilibrium data, instead of enthalpies of vaporization or densities. The RMSE of PAC-MAC is reduced to 0.099 kBT by optimizing 50 force field parameters. The resulting OPLS-PM force field has a comparable accuracy as the OPLS-AA force field in the calculation of mixing free energies using TI. PMID:28418655

Magnetic moment of solar plasma and the Kelvin force: -The driving force of plasma up-flow -

NASA Astrophysics Data System (ADS)

Shibasaki, Kiyoto

2017-04-01

Thermal plasma in the solar atmosphere is magnetized (diamagnetic). The magnetic moment does not disappear by collisions because complete gyration is not a necessary condition to have magnetic moment. Magnetized fluid is subjected to Kelvin force in non-uniform magnetic field. Generally, magnetic field strength decreases upwards in the solar atmosphere, hence the Kelvin force is directed upwards along the field. This force is not included in the fluid treatment of MHD. By adding the Kelvin force to the MHD equation of motion, we can expect temperature dependent plasma flows along the field which are reported by many observations. The temperature dependence of the flow speed is explained by temperature dependence of magnetic moment. From the observed parameters, we can infer physical parameters in the solar atmosphere such as scale length of the magnetic field strength and the friction force acting on the flowing plasma. In case of closed magnetic field lines, loop-top concentration of hot plasma is expected which is frequently observed.

Sarajevo 1914: An Examination of the Context by which Austria Hungary Responded to the Assassination of Archduke Franz Ferdinand

DTIC Science & Technology

2014-04-01

into the empire under separate arrangements offering varying degrees of autonomy. The Great Compromise of 1867 was the first political arrangement...considered it treasonous that the Hungarians demanded equal share in the Empire and criticized the Great Compromise of 1867. As the Slavs began to demand...lands.8 Kann goes on to say, “Undoubtedly, a great shift to the forces of ethnic and, to some extent, even racial nationalism occurred during the

The compensatory interaction between motor unit firing behavior and muscle force during fatigue

PubMed Central

De Luca, Carlo J.; Kline, Joshua C.

2016-01-01

Throughout the literature, different observations of motor unit firing behavior during muscle fatigue have been reported and explained with varieties of conjectures. The disagreement amongst previous studies has resulted, in part, from the limited number of available motor units and from the misleading practice of grouping motor unit data across different subjects, contractions, and force levels. To establish a more clear understanding of motor unit control during fatigue, we investigated the firing behavior of motor units from the vastus lateralis muscle of individual subjects during a fatigue protocol of repeated voluntary constant force isometric contractions. Surface electromyographic decomposition technology provided the firings of 1,890 motor unit firing trains. These data revealed that to sustain the contraction force as the muscle fatigued, the following occurred: 1) motor unit firing rates increased; 2) new motor units were recruited; and 3) motor unit recruitment thresholds decreased. Although the degree of these adaptations was subject specific, the behavior was consistent in all subjects. When we compared our empirical observations with those obtained from simulation, we found that the fatigue-induced changes in motor unit firing behavior can be explained by increasing excitation to the motoneuron pool that compensates for the fatigue-induced decrease in muscle force twitch reported in empirical studies. Yet, the fundamental motor unit control scheme remains invariant throughout the development of fatigue. These findings indicate that the central nervous system regulates motor unit firing behavior by adjusting the operating point of the excitation to the motoneuron pool to sustain the contraction force as the muscle fatigues. PMID:27385798

The compensatory interaction between motor unit firing behavior and muscle force during fatigue.

PubMed

Contessa, Paola; De Luca, Carlo J; Kline, Joshua C

2016-10-01

Throughout the literature, different observations of motor unit firing behavior during muscle fatigue have been reported and explained with varieties of conjectures. The disagreement amongst previous studies has resulted, in part, from the limited number of available motor units and from the misleading practice of grouping motor unit data across different subjects, contractions, and force levels. To establish a more clear understanding of motor unit control during fatigue, we investigated the firing behavior of motor units from the vastus lateralis muscle of individual subjects during a fatigue protocol of repeated voluntary constant force isometric contractions. Surface electromyographic decomposition technology provided the firings of 1,890 motor unit firing trains. These data revealed that to sustain the contraction force as the muscle fatigued, the following occurred: 1) motor unit firing rates increased; 2) new motor units were recruited; and 3) motor unit recruitment thresholds decreased. Although the degree of these adaptations was subject specific, the behavior was consistent in all subjects. When we compared our empirical observations with those obtained from simulation, we found that the fatigue-induced changes in motor unit firing behavior can be explained by increasing excitation to the motoneuron pool that compensates for the fatigue-induced decrease in muscle force twitch reported in empirical studies. Yet, the fundamental motor unit control scheme remains invariant throughout the development of fatigue. These findings indicate that the central nervous system regulates motor unit firing behavior by adjusting the operating point of the excitation to the motoneuron pool to sustain the contraction force as the muscle fatigues. Copyright © 2016 the American Physiological Society.

Measuring Stakeholder Participation in Evaluation: An Empirical Validation of the Participatory Evaluation Measurement Instrument (PEMI)

ERIC Educational Resources Information Center

Daigneault, Pierre-Marc; Jacob, Steve; Tremblay, Joel

2012-01-01

Background: Stakeholder participation is an important trend in the field of program evaluation. Although a few measurement instruments have been proposed, they either have not been empirically validated or do not cover the full content of the concept. Objectives: This study consists of a first empirical validation of a measurement instrument that…

Injury risk curves for the skeletal knee-thigh-hip complex for knee-impact loading.

PubMed

Rupp, Jonathan D; Flannagan, Carol A C; Kuppa, Shashi M

2010-01-01

Injury risk curves for the skeletal knee-thigh-hip (KTH) relate peak force applied to the anterior aspect of the flexed knee, the primary source of KTH injury in frontal motor-vehicle crashes, to the probability of skeletal KTH injury. Previous KTH injury risk curves have been developed from analyses of peak knee-impact force data from studies where knees of whole cadavers were impacted. However, these risk curves either neglect the effects of occupant gender, stature, and mass on KTH fracture force, or account for them using scaling factors derived from dimensional analysis without empirical support. A large amount of experimental data on the knee-impact forces associated with KTH fracture are now available, making it possible to estimate the effects of subject characteristics on skeletal KTH injury risk by statistically analyzing empirical data. Eleven studies were identified in the biomechanical literature in which the flexed knees of whole cadavers were impacted. From these, peak knee-impact force data and the associated subject characteristics were reanalyzed using survival analysis with a lognormal distribution. Results of this analysis indicate that the relationship between peak knee-impact force and the probability of KTH fracture is a function of age, total body mass, and whether the surface that loads the knee is rigid. Comparisons between injury risk curves for the midsize adult male and small adult female crash test dummies defined in previous studies and new risk curves for these sizes of occupants developed in this study suggest that previous injury risk curves generally overestimate the likelihood of KTH fracture at a given peak knee-impact force. Future work should focus on defining the relationships between impact force at the human knee and peak axial compressive forces measured by load cells in the crash test dummy KTH complex so that these new risk curves can be used with ATDs.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

A Bayesian estimation of a stochastic predator-prey model of economic fluctuations

NASA Astrophysics Data System (ADS)

Dibeh, Ghassan; Luchinsky, Dmitry G.; Luchinskaya, Daria D.; Smelyanskiy, Vadim N.

2007-06-01

In this paper, we develop a Bayesian framework for the empirical estimation of the parameters of one of the best known nonlinear models of the business cycle: The Marx-inspired model of a growth cycle introduced by R. M. Goodwin. The model predicts a series of closed cycles representing the dynamics of labor's share and the employment rate in the capitalist economy. The Bayesian framework is used to empirically estimate a modified Goodwin model. The original model is extended in two ways. First, we allow for exogenous periodic variations of the otherwise steady growth rates of the labor force and productivity per worker. Second, we allow for stochastic variations of those parameters. The resultant modified Goodwin model is a stochastic predator-prey model with periodic forcing. The model is then estimated using a newly developed Bayesian estimation method on data sets representing growth cycles in France and Italy during the years 1960-2005. Results show that inference of the parameters of the stochastic Goodwin model can be achieved. The comparison of the dynamics of the Goodwin model with the inferred values of parameters demonstrates quantitative agreement with the growth cycle empirical data.

The normative background of empirical-ethical research: first steps towards a transparent and reasoned approach in the selection of an ethical theory.

PubMed

Salloch, Sabine; Wäscher, Sebastian; Vollmann, Jochen; Schildmann, Jan

2015-04-04

Empirical-ethical research constitutes a relatively new field which integrates socio-empirical research and normative analysis. As direct inferences from descriptive data to normative conclusions are problematic, an ethical framework is needed to determine the relevance of the empirical data for normative argument. While issues of normative-empirical collaboration and questions of empirical methodology have been widely discussed in the literature, the normative methodology of empirical-ethical research has seldom been addressed. Based on our own research experience, we discuss one aspect of this normative methodology, namely the selection of an ethical theory serving as a background for empirical-ethical research. Whereas criteria for a good ethical theory in philosophical ethics are usually related to inherent aspects, such as the theory's clarity or coherence, additional points have to be considered in the field of empirical-ethical research. Three of these additional criteria will be discussed in the article: (a) the adequacy of the ethical theory for the issue at stake, (b) the theory's suitability for the purposes and design of the empirical-ethical research project, and (c) the interrelation between the ethical theory selected and the theoretical backgrounds of the socio-empirical research. Using the example of our own study on the development of interventions which support clinical decision-making in oncology, we will show how the selection of an ethical theory as a normative background for empirical-ethical research can proceed. We will also discuss the limitations of the procedures chosen in our project. The article stresses that a systematic and reasoned approach towards theory selection in empirical-ethical research should be given priority rather than an accidental or implicit way of choosing the normative framework for one's own research. It furthermore shows that the overall design of an empirical-ethical study is a multi-faceted endeavor which has to balance between theoretical and pragmatic considerations.

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

PubMed Central

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

Empirical Green's tensor retrieved from ambient noise cross-correlations at The Geysers geothermal field, Northern California

NASA Astrophysics Data System (ADS)

Nayak, Avinash; Taira, Taka'aki; Dreger, Douglas S.; Gritto, Roland

2018-04-01

We retrieve empirical Green's functions in the frequency range (˜0.2-0.9 Hz) for interstation distances ranging from ˜1 to ˜30 km (˜0.22 to ˜6.5 times the wavelength) at The Geysers geothermal field, Northern California, from coherency of ambient seismic noise being recorded by a variety of sensors (broad-band, short-period surface and borehole sensors, and one accelerometer). The applied methodology preserves the intercomponent relative amplitudes of the nine-component Green's tensor that allows us to directly compare noise-derived Green's functions (NGFs) with normalized displacement waveforms of complete single-force synthetic Green's functions (SGFs) computed with various 1-D and 3-D velocity models using the frequency-wavenumber integration method and a 3-D finite-difference wave propagation method, respectively. These comparisons provide an effective means of evaluating the suitability of different velocity models to different regions of The Geysers, and assessing the quality of the sensors and the NGFs. In the T-Tangential, R-Radial, Z-Vertical reference frame, the TT, RR, RZ, ZR and ZZ components (first component: force direction, second component: response direction) of NGFs show clear surface waves and even body-wave phases for many station pairs. They are also broadly consistent in phase and intercomponent relative amplitudes with SGFs for the known local seismic velocity structure that was derived primarily from body-wave traveltime tomography, even at interstation distances less than one wavelength. We also find anomalous large amplitudes in TR, TZ, RT and ZT components of NGFs at small interstation distances (≲4 km) that can be attributed to ˜10°-30° sensor misalignments at many stations inferred from analysis of longer period teleseismic waveforms. After correcting for sensor misalignments, significant residual amplitudes in these components for some longer interstation distance (≳8 km) paths are better reproduced by the 3-D velocity model than by the 1-D models incorporating known values and fast axis directions of crack-induced VS anisotropy in the geothermal field. We also analyse the decay of Fourier spectral amplitudes of the TT component of NGFs at 0.72 Hz with distance in terms of geometrical spreading and attenuation. While there is considerable scatter in the NGF amplitudes, we find the average decay to be consistent with the decay expected from SGF amplitudes and with the decay of tangential component local-earthquake ground-motion amplitudes with distance at the same frequency.

Novel strategies in feedforward adaptation to a position-dependent perturbation.

PubMed

Hinder, Mark R; Milner, Theodore E

2005-08-01

To investigate the control mechanisms used in adapting to position-dependent forces, subjects performed 150 horizontal reaching movements over 25 cm in the presence of a position-dependent parabolic force field (PF). The PF acted only over the first 10 cm of the movement. On every fifth trial, a virtual mechanical guide (double wall) constrained subjects to move along a straight-line path between the start and target positions. Its purpose was to register lateral force to track formation of an internal model of the force field, and to look for evidence of possible alternative adaptive strategies. The force field produced a force to the right, which initially caused subjects to deviate in that direction. They reacted by producing deviations to the left, "into" the force field, as early as the second trial. Further adaptation resulted in rapid exponential reduction of kinematic error in the latter portion of the movement, where the greatest perturbation to the handpath was initially observed, whereas there was little modification of the handpath in the region where the PF was active. Significant force directed to counteract the PF was measured on the first guided trial, and was modified during the first half of the learning set. The total force impulse in the region of the PF increased throughout the learning trials, but it always remained less than that produced by the PF. The force profile did not resemble a mirror image of the PF in that it tended to be more trapezoidal than parabolic in shape. As in previous studies of force-field adaptation, we found that changes in muscle activation involved a general increase in the activity of all muscles, which increased arm stiffness, and selectively-greater increases in the activation of muscles which counteracted the PF. With training, activation was exponentially reduced, albeit more slowly than kinematic error. Progressive changes in kinematics and EMG occurred predominantly in the region of the workspace beyond the force field. We suggest that constraints on muscle mechanics limit the ability of the central nervous system to employ an inverse dynamics model to nullify impulse-like forces by generating mirror-image forces. Consequently, subjects adopted a strategy of slightly overcompensating for the first half of the force field, then allowing the force field to push them in the opposite direction. Muscle activity patterns in the region beyond the boundary of the force field were subsequently adjusted because of the relatively-slow response of the second-order mechanics of muscle impedance to the force impulse.

Cross-Field Comparison of Ethics Education: Golden Rules and Particulars.

PubMed

Mulhearn, Tyler J; Watts, Logan L; Torrence, Brett S; Todd, E Michelle; Turner, Megan R; Connelly, Shane; Mumford, Michael D

2017-01-01

Research misconduct negatively impacts the scientific community and society in general. Providing training in the responsible conduct of research (RCR) to researchers is one viable approach to minimizing research misconduct. Although recent evidence suggests ethics training can indeed be effective, little empirical work has examined the similarities and differences across fields. In the present study, we analyzed 62 empirical studies in engineering, biomedical science, social science, and mixed fields. The findings suggest certain instructional principles, or "golden rules," apply generally to all fields. These golden rules include maintaining a field-specific or field-general approach and emphasizing processes in training. The findings also suggest that content areas contributing to instructional effectiveness vary as a function of field. Generally, it appears that all fields may benefit from taking a multi-pronged approach to ethics education wherein the salient field issues are covered. Implications for RCR education are discussed.

Precise measurements of droplet-droplet contact forces in quasi-2D emulsions

NASA Astrophysics Data System (ADS)

Lowensohn, Janna; Orellana, Carlos; Weeks, Eric

2015-03-01

We use microscopy to visualize a quasi-2D oil-in-water emulsion confined between two parallel slides. We then use the droplet shapes to infer the forces they exert on each other. To calibrate our force law, we set up an emulsion in a tilted sample chamber so that the droplets feel a known buoyant force. By correlating radius of the droplet and length of contacts with the buoyant forces, we validate our empirical force law. We improve upon prior work in our lab by using a high-resolution camera to image each droplet multiple times, thus providing sub-pixel resolution and reducing the noise. Our new technique identifies contact forces with only a 1% uncertainty, five times better than prior work. We demonstrate the utility of our technique by examining the normal modes of the droplet contact network in our samples.

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

Liu, Hao; Song, Dong; Lu, Hui; Luo, Ray; Chen, Hai-Feng

2018-05-28

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X-ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here we report our development for the CHARMM community. Our residue-specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections of for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J-couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

How accurately do force fields represent protein side chain ensembles?

PubMed

Petrović, Dušan; Wang, Xue; Strodel, Birgit

2018-05-23

Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Characterizing Cyclostationary Features of Digital Modulated Signals with Empirical Measurements using Spectral Correlation Function

DTIC Science & Technology

2011-06-01

USING SPECTRAL CORRELATION FUNCTION THESIS Mujun Song, Captain, ROKA AFIT/GCE/ENG/11-09 DEPARTMENT OF THE AIR FORCE AIR UNIVERSITY AIR...Management Air Force Institute of Technology Air University Air Education and Training Command In Partial Fulfillment of the Requirements for the...generator, Agilent E4438C, ESG Vector Signal Generator. Universal Software Radio Peripheral 2 (USRP2), which is a Software Defined Radio (SDR), is used

Military Innovation in the Rise and Fall of Great Powers: Lessons for America

DTIC Science & Technology

2011-06-01

must institute forcing mechanisms to integrate the elements of national power toward this stated goal. Several of the forcing mechanisms proposed...about my thesis topic. CAPT Porter immediately took an interest in my ideas and gave me food for thought and book recommendations that shaped the...fighting mechanism . The inventive and martial nature of the Assyrian Empire allowed its people to develop, relatively quickly, the first concept of

Engineering analyses for railroad tank car head puncture resistance

DOT National Transportation Integrated Search

2006-11-06

This paper describes engineering analyses to estimate the : forces, deformations, and puncture resistance of railroad tank : cars. Different approaches to examine puncture of the tank car : head are described. One approach is semi-empirical equations...

Measuring Corporate Smarts.

ERIC Educational Resources Information Center

Delahoussaye, Martin; Ellis, Kristine; Bolch, Matt

2002-01-01

Provides empirical evidence that significant investment in work force development leads to increased shareholder value. Suggests that management should heed the evidence when considering cutting training and development budgets. Profiles 11 companies' stock performance and discusses their training and development initiatives. (JOW)

A method of self-pursued boundary value on a body and the Magnus effect calculated with this method

NASA Astrophysics Data System (ADS)

Yoshino, Fumio; Hayashi, Tatsuo; Waka, Ryoji

1991-03-01

A computational method, designated 'SPB', is proposed for the automatic determination of the stream function Phi on an arbitrarily profiled body without recourse to empirical factors. The method is applied to the case of a rotating, circular cross-section cylinder in a uniform shear flow, and the results obtained are compared with those of both the method in which the value of Phi is fixed on a body and the conventional empirical method; it is in view of this established that the SPB method is very efficient and applicable to both steady and unsteady flows. The SPB method, in addition to yielding the aerodynamic forces acting on a cylinder, shows that the Magnus effect lift force decreases as the velocity gradient of the shear flow increases while the cylinder's rotational speed is kept constant.

Full nonlinear treatment of the global thermospheric wind system. Part 1: Mathematical method and analysis of forces

NASA Technical Reports Server (NTRS)

Blum, P. W.; Harris, I.

1973-01-01

The equations of horizontal motion of the neutral atmosphere between 120 and 500 km are integrated with the inclusion of all the nonlinear terms of the convective derivative and the viscous forces due to vertical and horizontal velocity gradients. Empirical models of the distribution of neutral and charged particles are assumed to be known. The model of velocities developed is a steady state model. In part 1 the mathematical method used in the integration of the Navier-Stokes equations is described and the various forces are analysed.

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

DOE PAGES

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang; ...

2016-05-25

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

PubMed Central

Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

2010-01-01

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

Electron diamagnetic effect in a magnetic nozzle on a helicon plasma thruster performance

NASA Astrophysics Data System (ADS)

Takahashi, Kazunori; Lafleur, Trevor; Charles, Christine; Alexander, Peter; Boswell, Rod

2012-10-01

The axial force, which is called thrust sometimes, imparted from a magnetically expanding helicon plasma thruster is directly measured and the results are compared with a two-dimensional fluid theory. The force component solely transmitted to the expanding field is directly measured and identified as an axial force produced by the azimuthal current due to an electron diamagnetic drift and the radial component of the applied magnetic field. In this type of configuration, plasma diffusion in magnetic field affects a spatial profile of the plasma density and the resultant axial force onto the magnetic field. It is observed that the force component onto the magnetic field increases with an increase in the magnetic field strength, simultaneously with an increase in the plasma density downstream of the source exit, which could be due to suppression of the cross field diffusion in the magnetic nozzle.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle.

PubMed

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle

NASA Astrophysics Data System (ADS)

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Force fields for describing the solution-phase synthesis of shape-selective metal nanoparticles

NASA Astrophysics Data System (ADS)

Zhou, Ya; Al-Saidi, Wissam; Fichthorn, Kristen

2013-03-01

Polyvinylpyrrolidone (PVP) and polyethylene oxide (PEO) are structure-directing agents that exhibit different performance in the polyol synthesis of Ag nanostructures. The success of these structure-directing agents in selective nanostructure synthesis is often attributed to their selective binding to Ag(100) facets. We use first-principles, density-functional theory (DFT) calculations in a vacuum environment to show that PVP has a stronger preference to bind to Ag(100) than to Ag(111), whereas PEO exhibits much weaker selectivity. To understand the role of solvent in the surface-sensitive binding, we develop classical force fields to describe the interactions of the structure-directing (PVP and PEO) and solvent (ethylene glycol) molecules with various Ag substrates. We parameterize the force fields through force-and-energy matching to DFT results using simulated annealing. We validate the force fields by comparisons to DFT and experimental binding energies. Our force fields reproduce the surface-sensitive binding predicted by DFT calculations. Molecular dynamics simulations based on these force fields can be used to reveal the role of solvent, polymer chain length, and polymer concentration in the selective synthesis of Ag nanostructures.

Magnetodynamic stability of a fluid cylinder under the Lundquist force-free magnetic field

NASA Astrophysics Data System (ADS)

Radwan, Ahmed E.; Halawa, Mohamed A.

1990-04-01

The magnetodynamic (in)stability of a conducting fluid cylinder subject to the capillarity and electromagnetic forces has been developed. The cylinder is pervaded by a uniform magnetic field but embedded in the Lundquist force-free varying field that allows for flowing a current surrounding the fluid. A general eigenvalue relation is derived based on a study of the equilibrium and perturbed states. The stability criterion is discussed analytically in general terms. The surface tension is destabilizing for small axisymmetric mode and stable for all others. The principle of the exchange of stability is allowed for the present problem due to the non-uniform behavior of the force-free field. Each of the axial and transverse force-free fields separately exerts a stabilizing influence in the most dangerous mode but the combined contribution of them is strongly destabilizing. Whether the model is acted upon the electromagnetic force (with the Lundquist field) the stability restrictions or/and the capillarity force are identified. Several reported works can be recovered as limiting cases with appropriate simplifications.

Validation and Application of the ReaxFF Reactive Force Field to Hydrocarbon Oxidation Kinetics

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0278 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics Adrianus Van Duin...application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1-0355 5c.  PROGRAM...Chenoweth Dec14 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics DISTRIBUTION A: Distribution approved for

To empower or not to empower your sales force? An empirical examination of the influence of leadership empowerment behavior on customer satisfaction and performance.

PubMed

Ahearne, Michael; Mathieu, John; Rapp, Adam

2005-09-01

This research focuses on the impact of leadership empowerment behavior (LEB) on customer service satisfaction and sales performance, as mediated by salespeople's self-efficacy and adaptability. Moreover, the authors propose an interactive relationship whereby LEB will be differentially effective as a function of employees' empowerment readiness. The authors' hypotheses are tested using survey data from a sample of 231 salespeople in the pharmaceutical field, along with external ratings of satisfaction from 864 customers and archival sales performance information. Results indicated that contrary to popular belief, employees with low levels of product/industry knowledge and low experience benefit the most from leadership behaviors that are empowering, whereas high-knowledge and experienced employees reap no clear benefit. The authors conclude with directions for future research and application. Copyright 2005 APA, all rights reserved.

New perspectives on evolutionary medicine: the relevance of microevolution for human health and disease

PubMed Central

2013-01-01

Evolutionary medicine (EM) is a growing field focusing on the evolutionary basis of human diseases and their changes through time. To date, the majority of EM studies have used pure theories of hominin macroevolution to explain the present-day state of human health. Here, we propose a different approach by addressing more empirical and health-oriented research concerning past, current and future microevolutionary changes of human structure, functions and pathologies. Studying generation-to-generation changes of human morphology that occurred in historical times, and still occur in present-day populations under the forces of evolution, helps to explain medical conditions and warns clinicians that their current practices may influence future humans. Also, analyzing historic tissue specimens such as mummies is crucial in order to address the molecular evolution of pathogens, of the human genome, and their coadaptations. PMID:23627943

Use of observational and model-derived fields and regime model output statistics in mesoscale forecasting

NASA Technical Reports Server (NTRS)

Forbes, G. S.; Pielke, R. A.

1985-01-01

Various empirical and statistical weather-forecasting studies which utilize stratification by weather regime are described. Objective classification was used to determine weather regime in some studies. In other cases the weather pattern was determined on the basis of a parameter representing the physical and dynamical processes relevant to the anticipated mesoscale phenomena, such as low level moisture convergence and convective precipitation, or the Froude number and the occurrence of cold-air damming. For mesoscale phenomena already in existence, new forecasting techniques were developed. The use of cloud models in operational forecasting is discussed. Models to calculate the spatial scales of forcings and resultant response for mesoscale systems are presented. The use of these models to represent the climatologically most prevalent systems, and to perform case-by-case simulations is reviewed. Operational implementation of mesoscale data into weather forecasts, using both actual simulation output and method-output statistics is discussed.

Preparation and characterization of photoactive composite kaolinite/TiO(2).

PubMed

Mamulová Kutláková, K; Tokarský, J; Kovář, P; Vojtěšková, S; Kovářová, A; Smetana, B; Kukutschová, J; Čapková, P; Matějka, V

2011-04-15

Preparation of nanocomposite kaolinite/TiO(2), using hydrolysis of titanyl sulfate in the presence of kaolin was addressed. A variable (kaolin)/(titanyl sulfate) ratio has been used in order to achieve the desired TiO(2) content in prepared nanocomposites. Calcination of the composites at 600 °C led to the transformation of the kaolinite to metakaolinite and to origination of metakaolinite/TiO(2) composites. The prepared samples were investigated using X-ray fluorescence spectroscopy, X-ray powder diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, thermogravimetry and diffuse reflectance spectroscopy in the UV-VIS region. Structural ordering of TiO(2) on the kaolinite particle surface was modeled using empirical force field atomistic simulations in the Material Studio modeling environment. Photodegradation activity of the composites prepared was evaluated by the discoloration of Acid Orange 7 aqueous solution. Copyright © 2011 Elsevier B.V. All rights reserved.

Relativistic Quark Model Based Description of Low Energy NN Scattering

NASA Astrophysics Data System (ADS)

Antalik, R.; Lyubovitskij, V. E.

A model describing the NN scattering phase shifts is developed. Two nucleon interactions induced by meson exchange forces are constructed starting from π, η, η‧ pseudoscalar-, the ρ, ϕ, ω vector-, and the ɛ(600), a0, f0(1400) scalar — meson-nucleon coupling constants, which we obtained within a relativistic quantum field theory based quark model. Working within the Blankenbecler-Sugar-Logunov-Tavkhelidze quasipotential dynamics, we describe the NN phase shifts in a relativistically invariant way. In this procedure we use phenomenological form factor cutoff masses and effective ɛ and ω meson-nucleon coupling constants, only. Resulting NN phase shifts are in a good agreement with both, the empirical data, and the entirely phenomenological Bonn OBEP model fit. While the quality of our description, evaluated as a ratio of our results to the Bonn OBEP model χ2 ones is about 1.2, other existing (semi)microscopic results gave qualitative results only.

Theoretical investigation of the molecular structure of the isoquercitrin molecule

NASA Astrophysics Data System (ADS)

Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

1999-09-01

Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

Integrating positive psychology into health-related quality of life research.

PubMed

Park, Crystal L

2015-07-01

Positive psychology is an increasingly influential force in theory and research within psychology and many related fields, including behavioral medicine, sociology, and public health. This article aims to review the ways in which positive psychology and health-related quality of life (HRQOL) research currently interface and to suggest fruitful future directions. This article reviews the basic elements of positive psychology and provides an overview of conceptual and empirical links between positive psychology and HRQOL. The role of one central aspect of positive psychology (meaning) within HRQOL is highlighted, and unresolved issues (e.g., lack of definitional clarity) are discussed. Some research on HRQOL has taken a positive psychology perspective, demonstrating the usefulness of taking a positive psychology approach. However, many areas await integration. Once conceptual and methodological issues are resolved, positive psychology may profitably inform many aspects of HRQOL research and, perhaps, clinical interventions to promote HRQOL as well.

Reduction of magneto rheological dampers stiffness by incorporating of an eddy current damper

NASA Astrophysics Data System (ADS)

Asghar Maddah, Ali; Hojjat, Yousef; Reza Karafi, Mohammad; Reza Ashory, Mohammad

2017-05-01

In this paper, a hybrid damper is developed to achieve lower stiffness compared to magneto rheological dampers. The hybrid damper consists of an eddy current damper (ECD) and a Magneto Rheological Damper (MRD). The aim of this research is to reduce the stiffness of MRDs with equal damping forces. This work is done by adding an eddy current passive damper to a semi-active MRD. The ECDs are contactless dampers which show an almost viscous damping behavior without increasing the stiffness of a system. However, MRDs increase damping and stiffness of a system simultaneously, when a magnetic field is applied. Damping of each part is studied theoretically and experimentally. A semi-empirical model is developed to explain the viscoelastic behavior of the damper. The experimental results showed that the hybrid damper is able to dissipate energy as much as those of MRDs while its stiffness is 12% lower at a zero excitation current.

Economics and Health Reform: Academic Research and Public Policy.

PubMed

Glied, Sherry A; Miller, Erin A

2015-08-01

Two prior studies, conducted in 1966 and in 1979, examined the role of economic research in health policy development. Both concluded that health economics had not been an important contributor to policy. Passage of the Affordable Care Act offers an opportunity to reassess this question. We find that the evolution of health economics research has given it an increasingly important role in policy. Research in the field has followed three related paths over the past century-institutionalist research that described problems; theoretical research, which proposed relationships that might extend beyond existing institutions; and empirical assessments of structural parameters identified in the theoretical research. These three strands operating in concert allowed economic research to be used to predict the fiscal and coverage consequences of alternative policy paths. This ability made economic research a powerful policy force. Key conclusions of health economics research are clearly evident in the Affordable Care Act. © The Author(s) 2015.

Comparative study of three-nucleon potentials in nuclear matter

NASA Astrophysics Data System (ADS)

Lovato, Alessandro; Benhar, Omar; Fantoni, Stefano; Schmidt, Kevin E.

2012-02-01

A new generation of local three-body potentials providing an excellent description of the properties of light nuclei, as well as of the neutron-deuteron doublet scattering length, has been recently derived. We have performed a comparative analysis of the equations of state of both pure neutron matter (PNM) and symmetric nuclear matter (SNM) at zero temperature obtained using these models of three-nucleon forces. In particular, we have carried out both variational and auxiliary field diffusion Monte Carlo calculations of the equation of state of PNM, while in the case of SNM we have only the variational approach has been considered. None of the considered potentials simultaneously explains the empirical equilibrium density and binding energy of symmetric nuclear matter. However, two of them provide reasonable values of the saturation density. The ambiguity concerning the treatment of the contact term of the chiral inspired potentials is discussed.

Communication: Role of explicit water models in the helix folding/unfolding processes

NASA Astrophysics Data System (ADS)

Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

2016-09-01

In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

Reprint of "Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)"

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2017-02-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Theoretical description of metal/oxide interfacial properties: The case of MgO/Ag(001)

NASA Astrophysics Data System (ADS)

Prada, Stefano; Giordano, Livia; Pacchioni, Gianfranco; Goniakowski, Jacek

2016-12-01

We compare the performances of different DFT functionals applied to ultra-thin MgO(100) films supported on the Ag(100) surface, a prototypical system of a weakly interacting oxide/metal interface, extensively studied in the past. Beyond semi-local DFT-GGA approximation, we also use the hybrid DFT-HSE approach to improve the description of the oxide electronic structure. Moreover, to better account for the interfacial adhesion, we include the van de Waals interactions by means of either the semi-empirical force fields by Grimme (DFT-D2 and DFT-D2*) or the self-consistent density functional optB88-vdW. We compare and discuss the results on the structural, electronic, and adhesion characteristics of the interface as obtained for pristine and oxygen-deficient Ag-supported MgO films in the 1-4 ML thickness range.

Surface structure and stability of partially hydroxylated silica surfaces

DOE PAGES

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

2017-04-04

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

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

PubMed

Saito, Minoru; Okazaki, Isao

2009-12-01

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

An empirical method for computing leeside centerline heating on the Space Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Helms, V. T., III

1981-01-01

An empirical method is presented for computing top centerline heating on the Space Shuttle Orbiter at simulated reentry conditions. It is shown that the Shuttle's top centerline can be thought of as being under the influence of a swept cylinder flow field. The effective geometry of the flow field, as well as top centerline heating, are directly related to oil-flow patterns on the upper surface of the fuselage. An empirical turbulent swept cylinder heating method was developed based on these considerations. The method takes into account the effects of the vortex-dominated leeside flow field without actually having to compute the detailed properties of such a complex flow. The heating method closely predicts experimental heat-transfer values on the top centerline of a Shuttle model at Mach numbers of 6 and 10 over a wide range in Reynolds number and angle of attack.

Influence of uncertainties of the empirical models for inferring the E-region electric fields at the dip equator

NASA Astrophysics Data System (ADS)

Moro, Juliano; Denardini, Clezio Marcos; Resende, Laysa Cristina Araújo; Chen, Sony Su; Schuch, Nelson Jorge

2016-06-01

Daytime E-region electric fields play a crucial role in the ionospheric dynamics at the geomagnetic dip latitudes. Due to their importance, there is an interest in accurately measuring and modeling the electric fields for both climatological and near real-time studies. In this work, we present the daytime vertical ( Ez) and eastward ( Ey) electric fields for a reference quiet day (February 7, 2001) at the São Luís Space Observatory, Brazil (SLZ, 2.31°S, 44.16°W). The component Ez is inferred from Doppler shifts of type II echoes (gradient drift instability) and the anisotropic factor, which is computed from ion and electron gyro frequencies as well as ion and electron collision frequencies with neutral molecules. The component Ey depends on the ratio of Hall and Pedersen conductivities and Ez. A magnetic field-line-integrated conductivity model is used to obtain the anisotropic factor for calculating Ez and the ionospheric conductivities for calculating Ey. This model uses the NRLMSISE-00, IRI-2007, and IGRF-11 empirical models as input parameters for neutral atmosphere, ionosphere, and geomagnetic field, respectively. Consequently, it is worth determining the uncertainties (or errors) in Ey and Ez associated with these empirical model outputs in order to precisely define the confidence limit for the estimated electric field components. For this purpose, errors of ±10 % were artificially introduced in the magnitude of each empirical model output before estimating Ey and Ez. The corresponding uncertainties in the ionospheric conductivity and electric field are evaluated considering the individual and cumulative contribution of the artificial errors. The results show that the neutral densities and temperature may be responsible for the largest changes in Ey and Ez, followed by changes in the geomagnetic field intensity and electron and ions compositions.

The effect of power-law body forces on a thermally driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1986-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

The effect of power law body forces on a thermally-driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

The Electromotive Force in Different Reference Frames

NASA Astrophysics Data System (ADS)

Adler, Charles L.

2018-05-01

The electromotive force (EMF) is the work per unit charge around a wire loop caused by a time-varying magnetic flux threading the loop. It is due to a force moving the charges around the loop. This is true whether the change in flux is due to the wire loop being stationary and the field changing in time, or the loop moving through a spatially varying field. In the first case, we say that the time-varying magnetic field induces an electric field that provides the force; in the second, we say that the force is due to the magnetic field acting on the charges in the moving loop. The theory of relativity states that both viewpoints must be equivalent, but it is sometimes difficult to harmonize them.

Global Langevin model of multidimensional biomolecular dynamics.

PubMed

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-14

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F(). To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F(), which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Global Langevin model of multidimensional biomolecular dynamics

NASA Astrophysics Data System (ADS)

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-01

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

PubMed

Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.

Bespoke optical springs and passive force clamps from shaped dielectric particles

NASA Astrophysics Data System (ADS)

Simpson, S. H.; Phillips, D. B.; Carberry, D. M.; Hanna, S.

2013-09-01

By moulding optical fields, holographic optical tweezers are able to generate structured force fields with magnitudes and length scales of great utility for experiments in soft matter and biological physics. It has recently been noted that optically induced force fields are determined not only by the incident optical field, but by the shape and composition of the particles involved [Gluckstad J. Optical manipulation: sculpting the object. Nat Photonics 2011;5:7-8]. Indeed, there are desirable but simple attributes of a force field, such as orientational control, that cannot be introduced by sculpting optical fields alone. With this insight in mind, we show, theoretically, how relationships between force and displacement can be controlled by optimizing particle shapes. We exhibit a constant force optical spring, made from a tapered microrod and discuss methods by which it could be fabricated. In addition, we investigate the optical analogue of streamlining, and show how objects can be shaped so as to reduce the effects of radiation pressure, and hence switch from non-trapping to trapping regimes.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-02-01

A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

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

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

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

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE PAGES

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; ...

2017-02-01

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

Lipid14: The Amber Lipid Force Field

PubMed Central

2015-01-01

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

Lorentz Body Force Induced by Traveling Magnetic Fields

NASA Technical Reports Server (NTRS)

Volz, M. P.; Mazuruk, K.

2003-01-01

The Lorentz force induced by a traveling magnetic field (TMF) in a cylindrical container has been calculated. The force can be used to control flow in dectrically conducting melts and the direction of the magnetic field and resulting flow can be reversed. A TMF can be used to partially cancel flow driven by buoyancy. The penetration of the field into the cylinder decreases as the frequency increases, and there exists an optimal value of frequency for which the resulting force is a maximum. Expressions for the Lorentz force in the limiting cases of low frequency and infinite cylinder are also given and compared to the numerical calculations.

Physical stress modifies top-down and bottom-up forcing on plant growth and reproduction in a coastal ecosystem.

PubMed

Daleo, Pedro; Alberti, Juan; Bruschetti, Carlos Martin; Pascual, Jesos; Iribarne, Oscar; Silliman, Brian R

2015-08-01

Bottom-up and top-down effects act together to exert strong control over plant growth and reproduction, but how physical stress modifies those interactive forces remains unclear. Even though empirical evidence is scarce, theory predicts that the importance of both top-down- and bottom-up forces may decrease as physical stress increases. Here, we experimentally evaluate in the field the separate and interactive effect of salinity, nutrient availability, and crab herbivory on plant above- and belowground biomass, as well as on sexual and clonal reproduction in the salt marsh plant Spartina densiflora. Results show that the outcome of the interaction between nutrient availability and herbivory is highly context dependent, not only varying with the abiotic context (i.e., with or without increased salinity stress), but also with the dependent variable considered. Contrary to theoretical predictions, our results show that, consistently across different measured variables, salinity stress did not cancel bottom-up (i.e., nutrients) or top-down (i.e., consumers) control, but has additive effects. Our results support emerging theory by highlighting that, under many conditions, physical stress can act additively with, or even stimulate, consumer control, especially in cases where the physical stress is only experienced by basal levels of the trophic chain. Abiotic stress, as well as bottom-up and top-down factors, can affect salt marsh structure and function not only by affecting biomass production but also by having other indirect effects, such as changing patterns in plant biomass allocation and reproduction.

Long term, non-anthropogenic groundwater storage changes simulated by a global land surface model

NASA Astrophysics Data System (ADS)

Li, B.; Rodell, M.; Sheffield, J.; Wood, E. F.

2017-12-01

Groundwater is crucial for meeting agricultural, industrial and municipal water needs, especially in arid, semi-arid and drought impacted regions. Yet, knowledge on groundwater response to climate variability is not well understood due to lack of systematic and continuous in situ measurements. In this study, we investigate global non-anthropogenic groundwater storage variations with a land surface model driven by a 67-year (1948-204) meteorological forcing data set. Model estimates were evaluated using in situ groundwater data from the central and northeastern U.S. and terrestrial water storage derived from the Gravity Recovery and Climate Experiment (GRACE) satellites and found to be reasonable. Empirical orthogonal function (EOF) analysis was employed to examine modes of variability of groundwater storage and their relationship with atmospheric effects such as precipitation and evapotranspiration. The result shows that the leading mode in global groundwater storage reflects the influence of the El Niño Southern Oscillation (ENSO). Consistent with the EOF analysis, global total groundwater storage reflected the low frequency variability of ENSO and decreased significantly over 1948-2014 while global ET and precipitation did not exhibit statistically significant trends. This study suggests that while precipitation and ET are the primary drivers of climate related groundwater variability, changes in other forcing fields than precipitation and temperature are also important because of their influence on ET. We discuss the need to improve model physics and to continuously validate model estimates and forcing data for future studies.

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

PubMed Central

2015-01-01

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

New empirically-derived solar radiation pressure model for GPS satellites

NASA Technical Reports Server (NTRS)

Bar-Sever, Y.; Kuang, D.

2003-01-01

Solar radiation pressure force is the second largest perturbation acting on GPS satellites, after the gravitational attraction from the Earth, Sun, and Moon. It is the largest error source in the modeling of GPS orbital dynamics.

The influence of inhomogeneous magnetic field over a NdFeB guideway on levitation force of the HTS bulk maglev system

NASA Astrophysics Data System (ADS)

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.

U.S. Field Artillery after World War I: Modernizing the Force While Downsizing

DTIC Science & Technology

2014-06-13

weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and......weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and

The Energetics of Motivated Cognition: A Force-Field Analysis

ERIC Educational Resources Information Center

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

2012-01-01

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

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Violent Crime in Post-Civil War Guatemala: Causes and Policy Implications

DTIC Science & Technology

2015-03-01

on field research and case studies in Honduras, Bolivia, and Argentina. Bailey’s Security Trap theory is comprehensive in nature and derived from... research question. The second phase uses empirical data and comparative case studies to validate or challenge selected arguments that potentially...Contextual relevancy, historical inference, Tools: Empirics and case conclusions empirical data studies Figme2. Sample Research Methodology E

Bubble Dynamics, Two-Phase Flow, and Boiling Heat Transfer in Microgravity

NASA Technical Reports Server (NTRS)

Chung, Jacob N.

1996-01-01

The objective of the research is to study the feasibility of employing an external force to replace the buoyancy force in order to maintain nucleate boiling in microgravity. We have found that a bulk velocity field, an electric field and an acoustic field could each play the role of the gravity field in microgravity. Nucleate boiling could be maintained by any one of the three external force fields in space.

The feasibility of an efficient drug design method with high-performance computers.

PubMed

Yamashita, Takefumi; Ueda, Akihiko; Mitsui, Takashi; Tomonaga, Atsushi; Matsumoto, Shunji; Kodama, Tatsuhiko; Fujitani, Hideaki

2015-01-01

In this study, we propose a supercomputer-assisted drug design approach involving all-atom molecular dynamics (MD)-based binding free energy prediction after the traditional design/selection step. Because this prediction is more accurate than the empirical binding affinity scoring of the traditional approach, the compounds selected by the MD-based prediction should be better drug candidates. In this study, we discuss the applicability of the new approach using two examples. Although the MD-based binding free energy prediction has a huge computational cost, it is feasible with the latest 10 petaflop-scale computer. The supercomputer-assisted drug design approach also involves two important feedback procedures: The first feedback is generated from the MD-based binding free energy prediction step to the drug design step. While the experimental feedback usually provides binding affinities of tens of compounds at one time, the supercomputer allows us to simultaneously obtain the binding free energies of hundreds of compounds. Because the number of calculated binding free energies is sufficiently large, the compounds can be classified into different categories whose properties will aid in the design of the next generation of drug candidates. The second feedback, which occurs from the experiments to the MD simulations, is important to validate the simulation parameters. To demonstrate this, we compare the binding free energies calculated with various force fields to the experimental ones. The results indicate that the prediction will not be very successful, if we use an inaccurate force field. By improving/validating such simulation parameters, the next prediction can be made more accurate.

Numerical simulation and prediction of coastal ocean circulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, P.

1992-01-01

Numerical simulation and prediction of coastal ocean circulation have been conducted in three cases. 1. A process-oriented modeling study is conducted to study the interaction of a western boundary current (WBC) with coastal water, and its responses to upstream topographic irregularities. It is hypothesized that the interaction of propagating WBC frontal waves and topographic Rossby waves are responsible for upstream variability. 2. A simulation of meanders and eddies in the Norwegian Coastal Current (NCC) for February and March of 1988 is conducted with a newly developed nested dynamic interactive model. The model employs a coarse-grid, large domain to account formore » non-local forcing and a fine-grid nested domain to resolve meanders and eddies. The model is forced by wind stresses, heat fluxes and atmospheric pressure corresponding Feb/March of 1988, and accounts for river/fjord discharges, open ocean inflow and outflow, and M[sub 2] tides. The simulation reproduced fairly well the observed circulation, tides, and salinity features in the North Sea, Norwegian Trench and NCC region in the large domain and fairly realistic meanders and eddies in the NCC in the nested region. 3. A methodology for practical coastal ocean hindcast/forecast is developed, taking advantage of the disparate time scales of various forcing and considering wind to be the dominant factor in affecting density fluctuation in the time scale of 1 to 10 days. The density field obtained from a prognostic simulation is analyzed by the empirical orthogonal function method (EOF), and correlated with the wind; these information are then used to drive a circulation model which excludes the density calculation. The method is applied to hindcast the circulation in the New York Bight for spring and summer season of 1988. The hindcast fields compare favorably with the results obtained from the prognostic circulation model.« less

Empirical model of TEC response to geomagnetic and solar forcing over Balkan Peninsula

NASA Astrophysics Data System (ADS)

Mukhtarov, P.; Andonov, B.; Pancheva, D.

2018-01-01

An empirical total electron content (TEC) model response to external forcing over Balkan Peninsula (35°N-50°N; 15°E-30°E) is built by using the Center for Orbit Determination of Europe (CODE) TEC data for full 17 years, January 1999 - December 2015. The external forcing includes geomagnetic activity described by the Kp-index and solar activity described by the solar radio flux F10.7. The model describes the most probable spatial distribution and temporal variability of the externally forced TEC anomalies assuming that they depend mainly on latitude, Kp-index, F10.7 and LT. The anomalies are expressed by the relative deviation of the TEC from its 15-day mean, rTEC, as the mean value is calculated from the 15 preceding days. The approach for building this regional model is similar to that of the global TEC model reported by Mukhtarov et al. (2013a) however it includes two important improvements related to short-term variability of the solar activity and amended geomagnetic forcing by using a "modified" Kp index. The quality assessment of the new constructing model procedure in terms of modeling error calculated for the period of 1999-2015 indicates significant improvement in accordance with the global TEC model (Mukhtarov et al., 2013a). The short-term prediction capabilities of the model based on the error calculations for 2016 are improved as well. In order to demonstrate how the model is able to reproduce the rTEC response to external forcing three geomagnetic storms, accompanied also with short-term solar activity variations, which occur at different seasons and solar activity conditions are presented.

Is the notion of central fatigue based on a solid foundation?

PubMed

Contessa, Paola; Puleo, Alessio; De Luca, Carlo J

2016-02-01

Exercise-induced muscle fatigue has been shown to be the consequence of peripheral factors that impair muscle fiber contractile mechanisms. Central factors arising within the central nervous system have also been hypothesized to induce muscle fatigue, but no direct empirical evidence that is causally associated to reduction of muscle force-generating capability has yet been reported. We developed a simulation model to investigate whether peripheral factors of muscle fatigue are sufficient to explain the muscle force behavior observed during empirical studies of fatiguing voluntary contractions, which is commonly attributed to central factors. Peripheral factors of muscle fatigue were included in the model as a time-dependent decrease in the amplitude of the motor unit force twitches. Our simulation study indicated that the force behavior commonly attributed to central fatigue could be explained solely by peripheral factors during simulated fatiguing submaximal voluntary contractions. It also revealed important flaws regarding the use of the interpolated twitch response from electrical stimulation of the muscle as a means for assessing central fatigue. Our analysis does not directly refute the concept of central fatigue. However, it raises important concerns about the manner in which it is measured and about the interpretation of the commonly accepted causes of central fatigue and questions the very need for the existence of central fatigue. Copyright © 2016 the American Physiological Society.

Haptic Stylus and Empirical Studies on Braille, Button, and Texture Display

PubMed Central

Kyung, Ki-Uk; Lee, Jun-Young; Park, Junseok

2008-01-01

This paper presents a haptic stylus interface with a built-in compact tactile display module and an impact module as well as empirical studies on Braille, button, and texture display. We describe preliminary evaluations verifying the tactile display's performance indicating that it can satisfactorily represent Braille numbers for both the normal and the blind. In order to prove haptic feedback capability of the stylus, an experiment providing impact feedback mimicking the click of a button has been conducted. Since the developed device is small enough to be attached to a force feedback device, its applicability to combined force and tactile feedback display in a pen-held haptic device is also investigated. The handle of pen-held haptic interface was replaced by the pen-like interface to add tactile feedback capability to the device. Since the system provides combination of force, tactile and impact feedback, three haptic representation methods for texture display have been compared on surface with 3 texture groups which differ in direction, groove width, and shape. In addition, we evaluate its capacity to support touch screen operations by providing tactile sensations when a user rubs against an image displayed on a monitor. PMID:18317520

Haptic stylus and empirical studies on braille, button, and texture display.

PubMed

Kyung, Ki-Uk; Lee, Jun-Young; Park, Junseok

2008-01-01

This paper presents a haptic stylus interface with a built-in compact tactile display module and an impact module as well as empirical studies on Braille, button, and texture display. We describe preliminary evaluations verifying the tactile display's performance indicating that it can satisfactorily represent Braille numbers for both the normal and the blind. In order to prove haptic feedback capability of the stylus, an experiment providing impact feedback mimicking the click of a button has been conducted. Since the developed device is small enough to be attached to a force feedback device, its applicability to combined force and tactile feedback display in a pen-held haptic device is also investigated. The handle of pen-held haptic interface was replaced by the pen-like interface to add tactile feedback capability to the device. Since the system provides combination of force, tactile and impact feedback, three haptic representation methods for texture display have been compared on surface with 3 texture groups which differ in direction, groove width, and shape. In addition, we evaluate its capacity to support touch screen operations by providing tactile sensations when a user rubs against an image displayed on a monitor.

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

PubMed Central

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-01-01

Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases. PMID:19493356

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance.

PubMed

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-06-03

Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Empirical investigation of a field theory formula and Black's formula for the price of an interest-rate caplet

NASA Astrophysics Data System (ADS)

Baaquie, Belal E.; Liang, Cui

2007-01-01

The industry standard for pricing an interest-rate caplet is Black's formula. Another distinct price of the same caplet can be derived using a quantum field theory model of the forward interest rates. An empirical study is carried out to compare the two caplet pricing formulae. Historical volatility and correlation of forward interest rates are used to generate the field theory caplet price; another approach is to fit a parametric formula for the effective volatility using market caplet price. The study shows that the field theory model generates the price of a caplet and cap fairly accurately. Black's formula for a caplet is compared with field theory pricing formula. It is seen that the field theory formula for caplet price has many advantages over Black's formula.

Radiation Forces and Torques without Stress (Tensors)

ERIC Educational Resources Information Center

Bohren, Craig F.

2011-01-01

To understand radiation forces and torques or to calculate them does not require invoking photon or electromagnetic field momentum transfer or stress tensors. According to continuum electromagnetic theory, forces and torques exerted by radiation are a consequence of electric and magnetic fields acting on charges and currents that the fields induce…

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

PubMed Central

2016-01-01

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

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Commensurability effects in the critical forces of a superconducting film with Kagomé pinning array at submatching fields

NASA Astrophysics Data System (ADS)

Vizarim, Nicolas P.; Carlone, Maicon; Verga, Lucas G.; Venegas, Pablo A.

2017-09-01

Using molecular dynamics simulations, we find the commensurability force peaks in a two-dimensional superconducting thin-film with a Kagomé pinning array. A transport force is applied in two mutually perpendicular directions, and the magnetic field is increased up to the first matching field. Usually the condition to have pronounced force peaks in systems with periodic pinning is associated to the rate between the applied magnetic field and the first matching field, it must be an integer or a rational fraction. Here, we show that another condition must be satisfied, the vortex ground state must be ordered. Our calculations show that the pinning size and strength may dramatically change the vortex ground state. Small pinning radius and high values of pinning strength may lead to disordered vortex configurations, which fade the critical force peaks. The critical forces show anisotropic behavior, but the same dependence on pinning strength and radius is observed for both driven force directions. Different to cases where the applied magnetic field is higher than the first matching field, here the depinning process begins with vortices weakly trapped on top of a pinning site and not with interstitial vortices. Our results are in good agreement with recent experimental results.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

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

NASA Technical Reports Server (NTRS)

Ye, Gang; Voigt, Gerd-Hannes

1989-01-01

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

Particles with nonlinear electric response: Suppressing van der Waals forces by an external field.

PubMed

Soo, Heino; Dean, David S; Krüger, Matthias

2017-01-01

We study the classical thermal component of Casimir, or van der Waals, forces between point particles with highly anharmonic dipole Hamiltonians when they are subjected to an external electric field. Using a model for which the individual dipole moments saturate in a strong field (a model that mimics the charges in a neutral, perfectly conducting sphere), we find that the resulting Casimir force depends strongly on the strength of the field, as demonstrated by analytical results. For a certain angle between the external field and center-to-center axis, the fluctuation force can be tuned and suppressed to arbitrarily small values. We compare the forces between these particles with those between particles with harmonic Hamiltonians and also provide a simple formula for asymptotically large external fields, which we expect to be generally valid for the case of saturating dipole moments.

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

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

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

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

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

Ponderomotive Force in the Presence of Electric Fields

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Hydrophobic interactions between dissimilar surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, R.H.; Flinn, D.H.; Rabinovich, Y.I.

1997-01-15

An atomic force microscope (AFM) was used to measure surface forces between a glass sphere and a silica plate. When the measurements were conducted between untreated surfaces, a short-range hydration force with decay lengths of 0.4 and 3.0 nm was observed. When the surfaces were hydrophobized with octadecyltrichlorosilane (OTS), on the other hand, long-range hydrophobic forces with decay lengths in the range of 2--32 nm were observed. The force measurements were conducted between surfaces having similar and dissimilar hydrophobicities so that the results may be used for deriving an empirical combining rule. It was found that the power law forcemore » constants for asymmetric interactions are close to the geometric means of those for symmetric interactions. Thus, hydrophobic force constants can be combined in the same manner as the Hamaker constants. A plot of the power law force constants versus water contact angles suggests that the hydrophobic force is uniquely determined by contact angle. These results will be useful in predicting hydrophobic forces for asymmetric interactions and in estimating hydrophobic forces from contact angles.« less

Macro-level social forces and micro-level consequences: poverty, alternate occupations, and drug dealing.

PubMed

Dunlap, Eloise; Johnson, Bruce D; Kotarba, Joseph A; Fackler, Jennifer L

2010-01-01

This article is an empirical examination of the ways in which macro-level social forces have had micro-level consequences in the New Orleans drug market. The article illustrates a clear connection between poverty and entrance into the drug market, as mitigated by race, lack of societal opportunity, lack of social capital, distressed families, and closed neighborhoods. Specifically, the research illustrates the mechanisms by which macro-level social forces intersect to legitimize drug dealing as a viable alternative method of acquiring money and social capital. These intersecting macro-level social forces, such as poverty, race, family structure, and neighborhood characteristics, ultimately constrain the life chances of those living in the inner city irrespective of personal traits, individual motivations, or private achievements.

Validation of pavement performance curves for the mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2009-02-01

The objective of this research is to determine whether the nationally calibrated performance models used in the Mechanistic-Empirical : Pavement Design Guide (MEPDG) provide a reasonable prediction of actual field performance, and if the desired accu...

Error analysis regarding the calculation of nonlinear force-free field

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Explanation of relativistic phenomena on the basis of interactions of particle energy, applied energy, and field energy

NASA Astrophysics Data System (ADS)

Fernando, Viraj

2011-09-01

This paper formulates a coherent theory of occurrence of relativistic phenomena in their interconnection in a feedback loop, unlike other theories, by tracing back concepts that Newton held but suppressed, when he developed his mechanics in his Principia. Despite Newtonian mechanics being based on a closed system, Newton in the General Scholium has indicated that in reality thee is in an open system, where 'a certain most subtle spirit' participates and directs all interactions from motion of bodies, to motion of light, to how the human brain operates. We have identified this 'most subtle spirit' as the non-empirical 'universal governing field' and that no empirical interaction in this universe can occur without exchange of energy between the empirical interactants and the governing field. By analyzing the energy momentum equation, we have demonstrated that everything empirical has a non-empirical substratum, identified with Spinoza's primitive substance, which binds everything in the universe to the field and through it to one another. Algorithm of Motion is founded on the Pythagorean character of the energy-momentum equation, which is applicable to all velocities 0

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de; Kibies, Patrick

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

Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface.

PubMed

Sandoval-Perez, Angelica; Pluhackova, Kristyna; Böckmann, Rainer A

2017-05-09

Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.

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

PubMed

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

2016-04-14

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

Spinmotive force due to domain wall motion in high field regime

NASA Astrophysics Data System (ADS)

Ieda, Jun'ichi; Yamane, Yuta; Maekawa, Sadamichi

2012-02-01

Spinmotive force associated with a moving vortex domain wall is investigated numerically. Dynamics of magnetization textures such as a domain wall exerts a non-conservative spin-force on conduction electrons [1], offering a new concept of magnetic devices [2]. This spinmotive force in permalloy nanowires has been detected by voltage measurement [3] where magnitude of the signal is limited less than 500 nV. Theoretically it is suggested that the spinmotive force signal increases as a function of external magnetic fields. At higher magnetic fields, however, the wall propagation mode becomes rather chaotic involving transformations of the wall structure and it remains to be seen how the spinmotive force appears. Numerical simulations show that the spinmotive force scales with the field even in a field range where the wall motion is no longer associated coherent precession. This feature has been tested in a recent experiment [4]. Further enhancement of the spinmotive force is explored by designing ferromagnetic nanostructures [5] and materials. [1] S. Barnes and S. Maekawa, PRL (2007). [2] S. Barnes, J. Ieda, and S. Maekawa, APL (2006). [3] S. A. Yang et al., PRL (2009). [4] M. Hayashi, J. Ieda et al., submitted. [5] Y. Yamane, J. Ieda et al., APEX (2011).

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

PubMed

Marston, Philip L; Zhang, Likun

2017-05-01

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

Mixed and Complex Mixed Migration during Armed Conflict: Multidimensional Empirical Evidence from Nepal

PubMed Central

Williams, Nathalie E.

2015-01-01

Historically, legal, policy, and academic communities largely ascribed to a dichotomy between forced and voluntary migration, creating a black and white vision that was convenient for legal and policy purposes. More recently, discussions have begun addressing the possibility of mixed migration, acknowledging that there is likely a wide continuum between forced and voluntary, and most migrants likely move with some amount of compulsion and some volition, even during armed conflict. While the mixed migration hypothesis is well-received, empirical evidence is disparate and somewhat blunt at this point. In this article, I contribute a direct theoretical and causal pathway discussion of mixed migration. I also propose the complex mixed migration hypothesis, which argues that not only do non-conflict related factors influence migration during conflict, but they do so differently than during periods of relative peace. I empirically test both hypotheses in the context of the recent armed conflict in Nepal. Using detailed survey data and event history models, results provide strong evidence for both mixed migration and complex mixed migration during conflict hypotheses. These hypotheses and evidence suggest that armed conflict might have substantial impacts on long-term population growth and change, with significant relevance in both academic and policy spheres. PMID:26366007

Systematic Validation of Protein Force Fields against Experimental Data

PubMed Central

Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2012-01-01

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

77 FR 14006 - Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

... DEPARTMENT OF DEFENSE Department of the Air Force Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement... Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement (FEIS). The MHPI ROD...

High-Frequency Intermuscular Coherence between Arm Muscles during Robot-Mediated Motor Adaptation

PubMed Central

Pizzamiglio, Sara; De Lillo, Martina; Naeem, Usman; Abdalla, Hassan; Turner, Duncan L.

2017-01-01

Adaptation of arm reaching in a novel force field involves co-contraction of upper limb muscles, but it is not known how the co-ordination of multiple muscle activation is orchestrated. We have used intermuscular coherence (IMC) to test whether a coherent intermuscular coupling between muscle pairs is responsible for novel patterns of activation during adaptation of reaching in a force field. Subjects (N = 16) performed reaching trials during a null force field, then during a velocity-dependent force field and then again during a null force field. Reaching trajectory error increased during early adaptation to the force-field and subsequently decreased during later adaptation. Co-contraction in the majority of all possible muscle pairs also increased during early adaptation and decreased during later adaptation. In contrast, IMC increased during later adaptation and only in a subset of muscle pairs. IMC consistently occurred in frequencies between ~40–100 Hz and during the period of arm movement, suggesting that a coherent intermuscular coupling between those muscles contributing to adaptation enable a reduction in wasteful co-contraction and energetic cost during reaching. PMID:28119620

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

PubMed

Bandura, A V; Sofo, J O; Kubicki, J D

2006-04-27

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

Magnetic field exposure stiffens regenerating plant protoplast cell walls.

PubMed

Haneda, Toshihiko; Fujimura, Yuu; Iino, Masaaki

2006-02-01

Single suspension-cultured plant cells (Catharanthus roseus) and their protoplasts were anchored to a glass plate and exposed to a magnetic field of 302 +/- 8 mT for several hours. Compression forces required to produce constant cell deformation were measured parallel to the magnetic field by means of a cantilever-type force sensor. Exposure of intact cells to the magnetic field did not result in any changes within experimental error, while exposure of regenerating protoplasts significantly increased the measured forces and stiffened regenerating protoplasts. The diameters of intact cells or regenerating protoplasts were not changed after exposure to the magnetic field. Measured forces for regenerating protoplasts with and without exposure to the magnetic field increased linearly with incubation time, with these forces being divided into components based on the elasticity of synthesized cell walls and cytoplasm. Cell wall synthesis was also measured using a cell wall-specific fluorescent dye, and no changes were noted after exposure to the magnetic field. Analysis suggested that exposure to the magnetic field roughly tripled the Young's modulus of the newly synthesized cell wall without any lag.

Structural learning in feedforward and feedback control.

PubMed

Yousif, Nada; Diedrichsen, Jörn

2012-11-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control.

Structural learning in feedforward and feedback control

PubMed Central

Diedrichsen, Jörn

2012-01-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control. PMID:22896725

The inducement of planetary boundary layer mass convergence associated with varying vorticity beneath tropospheric wind maximum

NASA Technical Reports Server (NTRS)

Johnson, D. R.

1984-01-01

The effects of the vorticity distribution are applied to study planetary boundary layer mass convergence beneath free tropospheric wind maximum. For given forcing by viscous and pressure gradient forces beneath a wind maximum, boundary layer cross stream mass transport is increased by anticyclonic vorticity on the right flank and decreased by cyclonic vorticity on the left flank. Such frictionally forced mass transport induces boundary layer mass convergence beneath the relative wind maximum. This result is related to the empirical rule that the most intense convection and severe weather frequently develop beneath the 500 mb zero relative vorticity isopleth.

Force-field prediction of materials properties in metal-organic frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew

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

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Force-field prediction of materials properties in metal-organic frameworks

DOE PAGES

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew; ...

2016-12-23

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

Creation of Synthetic Surface Temperature and Precipitation Ensembles Through A Computationally Efficient, Mixed Method Approach

NASA Astrophysics Data System (ADS)

Hartin, C.; Lynch, C.; Kravitz, B.; Link, R. P.; Bond-Lamberty, B. P.

2017-12-01

Typically, uncertainty quantification of internal variability relies on large ensembles of climate model runs under multiple forcing scenarios or perturbations in a parameter space. Computationally efficient, standard pattern scaling techniques only generate one realization and do not capture the complicated dynamics of the climate system (i.e., stochastic variations with a frequency-domain structure). In this study, we generate large ensembles of climate data with spatially and temporally coherent variability across a subselection of Coupled Model Intercomparison Project Phase 5 (CMIP5) models. First, for each CMIP5 model we apply a pattern emulation approach to derive the model response to external forcing. We take all the spatial and temporal variability that isn't explained by the emulator and decompose it into non-physically based structures through use of empirical orthogonal functions (EOFs). Then, we perform a Fourier decomposition of the EOF projection coefficients to capture the input fields' temporal autocorrelation so that our new emulated patterns reproduce the proper timescales of climate response and "memory" in the climate system. Through this 3-step process, we derive computationally efficient climate projections consistent with CMIP5 model trends and modes of variability, which address a number of deficiencies inherent in the ability of pattern scaling to reproduce complex climate model behavior.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

Enhanced heat transfer with full circumferential ribs in helical pipe

NASA Astrophysics Data System (ADS)

Chang, S. W.; Su, L. M.; Yang, T. L.

2002-08-01

This paper describes an experimental study of heat transfers in the smooth-walled and rib-roughened helical pipes with reference to the design of enhanced cooling passages in the cylinder head and liner of a marine propulsive diesel engine. The manner in which the repeated ribs modify the forced heat convection in the helical pipe is considered for the case where the flow is turbulent upon entering the coil but laminar in further downstream. A selection of experimental results illustrates the individual and interactive effects of Dean vortices and rib-flows on heat transfer along the inner and outer helixes of coils. The experimental-based observations reveal that the centrifugal force modifies the heat transfer in a manner to generate circumferential heat transfer variation with better cooling performance on the outer edge relative to its inner counterpart even with the agitated flow field caused by the repeated ribs. Heat transfer augmentation factor in the range of 1.3 - 3 times of the smooth-walled level is achieved using the present ribbing geometry. A set of empirical correlations based on the experimental data has been developed to permit the evaluation of heat transfers along the inner and outer helixes of the smooth-walled and rib-roughened helical pipes.

Empirical research in bioethical journals. A quantitative analysis

PubMed Central

Borry, P; Schotsmans, P; Dierickx, K

2006-01-01

Objectives The objective of this research is to analyse the evolution and nature of published empirical research in the fields of medical ethics and bioethics. Design Retrospective quantitative study of nine peer reviewed journals in the field of bioethics and medical ethics (Bioethics, Cambridge Quarterly of Healthcare Ethics, Hastings Center Report, Journal of Clinical Ethics, Journal of Medical Ethics, Kennedy Institute of Ethics Journal, Nursing Ethics, Christian Bioethics, andTheoretical Medicine and Bioethics). Results In total, 4029 articles published between 1990 and 2003 were retrieved from the journals studied. Over this period, 435 (10.8%) studies used an empirical design. The highest percentage of empirical research articles appeared in Nursing Ethics (n = 145, 39.5%), followed by the Journal of Medical Ethics (n = 128, 16.8%) and the Journal of Clinical Ethics (n = 93, 15.4%). These three journals account for 84.1% of all empirical research in bioethics published in this period. The results of the χ2 test for two independent samples for the entire dataset indicate that the period 1997–2003 presented a higher number of empirical studies (n = 309) than did the period 1990–1996 (n = 126). This increase is statistically significant (χ2 = 49.0264, p<.0001). Most empirical studies employed a quantitative paradigm (64.6%, n = 281). The main topic of research was prolongation of life and euthanasia (n = 68). Conclusions We conclude that the proportion of empirical research in the nine journals increased steadily from 5.4% in 1990 to 15.4% in 2003. It is likely that the importance of empirical methods in medical ethics and bioethics will continue to increase. PMID:16574880

A comparison of measured and theoretical predictions for STS ascent and entry sonic booms

NASA Technical Reports Server (NTRS)

Garcia, F., Jr.; Jones, J. H.; Henderson, H. R.

1983-01-01

Sonic boom measurements have been obtained during the flights of STS-1 through 5. During STS-1, 2, and 4, entry sonic boom measurements were obtained and ascent measurements were made on STS-5. The objectives of this measurement program were (1) to define the sonic boom characteristics of the Space Transportation System (STS), (2) provide a realistic assessment of the validity of xisting theoretical prediction techniques, and (3) establish a level of confidence for predicting future STS configuration sonic boom environments. Detail evaluation and reporting of the results of this program are in progress. This paper will address only the significant results, mainly those data obtained during the entry of STS-1 at Edwards Air Force Base (EAFB), and the ascent of STS-5 from Kennedy Space Center (KSC). The theoretical prediction technique employed in this analysis is the so called Thomas Program. This prediction technique is a semi-empirical method that required definition of the near field signatures, detailed trajectory characteristics, and the prevailing meteorological characteristics as an input. This analytical procedure then extrapolates the near field signatures from the flight altitude to an altitude consistent with each measurement location.

SOCIO-EMOTIONAL AND CHARACTER DEVELOPMENT

PubMed Central

Snyder, Frank J.

2015-01-01

More and more researchers are studying socio-emotional and character development (SECD). The rise and progress in SECD research is encouraging, but there is a critical issue with such a multidisciplinary and fast-developing field: SECD research and evaluation can be more consistent to prevent heterogeneity in definitions and disparate theoretical, measurement, and program models. After summarizing SECD-related literature, I recommend the theory of triadic influence (TTI) as a force to generate consistency and a resource to assist in guiding the design and evaluation of SECD-related programs. The theory fills a gulf in the literature that seeks an ecological theory aligned with SECD-related programs and etiology. The recommendation of the TTI stems from 3 main advantages: (1) The TTI integrates a full range of risk and protective factors in a detailed mediation and moderation framework; (2) it takes a comprehensive view of all the stakeholders in the educational system (i.e., youth, schools, families, and communities); (3) and its utility has been substantiated by empirical evidence from a variety of fields. I discuss applications of the TTI in SECD-related work and suggest improvements for etiology research and the design and evaluation of SECD programs. PMID:26478721

Space-time modeling of soil moisture

NASA Astrophysics Data System (ADS)

Chen, Zijuan; Mohanty, Binayak P.; Rodriguez-Iturbe, Ignacio

2017-11-01

A physically derived space-time mathematical representation of the soil moisture field is carried out via the soil moisture balance equation driven by stochastic rainfall forcing. The model incorporates spatial diffusion and in its original version, it is shown to be unable to reproduce the relative fast decay in the spatial correlation functions observed in empirical data. This decay resulting from variations in local topography as well as in local soil and vegetation conditions is well reproduced via a jitter process acting multiplicatively over the space-time soil moisture field. The jitter is a multiplicative noise acting on the soil moisture dynamics with the objective to deflate its correlation structure at small spatial scales which are not embedded in the probabilistic structure of the rainfall process that drives the dynamics. These scales of order of several meters to several hundred meters are of great importance in ecohydrologic dynamics. Properties of space-time correlation functions and spectral densities of the model with jitter are explored analytically, and the influence of the jitter parameters, reflecting variabilities of soil moisture at different spatial and temporal scales, is investigated. A case study fitting the derived model to a soil moisture dataset is presented in detail.

Molecular Mechanics

PubMed Central

Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

2014-01-01

Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

Collisional model of the drag force of granular impact

NASA Astrophysics Data System (ADS)

Stevens Bester, Cacey; Behringer, Robert P.

2017-06-01

A dense, dry granular target can cause a free-falling intruding object to come to an abrupt stop as its momentum is lost to the grains. An empirical force law describes this process, characterizing the stopping force as the sum of depth-dependent friction and velocity-dependent inertial drag. However, a complete interpretation of the stopping force, incorporating grain-scale interactions during impact, remains unresolved. Here, the momentum transfer is proposed to occur through sporadic, normal collisions with clusters of high force-carrying grains at the intruder's surface. To test this model in impact experiments, we determine the forces acting on an intruder decelerating through a dense granular medium using high-speed imaging of its trajectory. We vary the geometry of the impacting object to infer intruder-grain interactions. As a result, we connect the inertial drag to the effect of intruder shape based on the proposed collisional model. These impact studies serve as an approach to understand dynamic force transmission in granular media.

Statistical field theory of futures commodity prices

NASA Astrophysics Data System (ADS)

Baaquie, Belal E.; Yu, Miao

2018-02-01

The statistical theory of commodity prices has been formulated by Baaquie (2013). Further empirical studies of single (Baaquie et al., 2015) and multiple commodity prices (Baaquie et al., 2016) have provided strong evidence in support the primary assumptions of the statistical formulation. In this paper, the model for spot prices (Baaquie, 2013) is extended to model futures commodity prices using a statistical field theory of futures commodity prices. The futures prices are modeled as a two dimensional statistical field and a nonlinear Lagrangian is postulated. Empirical studies provide clear evidence in support of the model, with many nontrivial features of the model finding unexpected support from market data.

A data-driven decomposition approach to model aerodynamic forces on flapping airfoils

NASA Astrophysics Data System (ADS)

Raiola, Marco; Discetti, Stefano; Ianiro, Andrea

2017-11-01

In this work, we exploit a data-driven decomposition of experimental data from a flapping airfoil experiment with the aim of isolating the main contributions to the aerodynamic force and obtaining a phenomenological model. Experiments are carried out on a NACA 0012 airfoil in forward flight with both heaving and pitching motion. Velocity measurements of the near field are carried out with Planar PIV while force measurements are performed with a load cell. The phase-averaged velocity fields are transformed into the wing-fixed reference frame, allowing for a description of the field in a domain with fixed boundaries. The decomposition of the flow field is performed by means of the POD applied on the velocity fluctuations and then extended to the phase-averaged force data by means of the Extended POD approach. This choice is justified by the simple consideration that aerodynamic forces determine the largest contributions to the energetic balance in the flow field. Only the first 6 modes have a relevant contribution to the force. A clear relationship can be drawn between the force and the flow field modes. Moreover, the force modes are closely related (yet slightly different) to the contributions of the classic potential models in literature, allowing for their correction. This work has been supported by the Spanish MINECO under Grant TRA2013-41103-P.

Force, torque, linear momentum, and angular momentum in classical electr odynamics

NASA Astrophysics Data System (ADS)

Mansuripur, Masud

2017-10-01

The classical theory of electrodynamics is built upon Maxwell's equations and the concepts of electromagnetic (EM) field, force, energy, and momentum, which are intimately tied together by Poynting's theorem and by the Lorentz force law. Whereas Maxwell's equations relate the fields to their material sources, Poynting's theorem governs the flow of EM energy and its exchange between fields and material media, while the Lorentz law regulates the back-and-forth transfer of momentum between the media and the fields. An alternative force law, first proposed by Einstein and Laub, exists that is consistent with Maxwell's equations and complies with the conservation laws as well as with the requirements of special relativity. While the Lorentz law requires the introduction of hidden energy and hidden momentum in situations where an electric field acts on a magnetized medium, the Einstein-Laub (E-L) formulation of EM force and torque does not invoke hidden entities under such circumstances. Moreover, total force/torque exerted by EM fields on any given object turns out to be independent of whether the density of force/torque is evaluated using the law of Lorentz or that of Einstein and Laub. Hidden entities aside, the two formulations differ only in their predicted force and torque distributions inside matter. Such differences in distribution are occasionally measurable, and could serve as a guide in deciding which formulation, if either, corresponds to physical reality.

Creativity as Mediator for Intrinsic Motivation and Sales Performance

ERIC Educational Resources Information Center

Bodla, Mahmood A.; Naeem, Basharat

2014-01-01

Substantial theoretical and empirical literature indicates inconsistent performance implications of intrinsic motivation, suggesting the possibility of some explanatory mechanisms. However, little is known about the factors that might explain intrinsic motivation and sales force performance relation, particularly in highly competitive and…

Psychological Contracts: Are They Still Relevant?

ERIC Educational Resources Information Center

Maguire, Heather

2002-01-01

Empirical evidence from a banking organization illustrated how change has an impact on psychological contracts. Concluded that maintenance of contracts makes an important contribution to relationships but organizations need to adjust psychological contracts to meet the needs of the work force. (Contains 58 references.) (JOW)

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

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.

Improved model predictive control of resistive wall modes by error field estimator in EXTRAP T2R

NASA Astrophysics Data System (ADS)

Setiadi, A. C.; Brunsell, P. R.; Frassinetti, L.

2016-12-01

Many implementations of a model-based approach for toroidal plasma have shown better control performance compared to the conventional type of feedback controller. One prerequisite of model-based control is the availability of a control oriented model. This model can be obtained empirically through a systematic procedure called system identification. Such a model is used in this work to design a model predictive controller to stabilize multiple resistive wall modes in EXTRAP T2R reversed-field pinch. Model predictive control is an advanced control method that can optimize the future behaviour of a system. Furthermore, this paper will discuss an additional use of the empirical model which is to estimate the error field in EXTRAP T2R. Two potential methods are discussed that can estimate the error field. The error field estimator is then combined with the model predictive control and yields better radial magnetic field suppression.

Dynamo Induced by Time-periodic Force

NASA Astrophysics Data System (ADS)

Wei, Xing

2018-03-01

To understand the dynamo driven by time-dependent flow, e.g., turbulence, we investigate numerically the dynamo induced by time-periodic force in rotating magnetohydrodynamic flow and focus on the effect of force frequency on the dynamo action. It is found that the dynamo action depends on the force frequency. When the force frequency is near resonance the force can drive dynamo, but when it is far away from resonance dynamo fails. In the frequency range near resonance to support dynamo, the force frequency at resonance induces a weak magnetic field and magnetic energy increases as the force frequency deviates from the resonant frequency. This is opposite to the intuition that a strong flow at resonance will induce a strong field. It is because magnetic field nonlinearly couples with fluid flow in the self-sustained dynamo and changes the resonance of driving force and inertial wave.

Evidence-based Nursing Education - a Systematic Review of Empirical Research

PubMed Central

Reiber, Karin

2011-01-01

The project „Evidence-based Nursing Education – Preparatory Stage“, funded by the Landesstiftung Baden-Württemberg within the programme Impulsfinanzierung Forschung (Funding to Stimulate Research), aims to collect information on current research concerned with nursing education and to process existing data. The results of empirical research which has already been carried out were systematically evaluated with aim of identifying further topics, fields and matters of interest for empirical research in nursing education. In the course of the project, the available empirical studies on nursing education were scientifically analysed and systematised. The over-arching aim of the evidence-based training approach – which extends beyond the aims of this project - is the conception, organisation and evaluation of vocational training and educational processes in the caring professions on the basis of empirical data. The following contribution first provides a systematic, theoretical link to the over-arching reference framework, as the evidence-based approach is adapted from thematically related specialist fields. The research design of the project is oriented towards criteria introduced from a selection of studies and carries out a two-stage systematic review of the selected studies. As a result, the current status of research in nursing education, as well as its organisation and structure, and questions relating to specialist training and comparative education are introduced and discussed. Finally, the empirical research on nursing training is critically appraised as a complementary element in educational theory/psychology of learning and in the ethical tradition of research. This contribution aims, on the one hand, to derive and describe the methods used, and to introduce the steps followed in gathering and evaluating the data. On the other hand, it is intended to give a systematic overview of empirical research work in nursing education. In order to preserve a holistic view of the research field and methods, detailed individual findings are not included. PMID:21818237

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

PubMed

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

2010-01-01

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

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

Treesearch

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

2015-01-01

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

The calculation of transport phenomena in electromagnetically levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation has been developed for the electromagnetic force field, fluid flow field, and solute concentration field of levitation-melted metal specimens. The governing equations consist of the conventional transport equations combined with the appropriate expressions for the electromagnetic force field. The predictions obtained by solving the governing equations numerically on a digital computer are in good agreement with lifting force and average temperature measurements reported in the literature.

Estimating trends in the global mean temperature record

NASA Astrophysics Data System (ADS)

Poppick, Andrew; Moyer, Elisabeth J.; Stein, Michael L.

2017-06-01

Given uncertainties in physical theory and numerical climate simulations, the historical temperature record is often used as a source of empirical information about climate change. Many historical trend analyses appear to de-emphasize physical and statistical assumptions: examples include regression models that treat time rather than radiative forcing as the relevant covariate, and time series methods that account for internal variability in nonparametric rather than parametric ways. However, given a limited data record and the presence of internal variability, estimating radiatively forced temperature trends in the historical record necessarily requires some assumptions. Ostensibly empirical methods can also involve an inherent conflict in assumptions: they require data records that are short enough for naive trend models to be applicable, but long enough for long-timescale internal variability to be accounted for. In the context of global mean temperatures, empirical methods that appear to de-emphasize assumptions can therefore produce misleading inferences, because the trend over the twentieth century is complex and the scale of temporal correlation is long relative to the length of the data record. We illustrate here how a simple but physically motivated trend model can provide better-fitting and more broadly applicable trend estimates and can allow for a wider array of questions to be addressed. In particular, the model allows one to distinguish, within a single statistical framework, between uncertainties in the shorter-term vs. longer-term response to radiative forcing, with implications not only on historical trends but also on uncertainties in future projections. We also investigate the consequence on inferred uncertainties of the choice of a statistical description of internal variability. While nonparametric methods may seem to avoid making explicit assumptions, we demonstrate how even misspecified parametric statistical methods, if attuned to the important characteristics of internal variability, can result in more accurate uncertainty statements about trends.

School Climate Research

ERIC Educational Resources Information Center

Thapa, Amrit

2013-01-01

School climate research is clearly evolving. The field demands rigorous and empirically sound research that focuses on relating specific aspects and activities of interventions to changes in specific components of school climate. We also need empirical evidence based on sound research techniques on how both interventions and climate affect…

Gravitation Theory: Empirical Status from Solar System Experiments: All observations to date are consistent with Einstein's general relativity theory of gravity.

PubMed

Nordtvedt, K L

1972-12-15

I have reviewed the historical and contemporary experiments that guide us in choosing a post-Newtonian, relativistic gravitational theory. The foundation experiments essentially constrain gravitation theory to be a metric theory in which matter couples solely to one gravitational field, the metric field, although other cosmological gravitational fields may exist. The metric field for any metric theory can be specified (for the solar system, for our present purposes) by a series of potential terms with several parameters. A variety of experiments specify (or put limits on) the numerical values of the seven parameters in the post-Newtonian metric field, and other such experiments have been planned. The empirical results, to date, yield values of the parameters that are consistent with the predictions of Einstein's general relativity.

Comparing Molecular Dynamics Force Fields in the Essential Subspace

PubMed Central

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

2015-01-01

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

Operational advances in ring current modeling using RAM-SCB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Welling, Daniel T; Jordanova, Vania K; Zaharia, Sorin G

The Ring current Atmosphere interaction Model with Self-Consistently calculated 3D Magnetic field (RAM-SCB) combines a kinetic model of the ring current with a force-balanced model of the magnetospheric magnetic field to create an inner magnetospheric model that is magnetically self consistent. RAM-SCB produces a wealth of outputs that are valuable to space weather applications. For example, the anisotropic particle distribution of the KeV-energy population calculated by the code is key for predicting surface charging on spacecraft. Furthermore, radiation belt codes stand to benefit substantially from RAM-SCB calculated magnetic field values and plasma wave growth rates - both important for determiningmore » the evolution of relativistic electron populations. RAM-SCB is undergoing development to bring these benefits to the space weather community. Data-model validation efforts are underway to assess the performance of the system. 'Virtual Satellite' capability has been added to yield satellite-specific particle distribution and magnetic field output. The code's outer boundary is being expanded to 10 Earth Radii to encompass previously neglected geosynchronous orbits and allow the code to be driven completely by either empirical or first-principles based inputs. These advances are culminating towards a new, real-time version of the code, rtRAM-SCB, that can monitor the inner magnetosphere conditions on both a global and spacecraft-specific level. This paper summarizes these new features as well as the benefits they provide the space weather community.« less

Operational Advances in Ring Current Modeling Using RAM-SCB

NASA Astrophysics Data System (ADS)

Morley, S.; Welling, D. T.; Zaharia, S. G.; Jordanova, V. K.

2010-12-01

The Ring current Atmosphere interaction Model with Self-Consistently calculated 3D Magnetic field (RAM-SCB) combines a kinetic model of the ring current with a force-balanced model of the magnetospheric magnetic field to create an inner magnetospheric model that is magnetically self consistent. RAM-SCB produces a wealth of outputs that are valuable to space weather applications. For example, the anisotropic particle distribution of the KeV-energy population calculated by the code is key for predicting surface charging on spacecraft. Furthermore, radiation belt codes stand to benefit substantially from RAM-SCB calculated magnetic field values and plasma wave growth rates - both important for determining the evolution of relativistic electron populations. RAM-SCB is undergoing development to bring these benefits to the space weather community. Data-model validation efforts are underway to assess the performance of the system. “Virtual Satellite” capability has been added to yield satellite-specific particle distribution and magnetic field output. The code’s outer boundary is being expanded to 10 Earth Radii to encompass previously neglected geosynchronous orbits and allow the code to be driven completely by either empirical or first-principles based inputs. These advances are culminating towards a new, real-time version of the code, rtRAM-SCB, that can monitor the inner magnetosphere conditions on both a global and spacecraft-specific level. This paper summarizes these new features as well as the benefits they provide the space weather community.

Acoustic forcing of a liquid drop

NASA Technical Reports Server (NTRS)

Lyell, M. J.

1992-01-01

The development of systems such as acoustic levitation chambers will allow for the positioning and manipulation of material samples (drops) in a microgravity environment. This provides the capability for fundamental studies in droplet dynamics as well as containerless processing work. Such systems use acoustic radiation pressure forces to position or to further manipulate (e.g., oscillate) the sample. The primary objective was to determine the effect of a viscous acoustic field/tangential radiation pressure forcing on drop oscillations. To this end, the viscous acoustic field is determined. Modified (forced) hydrodynamic field equations which result from a consistent perturbation expansion scheme are solved. This is done in the separate cases of an unmodulated and a modulated acoustic field. The effect of the tangential radiation stress on the hydrodynamic field (drop oscillations) is found to manifest as a correction to the velocity field in a sublayer region near the drop/host interface. Moreover, the forcing due to the radiation pressure vector at the interface is modified by inclusion of tangential stresses.

Beyond integrating social sciences: Reflecting on the place of life sciences in empirical bioethics methodologies.

PubMed

Mertz, Marcel; Schildmann, Jan

2018-06-01

Empirical bioethics is commonly understood as integrating empirical research with normative-ethical research in order to address an ethical issue. Methodological analyses in empirical bioethics mainly focus on the integration of socio-empirical sciences (e.g. sociology or psychology) and normative ethics. But while there are numerous multidisciplinary research projects combining life sciences and normative ethics, there is few explicit methodological reflection on how to integrate both fields, or about the goals and rationales of such interdisciplinary cooperation. In this paper we will review some drivers for the tendency of empirical bioethics methodologies to focus on the collaboration of normative ethics with particularly social sciences. Subsequently, we argue that the ends of empirical bioethics, not the empirical methods, are decisive for the question of which empirical disciplines can contribute to empirical bioethics in a meaningful way. Using already existing types of research integration as a springboard, five possible types of research which encompass life sciences and normative analysis will illustrate how such cooperation can be conceptualized from a methodological perspective within empirical bioethics. We will conclude with a reflection on the limitations and challenges of empirical bioethics research that integrates life sciences.

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2015-09-01

The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations of methane hydrate using polarizable force fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-06-14

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are foundmore » between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl« less

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

The force-free configuration of flux ropes in geomagnetotail: Cluster observations

NASA Astrophysics Data System (ADS)

Yang, Y. Y.; Shen, C.; Zhang, Y. C.; Rong, Z. J.; Li, X.; Dunlop, M.; Ma, Y. H.; Liu, Z. X.; Carr, C. M.; Rème, H.

2014-08-01

Unambiguous knowledge of magnetic field structure and the electric current distribution is critical for understanding the origin, evolution, and related dynamic properties of magnetic flux ropes (MFRs). In this paper, a survey of 13 MFRs in the Earth's magnetotail are conducted by Cluster multipoint analysis, so that their force-free feature, i.e., the kind of magnetic field structure satisfying J × B = 0, can be probed directly. It is showed that the selected flux ropes with the bipolar signature of the south-north magnetic field component generally lie near the equatorial plane, as expected, and that the magnetic field gradient is rather weak near the axis center, where the curvature radius is large. The current density (up to several tens of nA/m2) reaches their maximum values as the center is approached. It is found that the stronger the current density, the smaller the angles between the magnetic field and current in MFRs. The direct observations show that only quasi force-free structure is observed, and it tends to appear in the low plasma beta regime (in agreement with the theoretic results). The quasi force-free region is generally found to be embedded in the central portion of the MFRs, where the current is approximately field aligned and proportional to the strength of core field. It is shown that ~60% of surveyed MFRs can be globally approximated as force free. The force-free factor α is found to be nonconstantly varied through the quasi force-free MFR, suggesting that the force-free structure is nonlinear.

Place as a social space: fields of encounter relating to the local sustainability process.

PubMed

Dumreicher, Heidi; Kolb, Bettina

2008-04-01

The paper shows how sustainability questions relate to the local space. The local place is not a static entity, but a dynamic one, undergoing constant changes, and it is the rapid social and material processes within the given local situation that is a challenge for the Chinese villages and their integrity. The following article considers the cohesion between the dwellers' emotional co-ownership of their local space and the sustainability process as a driving force in social, economic and ecological development. We bring together the classification of the seven fields of encounter, which were developed out of the empirical data of the Chinese case study villages, and sustainability oriented management considerations for all levels of this concept. We do not pretend to know the solutions, but describe a set of interrelated fields that can be anchor points for placing the solutions and show in which fields action and intervention is possible. In our concept of sustainability, every spatial field has its special meaning, needs special measures and policies and has different connotations to concepts like responsibility, family values or communication systems. We see the social sustainability process as a support for the empowerment of the local dwellers, and the SUCCESS research has encouraged the villages to find suitable sustainability oriented solutions for their natural and societal situation. Before entering the discussion about the chances and potential of a sustainability approach for the Chinese villages, it is first necessary to accept the fact that rural villages play a primordial role in Chinese society and that their potential can strengthen future pathways for China.

Evaluation of the attractive force of different types of new-generation magnetic attachment systems.

PubMed

Akin, Hakan; Coskun, M Emre; Akin, E Gulsah; Ozdemir, A Kemal

2011-03-01

Rare earth magnets have been used in prosthodontics, but their tendency for corrosion in the oral cavity and insufficient attractive forces limit long-term clinical application. The purpose of this study was to evaluate the attractive force of different types of new-generation magnetic attachment systems. The attractive force of the neodymium-iron-boron (Nd-Fe-B) and samarium-cobalt (Sm-Co) magnetic attachment systems, including closed-field (Hilop and Hicorex) and open-field (Dyna and Steco) systems, was measured in a universal testing machine (n=5). The data were statistically evaluated with 1-way ANOVA and post hoc Tukey-Kramer multiple comparison test (α=.05). The closed-field systems exhibited greater (P<.001) attractive force than the open-field systems. Moreover, there was a statistically significant difference in attractive force between Nd-Fe-B and Sm-Co magnets (P<.001). The strongest attractive force was found with the Hilop system (9.2 N), and the lowest force was found with the Steco system (2.3 N). The new generation of Nd-Fe-B closed-field magnets, along with improved technology, provides sufficient denture retention for clinical application. Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Magnetic Control of Convection during Protein Crystallization

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2004-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular Crystals for diffraction analyses has been the central focus for bio-chemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and Sedimentation as is achieved in "microgravity", we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, f o d o n of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with counteracts on for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteract terrestrial gravity. The genera1 objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagentic salts and solutions in magnetic fields and compare them to analyticalprctions.

Gendered Subjectivities of Spacetimematter

ERIC Educational Resources Information Center

Juelskjaer, Malou

2013-01-01

This paper investigates enactments of human subjectivities with a focus on how subjectivities may be studied if spatiality and temporality are taken up as constituting forces in the production of subjectivities. By reading poststructuralist feminist theorising, agential realism and empirical material diffractively through each other I re-situate…

NONLINEAR FORCE-FREE FIELD MODELING OF A SOLAR ACTIVE REGION USING SDO/HMI AND SOLIS/VSM DATA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thalmann, J. K.; Wiegelmann, T.; Pietarila, A.

2012-08-15

We use SDO/HMI and SOLIS/VSM photospheric magnetic field measurements to model the force-free coronal field above a solar active region, assuming magnetic forces dominate. We take measurement uncertainties caused by, e.g., noise and the particular inversion technique, into account. After searching for the optimum modeling parameters for the particular data sets, we compare the resulting nonlinear force-free model fields. We show the degree of agreement of the coronal field reconstructions from the different data sources by comparing the relative free energy content, the vertical distribution of the magnetic pressure, and the vertically integrated current density. Though the longitudinal and transversemore » magnetic flux measured by the VSM and HMI is clearly different, we find considerable similarities in the modeled fields. This indicates the robustness of the algorithm we use to calculate the nonlinear force-free fields against differences and deficiencies of the photospheric vector maps used as an input. We also depict how much the absolute values of the total force-free, virial, and the free magnetic energy differ and how the orientation of the longitudinal and transverse components of the HMI- and VSM-based model volumes compare to each other.« less

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

Chameleon field is one of the promising candidates of dark energy scalar fields. As in all viable candidate field theories, a screening mechanism is implemented to be consistent with all existing tests of general relativity. The screening effect in the chameleon theory manifests its influence limited only to the thin outer layer of a bulk object, thus producing extra forces orders of magnitude weaker than that of the gravitational force of the bulk. For pointlike particles such as atoms, the depth of screening is larger than the size of the particle, such that the screening mechanism is ineffective and the chameleon force is fully expressed on the atomic test particles. Extra force measurements using atom interferometry are thus much more sensitive than bulk mass based measurements, and indeed have placed the most stringent constraints on the parameters characterizing chameleon field. In this paper, we present a conceptual measurement approach for chameleon force detection using atom interferometry in microgravity, in which multiloop atom interferometers exploit specially designed periodic modulation of chameleon fields. We show that major systematics of the dark energy force measurements, i.e., effects of gravitational forces and their gradients, can be suppressed below all hypothetical chameleon signals in the parameter space of interest.

Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations

PubMed Central

Larsson, Per; Kasson, Peter M.

2014-01-01

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce lipidconverter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes. PMID:25081234

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

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

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

Jet-induced ground effects on a parametric flat-plate model in hover

NASA Technical Reports Server (NTRS)

Wardwell, Douglas A.; Hange, Craig E.; Kuhn, Richard E.; Stewart, Vearl R.

1993-01-01

The jet-induced forces generated on short takeoff and vertical landing (STOVL) aircraft when in close proximity to the ground can have a significant effect on aircraft performance. Therefore, accurate predictions of these aerodynamic characteristics are highly desirable. Empirical procedures for estimating jet-induced forces during the vertical/short takeoff and landing (V/STOL) portions of the flight envelope are currently limited in accuracy. The jet-induced force data presented significantly add to the current STOVL configurations data base. Further development of empirical prediction methods for jet-induced forces, to provide more configuration diversity and improved overall accuracy, depends on the viability of this STOVL data base. The data base may also be used to validate computational fluid dynamics (CFD) analysis codes. The hover data obtained at the NASA Ames Jet Calibration and Hover Test (JCAHT) facility for a parametric flat-plate model is presented. The model tested was designed to allow variations in the planform aspect ratio, number of jets, nozzle shape, and jet location. There were 31 different planform/nozzle configurations tested. Each configuration had numerous pressure taps installed to measure the pressures on the undersurface of the model. All pressure data along with the balance jet-induced lift and pitching-moment increments are tabulated. For selected runs, pressure data are presented in the form of contour plots that show lines of constant pressure coefficient on the model undersurface. Nozzle-thrust calibrations and jet flow-pressure survey information are also provided.

The Introduction of Fields in Relation to Force

ERIC Educational Resources Information Center

Brunt, Marjorie; Brunt, Geoff

2012-01-01

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

Phytoplankton pigment patterns and wind forcing off central California

NASA Technical Reports Server (NTRS)

Abbott, Mark R.; Barksdale, Brett

1991-01-01

Mesoscale variability in phytoplankton pigment distributions of central California during the spring-summer upwelling season are studied via a 4-yr time series of high-resolution coastal zone color scanner imagery. Empirical orthogonal functions are used to decompose the time series of spatial images into its dominant modes of variability. The coupling between wind forcing of the upper ocean and phytoplankton distribution on mesoscales is investigated. Wind forcing, in particular the curl of the wind stress, was found to play an important role in the distribution of phytoplankton pigment in the California Current. The spring transition varies in timing and intensity from year to year but appears to be a recurrent feature associated with the rapid onset of the upwelling-favorable winds. Although the underlying dynamics may be dominated by processes other than forcing by wind stress curl, it appears that curl may force the variability of the filaments and hence the pigment patterns.

The hierarchical stability of the seven known large size ratio triple asteroids using the empirical stability parameters.

PubMed

Liu, Xiaodong; Baoyin, Hexi; Marchis, Franck

In this study, the hierarchical stability of the seven known large size ratio triple asteroids is investigated. The effect of the solar gravity and primary's J 2 are considered. The force function is expanded in terms of mass ratios based on the Hill's approximation and the large size ratio property. The empirical stability parameters are used to examine the hierarchical stability of the triple asteroids. It is found that the all the known large size ratio triple asteroid systems are hierarchically stable. This study provides useful information for future evolutions of the triple asteroids.

Measurement and Ontology: What Kind of Evidence Can We Have for Quantum Fields?

NASA Astrophysics Data System (ADS)

Falkenburg, Brigitte

In the following, I deal with the ontology of quantum field theory (QFT) from a Kantian point of view, in terms of parts of empirical reality and their relations. In contradistinction to a formal ontology of QFT that is based primarily on the formal structure of the theory, I focus on the ways in which quantum fields can be measured, and on the structural features of empirical reality to which these measurements give rise. To approach the ontology of quantum fields in terms of measurement results in two paradoxes. First, ontology is about the structure of independent entities which belong to the furniture of the world, but measurements rely on interaction. Second, experimental evidence for quantum field theories is mainly based on particle tracks and other local phenomena. Thus, what kind of evidence can we have for the field structure of quantum fields? My paper attempts to unravel these paradoxes in the following steps. First, I give a rough sketch of the appearances of particle physics, the kinds of experimental evidence which count as tests of quantum electrodynamcs (QED) and the standard model of particle physics (1). In an intermezzo on Kant's view of scientific experience, I explain in which terms we might conceive of empirical reality beyond the claims of strict empiricism (2). Finally, I apply these ideas to the appearances of particle physics and suggest that they commit us to a relational ontology of QFT (3).

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afanas'ev, A A; Rubinov, A N; Gaida, L S

2015-10-31

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

The Tai Chi in Star Formation

NASA Astrophysics Data System (ADS)

Li, Hua-bai

2017-10-01

Tai Chi, a Chinese martial art developed based on the laws of nature, emphasises how 'to conquer the unyielding with the yielding'. The recent observation of star formation shows that stars result from the interaction between gravity, turbulence and magnetic fields. This interaction again follows the nature rules that inspired Tai Chi. For example, if self-gravity is the force that dominates, the molecular cloud will collapse isotropically, which compresses magnetic field lines. The density of the yielding field lines increases until magnetic pressure reaches the critical value to support the cloud against the gravitational force in directions perpendicular to the field lines (Lorentz force). Then gravity gives way to Lorentz force, accumulating gas only along the field lines till the gas density achieves the critical value to again compress the field lines. The Tai Chi goes on in a self-similar way.

Driving Force of Plasma Bullet in Atmospheric-Pressure Plasma

NASA Astrophysics Data System (ADS)

Yambe, Kiyoyuki; Masuda, Seiya; Kondo, Shoma

2018-06-01

When plasma is generated by applying high-voltage alternating current (AC), the driving force of the temporally and spatially varying electric field is applied to the plasma. The strength of the driving force of the plasma at each spatial position is different because the electrons constituting the atmospheric-pressure nonequilibrium (cold) plasma move at a high speed in space. If the force applied to the plasma is accelerated only by the driving force, the plasma will be accelerated infinitely. The equilibrium between the driving force and the restricting force due to the collision between the plasma and neutral particles determines the inertial force and the drift velocity of the plasma. Consequently, the drift velocity depends on the strength of the time-averaged AC electric field. The pressure applied by the AC electric field equilibrates with the plasma pressure. From the law of conservation of energy, the pressure equilibrium is maintained by varying the drift velocity of the plasma.

Flows, Fields, and Forces in the Mars-Solar Wind Interaction

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Brain, D. A.; Luhmann, J. G.; DiBraccio, G. A.; Ruhunusiri, S.; Harada, Y.; Fowler, C. M.; Mitchell, D. L.; Connerney, J. E. P.; Espley, J. R.; Mazelle, C.; Jakosky, B. M.

2017-11-01

We utilize suprathermal ion and magnetic field measurements from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, organized by the upstream magnetic field, to investigate the morphology and variability of flows, fields, and forces in the Mars-solar wind interaction. We employ a combination of case studies and statistical investigations to characterize the interaction in both quasi-parallel and quasi-perpendicular regions and under high and low solar wind Mach number conditions. For the first time, we include a detailed investigation of suprathermal ion temperature and anisotropy. We find that the observed magnetic fields and suprathermal ion moments in the magnetosheath, bow shock, and upstream regions have observable asymmetries controlled by the interplanetary magnetic field, with particularly large asymmetries found in the ion parallel temperature and anisotropy. The greatest temperature anisotropies occur in quasi-perpendicular regions of the magnetosheath and under low Mach number conditions. These results have implications for the growth and evolution of wave-particle instabilities and their role in energy transport and dissipation. We utilize the measured parameters to estimate the average ion pressure gradient, J × B, and v × B macroscopic force terms. The pressure gradient force maintains nearly cylindrical symmetry, while the J × B force has larger asymmetries and varies in magnitude in comparison to the pressure gradient force. The v × B force felt by newly produced planetary ions exceeds the other forces in magnitude in the magnetosheath and upstream regions for all solar wind conditions.

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

2015-08-06

Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna–Matthews–Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbitalmore » (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.« less

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, D.O.; Alexeff, I.; Sikka, V.K.

1987-08-10

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to ''float'' in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields. 6 figs.

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, David O.; Alexeff, Igor; Sikka, Vinod K.

1988-01-01

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to "float" in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields.

Empirical seasonal forecasts of the NAO

NASA Astrophysics Data System (ADS)

Sanchezgomez, E.; Ortizbevia, M.

2003-04-01

We present here seasonal forecasts of the North Atlantic Oscillation (NAO) issued from ocean predictors with an empirical procedure. The Singular Values Decomposition (SVD) of the cross-correlation matrix between predictor and predictand fields at the lag used for the forecast lead is at the core of the empirical model. The main predictor field are sea surface temperature anomalies, although sea ice cover anomalies are also used. Forecasts are issued in probabilistic form. The model is an improvement over a previous version (1), where Sea Level Pressure Anomalies were first forecast, and the NAO Index built from this forecast field. Both correlation skill between forecast and observed field, and number of forecasts that hit the correct NAO sign, are used to assess the forecast performance , usually above those values found in the case of forecasts issued assuming persistence. For certain seasons and/or leads, values of the skill are above the .7 usefulness treshold. References (1) SanchezGomez, E. and Ortiz Bevia M., 2002, Estimacion de la evolucion pluviometrica de la Espana Seca atendiendo a diversos pronosticos empiricos de la NAO, in 'El Agua y el Clima', Publicaciones de la AEC, Serie A, N 3, pp 63-73, Palma de Mallorca, Spain

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Weimin; Niu, Haitao; Lin, Tong

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 externalmore » 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.« less

On the debris-level origins of adhesive wear

NASA Astrophysics Data System (ADS)

Aghababaei, Ramin; Warner, Derek H.; Molinari, Jean-François

2017-07-01

Every contacting surface inevitably experiences wear. Predicting the exact amount of material loss due to wear relies on empirical data and cannot be obtained from any physical model. Here, we analyze and quantify wear at the most fundamental level, i.e., wear debris particles. Our simulations show that the asperity junction size dictates the debris volume, revealing the origins of the long-standing hypothesized correlation between the wear volume and the real contact area. No correlation, however, is found between the debris volume and the normal applied force at the debris level. Alternatively, we show that the junction size controls the tangential force and sliding distance such that their product, i.e., the tangential work, is always proportional to the debris volume, with a proportionality constant of 1 over the junction shear strength. This study provides an estimation of the debris volume without any empirical factor, resulting in a wear coefficient of unity at the debris level. Discrepant microscopic and macroscopic wear observations and models are then contextualized on the basis of this understanding. This finding offers a way to characterize the wear volume in atomistic simulations and atomic force microscope wear experiments. It also provides a fundamental basis for predicting the wear coefficient for sliding rough contacts, given the statistics of junction clusters sizes.

On the debris-level origins of adhesive wear.

PubMed

Aghababaei, Ramin; Warner, Derek H; Molinari, Jean-François

2017-07-25

Every contacting surface inevitably experiences wear. Predicting the exact amount of material loss due to wear relies on empirical data and cannot be obtained from any physical model. Here, we analyze and quantify wear at the most fundamental level, i.e., wear debris particles. Our simulations show that the asperity junction size dictates the debris volume, revealing the origins of the long-standing hypothesized correlation between the wear volume and the real contact area. No correlation, however, is found between the debris volume and the normal applied force at the debris level. Alternatively, we show that the junction size controls the tangential force and sliding distance such that their product, i.e., the tangential work, is always proportional to the debris volume, with a proportionality constant of 1 over the junction shear strength. This study provides an estimation of the debris volume without any empirical factor, resulting in a wear coefficient of unity at the debris level. Discrepant microscopic and macroscopic wear observations and models are then contextualized on the basis of this understanding. This finding offers a way to characterize the wear volume in atomistic simulations and atomic force microscope wear experiments. It also provides a fundamental basis for predicting the wear coefficient for sliding rough contacts, given the statistics of junction clusters sizes.

On the debris-level origins of adhesive wear

PubMed Central

Warner, Derek H.; Molinari, Jean-François

2017-01-01

Every contacting surface inevitably experiences wear. Predicting the exact amount of material loss due to wear relies on empirical data and cannot be obtained from any physical model. Here, we analyze and quantify wear at the most fundamental level, i.e., wear debris particles. Our simulations show that the asperity junction size dictates the debris volume, revealing the origins of the long-standing hypothesized correlation between the wear volume and the real contact area. No correlation, however, is found between the debris volume and the normal applied force at the debris level. Alternatively, we show that the junction size controls the tangential force and sliding distance such that their product, i.e., the tangential work, is always proportional to the debris volume, with a proportionality constant of 1 over the junction shear strength. This study provides an estimation of the debris volume without any empirical factor, resulting in a wear coefficient of unity at the debris level. Discrepant microscopic and macroscopic wear observations and models are then contextualized on the basis of this understanding. This finding offers a way to characterize the wear volume in atomistic simulations and atomic force microscope wear experiments. It also provides a fundamental basis for predicting the wear coefficient for sliding rough contacts, given the statistics of junction clusters sizes. PMID:28696291

Calculation of vortex lift effect for cambered wings by the suction analogy

NASA Technical Reports Server (NTRS)

Lan, C. E.; Chang, J. F.

1981-01-01

An improved version of Woodward's chord plane aerodynamic panel method for subsonic and supersonic flow is developed for cambered wings exhibiting edge separated vortex flow, including those with leading edge vortex flaps. The exact relation between leading edge thrust and suction force in potential flow is derived. Instead of assuming the rotated suction force to be normal to wing surface at the leading edge, new orientation for the rotated suction force is determined through consideration of the momentum principle. The supersonic suction analogy method is improved by using an effective angle of attack defined through a semi-empirical method. Comparisons of predicted results with available data in subsonic and supersonic flow are presented.

Machining of bone: Analysis of cutting force and surface roughness by turning process.

PubMed

Noordin, M Y; Jiawkok, N; Ndaruhadi, P Y M W; Kurniawan, D

2015-11-01

There are millions of orthopedic surgeries and dental implantation procedures performed every year globally. Most of them involve machining of bones and cartilage. However, theoretical and analytical study on bone machining is lagging behind its practice and implementation. This study views bone machining as a machining process with bovine bone as the workpiece material. Turning process which makes the basis of the actually used drilling process was experimented. The focus is on evaluating the effects of three machining parameters, that is, cutting speed, feed, and depth of cut, to machining responses, that is, cutting forces and surface roughness resulted by the turning process. Response surface methodology was used to quantify the relation between the machining parameters and the machining responses. The turning process was done at various cutting speeds (29-156 m/min), depths of cut (0.03 -0.37 mm), and feeds (0.023-0.11 mm/rev). Empirical models of the resulted cutting force and surface roughness as the functions of cutting speed, depth of cut, and feed were developed. Observation using the developed empirical models found that within the range of machining parameters evaluated, the most influential machining parameter to the cutting force is depth of cut, followed by feed and cutting speed. The lowest cutting force was obtained at the lowest cutting speed, lowest depth of cut, and highest feed setting. For surface roughness, feed is the most significant machining condition, followed by cutting speed, and with depth of cut showed no effect. The finest surface finish was obtained at the lowest cutting speed and feed setting. © IMechE 2015.

Empirical Psycho-Aesthetics and Her Sisters: Substantive and Methodological Issues--Part II

ERIC Educational Resources Information Center

Konecni, Vladimir J.

2013-01-01

Empirical psycho-aesthetics is approached in this two-part article from two directions. Part I, which appeared in the Winter 2012 issue of "JAE," addressed definitional and organizational issues, including the field's origins, its relation to "sister" disciplines (experimental philosophy, cognitive neuroscience of art, and neuroaesthetics), and…

AN IMPROVED STRATEGY FOR REGRESSION OF BIOPHYSICAL VARIABLES AND LANDSAT ETM+ DATA. (R828309)

EPA Science Inventory

Empirical models are important tools for relating field-measured biophysical variables to remote sensing data. Regression analysis has been a popular empirical method of linking these two types of data to provide continuous estimates for variables such as biomass, percent wood...

Field verification of KDOT's Superpave mixture properties to be used as inputs in the NCHRP mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2009-01-01

In the MechanisticEmpirical Pavement Design Guide (M-EPDG), prediction of flexible pavement response and performance needs an input of dynamic modulus of hot-mix asphalt (HMA) at all three levels of hierarchical inputs. This study was intended to ...

An Empirical Investigation into Programming Language Syntax

ERIC Educational Resources Information Center

Stefik, Andreas; Siebert, Susanna

2013-01-01

Recent studies in the literature have shown that syntax remains a significant barrier to novice computer science students in the field. While this syntax barrier is known to exist, whether and how it varies across programming languages has not been carefully investigated. For this article, we conducted four empirical studies on programming…