Note: This page contains sample records for the topic force field ff from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: August 15, 2014.
1

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

PubMed

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ . PMID:23146088

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

2

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data.  

PubMed

Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement between experimental and calculated order parameters and residual dipolar calculations. However, recent studies have suggested that ff99SB demonstrates poor agreement with J-coupling constants for short polyalanines. We performed extensive replica-exchange molecular-dynamics simulations on Ala(3) and Ala(5) in TIP3P and TIP4P-Ew solvent models. Our results suggest that the performance of ff99SB is among the best of currently available models. In addition, scalar coupling constants derived from simulations in the TIP4P-Ew model show a slight improvement over those obtained using the TIP3P model. Despite the overall excellent agreement, the data suggest areas for possible improvement. PMID:19651043

Wickstrom, Lauren; Okur, Asim; Simmerling, Carlos

2009-08-01

3

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

NASA Astrophysics Data System (ADS)

Understanding the response of energetic materials to thermal or shock loading at the atomistic level demands a highly accurate description of the reaction dynamics of million atom systems to capture the complex chemical and mechanical behavior involved: nonequilibrium energy/mass transfer, molecule excitation and decomposition under high strain/heat rates, formation of defects, plastic flow, and phase transitions. To enable such simulations, we developed the ReaxFF reactive force fields based on quantum mechanics (QM) calculations of reactants, products, high-energy intermediates and transition states, but using functional forms suitable for large-scale molecular dynamics simulations of chemical reactions under extreme conditions. We will present an overview of recent progress in ReaxFF developments, including the extension of ReaxFF to new nitramine- based (nitromethane, HMX, PETN, TATB) and peroxide-based (TATP) explosives. To demonstrate the versatility and transferability of ReaxFF, we will present applications to solid composite propellants such as Al/Al2O3-metal nanoparticles embedded into solid explosive matrices (RDX, PETN).

Goddard, W. A., III; Strachan, A.

2005-07-01

4

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges  

PubMed Central

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A “penalty score” is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.

Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.

2012-01-01

5

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.  

PubMed

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A "penalty score" is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data. PMID:23145473

Vanommeslaeghe, K; Raman, E Prabhu; MacKerell, A D

2012-12-21

6

ReaxFF SiO Reactive Force Field for Silicon and Silicon Oxide Systems  

Microsoft Academic Search

To predict the structures, properties, and chemistry of materials involving silicon and silicon oxides; interfaces between these materials; and hydrolysis of such systems, we have developed the ReaxFFSiO, reactive force field. The parameters for this force field were obtained from fitting to the results of quantum chemical (QC) calculations on the structures and energy barriers for a number of silicon

Adri C. T. van Duin; Alejandro Strachan; Shannon Stewman; Qingsong Zhang; Xin Xu; William A. Goddard

2003-01-01

7

ReaxFF reactive force field for solid oxide fuel cell systems with application to oxygen ion transport in yttria-stabilized zirconia.  

PubMed

We present the ReaxFF reactive force field developed to provide a first-principles-based description of oxygen ion transport through yttria-stabilized zirconia (YSZ) solid oxide fuel cell (SOFC) membranes. All parameters for ReaxFF were optimized to reproduce quantum mechanical (QM) calculations on relevant condensed phase and cluster systems. We validated the use of ReaxFF for fuel cell applications by using it in molecular dynamics (MD) simulations to predict the oxygen ion diffusion coefficient in yttria-stabilized zirconia as a function of temperature. These values are in excellent agreement with experimental results, setting the stage for the use of ReaxFF to model the transport of oxygen ions through the YSZ electrolyte for SOFC. Because ReaxFF descriptions are already available for some catalysts (e.g., Ni and Pt) and under development for other high-temperature catalysts, we can now consider fully first-principles-based simulations of the critical functions in SOFC, enabling the possibility of in silico optimization of these materials. That is, we can now consider using theory and simulation to examine the effect of materials modifications on both the catalysts and transport processes in SOFC. PMID:18348544

van Duin, Adri C T; Merinov, Boris V; Jang, Seung Soon; Goddard, William A

2008-04-10

8

The theoretical study on interaction of hydrogen with single-walled boron nitride nanotubes. I. The reactive force field ReaxFF(HBN) development.  

PubMed

We present a new reactive force field ReaxFF(HBN) derived to accurately model large molecular and condensed phase systems of H, B, and N atoms. ReaxFF(HBN) has been tested against quantum calculation data for B-H, B-B, and B-N bond dissociations and for H-B-H, B-N-B, and N-B-N bond angle strain energies of various molecular clusters. The accuracy of the developed ReaxFF(HBN) for B-N-H systems is also tested for (i) H-B and H-B bond energies as a function of out of plane in H-B(NH2)3 and H-N(BH2)3, respectively, (ii) the reaction energy for the B3N3H6+H2-->B3N3H8, and (iii) crystal properties such as lattice parameters and equations of states for the hexagonal type (h-BN) with a graphite structure and for the cubic type (c-BN) with a zinc-blende structure. For all these systems, ReaxFF(HBN) gives reliable results consistent with those from quantum calculations as it describes well bond breaking and formation in chemical processes and physical properties. Consequently, the molecular-dynamics simulation based on ReaxFF(HBN) is expected to give a good description of large systems (>2000 atoms even on the one-CPU machine) with hydrogen, boron, and nitrogen atoms. PMID:16392579

Han, Sang Soo; Kang, Jeung Ku; Lee, Hyuck Mo; van Duin, Adri C T; Goddard, William A

2005-09-15

9

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

SciTech Connect

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

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

2012-06-01

10

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

PubMed

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

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

2012-04-19

11

Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes.  

PubMed

With the aim of developing a computationally inexpensive method for modeling the high-temperature reaction dynamics of transition metal catalyzed reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial quantum mechanics (QM) training set, containing full reaction pathways for relevant reactions. In this paper we apply this approach to reactions involving carbon materials plus Co, Ni, and Cu atoms. We find that ReaxFF reproduces the QM reaction data with good accuracy while also reproducing the binding characteristics of Co, Ni, and Cu atoms to hydrocarbon fragments. To demonstrate the applicability of ReaxFF we performed high-temperature (1500 K) molecular dynamics simulations on a nonbranched all-carbon feedstock in the presence and absence of Co, Ni, and Cu atoms. We find that the presence of Co and Ni leads to substantial amounts of branched carbon atoms, leading eventually to the formation of carbon-nanotube-like species. In contrast, we find that under the same simulation conditions Cu leads to very little branching and leads to products with no nanotube character. In the absence of metals no branching is observed at all. These results suggest that Ni and Co catalyze the production of nanotube-like species whereas Cu does not. This is in excellent agreement with experimental observations, demonstrating that ReaxFF can provide a useful and computational tractable tool for studying the dynamics of transition metal catalytic chemistry. PMID:16833370

Nielson, Kevin D; van Duin, Adri C T; Oxgaard, Jonas; Deng, Wei-Qiao; Goddard, William A

2005-01-27

12

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.  

PubMed

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed. PMID:22845837

Meher, Biswa Ranjan; Kumar, Mattaparthi Venkata Satish; Sharma, Smriti; Bandyopadhyay, Pradipta

2012-12-01

13

Multiparadigm Modeling of Dynamical Crack Propagation in Silicon Using a Reactive Force Field  

NASA Astrophysics Data System (ADS)

We report a study of dynamic cracking in a silicon single crystal in which the ReaxFF reactive force field is used for several thousand atoms near the crack tip, while more than 100 000 atoms are described with a nonreactive force field. ReaxFF is completely derived from quantum mechanical calculations of simple silicon systems without any empirical parameters. Our results reproduce experimental observations of fracture in silicon including changes in crack dynamics for different crack orientations.

Buehler, Markus J.; van Duin, Adri C. T.; Goddard, William A., III

2006-03-01

14

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations  

PubMed Central

We have compared molecular dynamics (MD) simulations of a ?-hairpin forming peptide derived from the protein Nrf2 with 10 biomolecular force fields using trajectories of at least 1 ?s. The total simulation time was 37.2 ?s. Previous studies have shown that different force fields, water models, simulation methods, and parameters can affect simulation outcomes. The MD simulations were done in explicit solvent with a 16-mer Nrf2 ?-hairpin forming peptide using Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, GROMOS96 53a6, CHARMM27, and OPLS-AA/L force fields. The effects of charge-groups, terminal capping, and phosphorylation on the peptide folding were also examined. Despite using identical starting structures and simulation parameters, we observed clear differences among the various force fields and even between replicates using the same force field. Our simulations show that the uncapped peptide folds into a native-like ?-hairpin structure at 310 K when Amber ff99SB-ILDN, Amber ff99SB*-ILDN, Amber ff99SB, Amber ff99SB*, Amber ff03, Amber ff03*, GROMOS96 43a1p, or GROMOS96 53a6 were used. The CHARMM27 simulations were able to form native hairpins in some of the elevated temperature simulations, while the OPLS-AA/L simulations did not yield native hairpin structures at any temperatures tested. Simulations that used charge-groups or peptide capping groups were not largely different from their uncapped counterparts with single atom charge-groups. On the other hand, phosphorylation of the threonine residue located at the ?-turn significantly affected the hairpin formation. To our knowledge, this is the first study comparing such a large set of force fields with respect to ?-hairpin folding. Such a comprehensive comparison will offer useful guidance to others conducting similar types of simulations.

2012-01-01

15

Approximate photochemical dynamics of azobenzene with reactive force fields  

SciTech Connect

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

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

2013-12-14

16

Conformational preferences of modified uridines: comparison of AMBER derived force fields.  

PubMed

The widespread occurrence of modified residues in RNA sequences necessitates development of accurate parameters for these modifications for reliable modeling of RNA structure and dynamics. A comprehensive set of parameters for the 107 naturally occurring RNA modifications was proposed by Aduri et al. (J. Chem. Theory Comput. 2007, 3, 1464-1475) for the AMBER FF99 force field. In this work, we tested these parameters on a set of modified uridine residues, namely, dihydrouridine, 2-thiouridine, 4-thiouridine, pseudouridine, and uridine-5-oxyacetic acid, by performing molecular dynamics and replica exchange molecular dynamics simulations of these nucleosides. Although our simulations using the FF99 force field did not, in general, reproduce the experimentally observed conformational characteristics well, combination of the parameter set with recent revisions of the FF99 force field for RNA showed noticeable improvement for some of the nucleosides. PMID:24697757

Deb, Indrajit; Sarzynska, Joanna; Nilsson, Lennart; Lahiri, Ansuman

2014-04-28

17

Empirical force fields for complex hydrated calcio-silicate layered materials.  

PubMed

The use of empirical force fields is now a standard approach in predicting the properties of hydrated oxides which are omnipresent in both natural and engineering applications. Transferability of force fields to analogous hydrated oxides without rigorous investigations may result in misleading property predictions. Herein, we focus on two common empirical force fields, the simple point charge ClayFF potential and the core-shell potential to study tobermorite minerals, the most prominent family of Calcium-Silicate-Hydrates that are complex hydrated oxides. We benchmark the predictive capabilities of these force fields against first principles results. While the structural information seem to be in close agreement with DFT results, we find that for higher order properties such as elastic constants, the core-shell potential quantitatively improves upon the simple point charge model, and shows a larger degree of transferability to complex materials. In return, to remedy the deficiencies of the simple point charge potential for hydrated calcio-silicates, we suggest using both structural data and elasticity data for potential calibration, a new force field potential, CSH-FF. This re-parameterized version of ClayFF is then applied to simulating an atomistic model of cement (Pellenq et al., PNAS, 2009). We demonstrate that this force field improves the predictive capabilities of ClayFF, being considerably less computational intensive than the core-shell model. PMID:21069228

Shahsavari, Rouzbeh; Pellenq, Roland J-M; Ulm, Franz-Josef

2011-01-21

18

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

SciTech Connect

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

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

2010-10-21

19

The dynamics of highly excited electronic systems: Applications of the electron force field  

Microsoft Academic Search

Highly excited heterogeneous complex materials are essential elements of important processes, ranging from inertial confinement fusion to semiconductor device fabrication. Understanding the dynamics of these systems has been challenging because of the difficulty in extracting mechanistic information from either experiment or theory. We describe here the electron force field (eFF) approximation to quantum mechanics which provides a practical approach to

Julius T. Su; William A. Goddard

2009-01-01

20

Development of accurate force fields for the simulation of biomineralization.  

PubMed

The existence of an accurate force field (FF) model that reproduces the free-energy landscape is a key prerequisite for the simulation of biomineralization. Here, the stages in the development of such a model are discussed including the quality of the water model, the thermodynamics of polymorphism, and the free energies of solvation for the relevant species. The reliability of FFs can then be benchmarked against quantities such as the free energy of ion pairing in solution, the solubility product, and the structure of the mineral-water interface. PMID:24188760

Raiteri, Paolo; Demichelis, Raffaella; Gale, Julian D

2013-01-01

21

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

Microsoft Academic Search

Gamma-ray emission from pulsars has long been modeled using a vacuum dipole field. This approximation ignores changes in the field structure caused by the magnetospheric plasma and strong plasma currents. We present the first results of gamma-ray pulsar light-curve modeling using the more realistic field taken from three-dimensional force-free (FF) magnetospheric simulations. Having the geometry of the field, we apply

Xue-Ning Bai; Anatoly Spitkovsky

2010-01-01

22

Evaluating the strength of salt bridges: a comparison of current biomolecular force fields.  

PubMed

Recent advances in computer hardware and software have made rigorous evaluation of current biomolecular force fields using microsecond-scale simulations possible. Force fields differ in their treatment of electrostatic interactions, including the formation of salt bridges in proteins. Here we conducted an extensive evaluation of salt bridge interactions in the latest AMBER, CHARMM, and OPLS force fields, using microsecond-scale molecular dynamics simulations of amino acid analogues in explicit solvent. We focused on salt bridges between three different pairs of oppositely charged amino acids: Arg/Asp, Lys/Asp, and His(+)/Asp. Our results reveal considerable variability in the predicted KA values of the salt bridges for these force fields, as well as differences from experimental data: almost all of the force fields overestimate the strengths of the salt bridges. When amino acids are represented by side-chain analogues, the AMBER ff03 force field overestimates the KA values the least, while for complete amino acids, the AMBER ff13? force field yields the lowest KA value, most likely caused by an altered balance of side-chain/side-chain and side-chain/backbone contacts. These findings confirm the notion that the implicit incorporation of solvent polarization improves the accuracy of modeling salt bridge interactions. PMID:24702709

Debiec, Karl T; Gronenborn, Angela M; Chong, Lillian T

2014-06-19

23

The dynamics of highly excited electronic systems: applications of the electron force field.  

PubMed

Highly excited heterogeneous complex materials are essential elements of important processes, ranging from inertial confinement fusion to semiconductor device fabrication. Understanding the dynamics of these systems has been challenging because of the difficulty in extracting mechanistic information from either experiment or theory. We describe here the electron force field (eFF) approximation to quantum mechanics which provides a practical approach to simulating the dynamics of such systems. eFF includes all the normal electrostatic interactions between electrons and nuclei and the normal quantum mechanical description of kinetic energy for the electrons, but contains two severe approximations: first, the individual electrons are represented as floating Gaussian wave packets whose position and size respond instantaneously to various forces during the dynamics; and second, these wave packets are combined into a many-body wave function as a Hartree product without explicit antisymmetrization. The Pauli principle is accounted for by adding an extra spin-dependent term to the Hamiltonian. These approximations are a logical extension of existing approaches to simulate the dynamics of fermions, which we review. In this paper, we discuss the details of the equations of motion and potentials that form eFF, and evaluate the ability of eFF to describe ground-state systems containing covalent, ionic, multicenter, and/or metallic bonds. We also summarize two eFF calculations previously reported on electronically excited systems: (1) the thermodynamics of hydrogen compressed up to ten times liquid density and heated up to 200,000 K; and (2) the dynamics of Auger fragmentation in a diamond nanoparticle, where hundreds of electron volts of excitation energy are dissipated over tens of femtoseconds. These cases represent the first steps toward using eFF to model highly excited electronic processes in complex materials. PMID:20059073

Su, Julius T; Goddard, William A

2009-12-28

24

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

NASA Astrophysics Data System (ADS)

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

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

2006-07-01

25

Extension of the AMBER force field to cyclic ?,? dialkylated peptides.  

PubMed

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing ?,? dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, ?-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and ?-helical structures is established in aqueous solution, in agreement with EPR data. PMID:23051698

Grubiši?, Sonja; Brancato, Giuseppe; Pedone, Alfonso; Barone, Vincenzo

2012-11-28

26

Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces  

NASA Technical Reports Server (NTRS)

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

Kory, Carol L.; Dayton, James A.

1998-01-01

27

Energetic materials under mechanical shock and shear: Molecular dynamics simulation with reactive force field  

Microsoft Academic Search

The initial physical and chemical response of energetic materials under mechanical shock or shear loading has been investigated for RDX, PETN and HMX by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a shock wave and shock-induced chemical reactions created by moving piston mimicked by a potential wall. We simulate both

Sergey Zybin; Peng Xu; Adri van Duin; William Goddard

2007-01-01

28

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

SciTech Connect

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

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

2010-06-01

29

Near-field photonic forces  

Microsoft Academic Search

A review of recent advancements in photonic forces is presented. We discuss in detail the interaction of light and sub-wavelength particles on a substrate illuminated by total internal reflection, and we study the optical forces experienced by the particles. The effects of plasmon-mode excitations on the resulting photonic forces on metallic particles are also addressed. Moreover, we explore the possibility

P. C. C haumet

2004-01-01

30

Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models.  

PubMed

Here, we systematically investigated how the force fields and the partial charge models for ligands affect the ranking performance of the binding free energies predicted by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) approaches. A total of 46 small molecules targeted to five different protein receptors were employed to test the following issues: (1) the impact of five AMBER force fields (ff99, ff99SB, ff99SB-ILDN, ff03, and ff12SB) on the performance of MM/GBSA, (2) the influence of the time scale of molecular dynamics (MD) simulations on the performance of MM/GBSA with different force fields, (3) the impact of five AMBER force fields on the performance of MM/PBSA, and (4) the impact of four different charge models (RESP, ESP, AM1-BCC, and Gasteiger) for small molecules on the performance of MM/PBSA or MM/GBSA. Based on our simulation results, the following important conclusions can be obtained: (1) for short time-scale MD simulations (1 ns or less), the ff03 force field gives the best predictions by both MM/GBSA and MM/PBSA; (2) for middle time-scale MD simulations (2-4 ns), MM/GBSA based on the ff99 force field yields the best predictions, while MM/PBSA based on the ff99SB force field does the best; however, longer MD simulations, for example, 5 ns or more, may not be quite necessary; (3) for most cases, MM/PBSA with the Tan's parameters shows better ranking capability than MM/GBSA (GB(OBC1)); (4) the RESP charges show the best performance for both MM/PBSA and MM/GBSA, and the AM1-BCC and ESP charges can also give fairly satisfactory predictions. Our results provide useful guidance for the practical applications of the MM/GBSA and MM/PBSA approaches. PMID:23789789

Xu, Lei; Sun, Huiyong; Li, Youyong; Wang, Junmei; Hou, Tingjun

2013-07-18

31

Energetic materials under mechanical shock and shear: Molecular dynamics simulation with reactive force field  

NASA Astrophysics Data System (ADS)

The initial physical and chemical response of energetic materials under mechanical shock or shear loading has been investigated for RDX, PETN and HMX by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a shock wave and shock-induced chemical reactions created by moving piston mimicked by a potential wall. We simulate both the continuous and impulsive piston loading to investigate its influence on the initiation and decomposition reactions in energetic materials as well as the orientational dependence using large-scale parallel ReaxFF-MD simulations. Besides, we perform a series of simulations of pure shear at high strain rate as well as static uniaxial compression of energetic crystals to study their transformation and decomposition under various loading conditions. The mechanism and evolution of chemical reactions induced by mechanical shock and pure shear is discussed along with the propagation of heat, mass, pressure, and reaction waves.

Zybin, Sergey; Xu, Peng; van Duin, Adri; Goddard, William

2007-06-01

32

Polarization effects in molecular mechanical force fields  

PubMed Central

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

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

2014-01-01

33

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids.  

PubMed

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

Jämbeck, Joakim P M; Lyubartsev, Alexander P

2012-03-15

34

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

PubMed Central

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

2012-01-01

35

Force Field for SiF4.  

National Technical Information Service (NTIS)

The force field of SiF4 has been determined using both Coriolis coupling constants obtained from an investigation of the band contour of v3 at 195 K and isotopic shifts. The force fields are equally well determined using both methods and are in agreement....

I. W. Levin S. Abramowitz

1968-01-01

36

Force field feature extraction for ear biometrics  

Microsoft Academic Search

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

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

2005-01-01

37

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

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

38

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

PubMed Central

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

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

2012-01-01

39

Vorticity Field Evolution in a Forced Wake.  

National Technical Information Service (NTIS)

The purpose of this work is to quantify the vorticity evolution in the flow field of the forced wake of a splitter plate inside a confining geometry. The interest in this flow stems from the fact that forcing a low Reynolds number 2-D wake can lead to a h...

R. Cohn, M. Koochesfahani

1999-01-01

40

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

Microsoft Academic Search

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

W. A. Goddard III; A. Strachan

2005-01-01

41

Multi robot mapping using force field simulation  

Microsoft Academic Search

This paper describes a novel approach, called Force Field Simulation, to multi robot map- ping that works under the constraints given in autonomous search and rescue robotics. Extremely poor prealignment, lack of landmarks, and minimal overlap between scans are the main challenges. The presented algorithm solves the alignment problem of such laser scans utilizing a gradient descent approach motivated by

Rolf Lakaemper; Nagesh Adluru; Longin Jan Latecki; Raj Madhavan

2007-01-01

42

Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion.  

PubMed

We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H2 to form H2O product is ?538 s, whereas the computational cost was just 1289 ps, a speed increase of ?0.42 trillion (10(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF-OH2014 force field that was used in the simulations. PMID:24885152

Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A; Sun, Huai

2014-07-01

43

Harmonic force field for nitro compounds.  

PubMed

Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule). PMID:22119786

Bellido, Edson P; Seminario, Jorge M

2012-06-01

44

Field study on moving force identification  

NASA Astrophysics Data System (ADS)

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

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

2001-08-01

45

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

SciTech Connect

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

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

2007-11-01

46

Vibrational spectra and force field of dimethylphosphines  

NASA Astrophysics Data System (ADS)

Vibrational spectra in the range 200-3000 cm -1 are reported and assigned for the species (CH 3) 2PH, (CH 3) 2PD, (CD 3) 2PH, (CD 3) 2PD, CH 3CD 3PH and CH 3CD 3PD. The spectra in the range 1020-500 cm -1 are complicated due to the coupling between ?PH, ?Me and the skeletal modes of the molecule. Interpretation is only possible through a force field which is markedly different from an earlier one of dimethyl sulphide. This force field predicts uncoupled ?PH frequencies of 835 ( a) and 909 cm -1 ( a), couples PH bending largely to out-of-skeletal plane methyl rocking (? i) and includes a low p¦¦( a) bending constant, a high skeletal bending constant and unusual signs for two interaction constants. In the crystalline phase at 78 K, the two methyl groups are non-equivalent.

McKean, D. C.; McQuillan, G. P.

1980-04-01

47

All-atom polarizable force field for DNA based on the classical drude oscillator model.  

PubMed

Presented is a first generation atomistic force field (FF) 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 quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates 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 FF, 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. © 2014 Wiley Periodicals, Inc. PMID:24752978

Savelyev, Alexey; Mackerell, Alexander D

2014-06-15

48

A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field.  

PubMed

A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2 O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available. © 2014 Wiley Periodicals, Inc. PMID:24965869

Devereux, Mike; Gresh, Nohad; Piquemal, Jean-Philip; Meuwly, Markus

2014-08-01

49

Energetic materials under thermal shock: Molecular dynamics simulation with reactive force field  

NASA Astrophysics Data System (ADS)

The physical and chemical response of energetic materials under thermal shock loading has been investigated for RDX, PETN and HMX by molecular dynamics method with ReaxFF reactive force field parameterized from first-principles calculations. We study the propagation of a thermal front and following reactive wave from the hot spot created by fast heating of a local region and keeping it at high constant temperature. The hot spot serves as heat source to heat up adjacent materials where no temperature constraint is imposed, and trigger the chemical decomposition of energetic molecules. The mechanism and evolution of chemical reactions induced by thermal shock is discussed along with the propagation of heat, mass, pressure, and reaction waves.

Liu, Yi; Zybin, Sergey; van Duin, Adri; Goddard, William

2007-06-01

50

Simulation of Multiphase Systems Utilizing Independent Force Fields to Control Intra-Phase and Inter-Phase Behavior  

PubMed Central

Fixed-charge empirical force fields have been developed and widely used over the past three decades for all-atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. While this is generally suitable for single-phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. While nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual-force-field approach (Dual-FF) to address this problem and implemented it in the CHARMM simulation package. This Dual-FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intra-phase interactions and a separate set to represent inter-phase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intra-phase and inter-phase molecular behavior to be accurately and efficiently modeled in the same simulation.

Vellore, Nadeem A.; Yancey, Jeremy A.; Kucukkal, Tugba G.; Collier, Galen; Brooks, Bernard R.; Stuart, Steven J.

2013-01-01

51

Total Petroleum Hydrocarbon Criteria Working Group (TPHCWG) Field Demonstration Report: Air Force Plant Number 6 Fuel Farm Dobbins AFB, Georgia.  

National Technical Information Service (NTIS)

A demonstration of the Total Petroleum Hydrocarbon Criteria Working Group (TPHCWG) approach for assessing human health risk at weathered petroleum release sites was performed at a former above ground storage fuel farm (FF) located at Dobbins Air Force Bas...

D. A. Reed T. R. Sterner

2002-01-01

52

Carbynes phonons: A tight binding force field  

NASA Astrophysics Data System (ADS)

Modeling the vibrational structure of linear carbon chains has proved to be a difficult task with present first-principles calculations. This limits their applicability for the interpretation of experimental data, such as Raman scattering experiments on linear carbon chains within nanotubes. These limitations can be overcome by means of a simple tight binding scheme for ?-electrons. In this work a force field for the calculation of longitudinal phonon dispersion branches is built on the basis of bond-bond polarizabilities and just three parameters. The so obtained phonon dispersion branches are in very good agreement with the experimental data on carbynes in different environments and polyynes of any length. The model is discussed in relation to the importance of long range vibrational interactions in carbynes. The physical phenomena affecting their vibrational properties (i.e., Kohn anomaly, electron-phonon coupling) can be accurately and analytically described by the present approach.

Milani, Alberto; Tommasini, Matteo; Zerbi, Giuseppe

2008-02-01

53

The Energetics of Motivated Cognition: A Force-Field Analysis  

ERIC Educational Resources Information Center

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…

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

2012-01-01

54

Force-Field Analysis: Incorporating Critical Thinking in Goal Setting.  

ERIC Educational Resources Information Center

Force field analysis encourages members to examine the probability of reaching agreed-upon goals. It can help groups avoid working toward goals that are unlikely to be reached. In every situation are three forces: forces that encourage maintenance of the status quo or change; driving or helping forces that push toward change; and restraining…

Hustedde, Ron; Score, Michael

1995-01-01

55

The Introduction of Fields in Relation to Force  

ERIC Educational Resources Information Center

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.)

Brunt, Marjorie; Brunt, Geoff

2012-01-01

56

Reactive Force Fields via Explicit Valency  

NASA Astrophysics Data System (ADS)

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

Kale, Seyit

57

Force-Freeness of Solar Magnetic Fields in the Photosphere  

Microsoft Academic Search

It is widely believed that solar magnetic fields are force-free in the solar corona but not in the solar photosphere at all. In order to examine the force-freeness of active region magnetic fields at the photospheric level, we have calculated the integrated magnetic forces for 12 vector magnetograms of three flare-productive active regions. The magnetic field vectors are derived from

Y.-J. Moon; G. S. Choe; H. S. Yun; Y. D. Park; D. L. Mickey

2002-01-01

58

Force-Freeness of Solar Magnetic Fields in the Photosphere  

Microsoft Academic Search

It is widely believed that solar magnetic fields are force-free in the solar corona, but not in the solar photosphere. In order to examine the force-freeness of active region magnetic fields at the photospheric level, we have calculated the integrated magnetic forces for 33 vector magnetograms of four flare-productive active regions. The magnetic field vectors are derived from simultaneous Stokes

Y. Moon; G. S. Choe; H. S. Yun; Y. D. Park; D. L. Mickey

2001-01-01

59

Force?Freeness of Solar Magnetic Fields in the Photosphere  

Microsoft Academic Search

Q2 It is widely believed that solar magnetic fields are force-free in the solar corona but not in the solar photo- sphere at all. In order to examine the force-freeness of active region magnetic fields at the photospheric level, we have calculated the integrated magnetic forces for 12 vector magnetograms of three flare-productive active regions. The magnetic field vectors are

G. S. Choe; H. S. Yun; Y. D. Park; D. L. Mickey

2002-01-01

60

Brief: Field measurements of casing tension forces  

SciTech Connect

Tension forces acting on individual casing joints were accurately measured during installation of 10,158 ft of 9 5/8-in. {times} 47-lbm/ft casing and 11,960 ft of 11 7/8-in. {times} 71.8-lbm/ft casing. A unique casing load table (CLT) weighed the casing string after the addition of each casing joint. Strain gauges attached inside the pin ends of instrumented casing joints (ICJ`s) directly measured tension force on those joints. A high-speed computer data-acquisition system (DAS) automatically recorded data from all the sensors. Several casing joints were intentionally subjected to extreme deceleration to determine upper limits for dynamic tension forces. Data from these tests clearly show effects of wellbore friction and casing handling conditions. In every case, tension forces in the casing during maximum deceleration were considerably less than expected. In some cases, the highest tension forces occurred when the casing lifted out of the slips. Peak tension forces caused by setting the casing slips were typically no more than 5% greater than tension forces in the casing at rest. This dynamic amplification was far less than the 60% value used in the previous casing design method. Reducing the safety factor for installation loads has permitted use of lighter, less-expensive casing than dictated by older design criteria.

Quigley, M.S.; Lewis, D.B. [Mobil E and P Technical Center, Dallas, TX (United States); Boswell, R.S. [Stress Engineering Services, Houston, TX (United States)

1995-02-01

61

Forces on Dust Grains Exposed to Anisotropic Interstellar Radiation Fields  

Microsoft Academic Search

Grains exposed to anisotropic radiation fields are subjected to forces due to\\u000athe asymmetric photon-stimulated ejection of particles. These forces act in\\u000aaddition to the ``radiation pressure'' due to absorption and scattering. Here\\u000awe model the forces due to photoelectron emission and the photodesorption of\\u000aadatoms. The ``photoelectric'' force depends on the ambient conditions relevant\\u000ato grain charging. We find

Joseph C. Weingartner; B. T. Draine

2000-01-01

62

Lorentz Body Force Induced by Traveling Magnetic Fields  

NASA Technical Reports Server (NTRS)

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.

Volz, M. P.; Mazuruk, K.

2003-01-01

63

Measurement of the body force field of plasma actuators  

Microsoft Academic Search

A novel technique is proposed and investigated for the estimation of the body force field resulting from the operation of a dielectric barrier discharge plasma actuator. The technique relies on the measurement of the spatio-temporal evolution of the induced velocity field using high-speed particle image velocimetry (PIV). The technique has the advantage of providing spatial distribution of the body force

M. Kotsonis; S. Ghaemi; L. Veldhuis; F. Scarano

2011-01-01

64

Tailored Force Fields for Space-Based Construction  

Microsoft Academic Search

In Space, minor forces exerted over long periods can produce major results. Force fields of various kinds can be used to build large structures, superseding the human-intensive construction techniques of today. In this paper we consider how several techniques now used in other fields can be generalized and applied to Space-based construction. Radiation pressure exerted by coherent beams on scattering

Narayanan M. Komerath; Sameh S. Wanis; Joseph Czechowski

2003-01-01

65

Polarizable and nonpolarizable force fields for alkyl nitrates.  

PubMed

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

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

2008-01-24

66

Parallel Microassembly with Electrostatic Force Fields  

Microsoft Academic Search

Assembly is a fundamental issue in the volume productionof products that include microscopic (submillimeter)parts. These parts are often fabricated in parallelat high density but must then be assembled intopatterns with lower spatial density. In this paper wepropose a new approach to microassembly using 1) ultrasonicvibration to eliminate friction and adhesion,and 2) electrostatic forces to position and align partsin parallel. We

Karl-friedrich Böhringer; Kenneth Y. Goldberg; Michael Cohn; Roger Howe; Al Pisano

1998-01-01

67

Magnetic Forces and Field Line Density  

NSDL National Science Digital Library

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

68

Numerical simulation of Brownian particles in optical force fields  

NASA Astrophysics Data System (ADS)

Optical forces can affect the motion of a Brownian particle. For example, optical tweezers use optical forces to trap a particle at a desirable position. Using more complex force fields it is possible to generate more complex configurations. For example, by using two optical traps placed next to each other, it is possible to obtain a bistable potential where a particle can jump between the two potentials with a characteristic time scale. In this proceeding, we discuss a simple finite difference algorithm that can be used to simulate the motion of a Brownian particle in a one-dimensional field of optical forces.

Volpe, Giorgio; Volpe, Giovanni

2013-09-01

69

Petrographic Examination of Bell Canyon Tests (BCT) 1-FF Field Grouts over a Three-Year Period.  

National Technical Information Service (NTIS)

The Bell Canyon field test involving the placement of two grout plugs took place 26 September 1979 (Plug 1) and 14 February 1980 (Plug 2). Samples cast in the field were brought to WES and cured in hole AEC-7 (lease) brine. Samples were examined periodica...

J. P. Burkes J. E. Rhoderick

1983-01-01

70

Are Current Molecular Dynamics Force Fields too Helical?  

PubMed Central

Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that short polyalanine peptides in water populate the polyproline II structure almost exclusively. To investigate this apparent contradiction, with its ramifications for the assessment of molecular force fields and the structure of unfolded proteins, we performed extensive simulations of Ala5 in water (?5 ?s total time), using twelve different force fields and three different peptide terminal groups. Using either empirical or density-functional-based Karplus relations for the J-couplings, we find that most current force fields do overpopulate the ?-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini. Even after reweighting to match experiment, we find that Ala5 retains significant ?- and ?-populations. In fact, several force fields match the experimental data well before reweighting and have a significant helical population. We conclude that radical changes to the best current force fields are not necessary, based on the NMR data. Nevertheless, experiments on short peptides open the way toward the systematic improvement of current simulation models.

Best, Robert B.; Buchete, Nicolae-Viorel; Hummer, Gerhard

2008-01-01

71

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

PubMed

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

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

2013-05-30

72

Parametric study of ReaxFF simulation parameters for molecular dynamics modeling of reactive carbon gases  

NASA Astrophysics Data System (ADS)

The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions.

Jensen, Benjamin D.

73

Prediction of Mechanical Properties of Polymers With Various Force Fields  

NASA Technical Reports Server (NTRS)

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.

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

2005-01-01

74

Flow Field and Wall Forces of Yawed and Curved Cylinders  

Microsoft Academic Search

Measurements have been performed in an acoustic wind tunnel and tow tank to quantify the mean and fluctuating wall forces and flow fields on yawed and curved sections of cylinders. Of particular interest is the influence of inflow boundary layer thickness on the separation and shedding characteristics and the dynamic wall forces as a function of local yaw angle and

Stephen R. Snarski; William L. Keith

2003-01-01

75

Acculturation in Acquired Organizations: A Force-Field Perspective  

Microsoft Academic Search

The acculturation process involved when one organization is acquired by another, and the two organizational cultures merge, has not been adequately conceptualized in the strategic management literature. It is argued here that the acculturation process can be more fully understood by utilizing Lewin's (1951) force-field approach. In addition, major forces of cultural differentiation and organizational integration are identified. It is

Priscilla M. Elsass; John F. Veiga

1994-01-01

76

Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types  

PubMed Central

A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semi-empirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and x-ray diffraction experiments. NMR deuterium order parameters (SCD) are well predicted with the new FF, including proper splitting of the SCD for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of 13C NMR relaxation rates of DPPC, and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipids systems as well as heterogeneous systems including membrane proteins.

Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo; O'Connor, Joseph W.; Tobias, Douglas J.; Mondragon-Ramirez, Carlos; Vorobyov, Igor; MacKerell, Alexander D.; Pastor, Richard W.

2010-01-01

77

Contrasting studentsâ understanding of electric field and electric force  

NSDL National Science Digital Library

Students may have greater difficulties in understanding electric interactions because they have less day to day experience with them than with mechanics. There may also be differences in understanding of different electric concepts like electric force and field. This study presents the results of studentsâ responses to two sequences of superposition principle isomorphic questions in which the only difference was that in one of the sequences, the electric force was used and in the other, the electric field. We administered one of the sequences to 249 students at a large private Mexican university after covering electrostatics in an Electricity and Magnetism class. The studentsâ answers, reasoning and drawings were analyzed. We found that students who took the force sequence were better able to correctly answer the questions using the superposition principle than those students with the field sequence. The analysis of the studentsâ reasoning and drawings helped us to examine their understanding of electric field and the use of electric field lines.

Garza, Alejandro; Zavala, Genaro

2014-04-11

78

Contrasting students' understanding of electric field and electric force  

NASA Astrophysics Data System (ADS)

Students may have greater difficulties in understanding electric interactions because they have less day to day experience with them than with mechanics. There may also be differences in understanding of different electric concepts like electric force and field. This study presents the results of students' responses to two sequences of superposition principle isomorphic questions in which the only difference was that in one of the sequences, the electric force was used and in the other, the electric field. We administered one of the sequences to 249 students at a large private Mexican university after covering electrostatics in an Electricity and Magnetism class. The students' answers, reasoning and drawings were analyzed. We found that students who took the force sequence were better able to correctly answer the questions using the superposition principle than those students with the field sequence. The analysis of the students' reasoning and drawings helped us to examine their understanding of electric field and the use of electric field lines.

Garza, Alejandro; Zavala, Genaro

2013-01-01

79

Apparatus having reduced mechanical forces for supporting high magnetic fields  

DOEpatents

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

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

1991-01-01

80

Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants  

SciTech Connect

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

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

2011-01-01

81

Force field parameter estimation of functional perfluoropolyether lubricants  

NASA Astrophysics Data System (ADS)

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

Smith, Robert; Seung Chung, Pil; Steckel, Janice A.; Jhon, Myung S.; Biegler, Lorenz T.

2011-04-01

82

Alternating magnetic field forces for satellite formation flying  

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

83

Alternating Magnetic Field Forces for Satellite Formation Flying  

NASA Technical Reports Server (NTRS)

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

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

2012-01-01

84

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

NASA Technical Reports Server (NTRS)

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.

El-Kaddah, N.; Szekely, J.

1982-01-01

85

Force-Field Compensation in a Manual Tracking Task  

PubMed Central

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

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

2010-01-01

86

Visualization of Force Fields in Protein StructurePrediction  

SciTech Connect

The force fields used in molecular computational biology are not mathematically defined in such a way that their mathematical representation would facilitate the straightforward application of volume visualization techniques. To visualize energy, it is necessary to define a spatial mapping for these fields. Equipped with such a mapping, we can generate volume renderings of the internal energy states in a molecule. We describe our force field, the spatial mapping that we used for energy, and the visualizations that we produced from this mapping. We provide images and animations that offer insight into the computational behavior of the energy optimization algorithms that we employ.

Crawford, Clark; Kreylos, Oliver; Hamann, Bernd; Crivelli, Silvia

2005-04-26

87

Tracing optical force fields within graded-index media  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

88

Optical Near-field Interactions and Forces for Optoelectronic Devices  

NASA Astrophysics Data System (ADS)

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

Kohoutek, John Michael

89

Force-free magnetic fields - The magneto-frictional method  

NASA Technical Reports Server (NTRS)

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

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

1986-01-01

90

Force-free field model of ball lightning  

NASA Astrophysics Data System (ADS)

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

Tsui, K. H.

2001-03-01

91

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

PubMed Central

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

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

2010-01-01

92

Timing of pair production in time-dependent force fields  

NASA Astrophysics Data System (ADS)

We examine the creation and annihilation dynamics for electron-positron pairs in a time-dependent but subcritical electric force using a simplified model system. Numerical and semianalytical solutions to computational quantum field theory show that despite the continuity of the quantum field operator in time, the actual number of created particles can change in a discontinuous way if the field changes abruptly. The number of permanently created particles after the pulse, however, increases continuously with the duration of the electric field pulse, suggesting a transition from an exclusive annihilation to a creation regime.

Gerry, Christopher C.; Su, Q.; Grobe, R.

2006-10-01

93

A polarizable ellipsoidal force field for halogen bonds.  

PubMed

The anisotropic effects and short-range quantum effects are essential characters in the formation of halogen bonds. Since there are an array of applications of halogen bonds and much difficulty in modeling them in classical force fields, the current research reports solely the polarizable ellipsoidal force field (PEff) for halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated," which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion, and polarization interaction. Furthermore, it is largely compatible with existing, standard simulation packages. The fitted parameters are transferable and compatible with the general AMBER force field. This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2 level. Finally, the prediction of the halogen bond properties of human Cathepsin L (hcatL) has been found to be in excellent qualitative agreement with the cocrystal structures. PMID:23804187

Du, Likai; Gao, Jun; Bi, Fuzhen; Wang, Lili; Liu, Chengbu

2013-09-01

94

Operational Art in I Field Force, 1965 to 1967.  

National Technical Information Service (NTIS)

I Field Force effectively conducted operational art from 1965 through 1967 under the leadership of LTG Stanley Larsen in the II Corps Tactical Zone (II CORPS). This accomplishment is all the more noteworthy considering LTG Larsen and his staff built I Fie...

J. E. Turner

2012-01-01

95

Spatial confinement of ultrasonic force fields in microfluidic channels  

Microsoft Academic Search

We demonstrate and investigate multiple localized ultrasonic manipulation functions in series in microfluidic chips. The manipulation functions are based on spatially separated and confined ultrasonic primary radiation force fields, obtained by local matching of the resonance condition of the microfluidic channel. The channel segments are remotely actuated by the use of frequency-specific external transducers with refracting wedges placed on top

Otto Manneberg; S. Melker Hagsäter; Jessica Svennebring; Hans M. Hertz; Jörg P. Kutter; Henrik Bruus; Martin Wiklund

2009-01-01

96

Evaluation of TiO2 Force Fields.  

National Technical Information Service (NTIS)

A total of nine force fields for TiO2 have been compared and evaluated using bulk lattice and surface energy minimization procedures. Calculated crystal properties of four polymorphs of TiO2 (rutile, anatase, brookite and a high pressure phase TiO2(ii)) a...

D. R. Collins W. Smith

1996-01-01

97

Extending the AMBER Force Field to Describe Fluorescent Probes  

Microsoft Academic Search

We are developing a method for studying the structural dynamics of biomolecules, which couples fluorescence spectroscopy and computational modeling, providing a more complete understanding than is possible with either technique alone. The computational modeling will be based primarily on molecular dynamics (MD) simulation. Before running MD, dye parameters were determined that are consistent with the Cornell et al. force field

Andrew Cook; Arcelia Ortega; Alyssa Stevenson; Derek Summers; Alyssa Cassabaum; Christine Gobrogge; Bryan Leland; David Paul; Amy Speelman

2012-01-01

98

The effect of gravitational tidal forces on renormalized quantum fields  

NASA Astrophysics Data System (ADS)

The effect of gravitational tidal forces on renormalized quantum fields propagating in curved spacetime is investigated and a generalisation of the optical theorem to curved spacetime is proved. In the case of QED, the interaction of tidal forces with the vacuum polarization cloud of virtual e + e - pairs dressing the renormalized photon has been shown to produce several novel phenomena. In particular, the photon field amplitude can locally increase as well as decrease, corresponding to a negative imaginary part of the refractive index, in apparent violation of unitarity and the optical theorem. Below threshold decays into e + e - pairs may also occur. In this paper, these issues are studied from the point of view of a non-equilibrium initial-value problem, with the field evolution from an initial null surface being calculated for physically distinct initial conditions and for both scalar field theories and QED. It is shown how a generalised version of the optical theorem, valid in curved spacetime, allows a local increase in amplitude while maintaining consistency with unitarity. The picture emerges of the field being dressed and undressed as it propagates through curved spacetime, with the local gravitational tidal forces determining the degree of dressing and hence the amplitude of the renormalized quantum field. These effects are illustrated with many examples, including a description of the undressing of a photon in the vicinity of a black hole singularity.

Hollowood, Timothy J.; Shore, Graham M.

2012-02-01

99

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.  

PubMed

Structural preferences in the unfolded state of peptides determined by molecular dynamics still contradict experimental data. A remedy in this regard has been suggested by MD simulations with an optimized Amber force field ff03* ( Best, R. Hummer, G. J. Phys. Chem. B 2009 , 113 , 9004 - 9015 ). The simulations yielded a statistical coil distribution for alanine which is at variance with recent experimental results. To check the validity of this distribution, we investigated the peptide H-A(5)W-OH, which with the exception of the additional terminal tryptophan is analogous to the peptide used to optimize the force fields ff03*. Electronic circular dichroism, vibrational circular dichroism, and infrared spectroscopy as well as J-coupling constants obtained from NMR experiments were used to derive the peptide's conformational ensemble. Additionally, Fo?rster resonance energy transfer between the terminal chromophores of the fluorescently labeled peptide analogue H-Dbo-A(5)W-OH was used to determine its average length, from which the end-to-end distance of the unlabeled peptide was estimated. Qualitatively, the experimental (3)J(H(N),C(?)), VCD, and ECD indicated a preference of alanine for polyproline II-like conformations. The experimental (3)J(H(N),C(?)) for A(5)W closely resembles the constants obtained for A(5). In order to quantitatively relate the conformational distribution of A(5) obtained with the optimized AMBER ff03* force field to experimental data, the former was used to derive a distribution function which expressed the conformational ensemble as a mixture of polyproline II, ?-strand, helical, and turn conformations. This model was found to satisfactorily reproduce all experimental J-coupling constants. We employed the model to calculate the amide I' profiles of the IR and vibrational circular dichroism spectrum of A(5)W, as well as the distance between the two terminal peptide carbonyls. This led to an underestimated negative VCD couplet and an overestimated distance between terminal carbonyl groups. In order to more accurately account for the experimental data, we changed the distribution parameters based on results recently obtained for the alanine-based tripeptides. The final model, which satisfactorily reproduced amide I' profiles, J-coupling constant, and the end-to-end distance of A(5)W, reinforces alanine's high structural preference for polyproline II. Our results suggest that distributions obtained from MD simulations suggesting a statistical coil-like distribution for alanine are still based on insufficiently accurate force fields. PMID:21138254

Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

2010-12-30

100

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

NASA Astrophysics Data System (ADS)

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

Geng, Yanan; Wu, Weida

2014-05-01

101

Atomistic force field for alumina fit to density functional theory.  

PubMed

We present a force field for bulk alumina (Al2O3), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies. PMID:24289366

Sarsam, Joanne; Finnis, Michael W; Tangney, Paul

2013-11-28

102

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

SciTech Connect

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

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

2008-03-13

103

Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field.  

PubMed

A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A) -- where F and W are of aromatic character -- is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone-aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a '-D' symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals-not covering this energy-fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data. PMID:18464990

Valdes, Haydee; Pluhácková, Kristýna; Pitonák, Michal; Rezác, Jan; Hobza, Pavel

2008-05-21

104

An attempt in assessing contact forces from a kinematic field  

NASA Astrophysics Data System (ADS)

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

Richefeu, Vincent; Combe, Gaël; Maurin, Raphaël

2013-06-01

105

Spatial confinement of ultrasonic force fields in microfluidic channels.  

PubMed

We demonstrate and investigate multiple localized ultrasonic manipulation functions in series in microfluidic chips. The manipulation functions are based on spatially separated and confined ultrasonic primary radiation force fields, obtained by local matching of the resonance condition of the microfluidic channel. The channel segments are remotely actuated by the use of frequency-specific external transducers with refracting wedges placed on top of the chips. The force field in each channel segment is characterized by the use of micrometer-resolution particle image velocimetry (micro-PIV). The confinement of the ultrasonic fields during single- or dual-segment actuation, as well as the cross-talk between two adjacent fields, is characterized and quantified. Our results show that the field confinement typically scales with the acoustic wavelength, and that the cross-talk is insignificant between adjacent fields. The goal is to define design strategies for implementing several spatially separated ultrasonic manipulation functions in series for use in advanced particle or cell handling and processing applications. One such proof-of-concept application is demonstrated, where flow-through-mode operation of a chip with flow splitting elements is used for two-dimensional pre-alignment and addressable merging of particle tracks. PMID:18701122

Manneberg, Otto; Melker Hagsäter, S; Svennebring, Jessica; Hertz, Hans M; Kutter, Jörg P; Bruus, Henrik; Wiklund, Martin

2009-01-01

106

Mapping the force field of a hydrogen-bonded assembly.  

PubMed

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

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

2014-01-01

107

Mapping the force field of a hydrogen-bonded assembly  

PubMed Central

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

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

2014-01-01

108

A quantum mechanical scaled force field for tetranitromethane  

NASA Astrophysics Data System (ADS)

Infrared and Raman spectra of tetranitromethane have been recorded in the liquid and vapour phases as well as in solutions of several solvents. On the basis of theoretical predictions, the general assignment of the vibrational spectrum has been modified with respect to previous studies. The computed force field has been scaled to reproduce the experimental frequencies and the prediction capabilities of the method are discussed.

Arenas, J. F.; Otero, J. C.; Soto, J.

1993-10-01

109

Four-nucleon force in chiral effective field theory  

SciTech Connect

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

Evgeny Epelbaum

2005-10-25

110

Tuning the mass of chameleon fields in Casimir force experiments.  

PubMed

We have calculated the chameleon pressure between two parallel plates in the presence of an intervening medium that affects the mass of the chameleon field. As intuitively expected, the gas in the gap weakens the chameleon interaction mechanism with a screening effect that increases with the plate separation and with the density of the intervening medium. This phenomenon might open up new directions in the search of chameleon particles with future long-range Casimir force experiments. PMID:20867290

Brax, Ph; van de Bruck, C; Davis, A C; Shaw, D J; Iannuzzi, D

2010-06-18

111

Minds on Physics: Fundamental Forces and Fields, Activities and Reader  

NSDL National Science Digital Library

This is the fourth in a series of six books which involves activities designed for students. This volume deals with the basics of gravitational, electric, and magnetic forces and fields. The activities part contains guidelines with which teachers can base activities and many questions which can be raised in class. The reader part creates opportunity for discussion and summarizes content covered after the activities have been performed.

Leonard, William J.; Dufresne, Robert J.; Gerace, William J.; Mestre, Jose P.

2006-07-22

112

Quantum mechanical force field for water with explicit electronic polarization.  

PubMed

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes. PMID:23927266

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

2013-08-01

113

Molecular force field parametrization using multi-objective evolutionary algorithms  

Microsoft Academic Search

We suggest a novel tool for the parametrization of molecular force fields by using multi-objective optimization algorithms with a new set of physically motivated objective functions. The new approach is validated in the parametrization of the bonded terms for the homologous series of primary alcohols. Multi-objective evolutionary algorithms (MOEAs) and particularly multi-objective particle swarm optimization (MOPSO) are applied. The results

S. Mostaghim; M. Hoffmann; P. H. Konig; T. Frauenheim; J. Teich

2004-01-01

114

Quantum mechanical force field for water with explicit electronic polarization  

SciTech Connect

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

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

2013-08-07

115

From force fields to dynamics: Classical and quantal paths  

SciTech Connect

Reaction path provides a powerful tool for bridging the gap between electronic structure and chemical dynamics. Classical mechanical reaction paths may usually be understood in terms of the force field in the vicinity of a minimum energy path (MEP). When there is a significant component of hydrogenic motion along the MEP and a barrier much higher than the average energy of reactants, quantal tunneling paths must be considered, and these tend to be located on the corner-cutting side of the MEP. As the curvature of the MEP in mass-scaled coordinates is increased, the quantal reaction paths may deviate considerably from the classical ones, and the force field must be mapped out over a wider region, called the reaction swath. The required force fields may be presented by global or semiglobal analytic functions, or the dynamics may be computed directly from the electronic structure results without the intermediacy of potential energy functions. Applications to atom and diatom reactions in the gas phase and at gas-solid interfaces and to reactions of polyatomic molecules in the gas phase, in clusters, and in aqueous solution are discussed as examples. 106 refs., 2 figs.

Truhlar, D.G. (Univ. of Minnesota, Minneapolis (USA)); Gordon, M.S. (North Dakota State Univ., Fargo (USA))

1990-08-03

116

Molecular simulations of primary alkanolamines using an extendable force field.  

PubMed

A classical force field is proposed for the molecular simulation of primary alkanolamines containing a NH(2)-C-C-OH backbone. A method is devised to take into account the polar (H-bonding) environment of the alkanolamines by calculating electrostatic charges in the presence of explicit solvent molecules. The force field does not use a universal set of charges, but is rather constructed by following a general method for obtaining specific charges for the different alkanolamines. The model is parameterized on the two simplest primary alkanolamines and then validated by calculating thermodynamic properties of five other molecules. Experimental liquid densities and enthalpies of vaporization are also reported in order to complete existing literature data. The predicted ability of the force field is evaluated by comparing the simulation results with experimental densities and enthalpies of vaporization. Densities are predicted with an uncertainty of 1.5 % and enthalpies of vaporization with an uncertainty of 1 kJ mol(-1). A decomposition of the interaction energy into electrostatic and repulsive-dispersive interactions and an analysis of hydrogen-bond statistics lead to a complex picture. Some terms of these interactions are related to the molecular structure in a clear way, others are not. The results provide insights into the structure-property relations that contribute to a better description of the thermodynamic properties of alkanolamines. PMID:23047473

Simond, Mickaël R; Ballerat-Busserolles, Karine; Coxam, Jean-Yves; Pádua, Agílio A H

2012-12-01

117

Near field/far field (nf/ff) energy loss in electric-discharge lasers (EDL's): a mode-medium interaction. Technical report  

SciTech Connect

High-energy CO/sub 2/ EDL's (Electric Discharge Lasers) with unstable resonators exhibit a mode-medium interaction that spreads the focused beam and causes loss in the far-field. Mirror edge Fresnelling may result in amplified feedback, which causes a parallel-piped structure to be burned into the lasing medium. Possible confirming experiments are described.

Bentley, J.H.

1984-08-01

118

Design and optimization of force-reduced high field magnets  

NASA Astrophysics Data System (ADS)

High field magnets have many important applications in different areas of research, in the power industry and also for military purposes. For example, high field magnets are particularly useful in: material sciences, high energy physics, plasma physics (as fusion magnets), high power applications (as energy storage devices), and space applications (in propulsion systems). One of the main issues with high-field magnets is the presence of very large electromagnetic stresses that must be counteracted and therefore require heavy support structures. In superconducting magnets, the problems caused by Lorentz forces are further complicated by the fact that superconductors for high field applications are pressure sensitive. The current carrying capacity is greatly reduced under stress and strain (especially in the case of Nb 3Sn and the new high temperature superconductors) so the reduction of the acting forces is of even greater importance. Different force-reduced magnet concepts have been studied in the past, both numerical and analytical methods have been used to solve this problem. The developed concepts are based on such complex winding geometries that the realization and manufacturing of such coils is extremely difficult and these concepts are mainly of theoretical interest. In the presented research, a novel concept for force-reduced magnets has been developed and analyzed which is easy to realize and therefore is of practical interest. The analysis has been performed with a new methodology, which does not require the time consuming finite element calculations. The developed computer models describe the 3-dimensional winding configuration by sets of filaments (filamentary approximation). This approach is much faster than finite element analysis and therefore allows rapid optimization of concepts. The method has been extensively tested on geometries of force-reduced solenoids where even analytical solutions exist. As a further cross check, the developed computer codes have been tested against qualified finite element codes and found to be in excellent agreement. The developed concept of force-reduced coils is directly applicable to pulsed magnets and a conceptual design of a 25 Tesla magnet has been developed. Although no experimental proof was possible within the scope of this research, there is strong evidence to believe that the developed concept is also applicable to superconducting magnets operating in a constant current mode.

Rembeczki, Szabolcs

119

Vibrational spectra and harmonic force fields of pyrrolidine derivatives: comparison between HF, MP2 and DFT force fields  

Microsoft Academic Search

Infrared and Raman spectra are reported for the isotopic species of pyrrolidine-d0 (PY) and -d1 and for N-methylpyrrolidine-d0 (NMP), -d2, -d3 and -d8. A complete assignment of the experimentally observed bands to normal modes is presented and discussed in particular in the CH\\/CD stretching region. The molecular structures and harmonic force fields were calculated ab initio at the Hartree–Fock (HF),

Ferenc Billes; Ekkehard Geidel

1997-01-01

120

Ab initio valence force field calculations for quartz  

NASA Astrophysics Data System (ADS)

We have derived valence force constants for the tetrahedral SiO4 unit and the inter-tetrahedral SiOSi linkage from previous ab initio molecular orbital calculations on H4SiO4 and H6Si2O7 using a split-valence polarized Gaussian basis set (6-31G*), and used these to calculate the infrared and Raman active vibrational modes of ?-quartz. The calculation gives frequencies approximately 15% greater than experiment, as expected from harmonic force constants obtained at this level of Hartree-Fock theory, but the calculation gives the correct distribution of modes within each frequency range. Calculated 28 30 Si and 16 18 O isotope shifts and pressure shifts to 6 GPa are also in reasonable agreement with experiment. We have also used our ab initio force field to calculate the vibrational spectrum for ?-quartz. The results suggest either that inclusion of a torsional force constant is important for determining the stability of this high temperature polymorph, or that the ?-quartz has a disordered structure with lower symmetry (P62) domains, as suggested by earlier diffraction studies.

McMillan, Paul F.; Hess, Anthony C.

1990-03-01

121

Coarse-grained force field; general folding theory  

PubMed Central

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of ?-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described.

Liwo, Adam; He, Yi; Scheraga, Harold A.

2012-01-01

122

Field ion microscopy characterized tips in noncontact atomic force microscopy: Quantification of long-range force interactions  

NASA Astrophysics Data System (ADS)

Direct comparison of tip-sample forces obtained by dynamic force spectroscopy experiments with theoretical simulations is extremely difficult, since the precise tip shape and chemical identity of the apex atoms of the force sensing tip remain unknown in most experiments. Here, we present force curves measured with a tungsten tip on a Ag(111) surface obtained in a low-temperature atomic force microscope using tips that were analyzed by field ion microscopy down to atomic levels. The resulting van der Waals and electrostatic forces were found to be in quantitative agreement with analytical models, if the tip shape parameters from the field ion microscopy analysis were used. Furthermore, our analysis shows an additional long-range force interaction at tip-sample distances above 1.3 nm. We suggest that this unexpected force is related to patch charges arising from the inhomogeneous work function distribution on the surface of highly faceted sharp tips.

Falter, J.; Langewisch, G.; Hölscher, H.; Fuchs, H.; Schirmeisen, A.

2013-03-01

123

Kelvin probe force microscope with near-field photoexcitation  

NASA Astrophysics Data System (ADS)

We developed a combined probe microscope-a scanning probe near-field optical microscope (SNOM) combined with Kelvin probe force microscope (KFM) that uses a slim and bent optical fiber probe (S/B fiber probe). The developed SNOM-KFM system enables near-field photoexcitation through an apex of the S/B fiber probe during KFM measurement, so that the photoexcitation effects on surface potential (SP) can be measured with submicron spatial resolution. By measuring the SP of tris(8-hydroxyquinolinato) aluminum(III) (Alq3) thin films, we found that the S/B fiber probes have large negative values in the KFM transfer function. Near-field photoexcitation was performed on Alq3 thin films through the S/B fiber probes, and the spatial pattern of photoinduced reduction in SP was visualized by KFM measurement with the same probe.

Ozasa, Kazunari; Nemoto, Shigeyuki; Maeda, Mizuo; Hara, Masahiko

2010-05-01

124

Deformation field of the soft substrate induced by capillary force  

NASA Astrophysics Data System (ADS)

Prediction on the deformation of a soft substrate induced by capillary force has been widely paid attention in the broad range of applications, such as metallurgy, material science, astronavigation, micro/nano-technology, etc., which is also a supplementary result to the classical Young's equation. We quantitatively analyzed the deformation of an elastic substrate under capillary force by means of the energy principle and the continuum mechanics method. The actual drop's morphology was investigated and was compared with that calculated based on the classical spherical shape assumption of the droplet. The displacement field of the substrate was obtained, especially, its singularity at the droplet edge was also discussed. The results are beneficial to engineering application and micro/nano-measurement.

Liu, J. L.; Nie, Z. X.; Jiang, W. G.

2009-05-01

125

Force-free coronal magnetic field modeling using vector fields from Hinode and SDO  

NASA Astrophysics Data System (ADS)

Given the lack of routine direct measurements of the magnetic field in the solar corona, force-free reconstruction methods are a promising tool for the diagnostics of the magnetic structure there. Routine photospheric magnetic field measurements which monitor the temporal evolution of an active region and contain information on the non-potentiality of the field above are used as an input. Based on the assumption that magnetic forces dominate the solar atmosphere, these models allow estimates of the total and free magnetic energy content and the structure of the magnetic field above active regions. The outcome of force-free field modeling strongly depends on the vector magnetic field data used as boundary condition. We compare the model results based on simultaneously observed vector maps from the Helioseismic and Magnetic Imager (HMI) on board Solar Dynamics Observatory and from the Solar Optical Telescope Spectropolarimeter (SP) on board Hinode. We find substantial differences in the absolute estimates of the magnetic field energy but very similar relative estimates, e.g., the fraction of energy to be set free during an eruption or the fraction of flux linking distinct areas within an active region. Our study reveals that only relative estimates of coronal physical quantities from force-free models might be save and conclusions about the magnetic field topology might be drawn with caution.

Thalmann, Julia K.; Tiwari, Sanjiv K.; Wiegelmann, Thomas

2013-04-01

126

AFMM: A molecular mechanics force field vibrational parametrization program  

NASA Astrophysics Data System (ADS)

AFMM (Automated Frequency Matching Method) is a program package for molecular mechanics force field parametrization. The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference set is obtained. By implementing a Monte Carlo-like algorithm to vary the parameters, the tedious task of manual parametrization is replaced by an efficient automated procedure. The program is best suited for optimization of small rigid molecules in a well-defined energy minimum, for which the harmonic approximation to the energy surface is appropriate for describing the intra-molecular degrees of freedom. Program summaryTitle of program: AFMM Catalogue identifier: ADUZ Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: x86 PC, SGI, Sun Microsystems Operating system: GNU/Linux, BSD, IRIX, Solaris Programming language used: Python Memory required: 10 Mbytes No. of bits in a word: 32 or 64 No. of processors used: 1 Parallelized?: No No. of lines in distributed program, including test data, etc.:13 127 No. of bytes in distributed program, including test data, etc.: 182 550 Distribution format: tar.gz Typical running time: 24 h Nature of the physical problem: Molecular mechanics force field parametrization. Method of solution:Fitting of the molecular mechanics potential to normal modes derived from quantum chemical calculations. The missing force field parameters are optimized via a merit function to obtain the optimal fit with the reference quantum mechanical set.

Vaiana, A. C.; Cournia, Z.; Costescu, I. B.; Smith, J. C.

2005-04-01

127

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

PubMed

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968

Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

2012-01-10

128

Micro-gravity: current distributions creating a uniform force field  

NASA Astrophysics Data System (ADS)

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

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

2001-02-01

129

Context Rich Problems Online Archives: Electric Field and Electric Force  

NSDL National Science Digital Library

This page provides a set of context-rich physics problems relating to electric forces and fields. Each context-rich problem is based on a real-world situation, and includes both information that is relevant to solving the problem and extraneous information. Strategies for problem solving are not explicitly provided. Each problem is formulated so it is too difficult for one student to solve alone, yet not too difficult for a group to master. This resource is based on the research results of the Minnesota Physics Education Research group. See Related items on this page for a link to the full collection.

Group, University O.; Heller, Kenneth; Heller, Patricia

2008-09-29

130

Vector field statistical analysis of kinematic and force trajectories.  

PubMed

When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of 'non-directed' hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called 'statistical parametric mapping' (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems. PMID:23948374

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

2013-09-27

131

Automated conformational energy fitting for force-field development  

PubMed Central

We present a general conformational-energy fitting procedure based on Monte Carlo simulated annealing (MCSA) for application in the development of molecular mechanics force fields. Starting with a target potential energy surface and an unparameterized molecular mechanics potential energy surface, an optimized set of either dihedral or grid-based correction map (CMAP) parameters is produced that minimizes the root mean squared error (RMSE) between the parameterized and targeted energies. The fitting is done using an MCSA search in parameter space and consistently converges to the same RMSE irrespective of the randomized parameters used to seed the search. Any number of dihedral parameters can be simultaneously parameterized, allowing for fitting to multi-dimensional potential energy scans. Fitting options for dihedral parameters include non-uniform weighting of the target data, constraining multiple optimized parameters to the same value, constraining parameters to be no greater than a user-specified maximum value, including all or only a subset of multiplicities defining the dihedral Fourier series, and optimization of phase angles in addition to force constants. The dihedral parameter fitting algorithm’s performance is characterized through multi-dimensional fitting of cyclohexane, tetrahydropyran, and hexopyranose monosaccharide energetics, with the latter case having a 30-dimensional parameter space. The CMAP fitting is applied in the context of polypeptides, and is used to develop a parameterization that simultaneously captures the ?, ? energetics of the alanine dipeptide and the alanine tetrapeptide. Because the dihedral energy term is common to many force fields, we have implemented the dihedral-fitting algorithm in the portable Python scripting language and have made it freely available as Supplementary Material.

Guvench, Olgun; MacKerell, Alexander D.

2010-01-01

132

Improved force field for molecular modeling of poly(3-hexylthiophene).  

PubMed

An ab initio-based improved force field is reported for poly(3-hexylthiophene) (P3HT) in the solid state, deriving torsional parameters and partial atomic charges from ab initio molecular structure calculations with explicit treatment of the hexyl side chains. The force field is validated by molecular dynamics (MD) simulations of solid P3HT with different molecular weights including calculation of structural parameters, mass density, melting temperature, glass transition temperature, and surface tension. At 300 K, the P3HT crystalline structure features planar backbones with non-interdigitated all-trans hexyl side chains twisted ~90° from the plane of the backbone. For crystalline P3HT with infinitely long chains, the calculated 300 K mass density (1.05 g cm(-3)), the melting temperature (490 K), and the 300 K surface tension (32 mN/m) are all in agreement with reported experimental values, as is the glass transition temperature (300 K) for amorphous 20-mers. PMID:23899343

Bhatta, Ram S; Yimer, Yeneneh Y; Perry, David S; Tsige, Mesfin

2013-08-29

133

Development of force field parameters for molecular simulation of polylactide  

PubMed Central

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

McAliley, James H.; Bruce, David A.

2011-01-01

134

Reactive force field potential for carbon deposition on silicon surfaces  

NASA Astrophysics Data System (ADS)

In this paper a new interatomic potential based on the Kieffer force field and designed to perform molecular dynamics (MD) simulations of carbon deposition on silicon surfaces is implemented. This potential is a third-order reactive force field that includes a dynamic charge transfer and allows for the formation and breaking of bonds. The parameters for Si-C and C-C interactions are optimized using a genetic algorithm. The quality of the potential is tested on its ability to model silicon carbide and diamond physical properties as well as the formation energies of point defects. Furthermore, MD simulations of carbon deposition on reconstructed (100) silicon surfaces are carried out and compared to similar simulations using a Tersoff-like bond order potential. Simulations with both potentials produce similar results showing the ability to extend the use of the Kieffer potential to deposition studies. The investigation reveals the presence of a channelling effect when depositing the carbon at 45° incidence angle. This effect is due to channels running in directions symmetrically equivalent to the (110) direction. The channelling is observed to a lesser extent for carbon atoms with 30° and 60° incidence angles relative to the surface normal. On a pristine silicon surface, sticking coefficients were found to vary between 100 and 73%, depending on deposition conditions.

Briquet, Ludovic G. V.; Jana, Arindam; Mether, Lotta; Nordlund, Kai; Henrion, Gérard; Philipp, Patrick; Wirtz, Tom

2012-10-01

135

Thermomechanical properties of graphene: valence force field model approach.  

PubMed

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

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

2012-05-01

136

Developing Force Fields from the Microscopic Structure of Solutions  

PubMed Central

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

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

2009-01-01

137

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules  

Microsoft Academic Search

We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use

Wendy D. Cornell; Piotr Cieplak; Christopher I. Bayly; Ian R. Gould; Kenneth M. Merz; David M. Ferguson; David C. Spellmeyer; Thomas Fox; James W. Caldwell

1995-01-01

138

Electromagnetic self-forces and generalized Killing fields  

NASA Astrophysics Data System (ADS)

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

Harte, Abraham I.

2009-08-01

139

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

Microsoft Academic Search

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

Isabelle Quelven; Anne Roussin; Jean-marie Zajac

2005-01-01

140

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

SciTech Connect

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

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

2009-01-01

141

A comparison of sublimation enthalpies with lattice energies calculated using force fields  

NASA Astrophysics Data System (ADS)

Experimental sublimation enthalpies in a range of molecular crystals were compared with their lattice energies as calculated by molecular mechanics, using several force fields. This enables an evaluation of the capability of these force fields to determine intermolecular interaction energies. The best agreement between calculated energies and sublimation enthalpies is found in the case of Gavezzotti's force field, while significant discrepancies are found with the DREIDING force field and CVFF. With all force fields, the level of accuracy obtained in energy calculation is insufficient for confident use in determining the enthalpy difference between two polymorphs of a given compound.

Osborn, J. C.; York, P.

1999-01-01

142

A fast path integral method for polarizable force fields.  

PubMed

A quantum simulation of an imaginary time path integral typically requires around n times more computational effort than the corresponding classical simulation, where n is the number of ring polymer beads (or imaginary time slices) used in the calculation. It is however possible to improve on this estimate by decomposing the potential into a sum of slowly and rapidly varying contributions. If the slowly varying contribution changes only slightly over the length scale of the ring polymer, it can be evaluated on a contracted ring polymer with fewer than the full n beads (or equivalently on a lower order Fourier decomposition of the imaginary time path). Here we develop and test this idea for systems with polarizable force fields. The development consists of iterating the induction on the contracted ring polymer and applying an appropriate transformation to obtain the forces on the original n beads. In combination with a splitting of the Coulomb potential into its short- and long-range parts, this results in a method with little more than classical computational effort in the limit of large system size. The method is illustrated with simulations of liquid water at 300 K and hexagonal ice at 100 K using a recently developed flexible and polarizable Thole-type potential energy model. PMID:19739844

Fanourgakis, George S; Markland, Thomas E; Manolopoulos, David E

2009-09-01

143

Efficient parameterization of torsional terms for force fields.  

PubMed

A novel method is presented for fitting force-field dihedral angles using an ensemble of structures generated from an ab initio Monte Carlo simulation. Importance sampling is used to achieve an efficient algorithm using a low level of theory to minimize the system at each step with the dihedral angles constrained, followed by dihedral fitting using the single point energies at a higher level of theory. The resulting method is an order of magnitude more efficient than the traditional method of doing a constrained scan over each dihedral independently. Also as the sampling is more uniformly distributed, the full surface is approximated to a greater accuracy. The dihedral fitting is done with a nonlinear optimization method to vary the phase as well as the force constant. The utility of the method is demonstrated by fitting dihedrals of methyl L-lactate, diisopropyl fluorophosphate, isopentenyl phosphate, a leucine dipeptide, and two inhibitors of Signal Transducer and Activator of Transcription 5. The results show that the Monte Carlo scheme is more efficient than constrained scans and is particularly effective at approximating the underlying potential energy surface when the dihedral degrees are coupled. © 2014 Wiley Periodicals, Inc. PMID:24831846

Burger, Steven K; Ayers, Paul W; Schofield, Jeremy

2014-07-15

144

A quantum mechanical polarizable force field for biomolecular interactions  

PubMed Central

We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs.

Donchev, A. G.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, O. V.; Tarasov, V. I.

2005-01-01

145

A quantum mechanical polarizable force field for biomolecular interactions.  

PubMed

We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs. PMID:15911753

Donchev, A G; Ozrin, V D; Subbotin, M V; Tarasov, O V; Tarasov, V I

2005-05-31

146

Derivation of a Molecular Mechanics Force Field for Cholesterol  

SciTech Connect

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

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

2004-01-01

147

The Bonding Forces In Liquid Metals And Ultrasonic Field Action  

NASA Astrophysics Data System (ADS)

The understanding of the liquid metals properties is still imperfect. Assuming that the liquids are isotropic and show some elasticity properties, there are no physical reasons for rejecting the applicability of the fundamental ideas of the Debye theory to the description of the properties of liquid state. The approach is intended to relate the temperature Debye to the intensity of bonding forces between neighboring atoms and, in turn, to correlate this with the high power ultrasonic field action. In order to highlight the effect of the ultrasonic wave on the Debye temperature values, the experiments were carried out under similar conditions both with and without sonication. The relationship between the Debye temperature for both liquid and solid state is ?Dsolid / ?Dliquid = 0.85.

Moraru, Luminita; Murariu, Gabriel

2007-04-01

148

Investigation of crossed SAW fields by scanning acoustic force microscopy.  

PubMed

We used multimode scanning acoustic force microscopy (SAFM) for studying noncollinearly propagating Rayleigh and Love wave fields. By analyzing torsion and bending movement of SAFM cantilever, normal and in-plane wave oscillation components are accessible. The SAFM principle is the down-conversion of surface oscillations into cantilever vibrations caused by the nonlinearity of the tip-sample interaction. Through mixing of complementary oscillation components, phase velocities of crossed Rayleigh waves on GaAs and crossed Rayleigh and Love waves on the layered system SiO2/ST-cut quartz were obtained simultaneously. Now, it is possible to investigate elastic properties of submicron areas through multimode SAFM measurements. Finally, we present mixing experiments of four SAWs on GaAs and discuss the various influences on the measured SAFM amplitude and phase contrast. PMID:11477772

Behme, G; Hesjedal, T

2001-07-01

149

An accurate ab initio quartic force field for ammonia  

NASA Technical Reports Server (NTRS)

The quartic force field of ammonia is computed using basis sets of spdf/spd and spdfg/spdf quality and an augmented coupled cluster method. After correcting for Fermi resonance, the computed fundamentals and nu 4 overtones agree on average to better than 3/cm with the experimental ones except for nu 2. The discrepancy for nu 2 is principally due to higher-order anharmonicity effects. The computed omega 1, omega 3, and omega 4 confirm the recent experimental determination by Lehmann and Coy (1988) but are associated with smaller error bars. The discrepancy between the computed and experimental omega 2 is far outside the expected error range, which is also attributed to higher-order anharmonicity effects not accounted for in the experimental determination. Spectroscopic constants are predicted for a number of symmetric and asymmetric top isotopomers of NH3.

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

1992-01-01

150

The eccentric frame decomposition of central force fields  

NASA Astrophysics Data System (ADS)

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

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

2008-01-01

151

Diffusion through ordered force fields in nanopores represented by Smoluchowski equation  

Microsoft Academic Search

The classical Einstein or Fick diffusion equation was developed in random force fields. When the equation is applied to gas transport through coal, significant discrepancies are observed between experimental and simulation results. The explanation may be that the random force field assumption is violated. In this article, we analyze molecular transport driven by both random and ordered (directional) forces in

Fu Yang Wang; Zhong Hua Zhu; Victor Rudolph

2009-01-01

152

A Kirkwood-Buff Derived Force Field for Thiols, Sulfides, and Disulfides  

PubMed Central

A force field has been developed for molecular simulations of methanethiol, dimethyl sulfide, and dimethyl disulfide mixtures. The force field specifically attempts to balance the solvation and self-association of these solutes in solution mixtures with methanol. The force field is based on the Kirkwood–Buff (KB) theory of solutions and is parametrized using the KB integrals obtained from the experimental activity coefficients for the solution mixtures. The transferability of the force field was tested and confirmed by the accurate prediction of the activity coefficients for methanethiol/dimethyl sulfide solutions, which were not used in the initial parametrization of the force fields. The ideality of this latter solution is excellently reproduced. The applicability of the force field to simulations in water was corroborated with a reasonably accurate prediction for the low solubility of dimethyl sulfide in water. The aggregation of methanol molecules at low methanol mole fractions displayed by all the mixtures is reproduced and further analyzed.

Bentenitis, Nikolaos; Cox, Nicholas R.; Smith, Paul E.

2011-01-01

153

Magnetic field gradient measurement on magnetic cards using magnetic force microscopy  

Microsoft Academic Search

The magnetic field gradients of magnetic stripe cards, which are developed for classifying magnetic particles used in magnetic particle inspections, have been measured using a magnetic force microscope (MFM). The magnetic force exerted on a MFM probe by the stray field emanating from the card was measured to determine the field gradients. The results are in good agreement with the

C. C. H. Lo; J. Leib; D. C. Jiles; W. C. Chedister

2002-01-01

154

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

PubMed

In computational neuroscience it is generally accepted that human motor memory contains neural representations of the physics of the musculoskeletal system and the objects in the environment. These representations are called "internal models". Force field studies, in which subjects have to adapt to dynamic perturbations induced by a robotic manipulandum, are an established tool to analyze the characteristics of such internal models. The aim of the current study was to investigate whether catch trials during force field learning could influence the consolidation of motor memory in more complex tasks. Thereby, the force field was more than double the force field of previous studies (35 N·s/m). Moreover, the arm of the subjects was not supported. A total of 46 subjects participated in this study and performed center-out movements at a robotic manipulandum in two different force fields. Two control groups learned force field A on day 1 and were retested in the same force field on day 3 (AA). Two test groups additionally learned an interfering force field B (= -A) on day 2 (ABA). The difference between the two test and control groups, respectively, was the absence (0%) or presence (19%) of catch trials, in which the force field was turned-off suddenly. The results showed consolidation of force field A on day 3 for both control groups. Test groups showed no consolidation of force field A (19% catch trials) and even poorer performance on day 3 (0% catch trials). In conclusion, it can be stated that catch trials seem to have a positive effect on the performance on day 3 but do not trigger a consolidation process as shown in previous studies that used a lower force field viscosity with supported arm. These findings indicate that the results of previous studies in which less complex tasks were analyzed, cannot be fully transferred to more complex tasks. Moreover, the effects of catch trials in these situations are insufficiently understood and further research is needed. PMID:23898319

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

2013-01-01

155

Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC  

NASA Technical Reports Server (NTRS)

The quartic force fields of HCN and HNC are determined using atomic natural orbital one-particle basis sets of spdf/spd and spdfg/spdf quality in conjunction with the CCSD(T) electron correlation method (singles and doubles coupled-cluster theory plus a perturbation estimate of the effects of connected triple excitations). The HCN force field is in good agreement with a recent experimentally derived force field and also with the force field recently computed by Wong and Bacskay. On the basis of the good agreement obtained for HCN, it is argued that the ab initio quartic force field for HNC is superior to a prior force field derived from experiment. The harmonic frequencies of HNC are predicted to be 3822 +/- 10, 472 +/- 5, and 2051 +/- 10 cm(exp -1) for omega(sub 1), omega(sub 2), and omega(sub 3), respectively; the experimentally derived values are above these values and fall outside the estimated uncertainties. Using the quartic force field, spectroscopic constants are predicted for HNC based on a vibrational second-order perturbation theory analysis. It is also asserted that the gas-phase fundamental nu(sub 3) for HNC is slightly lower than the matrix isolation value. The range of validity of the quartic force fields is investigated by comparison of variational vibrational energies computed with the quartic force fields to those obtained from our recently reported global HCN/HNC potential energy surface and also to experimental data.

Lee, Timothy J.; Dateo, Christopher E.; Gazdy, Bela; Bowman, Joel M.

1993-01-01

156

Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC  

NASA Technical Reports Server (NTRS)

The quartic force fields of HCN and HNC are determined using atomic natural orbital one-particle basis sets of spdf/spd and spdfg/spdf quality in conjunction with the CCSD(T) electron correlation method (singles and doubles coupled-cluster theory plus a perturbational estimate of the effects of connected triple excitations). The HCN force field is in good agreement with a recent experimentally derived force field and also with the force field recently computed by Wong and Bacskay. On the basis of the good agreement obtained for HCN, it is argued that the ab initio quartic force field for HNC is superior to a prior force field derived from experiment. The harmonic frequencies of HNC are predicted to be 3822 +/- 10,472 +/- 5, and 2051 +/-10/cm for omega1, omega2, and omega3, respectively; the experimentally derived values are above these values and fall outside the estimated uncertainties. Using the quartic force field, spectroscopic constants are predicted for HNC based on a vibrational second-order perturbation theory analysis. It is also asserted that the gas-phase fundamental v(sub 3) for HNC is slightly lower than the matrix isolation value. The range of validity of the quartic force fields is investigated by comparison of variational vibrational energies computed with the quartic force fields to those obtained from our recently reported global HCN/HNC potential energy surface and also to experimental data.

Lee, Timothy J.; Dateo, Christopher E.; Gazdy, Bela; Bowman, Joel M.

1993-01-01

157

Using J-coupling constants for force field validation: application to hepta-alanine.  

PubMed

A computational solution to the protein folding problem is the holy grail of biomolecular simulation and of the corresponding force fields. The complexity of the systems used for folding simulations precludes a direct feedback between the simulations and the force fields, thus necessitating the study of simpler systems with sufficient experimental data to allow force field optimization and validation. Recent studies on short polyalanine peptides of increasing length (up to penta-alanine) indicated the presence of a systematic deviation between the experimental (NMR-derived) J-couplings and the great majority of biomolecular force fields, with the ?(2) values for even the best-performing force fields being in the 1.4-1.8 range. Here we show that by increasing the number of residues to seven and by achieving convergence through an increase of the simulation time to 2 ?s, we can identify one force field (the AMBER99SB force field, out of the three force fields studied) which when compared with the experimental J-coupling data (and for a specific set of Karplus equation parameters and estimated J-coupling errors previously used in the literature) gave a value of ?(2) = 0.99, indicating that full statistical consistency between experiment and simulation is feasible. However, and as a detailed analysis of the effects of estimated errors shows, the ?(2) values may be unsuitable as indicators of the goodness of fit of the various biomolecular force fields. PMID:22087590

Georgoulia, Panagiota S; Glykos, Nicholas M

2011-12-29

158

Magnetic field gradient measurement on magnetic cards using magnetic force microscopy  

NASA Astrophysics Data System (ADS)

The magnetic field gradients of magnetic stripe cards, which are developed for classifying magnetic particles used in magnetic particle inspections, have been measured using a magnetic force microscope (MFM). The magnetic force exerted on a MFM probe by the stray field emanating from the card was measured to determine the field gradients. The results are in good agreement with the field gradients estimated from the magnetizing field strengths used in the encoding process. .

Lo, C. C. H.; Leib, J.; Jiles, D. C.; Chedister, W. C.

2002-05-01

159

Focusing of Neutral Particle Beams by Fictitious Force Fields  

Microsoft Academic Search

In a rotating coordinate system the Coriolis force and centrifugal force can account for the curved trajectories followed by moving particles. It is shown that particle trajectories diverging from a source fixed in the rotating system may come to a focus at another point fixed in the system. Both first- and second-order focusing are obtained and an example of each

Daniel F. Dempsey

1963-01-01

160

Focusing of Neutral Particle Beams by Fictitious Force Fields  

Microsoft Academic Search

In a rotating coordinate system the Coriolis force and centrifugal force ; can account for the curved trajectories followed by movimg particles. It is ; shown that particle trajectories diverging from a source fixed in the rotating ; system may come to a focus at another point fixed in the system. Both first- and ; second-order focusing are obtained and

Daniel F. Dempsey

1963-01-01

161

Deformation field of the soft substrate induced by capillary force  

Microsoft Academic Search

Prediction on the deformation of a soft substrate induced by capillary force has been widely paid attention in the broad range of applications, such as metallurgy, material science, astronavigation, micro\\/nano-technology, etc., which is also a supplementary result to the classical Young's equation. We quantitatively analyzed the deformation of an elastic substrate under capillary force by means of the energy principle

J. L. Liu; Z. X. Nie; W. G. Jiang

2009-01-01

162

Near-field manipulation of interparticle forces through resonant absorption, optical binding, and dispersion forces  

NASA Astrophysics Data System (ADS)

The relative motions of two or more neutral particles, subject to optical trapping forces within a beam, are influenced by intrinsic inter-particle forces. The fundamental character of such forces is well-known and usually derives from dispersion interactions. However, the throughput of moderately intense (off-resonant) laser light can significantly modify the form and magnitude of these intrinsic forces. This optical binding effect is distinct from the optomechanical interactions involved in optical tweezers, and corresponds to a stimulated (pairwise) forward-scattering mechanism. In recent years, attention has begun to focus on optical binding effects at sub-micron and molecular dimensions. At this nanoscale, further manipulation of the interparticle forces is conceivable on the promotion of optically bound molecules to an electronic excited state. It is determined that such excitation may influence the intrinsic dispersion interaction without continued throughput of the laser beam, i.e. independent of any optical binding. Nevertheless, the forwardscattering mechanism is also affected by the initial excitation, so that both the optical binding and dispersion forces can be manipulated on input of the electromagnetic radiation. In addition, the rate of initial excitation of either molecule (or any energy transfer between them) may be influenced by an off-resonant input beam which, thus, acts as an additional actor in the modification of the interparticle force. A possible experimental set-up is proposed to enable the measurement of such changes in the interparticle coupling.

Bradshaw, David S.; Andrews, David L.

2013-09-01

163

Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects.  

PubMed

The methodology for deriving class II force fields has been applied to acetal, hemiacetal, and carbohydrate compounds. A set of eighteen model compounds containing one or more anomeric centers was selected for generating the quantum mechanical energy surface, from which the force field was derived and the functional form assessed. The quality of the fit was tested by comparing the energy surface predicted by the force field with ab initio results. Structural, energetic, and dynamic properties (vibrational frequencies) were analyzed. In addition, alpha and beta anomeric equilibrium structures and energies of 2-methoxytetrahydropyran, 2-deoxyribose, and glucose were computed at the HF/6-31G* and higher ab initio levels. These calculations provide test data from molecules outside the training set used to derive the force field. The quantum calculations were used to assess the ability of the class II force field and two quadratic diagonal (class I) force fields, CVFF, and Homans' extension of the AMBER force field, to account for the anomeric effects on the structural and energetic properties of carbohydrate systems. These class I force fields are unable to account for observed structural and energetic trends, exhibiting deviations as large as 5 kcal/mol in relative energies. The class II force field, on the other hand, is shown to reproduce anomeric structural as well as energetic differences. An energy component analysis of this force field shows that the anomeric differences are dominated by torsional energies, although coupling terms, especially angle/torsion, also make significant contributions (roughly 1 kcal/mol in glucose). In addition, the force field accurately accounts for both anomeric and exo-anomeric energy differences in 2-methoxytetrahydropyran, and anomeric energy differences in 2-deoxyribose and glucose. PMID:9538697

Hwang, M J; Ni, X; Waldman, M; Ewig, C S; Hagler, A T

1998-05-01

164

Non-force-free extrapolation of solar coronal magnetic field using vector magnetograms  

NASA Astrophysics Data System (ADS)

We report our recent improvement in non-force-free extrapolation of coronal magnetic field, using vector magnetograms. Based on the principle of minimum (energy) dissipation rate (MDR), a generally non-force-free magnetic field solution is expressed as the superposition of one potential field and two (constant-[alpha]) linear force-free fields, with distinct [alpha] parameters. With a known potential field, the system is reduced to a second-order one that can be solved using one single-layer vector magnetogram. We devise an iteration procedure to determine the potential field, by achieving satisfactory agreement between the MDR-model computed and measured transverse magnetic field vectors on the bottom boundary. We illustrate this approach by applying it to real magnetograph measurement of solar active region AR 10953. We show that the results are satisfactory as judged from the quantitative magnetic field measurement, and the behavior of the derived Lorentz force.

Hu, Qiang; Dasgupta, B.; Derosa, M. L.; Büchner, J.; Gary, G. A.

2010-02-01

165

Electromagnetic force analysis of HTS bulk in DC-magnetic fields due to electromagnet  

Microsoft Academic Search

A new type linear synchronous motor which is based on an idea considering pinning force of high temperature superconducting (HTS) bulk as synchronizing force in using current-carrying-armature winding is proposed. However, HTS bulk could not produce lift force enough to levitate the HTS bulk ship for basic experiments. To research larger lift force, DC-magnet which generates higher magnetic fields has

K. Yoshida; H. Matsumoto

2002-01-01

166

Shock induced decomposition and sensitivity of energetic materials by ReaxFF molecular dynamics  

NASA Astrophysics Data System (ADS)

Shock sensitivity of single crystal energetic materials can depend on the crystallographic direction. For example, sensitivity of PETN strongly correlates with orientational anisotropy of elastic precursor strength as well as steric hindrance to shear in some slip directions. In particular, deformation and excitation of energetic molecules can be affected by different slip systems and mechanisms of elastic-plastic transition for different directions. To study the influence of shock/impact orientation on initiation and decomposition of energetic materials we have performed a series of reactive molecular dynamics (MD) simulations using the ReaxFF reactive force field, capable to reproduce the quantum chemical (QM)-derived relative energies of the reactants, products, intermediates and transition states related to the RDX and HMX unimolecular decomposition. Our analysis shows that the sensitivity, pathways, and products of shock-induced decomposition in these single energetic crystals are dependent on the shock orientation as well as crystalline phases of energetic materials.

Zybin, S. V.

2005-07-01

167

Ridge forces, absolute plate motions, and the intraplate stress field  

Microsoft Academic Search

The study calculates torque poles for a variety of possible forces acting on the plates, including ridge push, slab pull, and collisional resistance. These poles are compared to the directions of the absolute plate motions. A strong correlation is found between ridge torque poles and the azimuth of absolute plate motions for the North American, South American, Pacific, Cocos, and

Randall M. Richardson

1992-01-01

168

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

PubMed Central

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.

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

169

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

PubMed

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

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

170

Determination of constant alpha force-free solar magnetic fields from magnetograph data  

Microsoft Academic Search

It is shown that a magnetic field that is force-free with alpha constant (alpha is not equal to 0) in the whole volume outside the sun cannot have a finite energy content and that such a field cannot be determined uniquely from only one magnetic field component given at the photosphere. Therefore, the extension of a global scale constant-alpha force-free

N. Seehafer

1978-01-01

171

Shape-induced force fields in optical trapping  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

172

A modified MM2 force field for bleomycin analysis  

NASA Astrophysics Data System (ADS)

New MM2 parameters for the cobalt binding site in cobalt-bleomycin, a potent antitumor antibiotic, are presented. These force constants were successfully used to model crystal structures of two cobalt-bleomycin analogues. Calculations on the bithiazole part of bleomycin show that the trans form is more stable than the cis form. It is also shown that conformational searches are necessary even in small inorganic molecules.

Charles, Robert; Ganly-Cunningham, Marcela; Warren, Rachel; Zimmer, Marc

1992-02-01

173

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

PubMed Central

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 ?-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 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.

Best, Robert B.; Hummer, Gerhard

2011-01-01

174

Parameters for the AMBER force field for the molecular mechanics modeling of the cobalt corrinoids  

NASA Astrophysics Data System (ADS)

Additional parameters for the AMBER force field have been developed for the molecular mechanics modeling of the cobalt corrinoids. Parameter development was based on a statistical analysis of the reported structures of these compounds. The resulting force field reproduces bond lengths, bond angles, and torsional angles within 0.01 Å, 0.8°, and 4.0° of the mean crystallographic values, respectively. Parameters for the Co-C bond length and the Co-C-C bond angle for modeling the alkylcobalamins were developed by modeling six alkylcobalamins. The validity of the force field was tested by comparing the results obtained with known experimental features of the structures of the cobalt corrinoids as well as with the results from their modeling using a parameter set for the MM2 force field that has been previously developed and extensively tested. The AMBER force field reproduces the structures of the cobalt corrinoids as well as the MM2 force field, although it tends to underestimate the corrin fold angle, the angle between mean planes through the corrin atoms in the northern and southern half of the molecules, respectively. The force field was applied to a study of the structures of 5'-deoxy-5'-(3-isoadenosyl)cobalamin, 2',5'-dideoxy-5'-adenosylcobalamin and 2',3',5'-trideoxy-5'-adenosylcobalamin. This expansion of the standard AMBER force field provides a force field that can be used for modeling the structures of the B 12-dependent proteins, the structures of some of which are now beginning to emerge. This was verified in a preliminary modeling of the coenzyme B 12 binding site of methylmalonyl coenzyme A mutase.

Marques, H. M.; Ngoma, B.; Egan, T. J.; Brown, K. L.

2001-04-01

175

Force-detected magnetic resonance in a field gradient of 250 000 Tesla per meter  

NASA Astrophysics Data System (ADS)

We report the detection of slice-selective electron spin resonance with an external magnetic field gradient comparable to local interatomic gradients, using the techniques of magnetic resonance force microscopy. An applied microwave field modulated the spin-gradient force between a paramagnetic DPPH sample and a micrometer-scale ferromagnetic tip on a force microscope cantilever. A sensitivity equivalent to 184 polarized electron moments in a one-Hertz detection bandwidth was attained. We mapped the tip magnetic field with a resonant slice thickness of order one nanometer, thereby demonstrating magnetic resonance on length scales comparable to molecular dimensions.

Bruland, K. J.; Dougherty, W. M.; Garbini, J. L.; Sidles, J. A.; Chao, S. H.

1998-11-01

176

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

NASA Astrophysics Data System (ADS)

I use the recently developed massive field approach to calculate the scalar self-force on a static particle in a Schwarzschild spacetime. In this approach the scalar self-force is obtained from the difference between the (massless) scalar field, and an auxiliary massive scalar field combined with a certain limiting process. By applying this approach to a static particle in Schwarzschild I show that the scalar self-force vanishes in this case. This result conforms with a previous analysis [A. G. Wiseman, Phys. Rev. D612000084014].

Rosenthal, Eran

2004-12-01

177

Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER\\/8 ff03 versus ECEPP\\/3  

Microsoft Academic Search

Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-d-Daa-Phe-Daa-NH2 (Daa=diamino acid): 1 combining d-Dab2 (?,?-diaminobutyryl) with Lys4, and 2 –d-Dap2 (?,?-diaminopropionyl) with Orn4. The ?-amino groups of d-Daa2 and Daa4 are coupled with ?CO into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and

Jerzy Ciarkowski; Sylwia ?uczak; Dawid Jagie?a; Emilia Sikorska; Jacek Wójcik; Marta Oleszczuk; Jan Izdebski

178

Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method  

NASA Astrophysics Data System (ADS)

A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn-Sham density functional theory with the Becke-Lee-Yang-Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car-Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper.

Akin-Ojo, Omololu; Song, Yang; Wang, Feng

2008-08-01

179

Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon.  

National Technical Information Service (NTIS)

Isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth's gravitational field using an image-analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. ...

S. DasGupta J. L. Plawsky P. C. Wayner

1995-01-01

180

Magnetic-field measurements of current-carrying devices by force-sensitive magnetic-force microscopy with potential correction  

Microsoft Academic Search

A scanning probe technique for current-carrying device imaging is proposed that combines magnetic-force microscopy with surface-potential nulling measurements. The device is ac biased at an off-resonant frequency and the current-induced magnetic field results in cantilever deflection which is detected by a lock-in amplifier. An ac bias at the resonant frequency is simultaneously applied to the tip and conventional scanning surface-potential

Tony Alvarez; Sergei V. Kalinin; Dawn A. Bonnell

2001-01-01

181

Observation of the switching fields of individual Permalloy particles in nanolithographic arrays via magnetic force microscopy  

Microsoft Academic Search

A technique has been developed for measuring the switching fields of individual submicron magnetic particles using a magnetic force microscope (MFM) in which an in situ magnetic field can be applied. This allows the study of the evolution of the particles' magnetic states as a function of applied field and the direct observation of cooperative switching. Observations of the switching

G. A. Gibson; J. F. Smyth; S. Schultz; D. P. Kern

1991-01-01

182

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

Microsoft Academic Search

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

Raya Fidel; Kristene Unsworth

2007-01-01

183

Terrestrial and microgravity boiling heat transfer in a dielectrophoretic force field  

Microsoft Academic Search

In order to maintain steady nucleate boiling in microgravity another force must be imposed on the boiling process to replace the buoyancy force. The objective of this study is to investigate the effectiveness of a static electric field for maintaining nucleate boiling in microgravity. Semi-transparent gold-film heaters are used to measure the instantaneous average heater surface temperature and to provide

T. J. Snyder; J. N. Chung

2000-01-01

184

Cell separation by non-inertial force fields in microfluidic systems  

Microsoft Academic Search

Cell and microparticle separation in microfluidic systems has recently gained significant attention in sample preparations for biological and chemical studies. Microfluidic separation is typically achieved by applying differential forces on the target particles to guide them into different paths. This paper reviews basic concepts and novel designs of such microfluidic separators with emphasis on the use of non-inertial force fields,

Hideaki Tsutsui; Chih-Ming Ho

2009-01-01

185

Electromagnetic field analysis and dynamic modeling of force for motor in Maglev train  

Microsoft Academic Search

Finite element model of a electromagnet module was established on the dimensions of long stator linear synchronous in TR08 Maglev vehicle in order to study the performance of the motor. The distribution of the electromagnetic field in the levitation air gap was analyzed in detail, then the curve of propulsive force and levitation force were obtained under different spans. The

Guirong Wang; Hong Xu; Jian Sun; Wei Wei

2008-01-01

186

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

PubMed Central

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

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

2006-01-01

187

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

PubMed

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

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

2006-06-01

188

The Rotational Spectrum and Anharmonic Force Field of Chlorine Dioxide, OClO  

NASA Technical Reports Server (NTRS)

The ground state rotational and quartic centrifugal distortion constants, their vibrational changes, and the sextic centrifugal distortion constants were used in a calculation of the quartic force field together with data from infrared studies.

Muller, Holger S. P.; Sorensen, G.; Birk, Manfred; Friedl, Randy R.

1997-01-01

189

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

NASA Astrophysics Data System (ADS)

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

Villegas, A.; Diez, F. J.

2014-04-01

190

Microscopic mean field approximation and beyond with the Gogny force  

NASA Astrophysics Data System (ADS)

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

Péru, S.; Martini, M.

2014-03-01

191

Microscopic mean field approximation and beyond with the Gogny force  

NASA Astrophysics Data System (ADS)

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

Péru, S.; Martini, M.

2014-05-01

192

H0bar ff and Zbar ff Interactions in Theeffective Lagrangian Approach  

NASA Astrophysics Data System (ADS)

We study possible effects induced by decoupled physics beyond the standard model on the decays Z-> bar ff and H0-> bar ff in the framework of effective Lagrangians. We consider only those dimension 6 [SUL (2) × UY (1)]-invariant fermionic operators that may be generated at tree level by the underlying physics. Using electroweak data, we get constraints on low energy new physics contributions to the partial widths ? (Z-> bar ff), including leptonic FCNC effects. We also discuss the underlying physics effects induced on BR (H0-> bar ff) of light fermions. In particular, we find a remarkable enhancement of the ?e, ?u and bar dd channels.

Hernández, J. M.; Sampayo, O. A.; Toscano, J. J.

193

Force field calculations for 2-amino-5-chloro- and 2-amino-5-bromo-benzotrifluorides  

Microsoft Academic Search

Force field calculations have been carried out for 2-amino-5-chloro- and 2-amino-5-bromo-benzotrifluorides using the earlier (Ref. [47] of this article) reported IR and Raman spectra. As the frequencies of the corresponding modes for the C–Br and the C–Cl groups do not differ widely the two molecules are assumed to be isotopomers for the purpose of the force field calculations. The calculated

R. A. Yadav; R. K. Yadav; N. P. Singh

2006-01-01

194

Nonlinear Force-Free Reconstruction of the Global Solar Magnetic Field: Methodology  

Microsoft Academic Search

We present a novel numerical method that allows the calculation of nonlinear force-free magnetostatic solutions above a boundary\\u000a surface on which only the distribution of the normal magnetic field component is given. The method relies on the theory of\\u000a force-free electrodynamics and applies directly to the reconstruction of the solar coronal magnetic field for a given distribution\\u000a of the photospheric

I. Contopoulos; C. Kalapotharakos; M. K. Georgoulis

2011-01-01

195

Comments on "Comments on solar linear force-free field and application of FFT analysis''  

NASA Astrophysics Data System (ADS)

The paper "Comments on Solar Linear Force-free Field and Application of FFT Analysis (Song & Zhang, 2004, 2005)" made some comments on linear force-free field problems and proposed a so-called improvement on the application of FFT. We argue that some points in Song & Zhang on available methods are misleading or incorrect. The FFT technique proposed in Song & Zhang is also controversial. Therefore some of their conclusions should not be solid.

Li, Z. H.; Yan, Y. H.; Song, G. X.

2006-01-01

196

Development and validation of new-generation molecular mechanical force fields and semiempirical Hamiltonians  

Microsoft Academic Search

This work describes the development and validation of many-body force fields and semiempirical Hamiltonians as part of a multi-scale modeling effort by the York Group targeted at biological applications. Basic science effort is spent towards the testing of existing polarizable force field functional forms in the areas of charge transfer and the coupling of polarization with many-body exchange. A new

Timothy John Giese

2005-01-01

197

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

Microsoft Academic Search

Accurate quartic anharmonic force fields for CF$_4$ and SiF$_4$ have been\\u000acalculated using the CCSD(T) method and basis sets of $spdf$ quality. Based on\\u000athe {\\\\it ab initio} force field with a minor empirical adjustment, the\\u000avibrational energy levels of these two molecules and their isotopomers are\\u000acalculated by means of high order Canonical Van Vleck Perturbation Theory(CVPT)\\u000abased on

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

1999-01-01

198

BIOREMEDIATION FIELD EVALUATION - HILL AIR FORCE BASE, UTAH  

EPA Science Inventory

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

199

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

NASA Technical Reports Server (NTRS)

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

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

1985-01-01

200

Improved united-atom force field for 1-alkyl-3-methylimidazolium chloride.  

PubMed

We have developed a united atom (UA) nonpolarizable force field for 1-alkyl-3-methyl-imidazolium chloride ([C(n)mim][Cl], n = 1, 2, 4, 6, 8), a potential solvent for the pretreatment of lignocellulosic biomass. The charges were assigned by fitting the electrostatic potential surface (ESP) of the ion pair dimers. The Lennard-Jones parameters of the hydrogen atoms on the imidazolium ring were adjusted to agree with the ab initio optimized geometries of isolated ion pairs. Molecular dynamics (MD) simulations were performed for a wide range of temperatures to validate the force field. Substantial improvements were found in both the dynamical properties and the fluid structures, as compared to those predicted using our previously developed UA force field (UA2006) (Phys. Chem. Chem. Phys. 2006, 8, 1096). Liquid densities were found to lie within 2% experimental data. The simulated heats of vaporization decreased about 30% relative to that predicted using the UA2006 force field. The site-site radial distribution functions between the hydrogen atoms on the imidazolium ring and the chloride anions were in good agreement with those determined by ab initio molecular dynamics. The newly developed force field gives a much better description of the self-diffusion coefficients and shear viscosities, which usually deviate by 1 order of magnitude when determined using other force fields. PMID:20235515

Liu, Zhiping; Chen, Ting; Bell, Alex; Smit, Berend

2010-04-01

201

First principles derived, transferable force fields for CO2 adsorption in Na-exchanged cationic zeolites.  

PubMed

The development of accurate force fields is vital for predicting adsorption in porous materials. Previously, we introduced a first principles-based transferable force field for CO2 adsorption in siliceous zeolites (Fang et al., J. Phys. Chem. C, 2012, 116, 10692). In this study, we extend our approach to CO2 adsorption in cationic zeolites which possess more complex structures. Na-exchanged zeolites are chosen for demonstrating the approach. These methods account for several structural complexities including Al distribution, cation positions and cation mobility, all of which are important for predicting adsorption. The simulation results are validated with high-resolution experimental measurements of isotherms and microcalorimetric heats of adsorption on well-characterized materials. The choice of first-principles method has a significant influence on the ability of force fields to accurately describe CO2-zeolite interactions. The PBE-D2 derived force field, which performed well for CO2 adsorption in siliceous zeolites, does not do so for Na-exchanged zeolites; the PBE-D2 method overestimates CO2 adsorption energies on multi-cation sites that are common in cationic zeolites with low Si/Al ratios. In contrast, a force field derived from the DFT/CC method performed well. Agreement was obtained between simulation and experiment not only for LTA-4A on which the force field fitting is based, but for other two common adsorbents, NaX and NaY. PMID:23807115

Fang, Hanjun; Kamakoti, Preeti; Ravikovitch, Peter I; Aronson, Matthew; Paur, Charanjit; Sholl, David S

2013-08-21

202

Asymptotic analysis of force-free magnetic fields of cylindrical symmetry  

NASA Technical Reports Server (NTRS)

It is known from computer calculations that if a force-free magnetic-field configuration is stressed progressively by footpoint displacements, the configuration expands and approaches the open configuration with the same surface flux distribution, and, in the process, the energy of the field increases progressively. Analysis of a simple model of force-free fields of cylindrical symmetry leads to simple asymptotic expressions for the extent and energy of such a configuration. The analysis is carried through for both spherical and planar source surfaces. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.

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

1995-01-01

203

Antrag Auf Gerichtliche Entscheidung, §§ 109 ff  

Microsoft Academic Search

\\u000a Die §§ 109 ff. gelten dann, wenn gemäß § 1 Freiheitsstrafe vollzogen wird. Selbst in den relativ wenigen Fällen, in denen\\u000a Freiheitsstrafe im Jugendstrafvollzug vollzogen wird, vgl. § 114 JGG, kann der Gefangene Antrag auf gerichtliche Entscheidung\\u000a gemäß den §§ 109 ff. stellen. Dies folgt u. a. auch aus der Nachrangigkeit des sonst im Jugendstrafvollzug geltenden Rechtsbehelfs\\u000a gemäß § 23

Peter Höflich; Wolfgang Schriever

204

High field-gradient dysprosium tips for magnetic resonance force microscopy  

NASA Astrophysics Data System (ADS)

Magnetic resonance force microscopy (MRFM) is based on measuring the attonewton-scale force between nuclear or electronic spins and a magnetic tip. The force is directly proportional to the magnetic field gradient generated by the tip, making a high moment nanoscale magnet desirable. Dysprosium, with a bulk magnetization 70% higher than iron, is a suitable candidate for such a tip. We have performed MRFM to quantitatively characterize two Dy nanomagnets. We find that magnetic field gradients as high as 6 MT/m (60 G/nm) can be generated, a 40% enhancement compared to our previous FeCo tips.

Mamin, H. J.; Rettner, C. T.; Sherwood, M. H.; Gao, L.; Rugar, D.

2012-01-01

205

Forces  

NSDL National Science Digital Library

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

206

The Pulsation Mode and Distance of the Cepheid FF Aquilae  

NASA Astrophysics Data System (ADS)

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

Turner, D. G.; Kovtyukh, V. V.; Luck, R. E.; Berdnikov, L. N.

2013-07-01

207

THE PULSATION MODE AND DISTANCE OF THE CEPHEID FF AQUILAE  

SciTech Connect

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

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

2013-07-20

208

Magnetooptical force in the resonance field formed by elliptically polarized light waves  

SciTech Connect

The dependence of the magnetooptical force on the ellipticity of the polarization of light beams is studied in terms of a one-dimensional model for closed J{sub g} {sup {yields}} J{sub e} optical transitions. A linear velocity and magnetic-field approximation is used to find analytical expressions for the magnetooptical force for a number of transitions. In the light fields formed by waves with an elliptical polarization, qualitatively new contributions are shown to appear; they have an even dependence on the detuning of the light field and do not disappear even in the case of an exact resonance. An analysis of these results demonstrates that a magnetooptical trap can stably operate at the zero detuning of the field. Numerical methods are used to investigate the nonlinear dependence of the force on the atom velocity and the magnetic field and to estimate the characteristic atom trapping rate and the number of trapped atoms.

Prudnikov, O. N., E-mail: llf@laser.nsc.ru; Taichenachev, A. V.; Tumaikin, A. M.; Yudin, V. I. [Novosibirsk State University (Russian Federation)

2008-05-15

209

Surface and thermodynamic interatomic force fields for silicon clusters and bulk phases  

NASA Astrophysics Data System (ADS)

We have developed new interatomic force fields which describe the phase stability of crystalline silicon and small clusters of silicon. We show that when three-body forces are adjusted to describe ``covalent-->metallic'' phase transitions instead of small-amplitude atomic vibrations, a simple and accurate force field is obtained. This force field can be easily modified to describe energies and structures of Sin vapor-phase clusters. A key aspect of the cluster problem is the transfer of bond strength from dangling bonds to back bonds. We expect our potential will have widespread applications to the formation and activation energies for diffusion of defects in crystalline Si and to the structural properties of amorphous and liquid silicon.

Chelikowsky, James R.; Phillips, J. C.

1990-03-01

210

Atomistic insight into orthoborate-based ionic liquids: force field development and evaluation.  

PubMed

We have developed an all-atomistic force field for a new class of halogen-free chelated orthoborate-phosphonium ionic liquids. The force field is based on an AMBER framework with determination of force field parameters for phosphorus and boron atoms, as well as refinement of several available parameters. The bond and angle force constants were adjusted to fit vibration frequency data derived from both experimental measurements and ab initio calculations. The force field parameters for several dihedral angles were obtained by fitting torsion energy profiles deduced from ab initio calculations. To validate the proposed force field parameters, atomistic simulations were performed for 12 ionic liquids consisting of tetraalkylphosphonium cations and chelated orthoborate anions. The predicted densities for neat ionic liquids and the [P6,6,6,14][BOB] sample, with a water content of approximately 2.3-2.5 wt %, are in excellent agreement with available experimental data. The potential energy components of 12 ionic liquids were discussed in detail. The radial distribution functions and spatial distribution functions were analyzed and visualized to probe the microscopic ionic structures of these ionic liquids. There are mainly four high-probability regions of chelated orthoborate anions distributed around tetraalkylphosphonium cations in the first solvation shell, and such probability distribution functions are strongly influenced by the size of anions. PMID:25020237

Wang, Yong-Lei; Shah, Faiz Ullah; Glavatskih, Sergei; Antzutkin, Oleg N; Laaksonen, Aatto

2014-07-24

211

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

PubMed

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

Savelyev, Alexey; MacKerell, Alexander D

2014-06-19

212

Theoretical prediction of the vibrational spectrum, geometry, and scaled quantum mechanical force field for phenylacetylene  

SciTech Connect

The optimized geometry and the complete harmonic force field of phenylacetylene have been determined by ab initio Hartree-Fock calculations, using a 4-21 Gaussian basis set. Systematic errors in the bond lengths, characteristic at this level of theory, were corrected by empirical offset values. Only at the ipso position does the equilibrium geometry obtained in this way differ significantly from the experimental one (MW; r{sub g}). A detailed analysis suggests that while the experimental ipso CCC angle may be correct, the ipso CC distance should be reconsidered. The force field was evaluated at the above geometry as a reference. To remove systematic deficiencies, the final scaled quantum mechanical (SQM) force field was obtained by applying scale factors optimized previously for benzene and acetylene. All force constants that occur both in phenylacetylene and in the isoelectronic molecule benzonitrile are very nearly the same. Frequencies calculated from the SQM force field of phenylacetylene confirm, with only a few exceptions, the published experimental assignments for all four isotopomers investigated. When the C-H (and C-D) stretching frequencies, perturbed by anharmonicity, are not considered, the average deviation between the observed and calculated frequencies is below 10 cm{sup {minus}1}. Theoretical dipole moment derivatives are discussed, and infrared intensities are presented. Quartic centrifugal distortion constants, calculated also from the SQM force field, agree well with the results of an incomplete experimental study.

Csaszar, A.G.; Fogarasi, G. (Eoetvoes Lorand Univ., Budapest (Hungary)); Boggs, J.E. (Univ. of Texas, Austin (USA))

1989-11-02

213

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

NASA Astrophysics Data System (ADS)

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.

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

2013-03-01

214

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

PubMed

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

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

2014-07-10

215

Determination of constant ? force-free solar magnetic fields from magnetograph data  

Microsoft Academic Search

At first it is shown that a magnetic field being force-free, i.e. satisfying ? × B = aB, with a = constant (a ? 0) in the whole exterior of the Sun cannot have a finite energy content and cannot be determined uniquely from only one magnetic field component given at the photosphere. Then the boundary value problem for a

N. Seehafer

1978-01-01

216

FIELD WINDING DRAG AND NORMAL FORCES OF LINEAR SYNCHRONOUS HOMOPOLAR MOTORS  

Microsoft Academic Search

Drag and normal forces caused by the homopolar field winding in a linear synchronous homopolar motor (LSHM), having a segmented secondary of solid iron, are calculated. The analysis is based on the electromagnetic field theory. Numerical results are computed and some experimental results are also given. It is concluded that solid iron segmented secondary is suitable for high speeds (100

I. BOLDEA; S. A. NASAR

1978-01-01

217

Characteristics of the convection of a conducting fluid in a complementary field of external forces  

NASA Astrophysics Data System (ADS)

The propagation of vortex perturbations in a conducting fluid along the induction vector of a constant magnetic field is investigated experimentally. In particular, an analysis is made of the formation of roll convective flows due to the magnetic field and Coriolis forces. The processes occurring at the intersection of roll structures with the surface of a rotating sphere are examined.

Mikel'Son, A. E.; Karklin', Ia. Kh.

1987-03-01

218

Characteristics of convection of an electrically conducting liquid in an additional external force field  

SciTech Connect

The authors analyze, theoretically and experimentally, the combined effects of gravitational and electric fields along with inertial forces on convective heat and mass transfer in liquid metals undergoing vortex flow in the presence of constant magnetic fields. The experimental data are derived for a eutectic indium-gallium-tin alloy. The flow model incorporates electrical conductivity and Hartmann number as well as other properties.

Mikel'son, A.E.; Karklin, Ya.Kh.

1987-07-01

219

Electrostatic Force Microscopy Study of the Electric Field Distribution in Semiconductor Laser Diodes Under Applied Biases.  

National Technical Information Service (NTIS)

In conclusion we present a new and direct electrostatic force microscopy method to resolve the electric field and capacitance distributions in laser diodes. Using this method we have investigated the fine structure of the electric field in AlGaAs/GaAs and...

A. Ankudinov A. Titkov D. Livshiz E. Kotelnikov V. Evtikhiev

2001-01-01

220

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase  

SciTech Connect

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

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

2012-05-09

221

Relativistic mean field model based on realistic nuclear forces  

SciTech Connect

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

Hirose, S.; Serra, M. [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Ring, P. [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Physik department, Technische Universitaet Muenchen, Garching (Germany); Otsuka, T. [Department of Physics, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Center for Nuclear Study, University of Tokyo, Hongo, Bunkyoku, Tokyo 113-0033 (Japan); RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 (Japan); Akaishi, Y. [RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 (Japan); Nihon University, Funabashi-shi, Chiba 274-8501 (Japan)

2007-02-15

222

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

PubMed

This study aims to clarify the mechanism of generating unsteady hydrodynamic forces acting on a hand during swimming in order to directly measure the forces, pressure distribution, and flow field around the hand by using a robotic arm and particle image velocimetry (PIV). The robotic arm consisted of the trunk, shoulder, upper arm, forearm, and hand, and it was independently computer controllable in five degrees of freedom. The elbow-joint angle of the robotic arm was fixed at 90°, and the arm was moved in semicircles around the shoulder joint in a plane perpendicular to the water surface. Two-component PIV was used for flow visualization around the hand. The data of the forces and pressure acting on the hand were sampled at 200Hz and stored on a PC. When the maximum resultant force acting on the hand was observed, a pair of counter-rotating vortices appeared on the dorsal surface of the hand. A vortex attached to the hand increased the flow velocity, which led to decreased surface pressure, increasing the hydrodynamic forces. This phenomenon is known as the unsteady mechanism of force generation. We found that the drag force was 72% greater and the lift force was 4.8 times greater than the values estimated under steady flow conditions. Therefore, it is presumable that swimmers receive the benefits of this unsteady hydrodynamic force. PMID:23764175

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

2013-07-26

223

Development of AMOEBA Force Field for 1,3-Dimethylimidazolium Based Ionic Liquids.  

PubMed

The development of AMOEBA (a multipolar polarizable force field) for imidazolium based ionic liquids is presented. Our parametrization method follows the AMOEBA procedure and introduces the use of QM intermolecular total interactions as well as QM energy decomposition analysis (EDA) to fit individual interaction energy components. The distributed multipoles for the cation and anions have been derived using both the Gaussian distributed multipole analysis (GDMA) and Gaussian electrostatic model-distributed multipole (GEM-DM) methods.1 The intermolecular interactions of a 1,3-dimethylimidazolium [dmim(+)] cation with various anions, including fluoride [F(-)], chloride [Cl(-)], nitrate [NO3(-)], and tetraflorouborate [BF4(-)], were studied using quantum chemistry calculations at the MP2/6-311G(d,p) level of theory. Energy decomposition analysis was performed for each pair using the restricted variational space decomposition approach (RVS) at the HF/6-311G(d,p) level. The new force field was validated by running a series of molecular dynamic (MD) simulations and by analyzing thermodynamic and structural properties of these systems. A number of thermodynamic properties obtained from MD simulations were compared with available experimental data. The ionic liquid structure reproduced using the AMOEBA force field is also compared with the data from neutron diffraction experiment and other MD simulations. Employing GEM-DM force fields resulted in a good agreement on liquid densities ?, enthalpies of vaporization ?Hvap, and diffusion coefficients D± in comparison with conventional force fields. PMID:24901255

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

2014-06-26

224

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

PubMed Central

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

Perez, Alberto; Marchan, Ivan; Svozil, Daniel; Sponer, Jiri; Cheatham, Thomas E.; Laughton, Charles A.; Orozco, Modesto

2007-01-01

225

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign  

PubMed Central

We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20–50% of the ordered structures with three force fields, but not with a fourth. A defining feature of the misfold is that Gly-7 adopts a ?PR conformation rather than ?L. By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for ?PR is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to the wild-type and does not populate the misfolded state in simulation. Our results highlight the complexity of interpreting NMR data for small, weakly structured, peptides in solution, as well as the importance of accurate glycine parameters in force fields, for a correct description of turn structures.

Kuhrova, Petra; De Simone, Alfonso; Otyepka, Michal; Best, Robert B.

2012-01-01

226

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

NASA Astrophysics Data System (ADS)

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

Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

2004-12-01

227

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

SciTech Connect

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

Sorin Zaharia; C.Z. Cheng

2002-06-18

228

Comparative study of energetic materials by classical interatomic potential ReaxFF and first-principles density functional theory  

NASA Astrophysics Data System (ADS)

Prediction of properties of energetic materials using atomic-scale simulations techniques is one of the challenging areas of energetic materials (EM) research. Molecular dynamics (MD) simulation of EM using classical reactive interatomic potentials is a powerful modeling technique that is capable of addressing sub-nanometer and sub-picosecond length and time scales of shock compression and detonation phenomena. However, the results of computer simulations can only be as reliable as the ability of the interatomic potentials to describe properly a variety of chemical effects including bond-breaking and bond-making. Recently, the reactive force field ReaxFF has been developed based on fitting of an ab-initio database of HCNO chemistry and is currently being actively used for MD simulations of EM. We performed a comparative study of static and thermodynamic properties of PETN, RDX and HMX using both density functional theory (DFT) and ReaxFF including static properties of different crystalline phases and equation of states (EOS). The transferability issues are discussed in the region of physical parameters relevant for MD simulation of initial decomposition and detonation in EM.

Oleynik, Ivan; Zybin, Sergey

2005-07-01

229

Tethyan collision forces and the stress field of the Eurasian Plate  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

230

Modeling of Gamma-Ray Pulsar Light Curves with Force-Free Magnetic Field  

Microsoft Academic Search

(Abridged) Gamma-ray emission from pulsars has long been modeled using a\\u000avacuum dipole field. This approximation ignores changes in the field structure\\u000acaused by the magnetospheric plasma and strong plasma currents. We present the\\u000afirst results of gamma-ray pulsar light curve modeling using the more realistic\\u000afield taken from 3D force-free magnetospheric simulations. Having the geometry\\u000aof the field, we

Xue-Ning Bai; Anatoly Spitkovsky

2009-01-01

231

Computing Nonlinear Force-Free Coronal Magnetic Fields in Spherical Geometry  

Microsoft Academic Search

We describe a newly developed code for the extrapolation of nonlinear force-free coronal magnetic fields in spherical coordinates.\\u000a The program uses measured vector magnetograms on the solar photosphere as input and solves the force-free equations in the\\u000a solar corona. The method is based on an optimization principle and the heritage of the newly developed code is a corresponding\\u000a method in

T. Wiegelmann

2007-01-01

232

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

DOEpatents

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

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

1991-04-09

233

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

DOEpatents

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

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

1991-01-01

234

On the numerical computation of nonlinear force-free magnetic fields. [from solar photosphere  

NASA Technical Reports Server (NTRS)

An algorithm has been developed to extrapolate nonlinear force-free magnetic fields from the photosphere, given the proper boundary conditions. This paper presents the results of this work, describing the mathematical formalism that was developed, the numerical techniques employed, and comments on the stability criteria and accuracy developed for these numerical schemes. An analytical solution is used for a benchmark test; the results show that the computational accuracy for the case of a nonlinear force-free magnetic field was on the order of a few percent (less than 5 percent). This newly developed scheme was applied to analyze a solar vector magnetogram, and the results were compared with the results deduced from the classical potential field method. The comparison shows that additional physical features of the vector magnetogram were revealed in the nonlinear force-free case.

Wu, S. T.; Sun, M. T.; Chang, H. M.; Hagyard, M. J.; Gary, G. A.

1990-01-01

235

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

NASA Astrophysics Data System (ADS)

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

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

1995-01-01

236

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

PubMed

The predictive power of biomolecular simulation critically depends on the quality of the force field or molecular model used and on the extent of conformational sampling that can be achieved. Both issues are addressed. First, it is shown that widely used force fields for simulation of proteins in aqueous solution appear to have rather different propensities to stabilize or destabilize ?-, ?-, and 310- helical structures, which is an important feature of a biomolecular force field due to the omni-presence of such secondary structure in proteins. Second, the relative stability of secondary structure elements in proteins can only be computationally determined through so-called free-energy calculations, the accuracy of which critically depends on the extent of configurational sampling. It is shown that the method of enveloping distribution sampling is a very efficient method to extensively sample different parts of configurational space. PMID:24410325

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

2014-06-19

237

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

NASA Astrophysics Data System (ADS)

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

Lekner, John

2013-12-01

238

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

PubMed

The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR-UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase. PMID:24620905

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

2014-06-19

239

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

NASA Astrophysics Data System (ADS)

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

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

2000-01-01

240

A regularization method for the extrapolationbreak of the photospheric solar magnetic field. I. Linear force-free field  

Microsoft Academic Search

We present a method for reconstructing the magnetic field B above the photosphere \\\\{z=0\\\\} as the solution of the boundary value problem (BVP) for a bounded regular force-free magnetic field in Omega =\\\\{z>0\\\\} from its boundary values supposed to be given on \\\\{z=0\\\\}. We propose a way for regularizing the class of standard extrapolation methods which turns out to diverge

T. Amari; T. Z. Boulmezaoud; Y. Maday

1998-01-01

241

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

242

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

NASA Astrophysics Data System (ADS)

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

Iwata, Natsumi; Kishimoto, Yasuaki

2014-01-01

243

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

PubMed

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

Iwata, Natsumi; Kishimoto, Yasuaki

2014-01-24

244

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

SciTech Connect

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

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

2013-05-10

245

The force field equation for the propagation of galactic cosmic rays applied to neutron monitor measurements  

NASA Astrophysics Data System (ADS)

The modulation of galactic cosmic rays is described in terms of a generalized force-field equation for a mixture of particles to which a neutron monitor is sensitive. The force-field solution is used to derive the modulation parameters from observations inside the atmosphere in an energy region well above the effective high-energy limit of satellite observations. The parameters are calculated in the rigidity range from about 2 to 15 GV and provide statistically accurate extensions in rigidity to existing results. The limitations of the modified convection-diffusion approximation for modulation studies in the rigidity range from about 2 to 15 GV are indicated.

Moraal, H.; Stoker, P. H.; Henning, J. J.

1974-11-01

246

On the numerical computation of nonlinear force-free magnetic fields  

NASA Technical Reports Server (NTRS)

An algorithm has been developed to extrapolate nonlinear force-free magnetic fields from a source surface, given the proper boundary conditions. The results of this work; describing the mathematical formalism that was developed, the numerical techniques employed, and the stability criteria developed for these numerical schemes are presented. An analytical solution is used for a test case; the results show that the computational accuracy for the case of a nonlinear force-free magnetic field was on the order of a few percent ( 5%).

Wu, S. T.; Chang, H. M.; Hagyard, M. J.

1985-01-01

247

A first-principles based force-field for Li+ and OH- in ethanolic solution  

NASA Astrophysics Data System (ADS)

We report on the development of force-field parameters for accurately modeling lithium and hydroxide ions in ethanol in solution. Based on quantum calculations of small molecular clusters mimicking the solvent structure of individual ions as well as the solvated LiOH dimer, significant improvements of off-the-shelf force-fields are obtained. The quality of our model is demonstrated by comparison to ab initio molecular dynamics of the bulk solution and to experimental data available for ethanol/water mixtures.

Milek, Theodor; Meyer, Bernd; Zahn, Dirk

2013-10-01

248

Transferability of Coarse-Grained Force Field for nCB Liquid Crystal Systems.  

PubMed

In this paper, the transferability of the coarse-grained (CG) force field originally developed for the liquid crystal (LC) molecule 5CB ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 2075 - 2089 ) was investigated by its homologues 6CB and 8CB molecules. Note that, to construct the 5CB CG force field, we combined the structure-based and thermodynamic quantities-based methods and at the same time attempted to use several fragment molecular systems to derive the CG nonbonded interaction parameters. The resultant 5CB CG force field exhibits a good transferability to some extent. For example, not only the experimental densities, the local packing of atom groups, and the antiparallel arrangements of nearest neighboring molecules, but also the unique LC mesophases as well as the nematic-isotropic phase transition temperatures of 6CB and 8CB were reproduced. Meanwhile, the limitations of this 5CB CG force field were also observed, such as the phase transition from nematic to smectic was postponed to the lower temperature and the resulting smectic phase structure is single-layer-like instead of partially interdigitated bilayer-like as observed in underlying atomistic model. Apparently, more attention should be paid when applying a CG force field to the state point which is quite different from which the force field is explicitly parametrized for. The origin of the above limitations can be potentially traced back to the inherent simplifications and some approximations often adopted in the creation process of CG force field, for example, choosing symmetric CG potentials which do not explicitly include electrostatic interactions and are parametrized by reproducing the target properties of the specific nematic 5CB phase at 300 K and 1 atm, as well as using soft nonbonded potential and excluding torsion barriers. Moreover, although by construction this CG force field could inevitably incorporate both thermodynamic and local structural information on the nematic 5CB phase, the anisotropic diffusion coefficient ratios for different LC phases in both 6CB and 8CB systems are reproduced well. All these findings suggest that the multiproperty parametrization route together with fragment-based method provides a new approach to maximize the possibility to simultaneously reproduce multiple physical properties of a given molecule or related molecules with similar chemical structures at other state points. PMID:24712306

Zhang, Jianguo; Guo, Hongxia

2014-05-01

249

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

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

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

250

A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins  

PubMed Central

Herein we introduce a novel practical strategy to overcome the well-known challenge of modeling the divalent zinc cation in metalloproteins. The main idea is to design short-long effective functions (SLEF) to describe charge interactions between the zinc ion and all other atoms. This SLEF approach has the following desired features: (1). It is pairwise, additive and compatible with widely used atomic pair-wise force fields for modeling biomolecules; (2). It only changes interactions between the zinc ion and other atoms, and does not affect force field parameters that model other interactions in the system; (3). It is a non-bonded model that is inherently capable to describe different zinc ligands and coordination modes. By optimizing two SLEF parameters as well as zinc vdW parameters through force matching based on Born-Oppenheimer ab initio QM/MM molecular dynamics simulations, we have successfully developed the first SLEF force field (SLEF1) to describe zinc interactions. Extensive molecular dynamics simulations of seven zinc enzyme systems with different coordination ligands and distinct chelation modes (4-,5-,6-fold), including the binuclear zinc active site, yielded zinc coordination numbers and binding distances in good agreement with the corresponding crystal structures as well as ab initio QM/MM MD results. This not only demonstrates the transferability and adequacy of the new SLEF1 force field in describing a variety of zinc proteins, but also indicates that this novel SLEF approach is a promising direction to explore for improving force field description of metal ion interactions.

Wu, Ruibo; Lu, Zhenyu; Cao, Zexing; Zhang, Yingkai

2010-01-01

251

Effects of speeds and force fields on submovements during circular manual tracking in humans.  

PubMed

Complex limb movements exhibit segmentation into submovements characterized as bell-shaped speed pulses. Submovements have been implicated in both feedback and feedforward control, reflecting an intermittent error-correction process. This study examines submovements occurring during a circular manual tracking task in humans, focusing on the amplitude-duration scaling of submovements and the properties of this scaling across changes in movement speed and external force load. The task consisted of intercepting and tracking a circularly moving target using a two-jointed, robotic arm that allowed external force fields to be imposed during tracking. Different speed levels and different levels of three types of force field were examined. Submovements were defined as fluctuations in the speed profile. The properties of the amplitude-duration ratio of the speed pulses were examined in relation to target speed and external force fields. The results show that the amplitude and duration of the submovements scale linearly in human manual tracking. The slope of the scaling was independently influenced by both target speed and external force fields. A common element in the increase in the scaling slope was increased tracking errors. Control experiments using passive movements and power spectral analysis showed that the submovements were not artifacts of the mechanical/acquisition system or the imposed force field. These results are consistent with the concept of stereotypy in which movements are constructed of scaled versions of a single prototype. Furthermore, the results support the hypothesis that submovements are integral to an error detection and correction control process. PMID:15668793

Pasalar, S; Roitman, A V; Ebner, T J

2005-05-01

252

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields  

PubMed Central

All-atom molecular dynamics simulations have been applied in the recent past to explore the free energetics underlying ion transport processes in biological ion channels. Roux and co-workers, Kuyucak and coworkers, Busath and coworkers, and others have performed rather elegant and extended timescale molecular dynamics simulations using current state-of-the-art fixed-charge (non-polarizable) force fields in order to calculate the potential of mean force defining the equilibrium flux of ions through prototypical channels such as Gramicidin A. An inescapable conclusion of such studies has been the gross overestimation of the equilibrium free energy barrier, generally predicted to be from 10 – 20 kcal/mole depending on the force field and simulation protocol used in the calculation; this translates to an underestimation of experimentally measurable single channel conductances by several orders of magnitude. Next-generation polarizable force fields have been suggested as possible alternatives for more quantitative predictions of the underlying free energy surface in such systems1. Presently, we consider ion permeation energetics in the gramicidin A channel using a novel polarizable force field. Our results predict a peak barrier height of 6 kcal/mole relative to the channel entrance; this is significantly lower than the uncorrected value of 12 kcal/mol for non-polarizable force fields such as GROMOS and CHARMM27 which do not account for electronic polarization. These results provide promising initial indications substantiating the long-conjectured importance of polarization effects in describing ion-protein interactions in narrow biological channels.

Patel, Sandeep; Davis, Joseph E.; Bauer, Brad A.

2009-01-01

253

A SELF-CONSISTENT NONLINEAR FORCE-FREE SOLUTION FOR A SOLAR ACTIVE REGION MAGNETIC FIELD  

SciTech Connect

Nonlinear force-free solutions for the magnetic field in the solar corona constructed using photospheric vector magnetic field boundary data suffer from a basic problem: the observed boundary data are inconsistent with the nonlinear force-free model. Specifically, there are two possible choices of boundary conditions on vertical current provided by the data, and the two choices lead to different force-free solutions. A novel solution to this problem is described. Bayesian probability is used to modify the boundary values on current density, using field-line connectivity information from the two force-free solutions and taking into account uncertainties, so that the boundary data are more consistent with the two nonlinear force-free solutions. This procedure may be iterated until a set of self-consistent boundary data (the solutions for the two choices of boundary conditions are the same) is achieved. The approach is demonstrated to work in application to Hinode/Solar Optical Telescope observations of NOAA active region 10953.

Wheatland, M. S. [Sydney Institute for Astronomy, School of Physics, University of Sydney, NSW 2006 (Australia); Regnier, S. [School of Mathematics and Statistics, University of St Andrews, St Andrews, Fife KY16 9SS (United Kingdom)], E-mail: m.wheatland@physics.usyd.edu.au, E-mail: stephane@mcs.st-andrews.ac.uk

2009-08-01

254

Force field inside the void in complex plasmas under microgravity conditions  

SciTech Connect

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

Kretschmer, M.; Khrapak, S.A.; Zhdanov, S.K.; Thomas, H.M.; Morfill, G.E.; Fortov, V.E.; Lipaev, A.M.; Molotkov, V.I.; Ivanov, A.I.; Turin, M.V. [Centre for Interdisciplinary Plasma Science, Max-Planck-Institut fuer extraterrestrische Physik, D-85741 Garching (Germany); Institute for High Energy Densities, Russian Academy of Sciences, Izhorskaya 13/19, 125412 Moscow (Russian Federation); RSC 'Energia' Korolev, 141070 Moscow Region (Russian Federation)

2005-05-01

255

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

NASA Astrophysics Data System (ADS)

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

Denisov, S. I.; Horsthemke, Werner

2000-09-01

256

Nonlinear force-free reconstruction of the global solar magnetic field: methodology  

Microsoft Academic Search

We present a novel numerical method that allows the calculation of nonlinear\\u000aforce-free magnetostatic solutions above a boundary surface on which only the\\u000adistribution of the normal magnetic field component is given. The method relies\\u000aon the theory of force-free electrodynamics and applies directly to the\\u000areconstruction of the solar coronal magnetic field for a given distribution of\\u000athe photospheric

Ioannis Contopoulos; Constantinos Kalapotharakos; Manolis Georgoulis

2010-01-01

257

Dilation of force-free magnetic flux tubes. [solar magnetic field profiles  

NASA Technical Reports Server (NTRS)

A general study is presented of the mapping functions which relate the magnetic-field profiles across a force-free rope in segments subjected to various external pressures. The results reveal that if the external pressure falls below a certain critical level (dependent on the flux-current relation which defines the tube), the magnetic profile consists of an invariant core sheathed in a layer permeated by an azimuthal magnetic field.

Frankenthal, S.

1977-01-01

258

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

ERIC Educational Resources Information Center

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

Veto, B.

2011-01-01

259

Active Contour External Force Using Vector Field Convolution for Image Segmentation  

Microsoft Academic Search

Snakes, or active contours, have been widely used in image processing applications. Typical roadblocks to consistent performance include limited capture range, noise sensitivity, and poor convergence to concavities. This paper proposes a new external force for active contours, called vector field convolution (VFC), to address these problems. VFC is calculated by convolving the edge map generated from the image with

Bing Li; Scott T. Acton

2007-01-01

260

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

SciTech Connect

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

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

1991-11-28

261

Making optimal use of empirical energy functions: force-field parameterization in crystal space.  

PubMed

Today's energy functions are not able yet to distinguish reliably between correct and almost correct protein models. Improving these near-native models is currently a major bottle-neck in homology modeling or experimental structure determination at low resolution. Increasingly accurate energy functions are required to complete the "last mile of the protein folding problem," for example during a molecular dynamics simulation. We present a new approach to reach this goal. For 50 high resolution X-ray structures, the complete unit cell was reconstructed, including disordered water molecules, counter ions, and hydrogen atoms. Simulations were then run at the pH at which the crystal was solved, while force-field parameters were iteratively adjusted so that the damage done to the structures was minimal. Starting with initial parameters from the AMBER force field, the optimization procedure converged at a new force field called YAMBER (Yet Another Model Building and Energy Refinement force field), which is shown to do significantly less damage to X-ray structures, often move homology models in the right direction, and occasionally make them look like experimental structures. Application of YAMBER during the CASP5 structure prediction experiment yielded a model for target 176 that was ranked first among 150 submissions. Due to its compatibility with the well-established AMBER format, YAMBER can be used by almost any molecular dynamics program. The parameters are freely available from www.yasara.org/yamber. PMID:15390263

Krieger, Elmar; Darden, Tom; Nabuurs, Sander B; Finkelstein, Alexei; Vriend, Gert

2004-12-01

262

Assessment of lower extremity motor adaptation via an extension of the Force Field Adaptation Paradigm  

Microsoft Academic Search

Lower extremity rehabilitation has seen recent increased interest. New tools are available to improve gait retraining in both adults and children. However, it remains difficult to determine optimal ways to plan interventions due to difficulties in continuously monitoring outcomes in patients undergoing rehabilitation. In this paper, we introduce an extension of the Force Field Adaptation Paradigm, used to quantitatively assess

Iahn Cajigas; Mary T. Goldsmith; Alexander Duschau-Wicke; Robert Riener; Maurice A. Smith; Emery N. Brown; Paolo Bonato

2010-01-01

263

Electromagnetic response of nanosphere pairs: Collective plasmon resonances, enhanced fields, and laser-induced forces  

Microsoft Academic Search

We present theoretical studies of the electromagnetic response of metallic nanosphere pairs, with emphasis on the role of their collective plasmon resonances in enhancing electromagnetic fields in their near vicinity, and also in enhancing laser-induced forces between the particles. We emphasize effects encountered when the two particles have dissimilar radii or are fabricated from dissimilar materials. The calculations explore the

Ping Chu; D. L. Mills

2008-01-01

264

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

EPA Science Inventory

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

265

Hydrogen bonding of DNA base pairs by consistent charge equilibration method combined with universal force field  

Microsoft Academic Search

By combining the consistent charge equilibration (CQEq) method with universal force field (UFF), we developed the CQEq with UFF (CUFF) method and confirmed its efficiency for investigating the hydrogen bonding of DNA base pairs. By using the new parameters together with reduced van der Waals radii for hydrogen atoms, the CUFF method was capable of yielding hydrogen-bonding lengths and energies

Tetsuji Ogawa; Noriyuki Kurita; Hideo Sekino; Osamu Kitao; Shigenori Tanaka

2003-01-01

266

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

USGS Publications Warehouse

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

Lee, M. W.; Meuwly, M.

2013-01-01

267

Classical diffusion of a particle in a one-dimensional random force field.  

National Technical Information Service (NTIS)

We present a comprehensive study of the motion of a damped Brownian particle evolving in a static, one dimensional gaussian random force field. We provide both a clear physical picture of the process and a variety of analytical techniques. As the average ...

J. P. Bouchaud A. Comtet A. Georges P. Le Doussal P. Le Doussal

1989-01-01

268

Decision support for the career field selection process at the US Air Force Academy  

Microsoft Academic Search

Each year, the US Air Force Academy graduates nearly 1000 young men and women. To support the decision of which cadets will be classified into which career fields, we describe a linear programming formulation with appealing computational properties that enable it as the core of a decision support tool. We explore methods for measuring and balancing cadets' class standing, Air

Andrew P. Armacost; James K. Lowe

2005-01-01

269

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

PubMed

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories. PMID:24170171

Lee, Myung Won; Meuwly, Markus

2013-12-14

270

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains.  

PubMed

To establish force-field-based (molecular) modeling capability that will accurately predict condensed-phase thermophysical properties for materials containing aliphatic azide chains, potential parameters for atom types unique to such chains have been developed and added to the COMPASS force field. The development effort identified the need to define four new atom types: one for each of the three azide nitrogen atoms and one for the carbon atom bonded to the azide. Calculations performed with the expanded force field yield (gas-phase) molecular structures and vibrational frequencies for hydrazoic acid, azidomethane, and the anti and gauche forms of azidoethane in good agreement with values determined experimentally and/or through computational quantum mechanics. Liquid densities calculated via molecular dynamics (MD) simulations were also in good agreement with published values for 13 of 15 training set compounds, the exceptions being hydrazoic acid and azidomethane. Of the 13 compounds whose densities are well simulated, nine have experimentally determined heats of vaporization reported in the open literature, and in all of these cases, MD simulated values for this property are in reasonable agreement with the published values. Simulations with the force field also yielded reasonable density estimates for a series of 2-azidoethanamines that have been synthesized and tested for use as hydrazine-alternative fuels. PMID:14634994

McQuaid, Michael J; Sun, Huai; Rigby, David

2004-01-15

271

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

ERIC Educational Resources Information Center

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

Mason, Elisa

1999-01-01

272

Limitations of the force field equation to describe cosmic ray modulation  

Microsoft Academic Search

The force field approximation to the transport equation which describes cosmic ray modulation in the heliosphere is a widely used tool. It is popular because it provides an easy to use, quasi-analytical method to describe the level of modulation with a single parameter. A simple numerical solution of the one-dimensional cosmic ray transport equation is used to show that this

R. A. Caballero-Lopez; H. Moraal

2004-01-01

273

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

SciTech Connect

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

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

2010-03-15

274

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

NASA Astrophysics Data System (ADS)

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

Asfaw, Tilaye Tadesse; Pevtsov, Alexei A.; Macneice, Peter J.

2014-06-01

275

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

PubMed

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices. PMID:24952518

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

2014-06-21

276

An improved DNA force field for ssDNA interactions with gold nanoparticles  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

277

Enzymatic degradation of neuropeptide FF and SQA-neuropeptide FF in the mouse brain  

Microsoft Academic Search

Degradation of neuropeptide FF (NPFF) and SQA-neuropeptide FF (SQA-NPFF) by mouse brain sections was investigated by using capillary electrophoresis with UV detection for the separation and the identification of the degradation products. The half disappearance time of SQA-NPFF was 2-fold greater than that of NPFF. NPFF was cleaved preferentially into an inactive metabolite, Gln-Arg-Phe-NH2, in the cerebrum slices. SQA-NPFF was

J. C. Sol; A. Roussin; S. Proto; H. Mazarguil; J. M. Zajac

1999-01-01

278

On the Force-free Nature of Photospheric Sunspot Magnetic Fields as Observed from Hinode (SOT/SP)  

NASA Astrophysics Data System (ADS)

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

Tiwari, Sanjiv Kumar

2012-01-01

279

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.  

PubMed

Hydration free energy calculations are often used to validate molecular simulation methodologies and molecular mechanics force fields. We use the free-energy perturbation method together with the AMOEBA polarizable force field and the Poltype parametrization protocol to predict the hydration free energies of 52 molecules as part of the SAMPL4 blind challenge. For comparison, similar calculations are performed using the non-polarizable General Amber force field. Against our expectations, the latter force field gives the better results compared to experiment. One possible explanation is the sensitivity of the AMOEBA results to the conformation used for parametrization. PMID:24577872

Manzoni, Francesco; Söderhjelm, Pär

2014-03-01

280

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

NASA Technical Reports Server (NTRS)

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

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

1995-01-01

281

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

282

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

283

Evaluation of Electromagnetic Force and Magnetic Laval Nozzle Acceleration in an Applied-Field MPD Thruster  

NASA Astrophysics Data System (ADS)

A magneto-plasma-dynamic thruster (MPDT) is expected as one of the promising electric propulsion systems owing to features of a relatively large thrust, high specific impulse that is unattainable by conventional chemical or nuclear propulsion required for space missions such as a manned Mars mission. To clarify the electromagnetic acceleration mechanism of a plasma flow in an applied-field MPDT, detailed flow field and electromagnetic force field are evaluated experimentally with spectroscopic technique and magnetic probe array. It is found that an axial drag force generated by an interaction between azimuthal plasma current and radial magnetic field cancels an acceleration force in a uniform magnetic field. A thermal energy component is much larger than a flow energy component in Bernoulli's equation and ion acoustic Mach number is limited less than unity in the muzzle region of MPD arcjet. In order to convert the thermal energy to the flow energy, magnetic Laval nozzle acceleration with a local magnetic coil is attempted. The ion Mach number after passing through the nozzle throat exceeds unity and a production of supersonic plasma flow is achieved. An optimum magnetic nozzle configuration is discussed with the experimental results.

Tobari, Hiroyuki; Sato, Ryuichi; Harata, Kenji; Hattori, Kunihiko; Ando, Akira; Inutake, Masaaki

2003-10-01

284

The AM1-FF Calculations of the Second Hyperpolarizabilities of Fullerenes and the Curvature  

NASA Astrophysics Data System (ADS)

By taking AM1 semiempirical quantum chemical calculations coupled with the finite field (FF) method, the second hyperpolarizabilities of higher fullerenes, C76, C78, C80, can be calculated efficiently. The structural factor, curvature, has also been explored in the higher fullerenes for their second hyperpolarizabilities.

Lin, Ying-Ting; Lee, Shyi-Long

2009-08-01

285

NONLINEAR FORCE-FREE MODELING OF MAGNETIC FIELDS IN A SOLAR FILAMENT  

SciTech Connect

We present a striking filament pattern in the nonlinear force-free (NLFF) chromospheric magnetic field of the active region NOAA 10956. The NLFF chromospheric field is extrapolated from the Hinode high-resolution photospheric vector magnetogram using the weighted optimization method. The modeled structure is characterized by a highly sheared field with strong horizontal magnetic components and has a virtually identical shape and location as the filament seen in H{alpha}. The modeled field strength agrees with the recent He I 10830 A observations by Kuckein et al.. The unequivocal resemblance between the NLFF extrapolation and the H{alpha} observation not only demonstrates the ability of the NLFF field to reproduce chromospheric features, but also provides a valuable diagnostic tool for the filament magnetic fields.

Jing Ju; Yuan Yuan; Xu Yan; Liu Rui; Wang Haimin [Space Weather Research Laboratory, New Jersey Institute of Technology, Newark, NJ 07102 (United States); Wiegelmann, Thomas, E-mail: ju.jing@njit.ed, E-mail: yy46@njit.ed, E-mail: yx2@njit.ed, E-mail: rui.liu@njit.ed, E-mail: haimin@flare.njit.ed, E-mail: wiegelmann@linmpi.mpg.d [Max Planck Institut fuer Sonnensystemforschung (MPS), Max-Planck-Strasse 2, 37191 Katlenburg-Lindau (Germany)

2010-08-10

286

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

NASA Astrophysics Data System (ADS)

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

Eminov, P. A.

2013-10-01

287

Near-Field Optical Forces: Photonics, Plasmonics and the Casimir Effect  

NASA Astrophysics Data System (ADS)

The coupling of macroscopic objects via the optical near-field can generate strong attractive and repulsive forces. Here, I explore the static and dynamic optomechanical interactions that take place in a geometry consisting of a silicon nanomembrane patterned with a square-lattice photonic crystal suspended above a silicon-on-insulator substrate. This geometry supports a hybridized optical mode formed by the coupling of eigenmodes of the membrane and the silicon substrate layer. This system is capable of generating nanometer-scale deflections at low optical powers for membrane-substrate gaps of less than 200 nm due to the presence of an optical cavity created by the photonic crystal that enhances both the optical force and a force that arises from photo-thermal-mechanical properties of the system. Feedback between Brownian motion of the membrane and the optical and photo-thermal forces lead to dynamic interactions that perturb the mechanical frequency and linewidth in a process known as ``back-action.'' The static and dynamic properties of this system are responsible for optical bistability, mechanical cooling and regenerative oscillations under different initial conditions. Furthermore, solid objects separated by a small distance experience the Casimir force, which results from quantum fluctuations of the electromagnetic field (i.e. virtual photons).The Casimir force supplies a strong nonlinear perturbation to membrane motion when the membrane-substrate separation is less than 150 nm. Taken together, the unique properties of this system makes it an intriguing candidate for transduction, accelerometry, and sensing applications. Second, near field optical forces were explored in two geometries involving surface plasmons. The first looked at the forces generated between two plasmonic waveguides at visible frequencies where flat metallic surfaces support tightly confined interface waves and at mid-infrared frequencies, where surface corrugations allow the propagation of surface waves known as ``spoof'' surface plasmons. The second involves the generation of a repulsive force on a low refractive index particle in a high refractive index fluid above a metal surface. This second geometry opens up a potential new avenue for frictionless waveguiding and the study of chemical and biological binding processes where it is desirable to have surfaces in the proximity of one another but not in contact.

Woolf, David Nathaniel

288

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

SciTech Connect

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

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

2012-01-01

289

Molecular dynamics simulation of tri-n-butyl-phosphate liquid: a force field comparative study.  

PubMed

Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has been demonstrated that the electric dipole moment can be approximated within 1% of the average experimental value by virtue of scaled atomic partial charges. The liquid mass density can be predicted within 0.5-1% of its experimentally determined value when using the corresponding charge scaling. However, in all cases, the predicted self-diffusion coefficient is significantly smaller than a commonly quoted experimental measurement; this result is qualified by the fact that the uncertainty of the experimental value was not available. PMID:22126596

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

2012-01-12

290

Inclusion of charge and polarizability fluxes provides needed physical accuracy in molecular mechanics force fields  

NASA Astrophysics Data System (ADS)

Physical accuracy in MM calculations requires maximally correct forces in addition to structures and energies. This requires inclusion of charge and polarizability fluxes in the energy function. Using our spectroscopically determined force field, which is designed to include these, we present three examples of the improved physical predictions that result from the incorporation of charge fluxes: the reproduction of the water angle opening on going from the isolated molecule to the liquid, the reproduction of the ? peptide torsion potential with only a single threefold (almost zero barrier) Fourier term, and reproduction of the quantum-mechanical MD ?, ? map of a dipeptide analog.

Palmo, Kim; Mannfors, Berit; Mirkin, Noemi G.; Krimm, Samuel

2006-10-01

291

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

NASA Technical Reports Server (NTRS)

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

Aly, J. J.

1984-01-01

292

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

Microsoft Academic Search

The Fourier transform infrared (FTIR) and Raman spectra of 2-amino-4-nitro-toluene; 2-amino-5-nitrotoluene; 2,4-dimethylaniline; 2,5-dimethylaniline; 2,6-dimethylaniline; 1,2,4-trimethylbenzene; 1,3,5-trimethylbenzene and pentamethyl-benzene have been recorded in the range 4000-400 Cm-1 and 4000-30 Cm-1, respectively. A normal coordinate analysis was carried out for both in-plane and out-of-plane vibrations of these molecules using an 81-parameter modified valence force field. The force constants were refined using 251

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

2011-01-01

293

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

USGS Publications Warehouse

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

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

1976-01-01

294

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.  

PubMed

Experimental NMR verification of MD simulations using 12 different force fields (AMBER, CHARMM, GROMOS, and OPLS-AA) and 5 different water models has been undertaken to identify reliable MD protocols for structure and dynamics elucidations of small open chain peptides containing Gly and Pro. A conformationally flexible tetrapeptide Gly-Pro-Gly-Gly was selected for NMR (3)J-coupling, chemical shift, and internuclear distance measurements, followed by their calculations using 2 ?s long MD simulations in water. In addition, Ramachandran population maps for Pro-2 and Gly-3 residues of GPGG obtained from MD simulations were used for detailed comparisons with similar maps from the protein data bank (PDB) for large number of Gly and Pro residues in proteins. The MD simulations revealed strong dependence of the populations and geometries of preferred backbone and side chain conformations, as well as the time scales of the peptide torsional transitions on the force field used. On the basis of the analysis of the measured and calculated data, AMBER99SB is identified as the most reliable force field for reproducing NMR measured parameters, which are dependent on the peptide backbone and the Pro side chain geometries and dynamics. Ramachandran maps showing the dependence of conformational populations as a function of backbone ?/? angles for Pro-2 and Gly-3 residues of GPGG from MD simulations using AMBER99SB, AMBER03, and CHARMM were found to resemble similar maps for Gly and Pro residues from the PDB survey. Three force fields (AMBER99, AMBER99?, and AMBER94) showed the least satisfactory agreement with both the solution NMR and the PDB survey data. The poor performance of these force fields is attributed to their propensity to overstabilize helical peptide backbone conformations at the Pro-2 and Gly-3 residues. On the basis of the similarity of the MD and PDB Ramachandran plots, the following sequence of transitions is suggested for the Gly backbone conformation: ?(L) ? ?(PR) ? ?(S) ? ?(P) ? ?, where backbone secondary structures ?(L) and ? are associated with helices and turns, ?(P) and ?(PR) correspond to the left- and right-handed polyproline II structures and ?(S) denotes the fully stretched backbone conformation. Compared to the force field dependence, less significant, but noteworthy, variations in the populations of the peptide backbone conformations were observed. For different solvent models considered, a correlation was noted between the number of torsional transitions in GPGG and the water self-diffusion coefficient on using TIP3P, TIP4P, and TIP5P models. In addition to MD results, we also report DFT derived Karplus relationships for Gly and Pro residues using B972 and B3LYP functionals. PMID:20825228

Aliev, Abil E; Courtier-Murias, Denis

2010-09-30

295

Evolving force-free magnetic fields. III - States of nonequilibrium and the preflare stage. [in solar atmosphere  

NASA Technical Reports Server (NTRS)

The paper considers whether a neighboring magnetostatic equilibrium exists to allow a magnetic field initially in a force-free configuration to accommodate any imposed weak pressure. The following problem is treated. The foot points of the field are fixed and the plasma is frozen into the field lines under the approximation of infinite electrical conductivity. A weak pressure is introduced. It is determined infinitesimal plasma displacements exist to adjust the field lines to a new equilibrium without changing the field line connectivity. The analysis is carried out for the bipolar force-free fields forming one of two evolutionary sequences modeling the development of the preflare stage. It was found that for the force-free field corresponding to the quasi-static stage of evolution, the neighboring magnetostatic equilibrium always exists and the imposed gas pressure can be accommodated with a slight departure of the field from being exactly force free.

Low, B. C.

1980-01-01

296

Force field effects on cerebellar Purkinje cell discharge with implications for internal models.  

PubMed

The cerebellum has been hypothesized to provide internal models for limb movement control. If the cerebellum is the site of an inverse dynamics model, then cerebellar neural activity should signal limb dynamics and be coupled to arm muscle activity. To address this, we recorded from 166 task-related Purkinje cells in two monkeys performing circular manual tracking under varying viscous and elastic loads. Hand forces and arm muscle activity increased with the load, and their spatial tuning differed markedly between the viscous and elastic fields. In contrast, the simple spike firing of 91.0% of the Purkinje cells was not significantly modulated by the force nor was their spatial tuning affected. For the 15 cells with a significant force effect, changes were small and isolated. These results do not support the hypothesis that Purkinje cells represent the output of an inverse dynamics model of the arm. Instead these neurons provide a kinematic representation of arm movements. PMID:17028585

Pasalar, S; Roitman, A V; Durfee, W K; Ebner, T J

2006-11-01

297

Direct actuation of cantilever in aqueous solutions by electrostatic force using high-frequency electric fields  

NASA Astrophysics Data System (ADS)

We recently developed a method to directly actuate a cantilever in aqueous solutions by electrostatic force [K.-I. Umeda et al., Appl. Phys. Express 3, 065205 (2010)]. However, the cantilever was actuated by surface stress in a low frequency regime. We solved this problem by applying amplitude-modulated high-frequency electric fields, which actuates the cantilever solely by electrostatic force. The time variations of the self-oscillation frequency of a cantilever and the Au(111) surface images by frequency-modulation atomic force microscopy using acoustic, photothermal, and the improved electrostatic actuation methods were compared, which demonstrates the advantages of the last method such as stability and simplicity in instrumentation.

Umeda, Ken-ichi; Kobayashi, Kei; Matsushige, Kazumi; Yamada, Hirofumi

2012-09-01

298

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

299

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

300

Mean Field with Tensor Force and Shell Structure of Exotic Nuclei  

SciTech Connect

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

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

2006-10-20

301

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

PubMed

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

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

2012-10-01

302

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

SciTech Connect

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

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

2012-08-10

303

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

NASA Astrophysics Data System (ADS)

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

Prior, C.; Berger, M. A.

2012-06-01

304

Molecular Tweezers: Using the Electric Field in a Synthetic Nanopore to Disrupt Biomolecular Binding Forces  

NASA Astrophysics Data System (ADS)

The forces binding proteins to DNA in an aqueous solution are vital to biology, but inadequately understood. In particular, restriction enzymes like EcoRI are extraordinarily sequence-specific and yet the complex with DNA is very stable. To stringently test these forces, we use the electric field inside a synthetic nanometer-diameter pore in a thin membrane to pull on double-stranded DNA bound to EcoRI and BamHI, introducing a shear between the enzyme and their respective cognate sites in DNA. We observe a sharp threshold near 1nN in the force required to disrupt the binding in the complex, which is in stark contrast with previous measurements of the force (10pN) accomplished by unzipping the DNA molecule at a constant loading rates (1nN/sec). This force, acting over a distance corresponding to the separation between bases, coincidentally corresponds to the free energy of formation for the EcoRI-DNA complex. Using molecular dynamics, we interpret the measurements and elucidate the binding with atomic precision.

Timp, Gregory

2007-03-01

305

Vapour-liquid coexistence curves of the united-atomand anisotropic united-atom force fields for alkane mixtures  

Microsoft Academic Search

The performances of two categories of force field for mixtures of alkanes are compared. Configurational-bias Monte Carlo simulations in the Gibbs ensemble were carried out to compute the vapour-liquid coexistence curves (VLCC) for pure n-pentane and n-dodecane and for binary mixtures of these components with methane. The united-atom (UA) force field (Siepmann and coworkers) and the anisotropic united-atom (AUA) force

Jerome Delhommelle; Anne Boutin; Bernard Tavitian; Allan D. Mackie; Alain H. Fuchs

1999-01-01

306

Numerical modeling of superparamagnetic sub-micronic particles trajectories under the coupled action of 3D force fields  

NASA Astrophysics Data System (ADS)

Trajectories of superparamagnetic sub-micronic particles submitted to a multi-force field are modeled numerically by a Finite Element Method. The first step is the computation of the magnetic forces and the carrier fluid velocity field, the second step is the computation of the trajectories using a Finite Difference Method with a predictor-corrector scheme.

Pham, P.; Massé, P.; Berthier, J.

2000-12-01

307

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

Microsoft Academic Search

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

Masato Akamatsu; Mitsuo Higano; Yoshio Takahashi; Hiroyuki Ozoe

2005-01-01

308

A scaled quantum mechanical force field for tetranitromethane and its intermediates  

NASA Astrophysics Data System (ADS)

The quadratic force field of TNM has been calculated by AM1, PM3 and 3-21G Hamiltonians and then scaled according to Pulay's method. The computed vibrational frequencies fit the experiment within ±2 cm -1. On the other hand, the mechanism of thermolysis of TNM has been investigated by the mentioned methods and all possible reaction channels have been explored. Up to date, we have established that the first step in the thermal decomposition of TNM involves dissociation of a C-N bond. With this assumption, computed values for the activation energy agree satisfactorily with the experimental ones. Given that no experimental vibrational spectrum is available for transition states, the force field for the relevant activated complex has been quantum mechanically computed and then scaled by using scale factors obtained for TNM in its ground state, then numerical values for the preexponential factor have been computed.

Arenas, J. F.; Marcos, J. I.; Otero, J. C.; Soto, J.

1995-04-01

309

Minimum radiation force target size for power measurements in focused ultrasonic fields with circular symmetry.  

PubMed

The time-averaged ultrasonic power emitted by medical ultrasonic equipment is mostly measured using a radiation force balance, and the question of the necessary target size is of practical importance. The question is answered here by calculations based on a Rayleigh integral algorithm for fields from circular, focusing transducers. This case occurs particularly in the field of high-intensity therapeutic ultrasound. The calculation yields the necessary size of an absorbing target so that the radiation force is 98% of that exerted on an absorber of infinite lateral size, and this as a function of the transducer-to-target distance, of the transducer radius in comparison with the wavelength and of the focus (half-)angle. Several distributions of the transducer vibration amplitude are considered. The Rayleigh integral strictly applies only to planar transducers, but among the amplitude distributions there is also one that allows the simulation of the spherically curved transducer type often found in practice. PMID:21218869

Beissner, K

2010-12-01

310

An Accurate Quartic Force Field and Vibrational Frequencies for HNO and DNO  

NASA Technical Reports Server (NTRS)

An accurate ab initio quartic force field for HNO has been determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T), in conjunction with the correlation consistent polarized valence triple zeta (cc-pVTZ) basis set. Improved harmonic frequencies were determined with the cc-pVQZ basis set. Fundamental vibrational frequencies were determined using a second-order perturbation theory analysis and also using variational calculations. The N-0 stretch and bending fundamentals are determined well from both vibrational analyses. The H-N stretch, however, is shown to have an unusually large anharmonic correction, and is not well determined using second-order perturbation theory. The H-N fundamental is well determined from the variational calculations, demonstrating the quality of the ab initio quartic force field. The zero-point energy of HNO that should be used in isodesmic reactions is also discussed.

Dateo, Christopher E.; Lee, Timothy J.; Schwenke, David W.

1994-01-01

311

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

PubMed

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

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

2012-08-01

312

Electron-phonon coupling in conjugated polymers: Reference force field and transferable coupling constants for polyacetylene  

Microsoft Academic Search

A Herzberg–Teller expansion for ? electrons in the ground state of conjugated polymers identifies quadratic electron–phonon (e–ph) contributions and suggests a ?+? reference force field F0 based on butadiene. Linear response theory then fixes linear e–ph coupling constants for the Raman shifts in polyacetylene (PA) due to ?-electron fluctuations. The same coupling constants and the known isotopic dependences of the

Alberto Girlando; Anna Painelli; Z. G. Soos

1993-01-01

313

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

PubMed

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

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

2014-01-01

314

Electron-diffraction study of the structure and force field of the zirconium tetrachloride molecule  

SciTech Connect

This study on zirconium tetrachloride completes a systematic study of the structures in the halides of the titanium subgroup. The previous electron-diffraction and spectroscopic studies of this compound and of other titanium-subgroup tetrahalides indicate that the equilibrium configurations in these compounds are tetrahedral. The purpose of the present study was to refine the observed molecular component of the scattering intensity in order to use it to determine the total force field of the ZrCl/sub 4/ molecule.

Utkin, A.N.; Petrova, V.N.; Girichev, G.V.; Petrov, V.M.

1987-01-01

315

OPLS all-atom force field for squaramides and squaric acid  

Microsoft Academic Search

The OPLS all-atom (AA) force field has been expanded to include squaramides and squaric acid. A complete set of stretching–bending, all-atom torsional and non-bonded parameters has been calculated. Starting from reported non-bonded parameters of amides, parameters were fitted to reproduce results from ab initio (MP2\\/6-31G?) calculations on squaramides and squaric acid. Their application in the solution phase was tested by

David Quiñonero; Salvador Tomàs; Antonio Frontera; Carolina Garau; Pablo Ballester; Antonio Costa; Pere M Deyà

2001-01-01

316

Field observations of basal forces and fluid pore pressure in a debris flow  

Microsoft Academic Search

Using results from an 8 m2 instrumented force plate we describe field measurements of normal and shear stresses, and fluid pore pressure for a debris flow. The flow depth increased from 0.1 to 1 m within the first 12 s of flow front arrival, remained relatively constant until 100 s, and then gradually decreased to 0.5 m by 600 s.

Brian W. McArdell; Perry Bartelt; Julia Kowalski

2007-01-01

317

Force-field dependence on the interfacial structure of oil-water interfaces  

Microsoft Academic Search

We investigate the performance of different force-fields for alkanes, united (TraPPE) and all atom (OPLS-AA) models, and water (SPC\\/E and TIP4P-2005), in the prediction of the interfacial structure of alkane (n-octane, and n-dodecane)–water interfaces. We report an extensive comparison of the interfacial thermodynamic properties as well as the interfacial structure (translational and orientational). We use the recently introduced intrinsic sampling

Fernando Bresme; Enrique Chacon; Pedro Tarazona

2010-01-01

318

Polarizable Water Model for the Coarse-Grained MARTINI Force Field  

PubMed Central

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

Sengupta, Durba; Marrink, Siewert J.

2010-01-01

319

Rigidity loss of protein macromolecule induced by force-Effective field theory.  

PubMed

In the framework of the effective field theory for the order parameter, which characterizes the degree of deviating the protein globule structure from its native state, the phase transition of the protein macromolecule from the elastic state into the plastic one under its mechanical stretching is considered. Elastic properties of a protein are studied as a function of the applied force, temperature, and the mean coordination number of the protein "network." Proteins 2014; 82:966-974. © 2013 Wiley Periodicals, Inc. PMID:24323674

Meilikhov, E Z; Farzetdinova, R M

2014-06-01

320

History force effects on contrast agent microbubbles in an ultrasound field  

Microsoft Academic Search

We study experimentally the radial and translational dynamics of an ultrasound contrast agent microbubble pair pulsating in an ultrasound field. The two bubbles attract each other through the so-called secondary Bjerknes force; quantifying these bubble-bubble interactions is therefore crucial for optimized medical imaging protocols. Using optical tweezers, we trap and control the distance between two microbubbles (BR-14, Bracco Research S.A.,

Valeria Garbin; Benjamin Dollet; Leen van Wijngaarden; Nico de Jong; Detlef Lohse; Michel Versluis

2008-01-01

321

Ab initio studies of the structures and force fields of ketenimine and related molecules  

NASA Astrophysics Data System (ADS)

Theoretical equilibrium geometries for ketenimine, aminoacetylene and ethynol have been obtained using the MP3/6-31G** ab initio method. Empirical scaling factors have been introduced to estimate the rotational constants Ao, Bo and Co. In addition the complete harmonic force fields for ketenimine, ketene and diazomethane have been computed, normal coordinate analyses have been performed and the quartic centrifugal distortion constants estimated.

Brown, R. D.; Rice, E. H. N.; Rodler, M.

1985-11-01

322

Molecular structure and harmonic force field of AsCl3 by microwave spectroscopy  

Microsoft Academic Search

The microwave spectrum of four isotopically substituted species of AsCl3 in the frequency range 100-220 GHz has been investigated. Four rs structures were determined resulting in the following average values of the bond length and bond angle: The harmonic force field of AsCl3 has been calculated and compared with that obtained without the aid of the centrifugal distortion constants.

G. Cazzoli; P. Forti; B. Lunelli

1978-01-01

323

Molecular structure and harmonic force field of SbCl3 by microwave spectroscopy  

Microsoft Academic Search

The microwave spectrum of six isotopically substituted molecules of SbCl3 in the frequency range 27-250 GHz has been investigated. Six rs structures were determined resulting in the following average values of the bond length and bond angle: rs(SbCl) = 2.3217 Å thetas(ClSbCl) = 97.19° The harmonic force field of SbCl3 has been calculated using the vibrational frequencies, the mean amplitudes,

G. Cazzoli; W. Caminati

1976-01-01

324

Anharmonic force field of ONCl and ONBr by combination of infrared and microwave data  

Microsoft Academic Search

From the analysis of the microwave spectra of ON35Cl and ON81Br in several vibrational excited states, vibro-rotational constants corresponding to the nu2 and nu3 vibrational modes have been determined for both molecules. In order to extract information on the anharmonic force field from these experimental data and anharmonicity xij constants obtained by other authors, the semiempirical potential function suggested by

A. M. Mirri; R. Cervellati; G. Cazzoli

1978-01-01

325

CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses  

PubMed Central

Presented is an extension of the CHARMM additive carbohydrate all-atom force field to enable modeling of polysaccharides containing furanose sugars. The new force field parameters encompass 1 ? 2, 1 ? 3, 1 ? 4 and 1 ? 6 pyranose-furanose linkages and 2 ? 1 and 2 ? 6 furanose-furanose linkages, building on existing hexopyranose and furanose monosaccharide parameters. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF) as to contain the key atoms in full carbohydrates. Target data for optimization included two-dimensional quantum mechanical (QM) potential energy scans of the ?/? glycosidic dihedral angles, with geometry optimization at the MP2/6-31G(d) level followed by MP2/cc-pVTZ single point energies. All possible chiralities of the model compounds at the linkage carbons were considered, and, for each geometry, the THF ring was constrained to the favorable South or North conformation. Target data also included QM vibrational frequencies and pair interaction energies and distances with water molecules. Force field validation included comparison of computed crystal properties, aqueous solution densities and NMR J-coupling constants to experimental reference values. Simulations of infinite crystals showed good agreement with experimental values for intramolecular geometries as well as for crystal unit cell parameters. Additionally, aqueous solution densities and available NMR data were reproduced to a high degree of accuracy, thus validating the hierarchically optimized parameters in both crystalline and aqueous condensed phases. The newly developed parameters allow for the modeling of linear, branched, and cyclic pyranose/furanose polysaccharides both alone and in heterogeneous systems including proteins, nucleic acids and/or lipids when combined with existing additive CHARMM biomolecular force fields.

Raman, E. Prabhu; Guvench, Olgun; MacKerell, Alexander D.

2010-01-01

326

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

PubMed Central

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

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

2012-01-01

327

Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field.  

PubMed

Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces. PMID:23440601

Schyman, Patric; Jorgensen, William L

2013-02-01

328

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

PubMed Central

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to ?m-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the ?m and nm scales.

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

2004-01-01

329

Reduction of the friction force in electron cooling systems due to magnetic field errors  

NASA Astrophysics Data System (ADS)

Magnetic field errors can limit the dynamical friction force on co-propagating ions and, hence, increase the cooling time. We present theoretical and numerical results for reduction of the friction force due to bounded transverse magnetic field errors, as a function of wavelength. VORPAL [1] simulations using a binary collision algorithm [2] show that small-wavelength field errors affect the friction logarithmically, via the Coulomb log, while long-wavelength errors reduce the friction by effectively increasing the transverse electron temperature. A complete understanding of finite-time effects and the role of small impact parameter collisions is required to correctly interpret the simulation results. We show that the distribution of electron-ion impact parameters is similar to a Pareto distribution, for which the central limit theorem does not apply. A new code has been developed to calculate the cumulative distribution function of electron-ion impact parameters and thus correctly estimate the expectation value and uncertainty of the friction force. [1] C. Nieter and J. Cary, J. Comp. Phys. 196 (2004), p. 448. [2] G. Bell et al., J. Comp. Phys. 227 (2008), p. 8714.

Sobol, Andrey; Bell, George; Bruhwiler, David; Fedotov, Alexei; Litvinenko, Vladimir

2009-05-01

330

A polarizable force field for water using an artificial neural network  

NASA Astrophysics Data System (ADS)

A force field for liquid water including polarization effects has been constructed using an artificial neural network (ANN). It is essential to include a many-body polarization effect explicitly into a potential energy function in order to treat liquid water which is dense and highly polar. The new potential energy function is a combination of empirical and nonempirical potentials. The TIP4P model was used for the empirical part of the potential. For the nonempirical part, an ANN with a back-propagation of error algorithm (BPNN) was introduced to reproduce the complicated many-body interaction energy surface from ab initio quantum mechanical calculations. BPNN, described in terms of a matrix, provides enough flexibility to describe the complex potential energy surface (PES). The structural and thermodynamic properties, calculated by isobaric-isothermal (constant-NPT) Monte Carlo simulations with the new polarizable force field for water, are compatible with experimental results. Thus, the simulation establishes the validity of using our estimated PES with a polarization effect for accurate predictions of liquid state properties. Applications of this approach are simple and systematic so that it can easily be applied to the development of other force fields besides the water-water system.

Cho, Kwang-Hwi; No, Kyoung Tai; Scheraga, Harold A.

2002-10-01

331

Molecular Dynamics Simulation of Hydrated DPPC Monolayers Using Charge Equilibration Force Fields  

PubMed Central

We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ± 1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ± 1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ± 0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. Since the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly-modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.

Lucas, Timothy R.; Bauer, Brad A.; Davis, Joseph E.; Patel, Sandeep

2012-01-01

332

A Kirkwood-Buff Force Field for the Aromatic Amino Acids  

PubMed Central

In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.

Ploetz, Elizabeth A.; Smith, Paul E.

2014-01-01

333

Lack of adaptation to random conflicting force fields of variable magnitude.  

PubMed

The concept of internal models has been used to explain how the brain learns and stores a variety of motor behaviors. A large body of work has shown that conflicting internal models could not be learned simultaneously; this suggests either a limited capacity or the unstable nature of short-term motor memories. However, it has been recently shown that multiple conflicting internal models of motor behavior could be acquired simultaneously if associated with appropriate contextual cues and random presentations. We re-examined this issue in a more complex environment in which the magnitude of the conflicting fields could vary randomly. Human subjects failed to show any evidence of learning the force fields themselves or the magnitude of the forces experienced, even with extended practice. Subjects did adapt to the applied perturbation when the field strength was kept constant but still did not form internal models. Our results show that neither random presentation nor specific contextual cues are sufficient for learning conflicting internal models when the magnitude of the forces is also unpredictable. The data suggest that multiple conflicting internal models cannot be learned in all environments, and provide support for the unstable nature or limited capacity of motor memories. PMID:17093124

Gupta, Rahul; Ashe, James

2007-01-01

334

Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study.  

PubMed

Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations. PMID:20449033

Künzel, Daniela; Markert, Thomas; Gross, Axel; Benoit, David M

2009-10-21

335

A uniqueness result for a simple force-free magnetic field submitted to a topological constraint  

NASA Astrophysics Data System (ADS)

A proof is given of the following statement: if B is a smooth force-free magnetic field contained in a cylindrical domain of axis parallel to z and of star-shaped cross-section, and if B is topologically equivalent to the uniform field B0=B0z, then B=B0. In addition to being a very first step in the general study of the uniqueness of a magnetostatic equilibrium subject to a topological constraint, this result has a direct relevance to the approach recently developed by Ng & Bhattacharjee (1998, Phys. Plasma, 5, 4028) to support Parker's theory of current sheets formation in the solar corona.

Aly, J. J.

2005-01-01

336

Integrated headgear for the future force warrior: results of the first field evaluations  

NASA Astrophysics Data System (ADS)

The development of an advanced ground soldier's integrated headgear system for the Army's Future Force Warrior Program passed a major milestone during 2006. Field testing of functional headgear systems by small combat units demonstrated that the headgear capabilities were mature enough to move beyond the advanced technology demonstration (ATD) phase. This paper will describe the final system with test results from the three field exercises and will address the strengths and weaknesses of the headgear system features, head mounted sensors, displays and sensor fusion.

Schuyler, W. Jeff; Melzer, James E.

2007-05-01

337

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

SciTech Connect

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

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

2011-12-15

338

Embedding Circular Force-Free Flux Ropes in Potential Magnetic Fields  

NASA Astrophysics Data System (ADS)

We propose a method for constructing approximate force-free equilibria in active regions that locally have a potential bipolar-type magnetic field with a thin force-free flux rope embedded inside it. The flux rope has a circular-arc axis and circular cross-section in which the interior magnetic field is predominantly toroidal (axial). Its magnetic pressure is balanced outside by that of the poloidal (azimuthal) field created at the boundary by the electric current sheathing the flux rope. To facilitate the implementation of the method in our numerical magnetohydrodynamic (MHD) code, the entire solution is described in terms of the vector potential of the magnetic field. The parameters of the flux rope can be chosen so that a subsequent MHD relaxation of the constructed configuration under line-tied conditions at the boundary provides a numerically exact equilibrium. Such equilibria are an approximation for the magnetic configuration preceding solar eruptions, which can be triggered in our model by imposing suitable photospheric flows beneath the flux rope. The proposed method is a useful tool for constructing pre-eruption magnetic fields in data-driven simulations of solar active events. Research supported by NASA's Heliophysics Theory and LWS Programs, and NSF/SHINE and NSF/FESD.

Titov, V. S.; Torok, T.; Mikic, Z.; Linker, J.

2013-12-01

339

Structure of kinematic and force fields in the Riemannian continuum model  

NASA Astrophysics Data System (ADS)

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

Guzev, M. A.

2011-09-01

340

Penetration and radial force balance in field-reversed configuration with large rotating magnetic field  

NASA Astrophysics Data System (ADS)

A field-reversed configuration (FRC) is formed by applying a rotating magnetic field (RMF) much larger than the axial magnetic field to a cylindrical glass vacuum chamber filled with 10 Pa argon gas without a preionization. The FRC with the plasma density 2.2×1019 m-3, the temperature 8.0 eV, the separatrix length 0.45 m, and the separatrix radius 0.035 m is sustained for the notably long period of 40 ms. It is observed that the antenna current which produces the RMF is reduced by about half after the FRC is formed. The interaction between the plasma and the antenna circuit increases the antenna resistance and changes the inductance of the antenna so that the circuit becomes nonresonant. The RMF is sufficiently large to fully penetrate to the center during the period and drive the current with a rigid rotor profile. The RMF is shown to play a major role in sustaining the plasma pressure.

Ohnishi, M.; Hugrass, W.; Fukuhara, M.; Masaki, T.; Osawa, H.; Chikano, T.

2008-10-01

341

Penetration and radial force balance in field-reversed configuration with large rotating magnetic field  

SciTech Connect

A field-reversed configuration (FRC) is formed by applying a rotating magnetic field (RMF) much larger than the axial magnetic field to a cylindrical glass vacuum chamber filled with 10 Pa argon gas without a preionization. The FRC with the plasma density 2.2x10{sup 19} m{sup -3}, the temperature 8.0 eV, the separatrix length 0.45 m, and the separatrix radius 0.035 m is sustained for the notably long period of 40 ms. It is observed that the antenna current which produces the RMF is reduced by about half after the FRC is formed. The interaction between the plasma and the antenna circuit increases the antenna resistance and changes the inductance of the antenna so that the circuit becomes nonresonant. The RMF is sufficiently large to fully penetrate to the center during the period and drive the current with a rigid rotor profile. The RMF is shown to play a major role in sustaining the plasma pressure.

Ohnishi, M.; Fukuhara, M.; Masaki, T.; Osawa, H.; Chikano, T. [Department of Electrical Engineering and Computer Science, Kansai University, 3-3-35 Yamate-cho, Suita-shi, Osaka 564-8680 (Japan); Hugrass, W. [School of Computing, University of Tasmania, Locked Bag 1359, Launceston, Tasmania 7250 (Australia)

2008-10-15

342

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

PubMed

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

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

2014-01-01

343

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

PubMed Central

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

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

2014-01-01

344

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

NASA Astrophysics Data System (ADS)

The focus of this study is the sustained body force (the so-called acoustic radiation force) in homogeneous tissue-like solids generated by an elevated-intensity, focused ultrasound field (Mach number=O(10-3)) in situations when the latter is modulated by a low-frequency signal. This intermediate-asymptotics problem, which bears relevance to a number of emerging biomedical applications, is characterized by a number of small (but non-vanishing) parameters including the Mach number, the ratio between the modulation and ultrasound frequency, the ratio of the shear to bulk modulus, and the dimensionless attenuation coefficient. On approximating the response of soft tissues as that of a nonlinear viscoelastic solid with heat conduction, the featured second-order problem is tackled via a scaling paradigm wherein the transverse coordinates are scaled by the width of the focal region, while the axial and temporal coordinate are each split into a "fast" and "slow" component with the twin aim of: (i) canceling the linear terms from the field equations governing the propagation of elevated-intensity ultrasound, and (ii) accounting for the effect of ultrasound modulation. In the context of the focused ultrasound analyses, the key feature of the proposed study revolves around the dual-time-scale treatment of the temporal variable, which allows one to parse out the contribution of ultrasound and its modulation in the nonlinear solution. In this way the acoustic radiation force (ARF), giving rise to the mean tissue motion, is exacted by computing the "fast" time average of the germane field equations. A comparison with the existing theory reveals a number of key features that are brought to light by the new formulation, including the contributions to the ARF of ultrasound modulation and thermal expansion, as well as the precise role of constitutive nonlinearities in generating the sustained body force in tissue-like solids by a focused ultrasound beam.

Dontsov, Egor V.; Guzina, Bojan B.

2012-10-01

345

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

NASA Astrophysics Data System (ADS)

The structure of liquid ethylene glycol at room temperature is examined by performing molecular dynamics (MD) simulation studies for several different liquid phase force fields. We compare the properties obtained and analyze the differences which arise from the use of these models. A thorough study of molecular conformation and intermolecular structure for the different potential models is carried out given that three of the studied force fields have the same intermolecular parameters and different intramolecular interactions. In addition, the effect of molecular shape on the intermolecular structure is discussed. Due to the important role played by the highly directional forces occurring in hydrogen bonded systems, in their intermolecular structure and in the macroscopic properties of the system, we pay special attention to the analysis of the features of the hydrogen bonding patterns present in the liquid. Revealing an overall agreement with the available structural experimental data, the results obtained show that, for the simulated models, the intermolecular structure is rather similar. The dynamics of the system is studied through the self-diffusion coefficients and, in contrast to the structural properties, the results obtained for the distinct models are quite different.

Saiz, L.; Padró, J. A.; Guàrdia, E.

2001-02-01

346

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

PubMed

For the first time the millimeter-wave spectra of the trans-35ClHC=CHF and trans-37ClHC=CHF isotopomers have been observed in natural abundance. Many DeltaJ=0, +/-1 DeltaK(-1)=+1 transitions for 35ClHC=CHF and DeltaJ=0 DeltaK(-1)=+1 transitions for 37ClHC=CHF have been detected and assigned. This allowed us to accurately determine the vibrational ground-state rotational constants, quartic and some sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for both 35Cl and 37Cl. The experimental investigation has been supported by highly accurate theoretical predictions. As far as ab initio computations are concerned, the complete set of cubic and quartic force constants have been evaluated by numerical differentiation of the analytic second-order Møller-Plesset many-body perturbation theory/correlation consistent polarized valence triple zeta second derivatives. The anharmonic part of the force field completes the theoretical study on the equilibrium structure, dipole moment, chlorine quadrupolar tensor, and harmonic force field previously carried out by the same authors. PMID:15267539

Cazzoli, Gabriele; Puzzarini, Cristina; Gambi, Alberto

2004-04-01

347

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

PubMed Central

Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field.

Xu, Dong; Zhang, Yang

2012-01-01

348

Atomic force microscopy and near-field optical imaging of a spin transition.  

PubMed

We report on atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) investigations of single crystals of the spin crossover complex {Fe(pyrazine)[Pt(CN)4]} across the first-order thermal spin transition. We demonstrate for the first time that the change in spin state can be probed with sub-micrometer spatial resolution through various topographic features extracted from AFM data. This original approach based on surface topography analysis should be easy to implement to any phase change material exhibiting sizeable electron-lattice coupling. In addition, AFM images revealed specific topographic features in the crystals, which were correlated with the spatiotemporal evolution of the transition observed by far-field and near-field optical microscopies. PMID:23881283

Lopes, Manuel; Quintero, Carlos M; Hernández, Edna M; Velázquez, Víctor; Bartual-Murgui, Carlos; Nicolazzi, William; Salmon, Lionel; Molnár, Gábor; Bousseksou, Azzedine

2013-09-01

349

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

PubMed Central

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

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

2012-01-01

350

Estimating unsteady aerodynamic forces on a cascade in a three-dimensional turbulence field  

NASA Technical Reports Server (NTRS)

An analytical method has been developed to estimate the unsteady aerodynamic forces caused by flow field turbulence on a wind tunnel turning vane cascade system (vane set). This method approximates dynamic lift and drag by linearly perturbing the appropriate steady state force equations, assuming that the dynamic loads are due only to free stream turbulence and that this turbulence is homogeneous, isotropic, and Gaussian. Correlation and unsteady aerodynamic effects are also incorporated into the analytical model. Using these assumptions, equations relating dynamic lift and drag to flow turbulence, mean velocity, and vane set geometry are derived. From these equations, estimates for the power spectra and rms (root mean squared value, delta) loading of both lift and drag can be determined.

Norman, T.; Johnson, W.

1985-01-01

351

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

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

352

Second Law Violations by Means of a Stratification of Temperature Due to Force Fields  

NASA Astrophysics Data System (ADS)

In 1868 J.C. Maxwell proved that a perpetual motion machine of the second kind would become possible, if the equilibrium temperature in a vertical column of gas subject to gravity were a function of height. However, Maxwell had claimed that the temperature had to be the same at all points of the column. So did Boltzmann. Their opponent was Loschmidt. He claimed that the equilibrium temperature declined with height, and that a perpetual motion machine of the second kind operating by means of such column was compatible with the second law of thermodynamics. Extending the general idea behind Loschmidt's concept to other force fields, gravity can be replaced by molecular forces acting on molecules that try to escape from the surface of a liquid into the vapor space. Experiments proving the difference of temperature between the liquid and the vapor phase were conducted in the 19th century already.

Trupp, Andreas

2002-11-01

353

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

PubMed Central

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

Lantada, Andres Diaz; Bris, Carlos Gonzalez; Morgado, Pilar Lafont; Maudes, Jesus Sanz

2012-01-01

354

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

PubMed

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

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

2012-01-01

355

Interfacial force field characterization of a constrained vapor bubble thermosyphon using IAI  

NASA Technical Reports Server (NTRS)

The isothermal profiles of the extended meniscus in a quartz cuvette were measured in a gravitational field using IAI (image analyzing interferometer) which is based on computer enhanced video microscopy of the naturally occurring interference fringes. The experimental results for heptane and pentane menisci were analyzed using the extended Young-Laplace Equation. These isothermal results characterized the interfacial force field in-situ at the start of the heat transfer experiments by quantifying the dispersion constant for the specific liquid-solid system. The experimentally obtained values of the disjoining pressures and the dispersion constants are compared to the subsequent non-isothermal experiments because one of the major variables in the heat sink capability of the CVBT is the dispersion constant. In all previous studies of micro heat pipes the value of the dispersion constant has been 'guesstimated'. The major advantages of the current glass cell is the ability to view the extended meniscus at all times. Experimentally, we find that the extended Young-Laplace Equation is an excellent model for for the force field at the solid-liquid vapor interfaces.

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

1994-01-01

356

Nonlinear Force-free Extrapolation of the Coronal Magnetic Field Based on the Magnetohydrodynamic Relaxation Method  

NASA Astrophysics Data System (ADS)

We develop a nonlinear force-free field (NLFFF) extrapolation code based on the magnetohydrodynamic (MHD) relaxation method. We extend the classical MHD relaxation method in two important ways. First, we introduce an algorithm initially proposed by Dedner et al. to effectively clean the numerical errors associated with ? · B . Second, the multigrid type method is implemented in our NLFFF to perform direct analysis of the high-resolution magnetogram data. As a result of these two implementations, we successfully extrapolated the high resolution force-free field introduced by Low & Lou with better accuracy in a drastically shorter time. We also applied our extrapolation method to the MHD solution obtained from the flux-emergence simulation by Magara. We found that NLFFF extrapolation may be less effective for reproducing areas higher than a half-domain, where some magnetic loops are found in a state of continuous upward expansion. However, an inverse S-shaped structure consisting of the sheared and twisted loops formed in the lower region can be captured well through our NLFFF extrapolation method. We further discuss how well these sheared and twisted fields are reconstructed by estimating the magnetic topology and twist quantitatively.

Inoue, S.; Magara, T.; Pandey, V. S.; Shiota, D.; Kusano, K.; Choe, G. S.; Kim, K. S.

2014-01-01

357

A Method for Embedding Circular Force-Free Flux Ropes in Potential Magnetic Fields  

NASA Astrophysics Data System (ADS)

We propose a method for constructing approximate force-free equilibria in pre-eruptive configurations that locally are a bipolar-type potential magnetic field with a thin force-free flux rope embedded inside it. The flux rope is assumed to have a circular-arc axis, circular cross-section, and electric current that is either concentrated in a thin layer at the boundary of the rope or smoothly distributed across it with a maximum of the current density at the center.The entire solution is described in terms of the magnetic vector potential in order to facilitate the implementation of the method in numerical magnetohydrodynamic (MHD) codes that evolve the vector potential rather than the magnetic field itself. The parameters of the flux rope can be chosen so that its subsequent MHD relaxation under photospheric line-tied boundary conditions leads to nearly exact numerical equilibria. To show the capabilities of our method, we apply it to several cases with different ambient magnetic fields and internal flux-rope structures. These examples demonstrate that the proposed method is a useful tool for initializing data-driven simulations of solar eruptions.

Titov, Viacheslav; Torok, Tibor; Mikic, Zoran; Linker, Jon A.

2014-06-01

358

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

PubMed

This paper provides a sociological model of the key transnational political and economic forces that are shaping the 'global football field'. The model draws upon, and significantly extends, the theory of the 'global field' developed previously by Robertson. The model features four quadrants, each of which contains a dominant operating principle, an 'elemental reference point', and an 'elemental theme'. The quadrants contain, first, neo-liberalism, associated with the individual and elite football clubs; second, neo-mercantilism, associated with nation-states and national football systems; third, international relations, associated with international governing bodies; and fourth, global civil society, associated with diverse institutions that pursue human development and/or social justice. We examine some of the interactions and tensions between the major institutional and ideological forces across the four quadrants. We conclude by examining how the weakest quadrant, featuring global civil society, may gain greater prominence within football. In broad terms, we argue that our four-fold model may be utilized to map and to examine other substantive research fields with reference to globalization. PMID:22670645

Giulianotti, Richard; Robertson, Roland

2012-06-01

359

A Fluxon Model for the Behavior of Solar Force-Free Magnetic Fields  

NASA Astrophysics Data System (ADS)

For years solar physics has sought to explain the incredible energy emissions of the sun, like coronal mass ejections and flares. One of the main reasons for this study is that areas of high solar activity can cause disruptions of technological equipment like our satellite network and power grids. It has been proven that magnetic fields are the main cause for all solar activity, and have therefore become the main focus of this branch of physics. I have been working with Dr. Charles Kankelborg of Montana State University on a computational model of the behavior of solar force-free magnetic fields and the ways in which they interact and release energy through relaxation of the field tension and repulsion. The model proposes that the field is composed of discrete bundles of constant magnetic flux called "fluxons," which are represented as distinct lines. With this new ability, it is possible to study various theoretical field configurations, how these fields interact, and what the final configuration may be after relaxation. (This work made possible by support from a National Science Foundation REU.)

Blane McCracken, Stephen; Kankelborg, Charles

2003-11-01

360

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

PubMed Central

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

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

361

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

PubMed

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

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

2012-05-01

362

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

PubMed Central

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

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

2012-01-01

363

Predicting the thermodynamic properties of gold nanoparticles using different force fields  

NASA Astrophysics Data System (ADS)

The objective of this research was to learn how to predict the thermodynamic properties of gold nanoparticles using computational tools. The lowest energy structures of gold nanoparticles of various sizes were determined and thermodynamic properties such as the free energy (F), internal energy (U), entropy (S), and specific heat (Cv) of the gold nanoparticles were investigated using a fully-atomistic Monte Carlo simulation method that utilizes a modified Wang-Landau algorithm. Eight well-known force fields for metallic systems were employed to model gold nanoparticles: the Lennard-Jones potential (LJ), the Lennard-Jones potential with Heinz's parameterization (LJH), the Gupta potential, the Sutton-Chen potential (SC), the Sutton-Chen potential with Pawluk's parameterization for small clusters (SCP), the Quantum Sutton-Chen potential (Q-SC), the Embedded Atom Method (EAM) by Cai and Ye, and the empirical potential for gold proposed by Olivier and coworkers (POT). Subsequently, we explored the accuracy of each force field in the description of the thermodynamic behavior of gold nanoparticles. The thermodynamic properties of gold nanoparticles were computed from the Density of States which was obtained as a result of the Monte Carlo simulation. Afterwards, the melting point of gold nanoparticles was determined from the behavior of the calculated thermodynamic properties and was compared with theory, experimental observations and other simulation results. The force fields employed predicted melting points of gold nanoparticles over a wide range of temperatures. A thorough comparison with the available experimental observations showed that the Quantum Sutton-Chen potential (Q-SC) correctly described the melting behavior of gold nanoparticles with sizes smaller than 1.3 nanometers.

Park, Yongjin

364

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins  

PubMed Central

Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments.

Shi, Yue; Xia, Zhen; Zhang, Jiajing; Best, Robert; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu

2013-01-01

365

CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose  

PubMed Central

An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields.

Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

2009-01-01

366

Solutions of the Helmholtz equation with boundary conditions for force-free magnetic fields  

NASA Technical Reports Server (NTRS)

It is shown that the solution, with one ignorable coordinate, for the Taylor minimum energy state (resulting in a force-free magnetic field) in either a straight cylindrical or a toroidal geometry with arbitrary cross section can be reduced to the solution of either an inhomogeneous Helmholtz equation or a Grad-Shafranov equation with simple boundary conditions. Standard Green's function theory is, therefore, applicable. Detailed solutions are presented for the Taylor state in toroidal and cylindrical domains having a rectangular cross section. The focus is on solutions corresponding to the continuous eigenvalue spectra. Singular behavior at 90 deg corners is explored in detail.

Rasband, S. N.; Turner, L.

1981-01-01

367

Clock field in arrayed magnetic logic gates with a magnetic force microscope tip  

NASA Astrophysics Data System (ADS)

A magnetic logic gate (MLG), which is based on magnetic quantum dot cellular automata (MQCA), is capable of NAND/NOR logic operations. By arranging MLGs in a two-dimensional periodic array, a highly functional circuit can be created. However, NAND/NOR gates are difficult to form into a two-dimensional periodic arrangement. Here, we propose NOT/AND/ORs gate based on MLGs, which can be arranged in a two-dimensional periodic array. To demonstrate logic operations, we performed numerical simulations based on the macro-spin model. To execute logic operation in the arrayed structure, we used the stray field from a magnetic force microscope tip.

Nomura, H.; Imanaga, Y.; Hiratsuka, Y.; Nakatani, R.

2012-08-01

368

Nonlinear force-free field extrapolation of the coronal magnetic field using the data obtained by the Hinode satellite  

NASA Astrophysics Data System (ADS)

The Hinode satellite can obtain high-quality photospheric vector magnetograms of solar active regions and the simultaneous coronal loop images in soft X-ray and extreme ultraviolet (EUV) bands. In this paper, we continue the work of He and Wang (2008) and apply the newly developed upward boundary integration computational scheme for the nonlinear force-free field (NLFFF) extrapolation of the coronal magnetic field to the photospheric vector magnetograms acquired by the Spectro-Polarimeter of the Solar Optical Telescope aboard Hinode. Three time series vector magnetograms of the same solar active region, NOAA 10930, are selected for the NLFFF extrapolations, which were observed within the time interval of 26 h during 10-11 December 2006 when the active region crossed the central area of the Sun's disk. Parallel computation of the NLFFF extrapolation code was realized through OpenMP multithreaded, shared memory parallelism and Fortran 95 programming language for the extrapolation calculations. The comparison between the extrapolated field lines and the coronal loop images obtained by the X-Ray Telescope and the EUV Imaging Spectrometer of Hinode shows that, in the central area of the active region, the field line configurations generally agree with the coronal images, and the orientations of the field lines basically coincide with the coronal loop observations for all three successive magnetograms. This result supports the NLFFF model being used for tracing the time series evolution of the 3-D coronal magnetic structures as the responses of the quasi-equilibrium solar atmosphere to the vector magnetic field changes in the photosphere.

He, Han; Wang, Huaning; Yan, Yihua

2011-01-01

369

Response of bedrock channel width to tectonic forcing: Insights from a numerical model, theoretical considerations, and comparison with field data  

Microsoft Academic Search

The morphology of bedrock river channels is controlled by climatic and tectonic conditions and substrate properties. Knowledge of tectonic controls remains scarce. This is partly due to slow tectonic rates and long response times of natural channels and partly due to the difficulty in isolating and constraining tectonic forcing conditions in the field. To study the effect of tectonic forcing

Jens M. Turowski; Dimitri Lague; Niels Hovius

2009-01-01

370

Lorentz Force on Sodium and Chlorine Ions in a Salt Water Solution Flow under a Transverse Magnetic Field  

ERIC Educational Resources Information Center

It is shown that, by applying elementary concepts in electromagnetism and electrochemistry to a system consisting of salt water flowing in a thin rectangular pipe at an average velocity v[subscript A] under the influence of a transverse magnetic field B[subscript 0], an electromotive force generator can be conceived. In fact, the Lorentz force

De Luca, R.

2009-01-01

371

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

NASA Astrophysics Data System (ADS)

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

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

2010-08-01

372

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

PubMed

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case. PMID:23389748

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

2013-03-21

373

A Non-Linear Force-Free Field Model for the Solar Magnetic Carpet  

NASA Astrophysics Data System (ADS)

The magnetic carpet is defined to be the small-scale photospheric magnetic field of the quiet-Sun. Recent high resolution, high cadence observations have shown that although small-scale, the magnetic carpet is far from 'quiet', it is continually evolving in a complex and dynamic manner. I will present a two-component model for the dynamic evolution of the Sun's magnetic carpet. The first component is a 2D model for the photospheric evolution of the small-scale solar magnetic field, that reproduces many observed parameters. The basic evolution of magnetic elements within the model is governed by a supergranular flow profile. In addition, magnetic elements may evolve through the processes of emergence, cancellation, coalescence and fragmentation. The synthetic magnetograms produced by the 2D model are then applied as photospheric boundary data to drive the continuous evolution of a 3D non-linear force-free coronal field. We studied the resultant complex, small-scale coronal magnetic field, in particular the energetics of the field.

Meyer, Karen; Mackay, D.; van Ballegooijen, A.; Parnell, C.

2013-07-01

374

The Congo River plume: Impact of the forcing on the far-field and near-field dynamics  

NASA Astrophysics Data System (ADS)

The first numerical simulations of the Congo River plume dynamics are presented in this study. The different forcing mechanisms responsible for the seasonal variations of the plume extend are separately analyzed and the Regional Ocean Modeling System (ROMS) is employed to carry out both a process orientated study—with simple baseline simulations and a sensitivity study—with realistic 1 year runs setup in 2005. The baseline model is forced only by the river flow, in the presence of realistic bathymetry. Tides, wind stress, surface heat flux, and ocean boundary conditions are the forcing added to the realistic model. The typical seasonal orientation of the Congo River plume is found to be northward during most of year except for the February-March (FM) season when the plume has a large westward extension (about 800 km) and its area nearly doubles. The northward extension of the plume is explained by a buoyancy-driven upstream coastal flow—due to the unique geomorphology of the Congo River estuary—and the combined influences of the ambient ocean currents and the wind. During the FM season, the surface ocean circulation is driving both (1) the westward extension of the plume and (2) the southward transport of the Nyanga River fresh waters which feed the Congo River plume. In the near-field region of the plume, the presence of the deep Congo canyon has two main effects: (1) its depth increases the intrusion of sea water into the river mouth and (2) its orientation initiates the formation of the upstream flow.

Denamiel, CléA.; Budgell, W. Paul; Toumi, Ralf

2013-02-01

375

Force field dependence of phospholipid headgroup and acyl chain properties: comparative molecular dynamics simulations of DMPC bilayers.  

PubMed

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united-atom Berger force field and three versions of all-atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut-off schemes were used to evaluate the long-range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long-range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P-C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid-lipid, protein-lipid, and ligand-lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. PMID:19475632

Prakash, Priyanka; Sankararamakrishnan, Ramasubbu

2010-01-30

376

Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L.  

PubMed

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

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

2014-06-26

377

Near field vortex dynamics in axially forced, co-flowing jets: quantitative description of a low-frequency configuration  

Microsoft Academic Search

This work presents an experimental study of the vortex structures that appear in the shear layer of co-flowing water jets subjected to a strong axial forcing. Quantitative, forcing-phase-locked measurements of the velocity in the near field were obtained using two-component Particle Image Velocimetry (PIV). Two-dimensional vorticity, strain and pressure fields were obtained from these data. Also, some information could be

Antonio Lecuona; Ulpiano Ruiz-Rivas; Pedro Rodr??guez-Aumente

2002-01-01

378

ReaxFF study of the oxidation of lignin model compounds for the most common linkages in softwood in view of carbon fiber production.  

PubMed

Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers. PMID:24428197

Beste, Ariana

2014-02-01

379

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

NASA Astrophysics Data System (ADS)

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

Sirivat, Anuvat; Kunanuruksapong, Ruksapong

2011-03-01

380

Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds.  

PubMed

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol). PMID:12868110

Allinger, Norman L; Chen, Kuo-Hsiang; Lii, Jenn-Huei; Durkin, Kathleen A

2003-09-01

381

Development and validation of new-generation molecular mechanical force fields and semiempirical Hamiltonians  

NASA Astrophysics Data System (ADS)

This work describes the development and validation of many-body force fields and semiempirical Hamiltonians as part of a multi-scale modeling effort by the York Group targeted at biological applications. Basic science effort is spent towards the testing of existing polarizable force field functional forms in the areas of charge transfer and the coupling of polarization with many-body exchange. A new semiempirical model (MNDO/d+CPE) is developed by a novel combination of the modified neglect of diatomic overlap with extension to d-orbitals (MNDO/d) semiempirical Hamiltonian with a set of charge-dependent, atom-centered, density response dipole functions. It is shown that existing semiempirical Hamiltonians severely under-predict the polarizability of atoms and molecules whereas the MNDO/d+CPE model reduces the errors across a wide range of charge states (2- to 2+) by an order of magnitude. Another semiempirical Hamiltonian (PM3 BP) is created through a reparametrization of the PM3 Hamiltonian to model hydrogen bonded nucleic acid base pairs. A large database of molecules (on-line at http://theory.chem.umn.edu/QCRNA) for the purpose of parametrizing future models is described. Semiempirical methods lack treatment for long-range London dispersion forces. Therefore, basic science work is performed on van der Waals systems with a large emphasis on rare gas dimers. The accurate calculation of dispersion interactions from ab initio is very computationally intensive. Therefore, a new multicoefficient correlation method is developed to decrease the computational effort required to obtain a large collection of van der Waals interaction energy reference data.

Giese, Timothy John

382

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

PubMed

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

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

2014-05-01

383

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

PubMed Central

Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 – 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures.

Baker, Christopher M.; Best, Robert B.

2013-01-01

384

Adsorption of amino acids on the magnetite-(111)-surface: a force field study.  

PubMed

Magnetite (Fe(3)O(4)) is an important biomineral, e.g., used by magnetotactic bacteria. The connection between the inorganic magnetite-(111)-surface and the organic parts of the bacteria is the magnetosome membrane. The membrane is built by different magnetosome membrane proteins (MMPs), which are dominated by the four amino acids glycine (Gly), aspartic acid (Asp), leucine (Leu) and glutamic acid (Glu). Force field simulations of the interaction of the magnetite-(111)-surface and the main amino acid compounds offer the possibility to investigate if and how the membrane proteins could interact with the mineral surface thus providing an atomistic view on the respective binding sites. In a force field simulation the four amino acids were docked on the Fe-terminated magnetite-(111)-surface. The results show that it is energetically favorable for the amino acids to adsorb on the surface with Fe-O-distances between 2.6 Å and 4.1 Å. The involved O-atoms belong to the carboxyl-group (Asp and Glu) or to the carboxylate-group (Gly, Leu and Glu). Electrostatic interactions dominate the physisorption of the amino acids. During the simulations, according to the frequency of the best results, the global minimum for the docking interaction could be attained for all amino acids analyzed. PMID:23070334

Bürger, Andreas; Magdans, Uta; Gies, Hermann

2013-02-01

385

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.  

PubMed

The implementation of molecular dynamics with the united-residue (UNRES) force field is extended to treat multichain proteins. Constant temperature was maintained in the simulations with Berendsen or Langevin thermostats. The method was tested on three alpha-helical proteins (1G6U and GCN4-p1, each with two chains, and 1C94, with four chains). Simulations were carried out for both the isolated single chains and the multichain complexes. The proteins were folded by starting from the extended conformation with random initial velocities and with the chains parallel to each other. No symmetry constraints or structure information were included for the single chains or the multichain complexes. In the case of single-chain simulations, a high percentage of the trajectories (100% for 1G6U, 90% for GCN4-p1, and 80% for 1C94) converged to nativelike structures (assumed as the experimental structure of a monomer in the multichain complex), showing that, for the proteins studied in this work with the UNRES force field, the interactions between chains are not critical for stabilization of the individual chains. In the case of multichain simulations, the native structures of the 1G6U and GCN4-p1 complexes, but not that of 1C94, are predicted successfully. The association of the subunits does not follow a unique mechanism; the monomers were observed to fold both before and simultaneously with their association. PMID:17201452

Rojas, Ana V; Liwo, Adam; Scheraga, Harold A

2007-01-11

386

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

SciTech Connect

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

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

1991-08-01

387

Predictive force-field calculations for the equilibrium dimerization of isoprene  

SciTech Connect

The Diels-Alder dimerization of isoprene is an important reaction. In the present work, the QCFF force field program was used to calculate gas-phase thermodynamic properties of the monomer (isoprene) and the dimers 1-methyl-5-(1-methylethenyl)cyclohexene (diprene) and 1-methyl-4-(1-methylethenyl)cyclohexene (dipentene) for the temperature range 298.15-1000 K. These QCFF-calculated thermodynamic values were compared, when possible, with corresponding values obtained experimentally or from other force field programs, and the agreement was found to be satisfactory. The QCFF values were further used to derive gas-phase equilibrium properties--[Delta]H[sup o], [Delta]S[sup o], [Delta]G[sup o], and K[sub p]--for the isoprene dimerization reaction at various temperatures. These computational results suggest that, based upon thermodynamics, diprene and dipentene are about equally favored dimerization products of isoprene and that reported experimental data reflect kinetic control of dipentene formation at lower temperatures. The equilibrium thermodynamics data for the isoprene dimerization reaction presented in this paper are felt to be sufficiently reliable that they can be utilized in the absence of any additional experimental data. 13 refs., 4 figs., 7 tabs.

Kar, M.; Lenz, T.G.; Vaughan, J.D. (Colorado State Univ., Fort Collins, CO (United States))

1994-03-03

388

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field  

PubMed Central

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting.

a Beccara, Silvio; Skrbic, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

2013-01-01

389

Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields.  

PubMed

Streptococcus pneumoniae causes meningitis, pneumonia and severe invasive disease (IPD) in young children. Although widespread infant immunisation with the PCV7 seven-valent pneumococcal conjugate vaccine has led to a dramatic decrease in IPD, infections due to non-vaccine serotypes, particularly serotype 19A, have increased. As the 19F polysaccharide differs from 19A at a single linkage position, it was assumed that PCV7 (containing 19F) would cross-protect against 19A disease. However, vaccination with PCV7 results in only 26% effectiveness against IPD caused by 19A. We explored the conformations and dynamics of the polysaccharide repeating units from serotypes 19F and 19A, comparing free energy surfaces for glycosidic linkages with 100ns aqueous molecular dynamics simulations of the di- and trisaccharide components. All calculations were performed with both the CHARMM and the GLYCAM carbohydrate force fields to establish whether the choice of model affects the predicted molecular behaviour. Although we identified key differences between the force fields, overall they were in agreement in predicting a 19F repeating unit with a wider range of conformation families than the more restricted 19A trisaccharide. This suggests a probable conformational difference between the 19F and 19A polysaccharides, which may explain the low cross-protection of 19F vaccines against 19A disease. PMID:24681444

Kuttel, Michelle; Gordon, Marc; Ravenscroft, Neil

2014-05-22

390

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations.  

PubMed

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM. PMID:23822223

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-28

391

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

392

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

NASA Astrophysics Data System (ADS)

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

Ahsan, Syed Amir

393

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

NASA Astrophysics Data System (ADS)

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

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

2008-04-01

394

The form of augmented force-feedback fields and the efficiency and satisfaction in computer-aided pointing tasks.  

PubMed

This study investigates operation efficiency and user satisfaction for spatial and temporal shapes of augmented force-feedback fields to be used with computer pointing devices in target acquisition tasks. In an experiment, three different force-field shapes at two different mean force levels were compared, with an electromechanical force-feedback trackball as control device and with efficiency and user satisfaction as dependent variables. Efficiency was measured by the time required to perform a certain task, and user satisfaction was measured through a subjective rating procedure. Satisfaction results indicate that to a rough approximation, participants can be grouped into those who prefer high and those who prefer low force levels. Members of the former group were most satisfied with force fields with a gradual start and an abrupt ending. This force-field shape also proved to be the most efficient for both groups. When all participants were considered as a single group, none of the effects was found to be statistically significant. A gender effect was also found; in both preference groups women achieved significantly shorter task completion times than men. Actual or potential applications of this research include enabling computer interaction for people prone to repetitive strain injuries and the increment of efficiency and satisfaction in human-computer interaction in general. PMID:16170947

Keuning, Hilde; Monné, Tom K J; IJsselsteijn, Wijnand A; Houtsma, Adrianus J M

2005-01-01

395

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

SciTech Connect

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

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

2013-11-15

396

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

NASA Astrophysics Data System (ADS)

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

Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

2013-11-01

397

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

NASA Astrophysics Data System (ADS)

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

Asano, Eiji; Uchida, Toshio; Matsumoto, Ryoji

2005-04-01

398

Forcing of dissolved organic carbon release by phytoplankton by anticyclonic mesoscale eddies in the subtropical NE Atlantic Ocean  

NASA Astrophysics Data System (ADS)

The organic carbon fluxes mediated by planktonic communities in two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) at the Canary Eddy Corridor were studied and compared with the dynamics in two far-field (FF) stations located outside the eddies. We observed favorable conditions and signs for upwelling at the center of CEs and for downwelling and mixing at the centers of AEs. CEs were characterized by a higher concentration of nutrients and the highest concentration of chlorophyll a (chl a), associated with the highest abundance of microphytoplankton and diatoms. AEs displayed concentrations of chl a values and nutrients similar to those at the FF stations, except for the highest ammonium concentration occurring at AE and a very low concentration of phosphorus at FF stations. AEs were transient systems characterized by an increasing abundance of picophytoplankton and heterotrophic bacteria. While primary production was similar between the systems, the production of dissolved organic carbon (PDOC) was significantly higher in the AEs. Phytoplankton cell mortality was lowest in the CEs, and we found higher cell mortality rates at AE than at FF stations, despite similar chl a concentration. Environmental changes in the AEs have been significantly prejudicial to phytoplankton as indicated by higher phytoplankton cell mortality (60% of diatoms cells were dead) and higher cell lysis rates. The adverse conditions for phytoplankton associated with the early-stage anticyclonic systems, mainly triggered by active downwelling, resulted in higher cell mortality, forcing photosynthesized carbon to fuel the dissolved pool.

Lasternas, S.; Piedeleu, M.; Sangrà, P.; Duarte, C. M.; Agustí, S.

2013-03-01

399

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

NASA Astrophysics Data System (ADS)

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

Zhang, Longcai; Wang, Suyu; Wang, Jiasu; Zheng, Jun

2007-12-01

400

Modelling of Tool Wear Based on Component Forces  

Microsoft Academic Search

Polynomial and exponential wear models of the joint effect of different combinations of component forces or ratios were fitted to determine the wear model that would give the best approximation of actual tool wear rates. Statistical analysis revealed the combination of force ratios: F1=Ff\\/Ft, F2=Fr\\/Ft and F4 = \\u000a$$\\\\sqrt {F_f^2 + F_r^2} \\/ \\\\sqrt {F_t^2 + F_f^2 + F_r^2}$$\\u000a to

E. O. Ezugwu; K. A. Olajire; J. Bonney

2001-01-01

401

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

SciTech Connect

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

Williams, Bruce A.

2005-08-01

402

Force field development for actinyl ions via quantum mechanical calculations: an approach to account for many body solvation effects.  

PubMed

Advances in computational algorithms and methodologies make it possible to use highly accurate quantum mechanical calculations to develop force fields (pair-wise additive intermolecular potentials) for condensed phase simulations. Despite these advances, this approach faces numerous hurdles for the case of actinyl ions, AcO2(n+) (high-oxidation-state actinide dioxo cations), mainly due to the complex electronic structure resulting from an interplay of s, p, d, and f valence orbitals. Traditional methods use a pair of molecules (“dimer”) to generate a potential energy surface (PES) for force field parametrization based on the assumption that many body polarization effects are negligible. We show that this is a poor approximation for aqueous phase uranyl ions and present an alternative approach for the development of actinyl ion force fields that includes important many body solvation effects. Force fields are developed for the UO2(2+) ion with the SPC/Fw, TIP3P, TIP4P, and TIP5P water models and are validated by carrying out detailed molecular simulations on the uranyl aqua ion, one of the most characterized actinide systems. It is shown that the force fields faithfully reproduce available experimental structural data and hydration free energies. Failure to account for solvation effects when generating PES leads to overbinding between UO2(2+) and water, resulting in incorrect hydration free energies and coordination numbers. A detailed analysis of arrangement of water molecules in the first and second solvation shell of UO2(2+) is presented. The use of a simple functional form involving the sum of Lennard-Jones + Coulomb potentials makes the new force field compatible with a large number of available molecular simulation engines and common force fields. PMID:22857380

Rai, Neeraj; Tiwari, Surya P; Maginn, Edward J

2012-09-01

403

Computerized planning for multiprobe cryosurgery using a force-field analogy.  

PubMed

Cryosurgery is the destruction of undesired biological tissues by freezing. For internal organs, multiple cryoprobes are inserted into the tissue with the goal of maximizing cryoinjury within a predefined target region, while minimizing cryoinjury to the surrounding tissues. The objective of this study is to develop a computerized planning tool to determine the best locations to insert the cryoprobes, based on bioheat transfer simulations. This tool is general and suitable for all available cooling techniques and hardware. The planning procedure employs a novel iterative optimization technique based on a force-field analogy. In each iteration, a single transient bioheat transfer simulation of the cryoprocedure is computed. At the end of the simulation, regions of tissue that would have undesired temperatures apply "