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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

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.

3

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.

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

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

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

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

10

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 Dehydrogenation on Vanadium Oxide Catalysts Kimberly Chenoweth, Adri C.T. van Duin, Petter Persson, Mu-Jeng Cheng, Jonas of hydrocarbons with vanadium oxide catalysts. The ReaxFF force field parameters have been fit to a large quantum

Goddard III, William A.

11

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

12

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

13

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

14

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.

15

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

16

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

17

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

18

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

19

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

20

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.

21

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.

22

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

PubMed Central

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

Hegazy, Lamees; Richards, Nigel G. J.

2013-01-01

23

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

24

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

25

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.

26

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.

27

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.

28

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

29

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

30

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

31

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

32

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

PubMed

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

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

2010-12-01

33

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

34

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

35

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

36

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

37

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

38

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

PubMed

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

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

2005-05-18

39

Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB.  

PubMed

Recently, we developed a residue-specific force field (RSFF1) based on conformational free-energy distributions of the 20 amino acid residues from a protein coil library. Most parameters in RSFF1 were adopted from the OPLS-AA/L force field, but some van der Waals and torsional parameters that effectively affect local conformational preferences were introduced specifically for individual residues to fit the coil library distributions. Here a similar strategy has been applied to modify the Amber ff99SB force field, and a new force field named RSFF2 is developed. It can successfully fold ?-helical structures such as polyalanine peptides, Trp-cage miniprotein, and villin headpiece subdomain and ?-sheet structures such as Trpzip-2, GB1 ?-hairpins, and the WW domain, simultaneously. The properties of various popular force fields in balancing between ?-helix and ?-sheet are analyzed based on their descriptions of local conformational features of various residues, and the analysis reveals the importance of accurate local free-energy distributions. Unlike the RSFF1, which overestimates the stability of both ?-helix and ?-sheet, RSFF2 gives melting curves of ?-helical peptides and Trp-cage in good agreement with experimental data. Fitting to the two-state model, RSFF2 gives folding enthalpies and entropies in reasonably good agreement with available experimental results. PMID:25358113

Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

2015-01-22

40

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

41

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

42

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

43

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

44

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF  

PubMed Central

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted.

2014-01-01

45

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

46

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

47

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

48

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

49

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.

50

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

51

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

52

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

PubMed

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

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

2012-04-19

53

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

54

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

55

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

56

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

57

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

58

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

59

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

60

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 to the dissociation energies of lithium-benzene sandwich compounds and the collision behavior of lithium atoms on lithium compounds is scarce. Also, because the application of high-level ab initio calculations demands

van Duin, Adri

61

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

62

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

63

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

PubMed

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

Srinivasan, Sriram Goverapet; van Duin, Adri C T

2011-11-24

64

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

65

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

E-print Network

force field on Morwell Brown coal structures Elodie Salmon a , Adri C.T. van Duin b , François Lorant Grandville, BP 20451, F-54001 Nancy, France d Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125, USA a r t i c l e i n f o Article history: Received 20 April

Goddard III, William A.

66

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

67

Reactive molecular dynamics simulation on the disintegration of Kapton, POSS polyimide, amorphous silica, and teflon during atomic oxygen impact using the ReaxFF reactive force-field method.  

PubMed

Atomic oxygen (AO) is the most abundant element in the low Earth orbit (LEO). It is the result of the dissociation of molecular oxygen by ultraviolet radiation from the sun. In the LEO, it collides with the materials used on spacecraft surfaces and causes degradation of these materials. The degradation of the materials on the surface of spacecrafts at LEO has been a significant problem for a long time. Kapton polyimide, polyhedral oligomeric silsesquioxane (POSS), silica, and Teflon are the materials extensively used in spacecraft industry, and like many other materials used in spacecraft industry, AO collision degradation is an important issue in their applications on spacecrafts. To investigate the surface chemistry of these materials in exposure to space AO, a computational chemical evaluation of the Kapton polyimide, POSS, amorphous silica, and Teflon was performed in separate simulations under similar conditions. For performing these simulations, the ReaxFF reactive force-field program was used, which provides the computational speed required to perform molecular dynamics (MD) simulations on system sizes sufficiently large to describe the full chemistry of the reactions. Using these simulations, the effects of AO impact on different materials and the role of impact energies, the content of material, and temperature of material on the behavior of the materials are studied. The ReaxFF results indicate that Kapton is less resistant than Teflon toward AO damage. These results are in good agreement with experiment. These simulations indicate that the amorphous silica shows the highest stability among these materials before the start of the highly exothermic silicon oxidation. We have verified that adding silicon to the bulk of the Kapton structure enhances the stability of the Kapton against AO impact. Our canonical MD simulations demonstrate that an increase in the heat transfer in materials during AO impact can provide a considerable decrease in the disintegration of the material. This effect is especially relevant in silica AO collision. Considerable experimental efforts have been undertaken to minimize such AO-based degradations. As our simulations demonstrate, ReaxFF can provide a cost-effective screening tool for future material optimization. PMID:24679339

Rahnamoun, A; van Duin, A C T

2014-04-17

68

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

E-print Network

Fields for Silicon Carbide Andres Jaramillo-Botero,* Saber Naserifar, and William A. Goddard, III: (1) the ReaxFF reactive force field for modeling the adiabatic reactive dynamics of silicon carbide, and atom coordinations; and used it to optimize a silicon-silicon force field. Handley and Deeth9 describe

Goddard III, William A.

69

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.

70

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

71

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.

72

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.

73

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

74

Correction to Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Hydrogen Combustion  

E-print Network

Correction to Adaptive Accelerated ReaxFF Reactive Dynamics with Validation from Simulating Information did not include the revised COH ReaxFF force field used for obtaining the published results, species generated in aARRDyn simulations with Vmax = 20 and 40 kcal at 2498 K; the new ReaxFF-OH2014 force

Goddard III, William A.

75

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

76

Rapid parameterization of small molecules using the Force Field Toolkit  

PubMed Central

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics (MD) simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, e.g., GAFF and CGenFF, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, set up multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). PMID:24000174

Mayne, Christopher G.; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C.

2013-01-01

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

The MSXX Force Field for the Barium Sulfate-Water Interface Yun Hee Jang,, Xiao Yan Chang, Mario Blanco, Sungu Hwang,, Yongchun Tang,  

E-print Network

The MSXX Force Field for the Barium Sulfate-Water Interface Yun Hee Jang,, Xiao Yan Chang, Mario, 2001; In Final Form: April 3, 2002 A new force field (MSXX FF) was developed for barium sulfate (BaSO4

Goddard III, William A.

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.  

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

81

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

82

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.

83

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

84

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

85

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

86

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

PubMed

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

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

2011-01-21

87

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

SciTech Connect

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

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

2010-10-21

88

Force field development for organic molecules: Modifying dihedral and 1-n pair interaction parameters.  

PubMed

We comprehensively illustrate a general process of fitting all-atom molecular mechanics force field (FF) parameters based on quantum mechanical calculations and experimental thermodynamic data. For common organic molecules with free dihedral rotations, this FF format is comprised of the usual bond stretching, angle bending, proper and improper dihedral rotation, and 1-4 scaling pair interactions. An extra format of 1-n scaling pair interaction is introduced when a specific intramolecular rotation is strongly hindered. We detail how the preferred order of fitting all intramolecular FF parameters can be determined by systematically generating characteristic configurations. The intermolecular Van der Waals parameters are initially taken from the literature data but adjusted to obtain a better agreement between the molecular dynamics (MD) simulation results and the experimental observations if necessary. By randomly choosing the molecular configurations from MD simulation and comparing their energies computed from FF parameters and quantum mechanics, the FF parameters can be verified self-consistently. Using an example of a platform chemical 3-hydroxypropionic acid, we detail the comparison between the new fitting parameters and the existing FF parameters. In particular, the introduced systematic approach has been applied to obtain the dihedral angle potential and 1-n scaling pair interaction parameters for 48 organic molecules with different functionality. We suggest that this procedure might be used to obtain better dihedral and 1-n interaction potentials when they are not available in the current widely used FF. © 2014 Wiley Periodicals, Inc. PMID:25487650

Chen, Siyan; Yi, Shasha; Gao, Wenmei; Zuo, Chuncheng; Hu, Zhonghan

2015-03-01

89

Force field parameters for aminoorganosilanes  

NASA Astrophysics Data System (ADS)

Force field parameters for new compound classes are an important prerequisite for the fast and reliable modeling of these compounds with commercial available modeling software. The development of MMX force field parameters for aminoorganosilanes is described in this work. Combined efforts have been undertaken including synthesis, structural characterization of suitable compounds, and quantum chemical calculation with a systematic set of model compounds. 1,2-Dibenzylamino-1,2-dichloro-dimethyldisilane has been synthesized and characterized by X-ray structure analysis. It is possible to calculate bond lengths and angles of this and other aminosilanes with the new force field parameters.

Meinel, Birgit; Günther, Betty; Böhme, Uwe

2015-01-01

90

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

91

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

92

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

93

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

94

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

95

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

96

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

97

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

NASA Astrophysics Data System (ADS)

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

Su, Julius T.; Goddard, William A.

2009-12-01

98

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

NASA Astrophysics Data System (ADS)

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

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

2006-07-01

99

Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces  

NASA Technical Reports Server (NTRS)

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

Kory, Carol L.; Dayton, James A.

1998-01-01

100

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

101

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

102

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

103

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

104

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

105

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

SciTech Connect

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

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

2010-06-01

106

The Force Field for Amino Acid Based Ionic Liquids: Polar Residues  

E-print Network

Ionic liquids (ILs) constitute one of the most active fields of research nowadays. Many organic and inorganic molecules can be converted into ions via relatively simple procedures. These ions can be combined into ILs. Amino acid based ILs (AAILs) represent a specific interest due to solubilization of biological species, participation in enzymatic catalysis, and capturing toxic gases. We develop a new force field (FF) for the seven selected AAILs comprising 1-ethyl-3-methylimidazolium cation and amino acid anions with polar residues. The anions were obtained via deprotonation of carboxyl group. We account for peculiar interactions between the anion and the cation by fitting electrostatic potential for an ion pair, in contrast to isolated ions. The van der Waals interactions were transferred from the CHARMM36 FF with minor modifications, as suggested by hybrid density functional theory. Compatibility between our parameters and CHARMM36 parameters is preserved. The developed interaction model fosters computation...

Fileti, Eudes Eterno

2015-01-01

107

Polarization effects in molecular mechanical force fields  

PubMed Central

The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594

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

2014-01-01

108

Lipid14: The Amber Lipid Force Field  

PubMed Central

The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package. The modular nature of this force field allows numerous combinations of head and tail groups to create different lipid types, enabling the easy insertion of new lipid species. The Lennard-Jones and torsion parameters of both the head and tail groups have been revised and updated partial charges calculated. The force field has been validated by simulating bilayers of six different lipid types for a total of 0.5 ?s each without applying a surface tension; with favorable comparison to experiment for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. As the derivation of this force field is consistent with the AMBER development philosophy, Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate, and small molecule force fields. PMID:24803855

2015-01-01

109

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

110

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

111

Modeling solar force-free magnetic fields  

Microsoft Academic Search

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

B. C. Low; Y. Q. Lou

1990-01-01

112

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

113

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

114

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

115

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; Höfinger, Siegfried

2013-01-01

116

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

117

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

PubMed

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

Savelyev, Alexey; MacKerell, Alexander D

2014-06-15

118

Field-regulated force by grafted polyelectrolytes  

E-print Network

Generation of mechanical force regulated by external electric field is studied both theoretically and by molecular dynamics (MD) simulations. The force arises in deformable bodies linked to the free end of a grafted polyelectrolyte chain which is exposed to electric field that favours its adsorption. We consider a few target bodies with different force-deformation relations including (i) linear and (ii) cubic dependences as well as (iii) Hertzian-like force. Such force-deformation relations mimic the behaviour of (i) coiled and (ii) stretched polymer chains, respectively, or (iii) that of a squeezed colloidal particle. The magnitude of the arising force varies over a wide interval although the electric field alters within a relatively narrow range only. The predictions of our theory agree quantitatively well with the results of numerical simulations. Both cases of zero and finite electrical current are investigated and we do not obtain substantial differences in the force generated. The phenomenon studied could possibly be utilised to design, e.g., vice-like devices to fix nano-sized objects.

Christian Seidel; Yury A. Budkov; Nikolay V. Brilliantov

2014-11-08

119

Current status of protein force fields for molecular dynamics simulations.  

PubMed

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

Lopes, Pedro E M; Guvench, Olgun; MacKerell, Alexander D

2015-01-01

120

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

121

Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations.  

PubMed

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized. PMID:25343332

Lundborg, Magnus; Lindahl, Erik

2015-01-22

122

Parallel optimization of a reactive force field for polycondensation of alkoxysilanes.  

PubMed

We have optimized a reactive force field (ReaxFF) in order to model the gelation of alkoxysilanes in bulk precursor solutions. The force field parameter set was refined using a parallelized local search algorithm. Using this approach, each processor is assigned a small list of parameters. At the end of every iteration, all parameters are updated simultaneously after being independently evaluated. In comparison to the serial evaluation of parameters, this results in faster parametrization of ReaxFF, as well as helps to prevent entrapment in local minima. The resulting model is found to reproduce hydrolysis and condensation reaction energies well. By applying the model to the condensation of silicic acid monomers at several temperatures, the activation energy of silane condensation is determined. The expected behavior, a gradual depletion of hydrolyzed silicon and growth of condensed silica clusters is observed over timescales of a few nanoseconds. The new model is also verified by modeling the early stages of clusterization in an alkoxysilane precursor solution. Both hydrolysis and condensation reactions are observed in a system containing a mixture of tetramethoxysilane, methanol, and water. PMID:25153668

Deetz, Joshua D; Faller, Roland

2014-09-18

123

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

124

eFF, a force field with electrons Julius Su and William A. Goddard III  

E-print Network

and C2H6 ionize (C-H) ionize (C-H) ionize (C-C) Leads to specific bond cleavage, cold fragments #12 ionization of C2H6 leads to C-C cleavage 1s electron ionized from C2H6 Electrons ejected from left carbon

Goddard III, William A.

125

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

126

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance  

PubMed Central

Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases. PMID:19493356

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-01-01

127

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

128

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

129

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

130

Reactive force field for electrophilic substitution at an aromatic system in twin polymerization  

NASA Astrophysics Data System (ADS)

Twin polymerization is a new synthesis concept, which enables the formation of two different macromolecular structures from organic-inorganic hybrid materials in one single process step. To gain insights into formation processes we implement a first-principles-based ReaxFF reactive force field for C/H/O/Si for the initial electrophilic substitution of an aromatic system. We show that established parametrizations that have been developed to model chemical reactions of (hydro) carbon or carbon nanotubes systems successfully cannot reproduce this reaction although they include the same chemical elements and in parts same reaction mechanisms. Thus, we develop a new parametrization being capable in reproducing this aromatic reaction properly and compare it to the established ones to identify the differences.

Schönfelder, Thomas; Friedrich, Joachim; Prehl, Janett; Seeger, Steffen; Spange, Stefan; Hoffmann, Karl Heinz

2014-08-01

131

Recent Developments and Applications of the CHARMM force fields  

PubMed Central

Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields. PMID:23066428

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

2011-01-01

132

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

133

An ab initio parametrized interatomic force field for silica  

NASA Astrophysics Data System (ADS)

We present a classical interatomic force field for liquid SiO2 which has been parametrized using the forces, stresses and energies extracted from ab initio calculations. We show how inclusion of more electronic effects in a phenomenological way and parametrization at the relevant conditions of pressure and temperature allow the creation of more accurate force fields. We compare the results of simulations with this force field both to experiment and to the results of ab initio molecular dynamics simulations and show how our procedure leads to comparisons which are greatly improved with respect to the most widely used force fields for silica.

Tangney, P.; Scandolo, S.

2002-11-01

134

Reactive Force Fields via Explicit Valency  

NASA Astrophysics Data System (ADS)

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

Kale, Seyit

135

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids  

Microsoft Academic Search

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

Swarnalatha Y. Reddy; Fabrice Leclerc; Martin Karplus

2003-01-01

136

Acceleration mechanisms 2: force-free reconnection  

Microsoft Academic Search

We suggest an unconventional view of the origin of most cosmic rays (CRs) in the universe. We propose that nearly every accelerated CR was part of the parallel current that maintains all force-free (f-f) magnetic fields. Charged particles are accelerated by the electric field E? produced by reconnection parallel to the magnetic field B. The inferred total energy in extragalactic

Stirling A. Colgate; Hui Li

2004-01-01

137

Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields  

Microsoft Academic Search

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

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

2012-01-01

138

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

Microsoft Academic Search

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

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

2006-01-01

139

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

Microsoft Academic Search

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

Feng Guo; Xinlu Cheng; Hong Zhang

2012-01-01

140

Drag forces on inclusions in classical fields with dissipative dynamics  

E-print Network

We study the drag force on uniformly moving inclusions which interact linearly with dynamical free field theories commonly used to study soft condensed matter systems. Drag forces are shown to be nonlinear functions of the inclusion velocity and depend strongly on the field dynamics. The general results obtained can be used to explain drag forces in Ising systems and also predict the existence of drag forces on proteins in membranes due to couplings to various physical parameters of the membrane such as composition, phase and height fluctuations.

Vincent Demery; D. S. Dean

2010-04-01

141

Magnetic Forces and Field Line Density  

NSDL National Science Digital Library

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

142

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

143

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

144

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

145

Molecular dynamics simulations of methane hydrate using polarizable force fields  

SciTech Connect

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

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

2007-06-14

146

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

147

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

148

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

149

Acceleration of particles in an isotropic random force field  

E-print Network

If we have a particle immersed in a field of random forces, each interaction of the particle with the field can enlarge or diminish its kinetic energy. In this work is shown that in general, for any field of random force with uniform distribution of directions, the probability to gain kinetic energy is larger that the probability to lose it. Therefore, if the particle is submitted to a great number of interactions with the force stochastic field, the final result will be that the particle will gain energy. The probability to gain energy in each interaction is Pg=1/2 (1+T/(2Po)), where T is the impulse given by the field and Po is the momentum of the particle before the interaction. The probability to lose energy in each interaction is Pl=1/2 (1-T/(2Po)).

Hector Javier Durand-Manterola

2012-04-18

150

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.

151

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

152

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 against expansion into the unbounded space. This property as a basic mechanism for solar coronal mass

Fornberg, Bengt

153

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

PubMed Central

A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed and applied to phospholipid bilayers with both choline and ethanolamine containing head groups and with both saturated and unsaturated aliphatic chains. Motivated by the current CHARMM lipid FF (C27 and C27r) systematically yielding values of the surface area per lipid that are smaller than experimental estimates and gel-like structures of bilayers well above the gel transition temperature, selected torsional, Lennard-Jones and partial atomic charge parameters were modified by targeting both quantum mechanical (QM) and experimental data. QM calculations ranging from high-level ab initio calculations on small molecules to semi-empirical QM studies on a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer in combination with experimental thermodynamic data were used as target data for parameter optimization. These changes were tested with simulations of pure bilayers at high hydration of the following six lipids: DPPC, 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC), 1,2-dilauroyl-sn-phosphatidylcholine (DLPC), 1-palmitoyl-2-oleoyl-sn-phosphatidylcholine (POPC), 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-phosphatidylethanolamine (POPE); simulations of a low hydration DOPC bilayer were also performed. Agreement with experimental surface area is on average within 2%, and the density profiles agree well with neutron and x-ray diffraction experiments. NMR deuterium order parameters (SCD) are well predicted with the new FF, including proper splitting of the SCD for the aliphatic carbon adjacent to the carbonyl for DPPC, POPE, and POPC bilayers. The area compressibility modulus and frequency dependence of 13C NMR relaxation rates of DPPC, and the water distribution of low hydration DOPC bilayers also agree well with experiment. Accordingly, the presented lipid FF, referred to as C36, allows for molecular dynamics simulations to be run in the tensionless ensemble (NPT), and is anticipated to be of utility for simulations of pure lipids systems as well as heterogeneous systems including membrane proteins. PMID:20496934

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

2010-01-01

154

Force-Field Compensation in a Manual Tracking Task  

PubMed Central

This study addresses force/movement control in a dynamic “hybrid” task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%), which is a function of the implicit accuracy of the tracking task. PMID:20567516

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

2010-01-01

155

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

156

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

157

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

158

niversal Force Field Can Uniquely Orient Non-Symmetric Parts  

Microsoft Academic Search

Recent work in parts handling advocates the investigation of a new generation of devices for parts feeding, sorting, positioning, and assembly. Unlike robot grippers, conveyor belts, or vibratory bowl feeders, these devices generate fo rce fields in which the parts move until they may reach a stable equilibrium pose. The development of the theory of programmable force fields has yielded

B. R. Donald; L. E. Kavraki; F. Lamiraux

159

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

160

Tailor-made force fields for crystal-structure prediction.  

PubMed

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom. PMID:18642947

Neumann, Marcus A

2008-08-14

161

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids  

PubMed Central

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

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

Force-field calculation and geometry of the HOOO radical.  

PubMed

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

Suma, Kohsuke; Sumiyoshi, Yoshihiro; Endo, Yasuki

2013-09-01

164

Water-Silica Force Field for Simulating Nanodevices  

PubMed Central

Amorphous silica is an inorganic material that is central for many nanotechnology appplications, such as nanoelectronics, microfluidics, and nanopore technology. In order to use molecular dynamics (MD) simulations to study the behavior of biomolecules with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet with silica served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water. PMID:17064100

Cruz-Chu, Eduardo R.; Aksimentiev, Aleksei; Schulten, Klaus

2008-01-01

165

Interaction Forces Between Multiple Bodies in a Magnetic Field  

NASA Technical Reports Server (NTRS)

Some of the results from experiments to determine the interaction forces between multiple bodies in a magnetic field are presented in this paper. It is shown how the force values and the force directions depend on the configuration of the bodies, their relative positions to each other, and the vector of the primary magnetic field. A number of efficient new automatic loading and assembly machines, as well as manipulators and robots, have been created based on the relationship between bodies and magnetic fields. A few of these patented magnetic devices are presented. The concepts involved open a new way to design universal grippers for robot and other kinds of mechanisms for the manipulation of objects. Some of these concepts can be used for space applications.

Joffe, Benjamin

1996-01-01

166

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

167

Comparison of Nonlinear Force-Free Field and Potential Field in the Quiet Sun  

Microsoft Academic Search

In this paper, a potential field extrapolation and three nonlinear force-free (NLFF) field extrapolations (optimization, direct boundary integral (DBIE), and approximate vertical integration (AVI) methods) are used to study the spatial configuration of magnetic field in the quiet Sun. It is found that differences in the computed field strengths among the three NLFF and potential fields exist in the low

S. Liu; H. Q. Zhang; J. T. Su

2011-01-01

168

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

169

PRIMO: A Transferable Coarse-grained Force Field for Proteins.  

PubMed

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

2013-08-13

170

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

171

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

172

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

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

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

175

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

176

Mitigated-force carriage for high magnetic field environments  

DOEpatents

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

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

2014-05-20

177

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

178

Amino acid similarity matrices based on force fields  

Microsoft Academic Search

Motivation: We propose a general method for deriving amino acid substitution matrices from low resolution force fields. Unlike current popular methods, the approach does not rely on evolutionary arguments or alignment of sequences or structures. Instead, residues are com- putationally mutated and their contribution to the total energy\\/score is collected. The average of these values over each position within a

Zsuzsanna Dosztányi; Andrew E. Torda

2001-01-01

179

Comparison of different force fields for the study of disaccharides  

Technology Transfer Automated Retrieval System (TEKTRAN)

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ß-cellobiose, a-maltose, and a-galabiose [a-D-Galp-(1'4)-a-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl and glycosidic linkage orientatio...

180

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

181

Energy buildup in sheared force-free magnetic fields  

NASA Technical Reports Server (NTRS)

Photospheric displacement of the footpoints of solar magnetic field lines results in shearing and twisting of the field, and consequently in the buildup of electric currents and magnetic free energy in the corona. The sudden release of this free energy may be the origin of eruptive events like coronal mass ejections, prominence eruptions, and flares. An important question is whether such an energy release may be accompanied by the opening of magnetic field lines that were previously closed, for such open field lines can provide a route for matter frozen into the field to escape the sun altogether. This paper presents the results of numerical calculations showing that opening of the magnetic field is permitted energetically, in that it is possible to build up more free energy in a sheared, closed, force-free magnetic field than is in a related magnetic configuration having both closed and open field lines. Whether or not the closed force-free field attains enough energy to become partially open depends on the form of the shear profile; the results presented compare the energy buildup for different shear profiles. Implications for solar activity are discussed briefly.

Wolfson, Richard; Low, Boon C.

1992-01-01

182

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

183

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

184

Optical forces in coupled plasmonic nanosystems: Near field and far field interaction regimes.  

PubMed

We study the forces generated by an electromagnetic field on two coupled gold nanowires at the vicinity of the plasmon resonance wavelength. Two different regimes are observed, depending on the separation distance between the wires. In the near field coupling regime, both attractive and repulsive forces can be generated, depending on and the illumination wavelength. Furthermore, at the plasmon resonance, it is possible to create forces 100 times larger than the radiation pressure. In the far field coupling regime, both particles are pushed by the incident field. However, the force amplitude applied on each wire is modulated as a function of , even for large separations. This indicates that the system behaves like a cavity and pseudo Fabry-Perot modes can be excited between the particles. The interaction of these modes with the plasmon resonances of the nanowires, determines the forces on the particles. Around the plasmon resonance wavelength, when the cavity is tuned to the incident light, forces are close to the average value corresponding to the radiation pressure of the incident field. On the other hand, when the cavity is detuned, the particles are retained or pushed anti-symmetrically. We finally study the forces applied on these nanowires in the centre of mass reference frame (CMRF) for the far field coupling regime. For any separation distance we observe equilibrium positions in the CMRF for at least one illumination wavelength. The stability of these equilibrium positions is discussed in detail. PMID:19547312

Lamothe, Elodie; Lévêque, Gaëtan; Martin, Olivier J F

2007-07-23

185

An attempt in assessing contact forces from a kinematic field  

NASA Astrophysics Data System (ADS)

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

Richefeu, Vincent; Combe, Gaël; Maurin, Raphaël

2013-06-01

186

Comparison of Nonlinear Force-Free Field and Potential Field in the Quiet Sun  

Microsoft Academic Search

In this paper, a potential field extrapolation and three nonlinear force-free (NLFF) field extrapolations (optimization, direct\\u000a boundary integral (DBIE), and approximate vertical integration (AVI) methods) are used to study the spatial configuration\\u000a of magnetic field in the quiet Sun. It is found that differences in the computed field strengths among the three NLFF and\\u000a potential fields exist in the low

S. Liu; H. Q. Zhang; J. T. Su

2011-01-01

187

Advancement of polarizable force field and its use for molecular modeling and design.  

PubMed

The most important requirement of biomolecular modeling is to deal with electrostatic energies. The electrostatic polarizability is an important part of electrostatic interaction for simulation systems. However, AMBER, CHARMM, OPLS, GROMOS, MMFF force fields etc. used in the past mostly apply fixed atomic center point charge to describe electrostatic energies, and are not sufficient for considering the influence of the electrostatic polarization. The emergence of polarizable force fields has solved this problem. In recent years, quickly developed polarizable force fields have involved a lot of fields. The chapter relating to polarizable force fields spread over several aspects. Firstly, we reviewed the history of the classical force fields and compared with polarizable force fields to elucidate the advancements of polarizable force fields. Secondly, it is introduced that the application of polarizable force fields to small molecules and biological macromolecules simulation, including molecular design. Finally, a brief development trend and perspective is given on rapidly growing polarizable force fields. PMID:25387957

Xu, Peijun; Wang, Jinguang; Xu, Yong; Chu, Huiying; Liu, Jiahui; Zhao, Meixia; Zhang, Depeng; Mao, Yingchen; Li, Beibei; Ding, Yang; Li, Guohui

2015-01-01

188

Spatial confinement of ultrasonic force fields in microfluidic channels.  

PubMed

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

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

2009-01-01

189

Direct computation of parameters for accurate polarizable force fields  

NASA Astrophysics Data System (ADS)

We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.

Verstraelen, Toon; Vandenbrande, Steven; Ayers, Paul W.

2014-11-01

190

In-plane force fields and elastic properties of graphene  

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

191

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

192

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

193

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

194

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

195

Current Status of the AMOEBA Polarizable Force Field  

PubMed Central

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models towards more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical. PMID:20136072

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

2010-01-01

196

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

197

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

198

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.

199

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

PubMed

The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described. PMID:23276161

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

2013-02-12

200

Dynamical effects in ab initio NMR calculations: Classical force fields fitted to quantum forces  

NASA Astrophysics Data System (ADS)

NMR chemical shifts for an L-alanine molecular crystal are calculated using ab initio plane wave density functional theory. Dynamical effects including anharmonicity may be included by averaging chemical shifts over an ensemble of structural configurations generated using molecular dynamics (MD). The time scales required mean that ab initio MD is prohibitively expensive. Yet the sensitivity of chemical shifts to structural details requires that the methodologies for performing MD and calculating NMR shifts be consistent. This work resolves these previously competing requirements by fitting classical force fields to reproduce ab initio forces. This methodology is first validated by reproducing the averaged chemical shifts found using ab initio molecular dynamics. Study of a supercell of L-alanine demonstrates that finite size effects can be significant when accounting for dynamics.

Robinson, Mark; Haynes, Peter D.

2010-08-01

201

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

202

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

203

Comparison of Nonlinear Force-free Field and Potential Field in the Quiet Sun  

E-print Network

In this paper, a potential field extrapolation and three nonlinear force-free (NLFF) field extrapolations (optimization, direct boundary integral (DBIE) and approximate vertical integration (AVI) methods) are used to study the spatial configuration of magnetic field in the quiet Sun. It is found that the strength differences between the three NLFF and potential fields exist in the low layers. However, they tend to disappear as the height increases, which are of the order of 0.1 G when the height exceeds $\\sim$ 2000 km above the photosphere. The absolute azimuth difference between one NLFF field and the potential field is as follows: for the optimization field, it decreases evidently as the height increases; for the DBIE field, it almost keeps constant and shows no significant change as the height increases; for the AVI field, it increases slowly as the height increases. The analysis shows that the reconstructed NLFF fields deviate significantly from the potential field in the quiet Sun.

S., Liu; T, Su J

2014-01-01

204

Continuum Polarizable Force Field within the Poisson-Boltzmann Framework  

PubMed Central

We have developed and tested a complete set of nonbonded parameters for a continuum polarizable force field. Our analysis shows that the new continuum polarizable model is consistent with B3LYP/cc-pVTZ in modeling electronic response upon variation of dielectric environment. Comparison with experiment also shows that the new continuum polarizable model is reasonable, with similar accuracy as B3LYP/cc-pVTZ in reproduction of dipole moments of selected organic molecules in the gas phase. We have further tested the validity to interchange the Amber van der Waals parameters between the explicit and continuum polarizable force fields with a series of dimers. It can be found that the continuum polarizable model agrees well with MP2/cc-pVTZ, with deviations in dimer binding energies less than 0.9 kcal/mol in the aqueous dielectric environment. Finally we have optimized atomic cavity radii with respect to experimental solvation free energies of 177 training molecules. To validate the optimized cavity radii, we have tested these parameters against 176 test molecules. It is found that the optimized PB atomic cavity radii transfer well from the training set to the test set, with an overall root-mean-squared deviation of 1.30 kcal/mol, unsigned average error of 1.07 kacl/mol, and correlation coefficient of 92% for all 353 molecules in both the training and test sets. Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework. PMID:18507452

Tan, Yu-Hong; Tan, Chunhu; Wang, Junmei; Luo, Ray

2008-01-01

205

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

PubMed Central

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

2011-01-01

206

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

207

Vector field statistical analysis of kinematic and force trajectories.  

PubMed

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

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

2013-09-27

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

Massive-Field Approach to the Scalar Self Force in Curved Spacetime  

E-print Network

We derive a new regularization method for the calculation of the (massless) scalar self force in curved spacetime. In this method, the scalar self force is expressed in terms of the difference between two retarded scalar fields: the massless scalar field, and an auxiliary massive scalar field. This field difference combined with a certain limiting process gives the expression for the scalar self-force. This expression provides a new self force calculation method.

Eran Rosenthal

2004-10-05

210

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

Microsoft Academic Search

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

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

1995-01-01

211

Evolution of Magnetic Field in AR 5747 and Its Approximation as a Linear Force Free Field  

E-print Network

The evolution of nonpotential characteristics of magnetic fields in AR 5747 is presented using Mees Solar Observatory magnetograms taken on Oct. 20, 1989 to Oct. 22, 1989. The active region showed such violent flaring activities during the observational span that strong X-ray flares took place including a 2B/X3 flare. The magnetogram data were obtained by the Haleakala Stokes Polarimeter which provides simultaneous Stokes profiles of the Fe I doublet 6301.5 and 6302.5. A nonlinear least square method was adopted to derive the magnetic field vectors from the observed Stokes profiles and a multi-step ambiguity solution method was employed to resolve the 180 degree ambiguity. From the ambiguity-resolved vector magnetograms, we have derived a set of physical quantities characterizing the field configuration, which are magnetic flux, vertical current density, magnetic shear angle, angular shear, magnetic free energy density and a measure of magnetic field discontinuity MAD (Maximum Angular Difference between two adjacent field vectors). In our results, all the physical parameters decreased with time, which implies that the active region was in a relaxation stage of its evolution. To examine the force-free characteristics of the field, we calculated the integrated Lorentz force and and also compared the longitudinal field component with the corresponding vertical current density. In this investigation, we found that the magnetic field in this active region was approximately linearly force-free throughout the observing period. The time variation of the linear force-free coefficient is consistent with the evolutionary trend of other nonpotentiality parameters. This suggests that the linear force-free coefficient could be a good indicator of the evolutionary status of active regions.

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

1999-10-05

212

A new spectroscopic molecular mechanics force field. Parameters for proteins  

NASA Astrophysics Data System (ADS)

We present the development of a new spectroscopic molecular mechanics potential for proteins. SPASIBA merges the torsional, van der Waals, electrostatic, and hydrogen bond potentials of AMBER with the Urey-Bradley-Shimanouchi terms for bond lengths and bond angles. To begin, SPASIBA was consistently parametrized to structural, energies, and vibrational frequency data of model compounds representative of the 16 nonaromatic acids: n-alkanes, alcohols, acids, ethyl methyl sulfide, methyl sulfide in water, ethanethiol, dimethyl disulfide, guanidium ion, propionamide, N-methylacetamide, N-methylisobutyramide, and N-isopropylacetamide. The parameters were then transferred to N-acetyl-X methylamides (where X=Gly, L-Ala, L-Pro), the L-Leu, L-Cys, and L-Thr amino acids blocked by the carboxylate and ammonium ions, and the right-handed deca-alanine and Gly-L-Pro-Gly-Gly peptides. Results show that SPASIBA reproduces vibrational frequencies (with much higher accuracy than present molecular mechanics potentials), as well as potential energy distributions of normal modes. For the 532 fundamental frequencies considered for refining the force field, the mean frequency error is 13 cm-1. This force field, which can be incorporated in molecular dynamics simulations, is also found to provide useful insights into the conformation/vibrational spectrum relationships. This ability is illustrated on the Gly and L-Ala dipeptides, as well as the polypeptides.

Derreumaux, Philippe; Vergoten, Gérard

1995-06-01

213

Reactive force field potential for carbon deposition on silicon surfaces  

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

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

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

PubMed

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

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

2013-08-15

217

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

2014-11-14

218

A density functional tight binding/force field approach to the interaction of molecules with rare gas clusters: Application to (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} clusters  

SciTech Connect

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 (C{sub 6}H{sub 6}){sup +/0}Ar{sub n} 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 [Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse (France)] [Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse (France)

2014-01-21

219

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

220

Reactive force fields for surface chemical reactions: A case study with hydrogen dissociation on Pd surfaces.  

PubMed

An approach based on reactive force fields is applied to the parametrization of potential energy surface (PES) for chemical reactions on surfaces with a benchmark system, H(2)/Pd(111). We show that a simple reactive force field based on the second moment approximation does not allow for obtaining reliable results of reaction dynamics for the considered system. With a more elaborate reactive force field, i.e., reactive bond order (REBO) force field, we succeeded in obtaining a reliable PES for H(2)/Pd(111). The accuracy of the constructed REBO force field is carefully checked through various tests including the comparison not only between energies calculated with density functional theory and those with REBO force field but also between the available results of ab initio molecular dynamics simulations and those with our force field. Moreover, our REBO force field is endowed with some transferability since the force field constructed with a database containing only information on H(2)/Pd(111) allows for obtaining also accurate results for H(2)/Pd(100) and qualitatively correct results for H(2)/Pd(110) without any refitting. With the help of our reactive force field, the molecular dynamics simulation for the dissociation of H(2) on the considered Pd surfaces is speeded up by five orders of magnitude compared to ab initio molecular dynamics method. The demonstrated reliability and the very high computational efficiency of reactive force fields open extremely attractive perspectives for studying large-scale complex reacting systems. PMID:20078177

Xiao, Y; Dong, W; Busnengo, H F

2010-01-01

221

Enhancing field emission from a carbon nanotube array by lateral control of electrodynamic force field  

Microsoft Academic Search

Fluctuation of field emission current from carbon nanotubes (CNTs) poses certain difficulties for their use in nano-biomedical X-ray devices and imaging probes. This problem arises due to deformation of the CNTs due to electrodynamic force field and electron–phonon interaction. It is of great importance to have precise control of emitted electron beams very near the CNT tips. In this paper,

D. Roy Mahapatra; S. V. Anand; N. Sinha; R. V. N. Melnik

2009-01-01

222

Local field loop measurements by magnetic force microscopy  

NASA Astrophysics Data System (ADS)

Magnetic force microscopy (MFM) is a valuable technique to investigate the reversal mechanisms of the magnetization in micrometric and sub-micrometric-patterned thin films that cannot be studied by means of magneto-optical methods because of their limited resolution. However, acquiring tens or hundreds of images consecutively at different applied magnetic fields is often impossible or impractical. Therefore, a field-dependent MFM-derived technique is discussed and applied on square and circular dots of different materials (Ni80Fe20, Co67Fe4Si14.5B14.5, Fe78Si9B13) having sizes ranging from 800 nm to 20 µm. Experimental local hysteresis loops are obtained by properly analysing the phase signal of the MFM along a selected profile of the studied patterned structure, as a function of the applied magnetic field. Characteristic features of the magnetization process, such as vortex nucleation and expulsion, transition from C-state to saturated state or domain wall motion in Landau-like domain configuration are identified, and their evolution with the applied field is followed. The necessity to combine experimental and theoretical analyses is addressed by micromagnetic simulations on a model system (a Ni80Fe20 square dot with a lateral size of 800 nm), comparable to one of the studied samples. The agreement between experimental and simulated MFM maps, at different applied fields, and hysteresis loops provides the necessary validation for the technique. Additionally, the simulations have been proven to be necessary to understand the magnetization reversal processes occurring in the studied sub-micrometric structures and to associate them with characteristic features of the hysteresis loops measured with the proposed technique.

Coïsson, Marco; Barrera, Gabriele; Celegato, Federica; Enrico, Emanuele; Manzin, Alessandra; Olivetti, Elena S.; Tiberto, Paola; Vinai, Franco

2014-08-01

223

On the Use of Quartic Force Fields in Variational Calculations  

NASA Technical Reports Server (NTRS)

The use of quartic force fields (QFFs) has been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this paper we outline and discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine(-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can effectively describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods. Cases are referenced where variational computations coupled with transformed QFFs produce accuracies compared to experiment for fundamental frequencies on the order of 5 cm(exp -1) and often as good as 1 cm(exp -1).

Fortenberry, Ryan C.; Huang, Xinchuan; Yachmenev, Andrey; Thiel, Walter; Lee, Timothy J.

2013-01-01

224

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

225

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

226

An accurate ab initio quartic force field for ammonia  

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

227

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

228

Molecular dynamics simulations of methane hydrate using polarizable force fields  

SciTech Connect

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

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

2007-03-01

229

instructions HisTrap FF crude,  

E-print Network

· p1 instructions HisTrap FF crude, 1 ml and 5 ml i 11-0012-38 Edition AA HisTrapTM FF crude, such as degradation and oxidation of sensitive target proteins, and is therefore of great importance. HisTrap FF crude properties HisTrap FF crude 1-ml and 5-ml columns are prepacked with the affinity medium Ni Sepharose 6 Fast

Lebendiker, Mario

230

Comparison of Nonlinear Force-Free Field and Potential Field in the Quiet Sun  

NASA Astrophysics Data System (ADS)

In this paper, a potential field extrapolation and three nonlinear force-free (NLFF) field extrapolations (optimization, direct boundary integral (DBIE), and approximate vertical integration (AVI) methods) are used to study the spatial configuration of magnetic field in the quiet Sun. It is found that differences in the computed field strengths among the three NLFF and potential fields exist in the low layers. However, they tend to disappear as the height increases, and the differences are of the order of 0.1 gauss when the height exceeds ? 2000 km above the photosphere. The difference in azimuth angles between each NLFF field model and the potential field is as follows: for the optimization field, it decreases evidently as the height increases; for the DBIE field, it almost stays constant and shows no significant change as the height increases; for the AVI field, it increases slowly as the height increases. Our analysis shows that the reconstructed NLFF fields deviate significantly from the potential field in the quiet Sun.

Liu, S.; Zhang, H. Q.; Su, J. T.

2011-05-01

231

Variations in Gravitational Field, Tidal Force, Electromagnetic Waves and Earthquakes  

NASA Astrophysics Data System (ADS)

This paper is the report on an experiment carried out between the month of December 2009 and the month of April 2010 between the Venetian Lagoon and the Northern Apennines in Italy, to check on a potential relationship between earthquakes and variations in the local gravitational field, the effect on the tide exercised by the interaction between the moon and the Sun, the appearance of anomalous light effects in the atmosphere ("Earth lights"), and the emission of radio waves caused by stresses in the Earth's crust. The cases studied show that there is indeed some concomitance between the periodic rising and falling of the sea level and the terrestrial tide effect, due to the gravitational attraction of the moon and sun on the Earth. In fact, changes in the local force of gravity coincided with the cycle of high and low tides and, in certain cases, with a variation in the electromagnetic field that preceded the occurrence of a seismic event by just a few hours. The o! bservations in the article are limited to the magnitude range discussed in the paper.

Strasser, Valentino

2010-12-01

232

Ordered behaviour in force-free magnetic fields  

NASA Astrophysics Data System (ADS)

Conditions in order that the trajectories of a force-free vectorfield lie on the level sets of a given function are studied. Force-free vectorfields symmetric under translations, rotations and roto-translations are also considered.

Gonzalez-Gascon, F.; Peralta-Salas, D.

2001-12-01

233

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method.  

PubMed

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF. PMID:16851738

Izvekov, Sergei; Voth, Gregory A

2005-04-14

234

Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields  

PubMed Central

Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM, GROMOS, OPLS, etc. Thus the model resolves the outstanding problem of incompatibility.

Leontyev, Igor V.

2014-01-01

235

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

PubMed Central

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

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

2013-01-01

236

Coarse-grained force fields for molecular simulations.  

PubMed

Molecular dynamics (MD) simulations at the atomic scale are a powerful tool to study the structure and dynamics of model biological systems. However, because of their high computational cost, the time and length scales of atomistic simulations are limited. Biologically important processes, such as protein folding, ion channel gating, signal transduction, and membrane remodeling, are difficult to investigate using atomistic simulations. Coarse-graining reduces the computational cost of calculations by reducing the number of degrees of freedom in the model, allowing simulations of larger systems for longer times. In the first part of this chapter we review briefly some of the coarse-grained models available for proteins, focusing on the specific scope of each model. Then we describe in more detail the MARTINI coarse-grained force field, and we illustrate how to set up and run a simulation of a membrane protein using the Gromacs software package. We explain step-by-step the preparation of the protein and the membrane, the insertion of the protein in the membrane, the equilibration of the system, the simulation itself, and the analysis of the trajectory. PMID:25330962

Barnoud, Jonathan; Monticelli, Luca

2015-01-01

237

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

238

The stability properties of cylindrical force-free fields - Effect of an external potential field  

NASA Technical Reports Server (NTRS)

A large-scale potential field with an embedded smaller-scale force-free structure gradient x B equals alpha B is studied in cylindrical geometry. Cases in which alpha goes continuously from a constant value alpha 0 on the axis to zero at large r are considered. Such a choice of alpha (r) produces fields which are realistic (few field reversals) but not completely stable. The MHD-unstable wavenumber regime is found. Since the considered equilibrium field exhibits a certain amount of magnetic shear, resistive instabilities can arise. The growth rates of the tearing mode in the limited MHD-stable region of k space are calculated, showing time-scales much shorter than the resistive decay time.

Chiuderi, C.; Einaudi, G.; Ma, S. S.; Van Hoven, G.

1980-01-01

239

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

240

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

241

Current Status of the AMOEBA Polarizable Force Field Jay W. Ponder and Chuanjie Wu  

E-print Network

#12;Current Status of the AMOEBA Polarizable Force Field Jay W. Ponder and Chuanjie Wu Department that should allow more accurate description of molecular properties. The recently introduced AMOEBA force, it has only received relatively limited validation, which we address here. We show that the AMOEBA force

Ponder, Jay

242

The lift forces acting on a submarine composite pipeline in a wave-current coexisting field  

SciTech Connect

The composite pipeline is defined as a main big pipe composed with one or several small pipes. The flow behavior around a submarine composite pipeline is more complicated than that around a single submarine pipeline. A series model test of composite pipelines in a wave-current coexisting field was conducted by the authors. Both in-line and lift forces were measured, and the resultant forces are also analyzed. The results of lift forces and resultant forces are reported in this paper. It is found that the lift force coefficients for composite pipelines are well related to the KC number. The lift force coefficients in an irregular wave-current coexisting field are smaller than those in regular wave-current coexisting field. The frequency of lift force is usually the twice or higher than the wave frequency. It is indicated by the authors` test that the resultant forces are larger than in-line forces (horizontal forces) about 10 to 20 percent. The effect of water depth was analyzed. Finally, the relationship between lift force coefficient C{sub l} and KC number, the statistical characteristics of lift and resultant forces, are given in this paper, which may be useful for practical engineering application.

Li, Y.C.; Zhang, N.C. [Dalian Univ. of Technology (China). Dept. of Civil Engineering

1994-12-31

243

Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force field Parameters for Calcite  

E-print Network

ARTICLES Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force field Parameters for Calcite Sungu Hwang, Mario Blanco, and William A. Goddard III* Materials and Process, 2001 We report a new force field for calcite suitable to study scale formation and squeeze treatments

Goddard III, William A.

244

Author's personal copy A reactive force-field for Zirconium and Hafnium Di-Boride  

E-print Network

Author's personal copy A reactive force-field for Zirconium and Hafnium Di-Boride Afif Gouissem reactions High temperature materials a b s t r a c t Zirconium and Hafnium Di-Boride are the two major. Introduction The aim of this study is to develop transferable reactive force fields for Zirconium and Hafnium

Sharma, Pradeep

245

A Single Universal Force Field Can Uniquely Orient Non-Symmetric Parts  

Microsoft Academic Search

Recent work in parts handling advocates the investigation of a new generation of devices for parts feeding, sorting, positioning, and assembly. Unlike robot grippers, conveyor belts, or vibratory bowl feeders, these devices generate force fields in which the parts move until they may reach a stable equilibrium pose. The development of the theory of programmable force fields has yielded a

B. R. Donald; L. E. Kavraki; F. Lamiraux

1999-01-01

246

Part orientation with one or two stable equilibria using programmable force fields  

Microsoft Academic Search

Programmable force fields are an abstraction to rep- resent a new class of devices for distributed, nonprehensile manip- ulation for applications in parts feeding, sorting, positioning, and assembly. Unlike robot grippers, conveyor belts, or vibratory bowl feeders, these devices generate force vector fields in which the parts move until they may reach a stable equilibrium pose. Recent research in the

Karl-Friedrich Böhringer; Bruce Randall Donald; Lydia E. Kavraki; Florent Lamiraux

2000-01-01

247

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins Jiajing Zhang,  

E-print Network

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins Yue Shi, Zhen Xia, Jiajing Zhang of the AMOEBA (atomic multi- pole optimized energetics for biomolecular simulation) force field for proteins is presented. The current version (AMOEBA- 2013) utilizes permanent electrostatic multipole moments through

Ponder, Jay

248

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field  

E-print Network

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field Jin Yu Xiang and Jay polarizable force field for transition-metal ions was developed based on AMOEBA and the angular overlap model). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number

Ponder, Jay

249

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

250

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

251

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

252

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

PubMed Central

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

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

253

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

Microsoft Academic Search

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

N. Seehafer

1978-01-01

254

Development of Field Excavator with Embedded Force Measurement  

NASA Technical Reports Server (NTRS)

A semi-intelligent excavation mechanism was developed for use with the NASA-built Centaur 2 rover prototype. The excavator features a continuously rotatable large bucket supported between two parallel arms, both of which share a single pivot axis near the excavator base attached to the rover. The excavator is designed to simulate the collection of regolith, such as on the Moon, and to dump the collected soil into a hopper up to one meter tall for processing to extract oxygen. Because the vehicle can be autonomous and the terrain is generally unknown, there is risk of damaging equipment or using excessive power when attempting to extract soil from dense or rocky terrain. To minimize these risks, it is critical for the rover to sense the digging forces and adjust accordingly. It is also important to understand the digging capabilities and limitations of the excavator. This paper discusses the implementation of multiple strain gages as an embedded force measurement system in the excavator's arms. These strain gages can accurately measure and resolve multi-axial forces on the excavator. In order to validate these sensors and characterize the load capabilities, a series of controlled excavation tests were performed at Glenn Research Center with the excavator at various depths and cut angles while supported by a six axis load cell. The results of these tests are both compared to a force estimation model and used for calibration of the embedded strain gages. In addition, excavation forces generated using two different types of bucket edge (straight vs. with teeth) were compared.

Johnson, K.; Creager, C.; Izadnegahdar, A.; Bauman, S.; Gallo, C.; Abel, P.

2012-01-01

255

Motor cortex single-neuron and population contributions to compensation for multiple dynamic force fields.  

PubMed

To elucidate how primary motor cortex (M1) neurons contribute to the performance of a broad range of different and even incompatible motor skills, we trained 2 monkeys to perform single-degree-of-freedom elbow flexion/extension movements that could be perturbed by a variety of externally-generated force fields. Fields were presented in a pseudo-random sequence of trial blocks. Different computer monitor background colors signalled the nature of the force field throughout each block. There were five different force fields: null field without perturbing torque (N), assistive (V-) and resistive (V+) viscous fields proportional to velocity, a resistive elastic force field (E+) proportional to position and a resistive visco-elastic field (VE) that was the linear combination of V+ and E+. After the monkeys were extensively trained in the 5 field conditions, neural recordings were subsequently made in M1 contralateral to the trained arm. Many caudal M1 neurons altered their activity systematically across most or all of the force fields in a manner that was appropriate to contribute to the compensation for each of the fields. The net activity of the entire sample population likewise provided a predictive signal about the differences in the time course of the external forces encountered during the movements across all force conditions. The neurons showed a broad range of sensitivities to the different fields and there was little evidence of a modular structure by which subsets of M1 neurons were preferentially activated during movements in specific fields or combinations of fields. PMID:25339714

Addou, Touria; Krouchev, Nedialko; Kalaska, John F

2014-10-22

256

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

257

Error analysis regarding the calculation of nonlinear force-free field  

NASA Astrophysics Data System (ADS)

Magnetic field extrapolation is an alternative method to study chromospheric and coronal magnetic fields. In this paper, two semi-analytical solutions of force-free fields (Low and Lou in Astrophys. J. 352:343, 1990) have been used to study the errors of nonlinear force-free (NLFF) fields based on force-free factor ?. Three NLFF fields are extrapolated by approximate vertical integration (AVI) Song et al. (Astrophys. J. 649:1084, 2006), boundary integral equation (BIE) Yan and Sakurai (Sol. Phys. 195:89, 2000) and optimization (Opt.) Wiegelmann (Sol. Phys. 219:87, 2004) methods. Compared with the first semi-analytical field, it is found that the mean values of absolute relative standard deviations (RSD) of ? along field lines are about 0.96-1.19, 0.63-1.07 and 0.43-0.72 for AVI, BIE and Opt. fields, respectively. While for the second semi-analytical field, they are about 0.80-1.02, 0.67-1.34 and 0.33-0.55 for AVI, BIE and Opt. fields, respectively. As for the analytical field, the calculation error of <| RSD|> is about 0.1˜0.2. It is also found that RSD does not apparently depend on the length of field line. These provide the basic estimation on the deviation of extrapolated field obtained by proposed methods from the real force-free field.

Liu, S.; Zhang, H. Q.; Su, J. T.

2012-02-01

258

Forces acting on a particle in a concentration gradient under an externally applied oscillating electric field  

NASA Astrophysics Data System (ADS)

We report a force field on a particle in a concentration (conductivity) gradient under an externally applied oscillating electric field. The conductivity gradient was established through integrated microcapillaries bridging high- and low-conductivity streams in dedicated microchannels. Particles in low-conductivity electrolyte were observed to experience a strong force with the application of an oscillating field and pulled to the microcapillary openings where they were held against the flow. Particle trapping was accompanied by a concurrent electrolyte injection from high- to low-conductivity channel, triggered with the externally applied field and further contributed to the conductivity gradient near the trapping sites. We experimentally evaluated the force dependence on the magnitude and frequency of the excitation field for 10 ?m polystyrene particles immersed at various conductivity levels. The experiments suggest that the observed force cannot be simply explained by dielectrophoresis or diffusiophoresis alone and further requires the consideration of a so-called concentration polarization force. This force has been rather recently postulated based on a theoretical treatment and yet to be experimentally validated. Using the theoretical treatment of this force, together with fluidic drag and diffusiophoresis, we correctly predicted trapping trajectories of particles based on a simultaneous solution of Poisson-Nernst-Planck and Stokes equations. The predicted and measured trapping velocities were found in reasonable agreement (within a factor of <1.6), suggesting that the consideration of the concentration polarization force is necessary for describing the observed particle behavior.

Luo, Yuan; Yobas, Levent

2014-09-01

259

The influence of centrifugal forces on the B field structure of an axially symmetric equilibrium magnetosphere  

NASA Technical Reports Server (NTRS)

A model is presented of an axially symmetric pole-on magnetosphere in MHD force balance, in which both plasma thermal pressure gradients and centrifugal force are taken into account. Assuming that planetary rotation leads to differentially rotating magnetotail field lines, the deformation of magnetotail field lines under the influence of both thermal plasma pressure and centrifugal forces was calculated. Analytic solutions to the Grad-Shafranov equation are presented, which include the centrifugal force term. It is shown that the nonrotational magnetosphere with hot thermal plasma leads to a field configuration without a toroidal B(phi) component and without field-aligned Birkeland currents. The other extreme, a rapidly rotating magnetosphere with cold plasma, leads to a configuration in which plasma must be confined within a thin disk in a plane where the radial magnetic field component B(r) vanishes locally.

Ye, Gang; Voigt, Gerd-Hannes

1989-01-01

260

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

E-print Network

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

Eran Rosenthal

2004-10-05

261

Shape-induced force fields in optical trapping  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

262

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule  

NASA Astrophysics Data System (ADS)

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of Gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Pendás, A. Martín; Hernández-Trujillo, J.

2012-10-01

263

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

Microsoft Academic Search

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

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

2010-01-01

264

Bifurcation of force-free solar magnetic fields: A numerical approach  

Microsoft Academic Search

Numerical calculations of two-dimensional force-free fields as models of solar active regions are presented. For a given ‘toroidal’ component of the photospheric magnetic field two branches of solutions are numerically obtained which merge at the critical point of maximum allowed toroidal magnetic field. Depending on boundary conditions magnetic islands may or may not form. The results are discussed with respect

Klaus Jockers

1978-01-01

265

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

266

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

NASA Technical Reports Server (NTRS)

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

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

1997-01-01

267

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

268

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

NASA Astrophysics Data System (ADS)

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

Villegas, A.; Diez, F. J.

2014-04-01

269

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

270

Drag force in SYM plasma with B field from AdS/CFT  

E-print Network

We investigate drag force in a thermal plasma of N=4 super Yang-Mills theory via both fundamental and Dirichlet strings under the influence of non-zero NSNS $B$-field background. In the description of AdS/CFT correspondence the endpoint of these strings correspondes to an external monopole or quark moving with a constant electromagnetic field. We demonstrate how the configuration of string tail as well as the drag force obtains corrections in this background.

Toshihiro Matsuo; Dan Tomino; Wen-Yu Wen

2006-08-10

271

Improving the Q2MM method for transition state force field modeling.  

PubMed

The Quantum-to-molecular mechanics method (Q2MM) for converting quantum mechanical transition states (TSs) to molecular mechanical minima has been modified to allow a fit to the "natural" reaction mode eigenvalue. The resulting force field gives an improved representation of the energy curvature at the TS, but can potentially give false responses to steric interactions. Ways to address this problem while staying close to the "natural" TS force field are discussed. © 2014 Wiley Periodicals, Inc. PMID:25430788

Limé, Elaine; Norrby, Per-Ola

2015-02-01

272

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

273

Field-induced forces at dielectric interfaces as a possible mechanism of RF hearing effects  

Microsoft Academic Search

A possible mechanism for effects of microwave radiation on the auditory system is the generation of field-induced forces at\\u000a interfaces that divide materials of dissimilar electrical properties. A general expression for these “Maxwell stresses” is\\u000a derived and then used to calculate the approximate magnitude of field-induced force within the organ of Corti during microwave\\u000a exposure. Comparison of the results with

William T. Joines; Blake S. Wilson

1981-01-01

274

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.

275

Refining classical force fields for ionic liquids: theory and application to [MMIM][Cl].  

PubMed

Most of the force fields for ionic liquids cannot properly describe statics and dynamics. In this context, we propose an efficient method to adapt force fields, the basis of any classical molecular dynamics simulation. In the parameterisation process, a target function is minimized by a conjugate gradient based approach that vastly accelerates the tuning of the force field parameters through parallelization. As the description of the dynamics is captured in the parameterisation of the partial charges, we fit the short range parameters using only static properties, thus avoiding long simulations for the force field refinement. In the validation of the final parameterisation, the force field gives a good description of the dynamics in terms of the conductivity, especially in the temperature regime where the reference properties are matched very accurately. This method is sufficiently general and easily altered to fit an arbitrary set of reference properties, such that it can be considered for the construction of a versatile, transferable force field for ionic liquids. PMID:23262645

Dommert, Florian; Holm, Christian

2013-02-14

276

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

277

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

PubMed

A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange. PMID:25554163

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

2014-12-28

278

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...

Heffernan, Anna

2014-01-01

279

Asymptotic analysis of force-free magnetic fields of cylindrical symmetry  

NASA Technical Reports Server (NTRS)

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

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

1995-01-01

280

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

281

Blunt force cranial trauma in the Cambodian killing fields.  

PubMed

In this paper we present a unique pattern of blunt force cranial trauma that was observed in 10 of a sample of 85 crania from a Cambodian skeletal collection comprised of Khmer Rouge victims. Initial examination of the trauma, which presents as substantial damage to the occipital with fractures extending to the cranial base, suggested the pattern was classifiable as a basilar or ring fracture. However, further investigation, including trauma analysis and historical research, revealed that this fracture type is distinctive from basilar and ring fractures. Historical data indicate that a particular execution method was the likely source of the trauma. Recognition of this trauma pattern is significant because it exemplifies the distinct fracture configuration resulting from an apparently categorical and methodical execution technique. Identification of this fracture type could potentially assist forensic investigators in the recognition of specific methods of murder or execution. PMID:17018075

Ta'ala, Sabrina C; Berg, Gregory E; Haden, Kathryn

2006-09-01

282

Electrodynamics as a particular case of the most general relativistic force field  

E-print Network

A new approach to classical electrodynamics is presented, showing that it can be regarded as a particular case of the most general relativistic force field. In particular, at first it is shown that the structure of the Lorentz force comes directly from the structure of the three-force transformation law, and that E and B fields can be defined, which in general will depend not only on the space-time coordinate, but also on the velocity of the body acted upon. Then it is proved that these fields become independent from the body velocity if the force field propagates throughout space at the relativistic speed limit c. Finally, field sources are introduced by defining them as perturbations of the field itself, obtaining a generalization of Maxwell equations which allow to express the field in terms sources, if these last are known a priori. Electrodynamics follows simply assuming, in addition to the postulate of field propagation at the speed c, that scalar sources of the B field are missing and that electric charge is an invariant characteristic of matter, acting both as source of the field and sensing property. The presented approach may have valuable didactic effectiveness in showing that space-time structure, as defined by Special Relativity postulates, is the ultimate responsible of the structure of electrodynamics laws.

Stefano Re Fiorentin

2009-05-21

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 O2 on Pt(111) is an activated process at non-zero coverages, with an activation energy that monotonically increases with coverage. At a coverage of 0.25 ML, a highly ordered p(2 × 2) adlayer is found, in agreement with several low-energy electron diffraction observations. Isotherms obtained from the GCMC simulations compare qualitatively and quantitatively well with previous DFT-based state diagrams, but are in disagreement with the experimental data sets available. ReaxFF GCMC simulations at very high coverages show that O atoms prefer to bind in fcc hollow sites, at least up to 0.8 ML considered in the present work. At moderate coverages, little to no disorder appears in the Pt lattice. At high coverages, some Pt atoms markedly protrude out of the surface plane. This observation is in qualitative agreement with recent STM images of an oxygen covered Pt surface. The use of the GCMC technique based on a transferable potential is particularly valuable to produce more realistic systems (adsorbent and adsorbate) to be used in subsequent dynamical simulations (Molecular Dynamics) to address recombination reactions (via either Eley-Rideal or Langmuir-Hinshelwood mechanisms) on variously covered surfaces. By using GCMC and Molecular Dynamics simulations, the ReaxFF force field can be a valuable tool for understanding heterogeneous catalysis on a solid surface. Finally, the use of a reactive potential is a necessary requirement to investigate problems where dissociative adsorption occurs, as typical of many important catalytic processes.

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

2011-12-01

284

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

285

BIOREMEDIATION FIELD EVALUATION - HILL AIR FORCE BASE, UTAH  

EPA Science Inventory

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

286

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

287

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

288

MAGNETIC HELICITY OF SELF-SIMILAR AXISYMMETRIC FORCE-FREE FIELDS  

SciTech Connect

In this paper, we continue our theoretical studies addressing the possible consequences of magnetic helicity accumulation in the solar corona. Our previous studies suggest that coronal mass ejections (CMEs) are natural products of coronal evolution as a consequence of magnetic helicity accumulation and that the triggering of CMEs by surface processes such as flux emergence also have their origin in magnetic helicity accumulation. Here, we use the same mathematical approach to study the magnetic helicity of axisymmetric power-law force-free fields but focus on a family whose surface flux distributions are defined by self-similar force-free fields. The semi-analytical solutions of the axisymmetric self-similar force-free fields enable us to discuss the properties of force-free fields possessing a huge amount of accumulated magnetic helicity. Our study suggests that there may be an absolute upper bound on the total magnetic helicity of all bipolar axisymmetric force-free fields. With the increase of accumulated magnetic helicity, the force-free field approaches being fully opened up with Parker-spiral-like structures present around a current-sheet layer as evidence of magnetic helicity in the interplanetary space. It is also found that among the axisymmetric force-free fields having the same boundary flux distribution, the one that is self-similar is the one possessing the maximum amount of total magnetic helicity. This gives a possible physical reason why self-similar fields are often found in astrophysical bodies, where magnetic helicity accumulation is presumably also taking place.

Zhang Mei [Key Laboratory of Solar Activity, National Astronomical Observatory, Chinese Academy of Sciences, Datun Road A20, Chaoyang District, Beijing 100012 (China); Flyer, Natasha [Institute for Mathematics Applied to Geosciences, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307 (United States); Low, Boon Chye [High Altitude Observatory, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307 (United States)

2012-08-10

289

Surface properties of liquid mercury: a comparison of density-dependent and density-independent force fields  

E-print Network

The surface properties of liquid mercury (Hg) at a temperature of 293 K are investigated by classical Molecular Dynamics simulation using density-independent (DI) and density-dependent (DD) force fields. The latter force fields were introduced to improve the description of surface properties. Both force fields yield lower values of the surface tension in comparison to experimental data. Moreover, the density-dependent force field results in an anomalous thermodynamic behavior. These findings are rationalized by liquid-state theory. An optimized, density-independent force field is proposed that yields a higher surface tension and, at the same time, provides an accurate description of the liquid-vapor coexistence.

A. Iakovlev; D. Bedrov; M. Müller

2014-12-08

290

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

291

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

PubMed

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

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

2014-08-01

292

Theory and numerical calculation of the acoustic field exerted by eddy-current forces  

Microsoft Academic Search

The equations for calculating the acoustic field produced within a nonmagnetic metal by interaction of eddy currents with a static magnetic field were obtained on the assumptions that: (1) an ultrasonic wave is generated by the electromagnetic force through classical and macroscopic phenomena; (2) the electric, magnetic, and elastic properties of the metal are linear, isotropic, and homogeneous throughout the

K. Kawashima

1976-01-01

293

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.

294

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

295

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

Microsoft Academic Search

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

N. Seehafer

1978-01-01

296

Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force  

PubMed Central

A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends non-trivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability, and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation. PMID:23853423

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

2013-01-01

297

POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins.  

PubMed

Previously, we reported development of a fast polarizable force field and software named POSSIM (POlarizable Simulations with Second order Interaction Model). The second-order approximation permits the speed up of the polarizable component of the calculations by ca. an order of magnitude. We have now expanded the POSSIM framework to include a complete polarizable force field for proteins. Most of the parameter fitting was done to high-level quantum mechanical data. Conformational geometries and energies for dipeptides have been reproduced within average errors of ca. 0.5 kcal/mol for energies of the conformers (for the electrostatically neutral residues) and 9.7° for key dihedral angles. We have also validated this force field by running Monte Carlo simulations of collagen-like proteins in water. The resulting geometries were within 0.94 Å root-mean-square deviation (RMSD) from the experimental data. We have performed additional validation by studying conformational properties of three oligopeptides relevant in the context of N-glycoprotein secondary structure. These systems have been previously studied with combined experimental and computational methods, and both POSSIM and benchmark OPLS-AA simulations that we carried out produced geometries within ca. 0.9 Å RMSD of the literature structures. Thus, the performance of POSSIM in reproducing the structures is comparable with that of the widely used OPLS-AA force field. Furthermore, our fitting of the force field parameters for peptides and proteins has been streamlined compared with the previous generation of the complete polarizable force field and relied more on transferability of parameters for nonbonded interactions (including the electrostatic component). The resulting deviations from the quantum mechanical data are similar to those achieved with the previous generation; thus, the technique is robust, and the parameters are transferable. At the same time, the number of parameters used in this work was noticeably smaller than that of the previous generation of our complete polarizable force field for proteins; thus, the transferability of this set can be expected to be greater, and the danger of force field fitting artifacts is lower. Therefore, we believe that this force field can be successfully applied in a wide variety of applications to proteins and protein-ligand complexes. PMID:25400518

Li, Xinbi; Ponomarev, Sergei Y; Sigalovsky, Daniel L; Cvitkovic, John P; Kaminski, George A

2014-11-11

298

Tethyan collision forces and the stress field of the Eurasian Plate  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

299

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields.  

PubMed

Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between the currently accessible simulation time scale and the experimental time scale for many important protein folding processes. In this study, molecular dynamics simulations were carried out for both the wild-type and the mutant hen lysozyme (TRP62GLY) to study the single mutation effect on lysozyme stability and misfolding. Our thermal denaturing simulations at 400-500 K with both the OPLSAA and the CHARMM force fields show that the mutant structure is indeed much less stable than the wild-type, which is consistent with the recent urea denaturing experiment (Dobson et al. Science 2002, 295, 1719-1722; Nature 2003, 424, 783-788). Detailed results also reveal that the single mutation TRP62GLY first induces the loss of native contacts in the beta-domain region of the lysozyme protein at high temperatures, and then the unfolding process spreads into the alpha-domain region through Helix C. Even though the OPLSAA force field in general shows a more stable protein structure than does the CHARMM force field at high temperatures, the two force fields examined here display qualitatively similar results for the misfolding process, indicating that the thermal denaturing of the single mutation is robust and reproducible with various modern force fields. PMID:17031950

Eleftheriou, Maria; Germain, Robert S; Royyuru, Ajay K; Zhou, Ruhong

2006-10-18

300

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

NASA Astrophysics Data System (ADS)

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

Scaife, Thomas M.; Heckler, Andrew F.

2007-11-01

301

High-field magnetic force microscopy as susceptibility imaging Casey Israel, Weida Wu, and Alex de Lozannea  

E-print Network

High-field magnetic force microscopy as susceptibility imaging Casey Israel, Weida Wu, and Alex de an extension of variable-temperature magnetic force microscopy MFM that allows spatial discrimination between.1063/1.2221916 Magnetic force microscopy MFM was developed as a scanning probe technique for mapping out magnetic field

Wu, Weida

302

Fictitious forces and simulated magnetic fields in rotating reference frames.  

PubMed

We show that the Wigner-Bargmann program of grounding nonrelativistic quantum mechanics in the unitary projective representations of the Galilei group can be extended to include all noninertial reference frames. The key concept is the Galilean line group, the group of transformations that ties together all accelerating reference frames, and its representations. These representations are constructed under the natural constraint that they reduce to the well-known unitary, projective representations of the Galilei group when the transformations are restricted to inertial reference frames. This constraint can be accommodated only for a class of representations with a sufficiently rich cocycle structure. Unlike the projective representations of the Galilei group, these cocycle representations of the Galilean line group do not correspond to central extensions of the group. Rather, they correspond to a class of nonassociative extensions, known as loop prolongations, that are determined by three-cocycles. As an application, we show that the phase shifts due to the rotation of Earth that have been observed in neutron interferometry experiments and the rotational effects that lead to simulated magnetic fields in optical lattices can be rigorously derived from the representations of the loop prolongations of the Galilean line group. PMID:24182238

Klink, W H; Wickramasekara, S

2013-10-18

303

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.

304

Stress effects on the initial lithiation of crystalline silicon nanowires: reactive molecular dynamics simulations using ReaxFF.  

PubMed

Silicon (Si) has been recognized as a promising anode material for the next-generation high-capacity lithium (Li)-ion batteries because of its high theoretical energy density. Recent in situ transmission electron microscopy (TEM) revealed that the electrochemical lithiation of crystalline Si nanowires (c-SiNWs) proceeds by the migration of the interface between the lithiated Si (LixSi) shell and the pristine unlithiated core, accompanied by solid-state amorphization. The underlying atomic mechanisms of Li insertion into c-Si remain poorly understood. Herein, we perform molecular dynamics (MD) simulations using the reactive force field (ReaxFF) to characterize the lithiation process of c-SiNWs. Our calculations show that ReaxFF can accurately reproduce the energy barriers of Li migration from DFT calculations in both crystalline (c-Si) and amorphous Si (a-Si). The ReaxFF-based MD simulations reveal that Li insertion into interlayer spacing between two adjacent (111) planes results in the peeling-off of the (111) facets and subsequent amorphization, in agreement with experimental observations. We find that breaking of the Si-Si bonds between (111)-bilayers requires a rather high local Li concentration, which explains the atomically sharp amorphous-crystalline interface (ACI). Our stress analysis shows that lithiation induces compressive stress at the ACI layer, causing retardation or even the stagnation of the reaction front, also in good agreement with TEM observations. Lithiation at high temperatures (e.g. 1200 K) shows that Li insertion into c-SiNW results in an amorphous to crystalline phase transformation at Li?:?Si composition of ?4.2?:?1. Our modeling results provide a comprehensive picture of the effects of reaction and diffusion-induced stress on the interfacial dynamics and mechanical degradation of SiNW anodes under chemo-mechanical lithiation. PMID:25559797

Ostadhossein, Alireza; Cubuk, Ekin D; Tritsaris, Georgios A; Kaxiras, Efthimios; Zhang, Sulin; van Duin, Adri C T

2015-02-01

305

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

PubMed

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

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

2014-06-19

306

Controlling dispersion forces between small particles with artificially created random light fields  

E-print Network

Appropriate combinations of laser beams can be used to trap and manipulate small particles with "optical tweezers" as well as to induce significant "optical binding" forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir-Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light induced interactions open a path towards...

Bruegger, Georges; Scheffold, Frank; Saenz, Juan Jose

2015-01-01

307

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers  

NASA Technical Reports Server (NTRS)

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

308

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.  

PubMed

The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations. PMID:25018674

Abella, Jayvee R; Cheng, Sara Y; Wang, Qiantao; Yang, Wei; Ren, Pengyu

2014-07-01

309

Nonlinear force-free coronal magnetic field extrapolation scheme based on the direct boundary integral formulation  

NASA Astrophysics Data System (ADS)

The boundary integral equation (BIE) method was first proposed by Yan and Sakurai (2000) and used to extrapolate the nonlinear force-free magnetic field in the solar atmosphere. Recently, Yan and Li (2006) improved the BIE method and proposed the direct boundary integral equation (DBIE) formulation, which represents the nonlinear force-free magnetic field by direct integration of the magnetic field on the bottom boundary surface. On the basis of this new method, we devised a practical calculation scheme for the nonlinear force-free field extrapolation above solar active regions. The code of the scheme was tested by the analytical solutions of Low and Lou (1990) and was applied to the observed vector magnetogram of solar active region NOAA 9077. The results of the calculations show that the improvement of the new computational scheme to the scheme of Yan and Li (2006) is significant, and the force-free and divergence-free constraints are well satisfied in the extrapolated fields. The calculated field lines for NOAA 9077 present the X-shaped structure and can be helpful for understanding the magnetic configuration of the filament channel as well as the magnetic reconnection process during the Bastille Day flare on 14 July 2000.

He, Han; Wang, Huaning

2008-05-01

310

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations.  

PubMed

The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc. PMID:25413259

Betz, Robin M; Walker, Ross C

2015-01-15

311

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

312

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

313

Anomalous diffusion of field lines and charged particles in Arnold-Beltrami-Childress force-free magnetic fields  

SciTech Connect

The cosmic magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free in the sense that the Lorentz force vanishes. The three-dimensional Arnold-Beltrami-Childress (ABC) field is an example of a force-free, helical magnetic field. In fluid dynamics, ABC flows are steady state solutions of the Euler equation. The ABC magnetic field lines exhibit a complex and varied structure that is a mix of regular and chaotic trajectories in phase space. The characteristic features of field line trajectories are illustrated through the phase space distribution of finite-distance and asymptotic-distance Lyapunov exponents. In regions of chaotic trajectories, an ensemble-averaged variance of the distance between field lines reveals anomalous diffusion—in fact, superdiffusion—of the field lines. The motion of charged particles in the force-free ABC magnetic fields is different from the flow of passive scalars in ABC flows. The particles do not necessarily follow the field lines and display a variety of dynamical behavior depending on their energy, and their initial pitch-angle. There is an overlap, in space, of the regions in which the field lines and the particle orbits are chaotic. The time evolution of an ensemble of particles, in such regions, can be divided into three categories. For short times, the motion of the particles is essentially ballistic; the ensemble-averaged, mean square displacement is approximately proportional to t{sup 2}, where t is the time of evolution. The intermediate time region is defined by a decay of the velocity autocorrelation function—this being a measure of the time after which the collective dynamics is independent of the initial conditions. For longer times, the particles undergo superdiffusion—the mean square displacement is proportional to t{sup ?}, where ??>?1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics, both of magnetic field lines and of particles moving in these fields, strongly suggest that theories of transport in three-dimensional chaotic magnetic fields need a shift from the usual paradigm of quasilinear diffusion.

Ram, Abhay K. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Dasgupta, Brahmananda [Center for Space Plasma and Aeronomic Research, University of Alabama in Huntsville, Huntsville, Alabama 35805 (United States); Krishnamurthy, V. [Center for Ocean-Land-Atmosphere Studies, George Mason University, Fairfax, Virginia 22030 (United States); Mitra, Dhrubaditya [Nordita, KTH Royal Institute of Technology and Stockholm University, 10691 Stockholm (Sweden)

2014-07-15

314

Force field inside the void in complex plasmas under microgravity conditions  

SciTech Connect

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

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

2005-05-01

315

FORCE-FREENESS OF SOLAR MAGNETIC FIELDS IN THE PHOTOSPHERE Q1 Y.-J. Moon,1,2  

E-print Network

FORCE-FREENESS OF SOLAR MAGNETIC FIELDS IN THE PHOTOSPHERE Q1 Y.-J. Moon,1,2 G. S. Choe,3 H. S. Yun It is widely believed that solar magnetic fields are force-free in the solar corona but not in the solar photo: photosphere 1. INTRODUCTION It is generally believed that magnetic fields play a central role in solar

316

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

317

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

318

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

319

Simulation of the Brownian motion of the domain wall in a nonlinear force field of nanowires  

NASA Astrophysics Data System (ADS)

The paper proposes a computer simulation method of the thermo-fluctuational motion of domain walls in ferromagnetic polycrystalline nanowires, taking into account a non-linear force field of magnetic inhomogeneities. The method makes use of stochastic Langevin function. Into the Langevin equation we added a member describing random force pattern of domain wall fixation on magnetic inhomogeneities. A variety of statistic characteristics of domain wall propagation process have been obtained: magnetization jumps distribution, activation energies distribution, distribution of magnetization switch waiting times and distribution of magnetization jump times. Paper shows that it is incorrect to apply Einstein-Smoluchowski equation for particle's thermo-fluctuational motion in non-linear force field pattern.

Ivanov, Anatoly A.; Orlov, Vitaly A.

2015-02-01

320

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

321

Realtime characteristic of FF like centralized control fieldbus and its state-of-art  

Microsoft Academic Search

The temporal property of MAC protocol of fieldbus is critical to meet real-time constraints of field devices in factory floor. Among various types of MAC protocols, the one using centralized strategy is characterized by providing a feasible schedule to meet different temporal constraints of field devices online, and also providing schedulability analysis offline a priori. WorldFIP and FF, two popular

Zhi Wang; Zhou Yue; Jiming Chen; Ye-qiong SONG; Youxian Sun

2002-01-01

322

Analysis of the FF Aqr spectra  

NASA Astrophysics Data System (ADS)

We determine the atmospheric parameters of the secondary in the close binary system FF Aqr and analyze its chemical composition. A series of high-resolution spectra are taken at different orbital phases using the coude echelle spectrometer of the 1.5-m Russian-Turkish Telescope (RTT150). We show that the absorption line intensity of heavy elements varies with phase due to the spotty nature of the cool component. We determine the abundances of heavy elements in the star's atmosphere by modelling the synthetic spectra and performing a differential analysis of the chemical composition of FF Aqr relative to the solar composition. Our analysis of the averaged spectrum of FF Aqr yielded 539 abundance estimates for 21 chemical elements. We found the metallicity of the star ([ Fe/H] = -0.11 ± 0.08) to be close solar, in agreement with the hypothesis that FF Aqr should belong to the Galactic disk. The inferred chemical composition of the objects exhibits no anomalous abundances of the ?-, r-, and s-process elements like those earlier found in other systems (IN Com, LW Hya, V471 Tau). The lack of such anomalies in FF Aqr must be due to the fact that the elements heavier than 16 O cannot be synthesized in the core of the primary during the last stages of its evolution.

Shimanskaya, N. N.; Bikmaev, I. F.; Shimansky, V. V.

2011-07-01

323

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

324

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

Microsoft Academic Search

A proof is given of the following statement: if B is a smooth force-free magnetic field contained in a cylindrical domain of axis parallel to z and of star-shaped cross-section, and if B is topologically equivalent to the uniform field B0=B0z, then B=B0. In addition to being a very first step in the general study of the uniqueness of a

J. J. Aly

2005-01-01

325

Confinement of Plasma along Shaped Open Magnetic Fields from the Centrifugal Force of Supersonic Plasma Rotation  

SciTech Connect

Interferometric density measurements in plasmas rotating in shaped, open magnetic fields demonstrate strong confinement of plasma parallel to the magnetic field, with density drops of more than a factor of 10. Taken together with spectroscopic measurements of supersonic ExB rotation of sonic Mach 2, these measurements are in agreement with ideal MHD theory which predicts large parallel pressure drops balanced by centrifugal forces in supersonically rotating plasmas.

Teodorescu, C.; Young, W. C.; Swan, G. W. S.; Ellis, R. F.; Hassam, A. B.; Romero-Talamas, C. A. [University of Maryland, College Park, Maryland 20742 (United States)

2010-08-20

326

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

327

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

328

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

PubMed

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

Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

2013-11-12

329

Force Field Adaptation Can Be Learned Using Vision in the Absence of Proprioceptive Error  

Microsoft Academic Search

It has been shown that people can learn to perform a variety of motor tasks in novel dynamic environments without visual feedback, highlighting the importance of proprioceptive feedback in motor learning. However, our results show that it is possible to learn a viscous curl force field without proprioceptive error to drive adaptation, by providing visual information about the position error.

Alejandro Melendez-Calderon; Lorenzo Masia; Roger Gassert; Giulio Sandini; Etienne Burdet

2011-01-01

330

Binary Phases of Aliphatic N-Oxides and Water: Force Field Development and Molecular Dynamics Simulation  

E-print Network

-pressure conditions.10 TMAO even appears to play a role in possible therapies for Alzheimer's disease.11 Explanations with available biopolymer potential energy functions. Noto et al.20 were the first who constructed a force field at finite TMAO concentrations.19 They found some evidence regarding changes of water-water structure

Berry, R. Stephen

331

Generation of magnetic field, vortices and relativistic particles by the nonpotential ponderomotive force  

Microsoft Academic Search

Effects of nonpotential ponderomotive force on kinetic phenomena in a plasma are presented. The particle distribution function is derived, which allows one to calculate the particle and heat fluxes. A novel relativistic hydrodynamic equation of motion, incorporating self-generated magnetic fields, is obtained, which admits no frozen-in condition. The generation of electron fluid vortices by a laser pulse in initially unmagnetized

Nodar L. Tsintsadze; Kunioki Mima; Levan N. Tsintsadze; Kyoji Nishikawa

2002-01-01

332

Focused ion beam modification of atomic force microscopy tips for near-field scanning optical microscopy  

E-print Network

A probe for near-field scanning optical microscopy is demonstrated based on a high index glass sphere attached to the end of a conventional atomic force microscopy tip. The sphere is machined into a pyramid geometry using a focused ion beam...

Krogmeier, Jeffrey R.; Dunn, Robert C.

2001-12-01

333

A Single Universal Force Field Can Uniquely Orient Non-Symmetric Parts  

E-print Network

grippers, conveyor belts, or vibratory bowl feeders, these devices generate force fields in which the parts pose. Our latter result leads to the design of devices that can act as "universal parts feeders been performed with vibratory bowl feeders. These devices are cus- tomly designed for the orientation

Richardson, David

334

Fort Future: Virtual Installation supports rapidly changing needs of armed forces in the field  

E-print Network

and electric utility modeling and planning tools for the Virtual Instal- lation. For water utilities, ArgonneFort Future: Virtual Installation supports rapidly changing needs of armed forces in the field FORT- ports the Fort Future Program by developing modeling and simulation tools for the Virtual Installation

Kemner, Ken

335

A transferable force field to predict phase equilibria and surface tension of ethers and glycol ethers.  

PubMed

We propose a new transferable force field to simulate phase equilibrium and interfacial properties of systems involving ethers and glycol ethers. On the basis of the anisotropic united-atom force field, only one new group is introduced: the ether oxygen atom. The optimized Lennard-Jones (LJ) parameters of this atom are identical whatever the molecule simulated (linear ether, branched ether, cyclic ether, aromatic ether, diether, or glycol ether). Accurate predictions are achieved for pure compound saturated properties, critical properties, and surface tensions of the liquid-vapor interface, as well as for pressure-composition binary mixture diagrams. Multifunctional molecules (1,2-dimethoxyethane, 2-methoxyethanol, diethylene glycol) have also been studied using a recently proposed methodology for the calculation of the intramolecular electrostatic energy avoiding the use of additional empirical parameters. This new force field appears transferable for a wide variety of molecules and properties. It is furthermore worth noticing that binary mixtures have been simulated without introducing empirical binary parameters, highlighting also the transferability to mixtures. Hence, this new force field gives future opportunities to simulate complex systems of industrial interest involving molecules with ether functions. PMID:21800821

Ferrando, Nicolas; Lachet, Véronique; Pérez-Pellitero, Javier; Mackie, Allan D; Malfreyt, Patrice; Boutin, Anne

2011-09-15

336

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

EPA Science Inventory

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

337

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

ERIC Educational Resources Information Center

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

Veto, B.

2011-01-01

338

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

Microsoft Academic Search

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

Paul M. Collier

2001-01-01

339

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEM?? polarizable force field.  

PubMed

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEM?? fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEM?? polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEM?? PFF is close to that of the MP2 method. This shows that ABEEM?? model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. PMID:24322440

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

340

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements  

E-print Network

demonstrated direct calculation of NMR observables from protein simulations. Here, we quantitatively evaluate accuracy in our benchmark. For the two optimal force fields, the calculation error is comparable (MD) simulation is a versatile computa- tional tool that allows investigation of condensed phase

Das, Rhiju

341

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

PubMed

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

Manzoni, Francesco; Söderhjelm, Pär

2014-03-01

342

ON THE FORCE-FREE NATURE OF PHOTOSPHERIC SUNSPOT MAGNETIC FIELDS AS OBSERVED FROM HINODE (SOT/SP)  

SciTech Connect

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

Tiwari, Sanjiv Kumar, E-mail: tiwari@mps.mpg.de [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur 313 001 (India)

2012-01-01

343

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

344

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

PubMed

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

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

2014-06-21

345

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

SciTech Connect

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

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

2005-01-01

346

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

347

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

PubMed

Magnetic forces have been incorporated into orthodontic mechanics during recent years. However, the biocompatibility of magnet alloys and the possible risk of harmful or unusual reactions in tissues exposed to static magnetic fields have been characterized as inconsistent and often contradictory. It has also been questioned whether magnetic forces have significant advantages over traditional mechanics. The present series of studies aimed to analyse the force and field properties, the biocompatibility and the clinical effects of rare earth magnets as well as to compare the efficiency of tooth movement between magnets and another force system. Samarium-cobalt magnets for molar distalization were tested in experimental models for force and field properties. The cytotoxicity of different magnet alloys (rare earth types) as well as of clinically used and recycled magnets was assessed by two in vitro methods, the millipore filter method and an extraction method. The effect of static magnetic fields on human gingival tissue and dental pulp was examined histologically for alterations in cell pattern and cell morphology. The effects of using repelling samarium-cobalt magnets for simultaneous distalization of maxillary first and second molars were analysed in individuals with Class II malocclusion. The efficiency of molar distalization was also intra-individually compared between repelling magnets and superelastic NiTi-coils in individuals with Class II malocclusion and deep bite. The magnet forces decreased approximately with the reciprocal square of the separation distance between the magnets. No fatigue of force over time could be seen. The static magnetic fields were weak and had a limited extent and the flux density dropped exponentially in all directions with increased distance from the magnets, implying a small exposure area when the magnets are used clinically. Rare earth magnets showed good biocompatibility, particularly coated magnets. However, uncoated samarium-cobalt magnets showed significant cytotoxicity. It was also found that stainless-steel-coated samarium-cobalt magnets could be recycled with maintained good biocompatibility. After exposure to static magnetic fields, normal clinical and histological conditions in the human gingival tissue and normal histological features in the human dental pulp were found. Repelling magnets were effective in producing maxillary molar distalization but some side effects like anchorage loss and molar tipping were found. The superelastic coils were shown to be even more efficient than the repelling magnets for maxillary molar distalization in individuals with Class II malocclusion and deep bite. PMID:7801229

Bondemark, L

1994-01-01

348

MODELING MAGNETIC FIELD STRUCTURE OF A SOLAR ACTIVE REGION CORONA USING NONLINEAR FORCE-FREE FIELDS IN SPHERICAL GEOMETRY  

SciTech Connect

We test a nonlinear force-free field (NLFFF) optimization code in spherical geometry using an analytical solution from Low and Lou. Several tests are run, ranging from idealized cases where exact vector field data are provided on all boundaries, to cases where noisy vector data are provided on only the lower boundary (approximating the solar problem). Analytical tests also show that the NLFFF code in the spherical geometry performs better than that in the Cartesian one when the field of view of the bottom boundary is large, say, 20 Degree-Sign Multiplication-Sign 20 Degree-Sign . Additionally, we apply the NLFFF model to an active region observed by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory (SDO) both before and after an M8.7 flare. For each observation time, we initialize the models using potential field source surface (PFSS) extrapolations based on either a synoptic chart or a flux-dispersal model, and compare the resulting NLFFF models. The results show that NLFFF extrapolations using the flux-dispersal model as the boundary condition have slightly lower, therefore better, force-free, and divergence-free metrics, and contain larger free magnetic energy. By comparing the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the Atmospheric Imaging Assembly on board SDO, we find that the NLFFF performs better than the PFSS not only for the core field of the flare productive region, but also for large EUV loops higher than 50 Mm.

Guo, Y.; Ding, M. D. [School of Astronomy and Space Science, Nanjing University, Nanjing 210093 (China); Liu, Y.; Sun, X. D. [W. W. Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305 (United States); DeRosa, M. L. [Lockheed Martin Advanced Technology Center, 3251 Hanover Street, Palo Alto, CA 94304 (United States); Wiegelmann, T., E-mail: guoyang@nju.edu.cn [Max-Planck-Institut fuer Sonnensystemforschung, Max-Planck-Strasse 2, D-37191 Katlenburg-Lindau (Germany)

2012-11-20

349

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

350

The Effect of Electric Fields In A Classic Introductory Physics Treatment of Eddy Current Forces  

E-print Network

A simple model of eddy currents in which current is computed solely from magnetic forces acting on electrons proves accessible to introductory students and gives a good qualitative account of eddy current forces. However, this model cannot be complete; it ignores the electric fields that drive current outside regions of significant magnetic field. In this paper we show how to extend the model to obtain a boundary value problem for current density. Solution of this problem in polar coordinates shows that the electric field significantly affects the quantitative results and presents an exercise suitable for upper division students. We apply elliptic cylindrical coordinates to generalize the result and offer an exercise useful for teaching graduate students how to use non-standard coordinate systems.

P. J. Salzman; John Robert Burke; Susan M. Lea

2006-07-23

351

Analytical solutions and validation of electric field and dielectrophoretic force in a bio-microfluidic channel.  

PubMed

In a microbiological device, cell or particle manipulation and characterization require the use of electric field on different electrodes in several configurations and shapes. To efficiently design microelectrodes within a microfluidic channel for dielectrophoresis focusing, manipulation and characterization of cells, the designer will seek the exact distribution of the electric potential, electric field and hence dielectrophoresis force exerted on the cell within the microdevice. In this paper we describe the approach attaining the analytical solution of the dielectrophoretic force expression within a microchannel with parallel facing same size electrodes present on the two faces of channel substrates, with opposite voltages on the pair electrodes. Simple Fourier series mathematical expressions are derived for electric potential, electric field and dielectric force between two distant finite-size electrodes. Excellent agreement is found by comparing the analytical results calculated using MATLAB™ with numerical ones obtained by Comsol. This analytical result can help the designer to perform simple design parametric analysis. Bio-microdevices are also designed and fabricated to illustrate the theoretical solution results with the experimental data. Experiments with red blood cells show the dielectrophoretic force contour plots of the analytical data matched to the experimental results. PMID:22287173

Nerguizian, Vahé; Alazzam, Anas; Roman, Dacian; Stiharu, Ion; Burnier, Miguel

2012-02-01

352

Hydrophobic force field as molecular alternative to surface-area models  

SciTech Connect

An effective force field for hydrophobic interactions is developed based on a modified potential-of-mean-force (PMF) expansion of the effective many-body interactions between nonpolar molecules in water. For the simplest nonpolar solutes in water, hard particles, the modified PMF expansion is exact in both limiting cases of infinite separation and perfect overlap. The hydrophobic interactions are parametrized by using the information-theory model of hydrophobic hydration. The interactions between nonpolar solutes are short-ranged and can be evaluated efficiently on a computer. The force field is compared with simulation data for alkane conformational equilibria in water as well as a model for the formation of a hydrophobic core of a protein. The modified PMF expansion can be extended to solutes with attractive interactions. The observed accuracy, computational efficiency, and atomic detail of the model suggest that this simple hydrophobic force field can lead to a molecular alternative for phenomenological surface-area models with applications in ligand-binding and protein-folding studies.

Hummer, G.

1999-07-07

353

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

Microsoft Academic Search

A field-reversed configuration (FRC) is formed by applying a rotating magnetic field (RMF) much larger than the axial magnetic field to a cylindrical glass vacuum chamber filled with 10 Pa argon gas without a preionization. The FRC with the plasma density 2.2×1019 m-3, the temperature 8.0 eV, the separatrix length 0.45 m, and the separatrix radius 0.035 m is sustained

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

2008-01-01

354

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

355

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

356

A New Code for Nonlinear Force-free Field Extrapolation of the Global Corona  

NASA Astrophysics Data System (ADS)

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 × 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 & 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

2012-08-01

357

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids  

Microsoft Academic Search

The parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described. Parameters for both torsional and nonbonded energetics have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER all-atom force field. The torsional parameters were determined by fitting to rotational energy profiles obtained from ab initio

William L. Jorgensen; David S. Maxwell; Julian Tirado-Rives

1996-01-01

358

The Effect of Tension and a Longitudinal Magnetic Field on the ThermoelectroMotive Forces in Permalloy  

Microsoft Academic Search

Measurements have been made on the combined effect of tension and a longitudinal magnetic field on the thermoelectromotive force in three specimens of permalloy. The specimens were in the form of wires, the composition being 78, 81 and 84 percent nickel with the remaining part iron. In all cases the magnetic field produces a decrease in the thermoelectromotive force. Annealing

Alpheus W. Smith; Joy Dillinger

1929-01-01

359

Dielectrophoresis Force and Deflection of Dielectric Elastomers and Blends under AC field  

NASA Astrophysics Data System (ADS)

The effects of frequency and amplitude of AC electric field on the deflection distance and the dielectrophoresis force of the of acrylic elastomers (AR71), styrene copolymers (SAR and SBR), and blends with poly(p-phenylene) (AR71:PPP and SAR:PPP) were investigated. The dielectrophoresis forces of the dielectric elastomers and blends were measured by a vertical cantilever under various frequencies (0.3-60 Hz) and at the amplitudes of 200, 300, 500, 600 and 800 Vpp/mm. In addition, the effect of thickness of specimens and the particle concentration on the dielectrophoresis force were studied. Poly(p-phenylene) particles were added into AR71 and SAR with particle concentrations of 5, 10, 15 and 20 vol%. The forces were calculated from the non-linear deflection theory of the cantilever. The dielectrophoresis forces and deflection distances of the dielectric elastomers and blends generally increase with increasing amplitude but slightly decrease with increasing frequency, and they dramatically drop at the cut-off frequency. The cutoff frequencies are 12.0, 1.5 and 1.5 Hz for AR71, SAR, and SBR, at E = 800 Vpp/mm, respectively.

Kunanuraksapong, Ruksapong; Sirivat, Anuvat

2010-03-01

360

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

PubMed

Instrumented objects and multipurpose haptic displays have commonly been used to investigate sensorimotor control of grasping and manipulation. A major limitation of these devices, however, is the extent to which the experimenter can vary the interaction dynamics to fully probe sensorimotor control mechanisms. We propose a novel method to study precision grip control using a grounded robotic gripper with two moving, mechanically coupled finger pads instrumented with force sensors. The device is capable of stably rendering virtual mechanical properties with a wide dynamic range of achievable impedances. Eight viscoelastic force fields with different combinations of stiffness and damping parameters were implemented, and tested on eight healthy subjects performing 30 consecutive repetitions of a grasp, hold, and release task with time and position constraints. Rates of thumb and finger force were found to be highly correlated (r>0.9) during grasping, revealing that, despite the mechanical coupling of the two finger pads, subjects performed grasping movements in a physiological fashion. Subjects quickly adapted to the virtual dynamics (within seven trials), but, depending on the presented force field condition, used different control strategies to correctly perform the task. The proof of principle presented in this paper underscores the potential of such a one-degree-of-freedom robotic gripper to study neural control of grasping, and to provide novel insights on sensorimotor control mechanisms. PMID:25014953

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

2015-01-01

361

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

SciTech Connect

An axisymmetric force-free magnetic field B(r, ?) in spherical coordinates is defined by a function r?sin??B{sub ?}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r?sin??B{sub ?}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(?))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(?) 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(?,?))/(r{sup n+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. [Institut für Geowissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther Universität, D-06099 Halle (Germany); Low, B. C. [High Altitude Observatory, National Center for Atmospheric Research, Boulder, Colorado 80307 (United States)

2014-10-15

362

Polarizable empirical force field for hexopyranose monosaccharides based on the classical drude oscillator.  

PubMed

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins. PMID:24564643

Patel, Dhilon S; He, Xibing; MacKerell, Alexander D

2015-01-22

363

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator  

PubMed Central

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute–water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins. PMID:24564643

2015-01-01

364

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

365

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

PubMed Central

Presented is an extension of the CHARMM additive carbohydrate all-atom force field to enable modeling of polysaccharides containing furanose sugars. The new force field parameters encompass 1 ? 2, 1 ? 3, 1 ? 4 and 1 ? 6 pyranose-furanose linkages and 2 ? 1 and 2 ? 6 furanose-furanose linkages, building on existing hexopyranose and furanose monosaccharide parameters. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF) as to contain the key atoms in full carbohydrates. Target data for optimization included two-dimensional quantum mechanical (QM) potential energy scans of the ?/? glycosidic dihedral angles, with geometry optimization at the MP2/6-31G(d) level followed by MP2/cc-pVTZ single point energies. All possible chiralities of the model compounds at the linkage carbons were considered, and, for each geometry, the THF ring was constrained to the favorable South or North conformation. Target data also included QM vibrational frequencies and pair interaction energies and distances with water molecules. Force field validation included comparison of computed crystal properties, aqueous solution densities and NMR J-coupling constants to experimental reference values. Simulations of infinite crystals showed good agreement with experimental values for intramolecular geometries as well as for crystal unit cell parameters. Additionally, aqueous solution densities and available NMR data were reproduced to a high degree of accuracy, thus validating the hierarchically optimized parameters in both crystalline and aqueous condensed phases. The newly developed parameters allow for the modeling of linear, branched, and cyclic pyranose/furanose polysaccharides both alone and in heterogeneous systems including proteins, nucleic acids and/or lipids when combined with existing additive CHARMM biomolecular force fields. PMID:20845956

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

2010-01-01

366

Polarizable Water Model for the Coarse-Grained MARTINI Force Field  

PubMed Central

Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. PMID:20548957

Sengupta, Durba; Marrink, Siewert J.

2010-01-01

367

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

PubMed

Presented is an extension of the CHARMM additive carbohydrate all-atom force field to enable modeling of polysaccharides containing furanose sugars. The new force field parameters encompass 1 ? 2, 1 ? 3, 1 ? 4, and 1 ? 6 pyranose-furanose linkages and 2 ? 1 and 2 ? 6 furanose-furanose linkages, building on existing hexopyranose and furanose monosaccharide parameters. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF) as to contain the key atoms in full carbohydrates. Target data for optimization included two-dimensional quantum mechanical (QM) potential energy scans of the ?/? glycosidic dihedral angles, with geometry optimization at the MP2/6-31G(d) level followed by MP2/cc-pVTZ single-point energies. All possible chiralities of the model compounds at the linkage carbons were considered, and for each geometry, the THF ring was constrained to the favorable south or north conformations. Target data also included QM vibrational frequencies and pair interaction energies and distances with water molecules. Force field validation included comparison of computed crystal properties, aqueous solution densities, and NMR J-coupling constants to experimental reference values. Simulations of infinite crystals showed good agreement with experimental values for intramolecular geometries as well as for crystal unit cell parameters. Additionally, aqueous solution densities and available NMR data were reproduced to a high degree of accuracy, thus validating the hierarchically optimized parameters in both crystalline and aqueous condensed phases. The newly developed parameters allow for the modeling of linear, branched, and cyclic pyranose/furanose polysaccharides both alone and in heterogeneous systems including proteins, nucleic acids, and/or lipids when combined with existing additive CHARMM biomolecular force fields. PMID:20845956

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

2010-10-14

368

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

369

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

PubMed Central

We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ± 1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ± 1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ± 0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. Since the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly-modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems. PMID:21997857

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

2012-01-01

370

A first principles based polarizable O(N) interatomic force field for bulk silica.  

PubMed

We present a reformulation of the Tangney-Scandolo interatomic force field for silica [J. Chem. Phys. 117, 8898 (2002)], which removes the requirement to perform an Ewald summation. We use a Yukawa factor to screen electrostatic interactions and a cutoff distance to limit the interatomic potential range to around 10 A?. A reparametrization of the potential is carried out, fitting to data from density functional theory calculations. These calculations were performed within the local density approximation since we find that this choice of functional leads to a better match to the experimental structural and elastic properties of quartz and amorphous silica than the generalized gradient approximation approach used to parametrize the original Tangney-Scandolo force field. The resulting O(N) scheme makes it possible to model hundreds of thousands of atoms with modest computational resources, without compromising the force field accuracy. The new potential is validated by calculating structural, elastic, vibrational, and thermodynamic properties of ?-quartz and amorphous silica. PMID:20831310

Kermode, J R; Cereda, S; Tangney, P; De Vita, A

2010-09-01

371

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

PubMed

A conventional by hand construction and parameterization of a polymer model for the purpose of molecular simulations can quickly become very work-intensive and time-consuming. Using the example of polyglycerol, I present a polymer decompostion strategy yielding a set of five monomeric residues that are convenient for an instantaneous assembly and subsequent force field simulation of a polyglycerol polymer model. Force field parameters have been developed in accordance with the classical Amber force field. Partial charges of each unit were fitted to the electrostatic potential using quantum-chemical methods and slightly modified in order to guarantee a neutral total polymer charge. In contrast to similarly constructed models of amino acid and nucleotide sequences, the glycerol building blocks may yield an arbitrary degree of bifurcations depending on the underlying probabilistic model. The iterative development of the overall structure as well as the relation of linear to branching units is controlled by a simple Markov model which is presented with few algorithmic details. The resulting polymer is highly suitable for classical explicit water molecular dynamics simulations on the atomistic level after a structural relaxation step. Moreover, the decomposition strategy presented here can easily be adopted to many other (co)polymers. PMID:25428569

Durmaz, Vedat

2015-03-01

372

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

373

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

374

Anharmonic force fields of HOF and F/sub 2/O  

SciTech Connect

Ab initio predictions at the SCF, CISD, and CCSD levels are reported for the title compounds using DZP and TZP basis sets. The calculated geometries, rotational constants, dipole moments, fundamental frequencies, isotopic frequency shifts, vibration--rotation interaction constants, centrifugal distortion constants, Coriolis coupling constants, and infrared band intensities are compared with experimental data (if available). The best agreement is usually found for the CCSD results. The experimentally derived cubic force field of F/sub 2/O is reproduced well by our results so that the predicted cubic and quartic force fields of HOF and the predicted quartic force field of F/sub 2/O are also expected to be realistic. On the basis of our theoretical anharmonic constants, a new interpretation is suggested for the anomalous isotopic frequency shift of ..nu../sub 3/ in HOF and DOF. Finally, an experimentally derived r/sub e/ structure with R(O--F) = 1.4356 A, r(O--H) = 0.9664 A, and ..cap alpha..(H--O--F) = 97.72/sup 0/ is proposed for HOF on the basis of the TZP CCSD vibration--rotation interaction constants.

Thiel, W.; Scuseria, G.; Schaefer H.F. III; Allen, W.D.

1988-10-15

375

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

PubMed Central

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to ?m-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the ?m and nm scales. PMID:15326302

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

2004-01-01

376

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

SciTech Connect

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

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

1989-04-01

377

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

NASA Astrophysics Data System (ADS)

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

Schuyler, W. Jeff; Melzer, James E.

2007-04-01

378

Study on Two Methods for Nonlinear Force-Free Extrapolation Based on Semi-Analytical Field  

NASA Astrophysics Data System (ADS)

In this paper, two semi-analytical solutions of force-free fields (Low and Lou, Astrophys. J. 352, 343, 1990) have been used to test two nonlinear force-free extrapolation methods. One is the boundary integral equation (BIE) method developed by Yan and Sakurai ( Solar Phys. 195, 89, 2000), and the other is the approximate vertical integration (AVI) method developed by Song et al. ( Astrophys. J. 649, 1084, 2006). Some improvements have been made to the AVI method to avoid the singular points in the process of calculation. It is found that the correlation coefficients between the first semi-analytical field and extrapolated field using the BIE method, and also that obtained by the improved AVI method, are greater than 90% below a height 10 of the 64×64 lower boundary. For the second semi-analytical field, these correlation coefficients are greater than 80% below the same relative height. Although differences between the semi-analytical solutions and the extrapolated fields exist for both the BIE and AVI methods, these two methods can give reliable results for heights of about 15% of the extent of the lower boundary.

Liu, S.; Zhang, H. Q.; Su, J. T.; Song, M. T.

2011-03-01

379

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

SciTech Connect

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

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

2011-12-15

380

Using the atomic force microscope as a nanomechanical partner to support evanescent field imaging  

NASA Astrophysics Data System (ADS)

Quantum Dot (QD)/microsphere structures supporting Whispering Gallery Modes (WGMs) are attached to Atomic Force Microscope (AFM) cantilevers for characterization of the evanescent field around the QD/microsphere and utilization of the evanescent field for sensing at the apical surface of live cells. Following laser excitation, QD emission couples to WGMs that circumnavigate the microsphere via total internal reflection at the internal surfaces of the microsphere. The resulting evanescent field is characterized utilizing the high spatial control of an AFM in approaching a dye monolayer on a test surface. The measured evanescent field extends approximately 50 nm from the microsphere surface, matching theoretical predictions. This system was then used to sense the accumulation of integrin and formation of focal adhesions at the apical surface of cells.

Amini, S.; Sun, Z.; Meininger, G. A.; Meissner, K. E.

2014-09-01

381

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.  

PubMed

We present an extension of the CHARMM hexopyranose monosaccharide additive all-atom force field to enable modeling of glycosidic-linked hexopyranose polysaccharides. The new force field parameters encompass 1?1, 1?2, 1?3, 1?4, and 1?6 hexopyranose glycosidic linkages, as well as O-methylation at the C(1) anomeric carbon, and are developed to be consistent with the CHARMM all-atom biomolecular force fields for proteins, nucleic acids, and lipids. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates, in particular O-methyl-tetrahydropyran and glycosidic-linked dimers consisting of two molecules of tetrahyropyran or one of tetrahydropyran and one of cyclohexane. Target data for parameter optimization include full two-dimensional energy surfaces defined by the ?/? glycosidic dihedral angles in the disaccharide analogs as determined by quantum mechanical MP2/cc-pVTZ single point energies on MP2/6-31G(d) optimized structures (MP2/cc-pVTZ//MP2/6-31G(d)). In order to achieve balanced, transferable dihedral parameters for the ?/? glycosidic dihedral angles, surfaces for all possible chiralities at the ring carbon atoms involved in the glycosidic linkages are considered, resulting in over 5000 MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. Also included as target data are vibrational frequencies, pair interaction energies and distances with water molecules, and intramolecular geometries including distortion of the glycosidic valence angle as a function of the glycosidic dihedral angles. The model-compound optimized force field parameters are validated on full disaccharides through comparison of molecular dynamics results to available experimental data. Good agreement is achieved with experiment for a variety of properties including crystal cell parameters and intramolecular geometries, aqueous densities, and aqueous NMR coupling constants associated with the glycosidic linkage. The newly-developed parameters allow for the modeling of linear, branched, and cyclic hexopyranose glycosides both alone and in heterogenous systems including proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:20161005

Guvench, Olgun; Hatcher, Elizabeth R; Venable, Richard M; Pastor, Richard W; Mackerell, Alexander D

2009-08-20

382

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

PubMed Central

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

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

2014-01-01

383

A Dust-Penetrated Classification Scheme for Bars as Inferred from their Gravitational Force Fields  

NASA Astrophysics Data System (ADS)

The division of galaxies into barred (SB) and normal (S) spirals is a fundamental aspect of the Hubble galaxy classification system. This tuning fork view was revised by de Vaucouleurs, whose classification volume recognized apparent bar strength (SA, SAB, SB) as a continuous property of galaxies called the ``family.'' However, the SA, SAB, and SB families are purely visual judgments that can have little bearing on the actual bar strength in a given galaxy. Until recently, published bar judgments were based exclusively on blue light images, where internal extinction or star formation can completely mask a bar. Near-infrared camera arrays, which principally trace the old stellar population in both normal and barred galaxies, now facilitate a quantification of bar strength in terms of gravitational potentials and force fields. In this paper, we show that the maximum value of the ratio of the tangential force to the mean axisymmetric radial force is a quantitative measure of the strength of a bar that can be straightforwardly derived for many galaxies. We show that a wide range of true bar strengths characterizes the category SB, while category SAB corresponds to a narrower range of bar strengths. Based on the force ratio, we define seven classes of bar strength and incorporate these classes into a dust-penetrated classification system for spiral galaxies. This work was supported by NSF grant AST 9617154 and the Anglo-American Chairman's Fund, Mrs. M. Keeton, CEO.

Buta, R.; Block, D. L.

2001-05-01

384

Nanophotonic force microscopy: characterizing particle-surface interactions using near-field photonics.  

PubMed

Direct measurements of particle-surface interactions are important for characterizing the stability and behavior of colloidal and nanoparticle suspensions. Current techniques are limited in their ability to measure pico-Newton scale interaction forces on submicrometer particles due to signal detection limits and thermal noise. Here we present a new technique for making measurements in this regime, which we refer to as nanophotonic force microscopy. Using a photonic crystal resonator, we generate a strongly localized region of exponentially decaying, near-field light that allows us to confine small particles close to a surface. From the statistical distribution of the light intensity scattered by the particle we are able to map out the potential well of the trap and directly quantify the repulsive force between the nanoparticle and the surface. As shown in this Letter, our technique is not limited by thermal noise, and therefore, we are able to resolve interaction forces smaller than 1 pN on dielectric particles as small as 100 nm in diameter. PMID:25625877

Schein, Perry; Kang, Pilgyu; O'Dell, Dakota; Erickson, David

2015-02-11

385

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

386

A SVD-based approach to helicoidal NF-FF transformations  

Microsoft Academic Search

We propose a novel Near-Field-Far-Field (NF-FF) transformation technique for aperture antennas and cylindrical NF scanning. It exploits a proper aperture field representation, based on the use of the Prolate Spheroidal Wave Functions (PSWFs), accounting for the a priori information on shape and size of the Antenna Under Test (AUT). It furthermore allows a fast NF acquisition by employing a continuous

A. Capozzoli; C. Curcio; G. D'Elia; F. Ferrara; C. Gennarelli; R. Guerriero; A. Liseno

2010-01-01

387

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

NASA Astrophysics Data System (ADS)

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

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

2008-10-01

388

STUDY OF HORIZONTAL-SPRAY FLUX FORCE/CONDENSATION SCRUBBER  

EPA Science Inventory

The report gives results of a laboratory pilot-scale evaluation of a Flux Force/Condensation (FF/C) scrubber for collecting fine particles, those smaller than 2 micrometers in diameter. FF/C scrubbing includes the effects of diffusiophoresis, thermophoresis, Stefan flow, and part...

389

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

390

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

391

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, Benoît

2012-01-01

392

The fast multipole method and point dipole moment polarizable force fields  

NASA Astrophysics Data System (ADS)

We present an 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 a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.

Coles, Jonathan P.; Masella, Michel

2015-01-01

393

The fast multipole method and point dipole moment polarizable force fields.  

PubMed

We present an 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 a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems. PMID:25591340

Coles, Jonathan P; Masella, Michel

2015-01-14

394

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

395

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

NASA Technical Reports Server (NTRS)

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

Norman, T.; Johnson, W.

1985-01-01

396

Scaled quantum chemical force fields for 1,1-difluorocyclopropane and the influence of vibrational anharmonicity.  

PubMed

Potential functions and harmonic (omega(i)) and anharmonic (nu(i)) fundamental frequencies have been calculated for 1,1-difluorocyclopropane (DFCP) and its d4 and d2 isotopomers using the program Gaussian 03. B3LYP and MP2 models were employed, each with the bases 6-311++G** and cc-pVTZ. Anharmonicity corrections Delta(i) = omega(i) - nu(i) are listed and shown to be different for symmetric and antisymmetric CH stretching modes in situations where Fermi resonance appears to be absent. The same effect is missing in C2H4, for which similar calculations were made. The quadratic force fields for DFCP have been scaled in symmetry coordinate space with 15 scale factors both to observed frequencies nu(obsd)and also to omega (obsd), where omega(obsd) = nu(obsd) + Delta. With nu(obsd) especially, different scale factors are needed for the symmetric and antisymmetric CH stretching force constants due to their differing anharmonicities. The source of the latter in the quartic and cubic force field is explored. MP2 calculations of valence interaction force constants involving the stretching of bonds on a common carbon atom are preferred to those from a B3LYP model. In either model, scaling to omega(obsd) rather than to nu(obsd) does not remove the necessity of varying scale factors for differing types of motion in the same group. Theoretical values of the five quartic centrifugal distortion constants are listed for the normal species and compared with new experimental data. The predictions are sufficiently good to be useful in fitting pure rotational transitions. A weakness is identified in the current Gaussian 03 code for the calculation of vibration-rotation quantities, and limitations are noted in the manner in which Fermi resonance is handled. PMID:18582021

McKean, Donald C; Craig, Norman C; Law, Mark M

2008-07-24

397

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 González; Morgado, Pilar Lafont; Maudes, Jesús Sanz

2012-01-01

398

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

PubMed

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

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

2012-01-01

399

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

400

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

401

Rational design of ion force fields based on thermodynamic solvation properties  

NASA Astrophysics Data System (ADS)

Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H3O+) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the problem is almost underdetermined, i.e., there is a whole set of degenerate parameters that equally well describe, e.g., chloride and bromide ions. (iii) For the heavy cations the problem is overdetermined, i.e., no combination of Lennard-Jones parameters is able to reproduce simultaneously energy and entropy of solvation. We discuss various possibilities to deal with these problems and finally present an optimized force field for the halide anions that reproduces the free energy and the entropy of solvation. For the alkali metal cations there is no unambiguous choice of parameters. Therefore, we give three different parameter sets for every ion with a small, intermediate, or large Lennard-Jones interaction strength, where the Lennard-Jones diameters are optimized to reproduce the solvation free energy. The ionic radius is reproduced with acceptable accuracy by this optimization strategy, meaning that the proposed force fields are reliable beyond the target observables (i.e., free energy and entropy of solvation).

Horinek, Dominik; Mamatkulov, Shavkat I.; Netz, Roland R.

2009-03-01

402

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

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

403

Lorentz Force on Sodium and Chlorine Ions in a Salt Water Solution Flow under a Transverse Magnetic Field  

ERIC Educational Resources Information Center

It is shown that, by applying elementary concepts in electromagnetism and electrochemistry to a system consisting of salt water flowing in a thin rectangular pipe at an average velocity v[subscript A] under the influence of a transverse magnetic field B[subscript 0], an electromotive force generator can be conceived. In fact, the Lorentz force

De Luca, R.

2009-01-01

404

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

405

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

406

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?  

PubMed Central

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

407

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins  

PubMed Central

Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments. PMID:24163642

Shi, Yue; Xia, Zhen; Zhang, Jiajing; Best, Robert; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu

2013-01-01

408

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.  

PubMed

Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments. PMID:24163642

Shi, Yue; Xia, Zhen; Zhang, Jiajing; Best, Robert; Wu, Chuanjie; Ponder, Jay W; Ren, Pengyu

2013-01-01

409

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

2007-08-31

410

Solutions of the Helmholtz equation with boundary conditions for force-free magnetic fields  

NASA Technical Reports Server (NTRS)

It is shown that the solution, with one ignorable coordinate, for the Taylor minimum energy state (resulting in a force-free magnetic field) in either a straight cylindrical or a toroidal geometry with arbitrary cross section can be reduced to the solution of either an inhomogeneous Helmholtz equation or a Grad-Shafranov equation with simple boundary conditions. Standard Green's function theory is, therefore, applicable. Detailed solutions are presented for the Taylor state in toroidal and cylindrical domains having a rectangular cross section. The focus is on solutions corresponding to the continuous eigenvalue spectra. Singular behavior at 90 deg corners is explored in detail.

Rasband, S. N.; Turner, L.

1981-01-01

411

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

PubMed

We present a fibre-top probe fabricated by carving a tipped cantilever on an optical fibre, with the tip machined in correspondence of the fibre core. When approached to an optical prism illuminated under total internal reflection conditions, the tip of the cantilever detects the optical tunnelling signal, while the light coupled from the opposite end of the fibre measures the deflection of the cantilever. Our results suggest that fibre-top technology can be used for the development of a new generation of hybrid probes that can combine atomic force microscopy with scanning near field optical microscopy. PMID:21155996

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

2011-04-01

412

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for protein side-chain analogues  

PubMed Central

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:23420678

Li, Xinbi; Ponomarev, Sergei Y.; Sa, Qina; Sigalovsky, Daniel L.; Kaminski, George A.

2013-01-01

413

Joyce and Ulysses: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data.  

PubMed

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dye's ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case. PMID:23389748

Barone, Vincenzo; Cacelli, Ivo; De Mitri, Nicola; Licari, Daniele; Monti, Susanna; Prampolini, Giacomo

2013-03-21

414

On the representation of potential energy surfaces of polyatomic molecules in normal coordinates: II. Parameterisation of the force field  

NASA Astrophysics Data System (ADS)

By substituting the standard mass-weighted normal coordinates with either Morse-like or Gauss-like coordinates, it is demonstrated that significant improvements can be made to the vibrational spectra of polyatomic molecules calculated variationally. Quartic force fields in the form of Taylor expansions are generated by density functional theory for water, formaldehyde and methane, and their vibrational spectra calculated by the perturbation normal coordinate code SPECTRO. These are then compared with three sets of spectra arising from the variational code MULTIMODE. Initial spectra are obtained using the identical Taylor expansion force fields. A subsequent set of spectra are then obtained for which the symmetric normal coordinates of the force fields are replaced by Morse-like coordinates and a final set of spectra are obtained for which the asymmetric normal coordinates of the force field are replaced by Gauss-like coordinates. The restriction is imposed that the complete set of derivatives to quartic are preserved under these coordinate transformations.

Burcl, Rudolf; Carter, Stuart; Handy, Nicholas C.

2003-05-01

415

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

PubMed

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. PMID:19396813

Saito, Minoru; Okazaki, Isao

2009-12-01

416

Correlation between optical and topographical images from an external reflection near-field microscope with shear force feedback  

NASA Astrophysics Data System (ADS)

An external reflection scanning near-field optical microscope with shear force regulation of the tip-surface distance is described. Near-field optical and shear force topographical images are compared for various samples. It is shown that the most important correlative relationships between these images can be deduced from symmetry considerations. The possibility of extracting additional information from the optical images is demonstrated on images of human blood cells.

Bozhevolnyi, Sergey I.; Smolyaninov, Igor I.; Keller, Ole

1995-07-01

417

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

SciTech Connect

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

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

2014-01-28

418

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

NASA Astrophysics Data System (ADS)

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

Gao, Weimin; Niu, Haitao; Lin, Tong; Wang, Xungai; Kong, Lingxue

2014-01-01

419

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 stres