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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 and Validation of ReaxFF Reactive Force Field for Hydrocarbon Chemistry Catalyzed by Nickel  

E-print Network

Development and Validation of ReaxFF Reactive Force Field for Hydrocarbon Chemistry Catalyzed as a function of temperature and pressure, we have developed the ReaxFF reactive force field to describe surface. The ReaxFF parameters were determined by fitting to the geometries and energy surfaces from

Goddard III, William A.

3

The ReaxFF PolarizableReactiveForce Fields for Molecular Dynamics Simulationof  

E-print Network

The ReaxFF PolarizableReactiveForce Fields for Molecular Dynamics Simulationof Ferroelectrics. A key feature of the force field (denoted ReaxFF) is that charge transfer and atomic polarization) obtained using QM methods of cubic and tetragonal BaTiO3 over a wide pressure range. We then use the ReaxFF

Goddard III, William A.

4

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

E-print Network

The ReaxFF Polarizable Reactive Force Fields for Molecular Dynamics Simulation of Ferroelectrics. A key feature of the force field (denoted ReaxFF) is that charge transfer and atomic polarization pressure range obtained using QM methods. We then use the ReaxFF with MD to study thermal properties of Ba

Ã?agin, Tahir

5

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

E-print Network

Development of a ReaxFF Reactive Force Field for Glycine and Application to Solvent Effect, a ReaxFF reactive force field has been developed for glycine. A training set for the ReaxFF hydrocarbon mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate

Goddard III, William A.

6

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

E-print Network

Development and Application of a ReaxFF Reactive Force Field for Oxidative DehydrogenationVed: May 21, 2008 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

Goddard III, William A.

7

Application of the ReaxFF Reactive Force Field to Reactive Dynamics of Hydrocarbon Chemisorption and Decomposition  

E-print Network

Application of the ReaxFF Reactive Force Field to Reactive Dynamics of Hydrocarbon Chemisorption the recently developed ReaxFF reactive force field to describe decomposition, reactivity, and desorption (QM) energy surfaces, validating the accuracy of ReaxFF for studying hydrocarbon decomposition

Goddard III, William A.

8

Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride Obaidur Rahaman,  

E-print Network

Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride Obaidur inexpensive yet reliable method for simulation of aqueous-phase copper chemistry, ReaxFF reactive force field training them against configurations generated from ReaxFF MD simulations that are performed multiple times

Goddard III, William A.

9

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

E-print Network

Dynamics of the Dissociation of Hydrogen on Stepped Platinum Surfaces Using the ReaxFF Reactive(533), has been studied using molecular dynamics and the reactive force field, ReaxFF. The force field mechanism is observed. Because ReaxFF includes all degrees of freedom in the substrate, we carried out

10

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

2013-06-25

11

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

12

Thermal Decomposition of Hydrazines from Reactive Dynamics Using the ReaxFF Reactive Force Field  

E-print Network

Thermal Decomposition of Hydrazines from Reactive Dynamics Using the ReaxFF Reactive Force Field (RD) studies on: the decomposition of bulk hydrazine (N2H4); the decomposition of bulk monomethyl-hydrazine (CH3N2H3), hereafter referred to simply as methyl-hydrazine; the decomposition of hydrazine

Goddard III, William A.

13

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

14

ReaxFF: A Reactive Force Field for Hydrocarbons Adri C. T. van Duin,,| Siddharth Dasgupta, Francois Lorant, and William A. Goddard III*,  

E-print Network

ReaxFF: A Reactive Force Field for Hydrocarbons Adri C. T. van Duin,,| Siddharth Dasgupta, Francois reactive chemical systems (1000s of atoms), we developed ReaxFF, a force field for reactive systems. ReaxFF so that all these terms go to zero smoothly as bonds break. In addition, ReaxFF has Coulomb and Morse

van Duin, Adri

15

Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure Modes from Reactive Dynamics  

E-print Network

Development of a ReaxFF Reactive Force Field for Ettringite and Study of its Mechanical Failure 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

Goddard III, William A.

16

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

2011-02-17

17

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

18

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

19

Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases  

E-print Network

Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage-point quantum mechanices (QM) energies from [Cu(H2O)n]2+ clusters abstracted from a ReaxFF molecular dynamics

Goddard III, William A.

20

Formation of water at a Pt(111) surface: A study using reactive force fields (ReaxFF) Markus J. Buehler1  

E-print Network

Formation of water at a Pt(111) surface: A study using reactive force fields (ReaxFF) Markus J temperature, we describe the dynamics of water formation at a Pt catalyst using a new reactive ReaxFF of water formation at Pt surfaces using a new first principles based reactive force field (ReaxFF) capable

Barr, Al

21

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

E-print Network

Development of the ReaxFF reactive force field for mechanistic studies of catalytic selective a new reactive force field, ReaxFF, for use in molecular dynamics (MD) simulations to investigate the structures and reactive dynamics of complex metal oxide catalysts. The parameters in ReaxFF are derived

van Duin, Adri

22

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  

E-print Network

Development of the ReaxFF Reactive Force Field for Describing Transition Metal Catalyzed Reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial that ReaxFF reproduces the QM reaction data with good accuracy while also reproducing the binding

Goddard III, William A.

23

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

24

Development of a ReaxFF Reactive Force Field for Tetrabutylphosphonium Glycinate/CO2 Mixtures.  

PubMed

Carbon dioxide interacts with the ionic liquid tetrabutylphosphonium glycinate, [P(C4)4][Gly], through both physical and chemical absorption. We present a parametrization of the ReaxFF force field for this system that accounts for both chemical and physical interactions. The parametrization was developed from an extensive training set including periodic density functional theory (DFT) calculations of reaction pathways between CO2 and the anion [Gly](-) in the condensed phase, condensed-phase molecular dynamics (MD) configurations, gas-phase CO2-anion and CO2-cation interactions, and gas-phase cluster calculations for intra-ion interactions. The optimized ReaxFF parameters capture the essential features of both physical and chemical interactions between CO2 and [P(C4)4][Gly] as compared with experiments, van der Waals-corrected DFT calculations, or, in the case of physical interactions, classical force field calculations. The probability distributions of the distance between C (from CO2) and N (from the anion) and the CO2 bend angles calculated from MD simulations with the optimized ReaxFF force field are in good general agreement with those from DFT-based MD simulations. We predict that the density of CO2/[P(C4)4][Gly] mixtures increases with increasing CO2 concentration up to at least 50 mol % CO2. We attribute the significant increase in density to the small effective volume occupied by chemically bound CO2 in the mixture. The predicted increase in density may be tested experimentally. PMID:25285669

Zhang, Bo; van Duin, Adri C T; Johnson, J Karl

2014-10-16

25

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

NASA Astrophysics Data System (ADS)

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 core, described as a Gaussian distribution with fixed total charge (e.g. +4 for Ti), and a valence charge, also described as a Gaussian distribution. The valence charges can flow in response to its environment as described via Charge Equilibration (QEq). The restoring force between a core and its valence electrons is given be the electrostatic interaction between the two charge distributions. Thus each atom has four universal parameters describing the electrostatics which are determined once from fitting to the QM charge distributions on a representative set of finite clusters. The nonelectrostatic interactions (Pauli repulsion, dispersion) are described with a Morse potential, leading to 3 additional universal parameters for each pair of atoms. We optimized the Morse parameters to reproduce the zero temperature Equation of State (energy- and pressure-volume curves) obtained using QM methods of cubic and tetragonal BaTiO3 over a wide pressure range. We then use the ReaxFF with MD to study thermal properties of BaTiO3, in particular the cubic to tetragonal phase transition. Our MD simulations indicate that the transition temperature obtained using ReaxFF is in good agreement with experiment.

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

2002-08-01

26

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

2013-09-30

27

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

2011-10-13

28

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

E-print Network

dynamics simulations using the ReaxFF reactive force field Elodie Salmon a , Adri C.T. van Duin b Accepted 27 August 2008 Available online 17 October 2008 a b s t r a c t This paper reports ReaxFF MD, specifically, ReaxFF predictions on the pyrolysis of prototypical chemical structures involving aliphatic chain

Goddard III, William A.

29

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

E-print Network

ReaxFF Reactive Force Field for Solid Oxide Fuel Cell Systems with Application to Oxygen Ion, Pasadena, California 91125 ReceiVed: August 23, 2007; In Final Form: NoVember 21, 2007 We present the ReaxFF through yttria-stabilized zirconia (YSZ) solid oxide fuel cell (SOFC) membranes. All parameters for ReaxFF

Goddard III, William A.

30

ReaxFF Reactive Force Field for the Y-Doped BaZrO3 Proton Conductor with Applications to Diffusion Rates for Multigranular Systems  

E-print Network

ReaxFF Reactive Force Field for the Y-Doped BaZrO3 Proton Conductor with Applications to Diffusion resistance. In order to provide the basis for improving these materials, we developed the ReaxFF reactive. The parameters in ReaxFF were based entirely on the results of quantum mechanics (QM) calculations for systems

Goddard III, William A.

31

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

32

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

33

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

E-print Network

Early maturation processes in coal. Part 2: Reactive dynamics simulations using the ReaxFF reactive force field on Morwell Brown coal structures Elodie Salmon a , Adri C.T. van Duin b , François Lorant Brown coal using the ReaxFF reactive force field. We find that these reactive MD simulations

Goddard III, William A.

34

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

35

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, William A

2009-08-01

36

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

37

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

38

Optimization and Application of Lithium Parameters for the Reactive Force Field, ReaxFF Sang Soo Han, Adri C. T. van Duin, William A. Goddard III, and Hyuck Mo Lee*,  

E-print Network

Optimization and Application of Lithium Parameters for the Reactive Force Field, ReaxFF Sang Soo optimized parameters of the reactive force field (ReaxFF) for these systems. The parameters for this force parameters for condensed phases of Li. The accuracy of the developed ReaxFF was also tested by comparison

van Duin, Adri

39

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

40

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

PubMed Central

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

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

2012-01-01

41

Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.  

PubMed

We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings. PMID:24479769

Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

2014-02-27

42

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). PMID:21873210

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

2011-01-01

43

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

44

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

2011-01-20

45

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. PMID:21166434

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

2011-01-01

46

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

47

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

2013-10-10

48

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

2013-07-11

49

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

2010-08-21

50

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

51

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

52

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

53

Simulating the Initial Stage of Phenolic Resin Carbonization via the ReaxFF Reactive Force De-en Jiang,*,  

E-print Network

Simulating the Initial Stage of Phenolic Resin Carbonization via the ReaxFF Reactive Force Field De of this process by using the ReaxFF reactive force field, which bridges quantum mechanical and molecular (ReaxFF) was developed by van Duin et al.9 ReaxFF employs a relation- ship between bond orders and bond

Goddard III, William A.

54

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

55

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

56

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

57

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

PubMed Central

In order 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(H2O)n]2+-cluster structures and energies) is augmented by single-point QM-energies from [Cu(H2O)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 Cu2+/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(H2O)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

2010-01-01

58

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

59

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

60

Reactive Force Field & Molecular Dynamics Simulations  

E-print Network

: Parallel reactive molecular dynamics (MD) RMD ReaxFF · Applications: 1. Combustion of aluminum · Large scale (multimillion atoms) · Long time (nanosecond) #12;Reactive force field (RMD & ReaxFF (ReaxFF) #12;Classification of ReaxFF Potential Bonded Non-bonded E = Elp + Eover + Eunder + Ebond

Southern California, University of

61

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

NASA Astrophysics Data System (ADS)

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, and surface step composition for flat and stepped YSZ surfaces. It is thermodynamically favorable for yttrium atoms to segregate to the surface of YSZ, and specifically to step edge sites. Surface saturation of yttrium occurs at approximately 40% (40:60 Y:Zr ratio) while yttrium concentration at the step edge does not approach a saturation value, suggesting that steps on the YSZ surface are mainly yttria-terminated. We found that it is thermodynamically favorable for oxygen vacancies to occupy positions in the subsurface layer of YSZ, and a higher fraction of vacancies occupy positions NN to Y than NN to Zr. Yttrium segregation to step edges on the YSZ surface does not lower the surface formation energy of the stepped surface below that of the flat (111) termination, suggesting that the stability of YSZ surface steps observed experimentally is due to kinetic barriers for surface re-ordering.

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

2010-08-01

62

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

63

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

2012-12-13

64

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

65

General Multiobjective Force Field Optimization Framework, with Application to Reactive Force Fields for Silicon Carbide  

E-print Network

: (1) the ReaxFF reactive force field for modeling the adiabatic reactive dynamics of silicon carbide quantum mechanical data sets for demanding applications like ReaxFF, electronic fast forward (or electron

Goddard III, William A.

66

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

67

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

68

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

E-print Network

March 2006) We report a study of dynamic cracking in a silicon single crystal in which the ReaxFF are described with a nonreactive force field. ReaxFF is completely derived from quantum mechanical calculations based on the ReaxFF reac

Goddard III, William A.

69

Toward a Process-Based Molecular Model of SiC Membranes. 1. Development of a Reactive Force Field  

E-print Network

the ReaxFF reactive force field, validated for high temperature reactions of other materials, to describe and structures. Then, we develop a model of the HPCS polymer and utilize ReaxFF to describe the thermal

Goddard III, William A.

70

DFT SQM force field for cobalt corrinoids  

NASA Astrophysics Data System (ADS)

This Letter introduces a systematic development of a quantitative vibrational force field (FF) capable of modeling vibrational spectra of cobalt corrinoids (B 12 derivatives). The scaled quantum mechanical (SQM) method is used to refine density functional theory (DFT) based force constants calculated at the B3LYP level of theory. The reliability of the DFT-SQM FF for cobalt corrinoids is tested on a six-coordinate methylcobalamin Im-[Co III-corrin]-CH 3 model. It is shown that the computed frequencies and Raman intensities permit detailed vibrational assignment. This analysis illustrates the utility of DFT-SQM FF in making detailed connections between the structure of cobalt corrinoids and their vibrational spectra.

Andruniow, Tadeusz; Zgierski, Marek Z.; Kozlowski, Pawel M.

2000-12-01

71

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

72

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

PubMed

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

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

2012-12-01

73

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

E-print Network

. Towards this end we are parameterizing a force field, ReaxFF[2], to simulate large clusters containing NaH, NasAlHg, NaAlH4 and Al phases plus catalysts atoms. ReaxFF has already been shown to be able for hydrocarbons[5], ReaxFF has been successfully applied to study Si/Si02 interfaces[3], MgH2 systems and Al

Goddard III, William A.

74

Molecular Dynamics Simulations of Carbon-Supported Ni Clusters Using the Reax Reactive Force Field  

E-print Network

),20­25 and the Reax force field (ReaxFF). The latter is based on a bond-order model in conjunction with a charge-equilibration scheme,26 and it was first developed for hydrocarbons.27 Subsequently, the ReaxFF with a graphite platelet34 using a ReaxFF for C/Pt/H systems. We showed that an initial cluster-substrate mismatch

Goddard III, William A.

75

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

2013-05-15

76

A reactive force field for lithiumaluminum silicates with applications to eucryptite phases This article has been downloaded from IOPscience. Please scroll down to see the full text article.  

E-print Network

/015002 Abstract We have parameterized a reactive force field (ReaxFF) for lithium­aluminum silicates using density properties. We have found that (a) these ReaxFF parameters predict the correct order of stability of ReaxFF, and discussed the elastic anisotropy of these two polymorphs. Polycrystalline average

Ciobanu, Cristian

77

APS/123-QED Multi-paradigm modeling of dynamical crack propagation in silicon using the ReaxFF  

E-print Network

APS/123-QED Multi-paradigm modeling of dynamical crack propagation in silicon using the ReaxFF in which the ReaxFF reactive force field is used for several thousand atoms near the crack tip while more than 100,000 atoms of the model system are described with a simple nonreactive force field. The ReaxFF

van Duin, Adri

78

Approximate photochemical dynamics of azobenzene with reactive force fields.  

PubMed

We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis?trans- and trans?cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work). PMID:24329064

Li, Yan; Hartke, Bernd

2013-12-14

79

Approximate photochemical dynamics of azobenzene with reactive force fields  

SciTech Connect

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

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

2013-12-14

80

Approximate photochemical dynamics of azobenzene with reactive force fields  

NASA Astrophysics Data System (ADS)

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

Li, Yan; Hartke, Bernd

2013-12-01

81

Chemical Physics Letters, in press Predicting Mechanical Response of Crosslinked Epoxy using ReaxFF  

E-print Network

Chemical Physics Letters, in press 1 Predicting Mechanical Response of Crosslinked Epoxy using ReaxFF events can play a significant role in epoxy mechanical behavior, the reactive force field (ReaxFF that mechanical stiffness and strength values predicted with MD using ReaxFF show close agreement with experiment

Odegard, Gregory M.

82

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

83

The first hyperpolarizabilities of hemicyanine cationic derivatives studied by finite-field (FF) calculations  

Microsoft Academic Search

In this paper, we have designed 26 hemicyanine cationic derivatives by selecting ?-conjugated bond and increasing alkyl chain length of electron donor (D) group and of electron acceptor (A) in order to describe their structure–property relationship. The geometries and molecular frontier orbitals are obtained from semi-empirical PM3 method. The finite-field (FF) method is performed to calculate molecular first hyperpolarizability (?).

Haipeng Li; Kui Han; Xiaopeng Shen; Zhenping Lu; Zhimin Huang; Wentao Zhang; Zhaohui Zhang; Lei Bai

2006-01-01

84

Forces in electromagnetic field and gravitational field  

E-print Network

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

Zihua Weng

2008-06-21

85

Perfluoroalkane force field for lipid membrane environments.  

PubMed

In this work, we present atomic parameters of perfluoroalkanes for use within the CHARMM force field. Perfluorinated alkanes represent a special class of molecules. On the one hand, they are considerably more hydrophobic than lipids, but on the other hand, they are not lipophilic either. Instead, they represent an independent class of philicity, enabling a whole portfolio of applications within both materials science and biochemistry. We performed a thorough parametrization of all bonded and nonbonded parameters with a particular focus on van der Waals parameters. Here, the general framework of the CHARMM and CGenFF force fields has been followed. The van der Waals parameters have been fitted to experimental densities over a wide range of temperatures and pressures. This newly parametrized class of molecules will open the gate for a variety of simulations of biologically relevant systems within the CHARMM force field. A particular perspective for the present work is the influence of polyphilic transmembrane molecules on membrane properties, aggregation phenomena, and transmembrane channels. PMID:25275859

von Rudorff, Guido Falk; Watermann, Tobias; Sebastiani, Daniel

2014-10-30

86

Simulations on the Thermal Decomposition of a Poly(dimethylsiloxane) Polymer Using the ReaxFF Reactive  

E-print Network

Simulations on the Thermal Decomposition of a Poly(dimethylsiloxane) Polymer Using the ReaxFF 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

van Duin, Adri

87

Establishment of performance standards and a cut-score for the Canadian Forces Firefighter Physical Fitness Maintenance Evaluation (FF PFME).  

PubMed

The Bookmark method for setting cut-scores was used to re-set the cut-score for the Canadian Forces Firefighter Physical Fitness Maintenance Evaluation (FF PFME). The time required to complete 10 tasks that together simulate a first-response firefighting emergency was accepted as a measure of work capacity. A panel of 25 Canadian Forces firefighter supervisors set cut-scores in three rounds. Each round involved independent evaluation of nine video work samples, where the times systematically increased from 400 seconds to 560 seconds. Results for Round 1 were discussed before moving to Round 2 and results for Round 2 were discussed before moving to Round 3. Accounting for the variability among panel members at the end of Round 3, a cut-score of 481 seconds (mean Round 3 plus 2 SEM) was recommended. Firefighters who complete the FF PFME in 481 seconds or less have the physical capacity to complete first-response firefighting work. PMID:25102916

Todd Rogers, W; Docherty, David; Petersen, Stewart

2014-11-01

88

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

89

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

90

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

91

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

92

The Scaled-Charge Additive Force Field for Amino Acid Based Ionic Liquids  

E-print Network

Abstract. Ionic liquids (ILs) constitute an emerging field of research. New ILs are continuously introduced involving more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non- polarizable force field (FF) for the eight AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions have been taken into account by computing electrostatic potential for ion pairs, in contrast to isolated ions. The van der Waals interactions have been transferred from the CHARMM36 FF with minor modifications. Therefore, compatibility between our parameters and CHARMM36 parameters is preserved. Our FF can be easily implemented using a variety of popular molecular dynamics programs. It will find broad applications in computational investigation of ILs.

Fileti, Eudes Eterno

2014-01-01

93

Anharmonic force field for methanol  

NASA Astrophysics Data System (ADS)

An ab initio quartic anharmonic force field for methanol has been calculated at the equilibrium position using the CCSD(T) method for the structure and the harmonic potential energy surface, and the MP4(SDQ) method for the anharmonic part of the surface. A triple zeta basis set was employed with symmetrized curvilinear internal valence coordinates in all calculations. The internal coordinate force field constants have been transformed into force constants in the dimensionless normal coordinate representation for various isotopomers. Vibrational term values for CH3OH, CH3OD, CD3OH, and CD3OD have been obtained using second order perturbation theory. Particular care has been devoted to the inclusion of Fermi resonance interactions between different vibrational states. A good accuracy has been achieved in the calculation of the fundamentals for all the isotopomers, the mean absolute error being 5.8 cm-1.

Miani, Andrea; Hänninen, Vesa; Horn, Matthias; Halonen, Lauri

94

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

95

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field.  

PubMed

In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained. PMID:23925839

Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter; Joshi, Kaushik L; Shin, Yun Kyung; Oelschlaeger, Peter; van Duin, Adri C T; Barone, Vincenzo

2013-09-28

96

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

2011-10-01

97

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

98

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

99

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

100

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

101

Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides  

PubMed Central

Based on the AMBER polarizable model (ff02), we have reoptimized the parameters related to the main-chain (?, ?) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., ?, PII, ?R, and ?L regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the ?, PII and ?R regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)7-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization. PMID:16526038

WANG, ZHI-XIANG; ZHANG, WEI; WU, CHUN; LEI, HONGXING; CIEPLAK, PIOTR; DUAN, YONG

2014-01-01

102

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. PMID:22352995

2012-01-01

103

Static and dynamical Meissner force fields  

NASA Astrophysics Data System (ADS)

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

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

1991-01-01

104

Predicting mechanical response of crosslinked epoxy using ReaxFF  

NASA Astrophysics Data System (ADS)

The development of improved epoxy resins can be greatly facilitated using molecular dynamics (MD) techniques. Because molecular-level failure events can play a significant role in epoxy mechanical behavior, the reactive force field (ReaxFF) is an ideal tool for MD simulations of crosslinked epoxies. The results of this Letter demonstrate that mechanical stiffness and strength values predicted with MD using ReaxFF show close agreement with experiment. The results also indicate that despite the inherently large time-scale differences between experiments and MD modeling, the elastic/yield response from the vastly different characteristic strain rates can be easily correlated.

Odegard, Gregory M.; Jensen, Benjamin D.; Gowtham, S.; Wu, Jianyang; He, Jianying; Zhang, Zhiliang

2014-01-01

105

Molecular simulations: Force fields for carbon capture  

NASA Astrophysics Data System (ADS)

Force fields have been generated that enable accurate simulations of interactions occurring between CO2 molecules and metal-organic frameworks featuring 'open' metal sites, which are promising for carbon capture applications.

Getman, Rachel B.

2012-10-01

106

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

107

Common Force Field Thermodynamics of Cholesterol  

PubMed Central

Four different force fields are examined for dynamic characteristics using cholesterol as a case study. The extent to which various types of internal degrees of freedom become thermodynamically relevant is evaluated by means of principal component analysis. More complex degrees of freedom (angle bending, dihedral rotations) show a trend towards force field independence. Moreover, charge assignments for membrane-embedded compounds are revealed to be critical with significant impact on biological reasoning. PMID:24302856

Giangreco, Francesco; Yamamoto, Eiji; Hirano, Yoshinori; di Giosia, Matteo; Zerbetto, Francesco; Yasuoka, Kenji; Narumi, Tetsu; Yasui, Masato; Hofinger, Siegfried

2013-01-01

108

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

109

Simulations of the quart (101-bar1)/water interface: A comparison of classical force fields, ab initi molecular dynamics, and x-ray reflectivity experiments.  

SciTech Connect

Classical molecular dynamics (CMD) simulations of the (1011) surface of quartz interacting with bulk liquid water are performed using three different classical force fields, Lopes et al., ClayFF, and CHARMM water contact angle (CWCA), and compared to ab initio molecular dynamics (AIMD) and X-ray reflectivity (XR) results. The axial densities of the water and surface atoms normal to the surface are calculated and compared to previous XR experiments. Favorable agreement is shown for all the force fields with respect to the position of the water atoms. Analyses such as the radial distribution functions between water and hydroxyl atoms and the average cosine of the angle between the water dipole vector and the normal of the surface are also calculated for each force field. Significant differences are found between the different force fields from such analyses, indicating differing descriptions of the structured water in the near vicinity of the surface. AIMD simulations are also performed to obtain the water and hydroxyl structure for comparison among the predictions of the three classical force fields to better understand which force field is most accurate. It is shown that ClayFF exhibits the best agreement with the AIMD simulations for water hydroxyl radial distribution functions, suggesting that ClayFF treats the hydrogen bonding more accurately.

Skelton, Adam [ORNL; Fenter, Paul [Argonne National Laboratory (ANL); Kubicki, James D. [Pennsylvania State University; Wesolowski, David J [ORNL; Cummings, Peter T [ORNL

2011-01-01

110

Computing nonlinear force free coronal magnetic fields  

E-print Network

Knowledge of the structure of the coronal magnetic field is important for our understanding of many solar activity phenomena, e.g. flares and CMEs. However, the direct measurement of coronal magnetic fields is not possible with present methods, and therefore the coronal field has to be extrapolated from photospheric measurements. Due to the low plasma beta the coronal magnetic field can usually be assumed to be approximately force free, with electric currents flowing along the magnetic field lines. There are both observational and theoretical reasons which suggest that at least prior to an eruption the coronal magnetic field is in a nonlinear force free state. Unfortunately the computation of nonlinear force free fields is way more difficult than potential or linear force free fields and analytic solutions are not generally available. We discuss several methods which have been proposed to compute nonlinear force free fields and focus particularly on an optimization method which has been suggested recently. We compare the numerical performance of a newly developed numerical code based on the optimization method with the performance of another code based on an MHD relaxation method if both codes are applied to the reconstruction of a semi-analytic nonlinear force-free solution. The optimization method has also been tested for cases where we add random noise to the perfect boundary conditions of the analytic solution, in this way mimicking the more realistic case where the boundary conditions are given by vector magnetogram data. We find that the convergence properties of the optimization method are affected by adding noise to the boundary data and we discuss possibilities to overcome this difficulty.

T. Wiegelmann; T. Neukirch

2008-01-21

111

Additive empirical force field for hexopyranose monosaccharides  

PubMed Central

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 ?- and ?-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. Though 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.

2010-01-01

112

Modeling solar force-free magnetic fields  

NASA Astrophysics Data System (ADS)

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 and the free energy associated with the electric current are finite and can be calculated directly from the magnetic field at the plane boundary using the virial theorem. In the study of solar magnetic fields with data from vector magnetographs, there is a long-standing interest in devising algorithms to extrapolate for the force-free magnetic field in a given domain from prescribed field values at the boundary. The closed-form magnetic fields of this paper open up an opportunity for testing the reliability and accuracy of algorithms that claim the capability of performing this extrapolation. The extrapolation procedure as an ill-posed mathematical problem is discussed.

Low, B. C.; Lou, Y. Q.

1990-03-01

113

Multi robot mapping using force field simulation  

Microsoft Academic Search

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

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

2007-01-01

114

Multi Robot Mapping using Force Field Simulation  

Microsoft Academic Search

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

Rolf Lakaemper; Raj Madhavan; Gaithersburg NIST

115

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

116

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. PMID:20856692

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

2010-01-01

117

Force field calculation for inplane vibrations of ethylene using cndo \\/Force method  

Microsoft Academic Search

cndo\\/Force method is used to evaluate redundancy-free internal valence force field (rfivff) for inplane vibrations of ethylene. The bending force constants, the stretch-band and bend-bend interaction force constants\\u000a are predicted reasonably well in magnitude and sign by this method; whereas stretching force constants and stretch-stretch\\u000a interactions are overestimated. Initial force field is set up by transferring stretching force constants from

A Jothi; G Shanmugam; A Annamalai; Surjit Singh

1982-01-01

118

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

119

A compact high field magnetic force microscope.  

PubMed

We present the design and performance of a simple and compact magnetic force microscope (MFM), whose tip-sample coarse approach is implemented by the piezoelectric tube scanner (PTS) itself. In brief, a square rod shaft is axially spring-clamped on the inner wall of a metal tube which is glued inside the free end of the PTS. The shaft can thus be driven by the PTS to realize image scan and inertial stepping coarse approach. To enhance the inertial force, each of the four outer electrodes of the PTS is driven by an independent port of the controller. The MFM scan head is so compact that it can easily fit into the 52mm low temperature bore of a 20T superconducting magnet. The performance of the MFM is demonstrated by imaging a manganite thin film at low temperature and in magnetic fields up to 15T. PMID:25189114

Zhou, Haibiao; Wang, Ze; Hou, Yubin; Lu, Qingyou

2014-12-01

120

Adaptive accelerated ReaxFF reactive dynamics with validation from simulating hydrogen combustion.  

PubMed

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

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

2014-07-01

121

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

122

Reactive force fields for proton transfer dynamics.  

PubMed

A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I. PMID:18072179

Lammers, Sven; Lutz, Stephan; Meuwly, Markus

2008-05-01

123

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

2012-03-01

124

Effects of temperature on the properties of glycerol: a computer simulation study of five different force fields.  

PubMed

We perform molecular dynamics simulations of glycerol (propane-1,2,3-triol) at normal pressure and a wide range of temperatures (300-460 K) and study the sensitivity of simulation results to the force field (FF) considered. We employ five commonly used FFs: (i) AMBER, (ii) CHARMM22, and (iii) three versions of the OPLS-AA FF (OPLS1, OPLS2, and OPLS3). We study thermodynamic (density ?(T), thermal expansion coefficient ?P(T), isobaric specific heat cP(T)), dynamic (diffusion coefficient D(T)), as well as structural properties (molecular conformations and hydrogen-bond statistics). In comparison with experiments, FFs i and iii provide reasonable estimations of ?(T) with deviations of ?4.5%; for FF ii, deviations in density are more pronounced, ?9%. Values of ?P(T) vary considerably among the FFs; e.g., deviations are ?9% for OPLS1-FF and ?60% for FF ii. For all models studied, values of cP(T) are approximately twice the corresponding experimental values. Diffusion coefficients are very sensitive to the FFs considered. Specifically, for FFs i and ii and OPLS3, the values of D(T) are remarkably close to the experimental values over the whole range of temperatures studied. Instead, in the cases of OPLS1 and OPLS2-FFs, D(T) is underestimated by approximately 2 orders of magnitude. Interestingly, in all cases, D(T) can be well described by a Vogel-Tamman-Fulcher equation, as observed in experiments. We present a detailed characterization of glycerol backbone conformation based on the traditional classification introduced by Bastiansen, defined in terms of glycerol's OCCC dihedral angles. All FFs indicate that the conformer population varies smoothly with temperature. However, the FFs provide very different conformer distributions. This implies that, from the microscopic point of view, these glycerol models may provide very different liquid environments for, for example, guest biomolecules and hence may play a relevant role in interpreting simulation results involving glycerol-based solutions. We also discuss the statistics of inter- and intramolecular hydrogen bonds (HBs). The FFs are qualitatively comparable regarding HB statistics; however, quantitative differences remain. For example, molecules form a total of 5.5-7 HBs at T = 350 K, depending on the FF considered, including at least one intramolecular HB. PMID:25188739

Jahn, David A; Akinkunmi, Frederick O; Giovambattista, Nicolas

2014-09-25

125

The Energetics of Motivated Cognition: A Force-Field Analysis  

ERIC Educational Resources Information Center

A force-field theory of motivated cognition is presented and applied to a broad variety of phenomena in social judgment and self-regulation. Purposeful cognitive activity is assumed to be propelled by a "driving force" and opposed by a "restraining force". "Potential" driving force represents the maximal amount of energy an individual is prepared…

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

2012-01-01

126

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

2011-06-13

127

MAGNETIC FIELD CONFINEMENT IN THE SOLAR CORONA. I. FORCE-FREE MAGNETIC FIELDS B. Fornberg,2  

E-print Network

MAGNETIC FIELD CONFINEMENT IN THE SOLAR CORONA. I. FORCE-FREE MAGNETIC FIELDS N. Flyer,1 B Axisymmetric force-free magnetic fields external to a unit sphere are studied as solutions to boundary value to the formation of an azimuthal rope of twisted magnetic field embedded within the global field, and to the energy

Fornberg, Bengt

128

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

129

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

130

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

131

ForceFit: a code to fit classical force fields to quantum mechanical potential energy surfaces.  

PubMed

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. PMID:20340109

Waldher, Benjamin; Kuta, Jadwiga; Chen, Samuel; Henson, Neil; Clark, Aurora E

2010-09-01

132

Solutions and symmetries of force-free magnetic fields  

SciTech Connect

New analytical results concerning force-free magnetic fields are presented. A number of examples of exact solutions for two-dimensional nonlinear force-free fields described by the Liouville equation are shown. These include classical solutions, such as, the Gold-Hoyle field and the force-free Harris sheet as special cases. The connection between these solutions and the Lie point symmetries of the Liouville equation is illustrated. Lie point symmetries of the equation describing force-free magnetic fields in helical symmetry in cylindrical geometry are also investigated and an infinitesimal generator that, in the vicinity of the cylinder axis, makes it possible to transform purely radially dependent solutions into helically symmetric solutions, is found. Finally we point out the existence of a formal analogy between the equations for the vector potential components of a class of force-free fields and the equations of motion of a charged particle in a magnetic field. This analogy makes it possible to transfer known results from the theory of the motion of a charged particle, into the context of force-free magnetic fields. Explicit examples of such application are given.

Tassi, E. [Burning Plasma Research Group, Dipartimento di Energetica and CNISM, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Pegoraro, F. [Dipartimento di Fisica, E. Fermi and CNISM, Pisa (Italy); Cicogna, G. [Dipartimento di Fisica, E. Fermi and INFN, Pisa (Italy)

2008-09-15

133

Nuclear forces from chiral effective field theory: a primer  

E-print Network

This paper is a write-up of introductory lectures on the modern approach to the nuclear force problem based on chiral effective field theory given at the 2009 Joliot-Curie School, Lacanau, France, 27 September - 3 October 2009.

Evgeny Epelbaum

2010-01-19

134

Nuclear forces from chiral effective field theory: a primer  

E-print Network

This paper is a write-up of introductory lectures on the modern approach to the nuclear force problem based on chiral effective field theory given at the 2009 Joliot-Curie School, Lacanau, France, 27 September - 3 October 2009.

Epelbaum, Evgeny

2010-01-01

135

Generative morphologies of architectural organization in matter force field  

E-print Network

This thesis investigates generative methods of architectural form finding in matter force fields that produce spatial subdivision and organizational variation. Unlike the style driven contemporary free-form architecture ...

Mutlu, Murat

2010-01-01

136

Nonequilibrium Forces Between Neutral Atoms Mediated by a Quantum Field  

E-print Network

We study all known and as yet unknown 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 principle, systematic and unified description including the intrinsic field fluctuations 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 forces -- between neutral atoms in the long-time limit but also discover the existence of two new types of interatomic forces. The first, a `nonequilibrium force', arises when the field and atoms are not in thermal equilibrium, and the second, which we call an `entanglement force', originates from the correlations of the internal degrees of freedom of entangled atoms.

Ryan Orson Behunin; Bei-Lok Hu

2010-02-13

137

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

138

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

139

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

PubMed

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

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

2013-05-30

140

Brownian motion in a non-homogeneous force field and photonic force microscope  

E-print Network

The Photonic Force Microscope (PFM) is an opto-mechanical technique based on an optical trap that can be assumed to probe forces in microscopic systems. This technique has been used to measure forces in the range of pico- and femto-Newton, assessing the mechanical properties of biomolecules as well as of other microscopic systems. For a correct use of the PFM, the force field to measure has to be invariable (homogeneous) on the scale of the Brownian motion of the trapped probe. This condition implicates that the force field must be conservative, excluding the possibility of a rotational component. However, there are cases where these assumptions are not fulfilled Here, we show how to improve the PFM technique in order to be able to deal with these cases. We introduce the theory of this enhanced PFM and we propose a concrete analysis workflow to reconstruct the force field from the experimental time-series of the probe position. Furthermore, we experimentally verify some particularly important cases, namely the case of a conservative or rotational force-field.

Giorgio Volpe; Giovanni Volpe; Dmitri Petrov

2007-08-03

141

Contrasting studentsâ understanding of electric field and electric force  

NSDL National Science Digital Library

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

Garza, Alejandro; Zavala, Genaro

2014-04-11

142

Alternating Magnetic Field Forces for Satellite Formation Flying  

NASA Technical Reports Server (NTRS)

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

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

2012-01-01

143

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

144

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

NASA Technical Reports Server (NTRS)

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

El-Kaddah, N.; Szekely, J.

1982-01-01

145

A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C6H6)+/0Arn clusters  

NASA Astrophysics Data System (ADS)

We propose in the present paper a SCC-DFTB/FF (Self-Consistent-Charge Density Functional based Tight Binding/Force-Field) scheme adapted to the investigation of molecules trapped in rare gas environments. With respect to usual FF descriptions, the model involves the interaction of quantum electrons in a molecule with rare gas atoms in an anisotropic scheme. It includes polarization and dispersion contributions and can be used for both neutral and charged species. Parameters for this model are determined for hydrocarbon-argon complexes and the model is validated for small hydrocarbons. With the future aim of studying polycyclic aromatic hydrocarbons in Ar matrices, extensive benchmark calculations are performed on (C6H6)+/0Arn clusters against DFT and CCSD(T) calculations for the smaller sizes, and more generally against other experimental and theoretical data. Results on the structures and energetics (isomer ordering and energy separation, cohesion energy per Ar atom) are presented in detail for n = 1-8, 13, 20, 27, and 30, for both neutrals and cations. We confirm that the clustering of Ar atoms leads to a monotonous decrease of the ionization potential of benzene for n ? 20, in line with previous experimental and FF data.

Iftner, Christophe; Simon, Aude; Korchagina, Kseniia; Rapacioli, Mathias; Spiegelman, Fernand

2014-01-01

146

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

147

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

148

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

149

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

150

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

151

Weyl-type fields with geodesic lines of force  

Microsoft Academic Search

The static electrogravitational equations are studied and it is shown that an aligned type D metric that has a Weyl-type relationship between the gravitational and electric potential has shear-free geodesic lines of force. All such fields are then found and turn out to be the fields of a charged sphere, charged infinite rod and charged infinite plate. A further solution

Brendan S. Guilfoyle

1999-01-01

152

Visualization of Force Fields in Protein StructurePrediction  

SciTech Connect

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

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

2005-04-26

153

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

NASA Astrophysics Data System (ADS)

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

Jensen, Benjamin D.

154

Estimation of Cellular Adhesion Forces Using Mean Field Theory  

Microsoft Academic Search

A complete understanding of the interaction of the cell with the surrounding substrate requires a quantitative understanding\\u000a of the force with which they adhere to the matrix. Using mean field theory, we provide a new and robust method to calculate\\u000a this force of cellular adhesion to a ligand coated substrate in a system that contains receptors, ligands and solvent. Our

Tianyi Yang; Muhammad H. Zaman

2010-01-01

155

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

156

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

157

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

158

Force-field calculation and geometry of the HOOO radical  

NASA Astrophysics Data System (ADS)

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.

Suma, Kohsuke; Sumiyoshi, Yoshihiro; Endo, Yasuki

2013-09-01

159

PRIMO: A Transferable Coarse-grained Force Field for Proteins  

PubMed Central

We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (?/?) and side chains (?1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36–155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides. PMID:23997693

Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael

2013-01-01

160

Ponderomotive force in the presence of electric fields  

SciTech Connect

This paper presents averaged equations of particle motion in an electromagnetic wave of arbitrary frequency with its wave vector directed along the ambient magnetic field. The particle is also subjected to an E(vector sign) Multiplication-Sign B(vector sign) drift and a background electric field slowly changing in space and acting along the magnetic field line. The fields, wave amplitude, and the wave vector depend on the coordinate along the magnetic field line. The derivations of the ponderomotive forces are done by assuming that the drift velocity in the ambient magnetic field is comparable to the particle velocity. Such a scenario leads to new ponderomotive forces, dependent on the wave magnetic field intensity, and, as a result, to the additional energy exchange between the wave and the plasma particles. It is found that the parallel electric field can lead to the change of the particle-wave energy exchange rate comparable to that produced by the previously discussed ponderomotive forces.

Khazanov, G. V.; Krivorutsky, E. N. [NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States)

2013-02-15

161

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

E-print Network

of hydrogen from mole- cules to atoms to plasma, as well as the electron dynamics of the Auger decay is available via experiments in diamond anvil cells and gas guns (3­5), and from theoretical studies

Goddard III, William A.

162

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

163

Weyl-type Fields with Geodesic Lines of Force  

E-print Network

The static electrogravitational equations are studied and it is shown that an aligned type D metric which has a Weyl-type relationship between the gravitational and electric potential has shearfree geodesic lines of force. All such fields are then found and turn out to be the fields of a charged sphere, charged infinite rod and charged infinite plate. A further solution is also found with shearing geodesic lines of force. This new solution can have $m>|e|$ or $m<|e|$, but cannot be in the Majumdar-Papapetrou class (in which $m = |e|$). It is algebraically general and has flat equipotential surfaces.

Brendan S. Guilfoyle

1999-05-18

164

Weyl-Type Fields with Geodesic Lines of Force  

E-print Network

The static electrogravitational equations are studied and it is shown that an aligned type D metric which has a Weyl-type relationship between the gravitational and electric potential has shearfree geodesic lines of force. All such fields are then found and turn out to be the fields of a charged sphere, charged infinite rod and charged infinite plate. A further solution is also found with shearing geodesic lines of force. This new solution can have $m>|e|$ or $m<|e|$, but cannot be in the Majumdar-Papapetrou class (in which $m = |e|$). It is algebraically general and has flat equipotential surfaces.

Guilfoyle, B S

1999-01-01

165

Einstein's osmotic equilibrium of colloidal suspensions in conservative force fields  

NASA Astrophysics Data System (ADS)

Predicted by Einstein in his 1905 paper on Brownian motion, colloidal particles in suspension reach osmotic equilibrium under gravity. The idea was demonstrated by J.B. Perrin to win Nobel Prize in Physics in 1926. We show Einstein's equation for osmotic equilibrium can be applied to colloids in a conservative force field generated by optical gradient forces. We measure the osmotic equation of state of 100nm Polystyrene latex particles in the presence of KCl salt and PEG polymer. We also obtain the osmotic compressibility, which is important for determining colloidal stability and the internal chemical potential, which is useful for predicting the phase transition of colloidal systems. This generalization allows for the use of any conservative force fields for systems ranging from colloidal systems to macromolecular solutions.

Fu, Jinxin; Ou-Yang, H. Daniel

2014-09-01

166

Weyl-type Fields with Geodesic Lines of Force  

Microsoft Academic Search

The static electrogravitational equations are studied and it is shown that an\\u000aaligned type D metric which has a Weyl-type relationship between the\\u000agravitational and electric potential has shearfree geodesic lines of force. All\\u000asuch fields are then found and turn out to be the fields of a charged sphere,\\u000acharged infinite rod and charged infinite plate. A further solution

Brendan S. Guilfoyle

1999-01-01

167

Subdiffusion in a time-dependent force field  

SciTech Connect

Based on the random-barrier model and using the mean-field approximation, we derive an equation that describes the subdiffusion of particles in an external time-varying force field. The derived equation predicts the frequency dependence of the conductivity and, in this regard, is consistent with the experiment. We show that the response of the system to an external perturbation depends significantly on the structure of the inhomogeneous medium.

Shkilev, V. P., E-mail: shkilevv@ukr.net [National Academy of Sciences of Ukraine, Institute of Surface Chemistry (Ukraine)

2012-05-15

168

Force, current and field effects in single atom manipulation  

E-print Network

Force, current and field effects in single atom manipulation K.-F. Braun , S.-W. Hla , N. Pertaya present a detailed investigation of the manipulation of Ag and Au atoms with a STM tip on the Ag(111 of the atom during manipulation. The threshold tunnelling resistance and tip-height to move a Au/Ag atom have

Hla, Saw-Wai

169

Lattice Dynamics of Black Phosphorus. I. Valence Force Field Model  

Microsoft Academic Search

Calculation of the lattice dynamical properties of black phosphorus, which is a narrow-gap covalent semiconductor with a layered structure, based on the valence force field model is presented. The results obtained are in good agreement with the experiments, except for infrared active optical modes. The results are discussed in connection with the crystal structure and the chemical-bonding nature of black

Chioko Kaneta; Hiroshi Katayama-Yoshida; Akira Morita

1986-01-01

170

AFMM: A molecular mechanics force field vibrational parametrization program  

Microsoft Academic Search

AFMM (Automated Frequency Matching Method) is a program package for molecular mechanics force field parametrization. The method used fits the molecular mechanics potential function to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. The program optimizes an initial parameter set (either pre-existing or using chemically-reasonable estimation) by iteratively changing them until the optimal fit with the reference

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

2005-01-01

171

The Role of Search for Field Force Knowledge Management  

E-print Network

Chapter 8 The Role of Search for Field Force Knowledge Management Dyaa Albakour, Ge´ry Ducatel technical information and vital regulatory information, a knowledge management solution is concerned to innovative knowledge management applications for mobile workers. Integration of mobile devices

Kruschwitz, Udo

172

Using Force Fields as a User Interface Device  

Microsoft Academic Search

This paper discusses the use of force fields as a means of passing advice from a computer program to a user. It is suggested that this mechanism can be used as a replacement for traditional user interface pop-ups or other widgets when the task is a three dimensional one and a haptic device is available. The benefits and limitations are

Chris Gunn

173

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

174

Modeling High Rate Impact Sensitivity of Perfect RDX and HMX Crystals by ReaxFF Reactive Dynamics  

Microsoft Academic Search

We report a methodology for rapid assessment of impact sensitivity of energetic materials which uses the ReaxFF reactive force field in reactive dynamics (RD) simulations of the high rate compression\\/expansion of a perfect energetic crystal. This approach is validated here to study the high rate impact sensitivity of 1,3,5-trinitrohexahydro-s-triazine (RDX) crystal and octahydro-1,3,5,7-tetrazocine (HMX) crystal at different phases (?, ?,

Luzheng Zhang; Sergey V. Zybin; Adri C. T. Van Duin; William A. Goddard III

2010-01-01

175

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

176

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

177

Reaction analysis and visualization of ReaxFF molecular dynamics simulations.  

PubMed

ReaxFF MD (Reactive Force Field Molecular Dynamics) is a promising method for investigating complex chemical reactions in relatively larger scale molecular systems. The existing analysis tools for ReaxFF MD lack the capability of capturing chemical reactions directly by analyzing the simulation trajectory, which is critical in exploring reaction mechanisms. This paper presents the algorithms, implementation strategies, features, and applications of VARxMD, a tool for Visualization and Analysis of Reactive Molecular Dynamics. VARxMD is dedicated to detailed chemical reaction analysis and visualization from the trajectories obtained in ReaxFF MD simulations. The interrelationships among the atoms, bonds, fragments, species and reactions are analyzed directly from the three-dimensional (3D) coordinates and bond orders of the atoms in a trajectory, which are accomplished by determination of atomic connectivity for recognizing connected molecular fragments, perception of bond types in the connected fragments for molecules or radicals, indexing of all these molecules or radicals (chemical species) based on their 3D coordinates and recognition of bond breaking or forming in the chemical species for reactions. Consequently, detailed chemical reactions taking place between two sampled frames can be generated automatically. VARxMD is the first tool specialized for reaction analysis and visualization in ReaxFF MD simulations. Applications of VARxMD in ReaxFF MD simulations of coal and HDPE (high-density polyethylene) pyrolysis show that VARxMD provides the capabilities in exploring the reaction mechanism in large systems with complex chemical reactions involved that are difficult to access manually. PMID:25064439

Liu, Jian; Li, Xiaoxia; Guo, Li; Zheng, Mo; Han, Junyi; Yuan, Xiaolong; Nie, Fengguang; Liu, Xiaolong

2014-09-01

178

Collision avoidance and task planning using impedance force fields  

NASA Astrophysics Data System (ADS)

A recent progression of heavy lift assist device is to place the human operator closer to the end effector to provide close coupling of the operator input and the payload. This close coupling of the human for control and the power of a heavy lift assist device provides improved accuracy with ease of handling in the case of heavy and bulk objects. However, collisions with obstacles may still occur in a crowded manufacturing environment due to the large work piece inertia characteristics, inappropriate motion command from the operator and inattention or fatigue of the human operator. In this research, a fictitious force field is assigned to each obstacle in the workspace. As a work piece moves closer to an object, an impedance force is calculated and combined with the control forces, in order to prevent collisions. In addition, a set of impedance fields are developed and applied that associate desired trajectories with the layout of the workspace. Thus, the force fields guide the work piece to achieve advantageous orientations and positions during the material handling operation. This includes adjustment of the height of the work piece for placement on tables, orientation to preset positions, and optimizing the configuration of the lift assist robot during motion. Experimental results show that this approach to augmentation provides the operator with a natural and effective interface to the heavy lift assist device.

Luecke, Greg R.; Tan, Kok-Leong; Zafer, Naci

1999-11-01

179

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

PubMed

We present the realization of a mesoscopic imaging technique, namely, the Magnetoelectric Force Microscopy (MeFM), for visualization of local magnetoelectric effect. The basic principle of MeFM is the lock-in detection of local magnetoelectric response, i.e., the electric field-induced magnetization, using magnetic force microscopy. We demonstrate MeFM capability by visualizing magnetoelectric domains on single crystals of multiferroic hexagonal manganites. Results of several control experiments exclude artifacts or extrinsic origins of the MeFM signal. The parameters are tuned to optimize the signal to noise ratio. PMID:24880381

Geng, Yanan; Wu, Weida

2014-05-01

180

Atomistic force field for alumina fit to density functional theory  

SciTech Connect

We present a force field for bulk alumina (Al{sub 2}O{sub 3}), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.

Sarsam, Joanne [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom) [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Thomas Young Centre, Imperial College London, London SW7 2AZ (United Kingdom); Finnis, Michael W.; Tangney, Paul, E-mail: p.tangney@imperial.ac.uk [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom) [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Thomas Young Centre, Imperial College London, London SW7 2AZ (United Kingdom); Department of Physics, Imperial College London, London SW7 2AZ (United Kingdom)

2013-11-28

181

Once-daily fluticasone furoate (FF)/vilanterol reduces risk of severe exacerbations in asthma versus FF alone  

PubMed Central

Background Combination therapy with an inhaled corticosteroid (ICS) and long-acting ?2 agonist (LABA) is recommended for patients with asthma symptomatic on ICS alone. However, there is ongoing debate regarding the risk-benefit ratio of using LABA in asthma. Objective To evaluate the effect of the addition of a novel LABA, vilanterol (VI), to a once-daily ICS, fluticasone furoate (FF), on the risk of severe asthma exacerbations in patients with uncontrolled asthma. Methods This randomised double-blind comparative study of variable duration (?24–78?weeks) was designed to finish after 330 events (each patient's first on-treatment severe asthma exacerbation). 2019 patients with asthma aged ?12?years with ?1 recorded exacerbation within 1?year were randomised and received FF/VI 100/25??g or FF 100??g, administered once daily in the evening. The primary endpoint was time to first severe exacerbation; secondary endpoints were rate of severe asthma exacerbations per patient per year and change in trough evening forced expiratory volume in 1?s (FEV1) from baseline. Results Compared with FF, FF/VI delayed the time to first severe exacerbation (HR 0.795, 95% CI 0.642 to 0.985) and reduced the annualised rate of severe exacerbations (rate reduction 25%, 95% CI 5% to 40%). Significantly greater improvements in trough FEV1 (p<0.001) were observed with FF/VI than with FF at weeks 12, 36, 52 and at endpoint. Both treatments were well tolerated with similar rates of treatment-related adverse events and on-treatment serious adverse events. Conclusions Once-daily FF/VI reduced the risk of severe asthma exacerbations and improved lung function compared with FF alone, with good tolerability and safety profile in adolescents and adults with asthma currently receiving ICS. ClinicalTrials.gov No NCT01086384 PMID:24253831

Bateman, Eric D; O'Byrne, Paul M; Busse, William W; Lotvall, Jan; Bleecker, Eugene R; Andersen, Leslie; Jacques, Loretta; Frith, Lucy; Lim, Jessica; Woodcock, Ashley

2014-01-01

182

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

183

Forces on a spherical conducting particle in E × B fields  

NASA Astrophysics Data System (ADS)

The forces acting on a spherical conducting particle in a transversely flowing magnetized plasma are calculated in the entire range of magnetization and Debye length, using the particle code SCEPTIC3D (Patacchini and Hutchinson 2010 Plasma Phys. Control. Fusion 52 035005, 2011 Plasma Phys. Control. Fusion 53 025005). In short Debye length (i.e. high density) plasmas, both the ion-drag and Lorentz force arising from currents circulating inside the dust show strong components antiparallel to the convective electric field, suggesting that a free dust particle should gyrate faster than what predicted by its Larmor frequency. In intermediate to large Debye length conditions, by a downstream depletion effect already reported in unmagnetized strongly collisional regimes, the ion-drag in the direction of transverse flow can become negative. The internal Lorentz force, however, remains in the flow direction, and large enough in magnitude so that no spontaneous dust motion should occur.

Patacchini, Leonardo; Hutchinson, Ian H.

2011-06-01

184

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

185

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

186

Quantum mechanical force field for water with explicit electronic polarization  

PubMed Central

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 × 106 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

2013-01-01

187

Quantum mechanical force field for water with explicit electronic polarization  

SciTech Connect

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

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

2013-08-07

188

Tuning the mass of chameleon fields in Casimir force experiments.  

PubMed

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

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

2010-06-18

189

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

190

Computer simulation of trifluoromethane properties with ab initio force field.  

PubMed

Intermolecular interaction potentials of the trifluoromethane dimer in 15 orientations have been calculated using the Hartree-Fock (HF) self-consistent theory and the second-order Møller-Plesset (MP2) perturbation theory. Single point energies at important geometries were also calibrated by the coupled cluster with single and double and perturbative triple excitation [CCSD(T)] calculations. We have employed Pople's medium size basis sets [up to 6-311++G(3df,3pd)] and Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). Basis set limit potential values were obtained through well-studied extrapolation methods. The calculated MP2 potential data were employed to parameterize a 5-site force field for molecular simulations. We performed molecular dynamics simulations using the constructed ab initio force field and compared the simulation results with experiments. Quantitative agreements for the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori. PMID:21598276

Chung, Yi-Hsing; Li, Arvin Huang-Te; Chao, Sheng D

2011-08-01

191

Force-free magnetic fields - Generating functions and footpoint displacements  

NASA Technical Reports Server (NTRS)

This paper presents analytic and numerical calculations that explore equilibrium sequences of bipolar force-free magnetic fields in relation to displacments of their magnetic footpoints. It is shown that the appearance of magnetic islands - sometimes interpreted as marking the loss of equilibrium in models of the solar atmosphere - is likely associated only with physically unrealistic footpoint displacements such as infinite separation or 'tearing' of the model photosphere. The work suggests that the loss of equilibrium in bipolar configurations, sometimes proposed as a mechanism for eruptive solar events, probably requires either fully three-dimensional field configurations or nonzero plasma pressure. The results apply only to fields that are strictly bipolar, and do not rule out equilibrium loss in more complex structures such as quadrupolar fields.

Wolfson, Richard; Verma, Ritu

1991-01-01

192

Coarse-grained force field; general folding theory  

PubMed Central

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of ?-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described. PMID:21643583

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

2012-01-01

193

Casimir force for a scalar field in warped brane worlds  

SciTech Connect

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

Linares, Roman; Morales-Tecotl, Hugo A. [Departamento de Fisica, Universidad Autonoma Metropolitana Iztapalapa, San Rafael Atlixco 186, C.P. 09340, Mexico D.F. (Mexico); Pedraza, Omar [Departamento de Fisica, Universidad Autonoma Metropolitana Iztapalapa, San Rafael Atlixco 186, C.P. 09340, Mexico D.F. (Mexico); Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada, Unidad Legaria, Instituto Politecnico Nacional, Av. Legaria 694, C.P. 11500, Mexico D.F. (Mexico)

2008-03-15

194

Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon  

NASA Technical Reports Server (NTRS)

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 interfaces for heptane and pentane menisci on quartz and tetradecane on SFL6. The effects of refractive indices of the solid and liquid on the measurement techniques were demonstrated. Experimentally obtained values of the disjoining pressure and dispersion constants were compared to those predicted from the Dzyaloshinskii - Lifshitz - Pilaevskii theory for an ideal surface and reasonable agreements were obtained. A parameter introduced gives a quantitative measurement of the closeness of the system to equilibrium. The nonequilibrium behavior of this parameter is also presented

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

1995-01-01

195

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

196

Nonlinear gravitational self-force: Field outside a small body  

NASA Astrophysics Data System (ADS)

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

Pound, Adam

2012-10-01

197

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

198

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, Ga"lle; Siozade-Lamoine, Laure; Casadessus, Olivier; Deumié, Carole; Hoffart, Louis; Conrath, John

2011-10-01

199

AFMM: A molecular mechanics force field vibrational parametrization program  

NASA Astrophysics Data System (ADS)

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

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

2005-04-01

200

Coupling ReaxFF with Temperature Accelerated  

E-print Network

Coupling ReaxFF with Temperature Accelerated Dynamics CMDF: Summer 2005 Daniel Yi, Caltech `07 #12; ReaxFF Developed by Adri van Duin at Caltech Bond order calculations allow reactivity Coulombic Examples: #12;ReaxFF - Time scale limitations ReaxFF used to simulate scales of a few nanoseconds worth

Goddard III, William A.

201

The Anharmonic Force Field of BeH2 Revisited  

NASA Technical Reports Server (NTRS)

The anharmonic force field of BeH2 has been calculated near the basis set and n-particle space limits. The computed antisymmetric stretch frequencies of BeH2 and BeD2 are in excellent agreement with recent high-resolution gas-phase measurements. The agreement between theory and experiment for the other spectroscopic constants is also excellent, except for omega(sub 3) and X(sub 33) for BeH2 and G(sub 22) for BeD2. It is concluded that further experimental work is needed in order to resolve these discrepancies.

Martin, Jan M. L.; Lee, Timothy J.

2003-01-01

202

Force Field Parametrization through Fitting on Inflection Points in Isotherms  

NASA Astrophysics Data System (ADS)

We present a method to determine potential parameters in molecular simulations of confined systems through fitting on experimental isotherms with inflection points. The procedure uniquely determines the adsorbent-adsorbate interaction parameters and is very sensitive to the size parameter. The inflection points in the isotherms are often related to a subtle interplay between different adsorption sites. If a force field can predict this interplay, it also reproduces the remaining part of the isotherm correctly, i.e., the Henry coefficients and saturation loadings.

Dubbeldam, D.; Calero, S.; Vlugt, T. J.; Krishna, R.; Maesen, T. L.; Beerdsen, E.; Smit, B.

2004-08-01

203

Context Rich Problems Online Archives: Electric Field and Electric Force  

NSDL National Science Digital Library

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

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

2008-09-29

204

Comparison of ReaxFF, DFTB, and DFT for phenolic pyrolysis. 2. Elementary reaction paths.  

PubMed

Reaction paths for the loss of CO, H2, and H2O from atomistic models of phenolic resin are determined using the hybrid B3LYP approach. B3LYP energetics are confirmed using CCSD(T). The energetics along the B3LYP paths are also evaluated using the PW91 generalized gradient approximation (GGA), the more approximate self-consistent charge density functional tight binding (SCC-DFTB), and the reactive force field (ReaxFF). Compared with the CCSD(T)/cc-pVTZ level for bond and reaction energies and barrier heights, the B3LYP, PW91, DFTB(mio), DFTB(pbc), and ReaxFF have average absolute errors of 3.8, 5.1, 17.4, 13.2, and 19.6 kcal/mol, respectively. The PW91 is only slightly less accurate than the B3LYP approach, while the more approximate approaches yield somewhat larger errors. The SCC-DFTB paths are in better agreement with B3LYP than are those obtained with ReaxFF. PMID:24093151

Bauschlicher, Charles W; Qi, Tingting; Reed, Evan J; Lenfant, Antonin; Lawson, John W; Desai, Tapan G

2013-11-01

205

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

2012-10-11

206

Thermomechanical properties of graphene: valence force field model approach.  

PubMed

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

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

2012-05-01

207

6.641 Electromagnetic Fields, Forces, and Motion, Spring 2003  

E-print Network

Electric and magnetic quasistatic forms of Maxwell's equations applied to dielectric, conduction, and magnetization boundary value problems. Electromagnetic forces, force densities, and stress tensors, including magnetization ...

Zahn, Markus, 1946-

208

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

2013-09-01

209

Parametrization of a reactive force field for aluminum hydride  

NASA Astrophysics Data System (ADS)

A reactive force field, REAXFF, for aluminum hydride has been developed based on density functional theory (DFT) derived data. REAXFFAlH3 is used to study the dynamics governing hydrogen desorption in AlH3. During the abstraction process of surface molecular hydrogen charge transfer is found to be well described by REAXFFAlH3. 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 NaAlH4.

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

2009-07-01

210

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

211

Derivation of a Molecular Mechanics Force Field for Cholesterol  

SciTech Connect

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

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

2004-01-01

212

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

213

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

214

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

215

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

216

Development of a ReaxFF potential for Pt-O systems describing the energetics and dynamics of Pt-oxide formation.  

PubMed

ReaxFF force field parameters describing Pt-Pt and Pt-O interactions have been developed and tested. The Pt-Pt parameters are shown to accurately account for the chemical nature, atomic structures and other materials properties of bulk platinum phases, low and high-index platinum surfaces and nanoclusters. The Pt-O parameters reliably describe bulk platinum oxides, as well as oxygen adsorption and oxide formation on Pt(111) terraces and the {111} and {100} steps connecting them. Good agreement between the force field and both density functional theory (DFT) calculations and experimental observations is demonstrated in the relative surface free energies of high symmetry Pt-O surface phases as a function of the oxygen chemical potential, making ReaxFF an ideal tool for more detailed investigations of more complex Pt-O surface structures. Validation for its application to studies of the kinetics and dynamics of surface oxide formation in the context of either molecular dynamics (MD) or Monte Carlo simulations are provided in part by a two-part investigation of oxygen diffusion on Pt(111), in which nudged elastic band (NEB) calculations and MD simulations are used to characterize diffusion processes and to determine the relevant diffusion coefficients and barriers. Finally, the power of the ReaxFF reactive force field approach in addressing surface structures well beyond the reach of routine DFT calculations is exhibited in a brief proof-of-concept study of oxygen adsorbate displacement within ordered overlayers. PMID:25250822

Fantauzzi, Donato; Bandlow, Jochen; Sabo, Lehel; Mueller, Jonathan E; van Duin, Adri C T; Jacob, Timo

2014-10-01

217

Force.  

ERIC Educational Resources Information Center

Discusses pupil misconceptions concerning forces. Summarizes some of Assessment of Performance Unit's findings on meaning of (1) force, (2) force and motion in one dimension and two dimensions, and (3) Newton's second law. (YP)

Gamble, Reed

1989-01-01

218

Changes in corticospinal excitability during reach adaptation in force fields  

PubMed Central

Both abrupt and gradually imposed perturbations produce adaptive changes in motor output, but the neural basis of adaptation may be distinct. Here, we measured the state of the primary motor cortex (M1) and the corticospinal network during adaptation by measuring motor-evoked potentials (MEPs) before reach onset using transcranial magnetic stimulation of M1. Subjects reached in a force field in a schedule in which the field was introduced either abruptly or gradually over many trials. In both groups, by end of the training, muscles that countered the perturbation in a given direction increased their activity during the reach (labeled as the on direction for each muscle). In the abrupt group, in the period before the reach toward the on direction, MEPs in these muscles also increased, suggesting a direction-specific increase in the excitability of the corticospinal network. However, in the gradual group, these MEP changes were missing. After training, there was a period of washout. The MEPs did not return to baseline. Rather, in the abrupt group, off direction MEPs increased to match on direction MEPs. Therefore, we observed changes in corticospinal excitability in the abrupt but not gradual condition. Abrupt training includes the repetition of motor commands, and repetition may be the key factor that produces this plasticity. Furthermore, washout did not return MEPs to baseline, suggesting that washout engaged a new network that masked but did not erase the effects of previous adaptation. Abrupt but not gradual training appears to induce changes in M1 and/or corticospinal networks. PMID:23034365

Ahmadi-Pajouh, Mohammad Ali; Harran, Michelle D.; Salimpour, Yousef; Shadmehr, Reza

2013-01-01

219

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model  

PubMed Central

The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+–O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers. PMID:24670003

2014-01-01

220

A low-temperature dynamic mode scanning force microscope operating in high magnetic fields  

E-print Network

-field optical microscope designed for operation at low temperatures.5 In this setup, an optical fiber is glued scanning near field optical microscopy,5,7­10 magnetic force microscopy,11 and acoustic near field as a friction- force sensor. The advantages of these piezoelectric sensors are the availability, the low cost

Ihn, Thomas

221

Electric Field How does a charge, q1, exert a force on  

E-print Network

Electric Field How does a charge, q1, exert a force on another charge, q2, when the charges don't touch? The charge, q1, sets up an electric field in its surrounding space This electric field has both magnitude and direction which determine the magnitude and direction of the force acting on q2 #12;Electric

Bertulani, Carlos A. - Department of Physics and Astronomy, Texas A&M University

222

Inertia as a zero-point-field Lorentz force  

Microsoft Academic Search

Under the hypothesis that ordinary matter is ultimately made of subelementary constitutive primary charged entities or partons'' bound in the manner of traditional elementary Planck oscillators (a time-honored classical technique), it is shown that a heretofore uninvestigated Lorentz force (specifically, the magnetic component of the Lorentz force) arises in any accelerated reference frame from the interaction of the partons with

Bernhard Haisch; Alfonso Rueda; H. E. Puthoff

1994-01-01

223

Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

224

Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

225

BE.430J Fields, Forces, and Flows in Biological Systems, Fall 2004  

E-print Network

This course covers the following topics: conduction, diffusion, convection in electrolytes; fields in heterogeneous media; electrical double layers; Maxwell stress tensor and electrical forces in physiological systems; and ...

Grodzinsky, Alan J.

226

Update of the cholesterol force field parameters in CHARMM.  

PubMed

A modification of the CHARMM36 lipid force field (C36) for cholesterol, henceforth, called C36c, is reported. A fused ring compound, decalin, was used to model the steroid section of cholesterol. For decalin, C36 inaccurately predicts the heat of vaporization (~10 kJ/mol) and molar volume (~10 cc/mol), but C36c resulted in near perfect comparison with experiment. MD simulations of decalin and heptane at various compositions were run to estimate the enthalpy and volumes of mixing to compare to experiment for this simple model of cholesterol in a chain environment. Superior estimates for these thermodynamic properties were obtained with C36c versus C36. These new parameters were applied to cholesterol, and quantum mechanical calculations were performed to modify the torsional potential of an acyl chain torsion for cholesterol. This model was tested through simulations of DMPC/10% cholesterol, DMPC/30% cholesterol, and DOPC/10% cholesterol. The C36 and C36c results were similar for surface areas per lipid, deuterium order parameters, electron density profiles, and atomic form factors and generally agree well with experiment. However, C36 and C36c produced slightly different cholesterol angle distributions with C36c adopting a more perpendicular orientation with respect to the bilayer plane. The new parameters in the C36c modification should enable more accurate simulations of lipid bilayers with cholesterol, especially for those interested in the free energy of lipid flip/flop or transfer of phospholipids and/or cholesterol. PMID:22136112

Lim, Joseph B; Rogaski, Brent; Klauda, Jeffery B

2012-01-12

227

Forces  

NSDL National Science Digital Library

This page provides the background for a basic laboratory exercise on force. Included is an explanation of force and vector components and an interactive java applet to demonstrate vectors and vector algebra.

Sorokin, Vladimir

2004-11-28

228

Impulsive force phenomenon of electric field stress causing serious particle contamination in plasma etching equipment  

NASA Astrophysics Data System (ADS)

To demonstrate electric field stress acting as an impulsive force, the action of the stress is investigated using a standard particle. Particles floated from a substrate owing to electric field stress are observed using an in situ particle monitoring system. The results indicate that the more rapidly an electric field changes, the more the stress increases, which demonstrates the impulsive force effect of electric field stress. From the results of this study, we can conclude that the cause of the instantaneous generation of many flaked particles in plasma etching chambers is electric field stress working as an impulsive force.

Kasashima, Yuji; Uesugi, Fumihiko

2014-11-01

229

Force  

NSDL National Science Digital Library

Instructions: This is a webquest designed to help students understand force. It is specifically meant to teach the idea that the greater the force applied to an object the greater the change in speed or direction of the object depending on the mass. This is also known as Newton's Second Law of Motion. Lets Learn about Force! For this project your students will understand force. They will use Newton's second law to solve the problem presented. UT Core Curriculum: Science 3rd Grade. Standard 3- Students will understand the relationship between the force applied to an object and resulting motion of the ...

Brownie, Mrs.

2010-04-07

230

Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids  

E-print Network

Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions Recently, we reported new coarse grain (CG) force fields for lipids and phenyl/fullerene based molecules. In the C60 lipid systems, the fullerenes were shown to aggregate even at the lowest concentrations

Nielsen, Steven O.

231

A reactive force field simulation of liquidliquid phase transitions in phosphorus  

E-print Network

A reactive force field simulation of liquid­liquid phase transitions in phosphorus P. Ballone 2004; accepted 6 August 2004 A force field model of phosphorus has been developed based on density T of the black P to arsenic A17 structure observed in the solid state, and also corresponds to a semiconductor

232

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

E-print Network

. In particular, a haptic sensor for a robotic finger is considered to be an important device because the fingerFinger-Shaped GelForce: Sensor for Measuring Surface Traction Fields for Robotic Hand Katsunari in a robotic hand. Index Terms--Force sensor, surface traction field, finger shape, robotic hand. Ã? 1

Tachi, Susumu

233

Charge Equilibration Force Fields for Molecular Dynamics Simulations of Lipids, Bilayers, and Integral Membrane Protein Systems  

PubMed Central

With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and biophysical systems. We have constructed and applied polarizable force fields for lipids and lipid bilayers. In this review of our recent work, we discuss the formalism we have adopted for implementing the charge equilibration (CHEQ) method for lipid molecules. We discuss the methodology, related issues, and briefly discuss results from recent applications of such force fields. Application areas include DPPC-water monolayers, potassium ion permeation free energetics in the gramicidin A bacterial channel, and free energetics of permeation of charged amino acid analogues across the water-bilayer interface. PMID:21967961

Lucas, Timothy R.; Bauer, Brad A.; Patel, Sandeep

2014-01-01

234

Climate Field Reconstruction under Stationary and Nonstationary Forcing.  

NASA Astrophysics Data System (ADS)

The fidelity of climate reconstructions employing covariance-based calibration techniques is tested with varying levels of sparseness of available data during intervals of relatively constant (stationary) and increasing (nonstationary) forcing. These tests employ a regularized expectation-maximization algorithm using surface temperature data from both the instrumental record and coupled ocean-atmosphere model integrations. The results indicate that if radiative forcing is relatively constant over a data-rich calibration period and increases over a data-sparse reconstruction period, the imputed temperatures in the reconstruction period may be biased and may underestimate the true temperature trend. However, if radiative forcing is stationary over a data-sparse reconstruction period and increases over a data-rich calibration period, the imputed values in the reconstruction period are nearly unbiased. These results indicate that using the data-rich part of the twentieth-century instrumental record (which contains an increasing temperature trend plausibly associated with increasing radiative forcing) for calibration does not significantly bias reconstructions of prior climate.

Rutherford, S.; Mann, M. E.; Delworth, T. L.; Stouffer, R. J.

2003-02-01

235

ADVANCES IN FORCE FIELD TAILORING FOR CONSTRUCTION IN SPACE  

E-print Network

space is certainly a complex process requiring several years. It is essential meanwhile to have field, in microgravity. The hypothesis was that the particles would drift towards the nodal surfaces of the field and form walls, and this hypothesis was proven true. By tailoring field geometry, one can thus

236

Comparison of oxidation resistance of UHMWPE and POM in H2O2 solution from ReaxFF reactive molecular dynamics simulations.  

PubMed

The oxidation mechanism of ultra-high-molecular-weight polyethylene (UHMWPE) and polyoxymethylene (POM) in hydrogen peroxide solution was investigated by molecular dynamics (MD) simulations via reactive force field (ReaxFF) method. MD results from ReaxFF suggested that UHMWPE provided better antioxidation activity at high temperature (>373 K) than its POM counterpart in the same concentration of hydrogen peroxide solution. Furthermore, POM was relatively more susceptible to erosion and swelling because of the infiltration of H2O2 solution. Calculations of the diffusion coefficient at different temperatures permit further understanding of the chemical phenomena involved in the level of oxidation in the course of MD simulations. Results of the simulations are generally consistent with the previous experimental available in literature. The simulations also provide new insights into understanding the mechanism resulting oxidation products among the interested polymers. PMID:25133290

Chen, Wu; Duan, Hai-tao; Hua, Meng; Gu, Ka-li; Shang, Hong-fei; Li, Jian

2014-08-28

237

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

238

Non-linear Force-free Modeling Of Coronal Magnetic Fields  

NASA Astrophysics Data System (ADS)

We compare a variety of nonlinear force-free field (NLFFF) extrapolation algorithms, including optimization, magneto-frictional, and Grad-Rubin-like codes, applied to a solar-like reference model. The model used to test the algorithms includes realistic photospheric Lorentz forces and a complex field including a weakly twisted, right helical flux bundle. The codes were applied to both forced "photospheric'' and more force-free "chromospheric'' vector magnetic field boundary data derived from the model. When applied to the chromospheric boundary data, the codes are able to recover the presence of the flux bundle and the field's free energy, though some details of the field connectivity are lost. When the codes are applied to the forced photospheric boundary data, the reference model field is not well recovered, indicating that the Lorentz forces on the photosphere severely impact the extrapolation of the field. Preprocessing of the photospheric boundary does improve the extrapolations considerably, although the results depend sensitively on the details of the numerical codes. When applying the NLFFF codes to solar data, the problems associated with Lorentz forces present in the low solar atmosphere must be recognized: the various codes will not necessarily converge to the correct, or even the same, solution.

Metcalf, Thomas R.; De Rosa, M. L.; Schrijver, C. J.; Barnes, G.; van Ballegooijen, A.; Wiegelmann, T.; Wheatland, M. S.; Valori, G.; McTiernan, J. M.

2007-05-01

239

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

2011-05-26

240

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

241

Nonlinear force-free magnetic fields: Calculation and applicatin to astrophysics. Ph.D. Thesis  

NASA Technical Reports Server (NTRS)

The problem concerned in this work is that of calculating magnetic field configurations in which the Lorentz force (vector)j x (vector)B is everywhere zero, subject to specified boundary conditions. The magnetic field is represented in terms of Clebsch variables in the form (vector)B = del alpha x del beta. These variables are constant on any field line. The most appropriate choice of boundary conditions is to specify the values of alpha and beta on the bounding surface. It is proposed that the field lines move in the direction of local Lorentz force and relax towards a force-free field configuration. This concept leads to an iteration procedure for modifying the variables alpha and beta that tends asymptotically towards the force-free state. This method is first applied to a simple problem in two rectangular dimensions; the calculation shows that the convergence of magnetic field energy to a minimum state (force-free) is close to exponential. This method is then applied to study some astrophysical force-free magnetic fields, such as the structures and evolution of magnetic fields of rotating sunspots and accretion disks. The implication of the results, as related to the mechanisms of solar flares, extragalactic radio sources and radio jets, are discussed.

Yang, Wei-Hong

1987-01-01

242

Casimir forces between arbitrary compact objects: Scalar and electromagnetic field  

E-print Network

We develop an exact method for computing the Casimir energy between arbitrary compact objects, both with boundary conditions for a scalar field and dielectrics or perfect conductors for the electromagnetic field. The energy is obtained as an interaction between multipoles, generated by quantum source or current fluctuations. The objects' shape and composition enter only through their scattering matrices. The result is exact when all multipoles are included, and converges rapidly. A low frequency expansion yields the energy as a series in the ratio of the objects' size to their separation. As examples, we obtain this series for two spheres with Robin boundary conditions for a scalar field and dielectric spheres for the electromagnetic field. The full interaction at all separations is obtained for spheres with Robin boundary conditions and for perfectly conducting spheres.

T. Emig; R. L. Jaffe

2007-10-26

243

Nonconservative forces between dielectric particles in a time-dependent electric field  

NASA Astrophysics Data System (ADS)

When a time-dependent external electric field is applied to a system of small dielectric particles, the time-averaged forces between the particles are enhanced if the external field has a frequency such that surface modes can be excited. We find that the forces are nonconservative if the dielectric function is dissipative; this occurs because the surface modes on nearby particles are coupled, causing their frequencies to depend on the interparticle distances. If a variable surface mode frequency crosses the fixed frequency of the external field at certain interparticle distances, the forces between the particles can change direction in such a way that the force lines spiral into fixed points, where the force is zero. We illustrate these ideas with a simple system for which an analytic solution exists: two identical spheres with a complex dielectric function, in vacuum.

Fuchs, Ronald; Claro, Francisco

2004-03-01

244

Van der Waals forces and Photon-less Effective Field Theories  

E-print Network

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

E. Ruiz Arriola

2010-12-10

245

Van der Waals forces and Photon-less Effective Field Theories  

E-print Network

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

Arriola, E Ruiz

2010-01-01

246

Lévy flights in external force fields: Langevin and fractional Fokker-Planck equations and their solutions  

Microsoft Academic Search

We consider Levy flights subject to external force fields. This anomalous\\u000atransport process is described by two approaches, a Langevin equation with Levy\\u000anoise and the corresponding generalized Fokker-Planck equation containing a\\u000afractional derivative in space. The cases of free flights, constant force and\\u000alinear Hookean force are analyzed in detail, and we corroborate our findings\\u000awith results from numerical

Sune Jespersen; Hans C. Fogedby

1999-01-01

247

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

248

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

249

Influence of an external magnetic field on forced turbulence in a swirling flow of liquid metal  

Microsoft Academic Search

We report an experimental investigation on the influence of an external magnetic field on forced three-dimensional turbulence of liquid gallium in a closed vessel. We observe an exponential damping of the turbulent velocity fluctuations as a function of the interaction parameter N (ratio of Lorentz force over inertial terms of the Navier-Stokes equation). The flow structures develop some anisotropy but

Basile Gallet; Michael Berhanu; Nicolas Mordant

2009-01-01

250

An integrated pedestrian behavior model based on Extended Decision Field Theory and Social Force model  

Microsoft Academic Search

A novel pedestrian behavior model is proposed, which integrates 1) Extended Decision Field Theory (EDFT) for tactical level human decision-making, 2) Social Force model (SFM) to represent physical interactions and congestions among the people and the environment, and 3) dynamic planning algorithm involving AND\\/OR graphs. Furthermore, the Social Force model is enhanced with the vision of each individual, and both

Hui Xi; Young-Jun Son; Seungho Lee

2010-01-01

251

Gait Rehabilitation Therapy Using Robot Generated Force Fields Applied at the Pelvis  

E-print Network

Gait Rehabilitation Therapy Using Robot Generated Force Fields Applied at the Pelvis ABSTRACT The Robotic Gait Rehabilitation (RGR) Trainer was designed and built to target secondary gait deviations, which generate corrective forces as a response to deviations from normal pelvic motion. The device

Mavroidis, Constantinos

252

ENHANCED THERMAL CONDUCTIVITY IN NANOFLUIDS UNDER THE ACTION OF OSCILLATING FORCE FIELDS  

E-print Network

ENHANCED THERMAL CONDUCTIVITY IN NANOFLUIDS UNDER THE ACTION OF OSCILLATING FORCE FIELDS Clément Le forces in the radio frequency and microwave ranges, we show that the thermal conductivity of nanofluids. Active control of transport coefficients. Nanocolloïds. Cooling system Introduction Nanofluids (Eastman

Paris-Sud XI, Université de

253

The force acting on a polarizable nanoparticle in the quantized electromagnetic field  

E-print Network

In this letter we derive an expression for the force acting on a small (still macroscopic) particle in the field of the quantized electromagnetic radiation in any arbitrary quantum state. This result unifies in one simple formula all known expressions for the forces (i.e. van der Waals or frictional) acting on a small particle.

Vanik E. Mkrtchian

2009-01-14

254

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

E-print Network

Acoustic radiation force in tissue-like solids due to modulated sound field Egor V. Dontsov, Bojan wherein the transverse coordinates are scaled by the width of the focal region, while the axial plate, the radiation force of sound is a phenomenon that has been intensely studied for over a century

Guzina, Bojan

255

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

256

Management of Social Incentives in Air Force Technical Training: A Field Experiment. Final Report.  

ERIC Educational Resources Information Center

The report is a study of the utility of social reinforcement for improving Air Force training. It was conducted through a field evaluation of social incentive instructional systems which would serve to improve student motivation, classroom performance, and attitudes. The participants included a total of 300 trainees from two Air Force bases; 25…

Hakel, Milton D.; And Others

257

On the finite volume discretization of discontinuous body force field on collocated grid: Application to VOF method  

Microsoft Academic Search

Discontinuities in the body force field typically appear at the interface of two fluid systems. Modeled with the volume-of-fluid (VOF) and discretized with the finite volume method, the discontinuous body force fields are represented as abruptly variable. In the present study, gravity and continuum surface force (CSF) are considered. Such strongly variable body forces can produce unphysical spikes in the

Jure Mencinger; Iztok Žun

2007-01-01

258

The Self-Force Problem: Local Behaviour of the Detweiler-Whiting Singular Field  

E-print Network

The growing reality of gravitational wave astronomy is giving age-old problems a new lease of life; one such problem is that of the self-force. A charged or massive particle moving in a curved background space-time produces a field that affects its motion, pushing it off its expected geodesic. This self-field gives rise to a so-called self-force acting on the particle. In modelling this motion, the self-force approach uses a perturbative expansion in the mass ratio. One of the most interesting sources of gravitational waves are extreme mass ratio inspirals - systems perfectly suited to self-force modelling. One of the key problems within the self-force model is the divergence of the field at the particle. To resolve this, the field is split into a singular component and a smooth regular field. This regular-singular split, introduced by Detweiler and Whiting, is used in most modern self-force calculations. In this thesis, we derive high-order expansions of the Detweiler-Whiting singular field, and use these to push the boundaries on current precision limits of self-force calculations. Within the mode-sum scheme, we give over 14 previously unknown regularisation parameters, almost doubling the current regularisation parameter database. We also produce smooth effective sources to high order, and propose an application of the higher terms to improve accuracy in the m-mode scheme. Finally, we investigate the status of the cosmic censorship conjecture and the role that the self-force plays. To this end, we give regularisation parameters for non-geodesic motion. We also show the necessity of our results in the exciting area of second order self-force calculations, which benefit significantly from high-order coordinate expansions of the singular field. We calculate several parameters that these schemes require, and highlight the further advancements possible from the results of this thesis.

Anna Heffernan

2014-03-24

259

Topological constraints and the existence of force-free fields  

NASA Technical Reports Server (NTRS)

A fundamental problem in plasma theory is the question of the existence of MHD equilibria. The issue of topological constraints is of crucial importance for the problem of the existence of equilibria. Heuristic methods are used to discuss the coronal wrapping pattern. It is concluded that for a given set of footpoint positions the wrapping pattern in the corona is completely fixed. The topological constraints are included in the boundary conditions on the Euler potentials and impost no additional restrictions on possible equilibria. Although this does not prove that equilibria always exist, it does show that the force-free problem is not overdetermined and that existence of equilibria is still an open question.

Antiochos, S. K.

1986-01-01

260

Microscopic mean field approximation and beyond with the Gogny force  

NASA Astrophysics Data System (ADS)

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

Péru, S.; Martini, M.

2014-05-01

261

Design of a multi-axis force transducer with applications in track and field  

E-print Network

The objective of this thesis is the design and implementation of a multi-axis force transducer to be integrated into a set of track and field starting blocks. The feedback from this transducer can be used by athletes and ...

Traina, Zachary J

2005-01-01

262

Excitation of forced ion acoustic waves, large plasma sheets, and magnetic field fluctuations over Gakona, Alaska  

E-print Network

Two research subjects: (1) excitation of "forced ion acoustic waves", and (2) "simultaneous excitation of plasma density fluctuations and geomagnetic field fluctuations" are reported in my M.S. thesis. The data was acquired ...

Cohen, Joel (Joel A.)

2009-01-01

263

Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions.  

PubMed

Despite DNA being a very important target for several proteins and drugs, molecular dynamics simulations with nucleic acids still encompass many challenges, such as the reliability of the chosen force field. In this paper, we carried out molecular dynamics simulations of the Dickerson-Drew dodecamer comparing GROMOS 53A6 and AMBER 03 force fields. While the AMBER force field presents specific topologies for the 5' and 3' terminal nucleotides, the GROMOS force field considers all nucleotides in the same way. To investigate the effects of the terminal nucleotide definitions, both force fields were modified to be applied in the two possible ways: with or without specific terminal nucleotide topologies. The analysis of global stability (rmsd, number of base pairs and hydrogen bonds) showed that both systems simulated with AMBER were stable, while the system simulated with the original GROMOS topologies was very unstable after 5 ns. When specific terminal topologies were included for GROMOS force field, DNA denaturation was delayed until 15 ns, but not avoided. The alpha/gamma transitions also displayed a strong dependence on the force field, but not on the terminal nucleotide definitions: AMBER simulations mainly explored configurations corresponding to the global minimum, while GROMOS simulations exhibited, very early in the simulations, an extensive sampling of local minima that may facilitate transitions to A-DNA isoform. The epsilon/zeta sampling was dependent both on the force field and on the terminal nucleotide definitions: while the AMBER simulations displayed well-defined B-I --> B-II transitions, the GROMOS force field clearly favored the B-I conformation. Also, the system simulated with the original GROMOS topologies displayed uncoupled epsilon/zeta transitions, leading to noncanonical conformations, but this was reverted when the new terminal nucleotide topologies were applied. Finally, the GROMOS force field leads to strong geometrical deformations on the DNA (overestimated groove widths and roll and strongly underestimated twist and slide), which restrict the use of GROMOS force field in long time scale DNA simulations unless a further reparametrization is made. PMID:20614923

Ricci, Clarisse G; de Andrade, Alex S C; Mottin, Melina; Netz, Paulo A

2010-08-01

264

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

265

Anharmonic force field, vibrational energies, and barrier to inversion of SiH3-  

Microsoft Academic Search

The full quartic force field of the ground electronic state of the silyl anion (SiH3-) has been determined at the CCSD(T)-R12 level employing a [Si\\/H]=[16s11p6d5f\\/7s5p4d] basis set. The vibrational energy levels, using the quartic force field as a representation of the potential energy hypersurface around equilibrium, have been determined by vibrational perturbation theory carried out to second, fourth, and sixth

Kirsten Aarset; Attila G. Császár; Edwin L. Sibert; Wim Klopper; Jozef Noga

2000-01-01

266

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

SciTech Connect

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

Makarov, V. P., E-mail: vpmac@ran.gpi.ru; Rukhadze, A. A., E-mail: rukh@fpl.gpi.ru [Russian Academy of Sciences, Prokhorov General Physics Institute (Russian Federation)

2010-01-15

267

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Kimberly Chenoweth, Adri C. T. van Duin, and William A. Goddard, III*  

E-print Network

,18,19 decomposition of improvised explosive devices,20 thermal decomposition of polymers,21 Bi), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions

Goddard III, William A.

268

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

269

Photonic forces in the near field of statistically homogeneous fluctuating sources  

E-print Network

Electromagnetic sources, as e.g. lasers, antennas, diffusers or thermal sources, produce a wavefield that interacts with objects to transfer them its momentum. We show that the photonic force exerted on a small particle in the near field of a planar statistically homogeneous fluctuating source uniquely depends and acts along the coordinate perpendicular to its surface. The gradient part of this force is contributed by only the evanescent components of the emitted field, its sign being opposite to that of the real part of the particle polarizability. The non-conservative force part is uniquely due to the propagating components, being repulsive and constant. Also, the source coherence length adds a degree of freedom since it largely affects these forces. The excitation of plasmons in the source surface drastically enhances the gradient force. Hence, partially coherent wavefields from fluctuating sources constitute new concepts for particle manipulation at the subwavelength scale

Aunon, Juan Miguel

2012-01-01

270

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

271

Spinmotive force due to domain wall motion in high field regime  

NASA Astrophysics Data System (ADS)

Spinmotive force associated with a moving vortex domain wall is investigated numerically. Dynamics of magnetization textures such as a domain wall exerts a non-conservative spin-force on conduction electrons [1], offering a new concept of magnetic devices [2]. This spinmotive force in permalloy nanowires has been detected by voltage measurement [3] where magnitude of the signal is limited less than 500 nV. Theoretically it is suggested that the spinmotive force signal increases as a function of external magnetic fields. At higher magnetic fields, however, the wall propagation mode becomes rather chaotic involving transformations of the wall structure and it remains to be seen how the spinmotive force appears. Numerical simulations show that the spinmotive force scales with the field even in a field range where the wall motion is no longer associated coherent precession. This feature has been tested in a recent experiment [4]. Further enhancement of the spinmotive force is explored by designing ferromagnetic nanostructures [5] and materials. [1] S. Barnes and S. Maekawa, PRL (2007). [2] S. Barnes, J. Ieda, and S. Maekawa, APL (2006). [3] S. A. Yang et al., PRL (2009). [4] M. Hayashi, J. Ieda et al., submitted. [5] Y. Yamane, J. Ieda et al., APEX (2011).

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

2012-02-01

272

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.

273

Parametrization and validation of a force field for liquid-crystal forming molecules D. L. Cheung,1,2  

E-print Network

Parametrization and validation of a force field for liquid-crystal forming molecules D. L. Cheung,1 of liquid-crystal fragment molecules. The calculations have been used to derive a molecular mechanics force field that describes a subset of commonly occurring liquid-crystal molecules. The force field has been

Wilson, Mark R.

274

Nonlinear force-free modeling of the solar coronal magnetic field  

E-print Network

The coronal magnetic field is an important quantity because the magnetic field dominates the structure of the solar corona. Unfortunately direct measurements of coronal magnetic fields are usually not available. The photospheric magnetic field is measured routinely with vector magnetographs. These photospheric measurements are extrapolated into the solar corona. The extrapolated coronal magnetic field depends on assumptions regarding the coronal plasma, e.g. force-freeness. Force-free means that all non-magnetic forces like pressure gradients and gravity are neglected. This approach is well justified in the solar corona due to the low plasma beta. One has to take care, however, about ambiguities, noise and non-magnetic forces in the photosphere, where the magnetic field vector is measured. Here we review different numerical methods for a nonlinear force-free coronal magnetic field extrapolation: Grad-Rubin codes, upward integration method, MHD-relaxation, optimization and the boundary element approach. We briefly discuss the main features of the different methods and concentrate mainly on recently developed new codes.

T. Wiegelmann

2008-01-18

275

Nonlinear force-free modeling of the solar coronal magnetic field  

NASA Astrophysics Data System (ADS)

The coronal magnetic field is an important quantity because the magnetic field dominates the structure of the solar corona. Unfortunately, direct measurements of coronal magnetic fields are usually not available. The photospheric magnetic field is measured routinely with vector magnetographs. These photospheric measurements are extrapolated into the solar corona. The extrapolated coronal magnetic field depends on assumptions regarding the coronal plasma, for example, force-freeness. Force-free means that all nonmagnetic forces like pressure gradients and gravity are neglected. This approach is well justified in the solar corona owing to the low plasma beta. One has to take care, however, about ambiguities, noise and nonmagnetic forces in the photosphere, where the magnetic field vector is measured. Here we review different numerical methods for a nonlinear force-free coronal magnetic field extrapolation: Grad-Rubin codes, upward integration method, MHD relaxation, optimization, and the boundary element approach. We briefly discuss the main features of the different methods and concentrate mainly on recently developed new codes.

Wiegelmann, T.

2008-03-01

276

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

277

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

278

Self-enhanced catalytic activities of functionalized graphene sheets in the combustion of nitromethane: molecular dynamic simulations by molecular reactive force field.  

PubMed

Functionalized graphene sheet (FGS) is a promising additive that enhances fuel/propellant combustion, and the determination of its mechanism has attracted much interest. In the present study, a series of molecular dynamic simulations based on a reactive force field (ReaxFF) are performed to explore the catalytic activity (CA) of FGS in the thermal decay of nitromethane (NM, CH3NO2). FGSs and pristine graphene sheets (GSs) are oxidized in hot NM liquid to increase their functionalities and subsequently show self-enhanced CAs during the decay. The CAs result from the interatomic exchanges between the functional groups on the sheets and the NM liquid, i.e., mainly between H and O atoms. CA is dependent on the density of NM, functionalities of sheets, and temperature. The GSs and FGSs that originally exhibit different functionalities tend to possess similar functionalities and consequently similar CAs as temperature increases. Other carbon materials and their oxides can accelerate combustion of other fuels/propellants similar to NM, provided that they can be dispersed and their key reaction steps in combustion are similar to NM. PMID:25055727

Zhang, Chaoyang; Wen, Yushi; Xue, Xianggui

2014-08-13

279

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

280

FIELD EXPERIMENTATION OF COTS-BASED UAV NETWORKING Air Force Research Laboratory  

E-print Network

1 of 7 FIELD EXPERIMENTATION OF COTS-BASED UAV NETWORKING Dan Hague Air Force Research Laboratory Vehicles (UAVs). This new capability has inspired many novel application ideas in UAV networking. We argue that field experimentation of UAV networking is essential in collecting link meas- urement data, developing

Kung, H. T.

281

FIELD WINDING DRAG AND NORMAL FORCES OF LINEAR SYNCHRONOUS HOMOPOLAR MOTORS  

Microsoft Academic Search

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

I. BOLDEA; S. A. NASAR

1978-01-01

282

Unified Field Equations Coupling Four Forces and Theory of Dark Matter and Dark Energy  

E-print Network

Unified Field Equations Coupling Four Forces and Theory of Dark Matter and Dark Energy Tian Ma. Electroweak Theory VI. Unified Theory of Dark Energy and Dark Matter VII. Concluding Remarks 2 #12;References: 1. Tian Ma & Shouhong Wang, Gravitational Field Equations and Theory of Dark Matter and Dark Energy

Wang, Shouhong

283

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 O 2 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

284

Forcing a Global, Offline Land Surface Modeling System with Observation-Based Fields  

NASA Technical Reports Server (NTRS)

The Global Land Data Assimilation System (GLDAS) drives multiple uncoupled land surface models in order to produce optimal output fields of surface states in near-real time, globally, at 1/4 degree spatial resolution. These fields are then made available for coupled atmospheric model initialization and further research. One of the unique aspects of GLDAS is its ability to ingest both modeled and observation-derived forcing for running global scale land surface models. This paper compares results of runs forced by modeled and observed precipitation and shortwave radiation fields. Differences are examined and the impact of the observations on model skill is assessed.

Rodell, Matthew; Houser, Paul R.; Jambor, U.; Gottschalck, J.; Radakovich, J.; Arsenault, K.; Meng, C.-J.; Mitchell, K. E.

2002-01-01

285

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

286

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

PubMed

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

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

2013-07-26

287

Exploring the Parameter Space of the Coarse-Grained UNRES Force Field by Random Search: Selecting a Transferable Medium-Resolution Force Field  

PubMed Central

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal ?-helical and a minimal ?-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with ? or ? + ? structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. PMID:19242966

HE, YI; XIAO, YI; LIWO, ADAM; SCHERAGA, HAROLD A.

2009-01-01

288

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

289

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

290

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

291

The effect of thermal weakening and buoyancy forces on rift localization: Field evidences from the Gulf of Aden oblique rifting  

E-print Network

The effect of thermal weakening and buoyancy forces on rift localization: Field evidences from Buoyancy forces Analog models On the basis of field and geophysical data, analog and numerical models, we here discuss the role of buoyancy forces arising from thickness variations in the lithosphere during

Husson, Laurent

292

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

PubMed

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 Moller-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. PMID:20095686

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

2010-01-14

293

Force-field adaptation without proprioception: can vision be used to model limb dynamics?  

PubMed

Because our environment and our body can change from time to time, the efficiency of human motor behavior relies on the updating of the neural processes transforming intentions into actions. Adaptation to the context critically depends on sensory feedback such as vision, touch or hearing. Although proprioception is not commonly listed as one of the main senses, its role is determinant for the coordination of daily gestures like goal-directed arm movements. In particular, previous work suggests that proprioceptive information is critical to update the internal representation of limb dynamic properties. Here, we examined the motor behavior of a deafferented patient, deprived of proprioception below the nose, to assess adaptation to new dynamic conditions in the absence of limb proprioception. The patient, and age-matched control participants, reached toward visual targets in a new force field created by a rotating platform. Full vision of the limb and workspace was available throughout the experiment. Although her impairment was obvious in baseline reaching performance, the proprioceptively deafferented patient clearly adapted to the new force conditions. In fact, her time course of adaptation was similar to that observed in controls. Moreover, when tested in the normal force field after adaptation to the new force field, the patient exhibited after-effects similar to those of controls. These findings show that motor adaptation to a modified force field is possible without proprioception and that vision can compensate for the permanent loss of proprioception to update the central representation of limb dynamics. PMID:19695273

Sarlegna, Fabrice R; Malfait, Nicole; Bringoux, Lionel; Bourdin, Christophe; Vercher, Jean-Louis

2010-01-01

294

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

NASA Astrophysics Data System (ADS)

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

Iwata, Natsumi; Kishimoto, Yasuaki

2014-01-01

295

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

SciTech Connect

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

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

1993-04-01

296

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

PubMed

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis. PMID:25098651

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

2014-09-16

297

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

SciTech Connect

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

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

2013-05-10

298

Coupling ReaxFF and DREIDING toCoupling ReaxFF and DREIDING to Model Enzymatic ReactionsModel Enzymatic Reactions  

E-print Network

Coupling ReaxFF and DREIDING toCoupling ReaxFF and DREIDING to Model Enzymatic Reactions with QM/MM schemes ReaxFF can model much larger regionsReaxFF can model much larger regions involving took 10h 26mdynamics took 10h 26m #12;Comparison MM, ReaxFF, QMComparison MM, ReaxFF, QM yes months

Goddard III, William A.

299

The Pulsation Mode and Distance of the Cepheid FF Aquilae  

NASA Astrophysics Data System (ADS)

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

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

2013-07-01

300

THE PULSATION MODE AND DISTANCE OF THE CEPHEID FF AQUILAE  

SciTech Connect

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

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

2013-07-20

301

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

302

Force estimation from incompressible flow field data using a momentum balance approach  

NASA Astrophysics Data System (ADS)

This study investigates how aerodynamic forces on a body can be evaluated using only instantaneous or averaged velocity field data through a control volume approach in an incompressible flow. The method allows for velocity field data to be missing inside the control volume, but requires that the product of the acceleration, the volume of the solid body, and the fluid density are negligible compared to the forces of interest. Validation of the method for accuracy has been conducted using three-dimensional data from a numerical simulation of unsteady flow around a static airfoil and has shown good agreement between actual and estimated force. Additionally, the method is tested using phase-averaged PIV data from flexible flapping membrane wings to calculate flapping cycle averaged forces that are compared with directly measured time-averaged forces. The numerical validation suggests that the method is accurate, while it is only able to give a rough estimate for the noisier experimental data. The lower accuracy of the forces estimated from the PIV data can be explained through experimental constraints, such as too large grid spacing in one of the three dimensions (in one of the cases), having to interpolate data on the control volume surface especially where the PIV laser light is shaded by the wing, and not covering the entire span of the wing.

Sällström, Erik; Ukeiley, Lawrence

2014-01-01

303

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

NASA Astrophysics Data System (ADS)

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

Lerche, I.; Low, B. C.

2014-10-01

304

ReaxFF reactive molecular dynamics on silicon pentaerythritol tetranitrate crystal validates the mechanism for the colossal sensitivity.  

PubMed

Recently quantum mechanical (QM) calculations on a single Si-PETN (silicon-pentaerythritol tetranitrate) molecule were used to explain its colossal sensitivity observed experimentally in terms of a unique Liu carbon-silyl nitro-ester rearrangement (R3Si-CH2-O-R2? R3Si-O-CH2-R2). In this paper we expanded the study of Si-PETN from a single molecule to a bulk system by extending the ReaxFF reactive force field to describe similar Si-C-H-O-N systems with parameters optimized to reproduce QM results. The reaction mechanisms and kinetics of thermal decomposition of solid Si-PETN were investigated using ReaxFF reactive molecular dynamics (ReaxFF-RMD) simulations at various temperatures to explore the origin of the high sensitivity. We find that at lower temperatures, the decomposition of Si-PETN is initiated by the Liu carbon-silyl nitro-ester rearrangement forming Si-O bonds which is not observed in PETN. As the reaction proceeds, the exothermicity of Si-O bond formation promotes the onset of NO2 formation from N-OC bond cleavage which does not occur in PETN. At higher temperatures PETN starts to react by the usual mechanisms of NO2 dissociation and HONO elimination; however, Si-PETN remains far more reactive. These results validate the predictions from QM that the significantly increased sensitivity of Si-PETN arises from a unimolecular process involving the unusual Liu rearrangement but not from multi-molecular collisions. It is the very low energy barrier and the high exothermicity of the Si-O bond formation providing energy early in the decomposition process that is responsible. PMID:25272955

Zhou, Tingting; Liu, Lianchi; Goddard Iii, William A; Zybin, Sergey V; Huang, Fenglei

2014-11-21

305

Effect of 905 MHz microwave radiation on colony growth of the yeast Saccharomyces cerevisiae strains FF18733, FF1481 and D7  

PubMed Central

Background The aim of this study was to evaluate the effect of weak radiofrequency microwave (RF/MW) radiation emitted by mobile phones on colony growth of the yeast Saccharomyces cerevisiae. Materials and methods S. cerevisiae strains FF18733 (wild-type), FF1481 (rad1 mutant) and D7 (commonly used to detect reciprocal and nonreciprocal mitotic recombinations) were exposed to a 905 MHz electromagnetic field that closely matched the Global System for Mobile Communication (GSM) pulse modulation signals for mobile phones at a specific absorption rate (SAR) of 0.12 W/kg. Results Following 15-, 30- and 60-minutes exposure to RF/MW radiation, strain FF18733 did not show statistically significant changes in colony growth compared to the control sample. The irradiated strains FF1481 and D7 demonstrated statistically significant reduction of colony growth compared to non-irradiated strains after all exposure times. Furthermore, strain FF1481 was more sensitive to RF/MW radiation than strain D7. Conclusions The findings indicate that pulsed RF/MW radiation at a low SAR level can affect the rate of colony growth of different S. cerevisiae strains. PMID:22933904

Vrhovac, Ivana; Hrascan, Reno; Franekic, Jasna

2010-01-01

306

COMPARISON OF FORCE-FREE CORONAL MAGNETIC FIELD MODELING USING VECTOR FIELDS FROM HINODE AND SOLAR DYNAMICS OBSERVATORY  

SciTech Connect

Photospheric magnetic vector maps from two different instruments are used to model the nonlinear force-free coronal magnetic field above an active region. We use vector maps inferred from polarization measurements of the Solar Dynamics Observatory/Helioseismic and Magnetic Imager (HMI) and the Solar Optical Telescope's Spectropolarimeter (SP) on board Hinode. Besides basing our model calculations on HMI data, we use both SP data of original resolution and scaled down to the resolution of HMI. This allows us to compare the model results based on data from different instruments and to investigate how a binning of high-resolution data affects the model outcome. The resulting three-dimensional magnetic fields are compared in terms of magnetic energy content and magnetic topology. We find stronger magnetic fields in the SP data, translating into a higher total magnetic energy of the SP models. The net Lorentz forces of the HMI and SP lower boundaries verify their force-free compatibility. We find substantial differences in the absolute estimates of the magnetic field energy but similar relative estimates, e.g., the fraction of excess energy and of the flux shared by distinct areas. The location and extension of neighboring connectivity domains differ and the SP model fields tend to be higher and more vertical. Hence, conclusions about the magnetic connectivity based on force-free field models are to be drawn with caution. We find that the deviations of the model solution when based on the lower-resolution SP data are small compared to the differences of the solutions based on data from different instruments.

Thalmann, J. K.; Tiwari, S. K.; Wiegelmann, T., E-mail: thalmann@mps.mpg.de [Max-Plank-Institut fuer Sonnensystemforschung, Max-Planck-Str. 2, D-37191 Katlenburg-Lindau (Germany)

2013-05-20

307

Infiltration of fibrous preform by molten aluminum in a centrifugal force field  

SciTech Connect

The pressure to infiltrate molten aluminum into alumina short-fiber preforms was generated by centrifugal force, and it was proved that centrifugal force is effective as a motive force for the infiltration and sound composites that are produced. The initiation pressure of the infiltration was also calculated and obtained clearly. The start pressure agreed well with the threshold pressure obtained theoretically. The characteristics of the infiltration in the preform was discussed using a one-dimensional solution of D`Arcy`s law in a centrifugal force field. It was made clear that when preform surface pressure is low, the region having lower pressure than the threshold pressure appears in the infiltrated region.

Nishida, Yoshinori; Shirayanagi, Itaru [National Industrial Research Inst., Nagoya (Japan); Sakai, Yoshibumi [Daido Inst. of Tech., Nagoya (Japan)

1996-12-01

308

Influence of an external magnetic field on forced turbulence in a swirling flow of liquid metal  

E-print Network

We report an experimental investigation on the influence of an external magnetic field on forced 3D turbulence of liquid gallium in a closed vessel. We observe an exponential damping of the turbulent velocity fluctuations as a function of the interaction parameter N (ratio of Lorentz force over inertial terms of the Navier-Stokes equation). The flow structures develop some anisotropy but do not become bidimensional. From a dynamical viewpoint, the damping first occurs homogeneously over the whole spectrum of frequencies. For larger values of N, a very strong additional damping occurs at the highest frequencies. However, the injected mechanical power remains independent of the applied magnetic field. The simultaneous measurement of induced magnetic field and electrical potential differences shows a very weak correlation between magnetic field and velocity fluctuations. The observed reduction of the fluctuations is in agreement with a previously proposed mechanism for the saturation of turbulent dynamos and wit...

Gallet, Basile; Mordant, Nicolas

2009-01-01

309

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

310

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

311

Spinmotive force due to motion of magnetic bubble arrays driven by magnetic field gradient  

PubMed Central

Interaction between local magnetization and conduction electrons is responsible for a variety of phenomena in magnetic materials. It has been recently shown that spin current and associated electric voltage can be induced by magnetization that depends on both time and space. This effect, called spinmotive force, provides for a powerful tool for exploring the dynamics and the nature of magnetic textures, as well as a new source for electromotive force. Here we theoretically demonstrate the generation of electric voltages in magnetic bubble array systems subjected to a magnetic field gradient. It is shown by deriving expressions for the electric voltages that the present system offers a direct measure of phenomenological parameter ? that describes non-adiabaticity in the current induced magnetization dynamics. This spinmotive force opens a door for new types of spintronic devices that exploit the field-gradient. PMID:25365971

Yamane, Yuta; Hemmatiyan, Shayan; Ieda, Jun'ichi; Maekawa, Sadamichi; Sinova, Jairo

2014-01-01

312

Spinmotive force due to motion of magnetic bubble arrays driven by magnetic field gradient.  

PubMed

Interaction between local magnetization and conduction electrons is responsible for a variety of phenomena in magnetic materials. It has been recently shown that spin current and associated electric voltage can be induced by magnetization that depends on both time and space. This effect, called spinmotive force, provides for a powerful tool for exploring the dynamics and the nature of magnetic textures, as well as a new source for electromotive force. Here we theoretically demonstrate the generation of electric voltages in magnetic bubble array systems subjected to a magnetic field gradient. It is shown by deriving expressions for the electric voltages that the present system offers a direct measure of phenomenological parameter ? that describes non-adiabaticity in the current induced magnetization dynamics. This spinmotive force opens a door for new types of spintronic devices that exploit the field-gradient. PMID:25365971

Yamane, Yuta; Hemmatiyan, Shayan; Ieda, Jun'ichi; Maekawa, Sadamichi; Sinova, Jairo

2014-01-01

313

Physical forces exerted by microbubbles on a surface in a traveling wave field.  

PubMed

The effect of a wave with a varying traveling component on the bubble activity as well as the physical force generated by microbubbles on a surface has been studied. The acoustic emission from a collection of bubbles is measured in a 928 kHz sound field. Particle removal tests on a surface, which actually measures the applied physical force by the bubbles on that surface, indicate a very strong dependence on the angle of incidence. In other words, when the traveling wave component is maximized, the average physical force applied by microbubbles reaches a maximum. Almost complete particle removal for 78 nm silica particles was obtained for a traveling wave, while particle removal efficiency was reduced to only a few percent when a standing wave was applied. This increase in particle removal for a traveling wave is probably caused by a decrease in bubble trapping at nodes and antinodes in a standing wave field. PMID:24091148

Brems, S; Hauptmann, M; Camerotto, E; Mertens, P W; Heyns, M; Struyf, H; De Gendt, S

2014-02-01

314

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

NASA Technical Reports Server (NTRS)

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

Frankenthal, S.

1977-01-01

315

Active contour external force using vector field convolution for image segmentation.  

PubMed

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 the user-defined vector field kernel. We propose two structures for the magnitude function of the vector field kernel, and we provide an analytical method to estimate the parameter of the magnitude function. Mixed VFC is introduced to alleviate the possible leakage problem caused by choosing inappropriate parameters. We also demonstrate that the standard external force and the gradient vector flow (GVF) external force are special cases of VFC in certain scenarios. Examples and comparisons with GVF are presented in this paper to show the advantages of this innovation, including superior noise robustness, reduced computational cost, and the flexibility of tailoring the force field. PMID:17688214

Li, Bing; Acton, Scott T

2007-08-01

316

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

317

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

USGS Publications Warehouse

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

Lee, M.W.; Meuwly, M.

2013-01-01

318

Author's personal copy Comparison of implicit solvent models and force fields in molecular dynamics  

E-print Network

that the total solvation free energy ðDGðsolv�� comprises the sum of the solvent electrostatic free energy ðAuthor's personal copy Comparison of implicit solvent models and force fields in molecular dynamics) domain, which adopts an ubiquitin-like b-grasp fold, have been simulated using two implicit solvent

Garrahan, Juan P.

319

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units  

PubMed Central

The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

2013-01-01

320

Charged particles in higher dimensional homogeneous gravitational field: Self-energy and self-force  

E-print Network

A problem of self-energy and self-force for a charged point-like particle in a higher dimensional homogeneous gravitational field is considered. We study two cases, when a particle has usual electric charge and a case when it has a scalar charge, which is a source of a scalar massless minimally coupled field. We assume that a particle is at rest in the gravitational field, so that its motion is not geodesic and it has an acceleration a directed from the horizon. The self-energy of a point charge is divergent and the strength of the divergence grows with the number of dimensions. In order to obtain a finite contribution to the self- energy we use a covariant regularization method which is a modification of the proper time cut-off and other covariant regularizations. We analyze a relation between the self-energy and self-force and obtain explicit expressions for the self-forces for the electric and scalar charge in the spacetimes with the number of dimensions up to eight. General expressions for the case of higher dimensions are also obtained. We discuss special logarithmic factors ln(a), which are present both in the self-energy and self-force in odd dimensions. Finally, we compare the obtained results with the earlier known results both for the homogeneous gravitational field and for particles near black holes.

Valeri P. Frolov; Andrei Zelnikov

2014-07-11

321

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

322

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

323

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

324

Calculation of Confined Phonon Spectrum in Narrow Silicon Nanowires using the Valence Force Field Method  

E-print Network

- based devices for thermoelectric and thermal management applications. Index terms: Confined phonons1 Calculation of Confined Phonon Spectrum in Narrow Silicon Nanowires using the Valence Force Field}@iue.tuwien.ac.at Abstract We study the effect of confinement on the phonon properties of ultra-narrow silicon nanowires

325

Transferable force field for carboxylate esters: application to fatty acid methylic ester phase equilibria prediction.  

PubMed

In this work, a new transferable united-atoms force field for carboxylate esters is proposed. All Lennard-Jones parameters are reused from previous parametrizations of the AUA4 force field, and only a unique set of partial electrostatic charges is introduced for the ester chemical function. Various short alkyl-chain esters (methyl acetate, ethyl acetate, methyl propionate, ethyl propionate) and two fatty acid methylic esters (methyl oleate and methyl palmitate) are studied. Using this new force field in Monte Carlo simulations, we show that various pure compound properties are accurately predicted: saturated liquid densities, vapor pressures, vaporization enthalpies, critical properties, liquid-vapor surface tensions. Furthermore, a good accuracy is also obtained in the prediction of binary mixture pressure-composition diagrams, without introducing empirical binary interaction parameters. This highlights the transferability of the proposed force field and gives the opportunity to simulate mixtures of industrial interest: a demonstration is performed through the simulation of the methyl oleate + methanol mixture involved in the purification sections of biodiesel production processes. PMID:22369235

Ferrando, Nicolas; Lachet, Véronique; Boutin, Anne

2012-03-15

326

Liquid properties of dimethyl ether from molecular dynamics simulations using ab initio force fields.  

PubMed

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller-Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3-site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom-wise radial distribution functions, the self-diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. PMID:22278976

Wang, Shi-Bao; Li, Arvin Huang-Te; Chao, Sheng D

2012-04-01

327

An improved DNA force field for ssDNA interactions with gold nanoparticles  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

328

SwissParam: a fast force field generation tool for small organic molecules.  

PubMed

The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy estimation, both of which require force field parameterization for many drug candidates. Here, we present a fast force field generation tool, called SwissParam, able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field, but in a functional form that is compatible with the CHARMM force field. Output files can be used with CHARMM or GROMACS. The topologies and parameters generated by SwissParam are used by the docking software EADock2 and EADock DSS to describe the small molecules to be docked, whereas the protein is described by the CHARMM force field, and allow them to reach success rates ranging from 56 to 78%. We have also developed a rapid binding free energy estimation approach, using SwissParam for ligands and CHARMM22/27 for proteins, which requires only a short minimization to reproduce the experimental binding free energy of 214 ligand-protein complexes involving 62 different proteins, with a standard error of 2.0 kcal mol(-1), and a correlation coefficient of 0.74. Together, these results demonstrate the relevance of using SwissParam topologies and parameters to describe small organic molecules in computer-aided drug design applications, together with a CHARMM22/27 description of the target protein. SwissParam is available free of charge for academic users at www.swissparam.ch. PMID:21541964

Zoete, Vincent; Cuendet, Michel A; Grosdidier, Aurélien; Michielin, Olivier

2011-08-01

329

Multiscale analysis of the electromagnetic self-force in a weak gravitational field  

SciTech Connect

We examine the motion of a charged particle in a weak gravitational field. In addition to the Newtonian gravity exerted by a large central body, the particle is subjected to an electromagnetic self-force that contains both a conservative piece and a radiation-reaction piece. This toy problem shares many of the features of the strong-field gravitational self-force problem, and it is sufficiently simple that it can be solved exactly with numerical methods, and approximately with analytical methods. We submit the equations of motion to a multiscale analysis, and we examine the roles of the conservative and radiation-reaction pieces of the self-force. We show that the radiation-reaction force drives secular changes in the orbit's semilatus rectum and eccentricity, while the conservative force drives a secular regression of the periapsis and affects the orbital time function; neglect of the conservative term can hence give rise to an important phasing error. We next examine what might be required in the formulation of a reliable secular approximation for the orbital evolution; this would capture all secular changes in the orbit and discard all irrelevant oscillations. We conclude that such an approximation would be very difficult to formulate without prior knowledge of the exact solution.

Pound, Adam; Poisson, Eric [Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1 (Canada)

2008-02-15

330

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

NASA Technical Reports Server (NTRS)

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

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

1995-01-01

331

Scale Selection in Locally Forced Convective Fields and the Initiation of Deep Cumulus.  

NASA Astrophysics Data System (ADS)

Deep cumulus dynamics has often been treated as an initial value problem where the long time effect of surface energy fluxes are neglected. Initiation is often assumed to follow from a strong localized deformation of the flow field, which is elsewhere quiescent. In nature, however, the atmosphere is rarely found in an undisturbed condition just prior to the inception of deep growth. One likely cause of widespread motions is the natural modal response of the environment to surface energy fluxes which results in a field of disturbances. Evidence is presented in this paper for the possible existence of a class of solutions when deep convection is allowed to evolve in the context of a thermally forced field of shallow convection. This class of solutions is neglected when one visualizes the growth of severe local storms in term of buoyant bubbles in an otherwise tranquil atmosphere. Considering deep cumulus initiation as a field problem severely limits the concept of an isolated cloud. Individual clouds may owe much of their structure to the existence of, and interaction with, the field of thermally forced deep normal modes. The importance of the local forcing terms is demonstrated here through a numerical simulation of the evolution of deep and severe convection out of a locally forced shallow cloud field in the absence of large scale forcing.When convection is initiated over the entire domain locally through thermal forcing at the ground, the modal solution first observed corresponds to the Rayleigh solution which consist of modes confined to the boundary-layer. However, solutions in the deep linear equations show that a second modal solution also exists. The dominance of this solution, which consists of deep modes of longer horizontal wavelength, is shown here to lead to deep convection.While the contribution of local forcing terms to the overall energy budget may be negligible at the severe convective stage, the mechanism of initiation appears to influence the pattern of evolution even into the mature stage. At the stage of shallow cumulus, the well-known phenomenon of upshear cumulus development is observed. As clouds grow deeper, an interesting phenomenon of phase-decoupled modal solutions is observed:. the growth of clouds appears to decouple the boundary-layer horizontal motions in phase from the stable layer motions, an effect that cyclically enhances and suppresses cloud growth. A characteristic time may be computed, and average cloud longevity inferred. Finally; the interaction of a moving storm system in its severe stage with the boundary-layer modes appears to provide one explanation for the spatial and temporal distribution of new convective cells in a multicellular storm system.

Balaji, V.; Clark, Terry L.

1988-11-01

332

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

333

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

334

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

PubMed

Much effort has been undertaken for the estimation of propulsive force of swimmers in the front crawl. Estimation is typically based on steady flow theory: the so-called quasi-steady analysis. Flow fields around a swimmer, however, are extremely unsteady because the change direction of hand produces unsteady vortex motions. To evaluate the force correctly, it is necessary to know the unsteady properties determined from the vortex dynamics because that unsteadiness is known to make the force greater. Unsteady flow measurements were made for this study using a sophisticated technique called particle image velocimetry (PIV) in several horizontal planes for subjects swimming in a flume. Using that method, a 100 time-sequential flow fields are obtainable simultaneously. Each flow field was calculated from two particle images using the cross-correlation method. The intensity of vortices and their locations were identified. A strong vortex was generated near the hand and then shed by directional change of the hand in the transition phase from in-sweep to out-sweep. When the vortex was shed, a new vortex rotating in the opposite direction around the hand was created. The pair of vortices induced the velocity component in the direction opposite to the swimming. Results of this study show that the momentum change attributable to the increase in this velocity component is the origin of thrust force by the hand. PMID:19054519

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

2009-01-01

335

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

SciTech Connect

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

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

2012-01-01

336

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

NASA Astrophysics Data System (ADS)

Electron holography is applied for the study of the leakage field of thin-film ferromagnetic tips used as probes in magnetic force microscopy. We used commercially available pyramidal tips covered on one face with a thin NiCo film, which were then placed in a high external magnetic field directed along the pyramid axis. Good agreement between simulated and experimental electron phase difference maps allows to measure the local flux from the ferromagnetic tips and therefore to evaluate the perturbation induced by the microprobe stray field on the sample area.

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

1996-03-01

337

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. PMID:20463845

2010-01-01

338

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

2013-09-26

339

Shear-force distance control at megahertz frequencies for near-field scanning optical microscopy  

NASA Astrophysics Data System (ADS)

We show that the use of fiber overtone resonance modes up to 3 MHz for shear-force distance control has two advantages for near-field microscopy. The higher dither frequency allows a shorter feedback loop time delay, which in turn allows scanning speeds of 100 ?m/s on a sample with, for example, a 150 nm height variation over a 1 ?m distance. Experiments on a hard semiconductor device and on a soft polymer sample demonstrate a factor of 5 improvement in scanning speed when the dither frequency is increased by a factor of 20. The second advantage is a reduction of the minimum lateral force required for height regulation, which is important for soft samples. Modeling the piezoelectric detection system as a harmonic oscillator indicates a factor of 33 increase in lateral force sensitivity when using the third overtone resonance of a typical fiber tip. This result is confirmed experimentally by immersing the tip into water.

Simon, A.; Brunner, R.; White, J. O.; Hollricher, O.; Marti, O.

2001-11-01

340

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

NASA Astrophysics Data System (ADS)

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

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

2011-06-01

341

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

342

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

2012-07-01

343

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

SciTech Connect

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

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

2012-08-10

344

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

345

Accuracy of spatial localization depending on head posture in a perturbed gravitoinertial force field.  

PubMed

Spatial orientation is crucial when subjects have to accurately reach memorized visual targets. In previous studies modified gravitoinertial force fields were used to affect the accuracy of pointing movements in complete darkness without visual feedback of the moving limb. Target mislocalization was put forward as one hypothesis to explain this decrease in accuracy of pointing movements. The aim of this study was to test this hypothesis by determining the accuracy of spatial localization of memorized visual targets in a perturbed gravitoinertial force field. As head orientation is involved in localization tasks and carrying relevant sensory systems (visual, vestibular and neck muscle proprioceptive), we also tested the effect of head posture on the accuracy of localization. Subjects (n=10) were seated off-axis on a rotating platform (120 degrees s(-1)) in complete darkness with the head fixed (head-fixed session) or free to move (head-free session). They were required to report verbally the egocentric spatial localization of visual memorized targets. They gave the perceived target location in direction (i.e. left or right) and in amplitude (in centimeters) relative to the direction they thought to be straight ahead. Results showed that the accuracy of visual localization decreased when subjects were exposed to inertial forces. Moreover, subjects localized the memorized visual targets more to the right than their actual position, that was in the direction of the inertial forces. With further analysis, it appeared that this shift of localization was concomitant with a shift of the visual straight ahead (VSA) in the opposite direction. Thus, the modified gravitoinertial force field led to a modification in the orientation of the egocentric reference frame. Furthermore, this shift of localization increased when the head was free to move while the head was tilted in roll toward the center of rotation of the platform and turned in yaw in the same direction. It is concluded that the orientation of the egocentric reference frame was influenced by the gravitoinertial vector. PMID:15578170

Prieur, J-M; Bourdin, C; Vercher, J-L; Sarès, F; Blouin, J; Gauthier, G M

2005-03-01

346

Force-Free Magnetic Fields Calculated from Automated Tracing of Coronal Loops with AIA/SDO  

NASA Astrophysics Data System (ADS)

One of the most realistic magnetic field models of the solar corona is a nonlinear force-free field (NLFFF) solution. There exist about a dozen numeric codes that compute NLFFF solutions based on extrapolations of photospheric vector magnetograph data. However, since the photosphere and lower chromosphere is not force-free, a suitable correction has to be applied to the lower boundary condition. Despite of such "pre-processing" corrections, the resulting theoretical magnetic field lines deviate substantially from observed coronal loop geometries. - Here we developed an alternative method that fits an analytical NLFFF approximation to the observed geometry of coronal loops. The 2D coordinates of the geometry of coronal loop structures observed with AIA/SDO are traced with the "Oriented Coronal CUrved Loop Tracing" (OCCULT-2) code, an automated pattern recognition algorithm that has demonstrated the fidelity in loop tracing matching visual perception. A potential magnetic field solution is then derived from a line-of-sight magnetogram observed with HMI/SDO, and an analytical NLFFF approximation is then forward-fitted to the twisted geometry of coronal loops. We demonstrate the performance of this magnetic field modeling method for a number of solar active regions, before and after major flares observed with SDO. The difference of the NLFFF and the potential field energies allows us then to compute the free magnetic energy, which is an upper limit of the energy that is released during a solar flare.

Aschwanden, M. J.

2013-12-01

347

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. PMID:23019560

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

2012-01-01

348

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

349

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. PMID:15507688

Herges, T.; Wenzel, W.

2004-01-01

350

Crystal Structure Prediction (CSP) of Flexible Molecules using Parallel Genetic Algorithms with a Standard Force Field  

PubMed Central

This paper describes the application of our distributed computing framework for crystal structure prediction (CSP), 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 which includes a series of tightly integrated computer programs for generating the molecule’s force field, sampling crystal structures using a distributed parallel genetic algorithm, 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.

2009-01-01

351

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

PubMed

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

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

2012-08-01

352

A scaled quantum mechanical force field for tetranitromethane and its intermediates  

NASA Astrophysics Data System (ADS)

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

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

1995-04-01

353

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model.  

PubMed

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 nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward 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 nonpolarizable 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. PMID:20575015

Zhu, Xiao; MacKerell, Alexander D

2010-09-01

354

Impacts into cosmic ice surfaces: A molecular-dynamics study using the Reax force field  

NASA Astrophysics Data System (ADS)

We present molecular-dynamics simulations of collisions of cosmic ice mixtures (H2O, CO2, CH4, NH3). Both cluster-cluster collisions and the impact of a Ne ion into a flat target are studied. The Reax force field, which allows for chemical reactions among the species, is employed. We monitor and discuss the reactions occurring as well as the number of radicals, fragments and intermediate reaction products.

Anders, Christian; Urbassek, Herbert M.

2013-05-01

355

Incorporating ReaxFF into CMDF and Applications  

E-print Network

Incorporating ReaxFF into CMDF and Applications Si-ping Han, Markus J. Buehler, Adri van Duin, and William A. Goddard Incorporating ReaxFF into CMDF and Applications Si-ping Han, Markus J. Buehler, Adri van Duin, and William A. Goddard ReaxFF Central data structure (Extended OpenBabel) XOB Method 1 QM

Goddard III, William A.

356

Polarizable force field development and molecular dynamics simulations of ionic liquids.  

PubMed

A many-body polarizable force field has been developed and validated for ionic liquids (ILs) containing 1-methyl-3-alkylimidazolium, 1-alkyl-2-methyl-3-alkylimidazolium, N-methyl-N-alkylpyrrolidinium, N-alkylpyridinium, N-alkyl-N-alkylpiperidinium, N-alkyl-N-alkylmorpholinium, tetraalkylammonium, tetraalkylphosphonium, N-methyl-N-oligoetherpyrrolidinium cations and BF(4)(-), CF(3)BF(3)(-), CH(3)BF(3)(-), CF(3)SO(3)(-), PF(6)(-), dicyanamide, tricyanomethanide, tetracyanoborate, bis(trifluoromethane sulfonyl)imide (Ntf(2)(-) or TFSI(-)), bis(fluorosulfonyl)imide (FSI(-)) and nitrate anions. Classical molecular dynamics (MD) simulations have been performed on 30 ionic liquids at 298, 333, and 393 K. The IL density, heat of vaporization, ion self-diffusion coefficient, conductivity, and viscosity were found in a good agreement with available experimental data. Ability of the developed force field to predict ionic crystal cell parameters has been tested on four ionic crystals containing Ntf(2)(-) anions. The influence of polarization on the structure and ion transport has been investigated for [emim][BF(4)] IL. A connection between the structural changes in IL resulting from turning off polarization and slowing down of ion dynamics has been found. Developed force field has also provided accurate description/prediction of thermodynamic and transport properties of alkanes, fluoroalkanes, oligoethers (1,2-dimethoxyethane), ethylene carbonate, propylene carbonate, dimethyl carbonate, hydrazine, methyhydrazine, dimethylhydrazine, acetonitrile, dimethyl amine, and dimethyl ketone. PMID:19637900

Borodin, Oleg

2009-08-20

357

Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator  

PubMed Central

A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments, results in significant improvement in the treatment of the conformational energies, and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules. PMID:23703219

He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D.

2014-01-01

358

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

PubMed Central

Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C6H6) and coronene (C24H12) well; however, for acenes larger than circumcoronene (C54H18) and especially for C60, the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces. PMID:23440601

Schyman, Patric; Jorgensen, William L.

2013-01-01

359

Molecular dynamics simulation of protein crystal with polarized protein-specific force field.  

PubMed

Two 250 ns molecular simulations have been carried out to study the structure and dynamics of crystal toxin protein II from the scorpion Androctonus australis Hector employing the polarized protein-specific charge (PPC), as well as the standard AMBER99SB force field, to investigate the electrostatic polarization on the simulated crystal stability. Results show that under PPC, the monomers in unit cell as well as the lattice in supercell are more stable with smaller root-mean-square deviations and more accurate lattice atomic fluctuations compared with the crystallographic B-factors than under AMBER99SB force field. Most of the interactions at interfaces in the X-ray structure are quite well-preserved, underscoring the important effect of polarization on maintaining the crystal stability. However, the results also show that the hydrogen bond between Asp53 and Gln37 and the cation-? interaction between Arg56 and His64 are not stable, indicating that further optimization of force field, especially the van der Waals interaction parameters, is desired. PMID:25285919

Li, Yongxiu; Zhang, John Z H; Mei, Ye

2014-10-30

360

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

E-print Network

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 effect of a strong magnetic field on some bulk magnitudes such as isothermal compressibility and spin susceptibility is also investigated.

M. Angeles Perez-Garcia; J. Navarro; A. Polls

2009-04-06

361

Materials Bound by Non-Chemical Forces: External Fields and the Quantum Vacuum  

E-print Network

We discuss materials which owe their stability to external fields. These include: 1) external electric or magnetic fields, and 2) quantum vacuum fluctuations in these fields induced by suitable boundary conditions (the Casimir effect). Instances of the first case include the floating water bridge and ferrofluids in magnetic fields. An example of the second case is taken from biology where the Casimir effect provides an explanation of the formation of stacked aggregations or "rouleaux" by negatively charged red blood cells. We show how the interplay between electrical and Casimir forces can be used to drive self-assembly of nano-structured materials, and could be generalized both as a probe of Casimir forces and as a means of manufacturing nanoscale structures. Interestingly, all the cases discussed involve the generation of the somewhat exotic negative pressures. We note that very little is known about the phase diagrams of most materials in the presence of external fields other than those represented by the macroscopic scalar quantities of pressure and temperature. Many new and unusual states of matter may yet be undiscovered.

John Swain; Allan Widom; Yogendra Srivastava

2014-04-29

362

Embedding Circular Force-Free Flux Ropes in Potential Magnetic Fields  

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

363

Determination of best-fit potential parameters for a reactive force field using a genetic algorithm  

Microsoft Academic Search

The ReaxFF interatomic potential, used for organic materials, involves more than 600 adjustable parameters, the best-fit values\\u000a of which must be determined for different materials. A new method of determining the set of best-fit parameters for specific\\u000a molecules containing carbon, hydrogen, nitrogen and oxygen is presented, based on a parameter reduction technique followed\\u000a by genetic algorithm (GA) minimization. This work

Poonam Pahari; Shashank Chaturvedi

364

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

SciTech Connect

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

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

2008-10-15

365

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

NASA Astrophysics Data System (ADS)

We report on atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) investigations of single crystals of the spin crossover complex {Fe(pyrazine)[Pt(CN)4]} across the first-order thermal spin transition. We demonstrate for the first time that the change in spin state can be probed with sub-micrometer spatial resolution through various topographic features extracted from AFM data. This original approach based on surface topography analysis should be easy to implement to any phase change material exhibiting sizeable electron-lattice coupling. In addition, AFM images revealed specific topographic features in the crystals, which were correlated with the spatiotemporal evolution of the transition observed by far-field and near-field optical microscopies.We report on atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) investigations of single crystals of the spin crossover complex {Fe(pyrazine)[Pt(CN)4]} across the first-order thermal spin transition. We demonstrate for the first time that the change in spin state can be probed with sub-micrometer spatial resolution through various topographic features extracted from AFM data. This original approach based on surface topography analysis should be easy to implement to any phase change material exhibiting sizeable electron-lattice coupling. In addition, AFM images revealed specific topographic features in the crystals, which were correlated with the spatiotemporal evolution of the transition observed by far-field and near-field optical microscopies. Electronic supplementary information (ESI) available: Far-field and near-field movies of the spin transition and SEM images of the NSOM tip. See DOI: 10.1039/c3nr03030j

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

2013-08-01

366

Nonlinear Force-Free Modeling of Coronal Magnetic Fields. II. Modeling a Filament Arcade and Simulated Chromospheric and Photospheric Vector Fields  

NASA Astrophysics Data System (ADS)

We compare a variety of nonlinear force-free field (NLFFF) extrapolation algorithms, including optimization, magneto-frictional, and Grad Rubin-like codes, applied to a solar-like reference model. The model used to test the algorithms includes realistic photospheric Lorentz forces and a complex field including a weakly twisted, right helical flux bundle. The codes were applied to both forced “photospheric” and more force-free “chromospheric” vector magnetic field boundary data derived from the model. When applied to the chromospheric boundary data, the codes are able to recover the presence of the flux bundle and the field’s free energy, though some details of the field connectivity are lost. When the codes are applied to the forced photospheric boundary data, the reference model field is not well recovered, indicating that the combination of Lorentz forces and small spatial scale structure at the photosphere severely impact the extrapolation of the field. Preprocessing of the forced photospheric boundary does improve the extrapolations considerably for the layers above the chromosphere, but the extrapolations are sensitive to the details of the numerical codes and neither the field connectivity nor the free magnetic energy in the full volume are well recovered. The magnetic virial theorem gives a rapid measure of the total magnetic energy without extrapolation though, like the NLFFF codes, it is sensitive to the Lorentz forces in the coronal volume. Both the magnetic virial theorem and the Wiegelmann extrapolation, when applied to the preprocessed photospheric boundary, give a magnetic energy which is nearly equivalent to the value derived from the chromospheric boundary, but both underestimate the free energy above the photosphere by at least a factor of two. We discuss the interpretation of the preprocessed field in this context. When applying the NLFFF codes to solar data, the problems associated with Lorentz forces present in the low solar atmosphere must be recognized: the various codes will not necessarily converge to the correct, or even the same, solution.

Metcalf, Thomas R.; De Rosa, Marc L.; Schrijver, Carolus J.; Barnes, Graham; van Ballegooijen, Adriaan A.; Wiegelmann, Thomas; Wheatland, Michael S.; Valori, Gherardo; McTtiernan, James M.

2008-02-01

367

Developing the Pulsed Fission-Fusion (PuFF) Engine  

NASA Technical Reports Server (NTRS)

In September 2013 the NASA Innovative Advanced Concept (NIAC) organization awarded a phase I contract to the PuFF team. Our phase 1 proposal researched a pulsed fission-fusion propulsion system that compressed a target of deuterium (D) and tritium (T) as a mixture in a column, surrounded concentrically by Uranium. The target is surrounded by liquid lithium. A high power current would flow down the liquid lithium and the resulting Lorentz force would compress the column by roughly a factor of 10. The compressed column would reach criticality and a combination of fission and fusion reactions would occur. Our Phase I results, summarized herein, review our estimates of engine and vehicle performance, our work to date to model the fission-fusion reaction, and our initial efforts in experimental analysis.

Adams, Robert B.; Cassibry, Jason; Bradley, David; Fabisinski, Leo; Statham, Geoffrey

2014-01-01

368

Trial-by-Trial Adaptation of Movements during Mental Practice under Force Field  

PubMed Central

Human nervous system tries to minimize the effect of any external perturbing force by bringing modifications in the internal model. These modifications affect the subsequent motor commands generated by the nervous system. Adaptive compensation along with the appropriate modifications of internal model helps in reducing human movement errors. In the current study, we studied how motor imagery influences trial-to-trial learning in a robot-based adaptation task. Two groups of subjects performed reaching movements with or without motor imagery in a velocity-dependent force field. The results show that reaching movements performed with motor imagery have relatively a more focused generalization pattern and a higher learning rate in training direction. PMID:23737857

Anwar, Muhammad Nabeel

2013-01-01

369

Large-scale magnetic field generation by randomly forced shearing waves.  

PubMed

A rigorous theory for the generation of a large-scale magnetic field by random nonhelically forced motions of a conducting fluid combined with a linear shear is presented in the analytically tractable limit of low magnetic Reynolds number (Rm) and weak shear. The dynamo is kinematic and due to fluctuations in the net (volume-averaged) electromotive force. This is a minimal proof-of-concept quasilinear calculation aiming to put the shear dynamo, a new effect recently found in numerical experiments, on a firm theoretical footing. Numerically observed scalings of the wave number and growth rate of the fastest-growing mode, previously not understood, are derived analytically. The simplicity of the model suggests that shear dynamo action may be a generic property of sheared magnetohydrodynamic turbulence. PMID:22243085

Heinemann, T; McWilliams, J C; Schekochihin, A A

2011-12-16

370

The Fast Multipole Method and Point Dipole Moment Polarizable Force Fields  

E-print Network

We present a momentum conserving implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using both a standard integrator and a multiple time step one. Our tests show the applicability of FMM combined with state-of-the-art chemical models in molecular dynamical systems.

Coles, Jonathan P

2014-01-01

371

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

PubMed Central

The accuracy of the empirical force fields is critical for meaningful molecular dynamics simulations of concentrated ionic solutions. Current models are typically developed on the basis of single ion properties such as the monohydrate energy in the gas phase, or the absolute hydration free energy at infinite dilution. However, failure of these models to accurately represent the properties of concentrated solutions cannot be excluded. Here, these issues are illustrated for a polarizable potential based on classical Drude oscillators. To accurately model concentrated ionic solutions, the parameters of the potential functions are optimized to reproduce osmotic pressure data. The sodium-chloride potential of mean force in solution calculated from the empirically-adjusted model is consistent with the results from that calculated from ab initio CPMD simulations. PMID:23795497

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

2012-01-01

372

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

PubMed Central

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

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

2012-01-01

373

Catalyzed growth of carbon nanotube with definable chirality by hybrid molecular dynamics-force biased Monte Carlo simulations.  

PubMed

Metal-catalyzed growth mechanisms of carbon nanotubes (CNTs) were studied by hybrid molecular dynamics-Monte Carlo simulations using a recently developed ReaxFF reactive force field. Using this novel approach, including relaxation effects, a CNT with definable chirality is obtained, and a step-by-step atomistic description of the nucleation process is presented. Both root and tip growth mechanisms are observed. The importance of the relaxation of the network is highlighted by the observed healing of defects. PMID:20939511

Neyts, Erik C; Shibuta, Yasushi; van Duin, Adri C T; Bogaerts, Annemie

2010-11-23

374

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

375

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

PubMed

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

Giulianotti, Richard; Robertson, Roland

2012-06-01

376

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

377

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field  

PubMed Central

An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure–property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies ?Gsolubilityo=?Gsubo+?Gsolvo, which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals. PMID:22582032

Schnieders, Michael J.; Baltrusaitis, Jonas; Shi, Yue; Chattree, Gaurav; Zheng, Lianqing; Yang, Wei; Ren, Pengyu

2012-01-01

378

The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.  

PubMed

An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals. PMID:22582032

Schnieders, Michael J; Baltrusaitis, Jonas; Shi, Yue; Chattree, Gaurav; Zheng, Lianqing; Yang, Wei; Ren, Pengyu

2012-05-01

379

300-FF-1 remedial design report/remedial action work plan  

SciTech Connect

The 300 Area has been divided into three operable units 300-FF-1, 300-FF-2, and 300-FF-5 all of which are in various stages of the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA) process. The 300-FF-1 Operable Unit, the subject of this report, includes liquid waste disposal sites, landfills, and a burial ground. This Remedial Design Report/Remedial Action Work Plan (RDR/RAWP) provides a summary description of each waste site included in the 300-FF-1 Operable Unit, the basis for remedial actions to be taken, and the remedial action approach and management process for implementing these actions. The remedial action approach and management sections provide a description of the remedial action process description, the project schedule, the project team, required planning documentation, the remedial action change process, the process for verifying attainment of the remedial action goals, and the required CERCLA and RCRA closeout documentation. Appendix A provides additional details on each waste site. In addition to remediation of the waste sites, waste generated during the remedial investigation/feasibility study portions of the project will also be disposed at the Environmental Restoration Disposal Facility (ERDF). Appendix B provides a summary of the modeling performed in the 300-FF-1 Phase 3 FS and a description of the modeling effort to be used to show attainment of the remedial action goals. Appendix C provides the sampling and analysis plan (SAP) for all sampling and field-screening activities performed during remediation and for verification of attainment with the remedial action goals. Appendix D provides the public involvement plan, prepared to ensure information is provided to the public during remedial design and remedial action processes.

Gustafson, F.W.

1997-02-01

380

H-theorem for a mean field model describing coupled oscillator systems under external forces  

NASA Astrophysics Data System (ADS)

This article studies the asymptotic behavior of solutions of Fokker-Planck equations describing mean field approximations of weakly coupled oscillator systems subjected to external forces. Using an H-theorem we show that transient probability densities converge to stationary ones. Furthermore, stability criteria are derived for the stationary solutions of these Fokker-Planck equations. The obtained results are applied to a model that combines the Haken-Kelso-Bunz model and the models of weakly coupled oscillators proposed by Winfree and Kuramoto. The stability criteria based on the H-theorem agree with those derived in our earlier analyses.

Frank, T. D.; Daffertshofer, A.; Peper, C. E.; Beek, P. J.; Haken, H.

2001-04-01

381

Using Lewin's force field analysis in implementing a nursing information system.  

PubMed

Change is a regular occurrence in the healthcare environment. The computerization of nursing systems is one aspect of the changes taking place in the information revolution. As a result, nurses have widely varying attitudes toward computers and change in the workplace. To transition the nursing team effectively from one system to another, the nurse informaticist must be aware of the factors that encourage and those that impede the change. Strategies must be developed to assist nurses in moving forward with the transition. This article presents a theoretical discussion of how Lewin's Force Field Analysis Model could be applied in the practice setting to implement a nursing information system successfully. PMID:12802948

Bozak, Marilynn G

2003-01-01

382

Fields and forces in flywheel energy storage with high-temperature superconducting bearings  

SciTech Connect

The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stability subsystems.

Turner, L.R. [Argonne National Lab., IL (United States). Energy Technology Div.] [Argonne National Lab., IL (United States). Energy Technology Div.

1997-03-01

383

Fields and forces in flywheel energy storage with high-temperature superconducting bearings  

SciTech Connect

The development of low-loss bearings employing high-temperature superconductors has brought closer the advent of practical flywheel energy storage systems. These systems require magnetic fields and forces for levitation, stabilization, and energy transfer. This paper describes the status of experiments on flywheel energy storage at Argonne National Laboratory and computations in support of that project, in particular computations for the permanent-magnet rotor of the motor-generator that transfers energy to and from the flywheel, for other energy-transfer systems under consideration, and for the levitation and stabilization subsystem.

Turner, L.R. [Argonne National Lab., IL (United States). Energy Technology Div.

1996-05-01

384

Compatibility of the chameleon-field model with fifth-force experiments, cosmology, and PVLAS and CAST results  

E-print Network

We analyse the PVLAS results using a chameleon field whose properties depend on the environment. We find that, assuming a runaway bare potential $V(\\phi)$ and a universal coupling to matter, the chameleon potential is such that the scalar field can act as dark energy. Moreover the chameleon field model is compatible with the CAST results, fifth force experiments and cosmology.

Ph. Brax; C. van de Bruck; A. -C. Davis

2007-03-22

385

An accurate ab initio quartic force field for ammonia J. M. L. Martin*) and Timothy J. Lee  

E-print Network

, and combustion studies, presupposes the availability of anharmonic force fields.' Third, dynam- ics studies would be the kinetics of the "thermal de- NOx" reaction4 in which the NOx emission of a jet engine of symmetry-unique and nonvanishing internal coordinate force constants to be de- termined. Even the harmonic

Martin, Jan M.L.

386

Recovery patterns in electroencephalographic global field power during maximal isometric force production.  

PubMed

In previous work, cortical activity decreased with fatigue following novel movements or small muscle group actions. These muscle actions, however, do not appear related to the cortical activity seen with biologically relevant and highly trained movement patterns (i.e., ingrained patterns). The cortical recovery response to ingrained patterns-and how it differs with altered load, speed, or volume - is unknown. The purpose of this balanced, within-group study was to investigate differences in cortical activity 24 hours after physically distinct variations of a highly trained squat exercise (n = 7, minimum 4 years resistance training experience). Four resistance protocols were chosen: rate of force development (PWR, 6 × 3 squat jumps at 30% of 1 repetition maximum [1RM]); magnitude of force development (FOR, 6 × 3 squat at 95% of 1RM); volume of force development (VOL, 6 × 10 squat at 80% of their 1RM); and control (CTRL, 6 sets unracking an empty bar). Twenty-four hours later, subjects performed a peak isometric squat while electroencephalographic and biochemical markers of exertion and fatigue were obtained. Global field power detected the quantity of activity superficial to motor regions. Waveforms of activity throughout the isometric squats were obtained and grand averages calculated to produce quantitative depictions of cortical activity. Significance was P ? 0.05. Peak isometric squat force was not statistically different 24 hours postexercise (Force [N]: PWR: 2828.79 ± 461.17; FOR: 2887.64 ± 453.09; VOL: 2910.17 ± 625.81; CTRL 2768.53 ± 374.85). Subjects produced similar and characteristic cortical activity patterns during isometric squats despite varying indices of fatigue. Differences were observed based upon the use or nonuse of aerobic endurance exercise in their training program. Patterns of activity in data seem to have emerged based on differences in training preference. Global Field Power (uV) during the isometric squat for PWR was 26.98 ± 14.64; FOR 24.06 ± 19.05; VOL 23.05 ± 13.37; and CTRL 15.78 ± 8.11. Previous research suggests that cortical activity decreases with physical activity; however, despite substantial endocrine, perceptual, and biomechanical differences between protocols, cortical activity was not decreased below control during the performance of a maximal isometric squat 24 hours after various exercise protocols. PMID:21857362

Dunn-Lewis, Courtenay; Flanagan, Shawn D; Comstock, Brett A; Maresh, Carl M; Volek, Jeff S; Denegar, Craig R; Kupchak, Brian R; Kraemer, William J

2011-10-01

387

Field evidence of the viscous sublayer in a tidally forced developing boundary layer  

NASA Astrophysics Data System (ADS)

Field observations of boundary layer development within a tidally forced estuary revealed evidence of an observable viscous sublayer. Evidence is provided by several independent measures of the flow field, including hydrodynamic smoothness, an immobile bed, and characteristic velocity, constant stress, and higher-order moment structures. This investigation reports what may be the second comprehensive observation of the viscous sublayer in a marine environment, and what could be the first observation of a momentum balance that includes the viscous sublayer within a shallow estuarine environment. Hydrodynamic observations were made in a straight channel within the Great Bay Estuary of New Hampshire over a flat sandy mud with low water depth of 1.5 m at the sampling location. Beyond quantifying the role of the benthic boundary layer in nutrient dynamics, these observations are useful to provide insight into very near boundary stress estimates leading to incipient motion in estuarine and coastal environments.

Wengrove, M. E.; Foster, D. L.

2014-07-01

388

Opto-mechanical probe for combining atomic force microscopy and optical near-field surface analysis.  

PubMed

We have developed a new easy-to-use probe that can be used to combine atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM). We show that, using this device, the evanescent field, obtained by total internal reflection conditions in a prism, can be visualized by approaching the surface with the scanning tip. Furthermore, we were able to obtain simultaneous AFM and SNOM images of a standard test grating in air and in liquid. The lateral resolution in AFM and SNOM mode was estimated to be 45 and 160 nm, respectively. This new probe overcomes a number of limitations that commercial probes have, while yielding the same resolution. PMID:25121878

van Hoorn, C H; Chavan, D C; Tiribilli, B; Margheri, G; Mank, A J G; Ariese, F; Iannuzzi, D

2014-08-15

389

The Congo River plume: Impact of the forcing on the far-field and near-field dynamics  

NASA Astrophysics Data System (ADS)

The first numerical simulations of the Congo River plume dynamics are presented in this study. The different forcing mechanisms responsible for the seasonal variations of the plume extend are separately analyzed and the Regional Ocean Modeling System (ROMS) is employed to carry out both a process orientated study—with simple baseline simulations and a sensitivity study—with realistic 1 year runs setup in 2005. The baseline model is forced only by the river flow, in the presence of realistic bathymetry. Tides, wind stress, surface heat flux, and ocean boundary conditions are the forcing added to the realistic model. The typical seasonal orientation of the Congo River plume is found to be northward during most of year except for the February-March (FM) season when the plume has a large westward extension (about 800 km) and its area nearly doubles. The northward extension of the plume is explained by a buoyancy-driven upstream coastal flow—due to the unique geomorphology of the Congo River estuary—and the combined influences of the ambient ocean currents and the wind. During the FM season, the surface ocean circulation is driving both (1) the westward extension of the plume and (2) the southward transport of the Nyanga River fresh waters which feed the Congo River plume. In the near-field region of the plume, the presence of the deep Congo canyon has two main effects: (1) its depth increases the intrusion of sea water into the river mouth and (2) its orientation initiates the formation of the upstream flow.

Denamiel, CléA.; Budgell, W. Paul; Toumi, Ralf

2013-02-01

390

Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.  

PubMed

The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (?30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods. PMID:21812413

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

2011-09-15

391

ReaxFF molecular dynamics simulations of CO collisions on an O-preadsorbed silica surface.  

PubMed

A quasiclassical trajectory dynamics study was performed for carbon monoxide collisions over an oxygen preadsorbed ?-cristobalite (001) surface. A reactive molecular force field (ReaxFF) was used to model the potential energy surface. The collisions were performed fixing several initial conditions: CO rovibrational states (v?=?0-5 and j?=?0, 20, 35), collision energies (0.05 ? E(col) ? 2.5 eV), incident angles (?(v)?=?0°, 45°) and surface temperatures (T(surf)?=?300 K, 900 K). The principal elementary processes were the molecular reflection and the non-dissociative molecular adsorption. CO? molecules were also formed in minor extension via an Eley-Rideal reaction although some of them were finally retained on the surface. The scattered CO molecules tend to be translationally colder and internally hotter (rotationally and vibrationally) than the initial ones. The present study supports that CO?+?O(ad) reaction should be less important than O?+?O(ad) reaction over silica for similar initial conditions of reactants, in agreement with experimental data. PMID:24633769

Gamallo, Pablo; Prats, Hèctor; Sayós, Ramón

2014-04-01

392

Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.  

PubMed

We used the second-generation mining minima method (M2) to compute the binding affinities of the novel host-guest complexes in the SAMPL3 blind prediction challenge. The predictions were in poor agreement with experiment, and we conjectured that much of the error might derive from the force field, CHARMm with Vcharge charges. Repeating the calculations with other generalized force-fields led to no significant improvement, and we observed that the predicted affinities were highly sensitive to the choice of force-field. We therefore embarked on a systematic evaluation of a set of generalized force fields, based upon comparisons with PM6-DH2, a fast yet accurate semi-empirical quantum mechanics method. In particular, we compared gas-phase interaction energies and entropies for the host-guest complexes themselves, as well as for smaller chemical fragments derived from the same molecules. The mean deviations of the force field interaction energies from the quantum results were greater than 3 kcal/mol and 9 kcal/mol, for the fragments and host-guest systems respectively. We further evaluated the accuracy of force-fields for computing the vibrational entropies and found the mean errors to be greater than 4 kcal/mol. Given these errors in energy and entropy, it is not surprising in retrospect that the predicted binding affinities deviated from the experiment by several kcal/mol. These results emphasize the need for improvements in generalized force-fields and also highlight the importance of systematic evaluation of force-field parameters prior to evaluating different free-energy methods. PMID:22274835

Muddana, Hari S; Gilson, Michael K

2012-05-01

393

Matching of additive and polarizable force fields for multiscale condensed phase simulations  

PubMed Central

Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 – 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures. PMID:23997691

Baker, Christopher M.; Best, Robert B.

2013-01-01

394

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations  

NASA Astrophysics Data System (ADS)

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

395

Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface  

PubMed Central

Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of ?-quartz, ab initio vibrational spectra and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of ?-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and space-time correlations of water oxygen atoms in terms of Van Hove self correlation functions. The Vibrational Density of States (VDOS) spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level. PMID:16471886

Lopes, Pedro E. M.; Murashov, Vladimir; Tazi, Mouhsine; Demchuk, Eugene; MacKerell, Alexander D.

2008-01-01

396

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

PubMed

We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

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

2014-05-01

397

Predictive force-field calculations for the equilibrium dimerization of isoprene  

SciTech Connect

The Diels-Alder dimerization of isoprene is an important reaction. In the present work, the QCFF force field program was used to calculate gas-phase thermodynamic properties of the monomer (isoprene) and the dimers 1-methyl-5-(1-methylethenyl)cyclohexene (diprene) and 1-methyl-4-(1-methylethenyl)cyclohexene (dipentene) for the temperature range 298.15-1000 K. These QCFF-calculated thermodynamic values were compared, when possible, with corresponding values obtained experimentally or from other force field programs, and the agreement was found to be satisfactory. The QCFF values were further used to derive gas-phase equilibrium properties--[Delta]H[sup o], [Delta]S[sup o], [Delta]G[sup o], and K[sub p]--for the isoprene dimerization reaction at various temperatures. These computational results suggest that, based upon thermodynamics, diprene and dipentene are about equally favored dimerization products of isoprene and that reported experimental data reflect kinetic control of dipentene formation at lower temperatures. The equilibrium thermodynamics data for the isoprene dimerization reaction presented in this paper are felt to be sufficiently reliable that they can be utilized in the absence of any additional experimental data. 13 refs., 4 figs., 7 tabs.

Kar, M.; Lenz, T.G.; Vaughan, J.D. (Colorado State Univ., Fort Collins, CO (United States))

1994-03-03

398

Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem.  

PubMed

The derivation and optimization of most energy terms in modern force fields are aided by automated computational tools. It is therefore important to have algorithms to rapidly and precisely train large numbers of interconnected parameters to allow investigators to make better decisions about the content of molecular models. In particular, the traditional approach to deriving dihedral parameters has been a least-squares fit to target conformational energies through variational optimization strategies. We present a computational approach for simultaneously fitting force field dihedral amplitudes and phase constants which is analytic within the scope of the data set. This approach completes the optimal molecular mechanics representation of a quantum mechanical potential energy surface in a single linear least-squares fit by recasting the dihedral potential into a linear function in the parameters. We compare the resulting method to a genetic algorithm in terms of computational time and quality of fit for two simple molecules. As suggested in previous studies, arbitrary dihedral phases are only necessary when modeling chiral molecules, which include more than half of drugs currently in use, so we also examined a dihedral parametrization case for the drug amoxicillin and one of its stereoisomers where the target dihedral includes a chiral center. Asymmetric dihedral phases are needed in these types of cases to properly represent the quantum mechanical energy surface and to differentiate between stereoisomers about the chiral center. PMID:24960267

Hopkins, Chad W; Roitberg, Adrian E

2014-07-28

399

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

SciTech Connect

This volume contains the abstracts and presentation material from the Research Assistance Task Force Meeting Electrical Breakdown of Insulating Ceramics in a High-Radiation Field.'' The meeting was jointly sponsored by the Office of Basic Energy Sciences and the Office of Fusion Energy of the US Department of Energy in Vail, Colorado, May 28--June 1, 1991. The 26 participants represented expertise in fusion, radiation damage, electrical breakdown, ceramics, and semiconductor and electronic structures. These participants came from universities, industries, national laboratories, and government. The attendees represented eight nations. The Task Force meeting was organized in response to the recent discovery that a combination of temperature, electric field, and radiation for an extended period of time has an unexplained adverse effect in ceramics, termed radiation-enhanced electrical degradation (REED). REED occurs after an incubation period and continues to accelerate with irradiation until the ceramics can no longer be regarded as insulators. It appears that REED is irreversible and the ceramic insulators cannot be readily annealed or otherwise repaired for future services. This effect poses a serious threat for fusion reactors, which require electrical insulators in diagnostic devices, in radio frequency and neutral beam systems, and in magnetic assemblies. The problem of selecting suitable electrical insulating materials in thus far more serious than previously anticipated.

Green, P.H. (comp.) [comp.

1991-08-01

400

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field  

E-print Network

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native beta-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappr...

Beccara, Silvio a; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

2013-01-01

401

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field  

PubMed Central

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native -sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. PMID:23555232

a Beccara, Silvio; Skrbic, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

2013-01-01

402

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field  

E-print Network

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native beta-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting.

Silvio a Beccara; Tatjana Skrbic; Roberto Covino; Cristian Micheletti; Pietro Faccioli

2013-02-08

403

Folding pathways of a knotted protein with a realistic atomistic force field.  

PubMed

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology. By using the dominant-reaction pathway scheme we collected about 30 successful folding trajectories for the 82-amino acid long trefoil-knotted protein. Despite the dissimilarity of their initial unfolded configuration, these trajectories reach the natively-knotted state through a remarkably similar succession of steps. In particular it is found that knotting occurs essentially through a threading mechanism, involving the passage of the C-terminal through an open region created by the formation of the native [Formula: see text]-sheet at an earlier stage. The dominance of the knotting by threading mechanism is not observed in MJ0366 folding simulations using simplified, native-centric models. This points to a previously underappreciated role of concerted amino acid interactions, including non-native ones, in aiding the appropriate order of contact formation to achieve knotting. PMID:23555232

a Beccara, Silvio; Škrbi?, Tatjana; Covino, Roberto; Micheletti, Cristian; Faccioli, Pietro

2013-01-01

404

A consistent force field parameter set for zwitterionic amino acid residues.  

PubMed

Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species. PMID:25338816

Horn, Anselm H C

2014-11-01

405

Simulations of vibrational spectra from classical trajectories: Calibration with ab initio force fields  

NASA Astrophysics Data System (ADS)

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5fs. For a given integration time step, lower vibrational frequencies (˜0-2000cm-1) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. ?-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.

Horní?ek, Jan; Kaprálová, Petra; Bou?, Petr

2007-08-01

406

Determination of best-fit potential parameters for a reactive force field using a genetic algorithm.  

PubMed

The ReaxFF interatomic potential, used for organic materials, involves more than 600 adjustable parameters, the best-fit values of which must be determined for different materials. A new method of determining the set of best-fit parameters for specific molecules containing carbon, hydrogen, nitrogen and oxygen is presented, based on a parameter reduction technique followed by genetic algorithm (GA) minimization. This work has two novel features. The first is the use of a parameter reduction technique to determine which subset of parameters plays a significant role for the species of interest; this is necessary to reduce the optimization space to manageable levels. The second is the application of the GA technique to a complex potential (ReaxFF) with a very large number of adjustable parameters, which implies a large parameter space for optimization. In this work, GA has been used to optimize the parameter set to determine best-fit parameters that can reproduce molecular properties to within a given accuracy. As a test problem, the use of the algorithm has been demonstrated for nitromethane and its decomposition products. PMID:21667073

Pahari, Poonam; Chaturvedi, Shashank

2012-03-01

407

Formation of magnetic discontinuities through superposition of force-free magnetic fields: Periodic boundaries  

NASA Astrophysics Data System (ADS)

In ideal magnetohydrodynamics characterized by an infinite electrical conductivity, the magnetic flux across an arbitrary fluid surface is conserved in time. The magnetofluid then can be partitioned into contiguous subvolumes of fluid, each of which entraps its own subsystem of magnetic flux. During dynamical evolution of the magnetofluid, these subvolumes press into each other; and in the process, two such subvolumes may come into direct contact while ejecting a third interstitial subvolume. Depending on the orientations of magnetic fields of the two interacting subvolumes, the magnetic field at the common surface of interaction may become discontinuous and a current sheet is formed there. This process of current sheet formation and their subsequent decay is believed to be a plausible mechanism for coronal heating and may also be responsible for various eruptive phenomena at the solar corona. In this work, we explore this theoretical concept through numerical simulations of a viscous, incompressible magnetofluid characterized by infinite electrical conductivity. In particular, we show that if the initial magnetic field is prescribed by superposition of two linear force-free fields with different torsion coefficients, then formation of current sheets are numerically realizable in the neighborhood of magnetic nulls.

Kumar, Dinesh; Bhattacharyya, R.; Smolarkiewicz, P. K.

2013-11-01

408

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.  

PubMed

A polarizable force field for nucleic acid bases based on the classical Drude oscillator model is presented. Parameter optimization was performed to reproduce crystallographic geometries, crystal unit cell parameters, heats of sublimation, vibrational frequencies and assignments, dipole moments, molecular polarizabilities and quantum mechanical base-base and base-water interaction energies. The training and validation data included crystals of unsubstituted and alkyl-substituted adenine, guanine, cytosine, uracil, and thymine bases, hydrated crystals, and hydrogen bonded base pairs. Across all compounds, the RMSD in the calculated heats of sublimation is 4.1%. This equates to an improvement of more than 2.5 kcal/mol in accuracy compared to the nonpolarizable CHARMM27 force field. However, the level of agreement with experimental molecular volume decreased from 1.7% to 2.1% upon moving from the nonpolarizable to the polarizable model. The representation of dipole moments is significantly improved with the Drude polarizable force field. Unlike in additive force fields, there is no requirement for the gas-phase dipole moments to be overestimated, illustrating the ability of the Drude polarizable force field to treat accurately differently dielectric environments and indicating the improvements in the electrostatic model. Validation of the model was performed on the basis of the calculation of the gas-phase binding enthalpies of base pairs obtained via potential of mean force calculations; the additive and polarizable models both performed satisfactorily with average differences of 0.2 and 0.9 kcal/mol, respectively, and rms differences of 1.3 and 1.7 kcal/mol, respectively. Overall, considering the number of significant improvements versus the additive CHARMM force field, the incorporation of explicit polarizability into the force field for nucleic acid bases represents an additional step toward accurate computational modeling of biological systems. PMID:21166469

Baker, Christopher M; Anisimov, Victor M; MacKerell, Alexander D

2011-01-27

409

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field  

PubMed Central

Coarse-grained molecular-dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-?-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel ?-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes which are unimodal. In addition, a comparison, between the structures that are representative of the minima in the free-energy profile along the essential collective coordinates of protein folding (computed by principal component analysis) and the free-energy profile projected along the virtual-bond dihedral angles ? of the backbone, revealed the key residues involved in the transitions between the different basins of the folding free-energy profile, in agreement with existing experimental data for 1E0L. PMID:20166738

Maisuradze, Gia G.; Senet, Patrick; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

2010-01-01

410

Investigation of Force-Freeness of Solar Emerging Magnetic Field via Application of the Virial Theorem to MHD Simulations  

E-print Network

Force-freeness of a solar magnetic field is a key to reconstructing invisible coronal magnetic structure of an emerging flux region on the Sun where active phenomena such as flares and coronal mass ejections frequently occur. We have performed magnetohydrodynamic (MHD) simulations which are adjusted to investigate force-freeness of an emerging magnetic field by using the virial theorem. Our focus is on how the force-free range of an emerging flux region develops and how it depends on the twist of a pre-emerged magnetic field. As an emerging flux region evolves, the upper limit of the force-free range continuously increases while the lower limit is asymptotically reduced to the order of a photospheric pressure scale height above the solar surface. As the twist becomes small the lower limit increases and then seems to be saturated. We also discuss the applicability of the virial theorem to an evolving magnetic structure on the Sun.

Kang, Jihye

2014-01-01

411

Scanning near-field optical/atomic-force microscopy for biomedical applications  

NASA Astrophysics Data System (ADS)

We have developed scanning near-field optical/atomic force microscopy (SNOM/AFM). The SNOM/AFM uses a bent optical fiber simultaneously as a dynamic force AFM cantilever and a SNOM probe. Resonant frequency of the optical fiber cantilever is 15 - 40 kHz. Optical resolution of the SNOM/AFM images shows less than 50 nm. The SNOM/AFM system contains photon counting system and polychrometer/ICCD system to observe fluorescence image and spectrograph of micro areas, respectively. A SNOM-AFM system was newly applied to analyses of biological samples. In this system a feedback signal from AFM in the noncontact mode was used to scan the probe tip along the surface contour of the sample. An optical fiber with a sharp tip on one end was bent for use as cantilever, and ac amplitude of the cantilever deflection was held constant during scanning by moving the stage. Green fluorescent protein (GFP) absorbs blue light and emits green light. GFP should be a convenient indicator of transformation and one that could allow cells to be separated with fluorescence-activated cell sorting. The gene coding to GFP was cloned in recombinant E.coli and plant cells. Spatial distribution of GFP gene expression was clarified using a SNOM-AFM system. Fluorescent spectroscopic analyses supported GFP was surely produced in E.coli and plant cells. Applications to gene identification in human genomes were also discussed.

Tamiya, Eiichi; Iwabuchi, Shinichiro; Murakami, Yuji; Sakaguchi, Toshifumi; Yokoyama, Kenji; Chiba, Norio; Muramatsu, Hiroshi

1996-12-01

412

Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields  

PubMed Central

The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parameterization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and non-planar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 C) are also reported. PMID:23621692

Dahlgren, Markus K.; Schyman, Patric; Tirado-Rives, Julian; Jorgensen, William L.

2013-01-01

413

Atomistic polarizable force field for molecular dynamics simulations of azide anion containing ionic liquids and crystals.  

NASA Astrophysics Data System (ADS)

Atomistic polarizable force field has been developed for a number of azide anion containing ionic liquids and crystals. Hybrid Molecular Dynamics/Monte Carlo (MD/MC) simulations were performed on methylguanazinium azide and 1-(2-butynyl)-3-methyl-imidazolium azide crystals, while 1-butyl-2,3-dimethylimidazolium azide and 1-amino-3-methyl-1,2,3-triazolium azide ionic liquids were investigated using MD simulations. Crystal cell parameters and crystal structures of 1-(2-butynyl)-3-methyl-imidazolium azide were found in good agreement with X-ray experimental data. Density and ion transport of 1-butyl-2,3-dimethylimidazolium azide predicted from MD simulations were in good agreement with experiments. Details of the ionic liquid structure and relaxation mechanism will be discussed.

Starovoytov, Oleg; Hooper, Justin; Borodin, Oleg; Smith, Grant

2010-03-01

414

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides  

PubMed Central

A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide solutions (MX), where M = Li+, Na+, K+, Rb+, Cs+ and X = F?, Cl?, Br?, I?, and their interactions with biomolecules. The models are specifically designed to reproduce the experimental Kirkwood-Buff integrals, and thereby the solution salt activities, as a function of salt concentration. Additionally, we demonstrate that these models reasonably reproduce other experimental properties including ion diffusion constants, dielectric decrements, and the excess heats of mixing. The parameters are developed by considering the properties of aqueous NaX and MCl solutions using a previously established model for NaCl. Transferability of the parameters to other salts is then established by the successful simulation of additional aqueous salt solutions, KI and CsBr, not originally included in the parameterization procedure. PMID:21789033

Gee, Moon Bae; Cox, Nicholas R.; Jiao, Yuanfang; Bentenitis, Nikolaos; Weeerasinghe, Samantha; Smith, Paul E.

2011-01-01

415

Assessment of Lower Extremity Motor Adaptation via an Extension of the Force Field Adaptation Paradigm  

PubMed Central

Lower extremity rehabilitation has seen recent increased interest. New tools are available to improve gait retraining in both adults and children. However, it remains difficult to determine optimal ways to plan interventions due to difficulties in continuously monitoring outcomes in patients undergoing rehabilitation. In this paper, we introduce an extension of the Force Field Adaptation Paradigm, used to quantitatively assess upper extremity motor adaptation, to the lower extremity. The algorithm is implemented on the Lokomat lower extremity gait orthosis and utilized to assess short-term motor adaptation. Establishing an understanding of how healthy adults’ motor systems adapt to external perturbations will be important to understanding how the adaptive mechanisms involved in gait are altered by disease. PMID:21095786

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

2012-01-01

416

Carbon cluster formation during thermal decomposition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine and 1,3,5-triamino-2,4,6-trinitrobenzene high explosives from ReaxFF reactive molecular dynamics simulations.  

PubMed

We report molecular dynamics (MD) simulations using the first-principles-based ReaxFF reactive force field to study the thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) at various densities and temperatures. TATB is known to produce a large amount (15-30%) of high-molecular-weight carbon clusters, whereas detonation of nitramines such as HMX and RDX (1,3,5-trinitroperhydro-1,3,5-triazine) generate predominantly low-molecular-weight products. In agreement with experimental observation, these simulations predict that TATB decomposition quickly (by 30 ps) initiates the formation of large carbonaceous clusters (more than 4000 amu, or approximately 15-30% of the total system mass), and HMX decomposition leads almost exclusively to small-molecule products. We find that HMX decomposes readily on this time scale at lower temperatures, for which the decomposition rate of TATB is about an order of magnitude slower. Analyzing the ReaxFF MD results leads to the detailed atomistic structure of this carbon-rich phase of TATB and allows characterization of the kinetics and chemistry related to this phase and their dependence on system density and temperature. The carbon-rich phase formed from TATB contains mainly polyaromatic rings with large oxygen content, leading to graphitic regions. We use these results to describe the initial reaction steps of thermal decomposition of HMX and TATB in terms of the rates for forming primary and secondary products, allowing comparison to experimentally derived models. These studies show that MD using the ReaxFF reactive force field provides detailed atomistic information that explains such macroscopic observations as the dramatic difference in carbon cluster formation between TATB and HMX. This shows that ReaxFF MD captures the fundamental differences in the mechanisms of such systems and illustrates how the ReaxFF may be applied to model complex chemical phenomena in energetic materials. The studies here illustrate this for modestly sized systems and modest periods; however, ReaxFF calculations of reactive processes have already been reported on systems with approximately 10(6) atoms. Thus, with suitable computational facilities, one can study the atomistic level chemical processes in complex systems under extreme conditions. PMID:19791809

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

2009-10-01