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1

A reactive force field (ReaxFF) for zinc oxide  

Microsoft Academic Search

We have developed a reactive force field (FF) within the ReaxFF framework, for use in molecular dynamics (MD) simulations to investigate structures and reaction dynamics for ZnO catalysts. The force field parameters were fitted to a training set of data points (energies, geometries, charges) derived from quantum-mechanical (QM) calculations. The data points were chosen to give adequate descriptions of (the

David Raymand; Adri C. T. van Duin; Micael Baudin; Kersti Hermansson

2008-01-01

2

Development of a ReaxFF reactive force field for titanium dioxide/water systems.  

PubMed

A new ReaxFF reactive force field has been developed to describe reactions in the Ti-O-H system. The ReaxFF force field parameters have been fitted to a quantum mechanical (QM) training set containing structures and energies related to bond dissociation energies, angle and dihedral distortions, and reactions between water and titanium dioxide, as well as experimental crystal structures, heats of formation, and bulk modulus data. Model configurations for the training set were based on DFT calculations on molecular clusters and periodic systems (both bulk crystals and surfaces). ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. ReaxFF also describes the relative energetics for rutile, brookite, and anatase. The results of ReaxFF match reasonably well with those of QM for water binding energies, surface energies, and H2O dissociation energy barriers. To validate this ReaxFF description, we have compared its performance against DFT/MD simulations for 1 and 3 monolayers of water interacting with a rutile (110) surface. We found agreement within a 10% error between the DFT/MD and ReaxFF water dissociation levels for both coverages. PMID:23687907

Kim, Sung-Yup; Kumar, Nitin; Persson, Petter; Sofo, Jorge; van Duin, Adri C T; Kubicki, James D

2013-06-11

3

Molecular dynamic simulation of aluminum–water reactions using the ReaxFF reactive force field  

Microsoft Academic Search

In this study we employed the ReaxFF reactive force field to examine the dynamics associated with the dissociation of adsorbed water molecules on an aluminum nanocluster surface. We have investigated several different concentrations of water on an Al100 cluster to elucidate the dynamics of the dissociation phenomena. Our results indicate that the dissociation of an isolated water molecule on the

Michael F. Russo; Rong Li; Matthew Mench; Adri C. T. van Duin

2011-01-01

4

The ReaxFF Polarizable Reactive Force Fields for Molecular Dynamics Simulation of Ferroelectrics  

Microsoft Academic Search

We use ab initio Quantum Mechanical (QM) calculations to derive a force field that accurately describes the atomic interactions in BaTiO3 allowing, via Molecular Dynamics (MD), the simulation of thousands of atoms. A key feature of the force field (denoted ReaxFF) is that charge transfer and atomic polarization are treated self-consistently. The charge on each atom is separated into a

William A. Goddard III; Qingsong Zhang; Mustafa Uludogan; Alejandro Strachan; Tahir Cagin

2002-01-01

5

CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields  

PubMed Central

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.

Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.

2010-01-01

6

ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation.  

PubMed

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models. PMID:18197648

Chenoweth, Kimberly; van Duin, Adri C T; Goddard, William A

2008-01-16

7

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

PubMed

To investigate the reaction kinetics of hydrogen combustion at high-pressure and high-temperature conditions, we constructed a ReaxFF training set to include reaction energies and transition states relevant to hydrogen combustion and optimized the ReaxFF force field parameters against training data obtained from quantum mechanical calculations and experimental values. The optimized ReaxFF potential functions were used to run NVT MD (i.e., molecular dynamics simulation with fixed number of atoms, volume, and temperature) simulations for various H(2)/O(2) mixtures. We observed that the hydroperoxyl (HO(2)) radical plays a key role in the reaction kinetics at our input conditions (T ? 3000 K, P > 400 atm). The reaction mechanism observed is in good agreement with predictions of existing continuum-scale kinetic models for hydrogen combustion, and a transition of reaction mechanism is observed as we move from high pressure, low temperature to low pressure, high temperature. Since ReaxFF derives its parameters from quantum mechanical data and can simulate reaction pathways without any preconditioning, we believe that atomistic simulations through ReaxFF could be a useful tool in enhancing existing continuum-scale kinetic models for prediction of hydrogen combustion kinetics at high-pressure and high-temperature conditions, which otherwise is difficult to attain through experiments. PMID:21261320

Agrawalla, Satyam; van Duin, Adri C T

2011-01-25

8

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

PubMed Central

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

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

2010-01-01

9

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

PubMed

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

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

2010-06-01

10

Development of a ReaxFF reactive force field for aqueous chloride and copper chloride.  

PubMed

Copper ions play crucial roles in many enzymatic and aqueous processes. A critical analysis of the fundamental properties of copper complexes is essential to understand their impact on a wide range of chemical interactions. However the study of copper complexes is complicated by the presence of strong polarization and charge transfer effects, multiple oxidation states, and quantum effects like Jahn-Teller distortions. These complications make the experimental observations difficult to interpret. In order to provide a computationally inexpensive yet reliable method for simulation of aqueous-phase copper chemistry, ReaxFF reactive force field parameters have been developed. The force field parameters have been trained against a large set of DFT-derived energies for condensed-phase copper-chloride clusters as well as chloride/water and copper-chloride/water clusters sampled from molecular dynamics (MD) simulations. The parameters were optimized by iteratively training them against configurations generated from ReaxFF MD simulations that are performed multiple times with improved sets of parameters. This cycle was repeated until the ReaxFF results were in accordance with the DFT-derived values. We have performed MD simulations on chloride/water and copper-chloride/water systems to validate the optimized force field. The structural properties of the chloride/water system are in accord with previous experimental and computational studies. The properties of copper-chloride/water agreed with the experimental observations including evidence of the Jahn-Teller distortion. The results of this study demonstrate the applicability of ReaxFF for the precise characterization of aqueous copper chloride. This force field provides a base for the design of a computationally inexpensive tool for the investigation of various properties and functions of metal ions in industrial, environmental, and biological environments. PMID:20180586

Rahaman, Obaidur; van Duin, Adri C T; Bryantsev, Vyacheslav S; Mueller, Jonathan E; Solares, Santiago D; Goddard, William A; Doren, Douglas J

2010-03-18

11

Thermal decomposition of condensed nitromethane from molecular dynamics using the ReaxFF Reactive force field  

Microsoft Academic Search

We study the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molecular dynamics (MD) with the ReaxFF first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000-3000 K) and density 1.97 g\\/cm^3 for times up to 200 picosec. At T=3000 K the first reaction in the decomposition of

Si-Ping Han; Adri van Duin; Alejandro Strachan

2005-01-01

12

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

13

ReaxFF(MgH) reactive force field for magnesium hydride systems.  

PubMed

We have developed a reactive force field (ReaxFF(MgH)) for magnesium and magnesium hydride systems. The parameters for this force field were derived from fitting to quantum chemical (QM) data on magnesium clusters and on the equations of states for condensed phases of magnesium metal and magnesium hydride crystal. The force field reproduces the QM-derived cell parameters, density, and the equations of state for various pure Mg and MgH(2) crystal phases as well as and bond dissociation, angle bending, charge distribution, and reaction energy data for small magnesium hydride clusters. To demonstrate one application of ReaxFF(MgH), we have carried out MD simulations on the hydrogen absorption/desorption process in magnesium hydrides, focusing particularly on the size effect of MgH(2) nanoparticles on H(2) desorption kinetics. Our results show a clear relationship between grain size and heat of formation of MgH(2); as the particle size decreases, the heat of formation increases. Between 0.6 and 2.0 nm, the heat of formation ranges from -16 to -19 kcal/Mg and diverges toward that of the bulk value (-20.00 kcal/Mg) as the particle diameter increases beyond 2 nm. Therefore, it is not surprising to find that Mg nanoparticles formed by ball milling (20-100 nm) do not exhibit any significant change in thermochemical properties. PMID:16838956

Cheung, Sam; Deng, Wei-Qiao; van Duin, Adri C T; Goddard, William A

2005-02-10

14

Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups.  

PubMed

We report an optimized set of CGenFF parameters that can be used to model small molecules containing acylphosphate and N-phosphonosulfonimidoyl functional groups in combination with the CHARMM force field. Standard CGenFF procedures were followed to obtain bonded interaction parameters, which were validated by geometry optimizations, comparison to the results of calculations at the MP2/6-31+G(d) level of theory, and molecular dynamics simulations. In addition, partial atomic charges were assigned so that the energy of hydrogen bonding of the model compounds with water was correctly reproduced. The availability of these parameters will facilitate computational studies of enzymes that generate acyladenylate intermediates during catalytic turnover. In addition, given that the N-phosphonosulfonimidoyl moiety is a stable transition state analog for the reaction of ammonia with an acyladenylate, the parameters developed in this study should find use in efforts to develop novel and potent inhibitors of various glutamine-dependent amidotransferases that have been validated as drug targets. Topology and parameter files for the model compounds used in this study, which can be combined with other CGenFF parameters in computational studies of more complicated acylphosphates and N-phosphonosulfonimidates are made available. PMID:24085536

Hegazy, Lamees; Richards, Nigel G J

2013-10-02

15

Optimization and application of lithium parameters for the reactive force field, ReaxFF.  

PubMed

To make a practical molecular dynamics (MD) simulation of the large-scale reactive chemical systems of Li-H and Li-C, we have optimized parameters of the reactive force field (ReaxFF) for these systems. The parameters for this force field were obtained from fitting to the results of density functional theory (DFT) calculations on the structures and energy barriers for a number of Li-H and Li-C molecules, including Li(2), LiH, Li(2)H(2), H(3)C-Li, H(3)C-H(2)C-Li, H(2)C=C-LiH, HCCLi, H(6)C(5)-Li, and Li(2)C(2), and to the equations of state and lattice parameters for condensed phases of Li. The accuracy of the developed ReaxFF was also tested by comparison to the dissociation energies of lithium-benzene sandwich compounds and the collision behavior of lithium atoms with a C(60) buckyball. PMID:16833794

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

2005-05-26

16

Global optimization of parameters in the reactive force field ReaxFF for SiOH.  

PubMed

We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in-house GA code that is parallelized across reference data items via the message-passing interface (MPI). Details of GA tuning turn-ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive-ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force-field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields. PMID:23852672

Larsson, Henrik R; van Duin, Adri C T; Hartke, Bernd

2013-07-15

17

ReaxFF-lg: correction of the ReaxFF reactive force field for London dispersion, with applications to the equations of state for energetic materials.  

PubMed

The practical levels of density functional theory (DFT) for solids (LDA, PBE, PW91, B3LYP) are well-known not to account adequately for the London dispersion (van der Waals attraction) so important in molecular solids, leading to equilibrium volumes for molecular crystals ~10-15% too high. The ReaxFF reactive force field is based on fitting such DFT calculations and suffers from the same problem. In the paper we extend ReaxFF by adding a London dispersion term with a form such that it has low gradients (lg) at valence distances leaving the already optimized valence interactions intact but behaves as 1/R(6) for large distances. We derive here these lg corrections to ReaxFF based on the experimental crystal structure data for graphite, polyethylene (PE), carbon dioxide, and nitrogen and for energetic materials: hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX), pentaerythritol tetranitrate (PETN), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), and nitromethane (NM). After this dispersion correction the average error of predicted equilibrium volumes decreases from 18.5 to 4.2% for the above systems. We find that the calculated crystal structures and equation of state with ReaxFF-lg are in good agreement with experimental results. In particular, we examined the phase transition between ?-RDX and ?-RDX, finding that ReaxFF-lg leads to excellent agreement for both the pressure and volume of this transition occurring at ~4.8 GPa and ~2.18 g/cm(3) density from ReaxFF-lg vs 3.9 GPa and ~2.21 g/cm(3) from experiment. We expect ReaxFF-lg to improve the descriptions of the phase diagrams for other energetic materials. PMID:21888351

Liu, Lianchi; Liu, Yi; Zybin, Sergey V; Sun, Huai; Goddard, William A

2011-09-21

18

Investigation of Complex Iron Surface Catalytic Chemistry Using the ReaxFF Reactive Force Field Method  

NASA Astrophysics Data System (ADS)

To demonstrate the feasibility of classical reactive dynamics for studying complex surface chemistry, we performed a series of five reactive molecular dynamics simulations addressing the carbon monoxide methanation and the hydrocarbon chain initiation using the ReaxFF reactive force field method. We found that the catalytic surface hydrogenation initiates from the undissociated CO molecules absorbed on the surface of the catalyst as described in the oxygenate mechanism. This process leads to the generation of surface absorbed CH X - groups, which initiates the synthesis of methane and the hydrocarbon chain growth. Direct hydrogenation of the surface carbide was not observed in the simulation. Coordination analysis of the carbon atoms in the system provides possible explanations in that the surface carbon atoms are further stabilized by the surface deformation of the iron catalyst at elevated temperatures. Results from the simulations also indicated that the surface CH- could dissociate into surface carbon atoms or be further hydrogenated into CH2- radicals, which is an important intermediate species in the synthesis of methane as well as the chain initiation. Results from the C-C coupling simulation suggested the preference of coupling between CH- and CH2- groups, which agrees with the alkenyl scheme of the carbene mechanism. The overall results agree with the available experimental observations and quantum mechanics (QM) study. Furthermore, these simulations indicate the possible cooperation among different mechanisms and prove the serviceability of the ReaxFF method for studying the complex heterogeneous catalytic system. These simulations have also allowed us to evaluate the accuracy of the current ReaxFF Fe/C/O/H description, providing crucial information regarding areas where further improvement is required.

Zou, Chenyu; Van Duin, Adri

2012-12-01

19

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

PubMed

We have developed a new ReaxFF reactive force field to describe accurately reactions of hydrocarbons with vanadium oxide catalysts. The ReaxFF force field parameters have been fit to a large quantum mechanics (QM) training set containing over 700 structures and energetics related to bond dissociations, angle and dihedral distortions, and reactions between hydrocarbons and vanadium oxide clusters. In addition, the training set contains charge distributions for small vanadium oxide clusters and the stabilities of condensed-phase systems. We find that ReaxFF reproduces accurately the QM training set for structures and energetics of small clusters. Most important is that ReaxFF describes accurately the energetics for various oxidation states of the condensed phases, including V 2O 5, VO 2, and V 2O 3 in addition to metallic V (V (0)). To demonstrate the capability of the ReaxFF force field for describing catalytic processes involving vanadium oxides, we performed molecular dynamics (MD) simulation for reactions of a gas of methanol exposed to the (001) surface of V 2O 5. We find that formaldehyde is the major product, in agreement with experiment. These studies find that water desorption from surface V (III) sites is facilitated by interlayer bonding. PMID:18652441

Chenoweth, Kimberly; Duin, Adri C T van; Persson, Petter; Cheng, Mu-Jeng; Oxgaard, Jonas; Goddard Iii, William A

2008-07-25

20

Simulating the initial stage of phenolic resin carbonization via the ReaxFF reactive force field.  

PubMed

Pyrolysis of phenolic resins leads to carbon formation. Simulating this resin-to-carbon process atomistically is a daunting task. In this paper, we attempt to model the initial stage of this process by using the ReaxFF reactive force field, which bridges quantum mechanical and molecular mechanical methods. We run molecular dynamics simulations to examine the evolution of small molecules at different temperatures. The main small-molecule products found include H(2)O, H(2), CO, and C(2)H(2). We find multiple pathways leading to H(2)O formation, including a frequent channel via beta-H elimination, which has not been proposed before. We determine the reaction barrier for H(2)O formation from the reaction rates obtained at different temperatures. We also discuss the relevance of our simulations to previous experimental observations. This work represents a first attempt to model the resin-to-carbon process atomistically. PMID:19496580

Jiang, De-en; van Duin, Adri C T; Goddard, William A; Dai, Sheng

2009-06-25

21

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

Microsoft Academic Search

The dissociation of hydrogen on eight platinum surfaces, Pt(111), Pt(100), Pt(110), Pt(211), Pt(311), Pt(331), Pt(332), and Pt(533), has been studied using molecular dynamics and the reactive force field, ReaxFF. The force field, which includes the degrees of freedom of the atoms in the platinum substrate, was used unmodified with potential parameters determined from previous calculations performed on a training set

Jeffery Ludwig; Dionisios G. Vlachos; Adri C. T. van Duin; William A. Goddard

2006-01-01

22

Thermal decomposition of hydrazines from reactive dynamics using the ReaxFF reactive force field.  

PubMed

We report reactive dynamics (RD) studies on: the decomposition of bulk hydrazine (N(2)H(4)); the decomposition of bulk monomethyl-hydrazine (CH(3)N(2)H(3)), hereafter referred to simply as methyl-hydrazine; the decomposition of hydrazine in the presence of hydrogen peroxide (H(2)O(2)); and decomposition hydrazine on catalytic surfaces Pt[100] and Pt[111] under various conditions. These studies use the ReaxFF reactive force field to describe the multitude of chemical reactions in these systems for a variety of reaction conditions in order to show that this approach leads to realistic decomposition mechanisms and rates. In particular, we determined how the decomposition of hydrazine is affected by temperature, pressure, and heating rate. We analyzed chemical reaction mechanism of the decomposition of hydrazine at the studied conditions and found that at lower temperatures the initial product from hydrazine decomposition is NH(3), whereas at higher temperatures H(2) and N(2) are the dominant early products. Prominent intermediates observed during these decompositions include N(2)H(3), N(2)H(2,) and NH(2), in agreement with quantum mechanical studies (7.3 ps at 3000 K). As the heating rate is decreased, the onset for hydrazine decomposition shifts to lower temperatures. Using a constant heating rate, we found that higher pressure (increased density) favors formation of NH(3) over N(2) and H(2). In studies of the catalytic decomposition of hydrazine on surfaces Pt[100] and Pt[111], we found that the presence of a Pt-catalyst reduces the initial decomposition temperature of hydrazine by about 50%. We found that the Pt[100]-surface is 20 times more active for hydrazine decomposition than the Pt[111]-surface, in qualitative agreement with experiments. These studies indicate how ReaxFF RD can be useful in understanding the chemical processes involved in bulk and catalytic decomposition and in oxidation of reactive species under various reaction conditions. PMID:19601597

Zhang, Luzheng; Duin, Adri C T van; Zybin, Sergey V; Goddard Iii, William A

2009-08-01

23

ReaxFF Reactive Force Field for Solid Oxide Fuel Cell Systems with Application to Oxygen Ion Transport in Yttria-Stabilized Zirconia  

Microsoft Academic Search

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

Adri C. T. van Duin; Boris V. Merinov; William A. Goddard III

2008-01-01

24

Development of the ReaxFF reactive force field for mechanistic studies of catalytic selective oxidation processes on BiMoO x  

Microsoft Academic Search

We have developed a new reactive force field, ReaxFF, for use in molecular dynamics (MD) simulations to investigate the structures\\u000a and reactive dynamics of complex metal oxide catalysts. The parameters in ReaxFF are derived directly from QM and have been\\u000a validated to provide reasonable accuracy for a wide variety of reactions. We report the use of ReaxFF to study the

William A. Goddard III; Adri van Duin; Kimberly Chenoweth; Mu-Jeng Cheng; Sanja Pudar; Jonas Oxgaard; Boris Merinov; Yun Hee Jang; Petter Persson

2006-01-01

25

Molecular dynamics simulations of laser-induced incandescence of soot using an extended ReaxFF reactive force field.  

PubMed

Laser-induced incandescence (LII) of soot has developed into a popular method for making in situ measurements of soot volume fraction and primary particle sizes. However, there is still a lack of understanding regarding the generation and interpretation of the cooling signals. To model heat transfer from the heated soot particles to the surrounding gas, knowledge of the collision-based cooling as well as reactive events, including oxidation (exothermic) and evaporation (endothermic) is essential. We have simulated LII of soot using the ReaxFF reactive force field for hydrocarbon combustion. Soot was modeled as a stack of four graphene sheets linked together using sp(3) hybridized carbon atoms. To calculate the thermal accommodation coefficient of various gases with soot, graphene sheets of diameter 40 Å were used to create a soot particle containing 2691 atoms, and these simulations were carried out using the ReaxFF version incorporated into the Amsterdam Density Functional program. The reactive force field enables us to simulate the effects of conduction, evaporation, and oxidation of the soot particle on the cooling signal. Simulations were carried out for both reactive and nonreactive gas species at various pressures, and the subsequent cooling signals of soot were compared and analyzed. To correctly model N(2)-soot interactions, optimization of N-N and N-C-H force field parameters against DFT and experimental values was performed and is described in this paper. Subsequently, simulations were performed in order to find the thermal accommodation coefficients of soot with various monatomic and polyatomic gas molecules like He, Ne, Ar, N(2), CO(2), and CH(4). For all these species we find good agreement between our ReaxFF results and previously published accommodation coefficients. We thus believe that Molecular Dynamics using the ReaxFF reactive force field is a promising approach to simulate the physical and chemical aspects of soot LII. PMID:21067165

Kamat, Amar M; van Duin, Adri C T; Yakovlev, Alexei

2010-11-10

26

ReaxFF reactive force field development and applications for molecular dynamics simulations of ammonia borane dehydrogenation and combustion.  

PubMed

Ammonia borane (AB) has attracted significant attention due to its high hydrogen content (19.6% by mass). To investigate the reaction mechanism associated with the combustion of AB, a reactive force field (ReaxFF) has been developed for use in molecular dynamics (MD) simulations. The ReaxFF parameters have been derived directly from quantum mechanical data (QM). NVT-MD simulations of single- and polymolecular AB thermolysis were conducted in order to validate the force field. The release of the first equivalent H(2) is a unimolecular reaction, and MD simulations show an activation energy of 26.36 kcal mol(-1), which is in good agreement with experimental results. The release of the second H(2) is also a unimolecular reaction; however, the release of a third H(2) requires the formation of a B-N polymer. Similar simulations were conducted with a boron and oxygen system, since the oxidation of boron will be an integral step in AB combustion, and show good agreement with the established mechanism for this system. At low temperatures, boron atoms agglomerate into a cluster, which is oxidized at higher temperatures, eventually forming condensed and gas phase boron-oxide-species. These MD results provide confidence that ReaxFF can properly model the oxidation of AB and provide mechanistic insight into the AB dehydrogenation and combustion reactions. PMID:20384351

Weismiller, Michael R; van Duin, Adri C T; Lee, Jongguen; Yetter, Richard A

2010-05-01

27

High-temperature high-pressure phases of lithium from electron force field (eFF) quantum electron dynamics simulations  

PubMed Central

We recently developed the electron force field (eFF) method for practical nonadiabatic electron dynamics simulations of materials under extreme conditions and showed that it gave an excellent description of the shock thermodynamics of hydrogen from molecules to atoms to plasma, as well as the electron dynamics of the Auger decay in diamondoids following core electron ionization. Here we apply eFF to the shock thermodynamics of lithium metal, where we find two distinct consecutive phase changes that manifest themselves as a kink in the shock Hugoniot, previously observed experimentally, but not explained. Analyzing the atomic distribution functions, we establish that the first phase transition corresponds to (i) an fcc-to-cI16 phase transition that was observed previously in diamond anvil cell experiments at low temperature and (ii) a second phase transition that corresponds to the formation of a new amorphous phase (amor) of lithium that is distinct from normal molten lithium. The amorphous phase has enhanced valence electron-nucleus interactions due to localization of electrons into interstitial locations, along with a random connectivity distribution function. This indicates that eFF can characterize and compute the relative stability of states of matter under extreme conditions (e.g., warm dense matter).

Kim, Hyungjun; Su, Julius T.; Goddard, William A.

2011-01-01

28

Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field.  

PubMed

To investigate the failure of the poly(dimethylsiloxane) polymer (PDMS) at high temperatures and pressures and in the presence of various additives, we have expanded the ReaxFF reactive force field to describe carbon-silicon systems. From molecular dynamics (MD) simulations using ReaxFF we find initial thermal decomposition products of PDMS to be CH(3) radical and the associated polymer radical, indicating that decomposition and subsequent cross-linking of the polymer is initiated by Si-C bond cleavage, in agreement with experimental observations. Secondary reactions involving these CH(3) radicals lead primarily to formation of methane. We studied temperature and pressure dependence of PDMS decomposition by following the rate of production of methane in the ReaxFF MD simulations. We tracked the temperature dependency of the methane production to extract Arrhenius parameters for the failure modes of PDMS. Furthermore, we found that at increased pressures the rate of PDMS decomposition drops considerably, leading to the formation of fewer CH(3) radicals and methane molecules. Finally, we studied the influence of various additives on PDMS stability. We found that the addition of water or a SiO(2) slab has no direct effect on the short-term stability of PDMS, but addition of reactive species such as ozone leads to significantly lower PDMS decomposition temperature. The addition of nitrogen monoxide does not significantly alter the degradation temperature but does retard the initial production of methane and C(2) hydrocarbons until the nitrogen monoxide is depleted. These results, and their good agreement with available experimental data, demonstrate that ReaxFF provides a useful computational tool for studying the chemical stability of polymers. PMID:15884961

Chenoweth, Kimberly; Cheung, Sam; van Duin, Adri C T; Goddard, William A; Kober, Edward M

2005-05-18

29

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

30

A reactive force-field (ReaxFF) Monte Carlo study of surface enrichment and step structure on yttria-stabilized zirconia  

Microsoft Academic Search

To investigate surface segregation in yttria-stabilized zirconia (YSZ), DFT energies describing surface energy as a function of yttrium lattice position were used to parameterize a reactive-force field (ReaxFF). We used ReaxFF to perform Monte Carlo (MC) simulated annealing to sample structural configurations of flat YSZ (111) and vicinal YSZ (111) stepped surfaces. We evaluated yttrium surface segregation, oxygen vacancy position,

Adam D. Mayernick; Matthias Batzill; Adri C. T. van Duin; Michael J. Janik

2010-01-01

31

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.  

PubMed

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF ? ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment. PMID:21166434

Rahaman, Obaidur; van Duin, Adri C T; Goddard, William A; Doren, Douglas J

2010-12-17

32

Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization  

PubMed Central

Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF?ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.

Rahaman, Obaidur; van Duin, Adri C.T.; Goddard, William A.; Doren, Douglas J.

2011-01-01

33

Improved ReaxFF Force Field Parameters for Au-S-C-H Systems.  

PubMed

Evaluation and reparameterization of previously reported ReaxFF parameters (Järvi, T. T.; et al. J. Phys. Chem. A 2011, 115, 10315-10322) is carried out for Au-S-C-H systems. Changes in Au-S and Au-Au bond parameters and S-Au-S angle bending parameters yield improvements for bond bending potential energy surfaces. The new ReaxFF parameters lead to good agreement with density functional theory geometries of small clusters and gold-thiolate nanoparticles. The energies of Au38(SCH3)24 clusters are compared, and the new ReaxFF calculations are also in good agreement with PBE calculations for the isomer orderings. In addition, the relative energies of Au40(SCH3)24 nanoparticles and Au-thiolate SAMs are calculated using the updated parameters. These new ReaxFF parameters will enable the study of the geometries and reactivity of larger gold-thiolate nanoparticles. PMID:24041237

Bae, Gyun-Tack; Aikens, Christine M

2013-09-27

34

Simulation of titanium metal/titanium dioxide etching with chlorine and hydrogen chloride gases using the ReaxFF reactive force field.  

PubMed

In this study, a new ReaxFF reactive force field has been developed to describe reactions in Ti/O/Cl/H materials. This force field was applied to etching simulations for titanium metal and titanium dioxide with chlorine and hydrogen chloride gases. The ReaxFF force field parameters are fitted against a quantum mechanical (QM) training set containing structures and energies related to bond dissociations, angle and dihedral distortions, and reactions between titanium and chlorine gases as well as heats of formation of TiClx crystals. These newly developed Ti-Cl force field parameters were combined with a recently developed Ti-O-H force field. ReaxFF accurately reproduces the QM training set for structures and energetics of small clusters and TiClx crystals. In the etching simulations, titanium and titanium dioxide slab models with chlorine and hydrogen chloride gases were used in molecular dynamics simulations. The etching ratio between HCl and Cl2 are compared to experimental results, and satisfactory results are obtained, indicating that this ReaxFF extension provides a useful tool for studying the atomistic-scale details of the etching process. PMID:23750609

Kim, Sung-Yup; van Duin, Adri C T

2013-06-26

35

Dynamics of the dissociation of hydrogen on stepped platinum surfaces using the ReaxFF reactive force field.  

PubMed

The dissociation of hydrogen on eight platinum surfaces, Pt(111), Pt(100), Pt(110), Pt(211), Pt(311), Pt(331), Pt(332), and Pt(533), has been studied using molecular dynamics and the reactive force field, ReaxFF. The force field, which includes the degrees of freedom of the atoms in the platinum substrate, was used unmodified with potential parameters determined from previous calculations performed on a training set exclusive of the surfaces considered in this work. The energetics of the eight surfaces in the absence of hydrogen at 0 K were first compared to previous density functional theory (DFT) calculations and found to underestimate excess surface energy. However, taking Pt(111) as a reference state, we found that the trend between surfaces was adequately predicted to justify a relative comparison between the various stepped surfaces. To assess the strengths and weaknesses of the force field, we performed detailed simulations on two stepped surfaces, Pt(533) and Pt(211), and compared our findings to published experimental and theoretical results. In general, the absolute magnitude of reaction rate predictions was low, a result of the force field's tendency to underpredict surface energy. However, when normalized, the simulations show the correct linear scaling with incident energy and angular dependence at collision energies where a direct dissociation mechanism is observed. Because ReaxFF includes all degrees of freedom in the substrate, we carried out simulations aimed at understanding surface-temperature effects on Pt(533). On the basis of the results on Pt(533)/Pt(211), we studied the reaction of hydrogen at normal incidence on all eight surfaces in a range of energies where we anticipated the force field to give reasonable qualitative trends. These results were subsequently fit to a simple linear model that predicts the enhanced reactivity of surfaces containing 111-type atomic steps versus 100-type atomic steps. This model provides a simple framework for predicting high-energy/high-temperature kinetics of complex surfaces not vicinal to Pt(111). PMID:16509724

Ludwig, Jeffery; Vlachos, Dionisios G; van Duin, Adri C T; Goddard, William A

2006-03-01

36

Molecular dynamics simulations of stability of metal-organic frameworks against H2O using the ReaxFF reactive force field.  

PubMed

We introduce the reactive force field (ReaxFF) simulation to predict the hydrolysis reactions and water stability of metal-organic frameworks (MOFs) where the simulation showed that MOF-74 has superior water-resistance compared with isoreticular IRMOF-1 and IRMOF-10. PMID:20593095

Han, Sang Soo; Choi, Seung-Hoon; van Duin, Adri C T

2010-07-01

37

Molecular dynamics simulation of O2 sticking on Pt(111) using the ab initio based ReaxFF reactive force field  

Microsoft Academic Search

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O2 on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2010-01-01

38

Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures  

Microsoft Academic Search

This paper reports reactive dynamics (RD) simulations of a macro-model of Morwell Brown coal using the ReaxFF reactive force field. We find that these reactive MD simulations successfully reproduce thermal decomposition processes of defunctionalization, depolymerization and rearrangement of the residual structure observed in various experimental studies. For example, our simulations indicate that the decarboxylation and dehydroxylation of the lignin side

Elodie Salmon; Adri C. T. van Duin; François Lorant; Paul-Marie Marquaire; William A. Goddard III

2009-01-01

39

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  

Microsoft Academic Search

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

Kevin D. Nielson; Jonas Oxgaard; Wei-Qiao Deng; William A. Goddard III; William A. Goddard

2005-01-01

40

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

41

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

2008-03-19

42

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

43

Thermal Decomposition of Plastic Bonded Explosives by Molecular Dynamic Simulations with the ReaxFF Force Field  

NASA Astrophysics Data System (ADS)

Plastic bonded explosives (PBX) are a type of composite energetic materials in which a high explosive is dispersed in a polymer matrix. The main purpose of making such high explosive polymer bound is to reduce their sensitivity to shock, friction, impact, etc. Thermal decomposition is an essential process to characterize an energetic material, because it is one of main causes of initiation of the explosives. In this work, we used MD simulations with the reactive force field (ReaxFF) to study the thermal decomposition of RDX crystal boned with polyurethane chains (Estane) and with nitrocellulose chains. The simulation results showed that RDX's thermal decomposition processing varies when a polymer binder was bonded to the crystal. With addition of polymer binders, RDX's sensitivity is reduced. In all cases studied, the products such as N2, H2O, CO, CO2, OH, etc. can be identified. However, the contributions to these individual species are different: nitrocellulose has much more contributions to N2, CO2, and CO; but Estane has a little contributions to H2O and almost no contributions to N2, CO and CO2. In addition, we found that the decomposition of RDX with Estane along the Y-direction is slower than that along the X-direction.

Zhang, Luzheng

2005-03-01

44

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

2012-04-11

45

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

46

Development and validation of a ReaxFF reactive force field for Cu cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases.  

PubMed

To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis. PMID:20707333

van Duin, Adri C T; Bryantsev, Vyacheslav S; Diallo, Mamadou S; Goddard, William A; Rahaman, Obaidur; Doren, Douglas J; Raymand, David; Hermansson, Kersti

2010-09-01

47

ReaxFF reactive force field for the Y-doped BaZrO3 proton conductor with applications to diffusion rates for multigranular systems.  

PubMed

Proton-conducting perovskites such as Y-doped BaZrO 3 (BYZ) are promising candidates as electrolytes for a proton ceramic fuel cell (PCFC) that might permit much lower temperatures (from 400 to 600 degrees C). However, these materials lead to relatively poor total conductivity ( approximately 10 (-4) S/cm) because of extremely high grain boundary resistance. In order to provide the basis for improving these materials, we developed the ReaxFF reactive force field to enable molecular dynamics (MD) simulations of proton diffusion in the bulk phase and across grain boundaries of BYZ. This allows us to elucidate the atomistic structural details underlying the origin of this poor grain boundary conductivity and how it is related to the orientation of the grains. The parameters in ReaxFF were based entirely on the results of quantum mechanics (QM) calculations for systems related to BYZ. We apply here the ReaxFF to describe the proton diffusion in crystalline BYZ and across grain boundaries in BYZ. The results are in excellent agreement with experiment, validating the use of ReaxFF for studying the transport properties of these membranes. Having atomistic structures for the grain boundaries from simulations that explain the overall effect of the grain boundaries on diffusion opens the door to in silico optimization of these materials. That is, we can now use theory and simulation to examine the effect of alloying on both the interfacial structures and on the overall diffusion. As an example, these calculations suggest that the reduced diffusion of protons across the grain boundary results from the increased average distances between oxygen atoms in the interface, which necessarily leads to larger barriers for proton hopping. Assuming that this is the critical issue in grain boundary diffusion, the performance of BYZ for multigranular systems might be improved using additives that would tend to precipitate to the grain boundary and which would tend to pull the oxygens atoms together. Possibilities might be to use a small amount of larger trivalent ions, such as La or Lu or of tetravalent ions such as Hf or Th. Since ReaxFF can also be used to describe the chemical processes on the anode and cathode and the migration of ions across the electrode-membrane interface, ReaxFF opens the door to the possibility of atomistic first principles predictions on models of a complete fuel cell. PMID:18925731

van Duin, Adri C T; Merinov, Boris V; Han, Sang Soo; Dorso, Claudio O; Goddard, William A

2008-10-17

48

Molecular dynamics simulation of O2 sticking on Pt(111) using the ab initio based ReaxFF reactive force field  

NASA Astrophysics Data System (ADS)

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O2 on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF potential energy surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule's rotational energy) because of steric hindrance. In the energy range between 0.1 and 0.4 eV, the sticking probability increases, similar to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3 due to an overall less attractive ReaxFF PES compared to experiments and density functional theory. For oblique impacts, the trapping probability is reduced by the nonzero parallel momentum because of the PES corrugation and does not scale with the total incident kinetic energy. Furthermore, our simulations predict quasispecular (slightly supraspecular) distributions of angles of reflection, in accordance with molecular beam experiments. Increasing the beam energy (between 1.2 and 1.7 eV) causes the angular distributions to broaden and to exhibit a tail toward the surface normal because molecules have enough momentum to get very near the surface and thus probe more corrugated repulsive regions of the PES.

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2010-08-01

49

Molecular dynamics simulation of O2 sticking on Pt(111) using the ab initio based ReaxFF reactive force field.  

PubMed

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O(2) on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF potential energy surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule's rotational energy) because of steric hindrance. In the energy range between 0.1 and 0.4 eV, the sticking probability increases, similar to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3 due to an overall less attractive ReaxFF PES compared to experiments and density functional theory. For oblique impacts, the trapping probability is reduced by the nonzero parallel momentum because of the PES corrugation and does not scale with the total incident kinetic energy. Furthermore, our simulations predict quasispecular (slightly supraspecular) distributions of angles of reflection, in accordance with molecular beam experiments. Increasing the beam energy (between 1.2 and 1.7 eV) causes the angular distributions to broaden and to exhibit a tail toward the surface normal because molecules have enough momentum to get very near the surface and thus probe more corrugated repulsive regions of the PES. PMID:20815586

Valentini, Paolo; Schwartzentruber, Thomas E; Cozmuta, Ioana

2010-08-28

50

Formation of water at a Pt(111) surface: A study using reactive force fields (ReaxFF)  

Microsoft Academic Search

In this paper, we report preliminary studies of formation of water from molecular oxygen and hydrogen. Using a series of atomistic simulations carried at finite temperature, we describe the dynamics of water formation at a Pt catalyst using a new reactive ReaxFF potential. By performing a series of studies, we obtain statistically meaningful trajectories to extract rate constants of water

Markus J. Buehler; Adri C. T. van Duin; Timo Jacob; Yunhee Jang; Boris Berinov; William A. Goddard

51

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

PubMed

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

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

2012-11-30

52

ReaxFF Reactive Force Field Study of Oriented Attachment of TiO2 Nanocrystals in Vacuum and Humid Environments  

NASA Astrophysics Data System (ADS)

We use a ReaxFF reactive force field to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. The nanocrystals are in the 2-6nm size range, with shapes dictated by the Wulff construction. In vacuum, the nanocrystals tend to merge along their direction of approach, resulting in a polycrystal. By contrast, in the presence of water vapor, the nanocrystals tend to reorient themselves and aggregate via the oriented attachment mechanism to form a single or twinned crystal. We find that adsorbed water molecules and hydroxyl groups play multiple roles in oriented attachment. As the nanocrystals approach one another closely, adsorbed water molecules and surface hydroxyls prevent their immediate aggregation. These adsorbed species create a hydrogen bonding network, which aligns the nanoparticles in registry. Upon the eventual elimination of these species, the nanoparticles fuse into a single-crystal or twinned aggregate. We observe this aggregation mechanism for anatase(101), anatase(112), and anatase(001) surfaces, as is also seen experimentally. This indicates the important role that solvent plays in nanocrystal aggregation and how solvent can be a powerful tool for directing and controlling nanocrystal growth.

Raju, Muralikrishna; Fichthorn, Kristen; van Duin, Adri

2013-03-01

53

Molecular-dynamics-based study of the collisions of hyperthermal atomic oxygen with graphene using the ReaxFF reactive force field.  

PubMed

In this work, we have investigated the hyperthermal collisions of atomic oxygens with graphene through molecular dynamics simulations using the ReaxFF reactive force field. First, following Paci et al. (J. Phys. Chem. A 2009, 113, 4677 - 4685), 5-eV energetic collisions of atomic oxygen with a 24-atom pristine graphene sheet and a sheet with a single vacancy defect, both functionalized with oxygen atoms in the form of epoxides, were studied. We found that the removal of an O(2) molecule from the surface of the graphene sheet occurs predominantly through an Eley-Rideal-type reaction mechanism. Our results, in terms of the number of occurrences of various reactive events, compared well with those reported by Paci et al. Subsequently, energetic collisions of atomic oxygen with a 25-times-expanded pristine sheet were investigated. The steady-state oxygen coverage was found to be more than one atom per three surface carbon atoms. Under an oxygen impact, the graphene sheet was always found to buckle along its diagonal. In addition, the larger sheet exhibited trampoline-like behavior, as a result of which we observed a much larger number of inelastic scattering events than those reported by Paci et al. for the smaller system. Removal of O(2) from the larger sheet occurred strictly through an Eley-Rideal-type reaction. Investigation of the events leading to the breakup of a pristine unfunctionalized graphene sheet and the effects of the presence of a second layer beneath the graphene sheet in an AB arrangement was done through successive impacts with energetic oxygen atoms on the structures. Breakup of a graphene sheet was found to occur in two stages: epoxide formation, followed by the creation and growth of defects. Events leading to the breakup of a two-layer graphene stack included epoxide formation, transformation from an AB to an AA arrangement as a result of interlayer bonding, defect formation and expansion in the top layer, and finally erosion of the bottom layer. We observed that the breakup of the two-layer stack occurred through a sequential, layer-by-layer, erosion process. PMID:21942282

Srinivasan, Sriram Goverapet; van Duin, Adri C T

2011-10-25

54

Thermal decomposition process in algaenan of Botryococcus braunii race L. Part 2: Molecular dynamics simulations using the ReaxFF reactive force field  

Microsoft Academic Search

This paper reports ReaxFF MD simulation results on pyrolysis of a molecular model of the algaenan Botryococcus braunii race L biopolymer, specifically, ReaxFF predictions on the pyrolysis of prototypical chemical structures involving aliphatic chain esters and aldehydes. These preliminary computational experiments are then used to analyze the thermal cracking process within algaenan race L biopolymers. The simulations indicate that the

Elodie Salmon; Adri C. T. van Duin; François Lorant; Paul-Marie Marquaire; William A. Goddard III

2009-01-01

55

Combustion of an Illinois No. 6 coal char simulated using an atomistic char representation and the ReaxFF reactive force field  

Microsoft Academic Search

Coal or biomass chars are complex carbonaceous materials that are important energy sources for electricity production. Reactive molecular dynamics simulations are a useful tool to examine the chemical reactions occurring in complex processes, providing that a realistic structural representation and an applicable reactive force field can be utilized. Combustion of coal (or biomass) char is one such area were additional

Fidel Castro-Marcano; Amar M. Kamat; Michael F. Russo; Adri C. T. van Duin; Jonathan P. Mathews

56

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

Microsoft Academic Search

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

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

2006-01-01

57

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields  

Microsoft Academic Search

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds.

K. Vanommeslaeghe; E. Hatcher; C. Acharya; S. Kundu; S. Zhong; J. Shim; E. Darian; O. Guvench; P. Lopes; I. Vorobyov; A. D. Mackerell Jr.

2010-01-01

58

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.  

PubMed

The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467

Vanommeslaeghe, K; Hatcher, E; Acharya, C; Kundu, S; Zhong, S; Shim, J; Darian, E; Guvench, O; Lopes, P; Vorobyov, I; Mackerell, A D

2010-03-01

59

Parameterization of a reactive force field using a Monte Carlo algorithm.  

PubMed

Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single-parameter parabolic-search algorithm. In this study, we use a robust metropolis Monte-Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high-dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO4 hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO4 hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable. PMID:23420666

Iype, E; Hütter, M; Jansen, A P J; Nedea, S V; Rindt, C C M

2013-02-19

60

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

61

Multiparadigm modeling of dynamical crack propagation in silicon using a reactive force field.  

PubMed

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. PMID:16606278

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

2006-03-10

62

Polarizable force fields  

Microsoft Academic Search

Standard force fields used in biomolecular computing describe electrostatic interactions in terms of fixed, usually atom-centered, charges. Real physical systems, however, polarize substantially when placed in a high-dielectric medium such as water — or even when a strongly charged system approaches a neutral body in the gas phase. Such polarization strongly affects the geometry and energetics of molecular recognition. First

Thomas A Halgren; Wolfgang Damm

2001-01-01

63

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

Microsoft Academic Search

We have parameterized a reactive force field (ReaxFF) for lithium-aluminum silicates using density functional theory (DFT) calculations of structural properties of a number of bulk phase oxides, silicates and aluminates, as well as of several representative clusters. The force field parameters optimized in this study were found to predict lattice parameters and heats of formation of selected condensed phases in

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

2012-01-01

64

An atomistic simulation for 4-cyano-4'-pentylbiphenyl and its homologue with a reoptimized force field.  

PubMed

Liquid crystals playing a crucial role in material sciences show increasing potential applications in nanotechnology and industry. Generally, thermodynamic and dynamic properties of liquid crystals strongly depend on the corresponding force fields (FF); thus, it is necessary and urgent for us to establish a reliable force field for a given liquid crystal system. In this paper, we develop a new set of FF parameters for the 5CB (4-cyano-4'-pentylbiphenyl) molecule by reoptimizing some parameters of TraPPE-UA in order to reproduce the bulk density. This strategy for the construction of 5CB FF is rather advisable as it not only provides reliable values for the Lennard-Jones parameters but also reduces the computational cost and maintains FF transferability. Indeed, our simulation results show that the phase behavior, the order parameter, conformational features, neighboring molecular pair arrangements, and diffusion properties of 5CB can be reproduced very well. We further validate the transferability of this 5CB FF by extending it to the 8CB (4-cyano-4'-octylbiphenyl) system. As a result, both the nematic and the partial bilayer smectic phases (Sm-A(d)) and the nematic-isotropic and the smectic-nematic transition temperatures as well as the diffusion properties of 8CB are successfully reproduced. Therefore, this set of FF parameters originally designed for the 5CB molecule is reliable and transferable. Its effectiveness to model nCB series and molecules with similar chemical structures is expected. PMID:21338147

Zhang, Jianguo; Su, Jiaye; Guo, Hongxia

2011-02-22

65

Development of the CHARMM Force Field for Lipids  

PubMed Central

The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990’s to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed.

Pastor, R.W.; MacKerell, A.D.

2011-01-01

66

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

Microsoft Academic Search

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

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

2007-01-01

67

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

Microsoft Academic Search

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

M. Warrier; P. Pahari; S. Chaturvedi

2010-01-01

68

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

69

Development of a Reactive Force Field for Shock-Induced Chemistry in Ti/B Nanocomposite  

NASA Astrophysics Data System (ADS)

A ReaxFF reactive force field is under development for describing the physics and chemistry of Ti/B mixtures under shock compression. In this presentation, we will summarize the parameterization of the force field for the reactants and the most stable product of the reaction, TiB2 in the P6/mmm space group. We will describe the behavior of crystalline TiB2 under uniaxial and hydrostatic compression and the structure of the crystal with varying void densities as calculated with periodic DFT. In addition, we will compare the results obtained for these properties and others (e.g., lattice constants, elastic constants, bulk modulus) with the newly developed ReaxFF force field. The force field developed in this work for TiB2 is combined with Ti and B ReaxFF force fields developed previously to yield a force field suitable for describing shock-induced reactions of Ti and B. Preliminary molecular dynamics studies will also be detailed.

Quenneville, Jason

2013-03-01

70

Modeling the sorption dynamics of NaH using a reactive force field  

SciTech Connect

We have parametrized a reactive force field for NaH, ReaxFF{sub NaH}, against a training set of ab initio derived data. To ascertain that ReaxFF{sub NaH} is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF{sub NaH} was done. The results and trend of ReaxFF{sub NaH} are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF{sub NaH}. There is a good match between the two results, showing that ReaxFF{sub NaH} is correctly parametrized by the ab initio training set. ReaxFF{sub NaH} has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF{sub NaH} properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments.

Ojwang, J. G. O.; Santen, Rutger van; Kramer, Gert Jan [Schuit Institute of Catalysis, Eindhoven University of Technology, Postbus 513, 5600 MB, Den Dolech 2, Eindhoven (Netherlands); Duin, Adri C. T. van; Goddard, William A. III [Material Research Center, California Institute of Technology (Caltech), 1200 East California Boulevard, Pasadena, California 91125 (United States)

2008-04-28

71

Modeling the sorption dynamics of NaH using a reactive force field.  

PubMed

We have parametrized a reactive force field for NaH, ReaxFF(NaH), against a training set of ab initio derived data. To ascertain that ReaxFF(NaH) is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF(NaH) was done. The results and trend of ReaxFF(NaH) are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF(NaH). There is a good match between the two results, showing that ReaxFF(NaH) is correctly parametrized by the ab initio training set. ReaxFF(NaH) has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF(NaH) properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments. PMID:18447486

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

2008-04-28

72

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

73

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

74

HEMP-Hand-Displacement-Based Pseudo-Haptics: A Study of a Force Field Application  

Microsoft Academic Search

Abstract This paper introduces a novel pseudo-haptic approach called HEMP - hand-displacement-based pseudo-haptics. The main idea behind HEMP is to provide haptic-like sensations by dynamically displacing the visual representation of the user's hand. This paper studies the possible application of HEMP to the simulation of force fields (FF). The proposed hardware solution for simulating the hand displacement is based on

Andreas Pusch; Olivier Martin; Sabine Coquillart

2008-01-01

75

A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations  

Microsoft Academic Search

A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principles- based reactive force fields (ReaxFF) describe chemical reactions. Environment-dependent bond orders associated with atomic pairs and their derivatives are reused extensively with the aid of linked-list cells to minimize the computation associated with atomic n-tuple interactions (n 4 explicitly and 6 due

Ken-Ichi Nomura; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta

2008-01-01

76

Two theoretical simulations of hydrocarbons thermal cracking: Reactive force field and density functional calculations  

Microsoft Academic Search

The aim of this study was to simulate 1-methylnaphthalene (1-MNa) thermal cracking with the use of a new reactive force field, ReaxFF, and to compare it with experimental results of 1-MNa pyrolysis and density functional calculations. Thermal decomposition of polyaromatic compounds is important to understand the oils thermal cracking in geological reservoirs. Pyrolysis experiments and simulation provided useful information on

J-Philippe Leininger; Christian Minot; François Lorant

2008-01-01

77

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

78

A reactive force field for aqueous-calcium carbonate systems.  

PubMed

A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water. PMID:21850319

Gale, Julian D; Raiteri, Paolo; van Duin, Adri C T

2011-08-18

79

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

PubMed

We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for alpha-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed. PMID:20455552

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

2010-06-01

80

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

81

Improving an all-atom force field  

NASA Astrophysics Data System (ADS)

Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue ? -sheet peptide, we propose incremental changes that improve the force field’s range of applicability.

Mohanty, Sandipan; Hansmann, U. H. E.

2007-07-01

82

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles  

PubMed Central

We report a reparameterization of the glycosidic torsion ? of the Cornell et al. AMBER force field for RNA, ?OL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although ?OL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using ?OL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our ?OL force field is compared with several previous glycosidic torsion parametrizations.

2011-01-01

83

Predictions of melting, crystallization, and local atomic arrangements of aluminum clusters using a reactive force field.  

PubMed

A parametrized reactive force field model for aluminum ReaxFF(Al) has been developed based on density functional theory (DFT) data. A comparison has been made between DFT and ReaxFF(Al) outputs to ascertain whether ReaxFF(Al) is properly parametrized and to check if the output of the latter has correlation with DFT results. Further checks include comparing the equations of state of condensed phases of Al as calculated from DFT and ReaxFF(Al). There is a good match between the two results, again showing that ReaxFF(Al) is correctly parametrized as per the DFT input. Simulated annealing has been performed on aluminum clusters Al(n) using ReaxFF(Al) to find the stable isomers of the clusters. A plot of stability function versus cluster size shows the existence of highly stable clusters (magic clusters). Quantum mechanically these magic clusters arise due to the complete filling of the orbital shells. However, since force fields do not care about electrons but work on the assumption of validity of Born-Oppenheimer approximation, the magic clusters are therefore correlated with high structural symmetry. There is a rapid decline in surface energy contribution due to the triangulated nature of the surface atoms leading to higher coordination number. The bulk binding energy is computed to be 76.8 kcal/mol. This gives confidence in the suitability of ReaxFF for studying and understanding the underlying dynamics in aluminum clusters. In the quantification of the growth of cluster it is seen that as the size of the clusters increase there is preference for the coexistence of fcc/hcp orders at the expense of simple icosahedral ordering, although there is some contribution from distorted icosahedral ordering. It is found that even for aluminum clusters with 512 atoms distorted icosahedral ordering exists. For clusters with N>/=256 atoms fcc ordering dominates, which implies that at this point we are already on the threshold of bulklike bonding. PMID:19123516

Ojwang', J G O; van Santen, Rutger; Kramer, Gert Jan; van Duin, Adri C T; Goddard, William A

2008-12-28

84

Improving an all-atom force field.  

PubMed

Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516

Mohanty, Sandipan; Hansmann, U H E

2007-07-18

85

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

86

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

87

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

88

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

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

89

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

2012-03-01

90

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

91

Modeling solar force-free magnetic fields  

Microsoft Academic Search

A class of nonlinear force-free magnetic fields is presented, described in terms of the solutions to a second-order, nonlinear ordinary differential equation. These magnetic fields are three-dimensional, filling the infinite half-space above a plane where the lines of force are anchored. They model the magnetic fields of the sun over active regions with a striking geometric realism. The total energy

B. C. Low; Y. Q. Lou

1990-01-01

92

Force Potentials in Quantum Field Theory  

Microsoft Academic Search

As early as 1935 Yukawa conjectured that the nuclear force, which ties together the component nucleons into a solid nucleus, could be attributed to an intermediate field with an intrinsic mass corresponding to the range of the nuclear force. The general success of the meson theory that followed the discovery of such particles in cosmic rays, has been so great

Y. Nambu

1950-01-01

93

Multiscale modeling of interaction of alane clusters on Al(111) surfaces: A reactive force field and infrared absorption spectroscopy approach  

Microsoft Academic Search

We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to the formation of alanes via H-induced etching of aluminum atoms from the surface. The alanes

J. G. O. Ojwang; Santanu Chaudhuri; Adri C. T. van Duin; Yves J. Chabal; Jean-Francois Veyan; Rutger van Santen; Gert Jan Kramer; William A. Goddard

2010-01-01

94

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

95

A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principles-based reactive force fields (ReaxFF) describe chemical reactions. Environment-dependent bond orders associated with atomic pairs and their derivatives are reused extensively with the aid of linked-list cells to minimize the computation associated with atomic n-tuple interactions (n?4 explicitly and ?6 due to chain-rule differentiation). These n-tuple computations are made modular, so that they can be reconfigured effectively with a multiple time-step integrator to further reduce the computation time. Atomic charges are updated dynamically with an electronegativity equalization method, by iteratively minimizing the electrostatic energy with the charge-neutrality constraint. The ReaxFF-MD simulation algorithm has been implemented on parallel computers based on a spatial decomposition scheme combined with distributed n-tuple data structures. The measured parallel efficiency of the parallel ReaxFF-MD algorithm is 0.998 on 131,072 IBM BlueGene/L processors for a 1.01 billion-atom RDX system.

Nomura, Ken-Ichi; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2008-01-01

96

Additive empirical force field for hexopyranose monosaccharides.  

PubMed

We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the alpha- and beta-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute-water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids. PMID:18470966

Guvench, Olgun; Greene, Shannon N; Kamath, Ganesh; Brady, John W; Venable, Richard M; Pastor, Richard W; Mackerell, Alexander D

2008-11-30

97

Navigation guided by artificial force fields  

Microsoft Academic Search

This paper presents a new technique for controlling a user's navigation in a virtual environment. The approach intro- duces artificial force fields which act upon the user's vir- tual body such that he is guided around obstacles, rather than penetrating or colliding with them. The technique is extended to incorporate gravity into the environment. The problem of negotiating stairs during

Dongbo Xiao; Roger J. Hubbold

1998-01-01

98

Lessons Learned, Headquarters, I Field Force Vietnam Artillery.  

National Technical Information Service (NTIS)

During the period 1 November 1967 through 31 January 1968, I Field Force Vietnam Artillery continued to support United States, Vietnamese, and Free World Military Assistance Forces in II Corps Tactical Zone (CTZ). I Field Force Vietnam Artillery units, to...

1968-01-01

99

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF)  

PubMed Central

Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262–8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.

Peters, Martin B.; Yang, Yue; Wang, Bing; Fusti-Molnar, Laszlo; Weaver, Michael N.; Merz, Kenneth M.

2010-01-01

100

A 6-site force field for succinonitrile  

NASA Astrophysics Data System (ADS)

A 6-site succinonitrile force field has been developed. The model has produced proper proportions of the three succinonitrile conformers, which is necessary to avoid the thermal contraction of the plastic crystal phase around the melting point. The solid and liquid densities are about 1% lower or higher than the experimental values. The melting point of the model has been adjusted using the Gibbs-Duhem integration method. The theoretical melting point is in good agreement with experiment.

Feng, Xiaobing; Laird, Brian B.

101

Sustaining the US Air Force's Force Support Career Field through Officer Workforce Planning.  

National Technical Information Service (NTIS)

This dissertation recommends changes that can be made to the structure and management of the Air Force's Force Support officer career field to better align development of functional competencies with positional demand for those competencies. Data on Force...

K. O'Neill

2012-01-01

102

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

103

Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics.  

National Technical Information Service (NTIS)

We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molecular dynamics with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethan...

A. Strachan A. C. Van Duin I. W. Goddard S. Han

2011-01-01

104

Thermal decomposition of energetic materials by ReaxFF reactive molecular dynamics  

Microsoft Academic Search

Understanding the complex physicochemical processes that govern the initiation and decomposition kinetics of energetic materials can pave the way for modifying the explosive or propellant formulation to improve their performance and reduce the sensitivity. In this work, we used molecular dynamics (MD) simulations with the reactive force field (ReaxFF) to study the thermal decomposition of pure crystals (RDX, HMX) as

Luzheng Zhang; Sergey V. Zybin; Adri C. T. van Duin; Siddharth Dasgupta; William A. Goddard

2005-01-01

105

Fine Particle Flotation in a Centrifugal Force Field.  

National Technical Information Service (NTIS)

The effect of a centrifugal force field on hydrodynamic characteristics, flotation kinetics and separation behavior was examined. Flotation devices were designed that combine a centrifugal force field and flotation action in one apparatus. The relation be...

H. M. G. C. Tils

1990-01-01

106

Biomolecular simulations of membranes: Physical properties from different force fields  

Microsoft Academic Search

Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the

Shirley W. I. Siu; Robert Vácha; Pavel Jungwirth; Rainer A. Böckmann

2008-01-01

107

Ab initio based polarizable force field parametrization  

NASA Astrophysics Data System (ADS)

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ~30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

Masia, Marco

2008-05-01

108

Ab initio based polarizable force field parametrization.  

PubMed

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations. PMID:18532799

Masia, Marco

2008-05-14

109

Force field comparisons of the heat capacity of carbon nanotubes  

Microsoft Academic Search

The force fields Tersoff, CHARMM, COMPASS, CVFF and PCFF are compared using molecular calculations and simulations of SWNT thermal properties. The heat capacity results from the force fields vary significantly in the low (room) temperature range. The COMPASS force field best reproduces the phonon frequencies calculated from density functional theory and is consistent with the Raman scattering results. The temperature

C. Y. Guo; B. Montgomery Pettitt; L. T. Wheeler

2006-01-01

110

Hydration of calcium oxide surface predicted by reactive force field molecular dynamics.  

PubMed

In this work, we present the parametrization of Ca-O/H interactions within the reactive force field ReaxFF, and its application to study the hydration of calcium oxide surface. The force field has been fitted using density functional theory calculations on gas phase calcium-water clusters, calcium oxide bulk and surface properties, calcium hydroxide, bcc and fcc Ca, and proton transfer reactions in the presence of calcium. Then, the reactive force field has been used to study the hydration of the calcium oxide {001} surface with different water contents. Calcium oxide is used as a catalyzer in many applications such as CO(2) sequestration and biodiesel production, and the degree of surface hydroxylation is a key factor in its catalytic performance. The results show that the water dissociates very fast on CaO {001} bare surfaces without any defect or vacancy. The surface structure is maintained up to a certain amount of water, after which the surface undergoes a structural rearrangement, becoming a disordered calcium hydroxyl layer. This transformation is the most probable reason for the CaO catalytic activity decrease. PMID:22316164

Manzano, Hegoi; Pellenq, Roland J M; Ulm, Franz-Josef; Buehler, Markus J; van Duin, Adri C T

2012-02-22

111

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

112

Recent Developments and Applications of the CHARMM force fields  

PubMed Central

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

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

2011-01-01

113

Force field refinement from NMR scalar couplings  

NASA Astrophysics Data System (ADS)

NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants J reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined J couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed J couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.

Huang, Jing; Meuwly, Markus

2012-03-01

114

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

115

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

116

Motor imagery facilitates force field learning.  

PubMed

Humans have the ability to produce an internal reproduction of a specific motor action without any overt motor output. Recent findings show that the processes underlying motor imagery are similar to those active during motor execution and both share common neural substrates. This suggests that the imagery of motor movements might play an important role in acquiring new motor skills. In this study we used haptic robot in conjunction with motor imagery technique to improve learning in a robot-based adaptation task. Two groups of subjects performed reaching movements with or without motor imagery in a velocity-dependent and position-dependent mixed force field. The groups performed movements with motor imagery produced higher after effects and decreased muscle co-contraction with respect to no-motor imagery group. These results showed a positive influence of motor imagery on acquiring new motor skill and suggest that motor learning can be facilitated by mental practice and could be used to increase the rate of adaptation. PMID:21555118

Anwar, Muhammad Nabeel; Tomi, Naoki; Ito, Koji

2011-04-21

117

Theory of force-free electromagnetic fields. I. General theory  

Microsoft Academic Search

A general method to deal with the (relativistic) force-free electromagnetic field is developed. We formulate the theory without assuming symmetry of the electromagnetic field configuration. Thus we can apply it to any object where the force-free approximation is justified, e.g., the pulsar magnetosphere, the black-hole magnetosphere, and the magnetosphere around the accretion disk. We describe the force-free electromagnetic field by

Toshio Uchida

1997-01-01

118

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids  

Microsoft Academic Search

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the

Swarnalatha Y. Reddy; Fabrice Leclerc; Martin Karplus

2003-01-01

119

DREIDING: A generic force field for molecular simulations  

Microsoft Academic Search

The authors report the parameters for a new generic force field, DREIDING, that they find useful for predicting structures and dynamics of organic, biological, and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations rather than individual force constants and geometric parameters that depend on the particular combination

Stephen L. Mayo; Barry D. Olafson; Goddard Wa III

1990-01-01

120

FORCE FIELD DEVELOPMENT FOR SIMULATIONS OF CONDENSED PHASES  

Microsoft Academic Search

The focus of this review is on development of force fields for simulations of technologically important properties of fluids and materials. Of particular interest are models that can reproduce thermodynamic and transport properties over a broad range of temperatures and densities. Most existing force fields have been optimized to the configurational properties of isolated molecules and thermodynamic or structural properties

A. Z. Panagiotopoulos

121

Chapter 1 Considerations for Lipid Force Field Development  

Microsoft Academic Search

The underlying approach to development of the CHARMM lipid force field, and the current ab initio and molecular dynamics methods for optimization of each term are reviewed. Results from the recent revision of the alkane force field and new results for esters illustrate the dependence of torsional surfaces on level of theory and basis set, and how changes in the

Jeffery B. Klauda; Richard M. Venable; Alexander D. MacKerell; Richard W. Pastor

2008-01-01

122

Empirical force fields for biological macromolecules: Overview and issues  

Microsoft Academic Search

Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force

Alexander D. MacKerell Jr.

2004-01-01

123

Lessons Learned, Headquarters, I Field Force Vietnam.  

National Technical Information Service (NTIS)

During February, March, and April 1968 the United States and Free World Military Forces and the Army Republic of Vietnam (ARVN) continued operations in the 2 Corps Tactical Zone (2 CTZ); in the west along the Cambodian/Laotion/Republic of Vietnam (RVN) bo...

1968-01-01

124

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

125

Lessons Learned, Headquarters, I Field Force Vietnam.  

National Technical Information Service (NTIS)

In November, December 1966 and January 1967, United States and Free World Military Forces (FWMAF) with 41 maneuver battalions, 23 US and 18 ROK, supported by 23 artillery battalions, and Army Vietnam (ARVN) with 30 maneuver battalions supported by 6 artil...

1967-01-01

126

Structural equilibrium of DNA represented with different force fields.  

PubMed

We have recently indicated preliminary evidence of different equilibrium average structures with the CHARMM and AMBER force fields in explicit solvent molecular dynamics simulations on the DNA duplex d(C5T5) . d(A5G5) (Feig, M. and B.M. Pettitt, 1997, Experiment vs. Force Fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. (101:7361-7363). This paper presents a detailed comparison of DNA structure and dynamics for both force fields from extended simulation times of 10 ns each. Average structures display an A-DNA base geometry with the CHARMM force field and a base geometry that is intermediate between A- and B-DNA with the AMBER force field. The backbone assumes B form on both strands with the AMBER force field, while the CHARMM force field produces heterogeneous structures with the purine strand in A form and the pyrimidine strand in dynamical equilibrium between A and B conformations. The results compare well with experimental data for the cytosine/guanine part but fail to fully reproduce an overall B conformation in the thymine/adenine tract expected from crystallographic data, particularly with the CHARMM force field. Fluctuations between A and B conformations are observed on the nanosecond time scale in both simulations, particularly with the AMBER force field. Different dynamical behavior during the first 4 ns indicates that convergence times of several nanoseconds are necessary to fully establish a dynamical equilibrium in all structural quantities on the time scale of the simulations presented here. PMID:9649374

Feig, M; Pettitt, B M

1998-07-01

127

Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields  

SciTech Connect

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

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

2012-02-14

128

Is the solar chromospheric magnetic field force-free?  

NASA Astrophysics Data System (ADS)

We use observations of the Na I lambda 5896 spectral line, made with the Stokes Polarimeter at Mees Solar Observatory, to measure the chromospheric vector magnetic field in NOAA active region 7216. We compute the magnetic field from observations of the Stokes parameters at six wavelengths within this spectral line using a derivative method and calculate the height dependence of the net Lorentz force in the photosphere and low chromosphere. We conclude that the magnetic field is not force-free in the photosphere, but becomes force-free roughly 400 km above the photosphere.

Metcalf, Thomas R.; Jiao, Litao; McClymont, Alexander N.; Canfield, Richard C.; Uitenbroek, Han

1995-01-01

129

Combined shear force and near-field scanning optical microscopy  

NASA Astrophysics Data System (ADS)

A distance regulation method has been developed to enhance the reliability, versatility, and ease of use of near-field scanning optical microscopy (NSOM). The method relies on the detection of shear forces between the end of a near-field probe and the sample of interest. The system can be used solely for distance regulation in NSOM, for simultaneous shear force and near-field imaging, or for shear force microscopy alone. In the latter case, uncoated optical fiber probes are found to yield images with consistently high resolution.

Betzig, E.; Finn, P. L.; Weiner, J. S.

1992-05-01

130

New-generation amber united-atom force field.  

PubMed

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide. PMID:16805629

Yang, Lijiang; Tan, Chun-Hu; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Cieplak, Piotr; Caldwell, James; Kollman, Peter A; Luo, Ray

2006-07-01

131

Evolving Field Artillery Standard Tactical Missions for Force XXI.  

National Technical Information Service (NTIS)

This study examines the need to change the field artillery's four standard tactical missions because of the U.S. Army's evolution to Force XXI operations. Currently the field artillery organizes field artillery for combat and assigns a tactical mission (d...

N. R. Brehm

1995-01-01

132

Kelvin probe force microscopy using near-field optical tips  

Microsoft Academic Search

We report on the use of near-field optical force sensors for Kelvin probe force microscopy (KPFM) and surface potential measurements. It is shown that a very good potential sensitivity of less than 5 mV can be obtained using such tips. In addition, it is found that the contact potential difference measured using these tips is independent of the scanning height,

R. Shikler; Y Rosenwaks

2000-01-01

133

Body-force stress fields defined by caustic rosettes  

Microsoft Academic Search

The method of reflected caustics was extended to the study of elastic fields due to body forces. It was shown that gage perforations create caustics under the influence of body forces which are different in shape and size than those developed in usual cases. The elastic solution of a perforated strip under the influence of an external loadp and body

P. S. Theocaris

1988-01-01

134

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

135

Molecular dynamics simulations of methane hydrate using polarizable force fields  

SciTech Connect

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-06-14

136

Comparison of protein force fields for molecular dynamics simulations.  

PubMed

In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules. PMID:18446282

Guvench, Olgun; MacKerell, Alexander D

2008-01-01

137

Forces in Toroidal Magnetic Field Coils on the Current Unbalance.  

National Technical Information Service (NTIS)

Calculation values of mechanical loadings are presented, which influence the elements of construction and separate coils of the longitudinal field of the tokamak type device. These forces appear at the unbalance of currents neighbouring sectionized parts ...

A. S. Simakov

1980-01-01

138

Shock Induced Decomposition and Sensitivity of Energetic Materials by ReaxFF Molecular Dynamics  

Microsoft Academic Search

We develop strain-driven compression-expansion technique using molecular dynamics (MD) with reactive force fields (ReaxFF) to study the impact sensitivity of energetic materials. It has been applied to simulation of 1,3,5-trinitrohexahydro-s-triazine (RDX) crystal subjected to high-rate compression typical at the detonation front. The obtained results show that at lower compression ratio x = 1-V\\/V040%) all molecules decompose very quickly. We have

L. Zhang; S. V. Zybin; A. C. T. van Duin; S. Dasgupta; W. A. Goddard

2006-01-01

139

ReaxFF Molecular Dynamics Study of Initial Mechanism of JP-10 Combustion  

Microsoft Academic Search

By applying ReaxFF(Reactive Force field) molecular dynamics simulations, we offered a mechanism study of JP10 combustion process in perspective of statistics. Through analysis of the distribution of radicals such as H, O, OH and HO2, we discussed the chain reaction mechanisms, which related to the explosive characteristic of combustion. The first stage of combustion of JP10 is the developing of

Feng Guo; Xinlu Cheng; Hong Zhang

2012-01-01

140

Constructing ab initio force fields for molecular dynamics simulations  

Microsoft Academic Search

We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are “chemically accurate” and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body interactions in extended molecular systems. The interactions

Yi-Ping Liu; Kyungsun Kim; B. J. Berne; Richard A. Friesner; Steven W. Rick

1998-01-01

141

Constructing ab initio force fields for molecular dynamics simulations  

Microsoft Academic Search

We explore and discuss several important issues concerning the derivation of many-body force fields from ab initio quantum chemical data. In particular, we seek a general methodology for constructing ab initio force fields that are ``chemically accurate'' and are computationally efficient for large-scale molecular dynamics simulations. We investigate two approaches for modeling many-body interactions in extended molecular systems. The interactions

Yi-Ping Liu; Kyungsun Kim; B. J. Berne; Richard A. Friesner; Steven W. Rick

1998-01-01

142

Polarizable and Nonpolarizable Force Fields for Alkyl Nitrates  

Microsoft Academic Search

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

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

2008-01-01

143

Structural Equilibrium of DNA Represented with Different Force Fields  

Microsoft Academic Search

We have recently indicated preliminary evidence of different equilibrium average structures with the CHARMM and AMBER force fields in explicit solvent molecular dynamics simulations on the DNA duplex d(C5T5) · d(A5G5) (Feig, M. and B. M. Pettitt, 1997, Experiment vs. Force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. 101:7361–7363). This paper presents a detailed comparison of

Michael Feig; B. Montgomery Pettitt

1998-01-01

144

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

PubMed Central

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

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

2011-01-01

145

Multiscale modeling of interaction of alane clusters on Al(111) surfaces: A reactive force field and infrared absorption spectroscopy approach  

NASA Astrophysics Data System (ADS)

We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to the formation of alanes via H-induced etching of aluminum atoms from the surface. The alanes then agglomerate at the step edges forming stringlike conformations. The identification of these stringlike intermediates as a precursor to the bulk hydride phase allows us to explain the loss of resolution in surface IR experiments with increasing hydrogen coverage on single crystal Al(111) surface. This is in excellent agreement with the experimental works of Go et al. [E. Go, K. Thuermer, and J. E. Reutt-Robey, Surf. Sci. 437, 377 (1999)]. The mobility of alanes molecules has been studied using molecular dynamics and it is found that the migration energy barrier of Al2H6 is 2.99 kcal/mol while the prefactor is D0=2.82×10-3 cm2/s. We further investigated the interaction between an alane and an aluminum vacancy using classical molecular dynamics simulations. We found that a vacancy acts as a trap for alane, and eventually fractionates/annihilates it. These results show that ReaxFF can be used, in conjunction with ab initio methods, to study complex reactions on surfaces at both ambient and elevated temperature conditions.

Ojwang, J. G. O.; Chaudhuri, Santanu; van Duin, Adri C. T.; Chabal, Yves J.; Veyan, Jean-Francois; van Santen, Rutger; Kramer, Gert Jan; Goddard, William A.

2010-02-01

146

Multiscale modeling of interaction of alane clusters on Al(111) surfaces: a reactive force field and infrared absorption spectroscopy approach.  

PubMed

We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to the formation of alanes via H-induced etching of aluminum atoms from the surface. The alanes then agglomerate at the step edges forming stringlike conformations. The identification of these stringlike intermediates as a precursor to the bulk hydride phase allows us to explain the loss of resolution in surface IR experiments with increasing hydrogen coverage on single crystal Al(111) surface. This is in excellent agreement with the experimental works of Go et al. [E. Go, K. Thuermer, and J. E. Reutt-Robey, Surf. Sci. 437, 377 (1999)]. The mobility of alanes molecules has been studied using molecular dynamics and it is found that the migration energy barrier of Al(2)H(6) is 2.99 kcal/mol while the prefactor is D(0)=2.82 x 10(-3) cm(2)/s. We further investigated the interaction between an alane and an aluminum vacancy using classical molecular dynamics simulations. We found that a vacancy acts as a trap for alane, and eventually fractionates/annihilates it. These results show that ReaxFF can be used, in conjunction with ab initio methods, to study complex reactions on surfaces at both ambient and elevated temperature conditions. PMID:20192309

Ojwang, J G O; Chaudhuri, Santanu; van Duin, Adri C T; Chabal, Yves J; Veyan, Jean-Francois; van Santen, Rutger; Kramer, Gert Jan; Goddard, William A

2010-02-28

147

Force field parameters for the simulation of modified histone tails.  

PubMed

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all-atom force field. We also describe a CHARMM united-atom force field for modified sidechains suitable for use with fragment-based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united-atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all-atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post-translational modifications of histone tails. PMID:20652987

Grauffel, Cédric; Stote, Roland H; Dejaegere, Annick

2010-10-01

148

Vibrational spectrum and force field of dimethyldimethoxysilane  

SciTech Connect

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

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

1986-01-01

149

A transferable ab initio based force field for aqueous ions  

NASA Astrophysics Data System (ADS)

We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2 +, Ca2 +, Sr2 +, and Cl-) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.

Tazi, Sami; Molina, John J.; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu

2012-03-01

150

Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants  

SciTech Connect

The head disk interface in hard disk drive can be considered 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 the 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

151

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

152

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

153

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

154

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

155

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

156

Effective Interatomic Forces from One-Particle Crystal Field Parameters.  

National Technical Information Service (NTIS)

Theoretical results are obtained for the crystal field coefficient which enable to develop an approach to the use of the crystal field data for the derivation of information on the effective interatomic forces in crystals. The method is applied to the mag...

S. Adam G. Adam A. Corciovei

1982-01-01

157

Magnetic clouds and force-free fields with constant alpha  

Microsoft Academic Search

Magnetic clouds observed at 1 AU are modeled as cylindrically symmetric, constant alpha force-free magnetic fields. The model satisfactorily explains the types of variations of the magnetic field direction that are observed as a magnetic cloud moves past a spacecraft in terms of the possible orientations of the axis of a magnetic cloud. The model also explains why the magnetic

L. F. Burlaga

1988-01-01

158

Dielectrophoretic forces on particles in travelling electric fields  

Microsoft Academic Search

Computations are presented of the fields and forces experienced by dielectric uncharged particles subjected to travelling electric fields. The results provide an improved understanding of the various electrokinetic effects observed for particles exhibiting travelling wave dielectrophoresis, either over microelectrode structures or in channels between electrodes. The real and imaginary components of the complex dipole moment induced in a particle are

Michael P. Hughes; Ronald Pethig; Xiao-Bo Wang

1996-01-01

159

Pattern forced geophysical vector field segmentation based on Clifford FFT  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

160

Mechanical properties of amorphous LixSi alloys: a reactive force field study  

NASA Astrophysics Data System (ADS)

Silicon is a high-capacity anode material for lithium-ion batteries. Electrochemical cycling of Si electrodes usually produces amorphous LixSi (a-LixSi) alloys at room temperature. Despite intensive investigation of the electrochemical behaviors of a-LixSi alloys, their mechanical properties and underlying atomistic mechanisms remain largely unexplored. Here we perform molecular dynamics simulations to characterize the mechanical properties of a-LixSi with a newly developed reactive force field (ReaxFF). We compute the yield and fracture strengths of a-LixSi alloys under a variety of chemomechanical loading conditions, including the constrained thin-film lithiation, biaxial compression, uniaxial tension and compression. Effects of loading sequence and stress state are investigated to correlate the mechanical responses with the dominant atomic bonding, featuring a transition from the covalent to the metallic glass characteristics with increasing Li concentration. The results provide mechanistic insights for interpreting experiments, understanding properties and designing new experiments on a-LixSi alloys, which are essential to the development of durable Si electrodes for high-performance lithium-ion batteries.

Fan, Feifei; Huang, Shan; Yang, Hui; Raju, Muralikrishna; Datta, Dibakar; Shenoy, Vivek B.; van Duin, Adri C. T.; Zhang, Sulin; Zhu, Ting

2013-10-01

161

Defecting controllability of bombarding graphene with different energetic atoms via reactive force field model  

NASA Astrophysics Data System (ADS)

We study the bombardment of a suspended monolayer graphene sheet via different energetic atoms via classical molecular dynamics based on the reactive force field (ReaxFF). We find that the probability, quality, and controllability of defects are mainly determined by the impact site, the properties of the incident atom, and the incident energy. Through comparison with density functional theory calculations, we demonstrate that defects and vacancies in graphene form only in regions of sufficiently high electron density. Furthermore, the quality of defects is influenced by the bond order of the incident atom-carbon bonds, where a higher bond order leads to lower probability of pristine defects (vacancies) but a higher probability of direct-substitution. Finally, the incident energy plays an important role on the evolution and final pattern of defects in graphene. Based on the probability, quality, and controllability analysis performed, we depict a full-range energy spectrum for atomic bombardment, where we demonstrate that desirable defects such as single vacancies and direct-substitution can be created with the appropriate incident energy.

Liu, Xiao Yi; Wang, Feng Chao; Park, Harold S.; Wu, Heng An

2013-08-01

162

Simulating the Initial Stage of Phenolic-resin Carbonization via the Reactive Force Field  

SciTech Connect

Pyrolysis of phenolic resins leads to carbon formation. Simulating this resin-to-carbon process atomistically is a daunting task. In this paper, we attempt to model the initial stage of this process by using the ReaxFF reactive force field, which bridges quantum mechanical and molecular mechanical methods. We run molecular dynamics simulations to examine the evolution of small molecules at different temperatures. The main small-molecule products found include H{sub 2}O, H{sub 2}, CO, and C{sub 2}H{sub 2}. We find multiple pathways leading to H{sub 2}O formation, including a frequent channel via {beta}-H elimination, which has not been proposed before. We determine the reaction barrier for H{sub 2}O formation from the reaction rates obtained at different temperatures. We also discuss the relevance of our simulations to previous experimental observations. This work represents a first attempt to model the resin-to-carbon process atomistically.

Jiang, Deen [ORNL; Van Duin, Adri C. T. [Pennsylvania State University, University Park, PA; GoddardIII, William A [California Institute of Technology, Pasadena; Dai, Sheng [ORNL

2009-01-01

163

Predictions of melting, crystallization, and local atomic arrangements of aluminum clusters using a reactive force field  

NASA Astrophysics Data System (ADS)

A parametrized reactive force field model for aluminum ReaxFFAl has been developed based on density functional theory (DFT) data. A comparison has been made between DFT and ReaxFFAl outputs to ascertain whether ReaxFFAl is properly parametrized and to check if the output of the latter has correlation with DFT results. Further checks include comparing the equations of state of condensed phases of Al as calculated from DFT and ReaxFFAl. There is a good match between the two results, again showing that ReaxFFAl is correctly parametrized as per the DFT input. Simulated annealing has been performed on aluminum clusters Aln using ReaxFFAl to find the stable isomers of the clusters. A plot of stability function versus cluster size shows the existence of highly stable clusters (magic clusters). Quantum mechanically these magic clusters arise due to the complete filling of the orbital shells. However, since force fields do not care about electrons but work on the assumption of validity of Born-Oppenheimer approximation, the magic clusters are therefore correlated with high structural symmetry. There is a rapid decline in surface energy contribution due to the triangulated nature of the surface atoms leading to higher coordination number. The bulk binding energy is computed to be 76.8 kcal/mol. This gives confidence in the suitability of ReaxFF for studying and understanding the underlying dynamics in aluminum clusters. In the quantification of the growth of cluster it is seen that as the size of the clusters increase there is preference for the coexistence of fcc/hcp orders at the expense of simple icosahedral ordering, although there is some contribution from distorted icosahedral ordering. It is found that even for aluminum clusters with 512 atoms distorted icosahedral ordering exists. For clusters with N>=256 atoms fcc ordering dominates, which implies that at this point we are already on the threshold of bulklike bonding.

Ojwang', J. G. O.; van Santen, Rutger; Kramer, Gert Jan; van Duin, Adri C. T.; Goddard, William A.

2008-12-01

164

Optical forces on Mie particles in an Airy evanescent field.  

PubMed

Using vector potential and spectrum representation, we derive the expressions of the Airy evanescent field existed at the interface. Utilizing these expressions and the Arbitrary Beam Theory, the optical forces exerted on a Mie dielectric particle in the Airy evanescent field were theoretically investigated in detail. Numerical results show that the optical forces exhibit strong oscillations which are corresponding to the distributions of the evanescent field. With the increasing the size of particle radius, Morphology Dependent Resonance occurs for the particle with specific refractive index. PMID:23187386

Yang, Yang; Zang, Wei-Ping; Zhao, Zhi-Yu; Tian, Jian-Guo

2012-11-01

165

Interfacial force field characterization in a constrained vapor bubble thermosyphon  

Microsoft Academic Search

isothermal profiles of the extended meniscus in a quartz cuvette were measured in the earth`s gravitational field using an image analyzing interferometer that is based on computer-enhanced video microscopy of the naturally occurring interference fringes. These profiles are a function of the stress field. Experimentally, the augmented Young-Laplace equation is an excellent model for the force field at the solid-liquid-vapor

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

1995-01-01

166

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

167

Nonequilibrium forces between neutral atoms mediated by a quantum field  

SciTech Connect

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

Behunin, Ryan O. [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Hu, Bei-Lok [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States)

2010-08-15

168

Force-field calculation and geometry of the HOOO radical.  

PubMed

High-level ab initio calculations using the Davidson-corrected multireference configuration interaction (MRCI) level of theory with Dunning's correlation consistent basis sets and force-field calculations were performed for the HOOO radical. The harmonic vibrational frequencies and their anharmonic constants obtained by the force-field calculations reproduce the IR-UV experimental vibrational frequencies with errors less than 19 cm(-1). The rotational constants for the ground vibrational state obtained using the vibration-rotation interaction constants of the force-field calculations also reproduce the experimentally determined rotational constants with errors less than 0.9%, indicating that the present quantum chemical calculations and the derived spectroscopic constants have high accuracy. The equilibrium structure was determined from the experimentally determined rotational constants combined with the theoretically derived vibration-rotation interaction constants. The determined geometrical parameters agree well with the results of the present MRCI calculation. PMID:24028111

Suma, Kohsuke; Sumiyoshi, Yoshihiro; Endo, Yasuki

2013-09-01

169

An all-atom force field for metallocenes.  

PubMed

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations. PMID:17181343

Lopes, José N Canongia; do Couto, P Cabral; da Piedade, Manuel E Minas

2006-12-28

170

Development of a transferable reactive force field for cobalt.  

PubMed

ReaxFF provides a method to describe bond-breaking and bond-forming events that can be applied to large-scale molecular dynamics simulations. This article describes the development of a ReaxFF potential for cobalt. This potential is transferable to a wide variety of cobalt systems, including various crystal structures, surfaces, clusters, and defects. The potential parameters were obtained from an extensive set of ab initio calculations. We have tested these parameters against additional DFT calculations not included in the fitting data set and found that ReaxFF provides similar or superior agreement with the DFT results compared to accepted embedded atom method descriptions for Co. We validated this potential by performing large-scale molecular dynamics simulations to predict the melting point, diffusion coefficients for the liquid as a function of temperature, and vacancy-mediated diffusion coefficients in the solid as a function of temperature and vacancy concentration. Results are compared with other theoretical methods and experiments where available. Since the ReaxFF method allows straightforward extensions to alloys and heterogeneous materials, including first-row elements, the ReaxFF parameters described here provide a foundation for the simulation of a wide range of Co-containing materials. PMID:20394398

Labrosse, Matthew R; Johnson, J Karl; van Duin, Adri C T

2010-05-13

171

Minds on Physics: Fundamental Forces & Fields, Teacher's Guide  

NSDL National Science Digital Library

This teacher's guide corresponds with the Fundamental Forces & Fields book, and consists of two parts: Answers and Instructional Aids for Teachers, and Answer Sheets. The Answers and Instructional Aids for Teachers provides advice for how to optimize the effectiveness of the activities, as well as brief explanations and comments on each question in the student activities. The Answer Sheets may be duplicated and distributed to students as desired. This is the fourth in a series of six teacher guides for the Minds On Physics Activities and Reader series. This volume deals with the basics of gravitational, electric, and magnetic forces and fields.

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

2007-05-25

172

Nucleon dynamics in effective field theory of nuclear forces  

Microsoft Academic Search

Low energy nucleon dynamics in the effective field theory (EFT) of nuclear forces is investigated by using the formalism of the generalized quantum dynamics (GQD). This formalism is based on a generalized dynamical equation derived as the most general equation of motion consistent with the current concepts of quantum theory and allows one to extend quantum dynamics to the case

Renat Kh. Gainutdinov; Aigul A. Mutygullina

2002-01-01

173

A force field for virtual atom molecular mechanics of proteins.  

PubMed

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of C alpha atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes. PMID:19717427

Korkut, Anil; Hendrickson, Wayne A

2009-08-28

174

Evaluation of DNA Force Fields in Implicit Solvation  

PubMed Central

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.

Gaillard, Thomas; Case, David A.

2011-01-01

175

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

176

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations  

Microsoft Academic Search

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

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

2007-01-01

177

Force field energy functionals for image feature extraction  

Microsoft Academic Search

The overall objective in defining feature space is to reduce the dimensionality of pattern space yet maintaining discriminatory power for classification and invariant description. To meet this objective, in the context of ear biometrics, a novel force field transformation has been developed in which the image is treated as an array of Gaussian attractors that act as the source of

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

2002-01-01

178

A force field for virtual atom molecular mechanics of proteins  

PubMed Central

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of C? atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

Korkut, Anil; Hendrickson, Wayne A.

2009-01-01

179

Whole field decoupling of predistortion on polymeric cell force transducer  

NASA Astrophysics Data System (ADS)

Microfabricated polymer transducers have been developed to study cell mechanics. The key principle is to quantify the deformations on the sensor arrays induced by cell contractions and convert them into force distributions. The simplifications in deformation measurements come from the basic assumption that the deformation is solely attributed to cell contractions triggered by chemical or electrical stimuli. The diffraction moiré fringes via two polymer gratings provide whole field evolutions of distortion/strain on soft-lithography fabricated substrates. We found that the moiré patterns are able to decouple predistortions which were traditionally thought to be solely caused by cell contractile forces.

Zheng, Xiaoyu; Zhang, Xin

2011-04-01

180

Development and testing of a general amber force field.  

PubMed

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching. PMID:15116359

Wang, Junmei; Wolf, Romain M; Caldwell, James W; Kollman, Peter A; Case, David A

2004-07-15

181

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

2010-12-07

182

Thermal Decomposition of Plastic Bonded Explosives by Molecular Dynamic Simulations with the ReaxFF Force Field  

Microsoft Academic Search

Plastic bonded explosives (PBX) are a type of composite energetic materials in which a high explosive is dispersed in a polymer matrix. The main purpose of making such high explosive polymer bound is to reduce their sensitivity to shock, friction, impact, etc. Thermal decomposition is an essential process to characterize an energetic material, because it is one of main causes

Luzheng Zhang

2005-01-01

183

Field measurement of basal forces generated by erosive debris flows  

USGS Publications Warehouse

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

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

2013-01-01

184

Aggregation of carbon in an atmosphere of molecular hydrogen investigated by ReaxFF-molecular dynamics simulations  

Microsoft Academic Search

The formation of carbon and hydrocarbon molecules by aggregation of carbon in a H2 atmosphere was investigated by molecular dynamics simulations based on the Reax force field (ReaxFF). Systems of 500 carbon atoms and 1000 hydrogen molecules were simulated at different densities and temperatures from 1000K to 2000K. The majority of hydrocarbons formed during 4ns of simulation time consist of

N. Lümmen

2010-01-01

185

ReaxFF Grand Canonical Monte Carlo simulation of adsorption and dissociation of oxygen on platinum (111)  

Microsoft Academic Search

Atomic-level Grand Canonical Monte Carlo (GCMC) simulations equipped with a reactive force field (ReaxFF) are used to study atomic oxygen adsorption on a Pt(111) surface. The off-lattice GCMC calculations presented here rely solely on the interatomic potential and do not necessitate the pre-computation of surface adlayer structures and their interpolation. As such, they provide a predictive description of adsorbate phases.

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2011-01-01

186

Molecular Dynamics modeling of O2\\/Pt(111) gas-surface interaction using the ReaxFF potential  

Microsoft Academic Search

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence

Paolo Valentini; Thomas E. Schwartzentruber; Ioana Cozmuta

2011-01-01

187

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

188

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

2008-03-13

189

In-plane force fields and elastic properties of graphene  

NASA Astrophysics Data System (ADS)

Bond stretching and angle bending force fields, appropriate to describe in-plane properties of graphene sheets, are derived using first principles' methods. The obtained force fields are fitted by analytical anharmonic potential energy functions, providing efficient means of calculations in molecular mechanics simulations. Using both molecular dynamics simulations and first principles' methods, numerical results regarding the mechanical behavior of graphene monolayers under various loads, like uniaxial tension in different directions or hydrostatic tension, are presented and compared. Graphene's response in shear stress is also investigated using molecular dynamics, where a noticeable asymmetric mechanical behavior is found. Stress-strain curves and elastic constants, such as, Young modulus, Poisson's ratio, bulk modulus, and shear modulus, are calculated. Our results are compared with available experimental estimates, as well as, with corresponding theoretical calculations. Finally, the effects of the anharmonicity of the extracted bond stretching and angle bending potentials on the mechanical properties of graphene are discussed.

Kalosakas, G.; Lathiotakis, N. N.; Galiotis, C.; Papagelis, K.

2013-04-01

190

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

191

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

192

The FoldX web server: an online force field  

Microsoft Academic Search

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleicacids.ThecorefunctionalityofFoldX,namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http:\\/\\/ foldx.embl.de\\/. The current release allows the cal-

Joost Schymkowitz; Jesper Borg; Francois Stricher; Robby Nys; Frederic Rousseau; Luis Serrano

2005-01-01

193

Comparison of different force fields for the study of disaccharides  

Microsoft Academic Search

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ?-cellobiose, ?-maltose, and ?-galabiose [?-d-Galp-(1?4)-?-d-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and\\/or higher level density

Carlos A. Stortz; Glenn P. Johnson; Alfred D. French; Gábor I. Csonka

2009-01-01

194

Charge sensitivity analysis in force-field-atom resolution  

Microsoft Academic Search

Charge sensitivity analysis (CSA) was extended to AMBER force-field resolution. The effective electronegativity and hardness\\u000a data were found using evolutionary algorithms. Four model hardness matrices based on the classical electrostatic, Mataga–Nishimoto,\\u000a Ohno, and Louwen–Vogt interpolation formulae were considered. Mulliken population analysis and electrostatically derived charges\\u000a (CHELPG) were taken into account. It was demonstrated that the Ohno interpolation formula gives the

Anna Stachowicz; Anna Styrcz; Jacek Korchowiec

195

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

196

Distinct Haptic Cues Do Not Reduce Interference when Learning to Reach in Multiple Force Fields  

Microsoft Academic Search

Background: Previous studies of learning to adapt reaching movements in the presence of novel forces show that learning multiple force fields is prone to interference. Recently it has been suggested that force field learning may reflect learning to manipulate a novel object. Within this theoretical framework, interference in force field learning may be the result of static tactile or haptic

Nicholas Cothros; Jeremy Wong; Paul L. Gribble

2008-01-01

197

Comparison of different force fields for the study of disaccharides.  

PubMed

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms. PMID:19758584

Stortz, Carlos A; Johnson, Glenn P; French, Alfred D; Csonka, Gábor I

2009-08-22

198

Current Status of the AMOEBA Polarizable Force Field  

PubMed Central

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Ponder, Jay W.; Wu, Chuanjie; Ren, Pengyu; Pande, Vijay S.; Chodera, John D.; Schnieders, Michael J.; Haque, Imran; Mobley, David L.; Lambrecht, Daniel S.; DiStasio, Robert A.; Head-Gordon, Martin; Clark, Gary N. I.; Johnson, Margaret E.

2010-01-01

199

A Fast Current-Field Iteration Method for Calculating Nonlinear Force-Free Fields  

Microsoft Academic Search

Existing methods for calculating nonlinear force-free magnetic fields are slow, and are likely to be inadequate for reconstructing\\u000a coronal magnetic fields based on high-resolution vector magnetic field data from a new generation of spectro-polarimetric\\u000a instruments. In this paper a new implementation of the current-field iteration method is presented, which is simple, fast,\\u000a and accurate. The time taken by the method

M. S. Wheatland

2006-01-01

200

A Fast Current-Field Iteration Method for Calculating Nonlinear Force-Free Fields  

Microsoft Academic Search

Existing methods for calculating nonlinear force-free magnetic fields are slow, and are likely to be inadequate for reconstructing coronal magnetic fields based on high-resolution vector magnetic field data from a new generation of spectro-polarimetric instruments. In this paper a new implementation of the current-field iteration method is presented, which is simple, fast, and accurate. The time taken by the method

M. S. Wheatland

2006-01-01

201

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

Microsoft Academic Search

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

Gwen Trentham; Hans Jochen Scholl

2008-01-01

202

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

203

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

2013-07-31

204

Ab initio quantum force field for simulations of nanostructures  

NASA Astrophysics Data System (ADS)

It is demonstrated that the third generation of a recently introduced quantum mechanical polarizable force field (QMPFF) successfully reproduces experimental data on binding energies of polycyclic aromatic hydrocarbons and fullerene C60 with graphite. The QMPFF also provides an accurate description of bulk graphite and solid C60 properties. In all the studied systems, the electrostatics due to the penetration effect was found to be important and comparable in magnitude with the total interaction energy. The QMPFF predicts graphite exfoliation energy of 55meV /atom in agreement with the relatively large experimental value of 52±5meV /atom recently suggested by Zacharia [Phys. Rev. B 69, 155406 (2004)].

Donchev, A. G.

2006-12-01

205

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

2011-12-07

206

Dynamics of rotating gaseous ellipsoid in external force fields  

NASA Astrophysics Data System (ADS)

General and computationally-tractable equations are presented for the large-amplitude motion of a uniform gaseous ellipsoid rotating in an external force field. When this force is expressed as a linear function of the rectangular coordinates in the space under consideration, the equation of motion is reduced to a set of ordinary differential equations for the angular velocity, semimajor-axes of the ellipsoid, circulation, and temperature of the gaseous medium; they are integrated as an initial-value problem. Ad hoc (though fairly realistic) equations are used for cooling and viscosity to reproduce the gravitational contractions of the rotating gaseous ellipsoid. As one application, a series of equilibrium states of a uniform interstellar gas cloud in the tidal force of the Galaxy was determined, and their gravitational contraction was followed to a compact elongated structure. Two types of contractions are also found; the one is smooth contraction and the other is a violent one in which the prolate ellipsoid tumbles end-over-end with large-scale gas circulation within it.

Tatematsu, Yoshinori; Fujimoto, Mitsuaki

1990-04-01

207

Molecular Dynamics modeling of O2/Pt(111) gas-surface interaction using the ReaxFF potential  

NASA Astrophysics Data System (ADS)

We studied adsorption dynamics of O2 on Pt(111) using Molecular Dynamics (MD) simulations with the ab initio based reactive force field ReaxFF. We found good quantitative agreement with the experimental data at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF Potential Energy Surface (PES) and the progressive suppression of a steering mechanism as the translational kinetic energy (or the molecule's rotational energy) is increased. In the energy range between 0.1 eV and 0.4 eV, the sticking probability increases, similarly to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3, due to an overall less attractive ReaxFF PES compared to experiments and DFT.

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2011-05-01

208

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

209

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

210

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

211

Reactive force field potential for carbon deposition on silicon surfaces.  

PubMed

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. PMID:22914286

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

2012-08-23

212

Modeling enzymatic transition states by force field methods  

NASA Astrophysics Data System (ADS)

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

Hansen, M. B.; Jensen, H. J. A.; Jensen, F.

213

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

214

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

215

A comparison of different approaches based on force fields for coordination among multiple mobiles  

Microsoft Academic Search

This paper addresses the issue of real-time coordination among multiple mobiles, using the force fields approach. Firstly, a brief overview of different formulations of force fields is presented along with two techniques for handling multiple mobiles. Secondly, a new straight forward formulation of force fields is proposed based on the concept of closest point of approach, and following the principle

Karim ZEGHAL

1998-01-01

216

Mechanism change in hot dense liquid nitromethane decomposition: ReaxFF molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

The decomposition mechanism of hot liquid nitromethane (NM) at various compressions and temperatures was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two initial thermal decomposition schemes is observed, depending on compression. At low densities unimolecular C-N bond cleavage is the dominant route, whereas when approaching Chapman-Jouget detonation conditions the dominant mechanism switches to the formation of CH3NO fragment. The change in decomposition mechanism of hot liquid NM leads to different kinetic and energetic behavior and products distribution.

Rom, Naomi; Zybin, Sergey; van Duin, Adri; Goddard, William; Zeiri, Yehuda; Katz, Gil; Kosloff, Ronnie

2011-06-01

217

Parameterization of reactive force field: dynamics of the [Nb6O19H(x)]((8-x)-) Lindqvist polyoxoanion in bulk water.  

PubMed

We present results on parameterization of reactive force field [van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. ReaxFF: A Reactive Force Field for Hydrocarbons. J. Phys. Chem. A 2001, 105, 9396-9409] for investigating the properties of the [Nb6O19Hx]((8-x)-) Lindqvist polyoxoanion, x = 0-8, in water. Force-field parameters were fitted to an extensive data set consisting of structures and energetics obtained at the Perdew-Burke-Ernzerhof density functional level of theory. These parameters can reasonably describe pure water structure as well as water with an excess of H(+) and OH(-) ions. Molecular dynamics simulations were performed on [Nb6O19Hx]((8-x)-), x = 0-8, submerged in bulk water at 298 K. Analysis of the MD trajectories showed facile H atom transfer between the protonated polyoxoanion core and bulk water. The number of oxygen sites labeled with an H atom was found to vary depending on the pH of the solution. Detailed analysis shows that the total number of protons at bridging (terminal), ?-O (?2-O), sites ranges from 3(1) at pH 7, to 2(0) at pH 11, to 1(0) at pH 15. These findings closely reflect available experimental measurements. PMID:23394309

Kaledin, Alexey L; van Duin, Adri C T; Hill, Craig L; Musaev, Djamaladdin G

2013-03-01

218

Planetary Magnetic Fields and Solar Forcing: Implications for Atmospheric Evolution  

NASA Astrophysics Data System (ADS)

The solar wind and the solar XUV/EUV radiation constitute a permanent forcing of the upper atmosphere of the planets in our solar system, thereby affecting the habitability and chances for life to emerge on a planet. The forcing is essentially inversely proportional to the square of the distance to the Sun and, therefore, is most important for the innermost planets in our solar system—the Earth-like planets. The effect of these two forcing terms is to ionize, heat, chemically modify, and slowly erode the upper atmosphere throughout the lifetime of a planet. The closer to the Sun, the more efficient are these process. Atmospheric erosion is due to thermal and non-thermal escape. Gravity constitutes the major protection mechanism for thermal escape, while the non-thermal escape caused by the ionizing X-rays and EUV radiation and the solar wind require other means of protection. Ionospheric plasma energization and ion pickup represent two categories of non-thermal escape processes that may bring matter up to high velocities, well beyond escape velocity. These energization processes have now been studied by a number of plasma instruments orbiting Earth, Mars, and Venus for decades. Plasma measurement results therefore constitute the most useful empirical data basis for the subject under discussion. This does not imply that ionospheric plasma energization and ion pickup are the main processes for the atmospheric escape, but they remain processes that can be most easily tested against empirical data. Shielding the upper atmosphere of a planet against solar XUV, EUV, and solar wind forcing requires strong gravity and a strong intrinsic dipole magnetic field. For instance, the strong dipole magnetic field of the Earth provides a “magnetic umbrella”, fending of the solar wind at a distance of 10 Earth radii. Conversely, the lack of a strong intrinsic magnetic field at Mars and Venus means that the solar wind has more direct access to their topside atmosphere, the reason that Mars and Venus, planets lacking strong intrinsic magnetic fields, have so much less water than the Earth? Climatologic and atmospheric loss process over evolutionary timescales of planetary atmospheres can only be understood if one considers the fact that the radiation and plasma environment of the Sun has changed substantially with time. Standard stellar evolutionary models indicate that the Sun after its arrival at the Zero-Age Main Sequence (ZAMS) 4.5 Gyr ago had a total luminosity of ?70% of the present Sun. This should have led to a much cooler Earth in the past, while geological and fossil evidence indicate otherwise. In addition, observations by various satellites and studies of solar proxies (Sun-like stars with different age) indicate that the young Sun was rotating more than 10 times its present rate and had correspondingly strong dynamo-driven high-energy emissions which resulted in strong X-ray and extreme ultraviolet (XUV) emissions, up to several 100 times stronger than the present Sun. Further, evidence of a much denser early solar wind and the mass loss rate of the young Sun can be determined from collision of ionized stellar winds of the solar proxies, with the partially ionized gas in the interstellar medium. Empirical correlations of stellar mass loss rates with X-ray surface flux values allows one to estimate the solar wind mass flux at earlier times, when the solar wind may have been more than 1000 times more massive. The main conclusions drawn on basis of the Sun-in-time-, and a time-dependent model of plasma energization/escape is that: 1. Solar forcing is effective in removing volatiles, primarily water, from planets,

Lundin, Rickard; Lammer, Helmut; Ribas, Ignasi

2007-03-01

219

Towards a force field based on density fitting  

NASA Astrophysics Data System (ADS)

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n=16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.

Piquemal, Jean-Philip; Cisneros, G. Andrés; Reinhardt, Peter; Gresh, Nohad; Darden, Thomas A.

2006-03-01

220

Towards a force field based on density fitting.  

PubMed

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed. PMID:16542062

Piquemal, Jean-Philip; Cisneros, G Andrés; Reinhardt, Peter; Gresh, Nohad; Darden, Thomas A

2006-03-14

221

Towards a force field based on density fitting  

PubMed Central

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n=16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.

Piquemal, Jean-Philip; Cisneros, G. Andres; Reinhardt, Peter; Gresh, Nohad; Darden, Thomas A.

2007-01-01

222

Crowd instability analysis using velocity-field based social force model  

Microsoft Academic Search

This paper proposes a novel method to locate crowd behavior instability spatio-temporally using a velocity-field based social force model. Considering the impacts of velocity field on interaction force between individuals, we establish an improved social force model by introducing collision probability in view of velocity distribution. As compared with commonly-used social force model, which defines interaction force as a dependent

Jing Zhao; Yi Xu; Xiaokang Yang; Qing Yan

2011-01-01

223

ReaxFF molecular dynamics simulations of oxidation of toluene at high temperatures.  

PubMed

Aromatic hydrocarbon fuels, such as toluene, are important components in real jet fuels. In this work, reactive molecular dynamics (MD) simulations employing the ReaxFF reactive force field have been performed to study the high-temperature oxidation mechanisms of toluene at different temperatures and densities with equivalence ratios ranging from 0.5 to 2.0. From the ReaxFF MD simulations, we have found that the initiation consumption of toluene is mainly through three ways, (1) the hydrogen abstraction reactions by oxygen molecules or other small radicals to form the benzyl radical, (2) the cleavage of the C-H bond to form benzyl and hydrogen radicals, and (3) the cleavage of the C-C bond to form phenyl and methyl radicals. These basic reaction mechanisms are in good agreement with available chemical kinetic models. The temperatures and densities have composite effects on toluene oxidation; concerning the effect of the equivalence ratio, the oxidation reaction rate is found to decrease with the increasing of equivalence ratio. The analysis of the initiation reaction of toluene shows that the hydrogen abstraction reaction dominates the initial reaction stage at low equivalence ratio (0.5-1.0), while the contribution from the pyrolysis reaction increases significantly as the equivalence ratio increases to 2.0. The apparent activation energies, E(a), for combustion of toluene extracted from ReaxFF MD simulations are consistent with experimental results. PMID:22998396

Cheng, Xue-Min; Wang, Quan-De; Li, Juan-Qin; Wang, Jing-Bo; Li, Xiang-Yuan

2012-10-03

224

Micrometer scale resolution images of human corneal graft using full-field optical coherence tomography (FF-OCT)-link to polarimetric study of scattered field  

NASA Astrophysics Data System (ADS)

The suitability of a corneal graft for transplant surgery is based on different criteria. It may be rejected in particular due to a loss of transparency, directly linked to its scattering properties. Then, these become an important parameter. The aim of this paper is to quantify the influence of the cornea thickness and of the epithelial layer on scattering properties. The origin of scattering is discussed based on polarimetric analysis of scattered field (surface and/or bulk) and on full-field optical coherence tomography imaging (structural information).

Georges, Gaëlle; Siozade-Lamoine, Laure; Casadessus, Olivier; Deumié, Carole; Hoffart, Louis; Conrath, John

2011-09-01

225

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

226

Parametrization of a reactive force field for aluminum hydride.  

PubMed

A reactive force field, REAXFF, for aluminum hydride has been developed based on density functional theory (DFT) derived data. REAXFF(AlH(3)) is used to study the dynamics governing hydrogen desorption in AlH(3). During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by REAXFF(AlH(3)). Results on heat of desorption versus cluster size show that there is a strong dependence of the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. In the gas phase, it was observed that small alane clusters agglomerated into a bigger cluster. After agglomeration molecular hydrogen was desorbed from the structure. This thermodynamically driven spontaneous agglomeration followed by desorption of molecular hydrogen provides a mechanism on how mobile alane clusters can facilitate the mass transport of aluminum atoms during the thermal decomposition of NaAlH(4). PMID:19655888

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

2009-07-28

227

Parametrization of a reactive force field for aluminum hydride  

SciTech Connect

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

Ojwang, J. G. O. [Schuit Institute of Catalysis, Eindhoven University of Technology, Postbus 513, Den Dolech 2, Eindhoven 5600 MB (Netherlands); Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Rd. NW, Washington D.C. 20012 (United States); Santen, Rutger A. van; Kramer, Gert Jan [Schuit Institute of Catalysis, Eindhoven University of Technology, Postbus 513, Den Dolech 2, Eindhoven 5600 MB (Netherlands); Duin, Adri C. T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Goddard, William A. III [Materials and Process Simulation Center (MSC), California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125 (United States)

2009-07-28

228

Molecular dynamics simulations of methane hydrate using polarizable force fields  

SciTech Connect

Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.

Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

2007-03-01

229

Accounting for electronic polarization in non-polarizable force fields.  

PubMed

The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole ?? 3D reported in recent ab initio and experimental studies with the value ?(eff)? 2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value ?(eff) = ?/??(el), where ?(el) = 1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes. PMID:21212894

Leontyev, Igor; Stuchebrukhov, Alexei

2011-01-07

230

The effect of frequency on electric field induced surface force in red blood cell membrane  

Microsoft Academic Search

The use of electric field induced surface force acting on a red blood cell membrane to explain the observed sphering and hemolysis of the cell when exposed to the field is discussed. The frequency of the applied sinusoidal field inversely affects the field strengths at which sphering and hemolysis occur. Increase in frequency decreases the magnitude of the surface force.

Stephen K. W. Chang

1993-01-01

231

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface.  

PubMed

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from -22.9 to -33.9 kcal/mol for formaldehyde, and from -44.3 to -66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde ? HCO + H, HCO ? H + CO, and CO ? C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST-based rates are consistent with HREELS observation. PMID:23804527

Yamada, Takahiro; Phelps, Donald K; van Duin, Adri C T

2013-06-26

232

Development of a ReaxFF potential for Pd/O and application to palladium oxide formation  

NASA Astrophysics Data System (ADS)

Oxide formation on palladium surfaces impacts the activity and selectivity of Pd-based catalysts, which are widely employed under oxygen rich operating conditions. To investigate oxidation processes over Pd catalysts at time and length scales inaccessible to quantum based computational methods, we have developed a Pd/O interaction potential for the ReaxFF reactive force field. The parameters of the ReaxFF potential were fit against an extensive set of quantum data for both bulk and surface properties. Using the resulting potential, we conducted molecular dynamics simulations of oxide formation on Pd(111), Pd(110), and Pd(100) surfaces. The results demonstrate good agreement with previous experimental observations; oxygen diffusion from the surface to the subsurface occurs faster on the Pd(110) surface than on the Pd(111) and Pd(100) surfaces under comparable conditions at high temperatures and pressures. Additionally, we developed a ReaxFF-based hybrid grand canonical Monte Carlo/molecular dynamics (GC-MC/MD) approach to assess the thermodynamic stability of oxide formations. This method is used to derive a theoretical phase diagram for the oxidation of Pd935 clusters in temperatures ranging from 300 K to 1300 K and oxygen pressures ranging from 10-14 atm to 1 atm. We observe good agreement between experiment and ReaxFF, which validates the Pd/O interaction potential and demonstrates the feasibility of the hybrid GC-MC/MD method for deriving theoretical phase diagrams. This GC-MC/MD method is novel to ReaxFF, and is well suited to studies of supported-metal-oxide catalysts, where the extent of oxidation in metal clusters can significantly influence catalytic activity, selectivity, and stability.

Senftle, Thomas P.; Meyer, Randall J.; Janik, Michael J.; van Duin, Adri C. T.

2013-07-01

233

Development of a ReaxFF potential for Pd?O and application to palladium oxide formation.  

PubMed

Oxide formation on palladium surfaces impacts the activity and selectivity of Pd-based catalysts, which are widely employed under oxygen rich operating conditions. To investigate oxidation processes over Pd catalysts at time and length scales inaccessible to quantum based computational methods, we have developed a Pd?O interaction potential for the ReaxFF reactive force field. The parameters of the ReaxFF potential were fit against an extensive set of quantum data for both bulk and surface properties. Using the resulting potential, we conducted molecular dynamics simulations of oxide formation on Pd(111), Pd(110), and Pd(100) surfaces. The results demonstrate good agreement with previous experimental observations; oxygen diffusion from the surface to the subsurface occurs faster on the Pd(110) surface than on the Pd(111) and Pd(100) surfaces under comparable conditions at high temperatures and pressures. Additionally, we developed a ReaxFF-based hybrid grand canonical Monte Carlo?molecular dynamics (GC-MC?MD) approach to assess the thermodynamic stability of oxide formations. This method is used to derive a theoretical phase diagram for the oxidation of Pd935 clusters in temperatures ranging from 300 K to 1300 K and oxygen pressures ranging from 10(-14) atm to 1 atm. We observe good agreement between experiment and ReaxFF, which validates the Pd?O interaction potential and demonstrates the feasibility of the hybrid GC-MC?MD method for deriving theoretical phase diagrams. This GC-MC?MD method is novel to ReaxFF, and is well suited to studies of supported-metal-oxide catalysts, where the extent of oxidation in metal clusters can significantly influence catalytic activity, selectivity, and stability. PMID:23901962

Senftle, Thomas P; Meyer, Randall J; Janik, Michael J; van Duin, Adri C T

2013-07-28

234

Field-aligned electric field caused by the decay of force-free magnetic field and particle acceleration  

Microsoft Academic Search

Numerical simulation for the dynamics of a coronal filamentary magnetic loop has been made under the assumption that the field is initially force-free and an electric resistivity suddenly increases at a given moment due to an appearance of ion sound waves, which can be excited due to a high current density if a characteristic radius r0 of the magnetic loop

T. Takakura

1987-01-01

235

Automation of AMOEBA polarizable force field parameterization for small molecules  

PubMed Central

A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database.

Wu, Johnny C.; Chattree, Gaurav

2012-01-01

236

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

237

Distinct Haptic Cues Do Not Reduce Interference when Learning to Reach in Multiple Force Fields  

PubMed Central

Background Previous studies of learning to adapt reaching movements in the presence of novel forces show that learning multiple force fields is prone to interference. Recently it has been suggested that force field learning may reflect learning to manipulate a novel object. Within this theoretical framework, interference in force field learning may be the result of static tactile or haptic cues associated with grasp, which fail to indicate changing dynamic conditions. The idea that different haptic cues (e.g. those associated with different grasped objects) signal motor requirements and promote the learning and retention of multiple motor skills has previously been unexplored in the context of force field learning. Methodology/Principle Findings The present study tested the possibility that interference can be reduced when two different force fields are associated with differently shaped objects grasped in the hand. Human subjects were instructed to guide a cursor to targets while grasping a robotic manipulandum, which applied two opposing velocity-dependent curl fields to the hand. For one group of subjects the manipulandum was fitted with two different handles, one for each force field. No attenuation in interference was observed in these subjects relative to controls who used the same handle for both force fields. Conclusions/Significance These results suggest that in the context of the present learning paradigm, haptic cues on their own are not sufficient to reduce interference and promote learning multiple force fields.

Cothros, Nicholas; Wong, Jeremy; Gribble, Paul L.

2008-01-01

238

Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.  

PubMed

One of the conclusions drawn at the CASP4 meeting in Asilomar was that applying various force fields during refinement of template-based models tends to move predictions in the wrong direction, away from the experimentally determined coordinates. We have derived an all-atom force field aimed at protein and nucleotide optimization in vacuo (NOVA), which has been specifically designed to avoid this problem. NOVA resembles common molecular dynamics force fields but has been automatically parameterized with two major goals: (i) not to make high resolution X-ray structures worse and (ii) to improve homology models built by WHAT IF. Force-field parameters were not required to be physically correct; instead, they were optimized with random Monte Carlo moves in force-field parameter space, each one evaluated by simulated annealing runs of a 50-protein optimization set. Errors inherent to the approximate force-field equation could thus be canceled by errors in force-field parameters. Compared with the optimization set, the force field did equally well on an independent validation set and is shown to move in silico models closer to reality. It can be applied to modeling applications as well as X-ray and NMR structure refinement. A new method to assign force-field parameters based on molecular trees is also presented. A NOVA server is freely accessible at http://www.yasara.com/servers PMID:11948792

Krieger, Elmar; Koraimann, Günther; Vriend, Gert

2002-05-15

239

Fast docking using the CHARMM force field with EADock DSS.  

PubMed

The prediction of binding modes (BMs) occurring between a small molecule and a target protein of biological interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays, the universe of docking software ranges from fast and user friendly programs to algorithmically flexible and accurate approaches. EADock2 is an example of the latter. Its multiobjective scoring function was designed around the CHARMM22 force field and the FACTS solvation model. However, the major drawback of such a software design lies in its computational cost. EADock dihedral space sampling (DSS) is built on the most efficient features of EADock2, namely its hybrid sampling engine and multiobjective scoring function. Its performance is equivalent to that of EADock2 for drug-like ligands, while the CPU time required has been reduced by several orders of magnitude. This huge improvement was achieved through a combination of several innovative features including an automatic bias of the sampling toward putative binding sites, and a very efficient tree-based DSS algorithm. When the top-scoring prediction is considered, 57% of BMs of a test set of 251 complexes were reproduced within 2 Å RMSD to the crystal structure. Up to 70% were reproduced when considering the five top scoring predictions. The success rate is lower in cross-docking assays but remains comparable with that of the latest version of AutoDock that accounts for the protein flexibility. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011. PMID:21541955

Grosdidier, Aurélien; Zoete, Vincent; Michielin, Olivier

2011-05-01

240

Generating Distributed Forcing Fields for Spatial Hydrologic Modeling  

NASA Astrophysics Data System (ADS)

Spatial hydrologic modeling requires the development of distributed forcing fields of weather and precipitation. This is particularly difficult in mountainous regions of the western US, where measurement sites are limited and the landscape is dominated by complex terrain and variations in vegetation cover. The Reynolds Creek Experimental Watershed (RCEW), in southwestern Idaho offers a unique opportunity to evaluate the sensitivity of interpolation techniques to the number and location of measurement sites. The RCEW, a 239 km2 hydro-climatic observatory operated by the USDA Agricultural Research Service since the early 1960's, contains 36 hydro-climatic measurement sites for monitoring the range of weather, snow and precipitation conditions across this complex mountain watershed. The MicroMet weather distribution utility, a process and topographically based weather interpolation tool (Liston and Elder, 2006), is used to generate surfaces of temperature, humidity, wind and precipitation over the snow-dominated 55 km2 (elevation range1398-2244m) Tollgate sub-catchment of RCEW. Nineteen meteorological stations were used to simulate the distribution of weather and precipitation for a series of storms during the 2004 water year. Measured and simulated values were compared to evaluate the accuracy of the model, and a jackknife approach was used to evaluate its sensitivity to data from particular stations. To evaluate the effect of elevation and storm track, different combinations of stations were selected, and to evaluate topographic exposure and vegetation shelter stations were divided into groups based on wind exposure. Results show that, even using a sophisticated weather distribution utility like MicroMet, the interpolation is very sensitive to station location and wind exposure. A certain amount of smoothing occurs even when using all 19 stations, but significant differences occur if only protected sites (similar to NRCS Snotel sites), or only wind-exposed sites are used. This research shows that citing hydro-meteorological monitoring stations is critical to improved hydrologic modeling in mountainous regions.

Nayak, A.; Marks, D.; Chandler, D.; Winstral, A.

2006-12-01

241

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

242

Spatial Distribution of Lorentz Forces in an Applied-Field Magneto-Plasma-Dynamic Arcjet Plasma  

NASA Astrophysics Data System (ADS)

In order to clarify the electromagnetic acceleration mechanisms of an applied-field magneto-plasma-dynamic arcjet (MPDA), magnetic fields are measured in detail near the MPDA outlet. Plasma current density is calculated using the Maxwell equation (rotB=?0j), and then spatial distributions of Lorentz forces (j×B forces) are evaluated. A uniform external magnetic field is deformed by a strong diamagnetic effect near the MPDA outlet, and as a consequence, a converging magnetic nozzle configuration is formed. It is found that an axial Lorentz force Fz (=jrB?-j?Br) is almost eliminated by the deceleration force (the j?Br force), which results from the diamagnetic effect. The deceleration force can be converted to the acceleration one in an externally-applied diverging magnetic field.

Tobari, Hiroyuki; Inutake, Masaaki; Ando, Akira; Hattori, Kunihiko

243

Sales force modeling: State of the field and research agenda  

Microsoft Academic Search

Inspired by Erin Anderson’s contributions to sales force research, this paper focuses on research that utilizes quantitative\\u000a models to investigate important questions in sales force management. The purpose is to summarize several significant developments\\u000a in knowledge over the last 40 years and identify major opportunities for impactful theoretical, empirical, and decision model-based\\u000a research in the future.

Murali K. Mantrala; Sönke Albers; Fabio Caldieraro; Ove Jensen; Kissan Joseph; Manfred Krafft; Chakravarthi Narasimhan; Srinath Gopalakrishna; Andris Zoltners; Rajiv Lal; Leonard Lodish

2010-01-01

244

An optimization approach to reconstructing force-free fields from boundary data: I. Theoretical basis  

Microsoft Academic Search

The reconstruction of force-free fields from boundary data is an important problem in solar physics. Reliable reconstructions of fields in active regions may allow detailed tests of existing theories of the physics of solar flares and of coronal heating. A new method, based on minimizing a global objective function describing the departure from a force-free and solenoidal state, will be

G. Roumeliotis; M. S. Wheatland

1997-01-01

245

An optimization approach to reconstructing force-free fields from boundary data: II. Numerical results  

Microsoft Academic Search

The reconstruction of force-free fields from boundary data is an important problem in solar physics. Reliable reconstructions of fields in active regions may allow detailed tests of existing theories of the physics of solar flares and of coronal heating. A new method, based on minimizing a global objective function describing the departure from a force-free and solenoidal state, has been

M. S. Wheatland; G. Roumeliotis

1997-01-01

246

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

Microsoft Academic Search

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

David Haydock

2005-01-01

247

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software  

Microsoft Academic Search

The similarity of the AMBER force field's energy functional form with that of the CHARMM force field, gives the potential for direct translation of common bonding and nonbonding terms, along with their parameters, present in CHARMM topology and parameter files, with the intent of evaluation within the AMBER software; specifically the SANDER and PMEMD dynamics engines. To this extent, we

Michael F. Crowley; Mark J. Williamson; Ross C. Walker

2009-01-01

248

Optimisation of OPLS–UA force-field parameters for protein systems using protein data bank  

Microsoft Academic Search

We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force-field parameters for all-atom model gave structures more consistent with the experimental implications

Yoshitake Sakae; Yuko Okamoto

2010-01-01

249

Increase of force in magnetic levitation by using field cooled yttrium barium copper oxide trapped field magnets instead of ferromagnets  

NASA Astrophysics Data System (ADS)

This dissertation describes how forces in magnetic levitation systems can be increased by using YBa2Cu3Oy high temperature superconductors (HTS) cooled in the uniform field of an electromagnet (2.3 T), instead of ferromagnets. The HTS, cooled in a field greater than its maximum trapped field (Bt,max), is in the fully saturated critical state (fcsat). Hence, it produces fields equal to its Bt,max, up to 1.6 T in this work. Since commonly used permanent ferromagnets (PM), of the size used in this work, produce only up to 0.5 T, replacing the PM in levitation systems with such HTS ``trapped field magnets'' significantly increases the magnetic fields and thus the levitation forces. We also cool HTS in zero field (zfc) or adjacent to a PM or fc sat HTS (fcadj). We thus study six configurations of PM - HTS or HTS - HTS levitation: a PM or a fc sat HTS opposed by either a zfc, fcsat, or fcadj HTS. Levitation forces and lateral forces, as well as their behavior in multiple cycles of approach and retreat, are investigated. Compared to levitation systems with PM, forces increase by a factor of four to ten in configurations with fcsat HTS. Up to 393 N (125 N/cm2) are obtained. In multiple cycles, forces decrease 10-40% during the first 5-10 cycles, but then stabilize at a constant level. Experimental force-distance curves were fitted to phenomenological models. Furthermore, force maxima were calculated as functions of the maximum trapped field of the HTS following Bean's model. Lateral forces were used to estimate the stability of the different configurations. Arrangements of several zfc samples with high levitation force and good stability were demonstrated.

Hennig, Wolfgang

1999-11-01

250

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

SciTech Connect

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

G.S. Choe; C.Z. Cheng

2002-05-09

251

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.  

PubMed

Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed. PMID:15264259

Oostenbrink, Chris; Villa, Alessandra; Mark, Alan E; van Gunsteren, Wilfred F

2004-10-01

252

A novel forcing technique to simulate turbulent mixing in a decaying scalar field  

NASA Astrophysics Data System (ADS)

To realize the full potential of Direct Numerical Simulation in turbulent mixing studies, it is necessary to develop numerical schemes capable of sustaining the flow physics of turbulent scalar quantities. In this work, a new scalar field forcing technique, termed ``linear scalar forcing,'' is presented and evaluated for passive scalars. It is compared to both the well-known mean scalar gradient forcing technique and a low waveshell spectral forcing technique. The proposed forcing is designed to capture the physics of one-time scalar variance injection and the subsequent self-similar turbulent scalar field decay, whereas the mean scalar gradient forcing and low waveshell forcing techniques are representative of continuous scalar variance injection. The linear scalar forcing technique is examined over a range of Schmidt numbers, and the behavior of the proposed scalar forcing is analyzed using single and two-point statistics. The proposed scalar forcing technique is found to be perfectly isotropic, preserving accepted scalar field statistics (fluxes) and distributions (scalar quantity, dissipation rate). Additionally, it is found that the spectra resulting from the three scalar forcing techniques are comparable for unity Schmidt number conditions, but differences manifest at high Schmidt numbers. These disparities are reminiscent of those reported between scaling arguments suggested by theoretical predictions and experimental results for the viscous-convective subrange.

Carroll, Phares L.; Verma, Siddhartha; Blanquart, G.

2013-09-01

253

Prevalence of Magnetic Field Forces and Universal Symmetry of Nature  

Microsoft Academic Search

Prevalence and equivalence of attraction and repulsion forces of magnets were searched. The repulsion between S poles was stronger by 21.6 percent than the repulsion between N poles. Attraction of N pole was greater than S pole, and inverse relation of distance for magnetic attractions were different for two types of poles. Repulsion effects between the same types of poles

Yildirim Cinar

2003-01-01

254

Casimir force for a scalar field in a single brane world  

SciTech Connect

Vacuum force is an interesting low energy test for brane worlds due to its dependence on field's modes and its role in submillimeter gravity experiments. In this contribution we obtain the scalar field vacuum force between two parallel plates lying in the brane of a Randall-Sundrum scenario extended by p compact dimensions (RSII-{sub p}). We obtain the force using the Green's function technique and we compare our results with the ones obtained by using the zeta function regularization method. As a result we obtain agreement in the expression for the force independently of the method used, thus we solve a previous discrepancy between the two approaches.

Linares, R.; Morales-Tecotl, H. A. [Departamento de Fisica, Universidad Autonoma Metropolitana Iztapalapa, San Rafael Atlixco 186, C.P. 09340, Mexico D.F. (Mexico); Pedraza, O. [Centro de Estudios en Fisica y Matematicas Basicas y Aplicadas, Universidad Autonoma de Chiapas, 4a. Oriente Norte 1428, Tuxtla Gutierrez, Chiapas (Mexico)

2010-02-10

255

Reactive Molecular Dynamics of Shock and Shear-Induced Chemistry in Energetic Materials for Future Force Insensitive Munitions  

Microsoft Academic Search

We report an approach to large-scale atomistic simulations of chemical initiation processes in shocked energetic materials based on parallel implementation of the ReaxFF reactive force field. Here, we present results of reactive molecular dynamics (MD) simulations of shocked Pentaerythritol Tetranitrate (PETN) single crystal, a conventional high explosive. We study a planar wall impact to compare mechanical and chemical response at

S. V. Zybin; W. A. Goddard; Peng Xu; J. Budzien; A. Thompson

2009-01-01

256

Kirkwood-Buff derived force field for alkali chlorides in simple point charge water  

NASA Astrophysics Data System (ADS)

Solvated ions are a fundamental constituent of many biological systems. An important class consists of the alkali cations. In particular, potassium (K+) is the most abundant ion in the cytoplasm, whereas lithium (Li+), rubidium (Rb+), and cesium (Cs+) are of fundamental physicochemical and medical relevance. A powerful tool to understand ion specificity and cellular systems on a microscopic level is provided by molecular dynamics simulations. Previously, reliable force field parameters for Li+, K+, Rb+, and Cs+ in aqueous solution have not been available for the simple point charge (SPC) water model widely used in conjunction with the GROMOS force field. We used the Kirkwood-Buff theory to develop force fields for Li+, K+, Rb+, and Cs+ in SPC water to reproduce experimental data on respective aqueous alkali chloride solutions (LiCl, KCl, RbCl, CsCl). The force field developed reproduces many of the known properties of alkali metal chlorides solutions including densities and partial molar volumes. Our force field is shown to be superior to other common alkali chloride force fields in terms of reproducing the activity derivative, as a prerequisite for a realistic measure of ion-solute association underlying ion-specific phenomena (Hofmeister effects). For lithium and potassium, the ionic radii from cation-water oxygen pair correlation functions and hydration numbers are well reproduced. The force field developed will be useful for modeling physiological conditions and ion-specific phenomena for biomolecular systems.

Klasczyk, Benjamin; Knecht, Volker

2010-01-01

257

Introducing dielectrophoresis as a new force field for field-flow fractionation.  

PubMed

We present the principle of cell characterization and separation by dielectrophoretic field-flow fractionation and show preliminary experimental results. The operational device takes the form of a thin chamber in which the bottom wall supports an array of microelectrodes. By applying appropriate AC voltage signals to these electrodes, dielectrophoretic forces are generated to levitate cells suspended in the chamber and to affect their equilibrium heights. A laminar flow profile is established in the chamber so that fluid flows faster with increasing distance from the chamber walls. A cell carried in the flow stream will attain an equilibrium height, and a corresponding velocity, based on the balance of dielectrophoretic, gravitational, and hydrodynamic lift forces it experiences. We describe a theoretical model for this system and show that the cell velocity is a function of the mean fluid velocity, the voltage and frequency of the signals applied to the electrodes, and, most significantly, the cell dielectric properties. The validity of the model is demonstrated with human leukemia (HL-60) cells subjected to a parallel electrode array, and application of the device to separating HL-60 cells from peripheral blood mononuclear cells is shown. PMID:9251828

Huang, Y; Wang, X B; Becker, F F; Gascoyne, P R

1997-08-01

258

Report on geological surveys in the 300-FF-1 operable unit.  

National Technical Information Service (NTIS)

This report describes a set of geophysical surveys performed by the Pacific Northwest Laboratory at selected locations within the 300-FF-1 Operable Unit at Hanford. Field work and preliminary data processing activities were initiated in September 1989. Th...

G. A. Sandness

1991-01-01

259

Force and torque on an electric dipole by spinning light fields  

NASA Astrophysics Data System (ADS)

We calculate the optical force and torque applied to an electric dipole by a spinning light field. We find that the dissipative part of the force depends on the orbital energy flow of the field only, because the latter is related to the phase gradient generalized for such a light field. As for the remaining spin energy flow, it gives rise to an optical torque. The resulting change in the optical force is detailed for different experimentally relevant configurations, and we show in particular how this change is critical when surface plasmon modes are involved.

Canaguier-Durand, Antoine; Cuche, Aurélien; Genet, Cyriaque; Ebbesen, Thomas W.

2013-09-01

260

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

NASA Astrophysics Data System (ADS)

Parameterization of a reactive force field for NaH is done using ab initio derived data. The parameterized force field(ReaxFFNaH) is used to study the dynamics governing hydrogen desorption in NaH. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by the parameterized force field. To gain more insight into the mechanism governing structural transformation of NaH during thermal decomposition a heating run in a molecular dynamics simulation is done. The result shows that a clear signature of hydrogen desorption is the fall in potential energy surface during heating.

Ojwang', J. G. O.; van Santen, Rutger; Kramer, Gert Jan; van Duin, Adri C. T.; Goddard, William A.

2008-09-01

261

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

NASA Astrophysics Data System (ADS)

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

Knoop, Claas; Fritsching, Udo

2013-10-01

262

Singular field used to calculate the self-force on nonspinning and spinning particles  

SciTech Connect

The singular field of a point charge has recently been described in terms of a new Green's function of curved spacetime. This singular field plays an important role in the calculation of the self-force acting upon the particle. We provide a method for calculating the singular field and a catalog of expansions of the singular field associated with the geodesic motion of monopole and dipole sources for scalar, electromagnetic, and gravitational fields. These results can be used, for example, to calculate the effects of the self-force acting on a particle as it moves through spacetime.

Messaritaki, Eirini [Department of Physics, University of Florida, P.O. Box 118440, Gainesville, Florida 32611-8440 (United States) and Department of Physics, University of Wisconsin - Milwaukee, P.O. Box 413, Milwaukee, Wisconsin, 53201 (United States)

2007-05-15

263

Vertical Lorentz Force and Cross-Field Currents in the Photospheric Magnetic Fields of Solar Active Regions  

NASA Astrophysics Data System (ADS)

We demonstrate that the vertical Lorentz force and a corresponding lower limit of the cross-field electric current density can be calculated from vector magnetograms of solar active regions obtained at a single height in the solar atmosphere, provided that the vertical gradient of the magnetic field strength is known at this height. We use a predicted vertical magnetic field gradient derived from a previous analysis. By testing various force-free solutions, we find that the numerical accuracy of our method is satisfactory. Applying the method to active region photospheric vector magnetograms, we find vertical Lorentz forces ranging from several hundredths to a few tenths of the typical photospheric gravitational force, and typical cross-field current densities up to several times 10 mA m-2. The typical vertical current density is found to be 2-3 times smaller, on the order of 10-15 mA m-2. These differences are above the associated uncertainties. The values of the cross-field currents decrease in an averaged vector magnetogram, but the ratio of the cross-field to the vertical current density increases, also above the uncertainties. We conclude that the photospheric active region magnetic fields are not force-free, contrary to the conjectures of some recent studies.

Georgoulis, Manolis K.; LaBonte, Barry J.

2004-11-01

264

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

265

Gait Rehabilitation therapy using robot generated force fields applied at the pelvis  

Microsoft Academic Search

The Robotic Gait Rehabilitation (RGR) Trainer was designed and built to target secondary gait deviations in patients post - stroke. While patients ambulate on a treadmill, force fields are applied to the pelvis, which generate corrective forces as a response to deviations from normal pelvic motion. The device is coupled to the patient via an orthopedic brace, and a linear

M. Pietrusinski; I. Cajigas; Y. Mizikacioglu; M. Goldsmith; P. Bonato; C. Mavroidis

2010-01-01

266

Flow Forces on Seaweeds: Field Evidence for Roles of Wave Impingement and Organism Inertia  

Microsoft Academic Search

Hydrodynamic forces dislodge and kill large numbers of organisms in intertidal and subtidal habitats along rocky shores. Although this feature of wave-driven water motion is well recognized, the mechanics of force imposition on compliant organisms is incompletely under- stood. Here we undertake a field examination of two pro- cesses that are thought to impose many of the more dan- gerous

BRIAN GAYLORD; MARK W. DENNY; M. A. R. KOEHL

267

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

Microsoft Academic Search

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

J. J. Aly

1984-01-01

268

Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields  

Microsoft Academic Search

We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K+ ion is calculated along

Toby W. Allen; Turgut Ba?tu?; Serdar Kuyucak; Shin-Ho Chung

2003-01-01

269

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

270

Effect of magnetic fields on combustion electromotive force  

Microsoft Academic Search

A magnetic field is observed to affect the electrical response of a system burning under self-propagating high-temperature\\u000a synthesis conditions. With the synthesis of lithium ferrite as an example, it is shown that, depending on its strength and\\u000a direction, applying a magnetic field induces different forms of response. The greatest effect is observed in the postprocess\\u000a region. Possible reasons for the

Yu. G. Morozov; M. V. Kuznetsov

1999-01-01

271

Evaluation of Site 26CK3906 on the Air Force Auxiliary Field, Indian Springs, Nevada.  

National Technical Information Service (NTIS)

Archeological testing and evaluation of site 26CK3906 on the Indian Springs Air Force Auxiliary Field (AFAF), Clark County, Nevada, was conducted by the Quaternary Sciences Center, Desert Research Institute (DRI), under contract with the National Park Ser...

S. D. Livingston L. C. Pippin

1989-01-01

272

Radiation of sound from a plate excited by a nonuniform field of random forces  

NASA Astrophysics Data System (ADS)

The influence of nonuniformity in a field of random forces on the acoustic pressure generated by a plate in a fluid is investigated. It is shown that the nonuniformity of the acoustic pressure in the fluid is much smaller than in the field of the forces driving the plate, both in the case of a plate without reinforcing beams and in the case of a beam-reinforced plate.

Romanov, V. N.

1985-04-01

273

Electric Field Force Features-Harmonic Representation for 3D Shape Similarity  

Microsoft Academic Search

This paper proposes a novel shape representation “electric force features”, which is based on electric field theory. This\\u000a representation has several benefits. First, it is invariant to scale and rigid transform. Second, it can represent complex\\u000a and ill-defined models because of its physical background. 3D model supposed as charged body, we get the electric field force\\u000a distribution by placing some

Yujie Liu; Zongmin Li; Hua Li

2006-01-01

274

New force fields for nitrous oxide and oxygen and their application to phase equilibria simulations  

Microsoft Academic Search

New force fields for nitrous oxide and oxygen, based on a Lennard–Jones plus point charge functional form are reported. The Lennard–Jones parameters of size and energy as well as the point charges were determined by fitting to single-component vapor–liquid equilibrium data. The new force fields accurately describe the vapor–liquid coexistance curves of nitrous oxide and oxygen. It is shown that

Niels Hansen; Felix A. B. Agbor; Frerich J. Keil

2007-01-01

275

An amber compatible molecular mechanics force field for the anticancer drug topotecan  

Microsoft Academic Search

A molecular mechanics (MM) force field has been developed for the topotecan (TPT) molecule, an anticancer drug the only molecular\\u000a target of which is the human topoisomerase I-DNA covalent complex. We proceeded according to the amber03 force field parametrization protocol, based on quantum mechanical calculations with solvent effects included by means of\\u000a continuum models. An adequate description of the electronic

Giovanni ChillemiAndrea Coletta; Andrea Coletta; Giordano Mancini; Nico Sanna; Alessandro Desideri

2010-01-01

276

Conformational Study of MetEnkephalin Based on the ECEPP Force Fields  

Microsoft Academic Search

We report a computational study of the small peptide Met-enkephalin based on the ECEPP\\/2 and ECEPP\\/3 force fields using the basin paving method. We have located a new global minimum when using the ECEPP\\/3 force field with peptide angles ? fixed at 180°. With this new result, we can conclude that the lowest energy configurations of Met-enkephalin predicted based on

Lixin Zhan; Jeff Z. Y. Chen; Wing-Ki Liu

2006-01-01

277

Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field  

Microsoft Academic Search

A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acids was developed for 2-thiouracil and 4-thiouracil, two naturally modified RNA bases. The new parameters allow for molecular modeling and molecular dynamics simulations of RNA containing 2-thiouracil and 4-thiouracil. Over the last several years, the main goal of molecular biology became the understanding

J. Sarzy?ska; T. Kuli?ski

2005-01-01

278

Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids  

Microsoft Academic Search

GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional

M. B. Tessier; M. L. DeMarco; A. B. Yongye; R. J. Woods

2008-01-01

279

Thermal decomposition of energetic materials by ReaxFF reactive molecular dynamics  

NASA Astrophysics Data System (ADS)

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

Zhang, L.

2005-07-01

280

Thermal decomposition of condensed-phase nitromethane from molecular dynamics from ReaxFF reactive dynamics.  

PubMed

We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH(3)NO(2)) using molecular dynamics with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000-3000 K) and density 1.97 g/cm(3) for times up to 200 ps. At T = 3000 K the first reaction in the decomposition of nitromethane is an intermolecular proton transfer leading to CH(3)NOOH and CH(2)NO(2). For lower temperatures (T = 2500 and 2000 K) the first reaction during decomposition is often an isomerization reaction involving the scission of the C-N bond the formation of a C-O bond to form methyl nitrate (CH(3)ONO). Also at very early times we observe intramolecular proton transfer events. The main product of these reactions is H(2)O which starts forming following those initiation steps. The appearance of H(2)O marks the beginning of the exothermic chemistry. Recent quantum-mechanics-based molecular dynamics simulations on the chemical reactions and time scales for decomposition of a crystalline sample heated to T = 3000 K for a few picoseconds are in excellent agreement with our results, providing an important, direct validation of ReaxFF. PMID:21542572

Han, Si-ping; van Duin, Adri C T; Goddard, William A; Strachan, Alejandro

2011-05-04

281

Shock Induced Decomposition and Sensitivity of Energetic Materials by ReaxFF Molecular Dynamics  

NASA Astrophysics Data System (ADS)

We develop strain-driven compression-expansion technique using molecular dynamics (MD) with reactive force fields (ReaxFF) to study the impact sensitivity of energetic materials. It has been applied to simulation of 1,3,5-trinitrohexahydro-s-triazine (RDX) crystal subjected to high-rate compression typical at the detonation front. The obtained results show that at lower compression ratio x = 1-V/V0<40% only a few of RDX molecules are decomposed, while for higher compressions (x>40%) all molecules decompose very quickly. We have observed both primary and secondary reactions during the decomposition process as well as production of various intermediates (NO2, NO, HONO, OH) and final products (H2O, N2, CO, CO2). The results of strain-driven compression-expansion modeling are in a good agreement with previous ReaxFF-MD shock simulations in RDX. Proposed approach might be useful for a quick test of sensitivity of energetic materials under conditions of high strain rate loading.

Zhang, L.; Zybin, S. V.; van Duin, A. C. T.; Dasgupta, S.; Goddard, W. A.

2006-07-01

282

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

283

Spinmotive force with static and uniform magnetization induced by a time-varying electric field  

NASA Astrophysics Data System (ADS)

A new spinmotive force is predicted in ferromagnets with spin-orbit coupling. By extending the theory of spinmotive force, we show that a time-varying electric field can induce a spinmotive force with static and uniform magnetization. This spinmotive has two advantages; it can be detected free from the inductive voltage owing to the absence of dynamical magnetization and it can be tuned by electric fields. To observe the effect, we propose two experimental setups: electric voltage measurement in a single ferromagnet and spin injection from a ferromagnet into an attached nonmagnetic conductor.

Yamane, Yuta; Ieda, Jun'ichi; Maekawa, Sadamichi

2013-07-01

284

Controlling the optical dipole force for molecules with field-induced alignment  

SciTech Connect

We measure the role of field-induced alignment on the dipole force for molecules using a single focused nonresonant laser beam. We show that through the alignment process we can modify the effective polarizability by field polarization and thus control the center-of-mass motion of the molecule. We observe a maximum change of 20% in the dipole force on CS{sub 2} molecules when changing from linearly to circularly polarized light. Additionally, the effect of the dipole force on different vibrational states is also studied.

Purcell, S. M.; Barker, P. F. [Department of Physics and Astronomy, University College London, London, WC1E 6BT (United Kingdom)

2010-09-15

285

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

NASA Astrophysics Data System (ADS)

We present a novel numerical method that allows the calculation of nonlinear force-free magnetostatic solutions above a boundary surface on which only the distribution of the normal magnetic field component is given. The method relies on the theory of force-free electrodynamics and applies directly to the reconstruction of the solar coronal magnetic field for a given distribution of the photospheric radial field component. The method works as follows: we start with any initial magnetostatic global field configuration ( e.g. zero, dipole), and along the boundary surface we create an evolving distribution of tangential (horizontal) electric fields that, via Faraday's equation, give rise to a respective normal-field distribution approaching asymptotically the target distribution. At the same time, these electric fields are used as boundary condition to numerically evolve the resulting electromagnetic field above the boundary surface, modeled as a thin ideal plasma with non-reflecting, perfectly absorbing outer boundaries. The simulation relaxes to a nonlinear force-free configuration that satisfies the given normal-field distribution on the boundary. This is different from existing methods relying on a fixed boundary condition - the boundary evolves toward the a priori given one, at the same time evolving the three-dimensional field solution above it. Moreover, this is the first time that a nonlinear force-free solution is reached by using only the normal field component on the boundary. This solution is not unique, but it depends on the initial magnetic field configuration and on the evolutionary course along the boundary surface. To our knowledge, this is the first time that the formalism of force-free electrodynamics, used very successfully in other astrophysical contexts, is applied to the global solar magnetic field.

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

2011-04-01

286

Nonlinear force-free reconstruction of the global solar magnetic field  

NASA Astrophysics Data System (ADS)

We present a novel numerical method that allows the calculation of nonlinear force-free magnetostatic solutions above a boundary surface on which only the distribution of the normal magnetic field component is given. The method relies on the theory of force-free electrodynamics and applies directly to the reconstruction of the solar coronal magnetic field for a given distribution of the photospheric radial field component. The method works as follows: we start with any initial magnetostatic global field configuration (e.g. zero, dipole), and along the boundary surface we create an evolving distribution of tangential (horizontal) electric fields that, via Faraday's equation, give rise to a respective normal field distribution approaching asymptotically the target distribution. At the same time, these electric fields are used as boundary condition to numerically evolve the resulting electromagnetic field above the boundary surface, modeled as a thin ideal plasma with non-reflecting, perfectly absorbing outer boundaries. The simulation relaxes to a nonlinear force-free configuration that satisfies the given normal field distribution on the boundary. This is different from existing methods relying on a fixed boundary condition - the boundary evolves toward the a priori given one, at the same time evolving the three-dimensional field solution above it. Moreover, this is the first time a nonlinear force-free solution is reached by using only the normal field component on the boundary. This solution is not unique, but depends on the initial magnetic field configuration and on the evolutionary course along the boundary surface. To our knowledge, this is the first time that the formalism of force-free electrodynamics, used very successfully in other astrophysical contexts, is applied to the global solar magnetic field.

Contopoulos, I.

2012-01-01

287

Computerized magnetic studies on d, f, d–d, f–f, and d– S, f– S systems under varying ligand and magnetic fields  

Microsoft Academic Search

A computer program is introduced which analyses the magnetic susceptibility of mononuclear and exchange-coupled homodinuclear dN–dN and fN–fN systems as well as heterodinuclear dN–S and fN–S complexes (S standing for a pure spin centre with S=12,1,72) taking into consideration interelectronic repulsion, spin-orbit coupling, ligand field effect, isotropic exchange interactions, and applied magnetic field. The program is applied to interpret the

H. Schilder; H. Lueken

2004-01-01

288

Energetic Materials at High Compression: First-Principles Density Functional Theory and Reactive Force Field Studies  

NASA Astrophysics Data System (ADS)

We report the results of a comparative study of pentaerythritol tetranitrate (PETN) at high compression using classical reactive interatomic potential ReaxFF and first-principles density functional theory (DFT). Lattice parameters of PETN I, the ground state structure at ambient conditions, is obtained by ReaxFF and two different density functional methods (plane wave and LCAO pseudopotential methods) and compared with experiment. Calculated energetics and isothermal equation of state (EOS) upon hydrostatic compression obtained by DFT and ReaxFF are both in good agreement with available experimental data. Our calculations of the hydrostatic EOS at zero temperature are extended to high pressures up to 50 GPa. The anisotropic characteristics of PETN upon uniaxial compression were also calculated by both ReaxFF and DFT.

Oleynik, I. I.; Conroy, M.; Zybin, S. V.; Zhang, L.; van Duin, A. C.; Goddard, W. A.; White, C. T.

2006-07-01

289

Polarizable interatomic force field for TiO2 parametrized using density functional theory  

NASA Astrophysics Data System (ADS)

We report a classical interatomic force field for TiO2 , which has been parametrized using density functional theory forces, energies, and stresses in the rutile crystal structure. The reliability of this classical potential is tested by evaluating the structural properties, equation of state, phonon properties, thermal expansion, and some thermodynamic quantities such as entropy, free energy, and specific heat under constant volume. The good agreement of our results with ab initio calculations and with experimental data, indicates that our force field describes the atomic interactions of TiO2 in the rutile structure very well. The force field can also describe the structures of the brookite and anatase crystals with good accuracy.

Han, X. J.; Bergqvist, L.; Dederichs, P. H.; Müller-Krumbhaar, H.; Christie, J. K.; Scandolo, S.; Tangney, P.

2010-04-01

290

Validation of Tailored Force Fields Concept for Use in Space-Based Construction  

NASA Astrophysics Data System (ADS)

The Tailored Force Fields technology offers the potential of automatically assembling structures of specified wall shape in microgravity using resonant acoustic or electromagnetic fields. Scaled to radio wavelengths, it opens a way to build large radiation-shielded space stations. The scientific logic behind the technology is summarized in this paper. Experimental evidence in acoustics, ultrasonics, optics and microwave regimes is tied to first principles. Results show that the dominant features such as the forces on particles are predictable to good accuracy using simple solutions of the conservation equations. The detailed formation of walls involves secondary interactions between particles, an area requiring further modeling. Evidence to-date indicates that the interactions cause, if anything, attractive forces under the conditions of interest. However, the detailed particle behavior depends on the specifics of the materials and the wavelengths being used. Phenomena such as heating and surface sintering are seen to be possible to integrate into, or separate from, the force-field tailoring.

Wanis, Sameh S.; Komerath, Narayanan M.

2006-01-01

291

New force field for molecular simulation of guanidinium-based ionic liquids.  

PubMed

An all-atom force field was proposed for a new class of room temperature ionic liquids (RTILs), N,N,N',N'-tetramethylguanidinium (TMG) RTILs. The model is based on the AMBER force field with modifications on several parameters. The refinements include (1) fitting the vibration frequencies for obtaining force coefficients of bonds and angles against the data obtained by ab initio calculations and/or by experiments and (2) fitting the torsion energy profiles of dihedral angles for obtaining torsion parameters against the data obtained by ab initio calculations. To validate the force field, molecular dynamics (MD) simulations at different temperatures were performed for five kinds of RTILs, where TMG acts as a cation and formate, lactate, perchlorate, trifluoroacetate, and trifluoromethylsulfonate act as anions. The predicted densities were in good agreement with the experimental data. Radial distribution functions (RDFs) and spatial distribution functions (SDFs) were investigated to depict the microscopic structures of the RTILs. PMID:16800517

Liu, Xiaomin; Zhang, Suojiang; Zhou, Guohui; Wu, Guangwen; Yuan, Xiaoliang; Yao, Xiaoqian

2006-06-22

292

Thermal Decomposition of Energetic Materials by ReaxFF Reactive Molecular Dynamics  

NASA Astrophysics Data System (ADS)

We report the study of thermal decomposition of 1,3,5-trinitrohexahydro-s-triazine (RDX) bonded with polyurethane (Estane) and of the bulk hydrazine by molecular dynamics (MD) simulations equipped with the reactive force field (ReaxFF). For the polymer binder explosive, the simulation results show that the thermal decomposition of RDX is affected by the presence of the polymer binder Estane. Generally, with addition of Estane the decomposition of RDX slows down. Final products including N2, H2O, CO, CO2 and intermediates NO2, NO and HONO have been identified from the thermal decomposition processes. For the bulk hydrazine, it is found that with the increase of temperature, its decomposition increases and more N2 and H2 are generated, but NH3 molecules are consumed much faster at higher temperatures. This simulation work provides us an approach to quickly test the response of various energetic materials to thermal conditions.

Zhang, Luzheng; Zybin, Sergey V.; van Duin, Adri C. T.; Dasgupta, Siddharth; Goddard, William A.

2006-07-01

293

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

294

Energetic Materials at High Compression: First-Principles Density Functional Theory and Reactive Force Field Studies  

Microsoft Academic Search

We report the results of a comparative study of pentaerythritol tetranitrate (PETN) at high compression using classical reactive interatomic potential ReaxFF and first-principles density functional theory (DFT). Lattice parameters of PETN I, the ground state structure at ambient conditions, is obtained by ReaxFF and two different density functional methods (plane wave and LCAO pseudopotential methods) and compared with experiment. Calculated

I. I. Oleynik; M. Conroy; S. V. Zybin; L. Zhang; A. C. van Duin; W. A. Goddard; C. T. White

2006-01-01

295

Ionic force field optimization based on single-ion and ion-pair solvation properties  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely, CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional {?,?} parameter space of the Lennard-Jones interaction to a one dimensional line for each ion. From the finite-concentration simulations, the pair potential is extracted and the osmotic coefficient is calculated, which is compared to experimental data. We find a strong dependence of the osmotic coefficient on the force field, which is remarkable as the single-ion solvation free energy and the ion-water structure remain invariant under the parameter variation. Optimization of the force field is achieved for the cations Cs+ and K+, while for the anions I- and F- the experimental osmotic coefficient cannot be reached. This suggests that in the long run, additional parameters might have to be introduced into the modeling, for example by modified mixing rules.

Fyta, Maria; Kalcher, Immanuel; Dzubiella, Joachim; Vrbka, Luboš; Netz, Roland R.

2010-01-01

296

Rigorous upper bound for turbulent electromotive force in reversed-field pinches  

SciTech Connect

An upper bound is determined for the turbulently generated axial electromotive force in reversed-field pinches, constrained solely by energy conservation in the approximation of incompressible magnetohydrodynamics. The field reversal is predicted and comparisons are made with the minimum-energy state with the invariant magnetic helicity.

Kim, C. (Institute for Fusion Studies, University of Texas at Austin, Austin, TX (USA)); Krommes, J.A. (Plasma Physics Laboratory, Princeton University, Princeton, NJ (USA))

1990-12-15

297

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

298

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

Microsoft Academic Search

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

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

1994-01-01

299

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

EPA Science Inventory

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

300

Non-force-free Extrapolation of Coronal Magnetic Field with Applications to Vector Magnetograms  

Microsoft Academic Search

Motivated by increasingly more advanced solar observations, we recently develop a method of non-force-free extrapolation of the solar coronal magnetic field from vector magnetograms, especially those for a finite active region. Based on a more complex variational principle, the principle of minimum (energy) dissipation rate (MDR), we adopt and solve a more complex equation governing the coronal magnetic field that

Q. Hu; A. Wang; B. Dasgupta; G. A. Gary; S. Wu

2009-01-01

301

Yukawa-field approximation of electrostatic free energy and dielectric boundary force  

NASA Astrophysics Data System (ADS)

A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends nontrivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation.

Cheng, Hsiao-Bing; Cheng, Li-Tien; Li, Bo

2011-11-01

302

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

303

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.

304

Soil washing physical separations test procedure - 300FF1 operable unit  

Microsoft Academic Search

This procedure provides the operations approach, a field sampling plan, and laboratory procedures for a soil washing test to be conducted by Alternative Remedial Technologies, Inc. (ART) in the 300-FF-1 area at the Hanford site. The {open_quotes}Quality Assurance Project Plan for the Soil Washing Physical Separations Test, 300-FF-1 Operable Unit,{close_quotes} Hanford, Washington, Alternative Remedial Technologies, Inc., February 1994 (QAPP) is

Belden

1993-01-01

305

The Effect of Field Representation on Student Responses to Magnetic Force Questions  

NSDL National Science Digital Library

We examine student understanding of the magnetic force exerted on a charged particle and report three findings from a series of tests administered to introductory physics students. First, we expand on previous findings that many students believe in âchargedâ magnetic poles and find that although students may answer according to a model where a positive charge is attracted to a south pole and repulsed by a north, these students may not believe that the poles are charged. Additional models produce identical answer schemes, the primary being magnetic force parallel to magnetic field. Second, the representation format affects responses: students answer differently when the magnetic field is portrayed by a field source vs. by field lines. Third, after traditional instruction improvement in student performance is greater on questions portraying field lines than for questions portraying field sources.

Scaife, Thomas M.; Heckler, Andrew F.

2009-06-24

306

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

307

Fictitious Forces and Simulated Magnetic Fields in Rotating Reference Frames  

NASA Astrophysics Data System (ADS)

We show that the Wigner-Bargmann program of grounding nonrelativistic quantum mechanics in the unitary projective representations of the Galilei group can be extended to include all noninertial reference frames. The key concept is the Galilean line group, the group of transformations that ties together all accelerating reference frames, and its representations. These representations are constructed under the natural constraint that they reduce to the well-known unitary, projective representations of the Galilei group when the transformations are restricted to inertial reference frames. This constraint can be accommodated only for a class of representations with a sufficiently rich cocycle structure. Unlike the projective representations of the Galilei group, these cocycle representations of the Galilean line group do not correspond to central extensions of the group. Rather, they correspond to a class of nonassociative extensions, known as loop prolongations, that are determined by three-cocycles. As an application, we show that the phase shifts due to the rotation of Earth that have been observed in neutron interferometry experiments and the rotational effects that lead to simulated magnetic fields in optical lattices can be rigorously derived from the representations of the loop prolongations of the Galilean line group.

Klink, W. H.; Wickramasekara, S.

2013-10-01

308

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

309

Observation of the Intrinsic Abraham Force in Time-Varying Magnetic and Electric Fields  

NASA Astrophysics Data System (ADS)

The Abraham force exerted by a time-dependent electromagnetic field on neutral, polarizable matter has two contributions. The one induced by a time-varying magnetic field and a static electric field is reported here for the first time. We discuss our results in the context of the radiative momentum in matter. Our observations are consistent with Abraham’s and Nelson’s versions for radiative momentum.

Rikken, G. L. J. A.; van Tiggelen, B. A.

2012-06-01

310

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

311

A Poisson P 3 M Force Field Scheme for Particle-Based Simulations of Ionic Liquids  

Microsoft Academic Search

In this work we propose a force-field scheme for the self-consistent particle-based simulation of electrolytic solutions. Within this approach, the electrostatic interactions are modeled with a particle-particle-particle-mesh (P3M) algorithm, where the long-range components of the force are resolved in real space with an iterative multi-grid Poisson solver. Simulations are performed where the solute ions are treated as Brownian particles governed

S. Aboud; D. Marreiro; M. Saraniti; R. Eisenberg

2004-01-01

312

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

313

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

314

Radio flare from FF Tau  

NASA Astrophysics Data System (ADS)

The Arcminute Microkelvin Imager Large Array (AMI-LA) reports a radio flare in the emission of the Class III object FF Tau. The flare occurred on 2012 July 24th (mJD 56132.2) with a flux density of 3.24 +/-0.03 (rms) +/-0.16 (absolute calibration uncertainty) mJy at a frequency of 16GHz (1.8cm). The emission had a rising spectrum with a power-law index of 0.34+/-0.21, constrained between 13.88 - 17.63GHz.

Scaife, Anna M. M.; Owen, James; Ercolano, Barbara; Rumsey, Clare

2012-08-01

315

Experimental studies of protozoan response to intense magnetic fields and forces  

NASA Astrophysics Data System (ADS)

Intense static magnetic fields of up to 31 Tesla were used as a novel tool to manipulate the swimming mechanics of unicellular organisms. It is shown that homogenous magnetic fields alter the swimming trajectories of the single cell protozoan Paramecium caudatum, by aligning them parallel to the applied field. Immobile neutrally buoyant paramecia also oriented in magnetic fields with similar rates as the motile ones. It was established that the magneto-orientation is mostly due to the magnetic torques acting on rigid structures in the cell body and therefore the response is a non-biological, passive response. From the orientation rate of paramecia in various magnetic field strengths, the average anisotropy of the diamagnetic susceptibility of the cell was estimated. It has also been demonstrated that magnetic forces can be used to create increased, decreased and even inverted simulated gravity environments for the investigation of the gravi-responses of single cells. Since the mechanisms by which Earth's gravity affects cell functioning are still not fully understood, a number of methods to simulate different strength gravity environments, such as centrifugation, have been employed. Exploiting the ability to exert magnetic forces on weakly diamagnetic constituents of the cells, we were able to vary the gravity from -8 g to 10 g, where g is Earth's gravity. Investigations of the swimming response of paramecia in these simulated gravities revealed that they actively regulate their swimming speed to oppose the external force. This result is in agreement with centrifugation experiments, confirming the credibility of the technique. Moreover, the Paramecium's swimming ceased in simulated gravity of 10 g, indicating a maximum possible propulsion force of 0.7 nN. The magnetic force technique to simulate gravity is the only earthbound technique that can create increased and decreased simulated gravities in the same experimental setup. These findings establish a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

Guevorkian, Karine

316

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

317

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

318

Effects of spatial confinement of electromagnetic field on optical forces due to whispering-gallery modes  

NASA Astrophysics Data System (ADS)

Using ab initio approach to the theory of electromagnetic interaction of a small particle and spherical whispering gallery mode resonator, we derive the optical forces experienced by the particle and it's resulting motion. The form of the forces differs from that expected by the traditional gradient/scattering approach due to the modification of the field by the particle. The main effect of the confinement of the field in a cavity consists in making the component of the optical force usually interpreted as gradient, manifestly non-conservative, and hence not presentable in the gradient form. It is shown how the standard gradient/scattering formalism can be modified for the cavity confined optical field.

Rubin, J. T.; Deych, L.

2012-02-01

319

Measurement of interaction force between small distances sandwiched with magnetic fluid under magnetic field  

NASA Astrophysics Data System (ADS)

In this contribution, the interactive force measurement between 10nm distance under magnetic field is carried out. Previous measurement of the interactive force is reported by Israelachivili et al. However, its measurement under magnetic field has not been performed. The methodology described in this paper is easier as the distance between two surfaces is not measured optically but dynamically. Therefore, it is different from the previous reported studies. Based on the results of the measurement of the interactive force, the diameter of the particle suspended in a solution under magnetic field is also estimated. Moreover, it may be predictable how the clusters have been formed. The method described will be very useful for new productions based on magnetic fluid.

Miyazaki, T.; Shibayama, A.; Sato, T.; Fujita, T.

2002-11-01

320

Parametrization and application of a coarse grained force field for benzene/fullerene interactions with lipids.  

PubMed

Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. Here, we developed the cross parameters necessary to unite those force fields and then applied the model to investigate the nature of benzene and C(60) interactions with lipid bilayers. The interaction parameters between the phenyl and lipid CG sites are based on experimental and all atom (AA) molecular dynamics (MD) data. The resulting force field was tested on benzene rich lipid bilayers and shown to reproduce general behavior expected from experiments. The parameters were then applied to C(60) interactions with lipid bilayers. Overall, the results showed excellent agreement with AA MD and experimental observations. In the C(60) lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations investigated. PMID:21090655

DeVane, Russell; Jusufi, Arben; Shinoda, Wataru; Chiu, Chi-cheng; Nielsen, Steven O; Moore, Preston B; Klein, Michael L

2010-11-19

321

Molecular dynamics simulation of liquid carbon tetrachloride using ab initio force field  

NASA Astrophysics Data System (ADS)

Intermolecular interaction potentials of the carbon tetrachloride dimer in 12 orientations have been calculated using the Hartree-Fock self-consistent theory and the second-order Møller-Plesset (MP2) perturbation theory. We have employed basis sets from Pople's medium size basis sets [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). The calculated MP2 potential data were employed to parametrize a four-site force field for molecular simulations. We performed molecular dynamics simulations using the ab initio force field and compared the simulation results to experiments. Quantitative agreements for the atomwise radial distribution functions, the self-diffusion coefficients, and the neutron and x-ray diffraction scattering functions over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori.

Li, Arvin Huang-Te; Huang, Shou-Cheng; Chao, Sheng D.

2010-01-01

322

Ab initio parametrized MM3 force field for the metal-organic framework MOF-5.  

PubMed

A new valence force field has been developed and validated for a particular class of coordination polymers known as nanoporous metal-organic frameworks (MOFs), introduced recently by the group of Yaghi. The experimental, structural, and spectroscopic data in combination with density functional theory calculations on several model systems were used to parametrize the bonded terms of the force field, which explicitly treats the metal-oxygen interactions as partially covalent as well as distinguishes different types of oxygens in the framework. Both the experimental crystal structure of MOF-5 and vibrational infrared spectrum are reproduced reasonably well. The proposed force field is believed to be useful in atomistic simulations of adsorption/diffusion of guest molecules inside the flexible pores of this important class of MOF materials. PMID:17301955

Tafipolsky, Maxim; Amirjalayer, Saeed; Schmid, Rochus

2007-05-01

323

A force field for molecular simulation of tetrabutylphosphonium amino acid ionic liquids.  

PubMed

An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs. PMID:17552552

Zhou, Guohui; Liu, Xiaomin; Zhang, Suojiang; Yu, Guangren; He, Hongyan

2007-06-07

324

Super resolution mapping of the near optical field and the gradient optical force  

NASA Astrophysics Data System (ADS)

We have developed a NSOM technique that can map both the near optical field and the optical force using an atomic force microscope. This technique could be very useful for characterizing MEMs/NEMs devices, plasmonic nanoantennas, nano-photonic devices and biologically active substrates. Unlike conventional NSOM techniques that rely on an aperture fabricated on the end of an AFM tip to collect the optical signal this apertureless technique uses a lockin amplifier locked to the AFM tip vibrational frequency, to correlate the amplitude modulation of the back reflected optical signal to the strength of the optical field. And since we are not limited by the fabrication of an aperture the spatial resolution of the map is limited only by the size of a sharp AFM tip which for metallic coated tips can have a radius of curvature of 10 to 20 nm. For optical force mapping the incident laser is modulated and the lock-in amplifier is used to correlate the amplitude modulation of the vibrating AFM tip to strength of the optical gradient force. And in this way one can get a very accurate mapping of both the optical force and the optical field for any substrate of interest as long as it can be back illuminated. Lastly with an electrically monolithic substrate it is possible to correlate the amplitude modulation of the tunneling current to the optical field and obtain a spatial mapping that has a resolution of an STM, about 1 nm or maybe less.

Gelfand, Ryan M.; Bonakdar, Alireza; Memis, O. Gokalp; Mohseni, Hooman

2013-09-01

325

ReaxFF Grand Canonical Monte Carlo simulation of adsorption and dissociation of oxygen on platinum (111)  

NASA Astrophysics Data System (ADS)

Atomic-level Grand Canonical Monte Carlo (GCMC) simulations equipped with a reactive force field (ReaxFF) are used to study atomic oxygen adsorption on a Pt(111) surface. The off-lattice GCMC calculations presented here rely solely on the interatomic potential and do not necessitate the pre-computation of surface adlayer structures and their interpolation. As such, they provide a predictive description of adsorbate phases. In this study, validation is obtained with experimental evidence (steric heats of adsorption and isotherms) as well as DFT-based state diagrams available in the literature. The ReaxFF computed steric heats of adsorption agree well with experimental data, and this study clearly shows that indirect dissociative adsorption of O2 on Pt(111) is an activated process at non-zero coverages, with an activation energy that monotonically increases with coverage. At a coverage of 0.25 ML, a highly ordered p(2 × 2) adlayer is found, in agreement with several low-energy electron diffraction observations. Isotherms obtained from the GCMC simulations compare qualitatively and quantitatively well with previous DFT-based state diagrams, but are in disagreement with the experimental data sets available. ReaxFF GCMC simulations at very high coverages show that O atoms prefer to bind in fcc hollow sites, at least up to 0.8 ML considered in the present work. At moderate coverages, little to no disorder appears in the Pt lattice. At high coverages, some Pt atoms markedly protrude out of the surface plane. This observation is in qualitative agreement with recent STM images of an oxygen covered Pt surface. The use of the GCMC technique based on a transferable potential is particularly valuable to produce more realistic systems (adsorbent and adsorbate) to be used in subsequent dynamical simulations (Molecular Dynamics) to address recombination reactions (via either Eley-Rideal or Langmuir-Hinshelwood mechanisms) on variously covered surfaces. By using GCMC and Molecular Dynamics simulations, the ReaxFF force field can be a valuable tool for understanding heterogeneous catalysis on a solid surface. Finally, the use of a reactive potential is a necessary requirement to investigate problems where dissociative adsorption occurs, as typical of many important catalytic processes.

Valentini, Paolo; Schwartzentruber, Thomas E.; Cozmuta, Ioana

2011-12-01

326

Investigation of acoustic fields generated by eddy currents using an atomic force microscope  

NASA Astrophysics Data System (ADS)

This paper reports the experimental measurement and imaging of the acoustic fields generated by low-frequency eddy currents in metals in the absence of an external static magnetic field using a modified atomic force microscope. Acoustic displacements in a typical metal placed in eddy current field without static magnetic field were theoretically computed and found to be in the range of few hundred picometers. A modified atomic force microscope was used to detect and measure the acoustic displacements in a single crystal copper. The setup was also used to image acoustic fields in a titanium alloy sample. Details of the modified AFM to measure and image acoustic displacements are presented. The role of electrical and elastic properties on the contrast in acoustic images of Ti-6Al-4V sample is discussed.

Nalladega, V.; Sathish, S.; Blodgett, M.

2013-01-01

327

Soil washing physical separations test procedure - 300-FF-1 operable unit  

SciTech Connect

This procedure provides the operations approach, a field sampling plan, and laboratory procedures for a soil washing test to be conducted by Alternative Remedial Technologies, Inc. (ART) in the 300-FF-1 area at the Hanford site. The {open_quotes}Quality Assurance Project Plan for the Soil Washing Physical Separations Test, 300-FF-1 Operable Unit,{close_quotes} Hanford, Washington, Alternative Remedial Technologies, Inc., February 1994 (QAPP) is provided in a separate document that presents the procedural and organizational guidelines for this test. This document describes specifications, responsibilities, and general procedures to be followed to conduct physical separation soil treatability tests in the North Process Pond of the 300-FF-1 Operable Unit (OU) at the Hanford Site. These procedures are based on the {open_quotes}300-FF-1 Physical Separations CERCLA Treatability Test Plan, DOE/RL 92-2l,{close_quotes} (DOE-RL 1993).

Belden, R.D.

1993-10-08

328

Efficacy of Group Decision Support Systems: A Field Experiment to Evaluate Impacts on Air Force Decision Makers.  

National Technical Information Service (NTIS)

The research contributed to the study of Group Decision Support Systems (GDSS) in field experiments involving real managers making real decisions. This research was conducted by the Air Force Institute of Technology with the Air Force Armstrong Laboratory...

B. C. Huff

1992-01-01

329

Conformational Study of Met-Enkephalin Based on the ECEPP Force Fields  

PubMed Central

We report a computational study of the small peptide Met-enkephalin based on the ECEPP/2 and ECEPP/3 force fields using the basin paving method. We have located a new global minimum when using the ECEPP/3 force field with peptide angles ? fixed at 180°. With this new result, we can conclude that the lowest energy configurations of Met-enkephalin predicted based on all four versions of ECEPP have a classic ?-turn centered at residue Gly3 and a ?-turn at residues Gly3-Phe4. However, minor differences between the structures also exist.

Zhan, Lixin; Chen, Jeff Z. Y.; Liu, Wing-Ki

2006-01-01

330

Non-mean-field effects in systems with long-range forces in competition.  

PubMed

We investigate the canonical equilibrium of systems with long-range forces in competition. These forces create a modulation in the interaction potential and modulated phases appear at the system scale. The structure of these phases differentiate this system from monotonic potentials, where only the mean-field and disordered phases exist. With increasing temperature, the system switches from one ordered phase to another through a first-order phase transition. Both mean-field and modulated phases may be stable, even at zero temperature, and the long-range nature of the interaction will lead to metastability characterized by extremely long time scales. PMID:23214765

Bachelard, R; Staniscia, F

2012-11-26

331

Magnetic Forces on Orthodontic Wires in High Field Magnetic Resonance Imaging (MRI) at 3 Tesla  

Microsoft Academic Search

\\u000a Abstract\\u000a \\u000a \\u000a Background:\\u000a   In a previous investigation we reported on magnetic forces in the static magnetic field of a 1.5 Tesla MRI system. The aim\\u000a of the present investigation was to assess forces on orthodontic wires in a high field strength MRI system at 3 Tesla.\\u000a \\u000a \\u000a \\u000a \\u000a Materials and Methods:\\u000a   Thirty-two different orthodontic wires (21 archwires, eight ligature wires and three retainer

Arndt Klocke; Bärbel Kahl-Nieke; Gerhard Adam; Jörn Kemper

2006-01-01

332

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

333

A Kirkwood-Buff derived force field for sodium chloride in water  

NASA Astrophysics Data System (ADS)

A force field for the simulation of mixtures of sodium chloride and water is described. The model is specifically designed to reproduce the experimentally determined Kirkwood-Buff integrals as a function of salt concentration, ensuring that a good representation of the solution activity is obtained. In addition, the model reproduces many of the known properties of sodium chloride solutions including the density, isothermal compressibility, ion diffusion constants, relative permittivity, and the heat of mixing. The results are also compared to other common sodium chloride force fields.

Weerasinghe, Samantha; Smith, Paul E.

2003-12-01

334

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

PubMed

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. PMID:24116634

Milek, Theodor; Meyer, Bernd; Zahn, Dirk

2013-10-14

335

Nonequilibrium forces between atoms and dielectrics mediated by a quantum field  

SciTech Connect

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

Behunin, Ryan O. [Center for Nonlinear Studies (CNLS) and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States); Hu, Bei-Lok [Maryland Center for Fundamental Physics, Department of Physics, University of Maryland, College Park, Maryland 20742 (United States); Joint Quantum Institute, University of Maryland, College Park, Maryland 20742 (United States)

2011-07-15

336

Near-field light detection by conservative and dissipative force modulation methods using a piezoelectric cantilever  

NASA Astrophysics Data System (ADS)

We demonstrated near-field light detection by dynamic force microscope using a self-sensing piezoelectric cantilever having a lead zirconate titanate thin film layer. The cantilever tip was brought close to a glass plate with a patterned chromium film on a right angle prism. The backside of the prism was irradiated by an intensity modulated laser light to create an evanescent field at the glass surface. We obtained near-field optical images of the patterned glass by detecting the frequency shift modulation or the amplitude modulation induced by the near-field light while the tip-sample distance was regulated by the frequency modulation method in ambient condition.

Satoh, Nobuo; Fukuma, Takeshi; Kobayashi, Kei; Watanabe, Shunji; Fujii, Toru; Matsushige, Kazumi; Yamada, Hirofumi

2010-06-01

337

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

338

Nonlinear Force-Free Modeling of Coronal Magnetic Fields Part I: A Quantitative Comparison of Methods  

NASA Astrophysics Data System (ADS)

We compare six algorithms for the computation of nonlinear force-free (NLFF) magnetic fields (including optimization, magnetofrictional, Grad Rubin based, and Green's function-based methods) by evaluating their performance in blind tests on analytical force-free-field models for which boundary conditions are specified either for the entire surface area of a cubic volume or for an extended lower boundary only. Figures of merit are used to compare the input vector field to the resulting model fields. Based on these merit functions, we argue that all algorithms yield NLFF fields that agree best with the input field in the lower central region of the volume, where the field and electrical currents are strongest and the effects of boundary conditions weakest. The NLFF vector fields in the outer domains of the volume depend sensitively on the details of the specified boundary conditions; best agreement is found if the field outside of the model volume is incorporated as part of the model boundary, either as potential field boundaries on the side and top surfaces, or as a potential field in a skirt around the main volume of interest. For input field (B) and modeled field (b), the best method included in our study yields an average relative vector error E n = < |B-b|>/< |B|> of only 0.02 when all sides are specified and 0.14 for the case where only the lower boundary is specified, while the total energy in the magnetic field is approximated to within 2%. The models converge towards the central, strong input field at speeds that differ by a factor of one million per iteration step. The fastest-converging, best-performing model for these analytical test cases is the Wheatland, Sturrock, and Roumeliotis (2000) optimization algorithm as implemented by Wiegelmann (2004).

Schrijver, Carolus J.; De Rosa, Marc L.; Metcalf, Thomas R.; Liu, Yang; McTiernan, Jim; Régnier, Stéphane; Valori, Gherardo; Wheatland, Michael S.; Wiegelmann, Thomas

2006-05-01

339

Field forced antiferroelectric-to-ferroelectric switching in modified lead zirconate titanate stannate ceramics  

Microsoft Academic Search

Electric-field-forced antiferroelectric- to-ferroelectric phase transitions in several compositions of modified lead zirconate titanate stannate antiferroelectric ceramics are studied for ultra-high-field-induced strain actuator applications. Two types of fatigue effects are observed in these ceramic compositions. In one, the fatigue effects only proceed to a limited extent and the properties may be restored by annealing above the Curie temperature, while in the

Wuyi Pan; Qiming Zhang; Amar Bhalla; Leslie E. Cross

1989-01-01

340

Magnetic field and electromagnetic force analysis of 3-phase air-core superconducting power transformer  

Microsoft Academic Search

The superconducting windings of the air-core superconducting power transformer have possibilities of being exposed to a higher magnetic field than those of the iron-core transformer because of no special paths for magnetic flux. Thus, in this paper, the magnetic field and electromagnetic force acting on the windings of an experimental 3-phase air-core superconducting transformer are analyzed. From the results, it

Hiroshi Yamaguchi; Teruo Kataoka; Hiroki Matsuoka; Tomohide Mouri; Shoji Nishikata; Y. Sato

2001-01-01

341

Non-force-free Extrapolation of Coronal Magnetic Field with Applications to Vector Magnetograms  

NASA Astrophysics Data System (ADS)

Motivated by increasingly more advanced solar observations, we recently develop a method of non-force-free extrapolation of the solar coronal magnetic field from vector magnetograms, especially those for a finite active region. Based on a more complex variational principle, the principle of minimum (energy) dissipation rate (MDR), we adopt and solve a more complex equation governing the coronal magnetic field that is non-force-free in general. We describe the theoretical basis in the context of general solar atmosphere conditions, and derive the extrapolation approach utilizing vector magnetograms as bottom boundary conditions. We illustrate the approach using both MHD numerical simulation results, and real vector magnetograph measurements of solar active regions. We wish to establish the validity of our approach, especially by detailed inter-comparison with self-consistent, full MHD simulation results, and investigations of the dynamics associated with non-vanishing forces.

Hu, Q.; Wang, A.; Dasgupta, B.; Gary, G. A.; Wu, S.

2009-12-01

342

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation  

Microsoft Academic Search

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model

Xuejin Li; Dazhi Kou; Shuling Rao; Haojun Liang

2006-01-01

343

Robotically generated force fields for stroke patient pelvic obliquity gait rehabilitation  

Microsoft Academic Search

The Robotic Gait Rehabilitation (RGR) Trainer, was designed and built to target secondary gait deviations in patients post - stroke. Using an impedance control strategy and a linear electromagnetic actuator, the device applies a force field to control pelvic obliquity through an orthopedic brace while the patient ambulates on treadmill. Healthy human subject testing confirmed efficacy of the method to

Maciej Pietrusinski; Iahn Cajigas; Mary Goldsmith; Paolo Bonato; Constantinos Mavroidis

2010-01-01

344

Force field calculations and reassigments of Raman and IR frequencies of pyrazine- N, N'-dioxide  

NASA Astrophysics Data System (ADS)

Force field calculations have been carried out for the planar and non-planar modes of pyrazine- N, N'-O 2 using the observed vibrational frequencies obtained from the IR and Raman spectral studies on pyrazine- N, N'-O 2-h 4 and pyrazine- N, N'-O 2-d 4 reported in the literature [D.A. Thornton, P.F.M. Verhoeven, G.M. Watkins, Herman O. Desseyn, Benjamin J. Van der Veken, Spectrochim. Acta 46A (1990) 1439]. The purpose of the present work is to determine force fields for the pyrazine- N, N'-O 2 molecule and to present vibrational assignments for the observed IR and Raman frequencies to the fundamental modes, combination bands and overtones. The planar force field determined in the present case is expected to be better than that reported earlier [S. Szöke, G. Varsanyi, E. Baitz, Acta Chim. 53 (1967) 345] because of the inclusion of the observed frequencies due to pyrazine- N, N'-O 2-d 4 isotopomer. In addition, the non-planar force field for this molecule is reported for the first time.

Yadav, R. A.; Mukherjee, V.; Kumar, Manoj; Singh, Rashmi

2007-04-01

345

Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems  

Microsoft Academic Search

The past decade has seen intense development of what are anticipated to be the next generation of classical force fields to be used in computational statistical mechanical approaches to studying a broad class of physical and biological systems. Among the several approaches being actively pursued currently is the fluctuating charge (or equivalently charge equilibration or electronegativity equalization) method. Within this

Sandeep Patel; Charles L. Brooks III

2006-01-01

346

Electric Field Force-Based Detection of Rotational Symmetry in 3D Model  

Microsoft Academic Search

In this paper, we propose a method to describe the rotational symmetry in 3D shapes. This symmetry is deterministically found through the use of a physical quantity: electric field force. He describes the measure of the shape's rotational symmetry with respect to every axis passing through the center mass. This algorithm can deal with complex and ill-defined models because of

Yujie Liu; Zongmin Li; Hua Li

2007-01-01

347

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

348

Empirical anharmonic force field and equilibrium structure of hypochlorous acid, HOCl  

NASA Astrophysics Data System (ADS)

The cubic and quartic force fields of HOCl are investigated on the basis of the most recent experimental data on vibration-rotation interaction constants and anharmonicity constants. Some discrepancies with respect to previously reported ab initio results are found and discussed. The geometrical parameters of this molecule are also evaluated from recent data on the equilibrium values of the moments of inertia.

Escribano, R. M.; Di Lonardo, G.; Fusina, L.

1996-09-01

349

The power of accounting: a field study of local financial management in a police force  

Microsoft Academic Search

This paper describes the introduction of management accounting change in the form of local financial management in a police force, West Mercia Constabulary, using an ethnographic study. The study applies institutional theory to understand the context, process and consequences of the introduction of devolved budgeting systems to the organization.The field study explains how the devolution of budgets in West Mercia

Paul M. Collier

2001-01-01

350

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

SciTech Connect

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

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

1992-01-01

351

Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields.  

PubMed

Branched antimicrobial peptides are promising as a new class of antibiotics displaying high activity and low toxicity and appear to work through a unique mechanism of action. We explore the structural dynamics of a covalently branched 18 amino acid peptide (referred to as B2088) in aqueous and membrane mimicking environments through molecular dynamics (MD) simulations. Towards this, we carry out conventional MD simulations and supplement these with replica exchange simulations. The simulations are carried out using four different force fields that are commonly employed for simulating biomolecular systems. These force fields are GROMOS53a6, CHARMM27 with cMAP, CHARMM27 without cMAP and AMBER99sb. The force fields are benchmarked against experimental data available from circular dichroism and nuclear magnetic resonance spectroscopies, and show that CHARMM27 without cMAP correction is the most successful in reproducing the structural dynamics of B2088 both in water and in the presence of micelles. Although the four force fields predict different structures of B2088, they all show that B2088 stabilizes against the head group of the lipid through hydrogen bonding of its Lys and Arg side chains. This leads us to hypothesize that B2088 is unlikely to penetrate into the hydrophobic region of the membrane owing to the high free energy costs of transfer from water, and possibly acts by carpeting and thus disrupting the membrane. PMID:23231260

Li, Jianguo; Lakshminarayanan, Rajamani; Bai, Yang; Liu, Shouping; Zhou, Lei; Pervushin, Konstantin; Verma, Chandra; Beuerman, Roger W

2012-12-01

352

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...

353

Differentially rotating charged dust with a force-free electromagnetic field. II  

Microsoft Academic Search

The relativistic field equations for stationary axisymmetric differentially rotating charged dust with vanishing Lorentz force are derived and reduced to a single partial differential equation. It is found that the ratio of charge density to mass density in this system can only be constant throughout space-time if it is cylindrically symmetric. In that case, solutions have been shown to exist

P. Wils; N Van den Blergh

1984-01-01

354

MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry  

Microsoft Academic Search

The mathematical formulation, parametrization scheme, and structural results of a new, generally applicable molecular force field are presented. The central features are a scheme for automatic parameter assignments, the consistent united-atom approximation, the absence of atom types other than elements, the replacement of electrostatic terms by geometrical hydrogen-bonding terms, the concomitant lack of a need for partial atomic charge assignment

Paul R. Gerber; Klaus Müller

1995-01-01

355

Nonlinear force fields: a distributed system of control primitives for representing and learning movements  

Microsoft Academic Search

Electrophysiological studies have suggested the presence of a modular structure in the output stages of the motor system. In this structure, independent modules are connected to specific groups of muscles and generate nonlinear fields of force acting upon the controlled limbs. This paper explores the computational consequences of this structure in the framework of multivariate approximation. Movements are generated through

F. A. Mussa-Ivaldi

1997-01-01

356

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

357

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

358

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase  

Microsoft Academic Search

Over the past 4 years the GROMOS96 force field has been successfully used in biomolecular simulations, for example in peptide folding studies and detailed protein investigations, but no applications to lipid systems have been published yet. Here we provide a detailed investigation of aliphatic liquid systems. For liquids of larger aliphatic chains, n-heptane and longer, the standard GROMOS96 parameter sets

Lukas D. Schuler; Xavier Daura; Wilfred F. Van Gunsteren

2001-01-01

359

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

Microsoft Academic Search

This article describes the application of our distributed computing framework for crystal structure pre- diction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal struc- ture of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC dis- tributed computing framework includes a series of tightly integrated computer programs

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

2009-01-01

360

Calibrating nucleic acids torsional energetics in force-field: insights from model compounds  

Microsoft Academic Search

The development of force fields that accurately describe both the structure and the dynamics of nucleic acids in condensed phase is an ongoing effort. The development of the latest versions of the CHARMM and AMBER nucleic acids relied on ab initio as well as on experimental target data for the parametrization. Here we compare the two latest versions of the

D Bosch; N Foloppe; N Pastor; L Pardo; M Campillo

2001-01-01

361

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

362

Use of decoys to optimize an all-atom force field including hydration.  

PubMed

A novel method of parameter optimization is proposed. It makes use of large sets of decoys generated for six nonhomologous proteins with different architecture. Parameter optimization is achieved by creating a free energy gap between sets of nativelike and nonnative conformations. The method is applied to optimize the parameters of a physics-based scoring function consisting of the all-atom ECEPP05 force field coupled with an implicit solvent model (a solvent-accessible surface area model). The optimized force field is able to discriminate near-native from nonnative conformations of the six training proteins when used either for local energy minimization or for short Monte Carlo simulated annealing runs after local energy minimization. The resulting force field is validated with an independent set of six nonhomologous proteins, and appears to be transferable to proteins not included in the optimization; i.e., for five out of the six test proteins, decoys with 1.7- to 4.0-A all-heavy-atom root mean-square deviations emerge as those with the lowest energy. In addition, we examined the set of misfolded structures created by Park and Levitt using a four-state reduced model. The results from these additional calculations confirm the good discriminative ability of the optimized force field obtained with our decoy sets. PMID:18502794

Arnautova, Yelena A; Scheraga, Harold A

2008-05-23

363

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

Microsoft Academic Search

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

W. Jeff Schuyler; James E. Melzer

2007-01-01

364

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

National Technical Information Service (NTIS)

Magnetic fields and Lorentz forces of an LHC dipole magnet are calculated using the method of image currents to represent the effect of the iron shield. The calculation is performed for coils of finite length using a parametrization for coil heads of cons...

C. Daum D. Avest

1989-01-01

365

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

SciTech Connect

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

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

1992-04-01

366

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation.  

PubMed

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model. PMID:16774386

Li, Xuejin; Kou, Dazhi; Rao, Shuling; Liang, Haojun

2006-05-28

367

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation  

NASA Astrophysics Data System (ADS)

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model.

Li, Xuejin; Kou, Dazhi; Rao, Shuling; Liang, Haojun

2006-05-01

368

Force Field for Mica-Type Silicates and Dynamics of Octadecylammonium Chains Grafted to Montmorillonite  

SciTech Connect

Layered silicates are widely used in nanotechnology and composite materials. We describe a force field for phyllosilicates (mica, montmorillonite, and pyrophyllite) on the basis of physically justified atomic charges, van der Waals parameters, vibrational constants, and distributions of charge defects in agreement with solid state {sup 29}Si NMR data. Unit cell parameters deviate only {approx}0.5% relative to experimental X-ray measurements and surface (respectively cleavage) energies deviate less than 10% from experimental data, including the partition between Coulomb and van der Waals contributions. Reproduction of surface energies facilitates quantitative simulations of hybrid interfaces with water, organics, and biomolecules for which accurate force fields are available. Parameters are consistent with the force fields PCFF (polymer consistent force field), CVFF (consistent valence force field), CHARMM (chemistry at Harvard macromolecular mechanics), and GROMACS (Groningen machine for chemical simulations). As an example of interest, we investigate the structure and dynamics of octadecylammonium montmorillonite ('C{sub 18}'-montmorillonite, cation exchange capacity = 91 mmol/100 g) by molecular dynamics simulation. The surfactant chains assemble essentially as a bilayer with minimal interpenetration within the gallery while the ammonium headgroups are hydrogen-bonded to cavities in the montmorillonite surface. In contrast to quaternary ammonium ions, no rearrangements on the surface have been observed (cavity crossing barrier >5 kcal/mol). The alkyl chains are in a liquidlike state with approximately 30% gauche conformations, in agreement with previous Fourier-transform infrared and solid-state NMR measurements. Computed X-ray diffraction patterns of sodium and C18-montmorillonite agree very well with X-ray patterns from experiment, and the computational model can assist in the assignment of complex reflections.

Heinz,H.; Koerner, H.; Anderson, K.; Vaia, R.; Farmer, B.

2005-01-01

369

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

PubMed Central

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

2010-01-01

370

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

371

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

372

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

373

Structure of the Velocity and Vorticity Field in a Confined Forced Wake  

NASA Astrophysics Data System (ADS)

Previous results have shown that forcing a low Reynolds number 2D wake inside of a confining channel can lead to large increases in the amount of molecular mixing. The current work is part of an investigation to understand the behavior of this flow based on the structure of its vorticity field. Molecular Tagging Velocimetry (MTV) is used to map the u and v components of the velocity field at several streamwise and spanwise locations within the test section. Approximately 500 measurements are made in each region, which extends about two forcing wavelengths. These measurements allow the examination of the structure of the spanwise vorticity field, which is computed from the velocity data by a 2nd order finite difference scheme. Results show a spatial periodicity in the velocity rms, which can be explained by the existence of a phase difference between the shed spanwise vorticity and the free-stream perturbation. This is different from that usually observed in forced wakes with a steady free-stream. Data also show that the lateral spacing between vortices is highly dependent upon the forcing amplitude.

Cohn, R. K.; Koochesfahani, M. M.

1997-11-01

374

Analytic energy gradient in combined time-dependent density functional theory and polarizable force field calculation  

NASA Astrophysics Data System (ADS)

Formulas for evaluating analytic energy gradient are derived for combined time-dependent density functional theory (TDDFT) and polarizable force field methods that incorporate dipole polarizability tensors and linearly induced point dipoles. The Z-vector method for determining relaxed one-particle difference density matrix in regular TDDFT methods is extended to include induced dipoles. The analytic gradient of the mutual polarization energy of the force field and the TDDFT excited state can be formulated by using the TDDFT difference density-induced dipoles and the transition state density-induced dipoles. All the forces and torques involving induced dipoles can be efficiently evaluated using standard electrostatic formulas as if the induced dipoles were permanent dipoles. The formulas are given in the most general form and are applicable to various flavors of polarizable force fields. Implementation and tests with a polarizable five-point water model show that the formulas are rigorous. The carbonyl vibration modes and infrared spectrum intensities of a cluster formed by acetone and two water molecules are studied.

Si, Dejun; Li, Hui

2010-10-01

375

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software  

NASA Astrophysics Data System (ADS)

The similarity of the AMBER force field's energy functional form with that of the CHARMM force field, gives the potential for direct translation of common bonding and nonbonding terms, along with their parameters, present in CHARMM topology and parameter files, with the intent of evaluation within the AMBER software; specifically the SANDER and PMEMD dynamics engines. To this extent, we have created a tool, CHAMBER, which can take a CHARMM protein structure file (PSF), coordinate file (COR) and associated forcefield files, and convert these to an AMBER topology file (prmtop) and associated coordinate file (inpcrd). CHAMBER opens a conversion route which enables the simulation of CHARMM parameterized models using AMBER's PMEMD engine; thus providing improved serial efficiency as well as parallel efficiency over large numbers of CPUs. Significant effort has been expended in ensuring a true representation of the CHARMM force field in AMBER providing energies and forces that are the same to the limits of machine precision. This software will be released in the upcoming version 1.3 of the free AMBERTools suite.1

Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C.

376

Micro fluidic channel actuator using optical force induced by evanescent field material coupling  

NASA Astrophysics Data System (ADS)

A hollow optical fiber (HOF) has an unique modal distribution of a central evanescent field due to its structure. The HOF consists of a central air hole, a Ge-doped ring core placed at the inmost layer, and silica cladding, which induces the weak evanescent field at the central hole. By the structure with geometric symmetry, it is possible to inject a refractive fluid into the hole and to modify the modal distribution. When a refractive index of the fluid is same with or higher than the core's, guiding of light becomes dominant at the center and the ringshaped field turns into a LP01 mode. During the process, optical force is induced and the net momentum of the fluid is changed. The direction of optical force is opposite to that of light propagation, and the fluid come to be dragged along the central channel in the HOF. In order to further investigate the phenomenon, we have changed the refractive index of the fluid and measured resultant optical force. The direction and strength of the optical force was dependent on the refractive index of the central fluid, which shows ample potential of the HOF as a refractive index sensor.

Choi, Honggu; Ha, Woosung; Park, Minkyu; Oh, Kyunghwan

2011-05-01

377

Two-dimensional electrostatic force field measurements with simultaneous topography measurement on embedded interdigitated nanoelectrodes using a force distance curve based method  

SciTech Connect

Accurate simultaneous measurements on the topography and electrostatic force field of 500 nm pitch interdigitated electrodes embedded in a thin SiO{sub 2} layer in a plane perpendicular to the orientation of the electrodes are shown for the first time. A static force distance curve (FDC) based method has been developed, which allows a lateral and vertical resolution of 25 and 2 nm, respectively. The measured force field distribution remains stable as result of the well controlled fabrication procedure of Pt cantilever tips that allows thousands of FDC measurements. A numerical model is established as well which demonstrates good agreement with the experimental results.

Jenke, Martin Guenter; Santschi, Christian; Hoffmann, Patrik [Advanced Photonics Laboratory, Ecole Polytechnique Federale de Lausanne (EPFL), Station 17, CH-1015 Lausanne (Switzerland)

2008-02-11

378

Theoretical calculation of the modulated acoustic radiation force on spheres and cylinders in a standing plane wave-field  

Microsoft Academic Search

The acoustic radiation force on objects is the result of nonlinear properties of wave propagation in continuous media. The acoustic radiation force is known to be static for a continuous wave and is used for many applications. This force can also be dynamic (oscillatory) if the incident sound wave-field is modulated (slow time-variations). The purpose of the present paper is

F. G. Mitri

2005-01-01

379

Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields  

PubMed Central

We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5–5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is prevented, and also when using force fields that accurately reproduce experimental alkane hydration free energies. The magnitude of the average water dipole moment decreases from 2.6 Debye (in bulk) to 1.88 Debye (in membrane interior). This variation correlates with the change in a water molecule’s coordination number.

Bauer, Brad A.; Lucas, Timothy R.; Meninger, David J.; Patel, Sandeep

2011-01-01

380

Quantum field theories, nuclear forces, and the cosmic rays (1934--1938)  

SciTech Connect

During the 1930s, cosmic rays were the most important source of data on the high-energy behavior of both quantum electrodynamics and nuclear forces. In the period 1934--1938, with which this article is concerned, the dominant fundamental theory of nuclear forces was that of the Fermi field. In sorting out the various cosmic-ray phenomena in the atmosphere, it was found that the less penetrating components were associated with electromagnetic cascade showers, and that the more penetrating component contained a new elementary'' particle, the mesotron. However, there remained puzzling features of the cosmic rays that left adequate room for other interpretations.

Brown, L.M. (Northwestern University, Evanston, Illinois 60208 (USA)); Rechenberg, H. (Max-Planck-Institut fuer Physik und Astrophysik and Werner-Heisenberg-Institut fuer Physik, P.O. Box 40 12 12, D-8000, Muenchen 40 (Germany))

1991-07-01

381

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.

382

The Mean Electromotive Force for MHD Turbulence: The Case of a Weak Mean Magnetic Field and Slow Rotation  

Microsoft Academic Search

The mean electromotive force that occurs in the framework of mean-field magnetohydrodynamics is studied for cases in which magnetic field fluctuations are not only due to the action of velocity fluctuations on the mean magnetic field. The possibility of magnetic field fluctuations independent of a mean magnetic field, as they may occur as a consequence of a small-scale dynamo, is

Karl-Heinz Rädler; Nathan Kleeorin; Igor Rogachevskii

2003-01-01

383

The Topological Nature of Boundary Value Problems for Force-Free Magnetic Fields  

NASA Astrophysics Data System (ADS)

The difficulties of constructing a three-dimensional, continuous force-free magnetic field in the solar corona are investigated through a boundary value problem posed for the unbounded domain external to a unit sphere. The normal field component Bn and the boundary value ?b of the twist function ? on the unit sphere, combined with the demand for a vanishing field at infinity, do constitute sufficient conditions for determining a solution if it exists, but Bn and ?b cannot be prescribed independently. An exhaustive classification of the admissible (Bn,?b)-pairs is developed, using the topological properties of the ? flux surfaces implied by their footprints described by the constant-?b curves on the unit sphere. The incompatibilities arising from boundary conditions contradicting the field equations are distinguished from the interesting one of (Bn,?b) being, in principle, admissible but requiring a weak solution describing a force-free field containing inevitable magnetic tangential discontinuities. This particular incompatibility relates the boundary value problem to the Parker theory of spontaneous current sheets in magnetic fields embedded in electrically perfectly conducting fluids. Our investigation strategically skirts around some important but formidable mathematical problems to arrive at physically definite conclusions and insights on the construction of force-free fields, both in the practical task of modeling coronal magnetic fields with magnetopolarimetric data and in the basic understanding of the Parker theory. Two specific demonstrations of (Bn,?b) are given to illustrate circumstances under which a continuous solution to the boundary value may or may not exist.

Low, B. C.; Flyer, N.

2007-10-01

384

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

385

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

386

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

SciTech Connect

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

Sindelka, Milan; Moiseyev, Nimrod [Department of Chemistry and Minerva Center of Nonlinear Physics in Complex Systems, Technion, Israel Institute of Technology, Haifa 32000 (Israel); Cederbaum, Lorenz S. [Theoretische Chemie, Physikalisch-Chemisches Institut, Universitaet Heidelberg, D-69120 Heidelberg (Germany)

2006-11-15

387

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

PubMed

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. PMID:22411565

Xu, Dong; Zhang, Yang

2012-04-13

388

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

USGS Publications Warehouse

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

Geist, E. L.

1996-01-01

389

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

2012-07-17

390

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

391

Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction  

PubMed Central

Summary Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation. In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.

Dagdeviren, Omur E; Schwendemann, Todd C; Monig, Harry; Altman, Eric I

2012-01-01

392

Effect of forcing on the vorticity field in a confined wake  

NASA Astrophysics Data System (ADS)

Several recent studies have found that when a low Reynolds number, plane wake is forced with sufficient amplitude, the normalized mixing product, measured as the amount of mixed fluid per unit width of the wake, can be increased to levels larger than those seen in high Reynolds number mixing layers. However, no studies examining the velocity and vorticity fields of this flow have been conducted. The present study examines the velocity and vorticity field of a low Reynolds number plane wake within a confining channel in order to better understand the vortex-vortex and vortex-wall interactions in order to shed light on the mechanisms which lead to increases in the amount of mixed fluid within the wake. Molecular Tagging Velocimetry (MTV) is used to measure the velocity field in both the streamwise (u, v velocities in x, y plane) and cross-stream (v, w velocities in y, z plane) measurement planes. The spanwise and streamwise vorticity components are then computed from their respective velocity fields. Measurements in the streamwise plane have found that a distinct spatial periodicity exists in the urms field that is not found in either the unforced case or in unconfined forced flows. A model was developed which relates this spatial periodicity to the phase difference between the forcing input and the rolling up of the vorticity shed from the splitter plate. From these data, it was also determined that the phase at which vorticity is shed is dependent upon the forcing amplitude. The forced wake flow is dominated by the shedding of concentrated, spanwise vortex core rollers. As these cores develop downstream, the levels of peak vorticity within the core decrease. A very small amount of -6w/6z is sufficient to generate a very large decrease in peak vorticity levels. This same quantity has also been found to be a good predictor of the spatial location where mixing enhancement will occur in the forced wake. Mixing enhancement is accomplished by the generation of regions of streamwise vorticity from the reorientation of the primary spanwise vortex cores. A model was developed which describes how these cores develop. The multiple regions of streamwise vorticity are the result of the passage and reorientation of multiple spanwise rollers. These reoriented "legs" of streamwise vorticity interact with the regions of streamwise vorticity resulting from the passage of previous spanwise vortex rollers to generate the additional surface area necessary for mixing enhancement. (Abstract shortened by UMI.)

Cohn, Richard Keith

1999-11-01

393

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

NASA Astrophysics Data System (ADS)

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

Cheatham, Thomas

2008-03-01

394

A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals.  

PubMed

Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules. PMID:22281810

Özp?nar, Gül Alt?nba?; Beierlein, Frank R; Peukert, Wolfgang; Zahn, Dirk; Clark, Timothy

2012-01-27

395

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

2012-07-20

396

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

PubMed

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. PMID:19130496

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

2009-10-01

397

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

PubMed Central

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

Herges, T.; Wenzel, W.

2004-01-01

398

A comparison of force fields and calculation methods for vibration intervals of isotopic H+3 molecules  

Microsoft Academic Search

This paper reports (a) improved values for low-lying vibration intervals of H+3, H2D+, D2H+, and D+3 calculated using the variational method and Simons–Parr–Finlan representations of the Carney–Porter and Dykstra–Swope abinitio H+3 potential energy surfaces, (b) quartic normal coordinate force fields for isotopic H+3 molecules, (c) comparisons of variational and second-order perturbation theory, and (d) convergence properties of the Lai–Hagstrom internal

Grady D. Carney; Steven M. Adler-Golden; David C. Lesseski

1986-01-01

399

A comparison of force fields and calculation methods for vibration intervals of isotopic H3(+) molecules  

Microsoft Academic Search

This paper reports (1) improved values for low-lying vibration intervals of H3(+), H2D(+), D2H(+), and D3(+) calculated using the variational method and Simons-Parr-Finlan (1973) representations of the Carney-Porter (1976) and Dykstra-Swope (1979) ab initio H3(+) potential energy surfaces, (2) quartic normal coordinate force fields for isotopic H3(+) molecules, (3) comparisons of variational and second-order perturbation theory, and (4) convergence properties

G. D. Carney; S. M. Adler-Golden; D. C. Lesseski

1986-01-01

400

Observation of high field regions in GaAs MESFETs by using Kelvin probe force microscopy  

Microsoft Academic Search

We have succeeded in measuring potential profile of GaAs MESFETs by using Kelvin probe force microscopy and compared it with that of AlGaAs\\/InGaAs PHEMT (xln=0.2). The obtained potential profile was different from that of PHEMT. Two-dimensional (2D) device simulation taking the surface state into account revealed that the surface states relaxed the high field at the gate edge. The high

T. Mizutani; T. Takeyama; K. Matsunami; S. Kishimoto; K. Maezawa; M. Tomizawa; P. Schmid; K. M. Lipka; E. Kohn

1999-01-01

401

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

PubMed

The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field. PMID:20684636

Raabe, Gabriele; Maginn, Edward J

2010-08-12

402

Quantum effects in liquid water from an ab initio-based polarizable force field  

Microsoft Academic Search

The importance of quantum effects as well as the accuracy of the ab initio-based polarizable TTM2.1-F force field in describing liquid water are quantitatively assessed by a detailed analysis of the temperature dependence of several thermodynamic and dynamical properties computed using the path-integral molecular dynamics and centroid molecular dynamics methods. The results show that quantum effects are not negligible even

Francesco Paesani; Satoru Iuchi; Gregory A. Voth

2007-01-01

403

Modifying atomic-scale friction between two graphene sheets: A molecular-force-field study  

Microsoft Academic Search

Recently discovered ultralow friction (superlubricity) between incommensurate graphitic layers has raised great interest in understanding the interlayer interaction between graphene sheets under various physical conditions. In this work, we have studied the effects of interlayer distance change and in-sheet defects in modifying the interlayer friction in graphene sheets by extensive molecular-force-field statics calculations. The interlayer friction between graphene sheets with

Yufeng Guo; Wanlin Guo; Changfeng Chen

2007-01-01

404

Polarizable Empirical Force Field for Sulfur-Containing Compounds Based on the Classical Drude Oscillator Model  

PubMed Central

Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over non-polarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Towards development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 non-polarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins.

Zhu, Xiao; MacKerell, Alexander D.

2010-01-01

405

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

Microsoft Academic Search

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

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

2008-01-01

406

Computational nature of human adaptive control during learning of reaching movements in force fields  

Microsoft Academic Search

.   Learning to make reaching movements in force fields was used as a paradigm to explore the system architecture of the biological\\u000a adaptive controller. We compared the performance of a number of candidate control systems that acted on a model of the neuromuscular\\u000a system of the human arm and asked how well the dynamics of the candidate system compared with

Nikhil Bhushan; Reza Shadmehr

1999-01-01

407

Determination method of the balance of the secondary-structure-forming tendencies of force fields  

Microsoft Academic Search

We propose a new method of optimisation of backbone torsion-energy parameters in the force field for molecular simulations of protein systems. This method is based on the idea of balancing the secondary-structure-forming tendencies, namely, those of ?-helix and ?-sheet structures. We perform a minimisation of the backbone dihedral angle-based root-mean-square deviation of the helix and ? structure regions in many

Yoshitake Sakae; Yuko Okamoto

2010-01-01

408

Lipidbook: A Public Repository for Force-Field Parameters Used in Membrane Simulations  

Microsoft Academic Search

Lipidbook is a public database for force-field parameters with a special emphasis on lipids, detergents and similar molecules\\u000a that are of interest when simulating biological membrane systems. It stores parameter files that are supplied by the community.\\u000a Topologies, parameters and lipid or whole bilayer structures can be deposited in any format for any simulation code, preferably\\u000a under a license that

Jan Doma?ski; Phillip J. Stansfeld; Mark S. P. Sansom; Oliver Beckstein

2010-01-01

409

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.  

PubMed

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 conformations. 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. PMID:20845956

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

2010-10-14

410

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

PubMed

We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the divalent cations as the relevant single-ion property. As a probe for ion-pair properties we compute the activity derivatives of the salt solutions. The optimization of the ionic force fields is done in two consecutive steps. First, the cation solvation free energy is determined as a function of the Lennard-Jones (LJ) parameters. The peak in the ion-water radial distribution function (RDF) is used as a check of the structural properties of the ions. Second, the activity derivatives of the electrolytes MgY(2), CaY(2), BaY(2), SrY(2) are determined through Kirkwood-Buff solution theory, where Y = Cl(-), Br(-), I(-). The activity derivatives are determined for the restricted set of LJ parameters which reproduce the exact solvation free energy of the divalent cations. The optimal ion parameters are those that match the experimental activity data and therefore simultaneously reproduce single-ion and ion-pair thermodynamic properties. For Ca(2+), Ba(2+), and Sr(2+) such LJ parameters exist. On the other hand, for Mg(2+) the experimental activity derivatives can only be reproduced if we generalize the combination rule for the anion-cation LJ interaction and rescale the effective cation-anion LJ radius, which is a modification that leaves the cation solvation free energy invariant. The divalent cation force fields are transferable within acceptable accuracy, meaning the same cation force field is valid for all halide ions Cl(-), Br(-), I(-) tested in this study. PMID:23320702

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

2013-01-14

411

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

NASA Astrophysics Data System (ADS)

We develop force field parameters for the divalent cations Mg2+, Ca2+, Sr2+, and Ba2+ for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the divalent cations as the relevant single-ion property. As a probe for ion-pair properties we compute the activity derivatives of the salt solutions. The optimization of the ionic force fields is done in two consecutive steps. First, the cation solvation free energy is determined as a function of the Lennard-Jones (LJ) parameters. The peak in the ion-water radial distribution function (RDF) is used as a check of the structural properties of the ions. Second, the activity derivatives of the electrolytes MgY2, CaY2, BaY2, SrY2 are determined through Kirkwood-Buff solution theory, where Y = Cl-, Br-, I-. The activity derivatives are determined for the restricted set of LJ parameters which reproduce the exact solvation free energy of the divalent cations. The optimal ion parameters are those that match the experimental activity data and therefore simultaneously reproduce single-ion and ion-pair thermodynamic properties. For Ca2+, Ba2+, and Sr2+ such LJ parameters exist. On the other hand, for Mg2+ the experimental activity derivatives can only be reproduced if we generalize the combination rule for the anion-cation LJ interaction and rescale the effective cation-anion LJ radius, which is a modification that leaves the cation solvation free energy invariant. The divalent cation force fields are transferable within acceptable accuracy, meaning the same cation force field is valid for all halide ions Cl-, Br-, I- tested in this study.

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

2013-01-01

412

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

PubMed Central

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

Xie, Wangshen; Gao, Jiali

2008-01-01

413

Ionic force field optimization and modified ion-pair mixing rules  

NASA Astrophysics Data System (ADS)

We propose an optimization scheme to obtain good ionic force fields for classical simulations of salt solutions, also of biological relevance. Our work is based on Molecular Dynamics simulations with explicit (SPC/E) water for different halide and alkali ions forming salt solutions at finite ion concentration. The force field derivation technique we propose is based on a simultaneous optimization of single-ion and ion-pair properties and the determination of the cation-anion interaction parameters (traditionally given by the mixing rules). From the finite-concentration simulations, thermodynamic properties of the salt solutions are derived, using the Kirkwood-Buff theory of solutions, and compared to relevant experimental data. For the rather size-symmetric salt solutions involving bromide and chloride ions, this scheme using the standard mixing rules works fine. For the iodide and fluoride solutions, corresponding to the largest and smallest anion we have considered, a rescaling of the mixing rules was necessary. In this respect, we have introduced scaling factors for the cation-anion Lennard-Jones interaction that quantify deviations from the standard mixing rules. We discuss the efficiency and complications of the proposed ionic force field optimization scheme.

Fyta, Maria; Netz, Roland R.

2012-02-01

414

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

415

Neutron Fermi liquids under the presence of a strong magnetic field with effective nuclear forces  

NASA Astrophysics Data System (ADS)

Landau's Fermi liquid parameters are calculated for non-superfluid pure neutron matter in the presence of a strong magnetic field at zero temperature. The particle-hole interactions in the system, where a net magnetization may be present, are characterized by these parameters in the framework of a multipolar formalism. We use either zero- or finite-range effective nuclear forces to describe the nuclear interaction. Using the obtained Fermi liquid parameters, the contribution of a strong magnetic field on some bulk magnitudes such as isothermal compressibility and spin susceptibility is also investigated.

Pérez-García, M. Ángeles; Navarro, J.; Polls, A.

2009-08-01

416

Field forced antiferroelectric-to-ferroelectric switching in modified lead zirconate titanate stannate ceramics  

SciTech Connect

Electric-field-forced antiferroelectric- to-ferroelectric phase transitions in several compositions of modified lead zirconate titanate stannate antiferroelectric ceramics are studied for ultra-high-field-induced strain actuator applications. Two types of fatigue effects are observed in these ceramic compositions. In one, the fatigue effects only proceed to a limited extent and the properties may be restored by annealing above the Curie temperature, while in the other, the fatigue effects proceed to a large extent and the properties cannot be restored completely by heat treatment.

Pan, W.; Zhang, Q.; Bhalla, A.; Cross, L.E. (Materials Research Lab., Pennsylvania State Univ., University Park, PA (US))

1989-04-01

417

Screening in nanowires and nanocontacts: field emission, adhesion force, and contact resistance  

SciTech Connect

The explanations of several nanoscale phenomena such as the field enhancement factor in field emission, the large decay length of the adhesion force between a metallic tip and a surface, and the contact resistance in a nanowire break junction have been elusive. Here we develop an analytical theory of Thomas-Fermi screening in nanoscale structures. We demonstrate that nanoscale dimensions give rise to an effective screening length that depends on geometry and physical boundary conditions. The above phenomena are shown to be manifestations of the effective screening length.

Zhang, Xiaoguang [ORNL; Pantelides, Sokrates T. [Vanderbilt University

2009-01-01

418

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

419

Additional dc magnetic field response of magnetostrictive/piezoelectric magnetoelectric Laminates by Lorentz force effect  

NASA Astrophysics Data System (ADS)

We have discovered that traditional long-type magnetoelectric laminate composite of magnetostrictive Tb1-xDyxFe2-y and piezoelectric materials possesses additional ability of detecting dc magnetic field, using the product effect of the Lorentz force effect from Terfenol-D metal strips in dc magnetic field applied with an ac electrical current and the piezoelectric effect from piezoelectric material. The output voltage between the two faces of piezoelectric (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 single crystal shows a good linear response to applied dc magnetic field of 100-1200 Oe under different ac electrical current inputs (0.4-200 mA). The magnetoelectric coefficient is about ~64.1 mV/T A. The additional dc magnetic field response of magnetostrictive/piezoelectric magnetoelectric laminates driven by Lorentz force makes this composite hopeful for application in coil-free ac/dc magnetic-sensitive sensors. At the same time, for this composite, the additional ability will not affect the primal ability for detecting ac magnetic field.

Jia, Yanmin; Tang, Yanxue; Zhao, Xiangyong; Luo, Haosu; Or, Siu Wing; Chan, Helen Lai Wa

2006-12-01

420

Combustion of 1,5-Dinitrobiuret (DNB) in the Presence of Nitric Acid Using ReaxFF Molecular Dynamics Simulations.  

PubMed

In this study we have examined the combustion dynamics of 1,5-dinitrobiuret (DNB) and nitric acid using reactive molecular dynamics simulations. Simulations were performed using the ReaxFF force field with parameters that were fitted against quantum mechanical calculations on model compounds/clusters relevant for this particular chemical system. Several different compositions were investigated, at densities of 0.5 and 1.0 g/mL, to examine the reaction kinetics in a dense vapor and liquid phase of these mixtures. Our simulations show that at certain compositions of the mixture reaction kinetics result in a very sharp release of thermal energy, which we associate with spontaneous ignition or hypergolicity. Analysis of key reaction mechanisms responsible for this process is discussed. PMID:23985064

Russo, Michael F; Bedrov, Dmitry; Singhai, Shashank; van Duin, Adri C T

2013-09-13

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