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Sample records for force field ff

  1. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

    PubMed Central

    2015-01-01

    We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on ?-helical and ?-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

  2. ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.

    PubMed

    Cerutti, David S; Swope, William C; Rice, Julia E; Case, David A

    2014-10-14

    We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard-Jones combining rules. The force field gives strong performance on ?-helical and ?-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

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

    PubMed Central

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

    2010-01-01

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

  4. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations.

    PubMed

    Perez, Alberto; MacCallum, Justin L; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A

    2015-10-13

    Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments. PMID:26574266

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

    NASA Astrophysics Data System (ADS)

    Zou, Chenyu; Van Duin, Adri

    2012-12-01

    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.

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

    E-print Network

    Zhigilei, Leonid V.

    ReaxFF: A Reactive Force Field for Hydrocarbons Adri C. T. van Duin,,| Siddharth Dasgupta, Francois constant as Rij f 0. We report here the ReaxFF for hydrocarbons. The parameters were derived from quantum and geometry data for a number of stable hydrocarbon compounds. We find that the ReaxFF provides a good

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

    E-print Network

    Goddard III, William A.

    Development of a ReaxFF Reactive Force Field for Aqueous Chloride and Copper Chloride Obaidur-derived energies for condensed-phase copper-chloride clusters as well as chloride/water and copper-chloride with the DFT-derived values. We have performed MD simulations on chloride/water and copper-chloride

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

    E-print Network

    Goddard III, William A.

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

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

    E-print Network

    Goddard III, William A.

    -temperature stability, and corrosion resistance. In addition, many of these systems have superionic conductivity at highReaxFF Reactive Force Field for Solid Oxide Fuel Cell Systems with Application to Oxygen IonFF were optimized to reproduce quantum mechanical (QM) calculations on relevant condensed phase

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

    E-print Network

    van Duin, Adri

    the structures and reactive dynamics of complex metal oxide catalysts. The parameters in ReaxFF are derivedDevelopment of the ReaxFF reactive force field for mechanistic studies of catalytic selective, Sanja Pudar, Jonas Oxgaard, Boris Merinov, Yun Hee Jang, and Petter Persson Materials and Process

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

    PubMed

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

    2014-02-27

    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

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

    PubMed

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

    2011-09-13

    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

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

    PubMed Central

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

    2011-01-01

    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

  14. Residue-specific force field based on protein coil library. RSFF2: modification of AMBER ff99SB.

    PubMed

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

    2015-01-22

    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

  15. Parameterizing Complex Reactive Force Fields Using Multiple Objective Evolutionary Strategies (MOES): Part 2: Transferability of ReaxFF Models to C-H-N-O Energetic Materials.

    PubMed

    Rice, Betsy M; Larentzos, James P; Byrd, Edward F C; Weingarten, N Scott

    2015-02-10

    The Multiple Objective Evolutionary Strategies (MOES) algorithm was used to parametrize force fields having the form of the reactive models ReaxFF (van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. J. Phys. Chem. A 2001, 105, 9396) and ReaxFF-lg (Liu, L.; Liu, Y.; Zybin, S. V.; Sun, H.; Goddard, W. A. J. Phys. Chem. A 2011, 115, 11016) in an attempt to produce equal or superior ambient state crystallographic structural results for cyclotrimethylene trinitramine (RDX). Promising candidates were then subjected to molecular dynamics simulations of five other well-known conventional energetic materials to assess the degree of transferability of the models. Two models generated through the MOES search were shown to have performance better than or as good as ReaxFF-lg in describing the six energetic systems modeled. This study shows that MOES is an effective and efficient method to develop complex force fields. PMID:26580903

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

    SciTech Connect

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

    2012-06-01

    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.

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

    PubMed

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

    2012-04-19

    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

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

    E-print Network

    van Duin, Adri

    Dynamics of the Dissociation of Hydrogen on Stepped Platinum Surfaces Using the ReaxFF Reactive, Pasadena, California 91125 ReceiVed: October 24, 2005; In Final Form: January 7, 2006 The dissociation scaling with incident energy and angular dependence at collision energies where a direct dissociation

  19. Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field

    NASA Astrophysics Data System (ADS)

    Verlackt, C. C. W.; Neyts, E. C.; Jacob, T.; Fantauzzi, D.; Golkaram, M.; Shin, Y.-K.; van Duin, A. C. T.; Bogaerts, A.

    2015-10-01

    Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma-cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered time-scale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.

  20. Study of thermal conductivity of ice clusters after impact deposition on the silica surfaces using the ReaxFF reactive force field.

    PubMed

    Rahnamoun, A; van Duin, A C T

    2016-01-21

    During aircraft or spacecraft missions, ice accumulates on different parts of their surface elements. An important parameter affecting the ability to remove this ice from the surface is the heat transfer characteristics of the accumulated ice. The ice heat transfer is related to the process of ice formation and its density and internal structure. In this study we investigate the effects of the ice and silica structure and the ice cluster attachment mechanism to the silica surface on the thermal conductivity (TC) of the attached ice cluster using the ReaxFF reactive force field. The purpose of this study is to investigate the thermal transport in amorphous and crystalline ice after high-velocity deposition on the silica surfaces. A dual thermostat method has been applied for the calculation of TC values. The validity of this method has been verified by comparing the calculated values of TC for crystal and amorphous ice with available experimental values. Our calculations show that the TC values of both crystal and amorphous ice drop after deposition on the silica surfaces. This decrease in the TC is more significant for the ice deposition on suboxide silica surfaces. Furthermore, crystal ice shows higher TC values than amorphous ice after accumulation. However, when crystal ice impacts on the silica surface at 1 km s(-1) impact speed, the crystalline shape of the ice cluster is lost to a considerable level and the TC values obtained for the ice clusters in such cases are closer to amorphous ice TC values. We observed a decrease in the TC values when ionic species are added inside the ice clusters. PMID:26670950

  1. 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

    Rahnamoun, A; van Duin, A C T

    2014-04-17

    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

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

    E-print Network

    Goddard III, William A.

    Simulating the Initial Stage of Phenolic Resin Carbonization via the ReaxFF Reactive Force Field DeVed: May 7, 2009 Pyrolysis of phenolic resins leads to carbon formation. Simulating this resin atomistically. 1. Introduction Phenolic resins are a good source of carbon. Direct pyrolysis of neat phenolic

  3. Establishment of performance standards and a cut-score for the Canadian Forces firefighter physical fitness maintenance evaluation (FF PFME).

    PubMed

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

    2014-01-01

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

  4. Rapid parameterization of small molecules using the Force Field Toolkit

    PubMed Central

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

    2013-01-01

    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

  5. Approximate photochemical dynamics of azobenzene with reactive force fields

    NASA Astrophysics Data System (ADS)

    Li, Yan; Hartke, Bernd

    2013-12-01

    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).

  6. Approximate photochemical dynamics of azobenzene with reactive force fields

    SciTech Connect

    Li, Yan; Hartke, Bernd

    2013-12-14

    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)

  7. A test on reactive force fields for the study of silica dimerization reactions

    NASA Astrophysics Data System (ADS)

    Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; van Erp, Titus S.

    2015-11-01

    We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.

  8. A test on reactive force fields for the study of silica dimerization reactions.

    PubMed

    Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T; Åstrand, Per-Olof; van Erp, Titus S

    2015-11-14

    We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method. PMID:26567652

  9. Neutron Reference Benchmark Field Specification: ACRR Free-Field Environment (ACRR-FF-CC-32-CL).

    SciTech Connect

    Vega, Richard Manuel; Parma, Edward J.; Griffin, Patrick J.; Vehar, David W.

    2015-07-01

    This report was put together to support the International Atomic Energy Agency (IAEA) REAL- 2016 activity to validate the dosimetry community’s ability to use a consistent set of activation data and to derive consistent spectral characterizations. The report captures details of integral measurements taken in the Annular Core Research Reactor (ACRR) central cavity free-field reference neutron benchmark field. The field is described and an “a priori” calculated neutron spectrum is reported, based on MCNP6 calculations, and a subject matter expert (SME) based covariance matrix is given for this “a priori” spectrum. The results of 31 integral dosimetry measurements in the neutron field are reported.

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

    SciTech Connect

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

    2010-10-21

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

  11. Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics.

    PubMed

    Pantelopulos, George A; Mukherjee, Sudipto; Voelz, Vincent A

    2015-09-01

    The p53-MDM2 complex is both a major target for cancer drug development and a valuable model system for computational predictions of protein-ligand binding. To investigate the accuracy of molecular simulations of MDM2 and its complex with p53, we performed a number of long (200 ns to 1 µs) explicit-solvent simulations using a range of force fields. We systematically compared nine popular force fields (AMBER ff03, ff12sb, ff14sb, ff99sb, ff99sb-ildn, ff99sb-ildn-nmr, ff99sb-ildn-phi, CHARMM22*, and CHARMM36) against experimental chemical shift data, and found similarly accurate results, with microsecond simulations achieving better agreement compared to 200-ns trajectories. Although the experimentally determined apo structure has a closed binding cleft, simulations in all force fields suggest the apo state of MDM2 is highly flexible, and able to sample holo-like conformations, consistent with a conformational selection model. Initial structuring of the MDM2 lid region, known to competitively bind the binding cleft, is also observed in long simulations. Taken together, these results show molecular simulations can accurately sample conformations relevant for ligand binding. We expect this study to inform future computational work on folding and binding of MDM2 ligands. PMID:26138282

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

    E-print Network

    Goddard III, William A.

    The dynamics of highly excited electronic systems: Applications of the electron force field Julius provides a practical approach to simulating the dynamics of such systems. eFF includes all the normal, ranging from inertial confinement fusion to semiconductor device fabrication. Understanding the dynamics

  13. Force Field Model of Periodic Trends in Biomolecular Halogen Bonds.

    PubMed

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

    2015-07-23

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

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

    E-print Network

    Fileti, Eudes Eterno

    2014-01-01

    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.

  15. Computational Investigation of Helical Traveling Wave Tube Transverse RF Field Forces

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.; Dayton, James A.

    1998-01-01

    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.

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

    E-print Network

    Goddard III, William A.

    by Nickel Jonathan E. Mueller, Adri C. T. van Duin, and William A. Goddard III*, Materials and Process reactions catalyzed by nickel surfaces and particles using reactive molecular dynamics on thousands of atoms adsorption, decomposition, reformation and desorption of hydrocarbons as they interact with the nickel

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

    E-print Network

    Fileti, Eudes Eterno

    2015-01-01

    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...

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

    PubMed

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

    2014-07-01

    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

  19. ############: 7 ########. L j (ff; z) =

    E-print Network

    Zudilin, Wadim

    .36 ########## ########### ######## ################### ####### #.#. ######### ####################### ########### # ####### ######## ### ## ### ####### #######, ########## # #### ############### ##### ### # ######## ################# #######. # ## ####### ####### ## ###### ##### ### ########### ######## ############### ##### ### # ########## ##### ######### ############ #####. ############: 7 ########. ######### L j (ff; z) = 1 X m=1 z m (ff +m) j ; ### ff 2 Q , j 2 N. ###### ######## #### ## ######## ###### ###### ####### L j (ff l ; z ; : : : ; ! s ######### ######### ############ #####, j 2 Q , j 6= 0, jjj ! 1. ##### a 2 Z, a 6= 0, b 2 N , (a; b) = 1, fi fi a b fi fi \\Gamma 1 + jjj

  20. Polarization effects in molecular mechanical force fields

    PubMed Central

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

    2014-01-01

    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

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

    PubMed Central

    2012-01-01

    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

  2. Radiation Characterization Summary: ACRR Central Cavity Free-Field Environment with the 32-Inch Pedestal at the Core Centerline (ACRR-FF-CC-32-cl).

    SciTech Connect

    Vega, Richard Manuel; Parma, Edward J.; Naranjo, Gerald E.; Lippert, Lance L.; Vehar, David W.; Griffin, Patrick J.

    2015-08-01

    This document presents the facilit y - recommended characteri zation o f the neutron, prompt gamma - ray, and delayed gamma - ray radiation fields in the Annular Core Research Reactor ( ACRR ) for the cen tral cavity free - field environment with the 32 - inch pedestal at the core centerline. The designation for this environmen t is ACRR - FF - CC - 32 - cl. The neutron, prompt gamma - ray , and delayed gamma - ray energy spectra , uncertainties, and covariance matrices are presented as well as radial and axial neutron and gamma - ray fluence profiles within the experiment area of the cavity . Recommended constants are given to facilitate the conversion of various dosimetry readings into radiation metrics desired by experimenters. Representative pulse operations are presented with conversion examples . Acknowledgements The authors wish to th ank the Annular Core Research Reactor staff and the Radiation Metrology Laboratory staff for their support of this work . Also thanks to David Ames for his assistance in running MCNP on the Sandia parallel machines.

  3. The MS-Q Force Field for Clay Minerals: Application to Oil Production Sungu Hwang, Mario Blanco, Ersan Demiralp, Tahir Cagin, and William A. Goddard, III*

    E-print Network

    Çagin, Tahir

    The MS-Q Force Field for Clay Minerals: Application to Oil Production Sungu Hwang, Mario Blanco to model kaolinite and pyrophyllite clay minerals and their interactions with representative organic molecules. The MS-Q FF reproduces the structural parameters for these clay minerals and gives accurate

  4. Secondary Structure of Rat and Human Amylin across Force Fields

    PubMed Central

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, ?-helices, and ?-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of ?-helix and ?-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards ?-hairpins, while CHARMM22/CMAP predicts structures that are overly ?-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils. PMID:26221949

  5. Secondary structure of rat and human amylin across force fields

    DOE PAGESBeta

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, ?-helices, and ?-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore »determined as a function of ?-helix and ?-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards ?-hairpins, while CHARMM22/CMAP predicts structures that are overly ?-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.« less

  6. Secondary structure of rat and human amylin across force fields

    SciTech Connect

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, ?-helices, and ?-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of ?-helix and ?-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards ?-hairpins, while CHARMM22/CMAP predicts structures that are overly ?-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.

  7. 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

    Skelton, Adam; Fenter, Paul; Kubicki, James D.; Wesolowski, David J; Cummings, Peter T

    2011-01-01

    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.

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

    PubMed Central

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

    2012-01-01

    Presented is an extension of the CHARMM General force field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest. PMID:22821581

  9. The harmonic force field of propane

    NASA Astrophysics Data System (ADS)

    Gough, K. M.; Murphy, W. F.; Raghavachari, Krishnan

    1987-09-01

    The quadratic vibrational force field of propane has been obtained by scaling calculated ab initio force fields to fit well determined vibrational frequencies from the Raman and infrared spectra of gaseous propane-h8, propane-d8, 1,1,1,2,3,3,3-propane-d7, and the two rotational isomers of 1,1,2,2,3,3,3-propane-d7. Two different ab initio force fields were investigated, one using Hartree-Fock theory (HF/6-31G*) and the other including electron correlation effects by means of second-order Møller-Plesset perturbation theory (MP2/6-31G*). The scaled MP2/6-31G* force field gives a significantly better fit of the experimental frequencies, especially for those involving contributions from the CC stretching coordinate.

  10. Current Status of Protein Force Fields for Molecular Dynamics

    PubMed Central

    Lopes, Pedro E.M.; Guvench, Olgun

    2015-01-01

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

  11. Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

    PubMed

    Lundborg, Magnus; Lindahl, Erik

    2015-01-22

    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

  12. 7/15 Force current 1/7 FORCE ON A CURRENT IN A MAGNETIC FIELD

    E-print Network

    Gustafsson, Torgny

    7/15 Force current 1/7 FORCE ON A CURRENT IN A MAGNETIC FIELD PURPOSE: To study the force exerted in a magnetic field B, it experiences a magnetic force, called the Lorentz force, F qvBsin , (1) which results of the electrons with the ions, the wire itself experiences a magnetic force due to the interaction of the current

  13. Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and

    E-print Network

    Richardson, David

    Comparison of a QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine Department of Theoretical Physics, University of Paderborn, Paderborn, Germany ABSTRACT We compare mechanics (MM) force fields and with a fast com- bined quantum mechanics/molecular mechanics (QM/MM) force

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

    E-print Network

    Goddard III, William A.

    in such important industrial processes as the Haber Bosch synthesis of ammonia and the Fischer-Tropsch formation and Decomposition Jonathan E. Mueller, Adri C. T. van Duin,§ and William A. Goddard III*, Materials and Process on nickel clusters. 1.0. Introduction Nickel is the primary catalyst in the steam reforming process1

  15. Reduced yield stress for zirconium exposed to iodine: Reactive force field simulation

    SciTech Connect

    Rossi, Matthew L.; Taylor, Christopher D.; van Duin, Adri C. T.

    2014-11-04

    Iodine-induced stress-corrosion cracking (ISCC), a known failure mode for nuclear fuel cladding, occurs when iodine generated during the irradiation of a nuclear fuel pellet escapes the pellet through diffusion or thermal cracking and chemically interacts with the inner surface of the clad material, inducing a subsequent effect on the cladding’s resistance to mechanical stress. To complement experimental investigations of ISCC, a reactive force field (ReaxFF) compatible with the Zr-I chemical and materials systems has been developed and applied to simulate the impact of iodine exposure on the mechanical strength of the material. The study shows that the material’s resistance to stress (as captured by the yield stress of a high-energy grain boundary) is related to the surface coverage of iodine, with the implication that ISCC is the result of adsorption-enhanced decohesion.

  16. Reduced yield stress for zirconium exposed to iodine: Reactive force field simulation

    DOE PAGESBeta

    Rossi, Matthew L.; Taylor, Christopher D.; van Duin, Adri C. T.

    2014-11-04

    Iodine-induced stress-corrosion cracking (ISCC), a known failure mode for nuclear fuel cladding, occurs when iodine generated during the irradiation of a nuclear fuel pellet escapes the pellet through diffusion or thermal cracking and chemically interacts with the inner surface of the clad material, inducing a subsequent effect on the cladding’s resistance to mechanical stress. To complement experimental investigations of ISCC, a reactive force field (ReaxFF) compatible with the Zr-I chemical and materials systems has been developed and applied to simulate the impact of iodine exposure on the mechanical strength of the material. The study shows that the material’s resistance tomore »stress (as captured by the yield stress of a high-energy grain boundary) is related to the surface coverage of iodine, with the implication that ISCC is the result of adsorption-enhanced decohesion.« less

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

    PubMed Central

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

    2014-01-01

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

  18. Conformal field theory of critical Casimir forces

    NASA Astrophysics Data System (ADS)

    Emig, Thorsten; Bimonte, Giuseppe; Kardar, Mehran

    2015-03-01

    Thermal fluctuations of a critical system induce long-ranged Casimir forces between objects that couple to the underlying field. For two dimensional conformal field theories (CFT) we derive exact results for the Casimir interaction for a deformed strip and for two compact objects of arbitrary shape in terms of the free energy of a standard region (circular ring or flat strip) whose dimension is determined by the mutual capacitance of two conductors with the objects' shape; and a purely geometric energy that is proportional to conformal charge of the CFT, but otherwise super-universal in that it depends only on the shapes and is independent of boundary conditions and other details. The effect of inhomogenous boundary conditions is also discussed.

  19. FORCE FIELD DEVELOPMENT FOR SIMULATIONS OF CONDENSED PHASES

    E-print Network

    1 FORCE FIELD DEVELOPMENT FOR SIMULATIONS OF CONDENSED PHASES A. Z. Panagiotopoulos1 IPST of this review is on development of force fields for simulations of technologically important properties properties over a broad range of temperatures and densities. Most existing force fields have been optimized

  20. Transferable force field for alcohols and polyalcohols.

    PubMed

    Ferrando, Nicolas; Lachet, Véronique; Teuler, Jean-Marie; Boutin, Anne

    2009-04-30

    A new force field has been developed for alcohol and polyalcohol molecules. Based on the anisotropic united-atom force field AUA4 developed for hydrocarbons, it only introduces one new anisotropic united atom corresponding to the hydroxyl group OH. In the case of polyalcohols and complex molecules, the calculation of the intramolecular electrostatic energy is revisited. These interactions are calculated between charges belonging to the different local dipoles of the molecule, one dipole being defined as a group of consecutive charges globally neutral. This new method allows avoiding the use of empirical scaling parameters commonly introduced to calculate 1-4 electrostatic interactions. The transferability of the proposed potential is demonstrated through the simulation of a wide variety of alcohol families: primary alcohols (methanol, ethanol, propan-1-ol, hexan-1-ol, octan-1-ol), secondary alcohols (propan-2-ol), tertiary alcohols (2-methylpropan-2-ol), phenol, and diols (1,2-ethanediol, 1,3-propanediol, 1,5-pentanediol). Monte Carlo simulations carried out in the Gibbs ensemble lead to a good agreement between calculated and experimental data for the thermodynamic properties along the liquid/vapor saturation curve, for the critical point coordinates and for the liquid structure at room temperature. Additional simulations were performed on the methanol + n-butane system showing the capability of the proposed potential to reproduce the azeotropic behavior of such mixtures with a good agreement. PMID:19344171

  1. The Energetics of Motivated Cognition: A Force-Field Analysis

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

    Hustedde, Ron; Score, Michael

    1995-01-01

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

  3. The Introduction of Fields in Relation to Force

    ERIC Educational Resources Information Center

    Brunt, Marjorie; Brunt, Geoff

    2012-01-01

    The introduction of force at age 14-16 years is considered, starting with elementary student experiments using magnetic force fields. The meaningless use of terms such as "action" and "reaction", or "agent" and "receiver" is discussed. (Contains 6 figures.)

  4. Nanoscale Piezoelectric Properties of Self-Assembled Fmoc-FF Peptide Fibrous Networks.

    PubMed

    Ryan, Kate; Beirne, Jason; Redmond, Gareth; Kilpatrick, Jason I; Guyonnet, Jill; Buchete, Nicolae-Viorel; Kholkin, Andrei L; Rodriguez, Brian J

    2015-06-17

    Fibrous peptide networks, such as the structural framework of self-assembled fluorenylmethyloxycarbonyl diphenylalanine (Fmoc-FF) nanofibrils, have mechanical properties that could successfully mimic natural tissues, making them promising materials for tissue engineering scaffolds. These nanomaterials have been determined to exhibit shear piezoelectricity using piezoresponse force microscopy, as previously reported for FF nanotubes. Structural analyses of Fmoc-FF nanofibrils suggest that the observed piezoelectric response may result from the noncentrosymmetric nature of an underlying ?-sheet topology. The observed piezoelectricity of Fmoc-FF fibrous networks is advantageous for a range of biomedical applications where electrical or mechanical stimuli are required. PMID:25994251

  5. Reactive Force Fields via Explicit Valency

    NASA Astrophysics Data System (ADS)

    Kale, Seyit

    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.

  6. Dislocation core fields and forces in FCC metals

    SciTech Connect

    Henager, Charles H.; Hoagland, Richard G.

    2004-04-01

    Atomistic models were used to obtain dislocation core fields for edge, screw, and mixed dislocations in Al and Cu using EAM. Core fields are analyzed using a line force dipole representation, with dilatant and dipole terms. The core field contribution to the force between dislocations is shown to be significant for interactions within 50b.

  7. ReaxFF Study of the Oxidation of Softwood Lignin in View of Carbon Fiber Production

    SciTech Connect

    Beste, Ariana

    2014-01-01

    We investigate the oxidative, thermal conversion of softwood lignin by performing molecular dynamics simulations based on a reactive force field (ReaxFF). The lignin samples are constructed from coniferyl alcohol units, which are connected through linkages that are randomly selected from a natural distribution of linkages in softwood. The goal of this work is to simulate the oxidative stabilization step during carbon fiber production from lignin precursor. We find that at simulation conditions where stabilization reactions occur, the lignin fragments have already undergone extensive degradation. The 5-5 linkage shows the highest reactivity towards cyclization and dehydrogenation.

  8. Lorentz Body Force Induced by Traveling Magnetic Fields

    NASA Technical Reports Server (NTRS)

    Volz, M. P.; Mazuruk, K.

    2003-01-01

    The Lorentz force induced by a traveling magnetic field (TMF) in a cylindrical container has been calculated. The force can be used to control flow in dectrically conducting melts and the direction of the magnetic field and resulting flow can be reversed. A TMF can be used to partially cancel flow driven by buoyancy. The penetration of the field into the cylinder decreases as the frequency increases, and there exists an optimal value of frequency for which the resulting force is a maximum. Expressions for the Lorentz force in the limiting cases of low frequency and infinite cylinder are also given and compared to the numerical calculations.

  9. Biomolecular simulations of membranes: Physical properties from different force fields

    E-print Network

    Siu, Weng In "Shirley"

    Received 28 December 2007; accepted 22 February 2008; published online 27 March 2008 Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all

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

    E-print Network

    Fornberg, Bengt

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

  11. Drag forces on inclusions in classical fields with dissipative dynamics

    E-print Network

    Vincent Demery; D. S. Dean

    2010-04-01

    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.

  12. Prediction of Mechanical Properties of Polymers With Various Force Fields

    NASA Technical Reports Server (NTRS)

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

    2005-01-01

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

  13. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

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

    2007-06-14

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

  14. A Molecular Mechanics Force Field for Biologically Important Sterols

    E-print Network

    Ullmann, G. Matthias

    of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol

  15. Generative morphologies of architectural organization in matter force field

    E-print Network

    Mutlu, Murat

    2010-01-01

    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 ...

  16. Mitigated-force carriage for high magnetic field environments

    DOEpatents

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

    2015-05-19

    A carriage for high magnetic field environments includes a plurality of work-piece separators disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla for supporting and separating a plurality of work-pieces by a preselected, essentially equal spacing, so that, as a first work-piece is inserted into the magnetic field, a 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.

  17. A transferable ab initio based force field for aqueous ions

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

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

    SciTech Connect

    Jiang, Deen; Van Duin, Adri C. T.; GoddardIII, William A; Dai, Sheng

    2009-01-01

    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.

  19. Imaging the C black formation by acetylene pyrolysis with molecular reactive force field simulations.

    PubMed

    Zhang, Chaoyang; Zhang, Chi; Ma, Yu; Xue, Xianggui

    2015-05-01

    C black is a class of substantial materials with a long history of applications. However, apart from some descriptions of primary reactions, subsequent processes leading up to the final formation mechanism remain unclear. This mechanism is also crucial for understanding the formation of other carbonaceous materials. In this work, we visualize C black formation by acetylene pyrolysis using molecular dynamics simulations with a molecular reactive force field named ReaxFF. We find that the formation undergoes four stages: (1) chain elongation by H abstraction and polymerization of small C species, (2) chain branching, (3) cyclization and ring densification, and (4) condensed ring folding. The simulated C black particle possesses a structure of folded graphite layers, which is in good accordance with experimental observations. Cyclization and condensation are derived from fusion between neighboring chains, significantly varying from common experimental observations at relatively low temperatures that abide by the mechanism of H abstraction and C2H2 addition. Moreover, polyyne and polyene are usually found during acetylene pyrolysis, suggesting that the pyrolysis of acetylene and other hydrocarbons may be a feasible method of obtaining carbyne, a novel carbonaceous material with a high value. PMID:25854895

  20. Acceleration of particles in an isotropic random force field

    E-print Network

    Hector Javier Durand-Manterola

    2012-04-18

    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)).

  1. Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants

    SciTech Connect

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

    2011-01-01

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

  2. Alternating Magnetic Field Forces for Satellite Formation Flying

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  3. Apparatus having reduced mechanical forces for supporting high magnetic fields

    DOEpatents

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

    1991-01-01

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

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

    NASA Technical Reports Server (NTRS)

    El-Kaddah, N.; Szekely, J.

    1982-01-01

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

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

    PubMed

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

    2014-11-14

    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

  6. Visualization of Force Fields in Protein Structure Prediction

    SciTech Connect

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

    2005-04-26

    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.

  7. Extension of the AMBER force field for nitroxide radicals and combined QM/MM/PCM approach to the accurate determination of EPR parameters of DMPOH in solution

    PubMed Central

    Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo

    2015-01-01

    A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in ?-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116

  8. Benchmarking of Force Fields for Molecule-Membrane Interactions.

    PubMed

    Paloncýová, Markéta; Fabre, Gabin; DeVane, Russell H; Trouillas, Patrick; Berka, Karel; Otyepka, Michal

    2014-09-01

    Studies of drug-membrane interactions witness an ever-growing interest, as penetration, accumulation, and positioning of drugs play a crucial role in drug delivery and metabolism in human body. Molecular dynamics simulations complement nicely experimental measurements and provide us with new insight into drug-membrane interactions; however, the quality of the theoretical data dramatically depends on the quality of the force field used. We calculated the free energy profiles of 11 molecules through a model dimyristoylphosphatidylcholine (DMPC) membrane bilayer using five force fields, namely Berger, Slipids, CHARMM36, GAFFlipids, and GROMOS 43A1-S3. For the sake of comparison, we also employed the semicontinuous tool COSMOmic. High correlation was observed between theoretical and experimental partition coefficients (log K). Partition coefficients calculated by all-atomic force fields (Slipids, CHARMM36, and GAFFlipids) and COSMOmic differed by less than 0.75 log units from the experiment and Slipids emerged as the best performing force field. This work provides the following recommendations (i) for a global, systematic and high throughput thermodynamic evaluations (e.g., log K) of drugs COSMOmic is a tool of choice due to low computational costs; (ii) for studies of the hydrophilic molecules CHARMM36 should be considered; and (iii) for studies of more complex systems, taking into account all pros and cons, Slipids is the force field of choice. PMID:26588554

  9. Average Lorentz self-force from electric field lines

    NASA Astrophysics Data System (ADS)

    Aashish, Sandeep; Haque, Asrarul

    2015-09-01

    We generalize the derivation of electromagnetic fields of a charged particle moving with a constant acceleration Singal (2011 Am. J. Phys. 79 1036) to a variable acceleration (piecewise constants) over a small finite time interval using Coulomb's law, relativistic transformations of electromagnetic fields and Thomson's construction Thomson (1904 Electricity and Matter (New York: Charles Scribners) ch 3). We derive the average Lorentz self-force for a charged particle in arbitrary non-relativistic motion via averaging the fields at retarded time.

  10. Nonequilibrium forces between neutral atoms mediated by a quantum field

    SciTech Connect

    Behunin, Ryan O.; Hu, Bei-Lok

    2010-08-15

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

  11. Interaction Forces Between Multiple Bodies in a Magnetic Field

    NASA Technical Reports Server (NTRS)

    Joffe, Benjamin

    1996-01-01

    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.

  12. Water-Silica Force Field for Simulating Nanodevices

    PubMed Central

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

    2008-01-01

    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

  13. Transferable force fields for adsorption of small gases in zeolites.

    PubMed

    Martin-Calvo, A; Gutiérrez-Sevillano, J J; Parra, J B; Ania, C O; Calero, S

    2015-10-01

    We provide transferable force fields for oxygen, nitrogen, and carbon monoxide that are able to reproduce experimental adsorption in both pure silica and alumino-substituted zeolites at cryogenic and high temperatures. The force field parameters can be combined with those previously reported for carbon dioxide, methane, and argon, opening the possibility for studying mixtures of interest containing the six components. Using these force field parameters we obtained some adsorption isotherms at cryogenic temperatures that at first sight were in discrepancies with experimental values for certain molecules and structures. We attribute these discrepancies to the sensitiveness of the equipment and to kinetic impedimenta that can lead to erratic results. Additional problems can be found during simulations when extra-framework cations are present in the system as their lack of mobility at low temperatures could lead to kinetic effects that hinder experimental adsorption. PMID:26313242

  14. Force-free field model of ball lightning

    NASA Astrophysics Data System (ADS)

    Tsui, K. H.

    2001-03-01

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

  15. Mitigated-force carriage for high magnetic field environments

    SciTech Connect

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

    2014-05-20

    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.

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

    NASA Astrophysics Data System (ADS)

    Fu, Jinxin; Ou-Yang, H. Daniel

    2014-09-01

    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.

  17. Force, current and field effects in single atom manipulation

    E-print Network

    Braun, Kai-Felix

    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

  18. 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...

  19. Force-Field Analysis: A Functional Management System

    ERIC Educational Resources Information Center

    Sanders, Stanley G.

    1977-01-01

    Force field analysis combines the advantages of the basic organization, objectivity, and science of systems theory and systems methods, with a simplicity and clarity that allows its mastery by policy-makers and administrators who are not specialists in engineering, data processing, or programming. (Author/IRT)

  20. Energy buildup in sheared force-free magnetic fields

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard; Low, Boon C.

    1992-01-01

    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.

  1. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

    PubMed Central

    KIRSCHNER, KARL N.; YONGYE, AUSTIN B.; TSCHAMPEL, SARAH M.; GONZÁLEZ-OUTEIRIÑO, JORGE; DANIELS, CHARLISA R.; FOLEY, B. LACHELE; WOODS, ROBERT J.

    2015-01-01

    A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both ?- and ?-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. PMID:17849372

  2. Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields.

    PubMed

    Mou?ka, Filip; Nezbeda, Ivo; Smith, William R

    2015-04-14

    We describe a computationally efficient molecular simulation methodology for calculating the concentration dependence of the chemical potentials of both solute and solvent in aqueous electrolyte solutions, based on simulations of the salt chemical potential alone. We use our approach to study the predictions for aqueous NaCl solutions at ambient conditions of these properties by the recently developed polarizable force fields (FFs) AH/BK3 of Kiss and Baranyai ( J. Chem. Phys. 2013 , 138 , 204507 ) and AH/SWM4-DP of Lamoureux and Roux ( J. Phys. Chem. B 2006 , 110 , 3308 - 3322 ) and by the nonpolarizable JC FF of Joung and Cheatham tailored to SPC/E water ( J. Phys. Chem. B 2008 , 112 , 9020 - 9041 ). We also consider their predictions of the concentration dependence of the electrolyte activity coefficient, the crystalline solid chemical potential, the electrolyte solubility, and the solution specific volume. We first highlight the disagreement in the literature concerning calculations of solubility by means of molecular simulation in the case of the JC FF and provide strong evidence of the correctness of our methodology based on recent independently obtained results for this important test case. We then compare the predictions of the three FFs with each other and with experiment and draw conclusions concerning their relative merits, with particular emphasis on the salt chemical potential and activity coefficient vs concentration curves and their derivatives. The latter curves have only previously been available from Kirkwood-Buff integrals, which require approximate numerical integrations over system pair correlation functions at each concentration. Unlike the case of the other FFs, the AH/BK3 curves are nearly parallel to the corresponding experimental curves at moderate and higher concentrations. This leads to an excellent prediction of the water chemical potential via the Gibbs-Duhem equation and enables the activity coefficient curve to be brought into excellent agreement with experiment by incorporating an appropriate value of the standard state chemical potential in the Henry Law convention. PMID:26574385

  3. Developing accurate molecular mechanics force fields for conjugated molecular systems.

    PubMed

    Do, Hainam; Troisi, Alessandro

    2015-10-14

    A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel. PMID:26349916

  4. Atomistic force field for alumina fit to density functional theory

    SciTech Connect

    Sarsam, Joanne; Thomas Young Centre, Imperial College London, London SW7 2AZ ; Finnis, Michael W.; Tangney, Paul; Thomas Young Centre, Imperial College London, London SW7 2AZ; Department of Physics, Imperial College London, London SW7 2AZ

    2013-11-28

    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.

  5. Field measurement of basal forces generated by erosive debris flows

    USGS Publications Warehouse

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

    2013-01-01

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

  6. Particle energization in a chaotic force-free magnetic field

    NASA Astrophysics Data System (ADS)

    Li, Xiaocan; Li, Gang; Dasgupta, Brahmananda

    2015-04-01

    A force-free field (FFF) is believed to be a reasonable description of the solar corona and in general a good approximation for low-beta plasma. The equations describing the magnetic field of FFF is similar to the ABC fluid equations which has been demonstrated to be chaotic. This implies that charged particles will experience chaotic magnetic field in the corona. Here, we study particle energization in a time-dependent FFF using a test particle approach. An inductive electric field is introduced by turbulent motions of plasma parcels. We find efficient particle acceleration with power-law like particle energy spectra. The power-law indices depend on the amplitude of plasma parcel velocity field and the spatial scales of the magnetic field fluctuation. The spectra are similar for different particle species. This model provide a possible mechanism for seed population generation for particle acceleration by, e.g., CME-driven shocks. Generalization of our results to certain non-force-free-field (NFFF) is straightforward as the sum of two or multiple FFFs naturally yield NFFF.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

    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

    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

  9. Double-charge model for classical force-field simulations

    NASA Astrophysics Data System (ADS)

    Barrett, Christopher; Wang, Lin-Wang

    2015-06-01

    In a traditional classical force-field model, the atomic point charge that generates the electrostatic potential, and the Born charge induced by atomic movement, are represented by the same charge parameter. But their actual values can be very different, and correct values for both of them are needed in order to yield the correct atomic structure (electrostatic charge) and phonon spectrum (Born charge). This is particularly true for nanostructure calculations. Here, we introduce a double-charge model (DCM) to reconcile the difference between the electrostatic charge and Born charge. The DCM allows us to reproduce the accurate ab initio phonon spectrum not only in bulk systems, but also for nanostructures (slabs and nanowires). This enables the use of classical force fields to study phonon spectra of large nanostructures, which are important for many phenomena from carrier dynamics to thermo conductivities.

  10. Four-nucleon force in chiral effective field theory

    SciTech Connect

    Evgeny Epelbaum

    2005-10-25

    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.

  11. Parmbsc1: a refined force field for DNA simulations.

    PubMed

    Ivani, Ivan; Dans, Pablo D; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balaceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluis; González, Carlos; Vendruscolo, Michele; Laughton, Charles A; Harris, Sarah A; Case, David A; Orozco, Modesto

    2016-01-01

    We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ?140 ?s) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/. PMID:26569599

  12. Tuning the Mass of Chameleon Fields in Casimir Force Experiments

    E-print Network

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

    2010-03-08

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

  13. Current Status of the AMOEBA Polarizable Force Field

    PubMed Central

    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

    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

  14. Design and optimization of force-reduced high field magnets

    NASA Astrophysics Data System (ADS)

    Rembeczki, Szabolcs

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

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

    PubMed

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

    2013-02-12

    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

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

    SciTech Connect

    Belden, R.D.

    1993-10-08

    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).

  17. THE PULSATION MODE AND DISTANCE OF THE CEPHEID FF AQUILAE

    SciTech Connect

    Turner, D. G.; Kovtyukh, V. V.; Luck, R. E.; Berdnikov, L. N. E-mail: val@deneb1.odessa.ua E-mail: leonid.berdnikov@gmail.com

    2013-07-20

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

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

    E-print Network

    Goddard III, William A.

    , François Lorant a , Paul-Marie Marquaire c , William A. Goddard III b,* a Institut Français du Pétrole, BP Physique des Réactions, Nancy Université, CNRS, 1 rue Grandville, B.P.20451 F, 54001 Nancy cedex, France the processes that generate oil and gas in the subsurface, and that this thermal pro- cess can be described

  19. Casimir force for a scalar field in warped brane worlds

    E-print Network

    Roman Linares; Hugo A. Morales-Tecotl; Omar Pedraza

    2007-12-24

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

  20. Casimir force for a scalar field in warped brane worlds

    SciTech Connect

    Linares, Roman; Morales-Tecotl, Hugo A.; Pedraza, Omar

    2008-03-15

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

  1. Casimir force for a scalar field in warped brane worlds

    NASA Astrophysics Data System (ADS)

    Linares, Román; Morales-Técotl, Hugo A.; Pedraza, Omar

    2008-03-01

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

  2. Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching

    NASA Astrophysics Data System (ADS)

    Li, Jicun; Wang, Feng

    2015-11-01

    Simple non-polarizable potentials were developed for Na+, K+, Cl-, and Br- using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.

  3. Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching.

    PubMed

    Li, Jicun; Wang, Feng

    2015-11-21

    Simple non-polarizable potentials were developed for Na(+), K(+), Cl(-), and Br(-) using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration. PMID:26590540

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

    PubMed Central

    2011-01-01

    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

  5. Mechanics 1: Motion in a Central Force Field We now study the properties of a particle of (constant) mass m moving in a particular type of force

    E-print Network

    Kerswell, Rich

    Mechanics 1: Motion in a Central Force Field We now study the properties of a particle of (constant) mass m moving in a particular type of force field, a central force field. Central forces are very important in physics and engineering. For example, the gravitional force of attraction between two point

  6. Sodium Chloride, NaCl/? : New Force Field

    E-print Network

    Raul Fuentes-Azcatl; Marcia C. Barbosa

    2015-08-08

    A new computational model for Sodium Chloride, the NaCl/{\\epsilon}, is proposed. The Force Fields employed here for the description of the NaCl is based on a set of radial particle-particle pair potentials involving Lennard-Jones (LJ) and Coulombic forces. The parameterization is obtained fitting the density of the crystal and the density and the dielectric constant of the mixture of salt with water at diluted solution. Our model shows good agreement with the experimental values for the density and surface tension for the pure system and for the density, the viscosity, the diffusion, and the dielectric constant for the mixture with water at various molal concentrations. The NaCl/{\\epsilon} together with the water TIP4P/{\\epsilon} model provide a good approximation for studying electrolyte solutions.

  7. Interfacial Force Field Characterization in a Constrained Vapor Bubble Thermosyphon

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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

  8. Interfacial force field characterization in a constrained vapor bubble thermosyphon

    SciTech Connect

    DasGupta, S.; Plawsky, J.L.; Wayner, P.C. Jr.

    1995-09-01

    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. 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-Pitaevskii 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.

  9. 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

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

    2014-01-21

    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.

  10. Continuum Polarizable Force Field within the Poisson-Boltzmann Framework

    PubMed Central

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

    2008-01-01

    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

  11. Validating empirical force fields for molecular-level simulation of cellulose dissolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

  12. Three Force Fields' Views of the 310 Helix Kalliopi K. Patapati and Nicholas M. Glykos*

    E-print Network

    Glykos, Nikolaos

    Three Force Fields' Views of the 310 Helix Kalliopi K. Patapati and Nicholas M. Glykos* Department force fields as evidenced from simulations of proteins in the folded state does not hold true different force fields show irreconcilable differ- ences in their folding predictions, even

  13. AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

    E-print Network

    Schlegel, H. Bernhard

    AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA Raviprasad of biological macromolecules, ultimately, resulting in elucidation of biological function. The AMBER force field functional RNAs. We developed force field parameters for the 107 modified nucleotides currently known

  14. Accounting for electronic polarization in nonpolarizable force fields

    E-print Network

    Leontyev, Igor

    2015-01-01

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole $\\mu$~3D reported in recent ab initio and experimental s...

  15. Development of force field parameters for molecular simulation of polylactide

    PubMed Central

    McAliley, James H.; Bruce, David A.

    2011-01-01

    Polylactide is a biodegradable polymer that is widely used for biomedical applications, and it is a replacement for some petroleum based polymers in applications that range from packaging to carpeting. Efforts to characterize and further enhance polylactide based systems using molecular simulations have to this point been hindered by the lack of accurate atomistic models for the polymer. Thus, we present force field parameters specifically suited for molecular modeling of PLA. The model, which we refer to as PLAFF3, is based on a combination of the OPLS and CHARMM force fields, with modifications to bonded and nonbonded parameters. Dihedral angle parameters were adjusted to reproduce DFT data using newly developed CMAP dihedral cross terms, and the model was further adjusted to reproduce experimentally resolved crystal structure conformations, melt density, volume expansivity, and the glass transition temperature of PLA. We recommend the use of PLAFF3 in modeling PLA in its crystalline or amorphous states and have provided the necessary input files required for the publicly available molecular dynamics code GROMACS. PMID:22180734

  16. Development of the ReaxFFCBN reactive force field for the improved design of liquid CBN hydrogen storage materials.

    PubMed

    Pai, Sung Jin; Yeo, Byung Chul; Han, Sang Soo

    2016-01-21

    Liquid CBN (carbon-boron-nitrogen) hydrogen-storage materials such as 3-methyl-1,2-BN-cyclopentane have the advantage of being easily accessible for use in current liquid-fuel infrastructure. To develop practical liquid CBN hydrogen-storage materials, it is of great importance to understand the reaction pathways of hydrogenation/dehydrogenation in the liquid phase, which are difficult to discover by experimental methods. Herein, we developed a reactive force field (ReaxFFCBN) from quantum mechanical (QM) calculations based on density functional theory for the storage of hydrogen in BN-substituted cyclic hydrocarbon materials. The developed ReaxFFCBN provides similar dehydrogenation pathways and energetics to those predicted by QM calculations. Moreover, molecular dynamics (MD) simulations with the developed ReaxFFCBN can predict the stability and dehydrogenation behavior of various liquid CBN hydrogen-storage materials. Our simulations reveal that a unimolecular dehydrogenation mechanism is preferred in liquid CBN hydrogen-storage materials. However, as the temperature in the simulation increases, the contribution of a bimolecular dehydrogenation mechanism also increases. Moreover, our ReaxFF MD simulations show that in terms of thermal stability and dehydrogenation kinetics, liquid CBN materials with a hexagonal structure are more suitable materials than those with a pentagonal structure. We expect that the developed ReaxFFCBN could be a useful protocol in developing novel liquid CBN hydrogen-storage materials. PMID:26681481

  17. 6.641 Electromagnetic Fields, Forces, and Motion, Spring 2003

    E-print Network

    Zahn, Markus, 1946-

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

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

    SciTech Connect

    Henson, Neil Jon; Waldher, Benjamin; Kuta, Jadwiga; Clark, Aurora; Clark, Aurora E

    2009-01-01

    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.

  19. The exterior source surface for force-free fields. [solar atmosphere magnetic field model

    NASA Technical Reports Server (NTRS)

    Barbosa, D. D.

    1978-01-01

    Consideration is given to the exterior source surface for force-free fields. The spherical harmonic expansion is presented for boundary values on two concentric spheres. An upper limit on a constant which measures the strength of coronal currents is found to be a function of the lowest multipole moment of the prescribed boundary values. The solar atmosphere is in the class of magnetic fields for which the study is applicable.

  20. Application of polarizable ellipsoidal force field model to pnicogen bonds.

    PubMed

    Liu, Fang; Du, Likai; Gao, Jun; Wang, Lili; Song, Bo; Liu, Chengbu

    2015-03-15

    Noncovalent interactions, such as hydrogen bonds and halogen bonds, are frequently used in drug designing and crystal engineering. Recently, a novel noncovalent pnicogen bonds have been identified as an important driving force in crystal structures with similar bonding mechanisms as hydrogen bond and halogen bond. Although the pnicogen bond is highly anisotropic, the pnicogen bond angles range from 160° to 180° due to the complicated substituent effects. To understand the anisotropic characters of pnicogen bond, a modification of the polarizable ellipsoidal force field (PEff) model previously used to define halogen bonds was proposed in this work. The potential energy surfaces (PESs) of mono- and polysubstituted PH3 -NH3 complexes were calculated at CCSD(T), MP2, and density functional theory levels and were used to examine the modified PEff model. The results indicate that the modified PEff model can precisely characterize pnicogen bond. The root mean squared error of PES obtained with PEff model is less than 0.5 kcal/mol, compared with MP2 results. In addition, the modified PEff model may be applied to other noncovalent bond interactions, which is important to understand the role of intermolecular interactions in the self-assembly structures. PMID:25565043

  1. Investigation of crossed SAW fields by scanning acoustic force microscopy.

    PubMed

    Behme, G; Hesjedal, T

    2001-07-01

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

  2. On the Use of Quartic Force Fields in Variational Calculations

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

    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).

  3. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

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

    2007-03-01

    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.

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

    PubMed

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

    2015-02-01

    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

  5. Interactions of hydrogen with the iron and iron carbide interfaces: a ReaxFF molecular dynamics study.

    PubMed

    Islam, Md Mahbubul; Zou, Chenyu; van Duin, Adri C T; Raman, Sumathy

    2015-12-23

    Hydrogen embrittlement (HE) is a well-known material phenomenon that causes significant loss in the mechanical strength of structural iron and often leads to catastrophic failures. In order to provide a detailed atomistic description of HE we have used a reactive bond order potential to adequately describe the diffusion of hydrogen as well as its chemical interaction with other hydrogen atoms, defects, and the host metal. The currently published ReaxFF force field for Fe/C/H systems was originally developed to describe Fischer-Tropsch (FT) catalysis [C. Zou, A. C. T. van Duin and D. C. Sorescu, Top. Catal., 2012, 55, 391-401], and especially had been trained for surface formation energies, binding energies of small hydrocarbon radicals on different surfaces of iron and the barrier heights of surface reactions. We merged this force field with the latest ReaxFF carbon parameters [S. Goverapet Srinivasan, A. C. T. van Duin and P. Ganesh, J. Phys. Chem. A, 2015, 119, 1089-5639] and used the same training data set to refit the Fe/C interaction parameters. The present work is focused on evaluating the applicability of this reactive force field to describe material characteristics and study the role of defects and impurities in the bulk and at the precipitator interfaces. We study the interactions of hydrogen with pure and defective ?-iron (ferrite), Fe3C (cementite), and ferrite-cementite interfaces with a vacancy cluster. We also investigate the growth of nanovoids in ?-iron using a grand canonical Monte Carlo (GCMC) scheme. The calculated hydrogen diffusion coefficients for both ferrite and cementite phases predict a decrease in the work of separation with increasing hydrogen concentration at the ferrite-cementite interface, suggesting a hydrogen-induced decohesion behavior. Hydrogen accumulation at the interface was observed during molecular dynamics (MD) simulations, which is consistent with experimental findings. These results demonstrate the ability of the ReaxFF potential to elucidate various aspects of hydrogen embrittlement in ?-iron and hydrogen interactions at a more complex metal/metal carbide interface. PMID:26626108

  6. Enthalpy of formation and anharmonic force field of diacetylene.

    PubMed

    Simmonett, Andrew C; Schaefer, Henry F; Allen, Wesley D

    2009-01-28

    The enthalpy of formation of diacetylene (C4H2) is pinpointed using state-of-the-art theoretical methods, accounting for high-order electron correlation, relativistic effects, non-Born-Oppenheimer corrections, and vibrational anharmonicity. Molecular energies are determined from coupled cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples (CCSDT), and perturbative quadruples [CCSDT(Q)], in concert with correlation-consistent basis sets (cc-pVXZ, X=D, T, Q, 5, 6) that facilitate extrapolations to the complete basis set limit. The first full quartic force field of diacetylene is determined at the highly accurate all-electron CCSD(T) level with a cc-pCVQZ basis, which includes tight functions for core correlation. Application of second-order vibrational perturbation theory to our anharmonic force field yields fundamental frequencies with a mean absolute difference of only 3.9 cm(-1) relative to the experimental band origins, without the use of any empirical scale factors. By a focal point approach, we converge on an enthalpy change for the isogyric reaction 2 H-C[triple bond]C-H-->H-C[triple bond]C-C[triple bond]C-H+H2 of (+0.03, +0.81) kcal mol(-1) at (0, 298.15) K. With the precisely established fHdegrees of acetylene, we thus obtain DeltafHdegrees(C4H2)=(109.4,109.7)+/-0.3 kcal mol(-1) at (0, 298.15) K. Previous estimates of the diacetylene enthalpy of formation range from 102 to 120 kcal mol(-1). PMID:19191379

  7. Enthalpy of formation and anharmonic force field of diacetylene

    NASA Astrophysics Data System (ADS)

    Simmonett, Andrew C.; Schaefer, Henry F.; Allen, Wesley D.

    2009-01-01

    The enthalpy of formation of diacetylene (C4H2) is pinpointed using state-of-the-art theoretical methods, accounting for high-order electron correlation, relativistic effects, non-Born-Oppenheimer corrections, and vibrational anharmonicity. Molecular energies are determined from coupled cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples (CCSDT), and perturbative quadruples [CCSDT(Q)], in concert with correlation-consistent basis sets (cc-pVXZ, X =D, T, Q, 5, 6) that facilitate extrapolations to the complete basis set limit. The first full quartic force field of diacetylene is determined at the highly accurate all-electron CCSD(T) level with a cc-pCVQZ basis, which includes tight functions for core correlation. Application of second-order vibrational perturbation theory to our anharmonic force field yields fundamental frequencies with a mean absolute difference of only 3.9 cm-1 relative to the experimental band origins, without the use of any empirical scale factors. By a focal point approach, we converge on an enthalpy change for the isogyric reaction 2H-C?C-H?H-C?C-C?C-H+H2 of (+0.03, +0.81) kcal mol-1 at (0, 298.15) K. With the precisely established ?fH° of acetylene, we thus obtain ?fH°(C4H2)=(109.4,109.7)±0.3 kcal mol-1 at (0, 298.15) K. Previous estimates of the diacetylene enthalpy of formation range from 102 to 120 kcal mol-1.

  8. Ab initio parameterization of an all-atom polarizable and dissociable force field for water.

    PubMed

    Pinilla, Carlos; Irani, Amir H; Seriani, Nicola; Scandolo, Sandro

    2012-03-21

    A novel all-atom, dissociative, and polarizable force field for water is presented. The force field is parameterized based on forces, stresses, and energies obtained form ab initio calculations of liquid water at ambient conditions. The accuracy of the force field is tested by calculating structural and dynamical properties of liquid water and the energetics of small water clusters. The transferability of the force field to dissociated states is studied by considering the solvation of a proton and the ionization of water at extreme conditions of pressure and temperature. In the case of the solvated proton, the force field properly describes the presence of both Eigen and Zundel configurations. In the case of the pressure-induced ice VIII/ice X transition and the temperature-induced transition to a superionic phase, the force field is found to describe accurately the proton symmetrization and the melting of the proton sublattice, respectively. PMID:22443781

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

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Strasser, Valentino

    2010-12-01

    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.

  11. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

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

  12. Developing the Pulsed Fission-Fusion (PuFF) Engine

    NASA Technical Reports Server (NTRS)

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

    2014-01-01

    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.

  13. On radiation forces acting on a transparent nanoparticle in the field of a focused laser beam

    NASA Astrophysics Data System (ADS)

    Afanas'ev, A. A.; Gaida, L. S.; Guzatov, D. V.; Rubinov, A. N.; Svistun, A. Ch

    2015-10-01

    Radiation forces acting on a transparent spherical nanoparticle in the field of a focused Gaussian laser beam are studied theoretically in the Rayleigh scattering regime. Expressions are derived for the scattering force and Cartesian components of the gradient force. The resultant force acting on a nanoparticle located in the centre of a laser beam is found. The parameters of the focused beam and optical properties of the nanoparticle for which the longitudinal component of the gradient force exceeds the scattering force are determined. Characteristics of the transverse gradient force are discussed.

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

    E-print Network

    Leontyev, Igor

    2015-01-01

    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,...

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

    E-print Network

    Grodzinsky, Alan J.

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

  16. The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube.

    PubMed

    Jensen, Benjamin D; Wise, Kristopher E; Odegard, Gregory M

    2015-08-01

    As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon-based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress-strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress-strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed. PMID:26096628

  17. Submitted to Physical Review A Friction forces arising from fluctuating thermal fields

    E-print Network

    Novotny, Lukas

    Submitted to Physical Review A Friction forces arising from fluctuating thermal fields Jorge R-dependent damping in shear-force microscopy and it gives guidance for future experiments. Also, the theory should explored to what extent Casimir forces influence the performance of micrometer sized mechanical devices [1

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

    E-print Network

    Ponder, Jay

    #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

  19. Controlled limits of FORC theory: Mean field and Nucleation

    E-print Network

    fluctuations corrections 1.3 Test/verify theory experimentally on nanoparticle arrays 2. Strong exchange of pillar sample. FIG. 5. a The first-order reversal curve FORC data for nickel pillar sample. To make

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

    E-print Network

    Ponder, Jay

    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

  1. Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field

    E-print Network

    Buehler, Markus J.

    Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field Alfonso Gautieri, Massachusetts Received January 9, 2010 Abstract: Collagen is the most abundant protein in the human body of collagen molecules. We identify MARTINI force field parameters to describe hydroxyproline amino acid

  2. A reactive force field simulation of liquidliquid phase transitions in phosphorus

    E-print Network

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

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

    E-print Network

    Nielsen, Steven O.

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

  4. 300-FF-1 remedial design report/remedial action work plan

    SciTech Connect

    Gustafson, F.W.

    1997-02-01

    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.

  5. DFT-Derived Force Fields for Modeling Hydrocarbon Adsorption in MIL-47(V).

    PubMed

    Kulkarni, Ambarish R; Sholl, David S

    2015-08-01

    Generic force fields such as UFF and DREIDING are widely used for predicting molecular adsorption and diffusion in metal-organic frameworks (MOFs), but the accuracy of these force fields is unclear. We describe a general framework for developing transferable force fields for modeling the adsorption of alkanes in a nonflexible MIL-47(V) MOF using periodic density functional theory (DFT) calculations. By calculating the interaction energies for a large number of energetically favorable adsorbate configurations using DFT, we obtain a force field that gives good predictions of adsorption isotherms, heats of adsorption, and diffusion properties for a wide range of alkanes and alkenes in MIL-47(V). The force field is shown to be transferable to related materials such as MIL-53(Cr) and is used to calculate the free-energy differences for the experimentally observed phases of MIL-53(Fe). PMID:26158777

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

    PubMed

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

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water. PMID:26178083

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  8. Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage

    PubMed Central

    Sattar, Sadia; Bennett, Nicholas J.; Wen, Wesley X.; Guthrie, Jenness M.; Blackwell, Len F.; Conway, James F.; Rakonjac, Jasna

    2015-01-01

    F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70?C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative “dipstick” lateral flow diagnostic assay for human plasma fibronectin. PMID:25941520

  9. Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage.

    PubMed

    Sattar, Sadia; Bennett, Nicholas J; Wen, Wesley X; Guthrie, Jenness M; Blackwell, Len F; Conway, James F; Rakonjac, Jasna

    2015-01-01

    F-specific filamentous phage of Escherichia coli (Ff: f1, M13, or fd) are long thin filaments (860 nm × 6 nm). They have been a major workhorse in display technologies and bionanotechnology; however, some applications are limited by the high length-to-diameter ratio of Ff. Furthermore, use of functionalized Ff outside of laboratory containment is in part hampered by the fact that they are genetically modified viruses. We have now developed a system for production and purification of very short functionalized Ff-phage-derived nanorods, named Ff-nano, that are only 50 nm in length. In contrast to standard Ff-derived vectors that replicate in E. coli and contain antibiotic-resistance genes, Ff-nano are protein-DNA complexes that cannot replicate on their own and do not contain any coding sequences. These nanorods show an increased resistance to heating at 70(?)C in 1% SDS in comparison to the full-length Ff phage of the same coat composition. We demonstrate that functionalized Ff-nano particles are suitable for application as detection particles in sensitive and quantitative "dipstick" lateral flow diagnostic assay for human plasma fibronectin. PMID:25941520

  10. @h|i* _i A iLhi _ 5}?@* Vi?_hi_ e @h* 2ff c f ff2 ff

    E-print Network

    Tourneret, Jean-Yves

    @h|i* _i A iLhi _ 5}?@* Vi?_hi_ e @h* 2ff#12;c f ff2 ff @h|i* t@?t _LU 4i?|t EN?i ui **i e hi| it| *hi _ Thi4ih Lh_hi _i uL?U|L? _i |h@?tuih| MEs ' @n2Zs E@iU @ : f @||@^ i T@h ? t}?@* %E| ' rE| n KE|c L KE| it| ? Mh | M*@?U t|@|L??@hi

  11. @h|i* _i A iLhi _ 5}?@* Vi?_hi_ 22 4@ht 2ff2c f ff2 ff

    E-print Network

    Tourneret, Jean-Yves

    @h|i* _i A iLhi _ 5}?@* Vi?_hi_ 22 4@ht 2ff2c f ff2 ff @h|i* t@?t _LU 4i?|t EN?i ui **i e hiU|L ihtL it| @ |Lhtii , ihUUi 5L| fE| ? Mh | M*@?U t|@|L??@hi _i _i?t|i tTiU|h@*i rfEs ' Çf 2 @||@^ @?| *i t; ,? t TTLt@?| sf :: {s i| i? hi4@h^ @?| ^ i t EA @ *@ uLh4i _

  12. Real-space phase-field simulation of piezoresponse force microscopy accounting for stray electric fields

    NASA Astrophysics Data System (ADS)

    Yang, Lun; Dayal, Kaushik

    2012-04-01

    Piezoresponse force microscopy (PFM) is a powerful scanning-probe technique used to characterize important aspects of the microstructure in ferroelectrics. It has been widely applied to understand domain patterns, domain nucleation and the structure of domain walls. In this paper, we apply a real-space phase-field model to consistently simulate various PFM configurations. We model the PFM tip as a charged region that is external to the ferroelectric, and implement a boundary element method to efficiently and accurately account for the external stray fields that mediate the interactions between the tip and the ferroelectric. Our phase-field model and the solution method together are able to account for the electrical fields both within the specimen as well as those outside, and also consistently solve for the resulting electromechanical response with the same phase-field model. We apply this to various problems: first, the effect of crystal lattice orientation on the induced tip displacement and rotation; second, PFM scanning of a 90° domain wall that emerges at a free surface; third, the effect of closure domain microstructure on PFM response; fourth, the effect of surface modulations on PFM response; and fifth, the effect of surface charge compensation on PFM response.

  13. Casimir force for a scalar field in a single brane world

    SciTech Connect

    Linares, R.; Morales-Tecotl, H. A.; Pedraza, O.

    2010-02-10

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

  14. 6. FF coal pulverizer (ball mill inside). GG building in ...

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

    6. FF coal pulverizer (ball mill inside). GG building in background did preliminary crushing; pulverizer to left, coal conveyor and air cleaning towers to right; conveyor on left brought crushed coal to FF. Looking north/northeast - Rouge Steel Company, 3001 Miller Road, Dearborn, Wayne County, MI

  15. Development of Field Excavator with Embedded Force Measurement

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    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.

  16. On the accuracy of force fields for predicting the physical properties of dimethylnitramine.

    PubMed

    Zheng, Lianqing; Thompson, Donald L

    2006-08-17

    The accuracy of three force fields for predicting the physical properties of dimethylnitramine (DMNA) has been investigated by using molecular dynamics simulations. The Sorescu, Rice, and Thompson (SRT) (J. Phys. Chem. B 1997, 101, 798) rigid-molecule, flexible generalized AMBER (J. Comput. Chem. 2004, 25, 1157), and Smith et al. flexible force fields (J. Phys. Chem. B 1999, 103, 705) were tested. The density, lattice parameters, isotherm, and melting point of DMNA are calculated using classical molecular dynamics. Except for the melting point, the predictions of the three force fields are in reasonable agreement with experimental values. The calculated thermodynamic melting points (Tmp) for the SRT, AMBER, and Smith et al. force fields are 380, 360, and 260 K, respectively. The experimental value is 331 K. Modifications of the torsional barriers in the AMBER force field resulted in Tmp = 346 K, in good agreement with the experimental value of 331 K. The calculated lattice parameters and bulk modulus are also improved with the modifications of the AMBER potential. The results indicate that, although not sufficiently accurate without modifications, the general force fields such as AMBER provide the basis for developing force fields that correctly predict the physical properties of nitramines. PMID:16898765

  17. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

    PubMed

    Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J; Zweckstetter, Markus; de Groot, Bert L; Grubmüller, Helmut

    2015-11-10

    Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles generated by eight all-atom empirical force fields against primary small-angle X-ray scattering (SAXS) and NMR data. Ensembles obtained with different force fields exhibit marked differences in chain dimensions, hydrogen bonding, and secondary structure content. These differences are unexpectedly large: changing the force field is found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performs best in this force field comparison: it has the lowest error in chemical shifts and J-couplings and agrees well with the SAXS data. A high population of left-handed ?-helix is present in the CHARMM 36 ensemble, which is inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty is shown to be much smaller than the observed differences. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. PMID:26574339

  18. Error analysis regarding the calculation of nonlinear force-free field

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    Magnetic field extrapolation is an alternative method to study chromospheric and coronal magnetic fields. In this paper, two semi-analytical solutions of force-free fields (Low and Lou in Astrophys. J. 352:343, 1990) have been used to study the errors of nonlinear force-free (NLFF) fields based on force-free factor ?. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2001-04-01

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

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

    NASA Technical Reports Server (NTRS)

    Ye, Gang; Voigt, Gerd-Hannes

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    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.

  2. Transferable next-generation force fields from simple liquids to complex materials.

    PubMed

    Schmidt, J R; Yu, Kuang; McDaniel, Jesse G

    2015-03-17

    Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as physically motivated. We find that these physically motivated force fields exhibit both high accuracy and transferability, with the latter deriving from the universality of the fundamental physical laws governing intermolecular interactions. This basic methodology has been applied to a diverse set of systems, ranging from simple liquids to nanoporous metal-organic framework materials. A key conclusion is that, in many cases, it is feasible to account for nearly all of the relevant physics of intermolecular interactions within the context of the force field. In such cases, the structural, thermodynamic, and dynamic properties of the system become naturally emergent, even in the absence of explicit parameterization to bulk properties. We also find that, quite generally, the three-body contributions to the dispersion and exchange energies in bulk liquids are crucial for quantitative accuracy in a first-principles force field, although these contributions are almost universally neglected in existing empirical force fields. PMID:25688596

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

    E-print Network

    Li, Bo

    Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force Hsiao free energy of a molecular sol- vation system with an implicit or continuum solvent is constructed. The electrostatic free energy de- termines the dielectric boundary force that in turn influences crucially

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

    E-print Network

    Vanik E. Mkrtchian

    2009-01-14

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

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

    E-print Network

    Guzina, Bojan

    Acoustic radiation force in tissue-like solids due to modulated sound field Egor V. Dontsov, Bojan B. Guzina n Department of Civil Engineering, University of Minnesota, United States a r t i c l e i-called acoustic radiation force) in homogeneous tissue-like solids generated by an elevated-intensity, focused

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

    E-print Network

    Heckler, Andrew F.

    particle and report three findings from a series of tests administered to introductory physics students, first studied by Maloney, that a magnetic pole exerts a force on a charged particle, regardless of itsThe Effect of Field Representation on Student Responses to Magnetic Force Questions Thomas M

  7. Numerical Investigation of Flow Fields and Forces for 2-D Squeeze Film Dampers 

    E-print Network

    Neadkratoke, Terdsak

    2011-08-08

    A numerical method is used to predict flow fields and forces for squeeze film dampers (SFDs). A two dimensional SFD is modeled with different amplitudes and frequencies of the journal orbiting inside the wall. In addition to the typical circular...

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

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

    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.

  9. Wolf2Pack--portal based atomistic force-field development.

    PubMed

    Krämer-Fuhrmann, Ottmar; Neisius, Jens; Gehlen, Niklas; Reith, Dirk; Kirschner, Karl N

    2013-04-22

    In this contribution we introduce the technical concept and implementation details concerning the front end of our force-field optimization workflow package for intramolecular degrees of freedom, called Wolf2Pack. The package's design follows our belief that parameter optimization should be a user-driven, but program guided, workflow with specific modular tasks that reduce human errors and save time. Through this design, parameter optimization becomes more reliable and reproducible. Wolf2Pack can integrate common force fields from different research areas, allowing the user to optimize balanced parameters; alternatively users can develop highly specialized force fields that suite their chemical systems. Included in the package's front end is a force-field and molecular database whose contents facilitate parameter optimization. Wolf2Pack can be accessed at www.wolf2pack.com. PMID:23452048

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

    E-print Network

    Traina, Zachary J

    2005-01-01

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

  11. The validity of the force-field equation to describe modulation

    NASA Astrophysics Data System (ADS)

    Moraal, H.; Steenberg, C. D.

    2001-08-01

    The Force-Field equation is a classical, convenient means to describe modulation effects in the one-dimensional approximation. It serves mainly as a tool for experimentalists to give a concise description of modulation strength. By comparing the Force-Field solution to numerical solutions of the transport equation, however, we show that the Force-Field approximation gets progressively worse with increasing radial distance. The reason is that adiabatic losses in the outer heliosphere become unimportant, and the ForceField equation can not simulate that. It is shown that the convection-diffusion approximation is more appropriate in the outer heliosphere. This result has consequences for the interpretation of Pioneer/Voyager observations in the outer heliosphere.

  12. Conformations of methylcyclooctane. a combined iterative force field-cndo approach

    NASA Astrophysics Data System (ADS)

    Abdi, Sadegh; Yavari, Issa; Askari, Massoud

    A combined iterative force field-CNDO molecular orbital approach to conformations of methyleyclooctane is described. This hybrid method involves a full relaxation forcefield calculation of conformer structures, followed by a single CNDO calculation on each structure.

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

    NASA Astrophysics Data System (ADS)

    Villegas, A.; Diez, F. J.

    2014-04-01

    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.

  14. Force-Field Induced Bias in the Structure of A?21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.

    PubMed

    Smith, Micholas Dean; Rao, J Srinivasa; Segelken, Elizabeth; Cruz, Luis

    2015-12-28

    In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid ?, the A?21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and ? structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the A?21-30 peptide. PMID:26629886

  15. Gravitational self-force in nonvacuum spacetimes: An effective field theory derivation

    NASA Astrophysics Data System (ADS)

    Zimmerman, Peter

    2015-09-01

    In this paper we investigate the motion of small compact objects in nonvacuum spacetimes using methods from effective field theory in curved spacetime. Although a vacuum formulation is sufficient in many astrophysical contexts, there are applications such as the role of the self-force in enforcing cosmic censorship in the context of the overcharging problem, which necessitate an extension into the nonvacuum regime. The defining feature of the self-force problem in nonvacuum spacetimes is the coupling between gravitational and nongravitational field perturbations. The formulation of the self-force problem for nonvacuum spacetimes was recently provided in simultaneous papers by Zimmerman and Poisson [Gravitational self-force in nonvacuum spacetimes, Phys. Rev. D 90, 084030 (2014)] and Linz, Friedmann, and Wiseman [Combined gravitational and electromagnetic self-force on charged particles in electrovac spacetimes, Phys. Rev. D 90, 084031 (2014)]. Here we distinguish ourselves by working with the effective action rather than the field equations. The formalism utilizes the multi-index notation developed by Zimmerman and Poisson [Gravitational self-force in nonvacuum spacetimes, Phys. Rev. D 90, 084030 (2014) to accommodate the coupling between the different fields. Using dimensional regularization, we arrive at a finite expression for the local self-force expressed in terms of multi-index quantities evaluated in the background spacetime. We then apply the formalism to compute the coupled gravitational self-force in two explicit cases. First, we calculate the self-force on a massive particle possessing scalar charge and moving in a scalarvac spacetime. We then derive an expression for the self-force on an electrically charged, massive particle moving in an electrovac spacetime. In both cases, the force is expressed as a sum of local terms involving tensors defined in the background spacetime and evaluated at the current position of the particle, as well as tail integrals that depend on the past history of the particle.

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

    PubMed

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

    2010-08-01

    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

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

    E-print Network

    Toshihiro Matsuo; Dan Tomino; Wen-Yu Wen

    2006-08-10

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  19. Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

    PubMed Central

    Bergonzo, Christina; Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

    2015-01-01

    Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem–loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowledge the most complete RNA structure ensembles reported to date for these systems, we remove the coupling between force field errors and errors due to incomplete sampling, providing a comprehensive comparison between current top-performing MD force fields for RNA. Of the RNA force fields tested in this study, none demonstrate the ability to correctly identify the most thermodynamically stable structure for all three systems. We discuss the deficiencies present in each potential function and suggest areas where improvements can be made. The results imply that although “short” (nsec-?sec timescale) simulations may stay close to their respective experimental structures and may well reproduce experimental observables, inevitably the current force fields will populate alternative incorrect structures that are more stable than those observed via experiment. PMID:26124199

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

    SciTech Connect

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

    2014-12-28

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  2. Data validation summary report 300-FF-5 round 5 groundwater

    SciTech Connect

    Hulstrom, L.C.

    1993-07-15

    Laboratory data for Fifth Round Groundwater samples collected during the 300-FF-5 Operable Unit Remedial Investigation have been reviewed and validated to ensure that they are of sufficient quality to support decisions regarding further actions to be taken at the 300-FF-5 Operable Unit. Table 1-1 is a summary of the validated samples. This report summarizes the results previously presented to Westinghouse Hanford in a series of Preliminary Quality Assurance Reports (PQAR) for the 300-FF-5 Fifth Round Groundwater samples. In some instances, the data qualifiers originally presented in the PQARs have been changed based upon further review of the data; these changes are highlighted in the text.

  3. 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- sphere at all. In order to examine the force-freeness of active region magnetic fields

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

    SciTech Connect

    Makarov, V. P. Rukhadze, A. A.

    2010-01-15

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

  5. Asymptotic analysis of force-free magnetic fields of cylindrical symmetry

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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.

  6. Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl

    NASA Astrophysics Data System (ADS)

    Halonen, L.; Ha, T.-K.

    1988-03-01

    Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.

  7. Cluster evolution during the early stages of heating explosives and its relationship to sensitivity: a comparative study of TATB, ?-HMX and PETN by molecular reactive force field simulations.

    PubMed

    Wen, Yushi; Zhang, Chaoyang; Xue, Xianggui; Long, Xinping

    2015-05-14

    Clustering is experimentally and theoretically verified during the complicated processes involved in heating high explosives, and has been thought to influence their detonation properties. However, a detailed description of the clustering that occurs has not been fully elucidated. We used molecular dynamic simulations with an improved reactive force field, ReaxFF_lg, to carry out a comparative study of cluster evolution during the early stages of heating for three representative explosives: 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), ?-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and pentaerythritol tetranitrate (PETN). These representatives vary greatly in their oxygen balance (OB), molecular structure, stability and experimental sensitivity. We found that when heated, TATB, HMX and PETN differ in the size, amount, proportion and lifetime of their clusters. We also found that the clustering tendency of explosives decreases as their OB becomes less negative. We propose that the relationship between OB and clustering can be attributed to the role of clustering in detonation. That is, clusters can form more readily in a high explosive with a more negative OB, which retard its energy release, secondary decomposition, further decomposition to final small molecule products and widen its detonation reaction zone. Moreover, we found that the carbon content of the clusters increases during clustering, in accordance with the observed soot, which is mainly composed of carbon as the final product of detonation or deflagration. PMID:25872486

  8. Forced MHD turbulence in a uniform external magnetic field

    NASA Technical Reports Server (NTRS)

    Hossain, M.; Vahala, G.; Montgomery, D.

    1985-01-01

    Two-dimensional dissipative MHD turbulence is randomly driven at small spatial scales and is studied by numerical simulation in the presence of a strong uniform external magnetic field. A behavior is observed which is apparently distinct from the inverse cascade which prevails in the absence of an external magnetic field. The magnetic spectrum becomes dominated by the three longest wavelength Alfven waves in the system allowed by the boundary conditions: those which, in a box size of edge 2 pi, have wave numbers (kx' ky) = (1, 1), and (1, -1), where the external magnetic field is in the x direction. At any given instant, one of these three modes dominates the vector potential spectrum, but they do not constitute a resonantly coupled triad. Rather, they are apparently coupled by the smaller-scale turbulence.

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

    E-print Network

    Contopoulos, Ioannis; Georgoulis, Manolis

    2010-01-01

    We present a novel numerical method that allows the calculation of nonlinear force-free magnetostatic solutions above a boundary surface on which only the distribution of the normal magnetic field component is given. The method relies on the theory of force-free electrodynamics and applies directly to the reconstruction of the solar coronal magnetic field for a given distribution of the photospheric radial field component. The method works as follows: we start with any initial magnetostatic global field configuration (e.g. zero, dipole), and along the boundary surface we create an evolving distribution of tangential (horizontal) electric fields that, via Faraday's equation, give rise to a respective normal field distribution approaching asymptotically the target distribution. At the same time, these electric fields are used as boundary condition to numerically evolve the resulting electromagnetic field above the boundary surface, modelled as a thin ideal plasma with non-reflecting, perfectly absorbing outer b...

  10. 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...

  11. Nonlinear force-free modeling of the solar coronal magnetic field

    E-print Network

    T. Wiegelmann

    2008-01-18

    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.

  12. DFT-based polarizable force field for TiO2 and SiO2

    NASA Astrophysics Data System (ADS)

    Corradini, Dario; Ishii, Yoshiki; Ohtori, Norikazu; Salanne, Mathieu

    2015-10-01

    TiO2 and SiO2 are materials with unique importance in materials science. They are often modelled using conventional force fields, but including polarization effects is compulsory for enhancing the accuracy of the simulations. Here we parameterize a force field for the two materials in the framework of the polarizable ion model. The parameterization is performed via a generalized force-fitting methodology using DFT calculations as reference data. We show that it is possible to generate a force field in which the same parameters are used for the oxide ion in both SiO2 and TiO2, and which is able to reproduce accurately the equilibrium structure of their various crystalline polymorphs, as well as glassy silica.

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

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-19

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

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

    PubMed

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

    2014-07-24

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

  15. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

    PubMed Central

    2015-01-01

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

  16. Thermodynamic properties for applications in chemical industry via classical force fields.

    PubMed

    Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran

    2012-01-01

    Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown. PMID:21678137

  17. A Molecular Dynamics simulation of Hugoniot curves of HMX using ReaxFF and its application in SPH modeling of macroscale terminal effects

    NASA Astrophysics Data System (ADS)

    Liu, Gui-Rong; Wang, Gangyu; Peng, Qing; de, Suvranu

    2015-06-01

    HMX is a widely used high explosive. Hugoniot curve is a valuable tool for analyzing the equations of state, and is of importance for all energetic materials including HMX. The Hugoniot curves serve as one of the key character in continuum modeling of high explosives. It can be obtained from experimental measurements, and recently also from computational studies. In this study, the Hugoniot curve of HMX is calculated using a multi-scale shock technique via Molecular Dynamics (MD) simulations, where the reactive force field ReaxFF is obtained from Quantum Mechanics calculations and tailored for HMX. It is found that our MD Hugoniot curve of HMX from the optimized ReaxFF potential agree well with experiments. The MD Hugoniot curve of HMX is also incorporated in our in-house Smoothed Particle Hydrodynamics (SPH) code for the modeling of the macro-scale explosive behaviors of HMX explosives and HMX cased in a 3D cylinder. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant HDTRA1-13-1-0025.

  18. Nonpeptide Small Molecule Agonist and Antagonist Original Leads for Neuropeptide FF1 and FF2 Receptors

    PubMed Central

    2015-01-01

    Neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R), and their endogenous ligand NPFF, are one of only several systems responsible for mediating opioid-induced hyperalgesia, tolerance, and dependence. Currently, no small molecules displaying good affinity or selectivity for either subtype have been reported, to decipher the role of NPFF2-R as it relates to opioid-mediated analgesia, for further exploration of NPFF1-R, or for medication development for either subtype. We report the first nonpeptide small molecule scaffold for NPFF1,2-R, the guanidino-piperidines, and SAR studies resulting in the discovery of a NPFF1 agonist (7b, Ki = 487 ± 117 nM), a NPFF1 antagonist (46, Ki = 81 ± 17 nM), and a NPFF2 partial antagonist (53a, Ki = 30 ± 5 nM), which serve as leads for the development of pharmacological probes and potential therapeutic agents. Testing of 46 alone was without effect in the mouse 48 °C warm-water tail-withdrawal test, but pretreatment with 46 prevented NPFF-induced hyperalgesia. PMID:25268943

  19. Nonpeptide small molecule agonist and antagonist original leads for neuropeptide FF1 and FF2 receptors.

    PubMed

    Journigan, V Blair; Mésangeau, Christophe; Vyas, Neha; Eans, Shainnel O; Cutler, Stephen J; McLaughlin, Jay P; Mollereau, Catherine; McCurdy, Christopher R

    2014-11-13

    Neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R), and their endogenous ligand NPFF, are one of only several systems responsible for mediating opioid-induced hyperalgesia, tolerance, and dependence. Currently, no small molecules displaying good affinity or selectivity for either subtype have been reported, to decipher the role of NPFF2-R as it relates to opioid-mediated analgesia, for further exploration of NPFF1-R, or for medication development for either subtype. We report the first nonpeptide small molecule scaffold for NPFF1,2-R, the guanidino-piperidines, and SAR studies resulting in the discovery of a NPFF1 agonist (7b, K(i) = 487 ± 117 nM), a NPFF1 antagonist (46, K(i) = 81 ± 17 nM), and a NPFF2 partial antagonist (53a, K(i) = 30 ± 5 nM), which serve as leads for the development of pharmacological probes and potential therapeutic agents. Testing of 46 alone was without effect in the mouse 48 °C warm-water tail-withdrawal test, but pretreatment with 46 prevented NPFF-induced hyperalgesia. PMID:25268943

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

    E-print Network

    Kung, H. T.

    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

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

    EPA Science Inventory

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

  2. Flute stabilization due to ponderomotive force created by an rf field with a variable gradient

    SciTech Connect

    Yasaka, Y.; Itatani, R.

    1986-06-30

    An rf-stabilization experiment was performed in the axisymmetric single-mirror device HIEI by controlling the radial-gradient scale length of the rf field with the aid of an azimuthally phased antenna array. The flute stability depends sensitively on the scale length of the perpendicular rf electric field, which shows that rf stabilization is caused by the ponderomotive force for ions.

  3. Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

    SciTech Connect

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

    2012-05-09

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

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

    PubMed

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

    2013-07-26

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

  5. ReaxFF Study of the Oxidation of Lignin Model Compounds for the Most Common Linkages in Softwood in View of Carbon Fiber Production

    SciTech Connect

    Beste, Ariana

    2014-01-01

    Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic, and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers.

  6. EXCLUSIVE STUDY OF REACTIONS p(ff; ff 0 )X AND p( ~ IN THE REGION OF THE ROPER RESONANCE

    E-print Network

    Titov, Anatoly

    EXCLUSIVE STUDY OF REACTIONS p(ff; ff 0 )X AND p( ~ d; d 0 )X IN THE REGION OF THE ROPER RESONANCE to the isospin 0) and \\Delta + ß, studied in the ßN ! ßßN reaction, are of the order of 10--20% and 20--30%, respectively. In addition, a small decay branching into aeN has been deduced. Recently, in an attempt

  7. Tethyan collision forces and the stress field of the Eurasian Plate

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    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.

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

    PubMed Central

    Pérez, Alberto; Marchán, Iván; Svozil, Daniel; Sponer, Jiri; Cheatham, Thomas E.; Laughton, Charles A.; Orozco, Modesto

    2007-01-01

    We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the ?/? concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the ?/? = (g+,t) backbone that were seen in long (more than 10 ns) simulations with previous AMBER parameter sets (parm94-99). The force field has been derived by fitting to high-level quantum mechanical data and verified by comparison with very high-level quantum mechanical calculations and by a very extensive comparison between simulations and experimental data. The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 individual structures). The total simulation time used to validate the force field includes near 1 ?s of state-of-the-art molecular dynamics simulations in aqueous solution. PMID:17351000

  9. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.

    PubMed

    Götz, Andreas W; Bucher, Denis; Lindert, Steffen; McCammon, J Andrew

    2014-04-01

    The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem. 2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks. PMID:24803868

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

    SciTech Connect

    Sorin Zaharia; C.Z. Cheng

    2002-06-18

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

  11. Gravitational self-force in non-vacuum spacetimes: an effective field theory derivation

    E-print Network

    Peter Zimmerman

    2015-07-13

    In this paper we investigate the motion of small compact objects in non-vacuum spacetimes using methods from effective field theory in curved spacetime. Although a vacuum formulation is sufficient in many astrophysical contexts, there are applications such as the role of the self-force in enforcing cosmic-censorship in the context of the overcharging problem, which necessitate an extension into the non-vacuum regime. The defining feature of the self-force problem in non-vacuum spacetimes is the coupling between gravitational and non-gravitational field perturbations. The formulation of the self-force problem for non-vacuum spacetimes was recently provided in simultaneous papers by Zimmerman and Poisson [1] and Linz, Friedmann, Wiseman [2]. Here we distinguish ourselves by working with the effective action rather than the field equations. The formalism utilizes the multi-index notation developed by Zimmerman and Poisson [1] to accommodate the coupling between the different fields. Using dimensional regularization, we arrive at a finite expression for the local self-force expressed in terms of multi-index quantities evaluated in the background spacetime. We then apply the formalism to compute the coupled gravitational self-force in two explicit cases. First, we calculate the self-force on a massive particle possessing scalar charge and moving in an scalarvac spacetime. We then derive an expression for the self-force on an electrically charged, massive particle moving in an electrovac spacetime. In both cases, the force is expressed as a sum of local terms involving tensors defined in the background spacetime and evaluated at the current position of the particle, as well as tail integrals that depend on the past history of the particle.

  12. Force-free magnetosphere of an aligned rotator with differential rotation of open magnetic field lines

    E-print Network

    Andrey N. Timokhin

    2006-09-07

    Here we briefly report on results of self-consistent numerical modeling of a differentially rotating force-free magnetosphere of an aligned rotator. We show that differential rotation of the open field line zone is significant for adjusting of the global structure of the magnetosphere to the current density flowing through the polar cap cascades. We argue that for most pulsars stationary cascades in the polar cap can not support stationary force-free configurations of the magnetosphere.

  13. A long-lived coronal X-ray arcade. [force-free magnetic field analysis

    NASA Technical Reports Server (NTRS)

    Mcguire, J. P.; Tandberg-Hanssen, E.; Krall, K. R.; Wu, S. T.; Smith, J. B., Jr.; Speich, D. M.

    1977-01-01

    A large, long-lived, soft X-ray emitting arch system observed during a Skylab mission is analyzed. The supposition is that these arches owe their stability to the stable coronal magnetic-field configuration. A global constant alpha force-free magnetic field analysis, is used to describe the arches which stayed in the same approximate position for several solar rotations. A marked resemblance is noted between the theoretical magnetic field configuration and the observed X-ray emmitting feature.

  14. Statement of Work for Drilling Five CERCLA Groundwater Monitoring Wells During Fiscal Year 2006, 300-FF-5 Operable Unit

    SciTech Connect

    Williams, Bruce A.

    2005-08-01

    Pacific Northwest National Laboratory, the U.S. Department of Energy (DOE), and the regulators have agreed that two characterization wells along with three additional performance monitoring wells shall be installed in the 300-FF-5 Operable Unit as defined in the proposed Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement [TPA]) Milestone M-24-57 and the 300-FF-5 Limited Field Investigation plan (DOE/RL-2005-47). This document contains the statement of work required to drill, characterize, and construct the proposed groundwater monitoring wells during FY 2006.

  15. Web-based 3D digital pathology framework for large-mapping data scanned by FF-OCT

    NASA Astrophysics Data System (ADS)

    Chang, ChiaKai; Tsai, Chien-Chung; Chien, Meng-Ting; Li, Yu-I.; Shun, Chia-Tung; Huang, Sheng-Lung

    2015-03-01

    Full-Field Optical Coherence Tomography (FF-OCT) is a high resolution instrument in 3 dimensional (3D) space, including lateral and longitudinal direction. With FF-OCT, we can perform 3D scanning for excised biopsy or cell culture sample to obtain cellular information. In this work, we have set up a high resolution FF-OCT scanning instrument that can perform cellular resolution tomography scanning of skin tissue for histopathology study. In a scan range of 1cm(x), 1cm(y), 106?m(z), for example, digital data occupies 253 GB capacity. Copying these materials is time consuming, not to mention efficient browsing and analyzing of these data. To solve the problem of information delivery, we have established a network service to browse and analyze the huge volume data.

  16. Experimental studies of protozoan response to intense magnetic fields and forces

    NASA Astrophysics Data System (ADS)

    Guevorkian, Karine

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

  17. Subthalamic Nucleus Local Field Potential Activity Helps Encode Motor Effort Rather Than Force in Parkinsonism

    PubMed Central

    Pogosyan, Alek; Ashkan, Keyoumars; Cheeran, Binith; FitzGerald, James J.; Green, Alexander L.; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Brown, Peter

    2015-01-01

    Local field potential (LFP) recordings from patients with deep brain stimulation electrodes in the basal ganglia have suggested that frequency-specific activities correlate with force or effort, but previous studies have not been able to disambiguate the two. Here, we dissociated effort from actual force generated by contrasting the force generation of different fingers while recording LFP activity from the subthalamic nucleus (STN) in patients with Parkinson's disease who had undergone functional surgery. Patients were studied while on their normal dopaminergic medication. We investigated the relationship between frequency-specific oscillatory activity in the STN and voluntary flexion of either the index or little finger at different effort levels. At each tested effort level (10%, 25%, and 40% of the maximal voluntary contraction force of each individual finger), the index finger generated larger force than the little finger. Movement-related suppression of beta-band power in the STN LFP was significantly modulated by effort, but not by which finger was used, suggesting that the beta suppression in the STN LFP during sustained contraction serves as a proxy for effort. The absolute force scaled with beta power suppression, but with the scaling determined by the maximal voluntary contraction force of the motor effector. Our results argue against the hypothesis that the basal ganglia are directly involved in the parameterization of force during movement and support a role of the STN in the control of motor effort to be attributed to a response. PMID:25878267

  18. Subthalamic nucleus local field potential activity helps encode motor effort rather than force in parkinsonism.

    PubMed

    Tan, Huiling; Pogosyan, Alek; Ashkan, Keyoumars; Cheeran, Binith; FitzGerald, James J; Green, Alexander L; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Brown, Peter

    2015-04-15

    Local field potential (LFP) recordings from patients with deep brain stimulation electrodes in the basal ganglia have suggested that frequency-specific activities correlate with force or effort, but previous studies have not been able to disambiguate the two. Here, we dissociated effort from actual force generated by contrasting the force generation of different fingers while recording LFP activity from the subthalamic nucleus (STN) in patients with Parkinson's disease who had undergone functional surgery. Patients were studied while on their normal dopaminergic medication. We investigated the relationship between frequency-specific oscillatory activity in the STN and voluntary flexion of either the index or little finger at different effort levels. At each tested effort level (10%, 25%, and 40% of the maximal voluntary contraction force of each individual finger), the index finger generated larger force than the little finger. Movement-related suppression of beta-band power in the STN LFP was significantly modulated by effort, but not by which finger was used, suggesting that the beta suppression in the STN LFP during sustained contraction serves as a proxy for effort. The absolute force scaled with beta power suppression, but with the scaling determined by the maximal voluntary contraction force of the motor effector. Our results argue against the hypothesis that the basal ganglia are directly involved in the parameterization of force during movement and support a role of the STN in the control of motor effort to be attributed to a response. PMID:25878267

  19. 77 FR 61019 - Aquatic Nuisance Species Task Force Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-05

    ...Cost Center: FF09F14000, Fund: 134] Aquatic Nuisance Species Task Force Meeting AGENCY...This notice announces a meeting of the Aquatic Nuisance Species (ANS) Task Force...prevent introduction and dispersal of aquatic nuisance species; to monitor,...

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

    DOEpatents

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

    1991-01-01

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

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

    DOEpatents

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

    1991-04-09

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

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

    PubMed Central

    Brügger, Georges; Froufe-Pérez, Luis S.; Scheffold, Frank; José Sáenz, Juan

    2015-01-01

    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 a 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 the control of translationally invariant interactions with tuneable strength and range in colloidal systems. PMID:26096622

  3. Magnetic force of piezoelectric cantilever energy harvesters with external magnetic field

    NASA Astrophysics Data System (ADS)

    Tan, D.; Leng, Y. G.; Gao, Y. J.

    2015-11-01

    In piezoelectric cantilever energy harvesters with external magnetic field, one of the difficulties is the impact of the external magnetic field or magnetic force on vibration response and energy harvesting efficiency. Here we use the magnetizing current and magnetic dipoles approaches to analyze the magnetic force. The two calculation models are proposed for the energy harvesters. The calculation results of the two methods are compared with a set of experimental data. It has been proved that errors are produced with both methods while the magnet interval is sufficiently small. However, the calculation result achieved from magnetic dipoles approach is closer to experimental measurements than the one of magnetizing current approach. Consequently, the magnetic dipoles approach can be chosen preferably to calculate the magnetic force of piezoelectric cantilever energy harvesters with external magnetic field.

  4. A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field.

    PubMed

    Madej, Benjamin D; Gould, Ian R; Walker, Ross C

    2015-09-24

    The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field. PMID:26359797

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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).

  6. Calculation of the linear force-free magnetic field above a solar active region

    NASA Astrophysics Data System (ADS)

    Abramenko, V. I.

    1997-08-01

    Modeling the linear force-free fields above solar active regions involves the use of either Fourier transforms or Green functions. The modeling results depend on the a priori conditions specified for the edges of the volume studied. However, none of the methods that have been developed allow direct specification of the values for the field at the nonphotospheric boundaries of the volume. A method that allows this would make it possible to study the influence of lateral boundary conditions on the solution inside the volume of interest and to use a priori information about the field in the corona. Here, an algorithm is presented for calculation of the linear force-free field in a limited volume (in the shape of a parallelepiped, Omega) using the distribution of the Bz component of the field at all boundaries of Omega and the distribution of Bx and Bv in a frame made up by the intersection of a lateral surface of Omega and a single arbitrarily chosen plane z = const. The algorithm is verified using a numerical model, permitting calculation of the linear force-free field of a dipole in a half-space using exact formulas. The rms deviation of the calculated and analytical solutions at each layer along the z axis does not exceed 1 percent. Substituting potential boundary conditions for force-free conditions at the nonphotospheric border of the Omega volume leads to a substantial change in the resulting magnetic configuration.

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

    PubMed

    Betz, Robin M; Walker, Ross C

    2015-01-15

    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. PMID:25413259

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

    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.

  9. Levitation force and trapped magnetic field of multi-grain YBCO bulk superconductors

    NASA Astrophysics Data System (ADS)

    Choi, J. S.; Park, S. D.; Jun, B. H.; Han, Y. H.; Jeong, N. H.; Kim, B. G.; Sohn, J. M.; Kim, C. J.

    2008-09-01

    A levitation force (LF), attractive force (AF) and trapped magnetic field (TMF) at 77 K of the multi-seeded melt processed (MSMG) bulk samples (single grain to five grain) were studied. The LF and TMF values of the MSMG-processed samples, cooled by both field cooling and zero-field cooling method, were smaller than that of a single grain sample, depending on the number of a grain. The trapped magnetic field analysis showed the magnetic fields were easily penetrated through the grain boundaries of multi-grain samples, because of the weak connection of (1 0 0)/(1 0 0) junctions. The poorly connected grain boundaries are thought to be the cause for the low LF and TMF values of the multi-grain samples.

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

    PubMed

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

    2014-09-16

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

  11. Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent.

    PubMed

    A Beccara, S; Fant, L; Faccioli, P

    2015-03-01

    We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an ? and a ? protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller. PMID:25793854

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

    SciTech Connect

    Huyer, S. )

    1993-04-01

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

  13. Comparison and maximum principles for a class of flux-limited diffusions with external force fields

    E-print Network

    Manh Hong Duong

    2015-08-16

    In this paper, we are interested in a general equation that has finite speed of propagation compatible with Einstein's theory of special relativity. This equation without external force fields has been derived recently by means of optimal transportation theory. We first provide an argument to incorporate the external force fields. Then we are concerned with comparison and maximum principles for this equation. We consider both stationary and evolutionary problems. We show that the former satisfies a comparison principle and a strong maximum principle. While the latter fulfils weaker ones. The key technique is a transformation that matches well with the gradient flow structure of the equation.

  14. Leading three-baryon forces from SU(3) chiral effective field theory

    E-print Network

    Stefan Petschauer; Norbert Kaiser; Johann Haidenbauer; Ulf-G. Meißner; Wolfram Weise

    2015-11-06

    Leading three-baryon forces are derived within SU(3) chiral effective field theory. Three classes of irreducible diagrams contribute: three-baryon contact terms, one-meson exchange and two-meson exchange diagrams. We provide the minimal non-relativistic terms of the chiral Lagrangian, that contribute to these diagrams. SU(3) relations are given for the strangeness S=0 and -1 sectors. In the strangeness-zero sector we recover the well-known three-nucleon forces from chiral effective field theory. Explicit expressions for the lambda-nucleon-nucleon chiral potential in isospin space are presented.

  15. Explicit Polarization: A Quantum Mechanical Framework for Developing Next Generation Force Fields

    PubMed Central

    2015-01-01

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

  16. Pulmonary Function in Flight (PuFF) Experiment

    NASA Technical Reports Server (NTRS)

    2003-01-01

    In this International Space Station (ISS) onboard photo, Expedition Six Science Officer Donald R. Pettit works to set up the Pulmonary Function in Flight (PuFF) experiment hardware in the Destiny Laboratory. Expedition Six is the fourth and final crew to perform the PuFF experiment. The PuFF experiment was developed to better understand what effects long term exposure to microgravity may have on the lungs. The focus is on measuring changes in the everness of gas exchange in the lungs, and on detecting changes in respiratory muscle strength. It allows astronauts to measure blood flow through the lungs, the ability of the lung to take up oxygen, and lung volumes. Each PuFF session includes five lung function tests, which involve breathing only cabin air. For each planned extravehicular (EVA) activity, a crew member performs a PuFF test within one week prior to the EVA. Following the EVA, those crew members perform another test to document the effect of exposure of the lungs to the low-pressure environment of the space suits. This experiment utilizes the Gas Analyzer System for Metabolic Analysis Physiology, or GASMAP, located in the Human Research Facility (HRF), along with a variety of other Puff equipment including a manual breathing valve, flow meter, pressure-flow module, pressure and volume calibration syringes, and disposable mouth pieces.

  17. Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

    SciTech Connect

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-07-15

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

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

    SciTech Connect

    Ram, Abhay K.; Dasgupta, Brahmananda; Krishnamurthy, V.; Mitra, Dhrubaditya

    2014-07-15

    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.

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

    NASA Astrophysics Data System (ADS)

    Lerche, I.; Low, B. C.

    2014-10-01

    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.

  20. Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM

    PubMed Central

    Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger

    2015-01-01

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550?nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455

  1. Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM.

    PubMed

    Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I I; Chan, C T; Chan, H B; Tong, Penger

    2015-01-01

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550?nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455

  2. The effect of dissipation on the torque and force experienced by nanoparticles in an AC field

    NASA Astrophysics Data System (ADS)

    Claro, F.; Fuchs, R.; Robles, P.; Rojas, R.

    2015-09-01

    We discuss the force and torque acting on spherical particles in an ensemble in the presence of a uniform AC electric field. We show that for a torque causing particle rotation to appear the particle must be absorptive. Our proof includes all electromagnetic excitations, which in the case of two or more particles gives rise to one or more resonances in the spectrum of force and torque depending on interparticle distance. Several peaks are found in the force and torque between two spheres at small interparticle distances, which coalesce to just one as the separation grows beyond three particle radii. We also show that in the presence of dissipation the force on each particle is nonconservative and may not be derived from the classical interaction potential energy as has been done in the past.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

    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.

  4. Application of superconductivity for magnetic force control in medical and industrial fields

    NASA Astrophysics Data System (ADS)

    Nishijima, S.

    2008-09-01

    The magnetic force control technique has expanded the applied field with developing a superconductivity because a high magnetic field and a high magnetic field gradient can be produced using the superconducting magnet. The magnetic force control technique has been applied to industrial fields such as recycling of abrasives, removing ferromagnetic particles from powdered products and purifying waste water. The technique is also applied to the drug delivery system as the medical application. Open gradient of magnetic separation was used for the recycling of the abrasives in wasted slurry from solar battery factory. For the removing the ferromagnetic particles from powdered products the magnetic filters were designed not to be blocked with the aggregated powder. In the water purification system, the superconducting high gradient magnetic separation was employed. For the magnetic drug delivery system the superconducting bulk magnet was used to navigate the nanometer-sized ferromagnetic particles in the blood vessel.

  5. Transferability and Nonbond Functional Form of Coarse Grained Force Field - Tested on Linear Alkanes.

    PubMed

    Cao, Fenglei; Sun, Huai

    2015-10-13

    Whether or not a coarse grained force field (CGFF) can be made to be transferrable is an important question to be addressed. By comparing potential energy with potential of mean force (PMF) of a molecular dimer, we proposed to use a free energy function (FE-12-6) with the parameters in entropic and energetic terms explicitly to represent the nonbond interactions in CGFF. Although the FE-12-6 function cannot accurately describe the PMF curves, a cancelation of short radii and strong repulsion makes the function a good approximation. For nonpolar molecules represented by linear alkanes, FE-12-6 is demonstrated to be highly effective in representing the nonbond interactions in CGFF. The force field parameters are well transferrable among different alkane molecules, in different thermodynamic states and for predicting various thermodynamic properties including heats of vaporization, vapor-liquid-equilibrium coexistence curves, surface tensions, and liquid densities. PMID:26574265

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

    NASA Astrophysics Data System (ADS)

    Ivanov, Anatoly A.; Orlov, Vitaly A.

    2015-02-01

    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.

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

    PubMed Central

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

    2014-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Denisov, S. I.; Horsthemke, Werner

    2000-09-01

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

  9. Electric/magnetic dipolein an electromagnetic field: force, torque and energy

    NASA Astrophysics Data System (ADS)

    Kholmetskii, Alexander; Missevitch, Oleg; Yarman, T.

    2014-10-01

    In this paper we collect the relativistic expressions for the force, torque and energy of a small electric/magnetic dipole in an electromagnetic field, which we recently obtained (A.L. Kholmetskii et al., Eur. J. Phys. 33, L7 (2011), Prog. Electromagn. Res. B 45, 83 (2012), Can. J. Phys. 9, 576 (2013)) and consider a number of subtle effects, characterized the behavior of the dipole in an external field, which seem interesting from the practical viewpoint.

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

    SciTech Connect

    Teodorescu, C.; Young, W. C.; Swan, G. W. S.; Ellis, R. F.; Hassam, A. B.; Romero-Talamas, C. A.

    2010-08-20

    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.

  11. Turbulent relaxation to a force-free field-reversed state

    NASA Technical Reports Server (NTRS)

    Dahlburg, J. P.; Montgomery, D.; Doolen, G. D.; Turner, L.

    1986-01-01

    The evolution of nonequilibrium initial conditions of an incompressible magnetohydrodynamic Z pinch is described by a three-dimensional, pseudospectral numerical code. Magnetohydrodynamic turbulence develops in the resistive, nonviscous magnetofluid, resulting in the selective decay of the energy relative to the magnetic helicity, at Lundquist numbers of only a few hundred. An interior force-free region grows with time and achieves spontaneous reversal of the toroidal magnetic field at the wall, without the necessity of an external electric field.

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

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

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

  13. A "Sensitive Skin" for Robotic Companions Featuring Temperature, Force, and Electric Field Sensors

    E-print Network

    Breazeal, Cynthia

    A "Sensitive Skin" for Robotic Companions Featuring Temperature, Force, and Electric Field Sensors a wide variety of tactile inputs. Such "sensitive skins" can provide much benefit in human robot. In this paper we present a set of design criteria for how such "skins" should be designed. Based

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

    ERIC Educational Resources Information Center

    Veto, B.

    2011-01-01

    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…

  15. An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field

    SciTech Connect

    Yao, Jin

    2015-02-10

    A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.

  16. Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

    PubMed

    Henriques, João; Cragnell, Carolina; Skepö, Marie

    2015-07-14

    An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014 , 10 , 5113 - 5124 . ], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment. PMID:26575776

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

    PubMed

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

    2013-11-12

    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

  18. Friction forces arising from fluctuating thermal fields Jorge R. Zurita-Sanchez

    E-print Network

    Novotny, Lukas

    Friction forces arising from fluctuating thermal fields Jorge R. Zurita-Sa´nchez The Institute-dissipation theorem is applied to derive the linear-velocity damping coefficient . It turns out that is the result substrate and numerical values for are evaluated for particle and substrate materials made of silver

  19. APT a next generation QM-based reactive force field model

    NASA Astrophysics Data System (ADS)

    Rappé, A. K.; Bormann-Rochotte, L. M.; Wiser, D. C.; Hart, J. R.; Pietsch, M. A.; Casewit, C. J.; Skiff, W. M.

    Modelling reactivity at the nanoscale is a major computational challenge. Both reactive force field and combined QM-MM methodologies have been and are being developed to study reactivity at this boundary between molecules and the solid state. There have been more than 1500 publications since the mid-1990s, on combined QM-MM methodologies. Limitations in current models include the distortional characteristics of force field potential terms, the smooth transit from one potential surface to another, rather than surface hopping, and the blending of electrostatics between QM and MM portions of a QM-MM model. Functional forms, potential surface coupling terms, and parameterization strategies for the Approximate Pair Theory (APT), a next generation reactive force field model, are described. The APT model has been developed to correct a number of limitations in current reactive force field models as well as providing a foundation for a next generation QM-MM model. Chemical bonding concepts are used to develop fully dissociative bond stretch, bend, torsion, and inversion valence terms. Quantum mechanics also provides functional forms for potential surface coupling terms that permit a general description of reactivity from hydrogen bonding, through non-classical carbocations and cracking, to olefin polymerization, oxidation, and metathesis. Van der Waals, electrostatic, and metallic bonding models also derive from quantum mechanical resonance. Finally, Pauli Principle-based orthogonality provides a way to electrostatically couple the QM and MM portions of a QM-MM model that will support arbitrarily large basis sets.

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

    E-print Network

    Berry, R. Stephen

    processing. For instance, N-methylmorpholine-N-oxide (NMMO) in water dissolves cellulose, whereas NBinary Phases of Aliphatic N-Oxides and Water: Force Field Development and Molecular Dynamics, 2002; In Final Form: April 23, 2003 Aliphatic N-oxides as cosolvents with water play an important role

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

    NASA Astrophysics Data System (ADS)

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

    2007-04-01

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

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

    E-print Network

    Park, Harold S.

    Defecting controllability of bombarding graphene with different energetic atoms via reactive force field model Xiao Yi Liu, Feng Chao Wang, Harold S. Park, and Heng An Wu Citation: J. Appl. Phys. 114 of Contents: http://jap.aip.org/resource/1/JAPIAU/v114/i5 Published by the AIP Publishing LLC. Additional

  3. Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.

    PubMed

    Eichenberger, Andreas P; Huang, Wei; Riniker, Sereina; van Gunsteren, Wilfred F

    2015-07-14

    A supra-atomic coarse-grained (CG) force field for liquid n-alkanes is presented. The model was calibrated using experimental thermodynamic data and structural as well as energetic properties for 14 n-alkanes as obtained from atomistic fine-grained (FG) simulations of the corresponding hydrocarbons using the GROMOS 45A3 biomolecular force field. A variation of the nonbonded force-field parameters obtained from mapping the FG interactions onto the CG degrees of freedom to fit the density and heat of vaporization to experimental values turned out to be mandatory for a correct reproduction of these data by the CG model, while the bonded force-field parameters for the CG model could be obtained from a Boltzmann-weighted fit with some variations with respect to the corresponding properties from the FG simulations mapped onto the CG degrees of freedom. The model presents 6 different CG bead types, for bead sizes from 2 to 4 distinguishing between terminal and nonterminal beads within an alkane chain (end or middle). It contains different nonbonded Lennard-Jones parameters for the interaction of CG alkanes with CG water. The CG alkane model was further tested by comparing predictions of the excess free energy, the self-diffusion constant, surface tension, isothermal compressibility, heat capacity, thermal expansion coefficient, and shear viscosity for n-alkanes to experimental values. The CG model offers a thermodynamically calibrated basis for the development of CG models of lipids. PMID:26575730

  4. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

    PubMed Central

    2015-01-01

    The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan ?, ?, ?1, and ?2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields. PMID:26190950

  5. 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...

  6. Nonlinear restoring forces and geometry influence on stability in near-field acoustic levitation

    E-print Network

    Cao, Wenwu

    of NFAL is based on nonlinear vibration and nonuniform pressure distribution of a plate resonatorNonlinear restoring forces and geometry influence on stability in near-field acoustic levitation a theoretical analysis on the levitation stability using a nonlinear squeeze film model including inertia

  7. Behavioral/Systems/Cognitive Motor Force Field Learning Influences Visual Processing of

    E-print Network

    Gribble, Paul

    about how vision affects action than we do about how action affects vision. The motor system mayBehavioral/Systems/Cognitive Motor Force Field Learning Influences Visual Processing of Target on the visual control of movement, relatively little is known about how movement influences vision. The motor

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

    NASA Astrophysics Data System (ADS)

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

    1996-09-01

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

  9. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field

    NASA Astrophysics Data System (ADS)

    Mareš, Ji?í; Vaara, Juha

    2014-10-01

    An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6 ] 2 + complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

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

    E-print Network

    Koehl, Mimi

    Flow Forces on Seaweeds: Field Evidence for Roles of Wave Impingement and Organism Inertia BRIAN on flexible benthic seaweeds: impingement of breaking waves directly on emergent or- ganisms, and inertial abruptly reaches the extent of its range of motion. We focus on two common and important seaweed species

  11. Visualization of Force Fields in Protein Structure Clark Crawford, Oliver Kreylos, Bernd Hamann, Silvia Crivelli

    E-print Network

    Hamann, Bernd

    the straightforward application of volume visualization techniques. To visualize energy, it is necessary to define of the internal energy states in a molecule. We de- scribe our force field, the spatial mapping that we used for energy, and the visualizations that we produced from this mapping. We provide im- ages and animations

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

    PubMed

    Ferrando, Nicolas; Lachet, Véronique; Boutin, Anne

    2012-03-15

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

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

    SciTech Connect

    Tiwari, Sanjiv Kumar

    2012-01-01

    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.

  14. First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

    NASA Technical Reports Server (NTRS)

    Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

    2014-01-01

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

  15. Accurate Force Field Development for Modeling Conjugated Polymers Kateri H. DuBay, Michelle Lynn Hall, Chuanjie Wu, David R. Reichman, and Richard A. Friesner

    E-print Network

    Reichman, David

    Accurate Force Field Development for Modeling Conjugated Polymers Kateri H. DuBay, Michelle Lynn a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order

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

    SciTech Connect

    Jiang, Xiankai; Huai, Ping; Fan, Chunhai; Song, Bo E-mail: bosong@sinap.ac.cn; Gao, Jun; Huynh, Tien; Zhou, Ruhong E-mail: bosong@sinap.ac.cn

    2014-06-21

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  18. ReaxFF molecular dynamics simulations of intermediate species in dicyanamide anion and nitric acid hypergolic combustion

    NASA Astrophysics Data System (ADS)

    Weismiller, Michael R.; Junkermeier, Chad E.; Russo, Michael F., Jr.; Salazar, Michael R.; Bedrov, Dmitry; van Duin, Adri C. T.

    2015-10-01

    Ionic liquids based on the dicyanamide anion (DCA) are of interest as replacements for current hypergolic fuels, which are highly toxic. To better understand the reaction dynamics of these ionic liquid fuels, this study reports the results of molecular dynamics simulations performed for two predicted intermediate compounds in DCA-based ionic liquids/nitric acid (HNO3) combustion, i.e. protonated DCA (DCAH) and nitro-dicyanamide-carbonyl (NDC). Calculations were performed using a ReaxFF reactive force field. Single component simulations show that neat NDC undergo exothermic decomposition and ignition. Simulations with HNO3 were performed at both a low (0.25 g ml-1) and high (1.00 g ml-1) densities, to investigate the reaction in a dense vapor and liquid phase, respectively. Both DCAH and NDC react hypergolically with HNO3, and increased density led to shorter times for the onset of thermal runaway. Contrary to a proposed mechanism for DCA combustion, neither DCAH nor NDC are converted to 1,5-Dinitrobiuret (DNB) before thermal runaway. Details of reaction pathways for these processes are discussed.

  19. Aerosol Spectral Radiative Forcing Efficiency from Airborne Measurements During Multiple Field Missions

    NASA Astrophysics Data System (ADS)

    Schmidt, S.; Leblanc, S. E.; Pilewskie, P.; Redemann, J.; Hostetler, C. A.; Ferrare, R. A.; Hair, J. W.

    2012-12-01

    Measurements of shortwave spectral irradiance in conjunction with measurements of aerosol optical depth are used to determine the direct aerosol radiative forcing for various different regions and missions. To better compare cases with different air masses and solar geometry, we use the concept of top-of-layer and bottom-of-layer relative forcing efficiency. The aerosol layers were sampled from aircraft during several field campaigns, including the Megacity Initiative: Local and Global Research Observations (MILAGRO, Mexico, 2006); the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS, Alaska and Alberta, 2008), Research at the Nexus of Air Quality and Climate Change (CalNex, California, 2010); and the Deep Convective Clouds and Chemistry Experiment (DC3, central US, 2012). We show that the spectral shape of the relative forcing efficiency is similar for these aerosol layers regardless of the aerosol type. The spectral relative forcing efficiency at any one wavelength for the majority of the cases is constrained within a span of 20% per unit of midvisible aerosol optical depth. Single scattering albedo, asymmetry parameter, and surface albedo are secondary products for the various methods used to determine aerosol radiative forcing. Using these, we determine the diurnally averaged spectral and broadband top-of-atmosphere and surface radiative forcing efficiency for the various different aerosol types and surface conditions.

  20. Magnetic force microscopy of alternating magnetic field gradient by frequency modulation of tip oscillation

    NASA Astrophysics Data System (ADS)

    Saito, H.; Ikeya, H.; Egawa, G.; Ishio, S.; Yoshimura, S.

    2009-04-01

    A new magnetic force microscopy (MFM) technique for measuring alternating magnetic field (ac magnetic field) was proposed by using frequency modulation (FM) phenomenon of tip oscillation. We detected a narrowband FM phenomenon in the tip oscillation of a high-coercivity MFM tip by applying an ac magnetic field to the tip by using a metal-in-gap (MIG) type ring head. In the experiment, the MFM tip was driven at a constant frequency fc near the resonant frequency of the cantilever by a piezoelectric element, and the ac magnetic field with a frequency fm up to 10 kHz was applied to the MFM tip. Two sideband spectra with a frequency of fc±fm were observed by applying ac magnetic field. The intensity of sideband spectra increased linearly with increasing applied current value of the MIG head. It was observed that FM occurred from the analysis of frequency spectra of the MFM signals. This FM phenomenon is caused by the force applied on the cantilever by the field gradient of the head. The FM phenomenon is understood by solving the differential equation for the harmonic oscillator of which the effective spring constant is changed periodically by ac magnetic field. The FM phenomenon can be used for imaging ac magnetic fields.

  1. Streaming and removal forces due to second-order sound field during megasonic cleaning of silicon wafers

    E-print Network

    Deymier, Pierre

    Streaming and removal forces due to second-order sound field during megasonic cleaning of silicon September 2000 We calculate the second-order streaming force in a fluid in the vicinity of the solid. It is composed of one silicon slab wafer immersed in water. The components of the streaming force parallel

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

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

    E-print Network

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

    2006-07-23

    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.

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

    NASA Astrophysics Data System (ADS)

    Woolf, David Nathaniel

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

  5. Electromagnetic and gravitational self-force on a relativistic particle from quantum fields in curved space

    E-print Network

    Galley, C R; Lin, S Y; Galley, Chad R.; Lin, Shih-Yuin

    2006-01-01

    We provide a quantum field theoretical derivation of the Abraham-Lorentz-Dirac (ALD) equation, describing the motion of an electric point charge sourcing an electromagnetic field, which back-reacts on the charge as a self-force, and the Mino-Sasaki-Tanaka-Quinn-Wald (MSTQW) equation describing the motion of a point mass with self-force interacting with the linearized metric perturbations caused by the mass off an otherwise vacuous curved background spacetime. We regularize the formally divergent self-force by smearing the direct part of the retarded Green's function and using a quasilocal expansion. We also derive the ALD-Langevin and the MSTQW-Langevin equations with a classical stochastic force accounting for the effect of the quantum fluctuations in the field, which causes small fluctuations on the particle trajectory. These equations will be useful for studying the stochastic motion of charges and small masses under the influence of both quantum and classical noise sources, derived either self-consistentl...

  6. Electromagnetic and gravitational self-force on a relativistic particle from quantum fields in curved space

    E-print Network

    Chad R. Galley; B. L. Hu; Shih-Yuin Lin

    2006-03-24

    We provide a quantum field theoretical derivation of the Abraham-Lorentz-Dirac (ALD) equation, describing the motion of an electric point charge sourcing an electromagnetic field, which back-reacts on the charge as a self-force, and the Mino-Sasaki-Tanaka-Quinn-Wald (MSTQW) equation describing the motion of a point mass with self-force interacting with the linearized metric perturbations caused by the mass off an otherwise vacuous curved background spacetime. We regularize the formally divergent self-force by smearing the direct part of the retarded Green's function and using a quasilocal expansion. We also derive the ALD-Langevin and the MSTQW-Langevin equations with a classical stochastic force accounting for the effect of the quantum fluctuations in the field, which causes small fluctuations on the particle trajectory. These equations will be useful for studying the stochastic motion of charges and small masses under the influence of both quantum and classical noise sources, derived either self-consistently or put in by hand phenomenologically. We also show that history-dependent noise-induced drift motions could arise from such stochastic sources on the trajectory that could be a hidden feature of gravitational wave forms hitherto unknown.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Technical Reports Server (NTRS)

    Aly, J. J.

    1984-01-01

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

  9. Near-field infrared absorption of plasmonic semiconductor microparticles studied using atomic force microscope infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Felts, Jonathan R.; Law, Stephanie; Roberts, Christopher M.; Podolskiy, Viktor; Wasserman, Daniel M.; King, William P.

    2013-04-01

    We report measurements of near-field absorption in heavily silicon-doped indium arsenide microparticles using atomic force microscope infrared spectroscopy (AFM-IR). The microparticles exhibit an infrared absorption peak at 5.75 ?m, which corresponds to a localized surface plasmon resonance within the microparticles. The near-field absorption measurements agree with far-field measurements of transmission and reflection, and with results of numerical solutions of Maxwell equations. AFM-IR measurements of a single microparticle show the temperature increase expected from Ohmic heating within the particle, highlighting the potential for high resolution infrared imaging of plasmonic and metamaterial structures.

  10. Math. 467: Modern Geometry c S. A. Fulling 2009ff

    E-print Network

    Fulling, Stephen

    .tamu.edu/~fulling/m467/f15/handout.pdf Class web page: http://calclab.math.tamu.edu/~fulling/m467/f15/ [PutMath. 467: Modern Geometry c S. A. Fulling 2009ff First day [data above] Course handout: http://calclab.math on tests than in most math courses. Each homework assignment will contain one essay question

  11. Math. 467: Modern Geometry c S. A. Fulling 2009ff

    E-print Network

    Fulling, Stephen

    .tamu.edu/~fulling/m467/f15/handout.pdf Class web page: http://calclab.math.tamu.edu/~fulling/m467/f15/ 1 #12;[PutMath. 467: Modern Geometry c S. A. Fulling 2009ff First day [data above] Course handout: http://calclab.math on tests than in most math courses. Each homework assignment will contain one essay question

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

    SciTech Connect

    Jiang Chaowei; Feng Xueshang; Xiang Changqing

    2012-08-10

    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.

  13. Effects of auroral-particle anisotropies and mirror forces on high-latitude electric fields

    NASA Technical Reports Server (NTRS)

    Chiu, Y. T.; Schulz, M.; Cornwall, J. M.

    1981-01-01

    It is noted that, for most of the mechanisms for the strong electric fields that characterize the narrow regions in which there is acceleration and precipitation of ring current and/or plasma-sheet plasma, certain effects must be taken into account in simulations of auroral electric fields. The effects are those of auroral particle anisotropy, of mirror forces due to the inhomogeneous geomagnetic field, of auroral electron backscatter by the atmosphere, and of electron trapping by the combination of magnetic mirroring and electrostatic forces. What is more, the effects of the very strong perpendicular electric field must also be taken into account in a kinetic description of the Poisson equation in order to achieve a unified theory of the auroral electrostatic structure. Progress in these areas during the past few years is reviewed. It is shown that particle anisotropies and mirror forces can account for some basic electrostatic features of the quiet arc, while additional effects may be occurring in strong events in which the parallel potential drop is more than about 10 kV.

  14. Forced and free variations of the surface temperature field in a general circulation model

    SciTech Connect

    North, G.R.; Yip, K.J.J.; Laiyung Leung ); Chervin, R.M. )

    1992-03-01

    The concept of forced' and free' variations of large-scale surface temperature is examined by analyzing several long runs of the Community Climate Model (CCM0) with idealized boundary conditions and forcing. (1) The planet is all land with uniform sea-level topography and fixed soil moisture. (2) The planetary surface and prescribed ozone are reflection symmetric across the equator and there is no generation of snow. (3) The obliquity is set to zero so that the climate is for a perpetual equinox solar insolation (i.e., sun fixed over the equator). After examining some relevant aspects of the undisturbed climate (surface temperature field) such as temporal and spatial autocorrelations and the corresponding spectra, two types of changes in external forcing are imposed to study the model response: (1) sinusoidal changes of the solar constant (5%, 10%, 20%, and 40% amplitudes) at periods of 15 and 30 days (the latter is the autocorrelation time for the global average surface temperature) and 20% at 60 days and (2) insertion of steady heat sources (points and zonal bands) of variable strength at the surface. Then the temporal spectra of large scales for the periodically forced climate and the ensemble-averaged influence functions are examined for the point source disturbed climates. In each class of experiments the response of ensemble-averaged amplitudes was found to be proportional to the amplitude of the forcing. These results suggest that the lowest moments of the surface temperature field have a particularly simple dependence on forcing. Furthermore, the apparent finiteness of the variance spectrum at low frequencies suggest that estimates of long-term statistics are stable in this type of atmospheric general circulation model. 31 refs., 17 figs.

  15. Unsteady hydrodynamic forces acting on a hand and its flow field during sculling motion.

    PubMed

    Takagi, Hideki; Shimada, Shohei; Miwa, Takahiro; Kudo, Shigetada; Sanders, Ross; Matsuuchi, Kazuo

    2014-12-01

    The goal of this research is to clarify the mechanism by which unsteady forces are generated during sculling by a skilled swimmer and thereby to contribute to improving propulsive techniques. We used particle image velocimetry (PIV) to acquire data on the kinematics of the hand during sculling, such as fluid forces and flow field. By investigating the correlations between these data, we expected to find a new propulsion mechanism. The experiment was performed in a flow-controlled water channel. The participant executed sculling motions to remain at a fixed position despite constant water flow. PIV was used to visualize the flow-field cross-section in the plane of hand motion. Moreover, the fluid forces acting on the hand were estimated from pressure distribution measurements performed on the hand and simultaneous three-dimensional motion analysis. By executing the sculling motion, a skilled swimmer produces large unsteady fluid forces when the leading-edge vortex occurs on the dorsal side of the hand and wake capture occurs on the palm side. By using a new approach, we observed interesting unsteady fluid phenomena similar to those of flying insects. The study indicates that it is essential for swimmers to fully exploit vortices. A better understanding of these phenomena might lead to an improvement in sculling techniques. PMID:25310026

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

    PubMed

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

    2015-01-01

    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

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

    PubMed Central

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

    2012-01-01

    Summary Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation. In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface. PMID:23019560

  18. High sensitive space electric field sensing based on micro fiber interferometer with field force driven gold nanofilm

    NASA Astrophysics Data System (ADS)

    Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei

    2015-10-01

    The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120?nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200?V/m at 1?KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection.

  19. High sensitive space electric field sensing based on micro fiber interferometer with field force driven gold nanofilm.

    PubMed

    Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei

    2015-01-01

    The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection. PMID:26507680

  20. High sensitive space electric field sensing based on micro fiber interferometer with field force driven gold nanofilm

    PubMed Central

    Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei

    2015-01-01

    The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120?nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200?V/m at 1?KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection. PMID:26507680

  1. Force-free magnetic fields - Is there a 'loss of equilibrium'?

    NASA Technical Reports Server (NTRS)

    Klimchuk, J. A.; Sturrock, P. A.

    1989-01-01

    This paper examines concept in solar physics that is known as loss of equilibrium in which a sequence of force-free magnetic fields, said to represent a possible quasi-static evolution of solar magnetic fields, reaches a critical configuration beyond which no acceptable solution of the prescribed form exists. This concept is used to explain eruptive phenomena ranging from solar flares to coronal mass ejections. Certain sequences of force-free configurations are discussed that exhibit a loss of equilibrium, and it is argued that the concept is devoid of physical significance since each sequence is defined a way that does not represent an acceptable thought experiment. For example, the sequence may be defined in terms of a global constraint on the boundary conditions, or the evolution of the sequence may require the creation of mgnetic flux that is not connected to the photosphere and is not present in the original configuration. The global constraints typically occur in using the so-called generating function method. An acceptance thought experiment is proposed to specify the field configuration in terms of photospheric boundary conditions comprising the normal component of the field and the field-line connectivity. Consider a magnetic-field sequence that, when described in terms of a generating function, exhibits a loss of equilibrium and show that, when one instead defines the sequence in terms of the corresponding boundary conditions, the sequence is well behaved.

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

    SciTech Connect

    Lerche, I.; Low, B. C.

    2014-10-15

    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.

  3. Convenient recycling and reuse of bombarded [¹?O]H?O for the production and the application of [¹?F]F?.

    PubMed

    Rötering, Sven; Franke, Karsten; Zessin, Jörg; Brust, Peter; Füchtner, Frank; Fischer, Steffen; Steinbach, Jörg

    2015-07-01

    The limited availability and the increasing demands of [(18)O]H2O force the reuse of bombarded [(18)O]H2O for the production of [(18)F]F(-) at least for the purposes of research. Therefore, inorganic and organic contaminants have to be removed from the [(18)O]H2O after bombardment. We present a simple, effective, easy-handling and reliable method of [(18)O]H2O purification including oxidation and distillation. The obtained recycled [(18)O]H2O had comparable quality to commercially distributed [(18)O]water. This was confirmed by a detailed comparison of produced radionuclides and their activities and the application of [(18)F]F(-) for the automated synthesis of [(18)F]fluspidine. PMID:25827947

  4. AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes.

    PubMed

    Nikitin, Alexei; Milchevskiy, Yury; Lyubartsev, Alexander

    2015-11-19

    A molecular mechanics force field of the AMBER/OPLS family for perfluoroalkanes, noble gases, and their mixtures with alkanes has been proposed. We had to abandon the traditional Lorentz-Berthelot combining rules for the Lennard-Jones potential to be able to uniformly describe these substance classes and their mixtures. Instead, the Waldman-Hagler rules developed for noble gases were used for all of these elements except hydrogen. Hydrogen is considered to be a particular substance to which the usual Lorentz-Berthelot rules are applied. The proposed rules have little effect on the organic chemistry of H, C, N, and O elements but make it compliant with the chemistry of heavy elements. Because of assigning a relatively high partial charge of -0.37e to fluorine atoms, the new force field reproduces the mutual insolubility of higher liquid alkanes and perfluoroalkanes. PMID:26498002

  5. The Influence of Lorentz Force on Vacuum Arc Behaviors with AN Axial Magnetic Field

    NASA Astrophysics Data System (ADS)

    Cho, S. H.; Lee, H. G.; Choi, M. J.; Kwon, J. R.; Kim, Y. J.

    The necessity of the vacuum interrupters (VIs) has been widely recognized on switching and controlling the fault currents in medium voltage level. An axial magnetic field (AMF) electrode has more advantages of the switching capability than other contact designs such as securing higher current value for transferring from the constriction arc to the diffuse. The heat flux and the local temperature on the electrode are increased by arc constriction, which is influenced by Lorentz force. It has undesirable influence on the characteristics of vacuum arc. In this study, we simulated the influence of Lorentz force on vacuum arc behaviors with an AMF electrode by using a commercial FEM package, ANSYS. The vacuum arc has been modeled with the sequential coupling method of two different fields, which are on the electromagnetic and thermal-flow. Arc constriction with various applied currents could be predicted with the results of temperature distribution.

  6. Secondary resonance magnetic force microscopy using an external magnetic field for characterization of magnetic thin films

    NASA Astrophysics Data System (ADS)

    Liu, Dongzi; Mo, Kangxin; Ding, Xidong; Zhao, Liangbing; Lin, Guocong; Zhang, Yueli; Chen, Dihu

    2015-09-01

    A bimodal magnetic force microscopy (MFM) that uses an external magnetic field for the detection and imaging of magnetic thin films is developed. By applying the external modulation magnetic field, the vibration of a cantilever probe is excited by its magnetic tip at its higher eigenmode. Using magnetic nanoparticle samples, the capacity of the technique which allows single-pass imaging of topography and magnetic forces is demonstrated. For the detection of magnetic properties of thin film materials, its signal-to-noise ratio and sensitivity are demonstrated to be superior to conventional MFM in lift mode. The secondary resonance MFM technique provides a promising tool for the characterization of nanoscale magnetic properties of various materials, especially of magnetic thin films with weak magnetism.

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

    PubMed Central

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

    2009-01-01

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

  8. Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate.

    PubMed

    Zhang, Changsheng; Lu, Chao; Wang, Qiantao; Ponder, Jay W; Ren, Pengyu

    2015-11-10

    Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact both the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P-O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different. PMID:26574325

  9. Limitations of force-free magnetic field extrapolations: Revisiting basic assumptions

    NASA Astrophysics Data System (ADS)

    Peter, H.; Warnecke, J.; Chitta, L. P.; Cameron, R. H.

    2015-12-01

    Context. Force-free extrapolations are widely used to study the magnetic field in the solar corona based on surface measurements. Aims: The extrapolations assume that the ratio of internal energy of the plasma to magnetic energy, the plasma ?, is negligible. Despite the widespread use of this assumption observations, models, and theoretical considerations show that ? is of the order of a few percent to more than 10%, and thus not small. We investigate what consequences this has for the reliability of extrapolation results. Methods: We use basic concepts starting with force and energy balance to infer relations between plasma ? and free magnetic energy to study the direction of currents in the corona with respect to the magnetic field, and to estimate the errors in the free magnetic energy by neglecting effects of the plasma (? ? 1). A comparison with a 3D magneto-hydrodynamics (MHD) model supports our basic considerations. Results: If plasma ? is of the order of the relative free energy (the ratio of the free magnetic energy to the total magnetic energy) then the pressure gradient can balance the Lorentz force. This is the case in solar corona, and therefore the currents are not properly described. In particular, the error in terms of magnetic energy by neglecting the plasma is of the order of the free magnetic energy, so that the latter cannot be reliably determined by an extrapolation. Conclusions: While a force-free extrapolation might capture the magnetic structure and connectivity of the coronal magnetic field, the derived currents and free magnetic energy are not reliable. Thus quantitative results of extrapolations on the location and amount of heating in the corona (through current dissipation) and on the energy storage of the magnetic field (e.g. for eruptive events) are limited.

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

    PubMed

    Raabe, Gabriele; Maginn, Edward J

    2010-08-12

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

  11. Theoretical and experimental study of inclusion removal from molten metal under an alternating electromagnetic force field

    NASA Astrophysics Data System (ADS)

    Patel, Ashish D.

    One of the emerging technologies for the production of clean metals is electromagnetic filtration. This dissertation describes the work done on the theory of electromagnetic separation in alternating electromagnetic fields together with the experimental results obtained on the removal of silica particles from molten aluminum from an induced current separator. Analytical expressions have been developed for describing the electric and magnetic fields, and the separation force for a spherical particle in an infinite conducting medium subjected to an alternating magnetic field. It was found that the magnitude and direction of the separation force depends on the ratio of electrical conductivity of the fluid and the sphere as well as the frequency of the applied field. Analytical expressions were also developed for the MHD flow in and around the particle. The solutions revealed two characteristic secondary flows; one is driven by the distortion of the electric current around the particle, while the other is driven by forces resulting from the interaction of the current and the applied magnetic field. The results of the experimental study on removal of silica particles from aluminum showed complete removal of the particles from the melt, and the rate of inclusion removal was found to depend on the applied magnetic field strength and the particle size. A mathematical model has been developed for describing the rate of inclusion removal from the metal in the induced current separator. The model was found to accurately predict the measured removal rates. The effects of the processing parameters on time for complete removal of inclusions in induced current separators are discussed.

  12. Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

    PubMed Central

    2015-01-01

    We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

  13. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    PubMed

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 ?s metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

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

    PubMed Central

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

    2012-01-01

    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

  15. Simplified TiO2 force fields for studies of its interaction with biomolecules.

    PubMed

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-21

    Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules. PMID:26093545

  16. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    PubMed

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site. PMID:25410708

  17. Force-Field Based Quasi-Chemical Method for Rapid Evaluation of Binary Phase Diagrams.

    PubMed

    Sweere, Augustinus J M; Fraaije, Johannes G E M

    2015-11-01

    We present the Pair Configurations to Molecular Activity Coefficients (PAC-MAC) method. The method is based on the pair sampling technique of Blanco (Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L. Application of Molecular Simulation to Derive Phase Diagrams of Binary Mixtures. Macromolecules 1992, 25, 3667-3676) with an extension that takes the packing of the molecules into account by a free energy model. The intermolecular energy is calculated using classical force fields. PAC-MAC is able to predict activity coefficients and corresponding vapor-liquid equilibrium diagrams at least 4 orders of magnitude faster than molecular simulations. The accuracy of the PAC-MAC method is tested by comparing the results with experimental data and with the results of the COSMO-SAC model (Lin, S.-T.; Sandler, S. I. A Priori Phase Equilibrium Prediction from a Segment Contribution Solvation Model. Ind. Eng. Chem. Res. 2002, 41, 899-913). PAC-MAC (using the OPLS-aa force field) is shown to be comparable in accuracy to COSMO-SAC, at the considerable advantage that PAC-MAC in principle does not require quantum calculation, provided proper force fields to be available. PMID:26418484

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

    PubMed Central

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

    2004-01-01

    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

  19. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

    PubMed Central

    Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-01-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 ?s metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  20. Cost-Effective Force Field Tailored for Solid-Phase Simulations of OLED Materials.

    PubMed

    Moral, M; Son, W-J; Sancho-García, J C; Olivier, Y; Muccioli, L

    2015-07-14

    A united atom force field is empirically derived by minimizing the difference between experimental and simulated crystal cells and melting temperatures for eight compounds representative of organic electronic materials used in OLEDs and other devices: biphenyl, carbazole, fluorene, 9,9'-(1,3-phenylene)bis(9H-carbazole)-1,3-bis(N-carbazolyl)benzene (mCP), 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (pCBP), phenazine, phenylcarbazole, and triphenylamine. The force field is verified against dispersion-corrected DFT calculations and shown to also successfully reproduce the crystal structure for two larger compounds employed as hosts in phosphorescent and thermally activated delayed fluorescence OLEDs: N,N'-di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine (NPD), and 1,3,5-tri(1-phenyl-1H-benzo[d]imidazol-2-yl)phenyl (TPBI). The good performances of the force field coupled to the large computational savings granted by the united atom approximation make it an ideal choice for the simulation of the morphology of emissive layers for OLED materials in crystalline or glassy phases. PMID:26575772

  1. A Kirkwood-Buff Force Field for the Aromatic Amino Acids

    PubMed Central

    Ploetz, Elizabeth A.; Smith, Paul E.

    2014-01-01

    In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained. PMID:21931889

  2. Simplified TiO2 force fields for studies of its interaction with biomolecules

    NASA Astrophysics Data System (ADS)

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-06-01

    Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

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

    PubMed Central

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

    2014-01-01

    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

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

    SciTech Connect

    Weening, R. H.

    2011-12-15

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

    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.

  6. GENERATION OF SEED MAGNETIC FIELD AROUND FIRST STARS: EFFECTS OF RADIATION FORCE

    SciTech Connect

    Ando, Masashi; Doi, Kentaro; Susa, Hajime E-mail: mn921009@center.konan-u.ac.j

    2010-06-20

    We investigate seed magnetic field generation in the early universe by the radiation force of first stars. In a previous study with the steady assumption, large amplitudes ({approx}10{sup -15} G for first stars, {approx}10{sup -11} G for QSOs) are predicted. In this study, we formulate this issue in an unsteady framework. Then, we consider a specific model of magnetic field generation around a very massive first star. Consequently, we (1) find that the steady assumption is not valid in realistic situations and (2) obtain a much smaller magnetic field strength than that predicted by Langer et al. In addition, we find that the momentum transfer process during photoionization is more important than Thomson scattering. The resultant magnetic flux density around the first star is {approx_lt}10{sup -19} G. This seed magnetic field will not affect subsequent star formation in the neighborhood of first stars.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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.

  8. Math. 467: Modern Geometry c S. A. Fulling 2009ff

    E-print Network

    Fulling, Stephen

    .tamu.edu/~fulling/m467/f14/handout.pdf Class web page: http://calclab.math.tamu.edu/~fulling/m467/f14/ [PutMath. 467: Modern Geometry c S. A. Fulling 2009ff First day [data above] Course handout: http://calclab.math course. There is more emphasis on homework and term papers and less on tests than in most math courses

  9. Examinations of samples of Bell Canyon Test 1-FF grout

    SciTech Connect

    Rhoderick, J. E.; Wong, G. S.; Buck, A. D.

    1981-05-01

    Portland cement grout identified as BCT-1-FF (Bell Canyon Test 1-FF) was used in borehole plugging experiments of the Bell Canyon Tests in Holl AEC-7 at the Waste Isolation Pilot Plant site in New Mexico during September 1979 and February 1980. This grout was made with fresh water. A study of this grout was begun in August 1979 in the laboratory to evauate the possible effects of temperature, pressure, and storage in fresh water or simulated groundwater (brine) on its phase composition and compressive strength at early ages. Phase composition was determined by X-ray diffraction. Temperatures ranged up to about 150/sup 0/F and included elevation at a few hours age after mixing; pressure was as high as 1500 psi; specimens were stored in simulated groundwater (brine) or in fresh water. Data from 1 to 90 days showed: (a) Higher temperature accelerated early strength gain. These differences essentially vanished by 90 days age. (b) Hydration products as identified by X-ray diffraction were normal; this indicated that a temperature range of 78 to 153/sup 0/F was not significant. (c) Pressure did not affect composition. (d) Storage in simulated groundwater (brine) or fresh water had no detectable effect. (e) Since the BCT-1-FF grout mixture contained added sulfate, it formed more ettringite as judged by X-ray diffraction than comparable portland cement mixtures without added sulfate.

  10. Photoelectric photometry of the unusual eclipsing binary system FF Aquarii.

    NASA Astrophysics Data System (ADS)

    Sipahi, E.; Evren, S.; Tas, G.; ?bano?lu, C.

    FF Aqr is the first eclipsing binary (P = 9.2d) containing a hot subdwarf (sdOB) and a chromospherically active cool giant component classified as a G8-K0 III star. We observed the system in U, B, V and R filters during 2002, 2003 and 2004 observing seasons using two different telescopes and detectors. We obtained a total of 1171 observational points in each colour. The light curve reveals that FF Aqr has a totality in the primary eclipse, which lasts about 13h 02m. The shape of the light curve indicates that FF Aqr is an Algol type binary. The light curves display an asymmetrical wave-like distortion at outside of the eclipse which has a minimum at about 0.46P and a light amplitude of 0.050m, 0.204m, 0.277m, 0.282m in the U, B, V, and R bands, respectively. This variation can not be explained by the reflection effect alone. We used the Wilson-Devinney code for the geometric and physical parameters of the system. The asymmetry at outside of the eclipse light variation and the results obtained from the light curve analysis were discussed.

  11. Three-body system in leading order Effective Field Theory without three-body forces

    E-print Network

    B. Blankleider; J. Gegelia

    2000-09-05

    The use of leading order effective field theory (EFT) to describe neutron-deuteron scattering leads to integral equations that have unusual behaviour: when only two-body interactions are included, the scattering amplitude does not approach a limit when the cutoff used to solve the equations is removed. It has recently been shown that this cutoff dependence can be eliminated by the careful inclusion of a three-body force. In this paper we show that the cutoff dependence is just a reflection of the fact that the aforementioned integral equations admit an infinite number of solutions amongst which only one corresponds to the physical scattering amplitude. We show how to numerically extract the physical scattering amplitude from the general solution and in this way explicitly demonstrate that the amplitude for a particle scattering off a two-body bound state, in leading order EFT, is in fact determined entirely by two-body forces.

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

    NASA Astrophysics Data System (ADS)

    Coles, Jonathan P.; Masella, Michel

    2015-01-01

    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.

  13. Validity and reliability of pressure-measurement insoles for vertical ground reaction force assessment in field situations.

    PubMed

    Koch, Markus; Lunde, Lars-Kristian; Ernst, Michael; Knardahl, Stein; Veiersted, Kaj Bo

    2016-03-01

    This study aimed to test the validity and reliability of pressure-measurement insoles (medilogic(®) insoles) when measuring vertical ground reaction forces in field situations. Various weights were applied to and removed from the insoles in static mechanical tests. The force values measured simultaneously by the insoles and force plates were compared for 15 subjects simulating work activities. Reliability testing during the static mechanical tests yielded an average interclass correlation coefficient of 0.998. Static loads led to a creeping pattern of the output force signal. An individual load response could be observed for each insole. The average root mean square error between the insoles and force plates ranged from 6.6% to 17.7% in standing, walking, lifting and catching trials and was 142.3% in kneeling trials. The results show that the use of insoles may be an acceptable method for measuring vertical ground reaction forces in field studies, except for kneeling positions. PMID:26674403

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

    SciTech Connect

    Sandness, G.A.

    1991-03-01

    This report describes a set of geophysical surveys performed by the Pacific Northwest Laboratory at selected locations within the 300-FF-1 Operable Unit at Hanford. Field work and preliminary data processing activities were initiated in September 1989. These actions were terminated by the Westinghouse Hanford Company before completion in December 1989. Work was reinitiated in October 1990, to complete the processing of the data that had already been collected and to report the results. Because the field work was only partially completed, the task objectives, as presented in the Statement of Work, could not be fully met. This report is, therefore, a progress report covering the work performed through December 11, 1989. This task involved (1) ground-penetrating radar surveys of the 618-4 and 618-5 Burial Grounds, and (2) ground-penetrating radar and electromagnetic induction surveys along the assumed routes of the abandoned process sewers and radioactive liquid waste sewers in the 300-FF-1 Operable Unit. The surveys in the burial grounds were intended to identify burial trenches and pits, to determine the depth of fill, and to locate waste materials, including any that might be outside the perimeter fences. The surveys along the sewer routes were intended, first, to confirm the locations of the sewers as shown on existing maps or to otherwise accurately determine their locations, and second, to attempt to identify locations of possible leaks. 3 refs., 3 figs., 2 tabs.

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

    PubMed

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

    2012-01-01

    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

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

    PubMed Central

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

    2012-01-01

    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

  17. Simulation of the Elastic and Ultimate Tensile Properties of Diamond, Graphene, Carbon Nanotubes, and Amorphous Carbon Using a Revised ReaxFF Parametrization.

    PubMed

    Jensen, Benjamin D; Wise, Kristopher E; Odegard, Gregory M

    2015-09-17

    In light of the enduring interest in using nanostructured carbon materials as reinforcing elements in composite materials, there is a significant need for a reliable computational tool capable to predict the mechanical properties, both elastic properties and properties at the point of fracture, in large-scale atomistic simulations. A revised version of the ReaxFF reactive force field parametrization for carbon, ReaxFFC-2013, was recently published and is notable because of the inclusion of density functional theory (DFT)-derived mechanical data for diamond and graphite in the fitting set. The purpose of the present work is to assess the accuracy of this new force field for predicting the mechanical properties for several allotropes of carbon, both in the elastic regime and during fracture. The initial discussion focuses on the performance of ReaxFFC-2013 for diamond and graphene, the two carbon forms for which mechanical properties were included in the parametrization data set. After it is established that simulations conducted with the new force field yield results that agree well with DFT and experimental data for most properties of interest, its transferability to amorphous carbon and carbon nanotubes is explored. ReaxFFC-2013 is found to produce results that, for the most part, compare favorably with available experimental data for single and multiwalled nanotubes and for amorphous carbon models prepared over a range of densities. Although there is opportunity for improvement in some predicted properties, the ReaxFFC-2013 parametrization is shown to generally perform well for each form of carbon and to compare favorably with DFT and experimental data. PMID:26315717

  18. A method for embedding circular force-free flux ropes in potential magnetic fields

    SciTech Connect

    Titov, V. S.; Török, T.; Mikic, Z.; Linker, J. A.

    2014-08-01

    We propose a method for constructing approximate force-free equilibria in pre-eruptive configurations in which a thin force-free flux rope is embedded into a locally bipolar-type potential magnetic field. The flux rope is assumed to have a circular-arc axis, a 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.

  19. Perspectives on the simulation of protein-surface interactions using empirical force field methods.

    PubMed

    Latour, Robert A

    2014-12-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  1. Nonlinear force-free extrapolation of the coronal magnetic field based on the magnetohydrodynamic relaxation method

    SciTech Connect

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

    2014-01-01

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

  2. Advances in damage control resuscitation and surgery: implications on the organization of future military field forces

    PubMed Central

    Tien, Col Homer; Beckett, Maj Andrew; Garraway, LCol Naisan; Talbot, LCol Max; Pannell, Capt Dylan; Alabbasi, Thamer

    2015-01-01

    Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future. PMID:26100784

  3. Advances in damage control resuscitation and surgery: implications on the organization of future military field forces.

    PubMed

    Tien, Homer; Beckett, Andrew; Garraway, Naisan; Talbot, Max; Pannell, Dylan; Alabbasi, Thamer

    2015-06-01

    Medical support to deployed field forces is increasingly becoming a shared responsibility among allied nations. National military medical planners face several key challenges, including fiscal restraints, raised expectations of standards of care in the field and a shortage of appropriately trained specialists. Even so, medical services are now in high demand, and the availability of medical support may become the limiting factor that determines how and where combat units can deploy. The influence of medical factors on operational decisions is therefore leading to an increasing requirement for multinational medical solutions. Nations must agree on the common standards that govern the care of the wounded. These standards will always need to take into account increased public expectations regarding the quality of care. The purpose of this article is to both review North Atlantic Treaty Organization (NATO) policies that govern multinational medical missions and to discuss how recent scientific advances in prehospital battlefield care, damage control resuscitation and damage control surgery may inform how countries within NATO choose to organize and deploy their field forces in the future. PMID:26100784

  4. Non-linear force-free field modeling: model techniques, boundary conditions, hares, and hounds

    NASA Astrophysics Data System (ADS)

    Schrijver, C. J.; De Rosa, M. L.; Metcalf, T.

    2005-05-01

    Understanding the conditions under which solar magnetic fields can destabilize to erupt in flares and coronal mass ejections requires a quantitative understanding of the coronal magnetic field and of the currents that it carries. The increased availability of vector magnetograms, together with EUV and X-ray coronal images, should provide adequate constraints to model the coronal field, and thus to visualize its 3D geometry and to measure the available free energy and helicity. Non-linear force-free fields (NLFFF) are likely a useful model to use when extrapolating the solar surface field upward into the coronal volume. It may even be possible to use the observed trajectories of coronal loops, evident in EUV images of the corona, as a further constraint. We present initial results of a team effort to understand the intricacies of NLFFF modeling: we discuss and evaluate comparisons of NLFFF models computed with different models and applications of boundary conditions, and look ahead to full coronal field modeling for the upcoming Solar-B and SDO missions.

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

    E-print Network

    Martin, Jan M.L.

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

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

    ERIC Educational Resources Information Center

    De Luca, R.

    2009-01-01

    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

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

    E-print Network

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

    2007-08-31

    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.

  8. Computing Reaction Pathways of Rare Biomolecular Transitions using Atomistic Force-Fields.

    PubMed

    Faccioli, P; A Beccara, S

    2016-01-01

    The Dominant Reaction Pathway (DRP) method is an approximate variational scheme which can be used to compute reaction pathways in conformational transitions undergone by large biomolecules (up to ~10(3) amino-acids) using realistic all-atom force fields. We first review the status of development of this method. Next, we discuss its validation against the results of plain MD protein folding simulations performed by the DE-Shaw group using the Anton supercomputer. Finally, we review a few representative applications of the DRP approach to study reactions which are far too complex and rare to be investigated by plain MD, even on the Anton machine. PMID:26320390

  9. Infrared and Raman spectra, ab initio calculations, force field refinement and vibrational assignment of 3-aminophenol

    NASA Astrophysics Data System (ADS)

    Buyukmurat, Y.; Akyuz, S.

    2005-06-01

    The molecular geometry and molecular vibrations of 3-aminophenol and its some deuterated derivatives have been investigated with the aid of quantum chemical calculations, normal coordinate analysis using force field refinement method and vibrational spectroscopy. The barrier of the OH group pointing in the direction of the amino group with respect to the anti conformer for 3-aminophenol was computed to be 2.44 kJ/mol. The spectroscopic and theoretical results are compared to the corresponding properties for some similar molecules.

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

    SciTech Connect

    Turner, L.R.

    1996-05-01

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

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

    SciTech Connect

    Turner, L.R.

    1997-03-01

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

  12. On finding fields and self-force in a gauge appropriate to separable wave equations

    E-print Network

    Tobias S. Keidl; John L. Friedman; Alan G. Wiseman

    2007-05-29

    Gravitational waves from the inspiral of a stellar-size black hole to a supermassive black hole can be accurately approximated by a point particle moving in a Kerr background. This paper presents progress on finding the electromagnetic and gravitational field of a point particle in a black-hole spacetime and on computing the self-force in a ``radiation gauge.'' The gauge is chosen to allow one to compute the perturbed metric from a gauge-invariant component $\\psi_0$ (or $\\psi_4$) of the Weyl tensor and follows earlier work by Chrzanowski and Cohen and Kegeles (we correct a minor, but propagating, error in the Cohen-Kegeles formalism). The electromagnetic field tensor and vector potential of a static point charge and the perturbed gravitational field of a static point mass in a Schwarzschild geometry are found, surprisingly, to have closed-form expressions. The gravitational field of a static point charge in the Schwarzschild background must have a strut, but $\\psi_0$ and $\\psi_4$ are smooth except at the particle, and one can find local radiation gauges for which the corresponding spin $\\pm 2$ parts of the perturbed metric are smooth. Finally a method for finding the renormalized self-force from the Teukolsky equation is presented. The method is related to the Mino, Sasaki, Tanaka and Quinn and Wald (MiSaTaQuWa) renormalization and to the Detweiler-Whiting construction of the singular field. It relies on the fact that the renormalized $\\psi_0$ (or $\\psi_4$) is a {\\em sourcefree} solution to the Teukolsky equation; and one can therefore reconstruct a nonsingular renormalized metric in a radiation gauge.

  13. Rate of Force Development, Muscle Architecture, and Performance in Young Competitive Track and Field Throwers.

    PubMed

    Zaras, Nikolaos D; Stasinaki, Angeliki-Nikoletta E; Methenitis, Spyridon K; Krase, Argyro A; Karampatsos, Giorgos P; Georgiadis, Giorgos V; Spengos, Konstantinos M; Terzis, Gerasimos D

    2016-01-01

    Zaras, ND, Stasinaki, A-NE, Methenitis, SK, Krase, AA, Karampatsos, GP, Georgiadis, GV, Spengos, KM, and Terzis, GD. Rate of force development, muscle architecture, and performance in young competitive track and field throwers. J Strength Cond Res 30(1): 81-92, 2016-The rate of force development (RFD) is an essential component for performance in explosive activities, although it has been proposed that muscle architectural characteristics might be linked with RFD and power performance. The purpose of the study was to investigate the relationship between RFD, muscle architecture, and performance in young track and field throwers. Twelve young track and field throwers completed 10 weeks of periodized training. Before (T1) and after (T2) training performance was evaluated in competitive track and field throws, commonly used shot put tests, isometric leg press RFD, 1 repetition maximum (1RM) strength as well as vastus lateralis architecture and body composition. Performance in competitive track and field throwing and the shot put test from the power position increased by 6.76 ± 4.31% (p < 0.001) and 3.58 ± 4.97% (p = 0.019), respectively. Rate of force development and 1RM strength also increased (p ? 0.05). Vastus lateralis thickness and fascicle length increased by 5.95 ± 7.13% (p = 0.012) and 13.41 ± 16.15% (p = 0.016), respectively. Significant correlations were found at T1 and T2, between performance in the shot put tests and both RFD and fascicle length (p ? 0.05). Close correlations were found between RFD, muscle thickness, and fascicle length (p ? 0.05). Significant correlations were found between the % changes in lean body mass and the % increases in RFD. When calculated together, the % increase in muscle thickness and RFD could predict the % increase in shot put throw test from the power position (p = 0.019). These results suggest that leg press RFD may predict performance in shot put tests that are commonly used by track and field throwers. PMID:26049793

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

    PubMed

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

    2013-03-21

    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

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

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

    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.

  16. Trapping and micromanipulation using ultrasonic fields and dual ultrasonic/magnetic forces

    NASA Astrophysics Data System (ADS)

    Hill, Martyn; Glynne-Jones, Peter; Harris, Nicholas R.; Boltryk, Rosemary J.; Stanley, Christopher; Bond, Damian

    2010-08-01

    Ultrasonic fields can be used to trap and manipulate micron-scale particles and second-phase fluids, utilising energy densities that do not impair cell viability. The technology can be seen as complementary to optical trapping as the size of the potential wells generated can be relatively large, making ultrasound suitable for the formation and manipulation of cell agglomerates, but less suitable for the manipulation of individual cells. This paper discusses physical phenomena associated with ultrasonic manipulation, including radiation forces, cavitation, and acoustic streaming. The technology is well suited to integration within "Lab on a Chip" devices and can involve excitation by plane, focussed, flexural, or surface acoustic waves. Example applications of resonators are discussed including particle filtration and concentration, cell washing, and biosensor enhancement. A recently developed device that uses both ultrasonic and magnetic forces to enhance the detection of tuberculosis bacteria using magnetic beads is discussed in detail. This approach uses ultrasonic levitation forces to overcome some of the issues associated with purely magnetic trapping. The technology has been implemented in a device in which the main fluidic components are disposable to allow for low production costs and improved control of biohazards.

  17. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations.

    PubMed

    Graen, Timo; Hoefling, Martin; Grubmüller, Helmut

    2014-12-01

    Recent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized ?-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories. PMID:26583233

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

    PubMed

    Muddana, Hari S; Gilson, Michael K

    2012-05-01

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

  19. Forcing of dissolved organic carbon release by phytoplankton by anticyclonic mesoscale eddies in the subtropical NE Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Lasternas, S.; Piedeleu, M.; Sangrà, P.; Duarte, C. M.; Agustí, S.

    2013-03-01

    The organic carbon fluxes mediated by planktonic communities in two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) at the Canary Eddy Corridor were studied and compared with the dynamics in two far-field (FF) stations located outside the eddies. We observed favorable conditions and signs for upwelling at the center of CEs and for downwelling and mixing at the centers of AEs. CEs were characterized by a higher concentration of nutrients and the highest concentration of chlorophyll a (chl a), associated with the highest abundance of microphytoplankton and diatoms. AEs displayed concentrations of chl a values and nutrients similar to those at the FF stations, except for the highest ammonium concentration occurring at AE and a very low concentration of phosphorus at FF stations. AEs were transient systems characterized by an increasing abundance of picophytoplankton and heterotrophic bacteria. While primary production was similar between the systems, the production of dissolved organic carbon (PDOC) was significantly higher in the AEs. Phytoplankton cell mortality was lowest in the CEs, and we found higher cell mortality rates at AE than at FF stations, despite similar chl a concentration. Environmental changes in the AEs have been significantly prejudicial to phytoplankton as indicated by higher phytoplankton cell mortality (60% of diatoms cells were dead) and higher cell lysis rates. The adverse conditions for phytoplankton associated with the early-stage anticyclonic systems, mainly triggered by active downwelling, resulted in higher cell mortality, forcing photosynthesized carbon to fuel the dissolved pool.

  20. Optical gecko toe: Optically controlled attractive near-field forces between plasmonic metamaterials and dielectric or metal surfaces

    NASA Astrophysics Data System (ADS)

    Zhang, J.; MacDonald, K. F.; Zheludev, N. I.

    2012-05-01

    On the mesoscopic scale, electromagnetic forces are of fundamental importance to an enormously diverse range of systems, from optical tweezers to the adhesion of gecko toes. Here we show that a strong light-driven force may be generated when a plasmonic metamaterial is illuminated in close proximity to a dielectric or metal surface. This near-field force can exceed radiation pressure and Casimir forces to provide an optically controlled adhesion mechanism mimicking the gecko toe: At illumination intensities of just a few tens of nW/?m2 it is sufficient to overcome the Earth's gravitational pull.

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

    SciTech Connect

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

    2014-01-28

    The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform 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.

  2. 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)

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

    2014-01-01

    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.

  3. The Nuclear Spin-Orbit Force in Chiral Effective Field Theories

    E-print Network

    R. J. Furnstahl; John J. Rusnak; Brian D. Serot

    1997-09-28

    A compelling feature of relativistic mean-field phenomenology has been the reproduction of spin-orbit splittings in finite nuclei after fitting only to equilibrium properties of infinite nuclear matter. This successful result occurs when the velocity dependence of the equivalent central potential that leads to saturation arises primarily because of a reduced nucleon effective mass. The spin-orbit interaction is then also specified when one works in a four-component Dirac framework. Here the nature of the spin-orbit force in more general chiral effective field theories of nuclei is examined, with an emphasis on the role of the tensor coupling of the isoscalar vector meson (omega) to the nucleon.

  4. Modification of Bell Canyon Test (BCT) 1-FF grout. Final report

    SciTech Connect

    Buck, A.D.; Rhoderick, J.E.; Burkes, J.P.; Mather, K.; Reinhold, R.E.; Boa, J.A. Jr.

    1983-09-01

    Bell Canyon Test (BCT) 1-FF grout was developed as a candidate material for use in repository sealing applications and was actually used in two field tests in New Mexico. This grout and modifications of it were made in the laboratory and tested or examined for workability, compressive strength, restrained expansion, permeability, phase composition, and microstructure. Most of these were done to an age of 1 year. Compressive strength and expansion data were determined beyond this age (960 days). Modifications include use of three other cements, two other fly ashes, a silica fume, different water contents, and different amounts of expansive additive (plaster). Each cement and mineral admixture was characterized by conventional chemical and physical tests as well as by x-ray diffraction examination. In general, the results indicated that the modifcations to the basic BCT-1-FF grout produced other grouts that were as good as it. An exception to this was the grout mixture (M-8-C) made with shrinkage compensating expansive cement; it had an excessive flow time (>20 sec). Another grout mixture (M-9-C) also had excessive flow time and lower strength. It was thought that these problems could be solved with more modification to these two mixtures. 6 references, 24 figures, 7 tables.

  5. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor.

    PubMed

    Dennis, John Ojur; Ahmad, Farooq; Khir, M Haris Bin Md; Bin Hamid, Nor Hisham

    2015-01-01

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT. PMID:26225972

  6. Field investigation source area ST58 old Quartermaster service station, Eielson Air Force Base, Alaska

    SciTech Connect

    Liikala, T.L.; Evans, J.C.

    1995-01-01

    Source area ST58 is the site of the old Quartermaster service station at Eielson Air Force Base, Alaska. The source area is one of several Source Evaluation Report sites being investigated by Pacific Northwest Laboratory for the US Air Force as candidates for no further remedial action, interim removal action, or a remedial investigation/feasibility study under a Federal Facilities Agreement. The purpose of this work was to characterize source area ST58 and excavate the most contaminated soils for use in composting treatability studies. A field investigation was conducted to determine the nature and extent of soil contamination. The field investigation entailed a records search; grid node location, surface geophysical, and soil gas surveys; and test pit soil sampling. Soil excavation followed based on the results of the field investigation. The site was backfilled with clean soil. Results from this work indicate close spatial correlation between screening instruments, used during the field investigation and soil excavation, and laboratory analyses. Gasoline was identified as the main subsurface contaminant based on the soil gas surveys and test pit soil sampling. A center of contamination was located near the northcentral portion of the source area, and a center was located in the northwestern comer. The contamination typically occurred near or below a former soil horizon probably as a result of surface spills and leaks from discontinuities and/or breaks in the underground piping. Piping locations were delineated during the surface geophysical surveys and corresponded very well to unscaled drawings of the site. The high subsurface concentrations of gasoline detected in the northwestern comer of the source area probably reflect ground-water contamination and/or possibly floating product.

  7. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor

    PubMed Central

    Dennis, John Ojur; Ahmad, Farooq; Khir, M. Haris Bin Md; Hamid, Nor Hisham Bin

    2015-01-01

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT. PMID:26225972

  8. Inclusion of ionic interactions in force field calculations of charged biomolecules--DNA structural transitions.

    PubMed

    Klement, R; Soumpasis, D M; Kitzing, E V; Jovin, T M

    1990-01-01

    The potential of mean force (PMF) approach for treating polyion-diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116-5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER-PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C-G)6, and the B and heteronomous (H) conformations of dA12.dT12, as a function of salt concentration. In the case of d(C-G)6, the predicted B-ZI transition occurs at 2.4M and is essentially driven by the phosphate-diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B-DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl. In the range of 0.01-0.3M NaCl, the H form of dA12.dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence. PMID:2369618

  9. A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

    PubMed

    Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P

    2016-02-13

    We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure. PMID:26712642

  10. Point Defects in Carbon Nanotubes: ab initio and Force-Fields Based Simulations

    NASA Astrophysics Data System (ADS)

    Kroes, Jaap; Pietrucci, Fabio; Curioni, Alessandro; Andreoni, Wanda

    2014-03-01

    We present an extended investigation of point defects in carbon nanotubes (CNTs) and their effects on mechanical and electronic properties. This study is based on large-scale calculations using DFT with exchange and correlation functionals of the GGA - including empirical corrections for van-der-Waals interactions - and of the hybrid type. Additional simulations using classical interatomic potentials allow us to obtain a critical comparison between the outcome of DFT and force-fields. The CNT models adopted have a range of sizes and chiralities. In particular, (i) our simulations of oxygen chemisorption revealed a tendency to clustering and the existence of kinetic traps (epoxides), which explain STS data; (ii) the extension to oxygen isovalent species on CNTs and other graphitic surfaces has suggested a simple predictive model for the chemisorption pattern. Moreover, (iii) our analysis shows an intrinsic difficulty of available force fields to account for the energetics of vacancies and adsorption site preferences. Additional results aiming at characterizing the interaction of nitrogen oxides (NOx) with the CNT surface will also be presented. Work supported by SNSF Nano-Tera.ch and CSCS.

  11. Limitations of force-free magnetic field extrapolations: revisiting basic assumptions

    E-print Network

    Peter, H; Chitta, L P; Cameron, R H

    2015-01-01

    Force-free extrapolations are widely used to study the magnetic field in the solar corona based on surface measurements. The extrapolations assume that the ratio of internal energy of the plasma to magnetic energy, the plasma-beta is negligible. Despite the widespread use of this assumption observations, models, and theoretical considerations show that beta is of the order of a few percent to more than 10%, and thus not small. We investigate what consequences this has for the reliability of extrapolation results. We use basic concepts starting with the force and the energy balance to infer relations between plasma-beta and free magnetic energy, to study the direction of currents in the corona with respect to the magnetic field, and to estimate the errors in the free magnetic energy by neglecting effects of the plasma (beta<<1). A comparison with a 3D MHD model supports our basic considerations. If plasma-beta is of the order of the relative free energy (the ratio of the free magnetic energy to the total...

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

    PubMed Central

    Baker, Christopher M.; Best, Robert B.

    2013-01-01

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

  13. Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations

    PubMed Central

    Fadrná, Eva; Špa?ková, Nad'a; Štefl, Richard; Ko?a, Jaroslav; Cheatham, Thomas E.; Šponer, Ji?í

    2004-01-01

    A computational analysis of d(GGGGTTTTGGGG)2 guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanics, Poisson Boltzmann, surface area (MM-PBSA) calculations with explicit inclusion of structural monovalent cations. The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space. The results are independent of the starting structures. Major conformational transitions not seen in conventional MD simulations are observed when LES is applied. The favored LES structures consistently provide lower free energies (as estimated by molecular-mechanics, Poisson Boltzmann, surface area) than other structures. Unfortunately, the predicted optimal structure for the diagonal loop arrangement differs substantially from the atomic resolution experiments. This result is attributed to force field deficiencies, such as the potential misbalance between solute-cation and solvent-cation terms. The MD simulations are unable to maintain the stable coordination of the monovalent cations inside the diagonal loops as reported in a recent x-ray study. The optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture. PMID:15240460

  14. The Outflows Accelerated by the Magnetic Fields and Radiation Force of Accretion Disks

    NASA Astrophysics Data System (ADS)

    Cao, Xinwu

    2014-03-01

    The inner region of a luminous accretion disk is radiation-pressure-dominated. We estimate the surface temperature of a radiation-pressure-dominated accretion disk, \\Theta =c_s^2/r^2\\Omega _K^2\\ll (H/r)^2, which is significantly lower than that of a gas-pressure-dominated disk, ? ~ (H/r)2. This means that the outflow can be launched magnetically from the photosphere of the radiation-pressure-dominated disk only if the effective potential barrier along the magnetic field line is extremely shallow or no potential barrier is present. For the latter case, the slow sonic point in the outflow will probably be in the disk, which leads to a slow circular dense flow above the disk. This implies that hot gas (probably in the corona) is necessary for launching an outflow from the radiation-pressure-dominated disk, which provides a natural explanation for the observational evidence that the relativistic jets are related to hot plasma in some X-ray binaries and active galactic nuclei. We investigate the outflows accelerated from the hot corona above the disk by the magnetic field and radiation force of the accretion disk. We find that with the help of the radiation force, the mass loss rate in the outflow is high, which leads to a slow outflow. This may be why the jets in radio-loud narrow-line Seyfert galaxies are in general mildly relativistic compared with those in blazars.

  15. Distortion of magnetic field and magnetic force of a brushless dc motor due to deformed rubber magnet

    NASA Astrophysics Data System (ADS)

    Lee, C. J.; Jang, G. H.

    2008-04-01

    This paper investigates the distortion of magnetic field of a brushless dc (BLDC) motor due to deformed rubber magnet. Global or local deformation of rubber magnet in the BLDC motor is mathematically modeled by using the Fourier series. Distorted magnetic field is calculated by using the finite element method, and unbalanced magnetic force is calculated by using the Maxwell stress tensor. When the rubber magnet is globally or locally deformed, the unbalanced magnetic force has the frequencies with the first harmonic and the harmonics of slot number ±1. However, the harmonic deformation with multiple of common divisor of pole and slot does not generate unbalanced magnetic force due to the rotational symmetry.

  16. Determination of the viscous acoustic field for liquid drop positioning/forcing in an acoustic levitation chamber in microgravity

    NASA Technical Reports Server (NTRS)

    Lyell, Margaret J.

    1992-01-01

    The development of acoustic levitation systems has provided a technology with which to undertake droplet studies as well as do containerless processing experiments in a microgravity environment. Acoustic levitation chambers utilize radiation pressure forces to position/manipulate the drop. Oscillations can be induced via frequency modulation of the acoustic wave, with the modulated acoustic radiation vector acting as the driving force. To account for tangential as well as radial forcing, it is necessary that the viscous effects be included in the acoustic field. The method of composite expansions is employed in the determination of the acoustic field with viscous effects.

  17. An electrohydraulic actuated ankle foot orthosis to generate force fields and to test proprioceptive reflexes during human walking.

    PubMed

    Noël, Martin; Cantin, Benoit; Lambert, Sébastien; Gosselin, Clément M; Bouyer, Laurent J

    2008-08-01

    The control of human walking can be temporarily modified by applying forces to the leg. To study the neural mechanisms underlying this adaptive capacity, a device delivering controlled forces and high-velocity displacements to the ankle was designed. A new solution, involving a closed circuit hydraulic system composed of two cylinders (master-slave) mutually connected by hoses and controlled by an electric motor was preferred over classical mechanical/electrical approaches. The slave cylinder delivers desired torques to the ankle using a light weight, custom-designed ankle-foot orthosis. This electrohydraulic orthosis (EHO) can produce several types of force fields during walking, including constant, position-dependent, and phase-dependent. With phase-dependent force fields, active torque cancellation maintains low-residual torques ( < or = 1.85 Nm root mean square) outside of the zone of force application for walking speeds ranging from 0.2 to 4.5 km/h. Rapid ankle stretches/unloads ( > 200 degrees/s) can also be produced alone or during force field application, and elicited proprioceptive reflexes in ankle muscles. In conclusion, the EHO is capable of delivering controlled force fields and of activating proprioceptive reflexes during human walking. It will provide the flexibility needed to test the adaptability of healthy and pathological gait control, and to address some of its underlying neural mechanisms. PMID:18701385

  18. Structure and Stability of Magnetic Fields in Solar Active Region12192 Based on Nonlinear Force-Free Field Modeling

    E-print Network

    Inoue, S; Kusano, K

    2016-01-01

    We analyze a three-dimensional (3D) magnetic structure and its stability in large solar active region(AR) 12192, using the 3D coronal magnetic field constructed under a nonlinear force-free field (NLFFF) approximation. In particular, we focus on the magnetic structure that produced an X3.1-class flare which is one of the X-class flares observed in AR 12192. According to our analysis, the AR contains multiple-flux-tube system, {\\it e.g.}, a large flux tube, both of whose footpoints are anchored to the large bipole field, under which other tubes exist close to a polarity inversion line (PIL). These various flux tubes of different sizes and shapes coexist there. In particular, the later are embedded along the PIL, which produces a favorable shape for the tether-cutting reconnection and is related to the X-class solar flare. We further found that most of magnetic twists are not released even after the flare, which is consistent with the fact that no observational evidence for major eruptions was found. On the oth...

  19. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical forces are reviewed culminating with the research manuscript in section 3.4 of the development of the two-state worm-like chain, modeling the overstretching transition of B-DNA to S-DNA. Chapter 4 considers the behavior of DNA in an electric field, first reviewing DNA as a polyelectrolyte and of DNA electrophoresis in free solution and it's polarization and resulting stretched conformation as context for the study of the contrasting behavior of DNA in an AC electric field presented in the research manuscripts of the final two sections of chapter 4. In section 4.3 the collapse of DNA in ac electric fields is investigated with the experimental results and possible models for collapse presented with a scaling analysis of the frequency- and confinement-dependent critical field for collapse presented in section 4.4, contrasting a mean-field Flory-type model and a continuum, wormlike chain model. Chapter 5 investigates viral RNA; reviewing the encapsidation, life cycle and the evolutionary dynamics of single-stranded RNA viruses including the quasispecies model and it's prediction of the information or error catastrophe, providing context for the models developed in the research manuscripts presented in sections 2.5 and 5.3. In section 5.3, a simple ODE model of the evolution of positive-sense single-stranded RNA viruses is developed, adopting the two-state mean-field quasispecies model, to characterize the selection pressure associated with the encapsidation and independently, the degradation by RNAi of the wild-type relative to the mutant population and demonstrate their capacity to induce an information catastrophe and consequently support the evolution of intermediate encapsidation rates and of viral suppressors of RNA silencing, in addition to providing support for antiviral therapeutic pathways.

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

    SciTech Connect

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

    2013-11-15

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

  1. Optical response of magnetic fluorescent microspheres used for force spectroscopy in the evanescent field.

    PubMed

    Bijamov, Alex; Shubitidze, Fridon; Oliver, Piercen M; Vezenov, Dmitri V

    2010-07-20

    Force spectroscopy based on magnetic tweezers is a powerful technique for manipulating single biomolecules and studying their interactions. The resolution in magnetic probe displacement, however, needs to be commensurate with molecular sizes. To achieve the desirable sensitivity in tracking displacements of the magnetic probe, some recent approaches have combined magnetic tweezers with total internal reflection fluorescence microscopy. In this situation, a typical force probe is a polymer microsphere containing two types of optically active components: a pure absorber (magnetic nanoparticles for providing the pulling force) and a luminophore (semiconducting nanoparticles or organic dyes for fluorescent imaging). To assess the system's capability fully with regard to tracking the position of the force probe with subnanometer accuracy, we developed a body-of-revolution formulation of the method of auxiliary sources (BOR-MAS) to simulate the absorption, scattering, and fluorescence of microscopic spheres in an evanescent electromagnetic field. The theoretical formulation uses the axial symmetry of the system to reduce the dimensionality of the modeling problem and produces excellent agreement with the reported experimental data on forward scattering intensity. Using the BOR-MAS numerical model, we investigated the probe detection sensitivity for a high numerical aperture objective. The analysis of both backscattering and fluorescence observation modes shows that the total intensity of the bead image decays exponentially with the distance from the surface (or the length of a biomolecule). Our investigations demonstrate that the decay lengths of observable optical power are smaller than the penetration depth of the unperturbed excitation evanescent wave. In addition, our numerical modeling results illustrate that the expected sensitivity for the decay length changes with the angle of incidence, tracking the theoretical penetration depth for a two-media model, and is sensitive to the bead size. The BOR-MAS methodology developed in this work for near-field modeling of bead-tracking experiments fully describes the fundamental photonic response of microscopic BOR probes at the subwavelength level and can be used for future improvements in the design of these probes or in the setup of bead-tracking experiments. PMID:20486724

  2. Electric field and force modeling for electrostatic levitation of lossy dielectric plates

    NASA Astrophysics Data System (ADS)

    Woo, S. J.; Higuchi, T.

    2010-11-01

    Electrostatic levitation holds great promise for the semiconductor, solar panel, and flat-panel display industry where the handling of dielectrics in a contact-free manner can bring many advantages and solve long-standing contamination and particulate control problems. In this work an analytical model is developed for the electrostatic levitation field between a lossy dielectric plate and a generic stator electrode structure consisting of a regular planar array of parallel bar electrodes. Time-varying voltages of differing polarities are alternatingly applied to the bar electrodes. Atmospheric humidity-related surface conduction on the plate is explicitly taken into account in the model since it has a profound effect on the field dynamics. Based on this model, the electrostatic levitation force is calculated using the Maxwell stress tensor formulation. The levitation force dynamics are investigated by evaluating the transient response of the field under a step in the applied voltages. In this context, the rate of electric charge build up on the plate is characterized by the suspension initiation time (TSI), which is defined as the time elapsed between applying step voltages to the stator electrodes and start of lift-off of the dielectric plate from its initial position. TSI is theoretically predicted for 0.7 mm thick soda-lime glass substrates, typically used in the manufacturing of liquid crystal displays (LCDs), as a function of electrode geometry, air gap separation, ambient humidity, and step voltage magnitudes. The predicted results are shown to be in good agreement with previously published experimental data for soda-lime glass substrates.

  3. Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

    PubMed Central

    Buck, Patrick M.; Bystroff, Christopher

    2015-01-01

    Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for ?-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as ?-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 ?s trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

  4. Force Field for Peptides and Proteins based on the Classical Drude Oscillator

    PubMed Central

    Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

    2013-01-01

    Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone ?, ? conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

  5. The Reaction 70 Ge(ff,fl) 74 Se (p--process) Zs. Fulop y , '

    E-print Network

    Rauscher, Thomas

    The Reaction 70 Ge(ff,fl) 74 Se (p--process) Zs. F¨ul¨op y , ' A.Z. Kiss y , E. Somorjai y , C section of the reaction 70 Ge(ff,fl) 74 Se is measured in the bombarding energy range of 4.90!E ff !7.53 MeV. The experimental S--factor values are in good agreement with theoretical calculations. Reaction

  6. Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures.

    PubMed

    LuCore, Stephen D; Litman, Jacob M; Powers, Kyle T; Gao, Shibo; Lynn, Ava M; Tollefson, William T A; Fenn, Timothy D; Washington, M Todd; Schnieders, Michael J

    2015-08-18

    A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing of protein side chains. Although such interactions between residues are often approximated as being pairwise additive, in reality, higher-order many-body contributions that depend on environment drive hydrophobic collapse and cooperative electrostatics. Beginning from dead-end elimination, we derive the first algorithm, to our knowledge, capable of deterministic global repacking of side chains compatible with many-body energy functions. The approach is applied to seven PCNA x-ray crystallographic data sets with resolutions 2.5-3.8 Å (mean 3.0 Å) using an open-source software. While PDB_REDO models average an Rfree value of 29.5% and MOLPROBITY score of 2.71 Å (77th percentile), dead-end elimination with the polarizable AMOEBA force field lowered Rfree by 2.8-26.7% and improved mean MOLPROBITY score to atomic resolution at 1.25 Å (100th percentile). For structural biology applications that depend on side-chain repacking, including x-ray refinement, homology modeling, and protein design, the accuracy limitations of pairwise additivity can now be eliminated via polarizable or quantum mechanical potentials. PMID:26287633

  7. Single nanowire manipulation within dielectrophoretic force fields in the sub-crossover frequency regime

    NASA Astrophysics Data System (ADS)

    Palapati, N. K. R.; Pomerantseva, E.; Subramanian, A.

    2015-02-01

    This paper presents the quantitative relationship between the control parameters of a dielectrophoretic (DEP) force field and the resulting electrokinetic region of influence experienced by individual nanowires (NWs) in colloidal suspensions. Our results show that DEP operation at sub-crossover frequencies, which are defined as frequencies slightly below the transition from positive-to-negative DEP, offers a suitable but previously unexplored performance regime for single NW manipulation and assembly. The low-magnitude DEP forces at these frequencies, which are estimated to be 8 orders of magnitude smaller as compared to near-DC frequencies, provide an efficient avenue to controllably extend electrokinetic influence on suspension volumes that present isolated NWs. These results are demonstrated using ?-phase manganese dioxide NWs as a model one-dimensional construct. Based on experimentally extracted values for the NW intrinsic conductivity and dielectric permittivity, we employ computational models to explain each of the performance regimes observed in this nanoassembly system. In addition, we use a new approach to estimate the concentration of a NW suspension from experimentally observed data for deposition yields.

  8. Trihydrogen cation with neon and argon: structural, energetic, and spectroscopic data from quartic force fields.

    PubMed

    Theis, Riley A; Fortenberry, Ryan C

    2015-05-21

    The argonium cation, ArH(+), has been previously detected in nature for the first time. This cation is believed to form through the gas-phase reaction of Ar(+) and H2. In this work, quantum chemical techniques show that the reaction of Ar and H3(+) may be a viable alternative or contributor to the creation of ArH(+) corroborating previous analysis. In order to further evaluate this claim, highly accurate quartic force field computations are used to produce spectroscopic data and anharmonic vibrational frequencies for ArH3(+) in its 18 isotopologues. NeH3(+) is also analyzed but has a low Ne-H3(+) dissociation barrier. Therefore, it less likely to be observed. Consequently, NeH(+) is also unlikely to be formed from NeH3(+) as it was also not from NeH2(+). PMID:25923978

  9. Assessment of split-charge equilibration model for development of polarizable force fields

    NASA Astrophysics Data System (ADS)

    Smirnov, Konstantin S.

    2015-10-01

    Performance of split-charge equilibration model (SQE) for force field development was tested by computing static and response characteristics of water clusters. Results of the study show that SQE yields reliable results for the molecular electrostatic potential, dipole, and polarizability of clusters of increasing size. Intermolecular charge transfer needs to be considered for hydrogen bonded systems in order to accurately reproduce the dipole versus system size behavior. It was found that the model quantitatively mimics the IR intensities of intermolecular vibrational modes, but fails in the computation of the IR and Raman intensities of intramolecular vibrations. The response of charge distribution to perturbation by point charge is confidently modeled by SQE in the conditions corresponding to the linear-response regime.

  10. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.

    PubMed

    Thaunay, Florian; Dognon, Jean-Pierre; Ohanessian, Gilles; Clavaguéra, Carine

    2015-10-21

    The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes. PMID:26214153

  11. Generalized valence-force-field model of (Ga,In)(N,P) ternary alloys

    NASA Astrophysics Data System (ADS)

    Biswas, Koushik; Franceschetti, Alberto; Lany, Stephan

    2008-08-01

    We present a generalized valence-force-field (VFF) model for the ternary III V alloys ( III=Ga , In and V=N , P) to predict the formation energies and atomic structures of ordered and disordered alloy configurations. For each alloy (GaInN, GaInP, GaNP, and InNP) the VFF parameters, which include bond-angle/bond-length interactions, are fitted to the first-principles calculated formation energies of 30 ternary structures. Compared to standard approaches where the VFF parameters are transferred from the individual binary III V compounds, our generalized VFF approach predicts alloy formation energies and atomic structures with considerably improved accuracy. Using this generalized approach and random realizations in large supercells (4096 atoms), we determine the temperature-composition phase diagram, i.e., the binodal and spinodal decomposition curves, of the (Ga, In) (N, P) ternary alloys.

  12. Generalized Valence-Force-Field Model of (Ga,In)(N,P) Ternary Alloys

    SciTech Connect

    Biswas, K.; Franceschetti, A.; Lany, S.

    2008-01-01

    We present a generalized valence-force-field (VFF) model for the ternary III-V alloys (III=Ga, In and V=N, P) to predict the formation energies and atomic structures of ordered and disordered alloy configurations. For each alloy (GaInN, GaInP, GaNP, and InNP) the VFF parameters, which include bond-angle/bond-length interactions, are fitted to the first-principles calculated formation energies of 30 ternary structures. Compared to standard approaches where the VFF parameters are transferred from the individual binary III-V compounds, our generalized VFF approach predicts alloy formation energies and atomic structures with considerably improved accuracy. Using this generalized approach and random realizations in large supercells (4096 atoms), we determine the temperature-composition phase diagram, i.e., the binodal and spinodal decomposition curves, of the (Ga, In) (N, P) ternary alloys.

  13. Application of a polarizable force field to calculations of relative protein–ligand binding affinities

    PubMed Central

    Khoruzhii, Oleg; Donchev, Alexander G.; Galkin, Nikolay; Illarionov, Alexei; Olevanov, Mikhail; Ozrin, Vladimir; Queen, Cary; Tarasov, Vladimir

    2008-01-01

    An explicitly polarizable force field based exclusively on quantum data is applied to calculations of relative binding affinities of ligands to proteins. Five ligands, differing by replacement of an atom or functional group, in complexes with three serine proteases—trypsin, thrombin, and urokinase-type plasminogen activator—with available experimental binding data are used as test systems. A special protocol of thermodynamic integration was developed and used to provide sufficiently low levels of systematic error along with high numerical efficiency and statistical stability. The calculated results are in excellent quantitative (rmsd = 1.0 kcal/mol) and qualitative (R2 = 0.90) agreement with experimental data. The potential of the methodology to explain the observed differences in the ligand affinities is also demonstrated. PMID:18653760

  14. Phase I remedial investigation report for the 300-FF-5 operable unit, Volume 1

    SciTech Connect

    1994-01-01

    The focus of this remedial investigation (RI) is the 300-FF-5 operable unit, one of five operable units associated with the 300 Area aggregate of the U.S. Department of Energy`s (DOE`s) Hanford Site. The 300-FF-5 operable unit is a groundwater operable unit beneath the 300-FF-1, 300-FF-2, and 300-FF-3 source operable units. This operable unit was designated to include all contamination detected in the groundwater and sediments below the water table that emanates from the 300-FF-1, 300-FF-2, and 300-FF-3 operable units (DOE-RL 1990a). In November 1989, the U.S. Environmental Protection Agency (EPA) placed the 300 Area on the National Priorities List (NPL) contained within Appendix B of the National Oil and Hazardous Substance Pollution Contingency Plan (NCP, 53 FR 51391 et seq.). The EPA took this action pursuant to their authority under the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA, 42 USC 9601 et seq.). The DOE Richland Operations Office (DOE-RL), the EPA and Washington Department of Ecology (Ecology) issued the Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement), in May 1989 (Ecology et al. 1992, Rev. 2). This agreement, among other matters, governs all CERCLA efforts at the Hanford Site. In June 1990, a remedial investigation/feasibility study (RI/FS) workplan for the 300-FF-5 operable unit was issued pursuant to the Tri-Party Agreement.

  15. Current sheet scattering and ion isotropic boundary under 3-D empirical force-balanced magnetic field

    NASA Astrophysics Data System (ADS)

    Yue, Chao; Wang, Chih-Ping; Lyons, Larry; Liang, Jun; Donovan, Eric F.; Zaharia, Sorin G.; Henderson, Michael

    2014-10-01

    To determine statistically the extent to which current sheet scattering is sufficient to account for the observed ion isotropic boundaries (IBs) for <30 keV ions, we have computed IBs from our 3-D empirical force-balanced magnetic field, identified IBs in FAST observations, and investigated the model-observation consistency. We have found in both model and FAST results the same dependences of IB latitudes on magnetic local time, ion energy, Kp, and solar wind dynamic pressure (PSW) levels: IB moves to higher latitudes from midnight toward dawn/dusk and to lower latitudes as energy increases and as Kp or PSW increases. The model predicts well the observed energy dependence, and the modeled IB latitudes match fairly well with those from FAST for Kp = 0. As Kp increases, the latitude agreement at midnight remains good but a larger discrepancy is found near dusk. The modeled IBs at the equator are located around the earthward boundary of highly isotropic ions observed by Time History of Events and Macroscale Interactions during Substorms at midnight and postmidnight, but with some discrepancy near dusk under high Kp. Thus, our results indicate that current sheet scattering generally plays the dominant role. The discrepancies suggest the importance of pitch angle scattering by electromagnetic ion cyclotron waves, which occur more often from dusk to noon and are more active during higher Kp. The comparison with the observed IBs is better with our model than under the nonforce-balanced T89, indicating that using a forced-balanced model improves the description of the magnetic field configuration and reinforces our conclusions regarding the role of current sheet scattering.

  16. The Relativistic Quantized Force: Newton's Second Law, Inertial and Gravitational; Generalization of Schwarzschild Metric for Strong and Weak Gravitational Field

    NASA Astrophysics Data System (ADS)

    Almosallami, Azzam

    2011-03-01

    In this paper we derived the relativistic Quantized force, where the force given as a function of frequency [1]. Where, in this paper we defined the relativistic momentum as a function of frequency equivalent to the energy held by a body, and time, and then the quantized force is given as the first derivative of the momentum with respect to time. Subsequently we introduce in section one Newton's second law as it is relativistic quantized, and in section two we introduce the relativistic quantized inertial force, and then the relativistic quantized gravitational force, and the quantized gravitational time dilation. At the end we shall generalize the Schwartzschild metric to describe the weak and strong gravitational field.

  17. Concurrent field measurements of turbulent velocities, plant reconfiguration and drag forces on Ranunculus penicillatus

    NASA Astrophysics Data System (ADS)

    Paul, Maike; Thomas, Robert E.; Keevil, Gareth M.

    2013-04-01

    In lowland rivers, seasonal patterns of in-stream macrophyte growth and decay have significant implications for flood risk. For a given discharge, flood risk is increased when dense macrophyte canopies reduce flow areas, increase blockage ratios and alter reach-scale roughness values. These factors combine and can increase the flow depth. Conversely, submerged vegetation is exposed to drag forces exerted by the flow, which may be sufficient to damage limbs or dislodge plants. The classical drag equation suggests that the force exerted by fluid flows upon submerged vegetation is a function of the fluid properties, the projected area of the vegetation, and the square of the flow velocity. However, very few studies have simultaneously monitored all of these parameters, resulting in significant uncertainty in the estimation of the coefficient that relates these parameters to the drag force and also the related roughness parameters that control the flow depth for a given discharge. To our knowledge, this study presents the first concurrent field measurements of turbulent velocities, plant reconfigurations and drag forces acting on Ranunculus penicillatus ssp. pseudofluitans (Syme) S.D.Webster. Measurements were undertaken in an artificially straightened reach of the chalk-bed River Wylye, near Longbridge Deverill, Wiltshire, UK. The reach is 5.7 m wide and during measurements there was a mean flow depth of 0.28 m and an average discharge of 0.28 m³s-1. The reach is cleared of vegetation up to three times a year for flood defence purposes, but Ranunculus p. grows back within several weeks. Measurements were carried out after re-growth, when plants were fully developed with a mean length of 0.75 m and on average 6 nodes along the stem. The distances between the nodes increased from the base towards the tip and each node produced a capillary leaf, sometimes in conjunction with a branch. Floating leaves and flowers were not present. Plants were attached to a custom-made drag sensor that was deployed flush with the streambed. Simultaneously, a profiling Acoustic Doppler Velocimeter (Nortek Vectrino-II) was deployed 0.5 m upstream of the plants. Also, a video camera was installed with its field of view perpendicular to the mean flow direction, in order to record plant motion and reconfiguration associated with turbulent velocity and drag fluctuations. Measurements were repeated while the Vectrino-II was consecutively deployed at four vertical positions to: 1. obtain a velocity profile through the entire water column and 2. study which vertical position correlated most strongly to the drag force. Velocity measurements confirmed that turbulent structures were present throughout the water column and a response to these fluctuations was observed in the drag measurements. Responses lagged in time due to the horizontal distance between Vectrino-II and drag sensor position. Additionally, spectral analysis showed that the drag fluctuates with a frequency of 0.5 Hz which corresponds well with the undulating, quasi-sinusoidal, plant motion observed on the video footage. This motion was associated with the downstream propagation of coherent eddies.

  18. Yukawa-field approximation of electrostatic free energy and dielectric boundary force This article has been downloaded from IOPscience. Please scroll down to see the full text article.

    E-print Network

    Li, Bo

    Yukawa-field approximation of electrostatic free energy and dielectric boundary force This article.1088/0951-7715/24/11/011 Yukawa-field approximation of electrostatic free energy and dielectric boundary force Hsiao-Bing Cheng1. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially

  19. Statement of Work for Direct Push Technology Characterization Borehole Installations During Fiscal Year 2006, 300-FF-5 Operable Unit

    SciTech Connect

    Williams, Bruce A.

    2005-11-29

    This document specifies activities to be performed by FHI to fulfill Part II of the 300-FF-5 Operable Unit Limited Field Investigation. The scope includes driving up to 15 direct push technology boreholes to the water table for radiological geophysical logging of the vadose zone to define the vertical extent and concentration of process uranium waste in the subsurface. Drilling and sampling field activates will follow FHI waste management, risk assessment and QA process and procedures. The sampling and analysis of information recovered during this characterization will meet the Hanford Performance Assessment Project QAAP requirements.

  20. Compatibility of the Chameleon-Field Model with Fifth-Force Experiments, Cosmology, and PVLAS and CAST Results

    SciTech Connect

    Brax, Philippe; Bruck, Carsten van de; Davis, Anne-Christine

    2007-09-21

    We analyze 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 CERN Axion Solar Telescope results, fifth-force experiments, and cosmology.

  1. Accuracy analysis and application of extrapolation of force-free fields in solar active and quiet regions

    NASA Astrophysics Data System (ADS)

    Liu, Suo; Zhang, Hongqi; Su, Jiangtao; Song, Mutao

    2013-07-01

    In this paper, the availability, applicability and deviation of nonlinear force-free (NLFF) fields extrapolated by Approximate Vertical Integration (AVI), Boundary Integral Equation (BIE) and Optimization (Opt.) methods are studied based on the comparison with two semi-analytical fields (Low & Lou 1990). These NLFF extrapolations based on the observational vector magnetograms are used to study the spatial magnetic field in the quiet Sun.

  2. Atomic force microscope based near-field imaging for probing cell surface interactions

    NASA Astrophysics Data System (ADS)

    Amini, Sina

    Near-membrane and trans-membrane proteins and their interactions with the extracellular matrix (ECM) can yield valuable information about cell dynamics. However, advances in the field of nanoscale cellular processes have been hindered, in part, due to limits imposed by current technology. In this work, a novel evanescent field (EF) imaging technique is designed, modeled, created and tested for near-field imaging in the apical surface of cells. This technique and Forster resonance energy transfer (FRET) were used to investigate interactions between integrins on the cell surface and the ECM protein, fibronectin. The goal was to monitor changes in the integrin density at the cell surface as a function of clustering after binding to fibronectin on the microsphere surface. For the EF technique, quantum dot (QD)-embedded polystyrene microspheres were used to couple light into whispering gallery modes (WGMs) inside the microspheres; the resulting EF at the surface of the microsphere was used as a near-field excitation source with ~50 nm axial resolution for exciting fluorescently-labeled integrins. For FRET measurements (~10 nm axial resolution), QDs (donors) were coated on the surface of microspheres and energy transfer to red fluorescent protein (RFP)-integrin constructs (acceptors) studied. In both techniques, the QD-modified microspheres were mounted on atomic force microscope (AFM) cantilevers, functionalized with fibronectin, and brought into contact with fluorescently-labeled HeLa or vascular smooth muscle (VSM) cells. The results obtained from both methods show the clustering and activity of the integrins and are in good agreement with each other. Amsterdam discrete dipole approximation (ADDA) was used to study the effects of inhomogeneous surrounding refractive index on the quality factor and position of the WGMs due to the attachment of a microsphere to an AFM cantilever. WGMs of various QD-embedded microspheres mounted on AFM cantilevers were experimentally measured and shown to be consistent with the model.

  3. Application of Fourth Order Vibrational Perturbation Theory with Analytic Hartree-Fock Force Fields

    NASA Astrophysics Data System (ADS)

    Gong, Justin Z.; Matthews, Devin A.; Stanton, John F.

    2014-06-01

    Fourth-Order Rayleigh-Schrodinger Perturbation Theory (VPT4) is applied to a series of small molecules. The quality of results have been shown to be heavily dependent on the quality of the quintic and sextic force constants used and that numerical sextic force constants converge poorly and are unreliable for VPT4. Using analytic Hartree-Fock force constants, it is shown that these analytic higher-order force constants are comparable to corresponding force constants from numerical calculations at a higher level of theory. Calculations show that analytic Hartree-Fock sextic force constants are reliable and can provide good results with Fourth-Order Rayleigh-Schrodinger Perturbation Theory.

  4. Capillary Force-Driven, Hierarchical Co-Assembly of Dandelion-Like Peptide Microstructures.

    PubMed

    Wang, Yuefei; Huang, Renliang; Qi, Wei; Xie, Yanyan; Wang, Mengfan; Su, Rongxin; He, Zhimin

    2015-06-24

    The wetting and drying of drops on flexible fibers occurs ubiquitously in nature, and the capillary force underlying this phenomenon has motivated our great interest in learning how to direct supramolecular self-assembly. Here, the hierarchical co-assembly of two aromatic peptides, diphenylalanine (FF) and ferrocene-diphenylalanine (Fc-FF), is reported via sequential, combinatorial assembly. The resulting dandelion-like microstructures have highly complex architectures, where FF microtube arrays serve as the scapes and the Fc-FF nanofibers serve as the flower heads. Homogeneous FF microtubes with diameters tailored between 1 and 9 ?m and wall thickness ranging from 70 to 950 nm are initially formed by controlling the degree of supersaturation of the FF and the water content. Once the FF microtubes are formed, the growth of the dandelion-like microstructures is then driven by the capillary force, derived from the wetting and drying of the Fc-FF solution on the FF microtubes. This simple and ingenious strategy offers many opportunities to develop new and creative methods for controlling the hierarchical self-assembly of peptides and thus building highly complex nano and microstructures. PMID:25759325

  5. Current sheet formation in a sheared force-free-magnetic field. [in sun

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard

    1989-01-01

    This paper presents the results of a study showing how continuous shearing motion of magnetic footpoints in a tenuous, infinitely conducting plasma can lead to the development of current sheets, despite the absence of such sheets or even of neutral points in the initial state. The calculations discussed here verify the earlier suggestion by Low and Wolfson (1988) that extended current sheets should form due to the shearing of a force-free quadrupolar magnetic field. More generally, this work augments earlier studies suggesting that the appearance of discontinuities - current sheets - may be a necessary consequence of the topological invariance imposed on the magnetic field geometry of an ideal MHD system by virtue of its infinite conductivity. In the context of solar physics, the work shows how the gradual and continuous motion of magnetic footpoints at the solar photosphere may lead to the buildup of magnetic energy that can then be released explosively when finite conductivity effects become important and lead to the rapid dissipation of current sheets. Such energy release may be important in solar flares, coronal mass ejections, and other eruptive events.

  6. Forces and Phases: An Investigation of Azimuthal Plasma and Field Periodicities in Saturn's Inner Magnetosphere

    NASA Astrophysics Data System (ADS)

    Ramer, K. M.; Kivelson, M. G.; Khurana, K. K.; Sergis, N.; Walker, R. J.; Jia, X.

    2012-12-01

    In Saturn's magnetosphere, periodic fluctuations are ubiquitous; for example, periodicities have been observed in Saturn Kilometric Radiation (SKR), in auroral emissions, in magnetic perturbations, in electron density, and in energetic particle fluxes. In this study, we extend the search for periodicities at Saturn by examining additional plasma and magnetic field parameters in Saturn's inner magnetosphere near the equatorial plane. Our study uses data acquired by the Cassini spacecraft during the equatorial passes from Oct 11, 2005 to May 24, 2006. We have found that the intermittency of in situ measurements in the inner magnetosphere precludes the use of the frequency sweeping technique adopted by Gurnett et al. [2007] to establish the optimum rotation period. We, therefore, use rotation periods already in use: first the slowly changing SLS3 period based on SKR measurements, and second the period based on the magnetic field [Provan et al., 2011], to establish phases and obtain evidence that magnetic pressure, plasma pressure, density, and angular velocity are periodically modulated. We then establish the phase relationships among these parameters to test azimuthal force balance and we compare these results to simulations by Jia et al. [2012].

  7. A theoretical vibrational spectroscopic study with density functional theory and force field refinement calculation methods on free 4-aminopyrimidine molecule

    NASA Astrophysics Data System (ADS)

    Balci, K.; Akyuz, S.

    2005-06-01

    A detailed investigation of the geometric structure, force field, electro-optical parameters, relative IR intensities and harmonic vibrational wavenumbers of free 4-aminopyrimidine molecule (4APM) in the electronically ground state has been carried out by using both the DFT-B3LYP (with 6-31++G(d,p) double and 6-311++G(d,p) triple basis sets) and force field refinement calculation methods. The vibrational wavenumbers calculated with DFT method were scaled by using two different methods: (1) scaling with dual scaling factors, (2) deriving the scaling factors from the graph of observed versus calculated wavenumbers. In the case of force field refinement method, the force constants of the pyrimidine were slightly refined so as to fit the calculated wavenumbers to the experimental ones. In order to define the contributions of the internal coordinates of the molecule on its each normal vibrational mode, P.E.D. calculations were performed. In wavenumber and PED calculations, both methods have yield results in agreement with the experimental assignment and also with each other, particularly for ring vibrations. The relative IR intensities calculated by the force field refinement method are considerably in good agreement with experimental ones, however, the results of the IR intensities, obtained from the DFT method are found to be significantly different from the experimental values.

  8. Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields

    PubMed Central

    Allen, Toby W.; Andersen, Olaf S.; Roux, Benoit

    2006-01-01

    We investigate methods for extracting the potential of mean force (PMF) governing ion permeation from molecular dynamics simulations (MD) using gramicidin A as a prototypical narrow ion channel. It is possible to obtain well-converged meaningful PMFs using all-atom MD, which predict experimental observables within order-of-magnitude agreement with experimental results. This was possible by careful attention to issues of statistical convergence of the PMF, finite size effects, and lipid hydrocarbon chain polarizability. When comparing the modern all-atom force fields of CHARMM27 and AMBER94, we found that a fairly consistent picture emerges, and that both AMBER94 and CHARMM27 predict observables that are in semiquantitative agreement with both the experimental conductance and dissociation coefficient. Even small changes in the force field, however, result in significant changes in permeation energetics. Furthermore, the full two-dimensional free-energy surface describing permeation reveals the location and magnitude of the central barrier and the location of two binding sites for K+ ion permeation near the channel entrance—i.e., an inner site on-axis and an outer site off-axis. We conclude that the MD-PMF approach is a powerful tool for understanding and predicting the function of narrow ion channels in a manner that is consistent with the atomic and thermally fluctuating nature of proteins. PMID:16500984

  9. Measurements of the force fields within an acoustic standing wave using holographic optical tweezers

    SciTech Connect

    Bassindale, P. G.; Drinkwater, B. W.; Phillips, D. B.; Barnes, A. C.

    2014-04-21

    Direct measurement of the forces experienced by micro-spheres in an acoustic standing wave device have been obtained using calibrated optical traps generated with holographic optical tweezers. A micro-sphere, which is optically trapped in three dimensions, can be moved through the acoustic device to measure forces acting upon it. When the micro-sphere is subjected to acoustic forces, it's equilibrium position is displaced to a position where the acoustic forces and optical forces are balanced. Once the optical trapping stiffness has been calibrated, observation of this displacement enables a direct measurement of the forces acting upon the micro-sphere. The measured forces are separated into a spatially oscillating component, attributed to the acoustic radiation force, and a constant force, attributed to fluid streaming. As the drive conditions of the acoustic device were varied, oscillating forces (>2.5 pN{sub pp}) and streaming forces (<0.2 pN) were measured. A 5??m silica micro-sphere was used to characterise a 6.8?MHz standing wave, ??=?220??m, to a spatial resolution limited by the uncertainty in the positioning of the micro-sphere (here to within 2?nm) and with a force resolution on the order of 10 fN. The results have application in the design and testing of acoustic manipulation devices.

  10. Atmospheric and Oceanic forcing of sea ice drift and deformation during the SEDNA field campaign

    NASA Astrophysics Data System (ADS)

    Roberts, A.; Hutchings, J.; Hibler, W. D.; Seefeldt, M.

    2007-12-01

    This paper provides a synopsis of the surface atmospheric and oceanic forcing of sea ice drift and deformation during the Sea ice Experiment: Dynamical Nature of the Arctic (SEDNA) Beaufort Sea campaign of April 2007. During the campaign two hexagonal arrays of GPS buoys were deployed with maximum diameters of 10km and 70km, respectively, providing an excellent record of sea ice drift and deformation. This record is analyzed in light of in situ surface wind and current measurements, high resolution Weather Research and Forecast Model (WRF) simulations focussed on the Beaufort Sea, and pan-arctic synoptic weather events represented in NCEP II atmospheric analyses. Analysis of the drift track and wind-forcing in the time domain suggests little trace of inertial or tidally induced motion during the field camp. A broader understanding of the relative contribution of semi-diurnal motion to Beaufort Sea ice drift and deformation is gained by comparing barotropic ice-tide model output with a 12-month Beaufort Sea ice-drift time series of buoys deployed in August 2006. Spectral comparisons of the buoy-drift with our model's output reveal that semi-diurnal deformation spectra does not always result from strong local surface winds, regardless of sea ice concentration. This result is particularly significant because the ice camp was located close to the latitude at which the M2 tide oscillates at the resonant inertial frequency, potentially making excitation of the oceanic boundary layer by storms more likely. One interpretation of this result is that specific ice-ocean boundary layer treatments in ocean models may have some baring on their estimates of the ice mass balance of the Arctic Ocean.

  11. Sugmut field: A forced regression deposit within the Neocomian prograding clinoform complex, West Siberian Basin, Russia

    SciTech Connect

    Armentrout, J.M. ); Oleg, M.; Igirgi, M.

    1996-01-01

    The Volgian-Neocomian interval of the Middle Ob Region of the intracratonic West Siberian Basin consists of between 35 and 45 regional transgressive/regressive cycles infilling a basin which had an average water depth of approximately 200 meters. Within local clinoforms, wells have encountered elongate shelf-edge sandstone bodies ranging from 15 to 100 kilometers in strike-oriented length. In most areas the seismic interval correlative to the reservoir sandstone pinches-out against the foreset of the preceding clinoform. This geometric relationship, and the sharp-based log pattern of sandstones along the more landward margin of the sandstone body, suggests that the sandstone may have been deposited as a consequence of marked downward shift in baselevel as part of a lowstand prograding complex, or possibly as a late highstand forced regression deposit. The Sugmut field, located in the northeast part of the study area, is 12 km wide east-west and 75 km long north-south, and grades laterally into shale to the west, south and east. Relative to the regressive phase isopach, the transgressive phase isopach thick shifts slightly northward and eastward indicating the direction of littoral drift and marginward transgression. In the northern part of the field the shelf-edge sandstone interval may correlate with a thin depositional-dip oriented shelf sandstone mapped within the transgressive interval. This mapped pattern may be interpreted as lowstand incision of a fluvial system supplying sand to a shelf-edge delta followed by infilling of the fluvial valley during transgression. Subsequent down-to-the-north regional tilt resulted in structural closure forming the Sugmut field trap.

  12. Sugmut field: A forced regression deposit within the Neocomian prograding clinoform complex, West Siberian Basin, Russia

    SciTech Connect

    Armentrout, J.M.; Oleg, M.; Igirgi, M.

    1996-12-31

    The Volgian-Neocomian interval of the Middle Ob Region of the intracratonic West Siberian Basin consists of between 35 and 45 regional transgressive/regressive cycles infilling a basin which had an average water depth of approximately 200 meters. Within local clinoforms, wells have encountered elongate shelf-edge sandstone bodies ranging from 15 to 100 kilometers in strike-oriented length. In most areas the seismic interval correlative to the reservoir sandstone pinches-out against the foreset of the preceding clinoform. This geometric relationship, and the sharp-based log pattern of sandstones along the more landward margin of the sandstone body, suggests that the sandstone may have been deposited as a consequence of marked downward shift in baselevel as part of a lowstand prograding complex, or possibly as a late highstand forced regression deposit. The Sugmut field, located in the northeast part of the study area, is 12 km wide east-west and 75 km long north-south, and grades laterally into shale to the west, south and east. Relative to the regressive phase isopach, the transgressive phase isopach thick shifts slightly northward and eastward indicating the direction of littoral drift and marginward transgression. In the northern part of the field the shelf-edge sandstone interval may correlate with a thin depositional-dip oriented shelf sandstone mapped within the transgressive interval. This mapped pattern may be interpreted as lowstand incision of a fluvial system supplying sand to a shelf-edge delta followed by infilling of the fluvial valley during transgression. Subsequent down-to-the-north regional tilt resulted in structural closure forming the Sugmut field trap.

  13. Source evaluation report phase 2 investigation: Limited field investigation. Final report: United States Air Force Environmental Restoration Program, Eielson Air Force Base, Alaska

    SciTech Connect

    Not Available

    1994-10-01

    This report describes the limited field investigation work done to address issues and answer unresolved questions regarding a collection of potential contaminant sources at Eielson Air Force Base (AFB), near Fairbanks, Alaska. These sources were listed in the Eielson AFB Federal Facility Agreement supporting the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) cleanup of the base. The limited field investigation began in 1993 to resolve all remaining technical issues and provide the data and analysis required to evaluate the environmental hazard associated with these sites. The objective of the limited field investigation was to allow the remedial project managers to sort each site into one of three categories: requiring remedial investigation/feasibility study, requiring interim removal action, or requiring no further remedial action.

  14. Constraining Carbonaceous Aerosol Climate Forcing by Bridging Laboratory, Field and Modeling Studies

    NASA Astrophysics Data System (ADS)

    Dubey, M. K.; Aiken, A. C.; Liu, S.; Saleh, R.; Cappa, C. D.; Williams, L. R.; Donahue, N. M.; Gorkowski, K.; Ng, N. L.; Mazzoleni, C.; China, S.; Sharma, N.; Yokelson, R. J.; Allan, J. D.; Liu, D.

    2014-12-01

    Biomass and fossil fuel combustion emits black (BC) and brown carbon (BrC) aerosols that absorb sunlight to warm climate and organic carbon (OC) aerosols that scatter sunlight to cool climate. The net forcing depends strongly on the composition, mixing state and transformations of these carbonaceous aerosols. Complexities from large variability of fuel types, combustion conditions and aging processes have confounded their treatment in models. We analyse recent laboratory and field measurements to uncover fundamental mechanism that control the chemical, optical and microphysical properties of carbonaceous aerosols that are elaborated below: Wavelength dependence of absorption and the single scattering albedo (?) of fresh biomass burning aerosols produced from many fuels during FLAME-4 was analysed to determine the factors that control the variability in ?. Results show that ? varies strongly with fire-integrated modified combustion efficiency (MCEFI)—higher MCEFI results in lower ? values and greater spectral dependence of ? (Liu et al GRL 2014). A parameterization of ? as a function of MCEFI for fresh BB aerosols is derived from the laboratory data and is evaluated by field data, including BBOP. Our laboratory studies also demonstrate that BrC production correlates with BC indicating that that they are produced by a common mechanism that is driven by MCEFI (Saleh et al NGeo 2014). We show that BrC absorption is concentrated in the extremely low volatility component that favours long-range transport. We observe substantial absorption enhancement for internally mixed BC from diesel and wood combustion near London during ClearFlo. While the absorption enhancement is due to BC particles coated by co-emitted OC in urban regions, it increases with photochemical age in rural areas and is simulated by core-shell models. We measure BrC absorption that is concentrated in the extremely low volatility components and attribute it to wood burning. Our results support enhanced light absorption by internally mixed BC parameterizations in models and identify mixed biomass and fossil combustion regions where this effect is large. We unify the treatment of carbonaceous aerosol components and their interactions to simplify and verify their representation in climate models, and re-evaluate their direct radiative forcing.

  15. Protein adsorption to poly(ethylenimine)-modified Sepharose FF. IV. Dynamic adsorption and elution behaviors.

    PubMed

    Liu, Na; Yu, Lin-Ling; Sun, Yan

    2014-10-01

    We have previously investigated bovine serum albumin (BSA) uptake to poly(ethylenimine) (PEI)-grafted Sepharose FF. It was found that there was a critical ionic capacity (cIC; 600mmol/L) for BSA, above which the protein adsorption capacity and uptake kinetics increased drastically. In this work, two poly(ethylenimine) (PEI)-grafted resins with IC values of 271mmol/L (FF-PEI-L270) and 683mmol/L (FF-PEI-L680), which were below and above the cIC, respectively, were chosen to investigate the breakthrough and linear gradient elution (LGE) behaviors of BSA. Commercially available anion exchanger, Q Sepharose FF, was used for comparison. The DBC values of FF-PEI-L680 were much higher in the entire residence time range (2-10min) than the other two resins due to its high static adsorption capacity and uptake kinetics. At a residence time of 5.0min, the DBC of FF-PEI-L680 (104mg/mL) was about seven times that of FF-PEI-L270 and three times that of Q Sepharose FF. A rise-fall trend of the DBCs with increasing ionic strength (IS) was found for all the three resins studied, indicating the presence of electrostatic exclusion for protein uptake at low IS. With increasing NaCl concentration from 20 to 200mmol/L, FF-PEI-L680 kept very high DBC values (64-114mg/mL). In addition, FF-PEI-L270 showed more favorable adsorption properties than Q Sepharose FF at 100-300mmol/L NaCl. These results proved that the three-dimensional grafting ion exchange layer on the PEI resins enhanced their tolerance to IS. In the study of LGE, the three resins showed similar elution behaviors and no distinct peak tailings were observed. The salt concentrations at the elution peaks (IR) were in the order of FF-PEI-L680>FF-PEI-L270>Q Sepharose FF, indicating that the elution for the PEI resins needed higher salt concentrations, which was also an appearance of the salt-tolerant feature of the PEI resins. When protein loading amount was increased to the value equivalent to the DBC at 10% breakthrough, the adsorbed BSA could be eluted at lower salt concentrations. The chromatographic study has provided new insights into the practical application of the PEI-based anion exchangers. PMID:25179288

  16. Mechanical characterization and modelling of Lorentz force based MEMS magnetic field sensors

    NASA Astrophysics Data System (ADS)

    Gkotsis, P.; Lara-Castro, M.; López-Huerta, F.; Herrera-May, A. L.; Raskin, J.-P.

    2015-10-01

    In this work we present experimental results from dynamic and static tests on miniature magnetic field sensors which are based on Micro Electro Mechanical Systems (MEMS) technologies. These MEMS magnetometers were fabricated on SOI wafers using Si bulk micromachining techniques and they operate at the first resonant frequency under the action of the Lorentz force which arises when a current flows through them in the presence of an external magnetic field. Sensing is based on piezoresistive principles and high sensitivity is expected from devices that show high total quality factors Qtot. We investigate here the energy loss mechanisms and the temperature rise due to Joule heating effects in the resonators of the magnetometers by performing tests both in air and under vacuum conditions. Testing was performed using laser Doppler Vibrometry and white light interferometry. At each pressure different driving currents have been applied and Qtot was extracted. It is found that Qtot varies with pressure between two limiting values: a low one in air which was between 17 and 500 for the tested devices and a high one in vacuum which in the case of one of our devices was equal to 2800. The amplitude of the applied current is also affecting the Q value at a certain pressure due to the rise of thermal stress in the resonating structures. The sensitivity of the sensors in air was experimentally measured using a Helmholtz coil and an oscilloscope and values between 72 mV T-1 and 513 mV T-1 were obtained from the tested devices. We further attempt to estimate the temperature rise in the devices due to Joule heating effects by combining the topography scans which were experimentally obtained with results from thermomechanical analysis of the sensors using Finite Element Modelling.

  17. Mode Transition of RNA Trap by Electric and Hydraulic Force Field in Microfluidic Taper Shape Channel

    NASA Astrophysics Data System (ADS)

    Takamura, Yuzuru; Ueno, Kunimitsu; Nagasaka, Wako; Tomizawa, Yuichi; Tamiya, Eiichi

    2007-03-01

    We have discovered a phenomenon of accumulation of DNA near the constricted position of a microfluidic chip with taper shaped channel when both hydro pressure and electric field are applied in opposite directions. However, RNA has not been able to trap so far, unlike huge and uniformly double stranded DNA molecules, RNAs are smaller in size and single stranded with complicated conformation like blocks in lysed cell solution. In this paper, we will report not only large but also small RNA (100˜10b) are successfully trapped in relatively large microfluidic taper shape channel (width >10um). RNA are trapped in circular motion near the constricted position of taper shape channel, and the position and shape of the trapped RNA are controlled and make mode transition by changing the hydraulic and the electric force. Using this technique, smaller size molecule can be trapped in larger micro fluidic structure compared to the trap using dielectrophoresis. This technique is expected to establish easy and practical device as a direct total RNA extraction tool from living cells or tissues.

  18. Penetration Barrier of Water through Graphynes' Pores: First-Principles Predictions and Force Field Optimization.

    PubMed

    Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I; Campos-Martínez, José; Pirani, Fernando; Giorgi, Giacomo; Yamashita, Koichi

    2014-02-20

    Graphynes are novel two-dimensional carbon-based materials that have been proposed as molecular filters, especially for water purification technologies. We carry out first-principles electronic structure calculations at the MP2C level of theory to assess the interaction between water and graphyne, graphdiyne, and graphtriyne pores. The computed penetration barriers suggest that water transport is unfeasible through graphyne while being unimpeded for graphtriyne. For graphdiyne, with a pore size almost matching that of water, a low barrier is found that in turn disappears if an active hydrogen bond with an additional water molecule on the opposite side of the opening is considered. Thus, in contrast with previous determinations, our results do not exclude graphdiyne as a promising membrane for water filtration. In fact, present calculations lead to water permeation probabilities that are 2 orders of magnitude larger than estimations based on common force fields. A new pair potential for the water-carbon noncovalent component of the interaction is proposed for molecular dynamics simulations involving graphdiyne and water. PMID:26270848

  19. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization

    SciTech Connect

    Mazack, Michael J. M.; Gao, Jiali

    2014-05-28

    The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

  20. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  1. Modeling Cu(II) Binding to Peptides Using the Extensible Systematic Force Field

    PubMed Central

    Ryvkin, Faina; Greenaway, Frederick T.

    2010-01-01

    The utility of the extensible systematic force field (ESFF) was tested for copper(II) binding to a 34-amino-acid Cu(II) peptide, which includes five histidine residues and is the putative copper-binding site of lysyl oxidase. To improve computational efficiency, distance geometry calculations were used to constrain all combinations of three histidine ligands to be within bonding distance of the copper and the best results were utilized as starting structures for the ESFF computations. All likely copper geometries were modeled, but the results showed only a small dependence on the geometrical model in that all resulted in a distorted square pyramidal geometry about the copper, some of the imidazole rings were poorly oriented for ligation to the Cu(II), and the copper-nitrogen bond distances were too long. The results suggest that ESFF should be used with caution for Cu(II) complexes where the copper-ligand bonds have significant covalency and when the ligands are not geometrically constrained to be planar. PMID:20300581

  2. Polarizable Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds Based on the Classical Drude Oscillator

    PubMed Central

    Lopes, Pedro E. M.; Lamoureux, Guillaume; MacKerell, Alexander D.

    2009-01-01

    The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the nitrogen-containing heteroaromatic compounds pyridine, pyrimidine, pyrrole, imidazole, indole and purine. Initial parameters for the 6-membered rings were based on benzene with non-bond parameter optimization focused on the nitrogen atoms and adjacent carbons and attached hydrogens. In the case of 5-member rings, parameters were first developed for imidazole and transferred to pyrrole. Optimization of all parameters was performed against an extensive set of quantum mechanical and experimental data. Ab initio data was used for determination of the initial electrostatic parameters, the vibrational analysis, and in the optimization of the relative magnitudes of the Lennard-Jones parameters, through computations of the interactions of dimers of model compounds, model compound-water interactions and interactions of rare gases with model compounds. The absolute values of the Lennard-Jones parameters were determined targeting experimental heats of vaporization, molecular volumes, heats of sublimation, crystal lattice parameters and free energies of hydration. Final scaling of the polarizabilities from the gas phase values by 0.85 was determined by reproduction of the dielectric constants of pyridine and pyrrole. The developed parameter set was extensively validated against additional experimental data such as diffusion constants, heat capacities and isothermal compressibilities, including data as a function of temperature. PMID:19090564

  3. Nano-imaging collagen by atomic force, near-field and nonlinear microscope

    NASA Astrophysics Data System (ADS)

    Lim, Ken Choong; Tang, Jinkai; Li, Hao; Ng, Boon Ping; Kok, Shaw Wei; Wang, Qijie; Zhang, Ying

    2015-03-01

    As the most abundant protein in the human body, collagen has a very important role in vast numbers of bio-medical applications. The unique second order nonlinear properties of fibrillar collagen make it a very important index in nonlinear optical imaging based disease diagnosis of the brain, skin, liver, colon, kidney, bone, heart and other organs in the human body. The second-order nonlinear susceptibility of collagen has been explored at the macroscopic level and was explained as a volume-averaged molecular hyperpolarizability. However, details about the origin of optical second harmonic signals from collagen fibrils at the molecular level are still not clear. Such information is necessary for accurate interpolation of bio-information from nonlinear optical imaging techniques. The later has shown great potential in collagen based disease diagnosis methodologies. In this paper, we report our work using an atomic force microscope (AFM), near field (SNOM) and nonlinear laser scanning microscope (NLSM) to study the structure of collagen fibrils and other pro-collagen structures.

  4. Exploring LacI-DNA Dynamics by Multiscale Simulations Using the SIRAH Force Field.

    PubMed

    Machado, Matias R; Pantano, Sergio

    2015-10-13

    The lac repressor protein (LacI) together with its target regulatory sequence are a common model for studying DNA looping and its implications on transcriptional control in bacteria. Owing to the molecular size of this system, standard all-atom (AA) simulations are prohibitive for achieving relevant biological time scales. As an alternative, multiscale models, which combine AA descriptions at particular regions with coarse-grained (CG) representations of the remaining components, were used to address this computational challenge while preserving the relevant details of the system. In this work, we implement a new multiscale approach based on the SIRAH force field to gain deeper insights into the dynamics of the LacI-DNA system. Our methodology allows for a dual resolution treatment of the solute and solvent, explicitly representing the protein, DNA, and solvent environment without compromising the AA region. Starting from the P1 loop configuration in an undertwisted conformation, we were able to observe the transition to the more stable overtwisted state. Additionally, a detailed characterization of the conformational space sampled by the DNA loop was done. In agreement with experimental and theoretical evidence, we observed the transient formation of kinks at the loop, which were stabilized by the presence of counterions at the minor groove. We also show that the loop's intrinsic flexibility can account for reported FRET measurements and bent conformations required to bind the CAP transcription factor. PMID:26574286

  5. Ion solvation in water from molecular dynamics simulation with the ABEEM/MM force field.

    PubMed

    Yang, Zhong-Zhi; Li, Xin

    2005-04-28

    A systematic study on monovalent ions in water clusters and in aqueous solution is presented for providing insight into their solvation structures, charge distributions, binding energies, as well as dynamic and thermodynamic properties in terms of the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges into the Coulomb term in MM. For hydrated systems of M+(H2O)n, M+ being Li+, Na+, and K+, as well as X-(H2O)n, X- being F-, Cl-, and Br-, with n = 1-6, parameters for the effective interaction between the ion and the water molecules were determined, so as to reproduce the experimental or ab initio results. The corresponding parameters were tested with molecular dynamics (MD) simulations of these ions in liquid water and with solvation free energy calculations using the perturbation technique. The results of aqueous ionic solution simulations with the ABEEM/MM force field provide a reasonable description of many important properties, which are in good agreement with the experimental measurements. This work demonstrates that the combination of ABEEM/MM-MD provides a powerful tool in analyzing solvation processes of monovalent ions in water. PMID:16839014

  6. Semi-quartic force fields retrieved from multi-mode expansions: Accuracy, scaling behavior, and approximations.

    PubMed

    Ramakrishnan, Raghunathan; Rauhut, Guntram

    2015-04-21

    Semi-quartic force fields (QFF) rely on a Taylor-expansion of the multi-dimensional Born-Oppenheimer potential energy surface (PES) and are frequently used within the calculation of anharmonic vibrational frequencies based on 2nd order vibrational perturbation theory (VPT2). As such they are usually determined by differentiation of the electronic energy with respect to the nuclear coordinates. Alternatively, potential energy surfaces can be expanded in terms of multi-mode expansions, which typically do not require any derivative techniques. The computational effort to retrieve QFF from size-reduced multi-mode expansions has been studied and has been compared with standard Taylor-expansions. As multi-mode expansions allow for the convenient introduction of subtle approximations, these will be discussed in some detail. In addition, a preliminary study about the applicability of a generalized Duschinsky transformation to QFFs is provided. This transformation allows for the efficient evaluation of VPT2 frequencies of isotopologues from the PES of the parent compound and thus avoids the recalculation of PESs in different axes systems. PMID:25903877

  7. 1 = \\Gamma0:30104661 ff 1 = 2:1810429 \\Delta 10 \\Gamma2 2 = \\Gamma6:3319840 \\Delta 10 \\Gamma3 ff 2 = 7:5714590 \\Delta 10 \\Gamma2

    E-print Network

    van Baal, Pierre

    Table I Ÿ 1 = \\Gamma0:30104661 ff 1 = 2:1810429 \\Delta 10 \\Gamma2 Ÿ 2 = \\Gamma6:3319840 \\Delta 10 \\Gamma3 ff 2 = 7:5714590 \\Delta 10 \\Gamma2 Ÿ 3 = 5:6289546 \\Delta 10 \\Gamma4 ff 3 = 1:1130266 \\Delta 10 \\Gamma4 Ÿ 4 = \\Gamma1:5687855 \\Delta 10 \\Gamma3 ff 4 = \\Gamma2:1475176 \\Delta 10 \\Gamma4 Ÿ 5 = 4

  8. A CRITICAL ASSESSMENT OF NONLINEAR FORCE-FREE FIELD MODELING OF THE SOLAR CORONA FOR ACTIVE REGION 10953

    SciTech Connect

    DeRosa, Marc L.; Schrijver, Carolus J.; Aschwanden, Markus J.; Cheung, Mark C. M.; Lites, Bruce W.; Amari, Tahar; Canou, Aurelien; McTiernan, James M.; Regnier, Stephane; Thalmann, Julia K.; Wiegelmann, Thomas; Inhester, Bernd; Tadesse, Tilaye; Valori, Gherardo; Wheatland, Michael S.; Conlon, Paul A.; Fuhrmann, Marcel

    2009-05-10

    Nonlinear force-free field (NLFFF) models are thought to be viable tools for investigating the structure, dynamics, and evolution of the coronae of solar active regions. In a series of NLFFF modeling studies, we have found that NLFFF models are successful in application to analytic test cases, and relatively successful when applied to numerically constructed Sun-like test cases, but they are less successful in application to real solar data. Different NLFFF models have been found to have markedly different field line configurations and to provide widely varying estimates of the magnetic free energy in the coronal volume, when applied to solar data. NLFFF models require consistent, force-free vector magnetic boundary data. However, vector magnetogram observations sampling the photosphere, which is dynamic and contains significant Lorentz and buoyancy forces, do not satisfy this requirement, thus creating several major problems for force-free coronal modeling efforts. In this paper, we discuss NLFFF modeling of NOAA Active Region 10953 using Hinode/SOT-SP, Hinode/XRT, STEREO/SECCHI-EUVI, and SOHO/MDI observations, and in the process illustrate three such issues we judge to be critical to the success of NLFFF modeling: (1) vector magnetic field data covering larger areas are needed so that more electric currents associated with the full active regions of interest are measured, (2) the modeling algorithms need a way to accommodate the various uncertainties in the boundary data, and (3) a more realistic physical model is needed to approximate the photosphere-to-corona interface in order to better transform the forced photospheric magnetograms into adequate approximations of nearly force-free fields at the base of the corona. We make recommendations for future modeling efforts to overcome these as yet unsolved problems.

  9. Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field

    E-print Network

    Jayaram, Bhyravabotla

    Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model provides rapid estimates of the electrostatic free energies of solvation for diverse molecules of parameters compatible with the AMBER force field is described. The method is used to estimate free energies

  10. Induced Electromotive Force (EMF) Profile in a Circular Loop Passing a Limited Rectangular Area with Perpendicular Uniform Constant Magnetic Field

    E-print Network

    Viridi, Sparisoma; Khairurrijal,

    2012-01-01

    Profile of induced eletromotive force (EMF) for a circular loop (CL) entering and leaving a limited rectangular area which has perpendicular uniform magnetic field is reported in this work. The influence of parameters of the sytem to the induced EMF profile is discussed.

  11. Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ?/? force field reparametrizations.

    PubMed

    Mlýnský, Vojt?ch; Kührová, Petra; Zgarbová, Marie; Jure?ka, Petr; Walter, Nils G; Otyepka, Michal; Šponer, Ji?í; Banáš, Pavel

    2015-03-19

    X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme's active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozyme's active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used. Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of ?/? torsions significantly improves the description of the hairpin ribozyme's scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH contributes to the conformational behavior observed for the scissile phosphate in the presence of a deprotonated G8(-). On the basis of the new force field, we obtain a reactive conformation for the hairpin ribozyme active site that is consistent with the most recent mechanistic and structural data. PMID:25692537

  12. Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene.

    PubMed

    Abramyan, Tigran M; Snyder, James A; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

    2015-01-01

    Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG-X-GTGT host-guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5?kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard-Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid-liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122

  13. Molecular dynamic study of Shock wave response of bulk amorphous polyvinyl chloride: effect of chain length and force field

    NASA Astrophysics Data System (ADS)

    Neogi, Anupam; Mitra, Nilanjan

    2015-06-01

    Atomistic molecular dynamics in conjunction with multi-scale shock technique is utilized to investigate shock wave response of bulk amorphous polyvinyl chloride. Dependence of chain length on physical and mechanical behaviour of polymeric material at ambient condition of temperature and pressure are well known but unknown for extreme conditions. Non-reactive force fields PCFF, COMPASS and PCFF+ were used to determine applicability of the force field for the study of the material subjected to shock loads. Several samples of PVC with various chain lengths were subjected to a range of shock compression from 1.5-10.0 km/s. Even though dependence of chain length was observed for lower shock strengths but was not for intense shock loads. The principle Hugoniot points, calculated by applying hydrostatic Rankine-Hugoniot equations and as well as multi-scale shock technique, were compared against LASL experimental shock data, demonstrating superior performance of PCFF+ force-field over PCFF and COMPASS. Shock induced melting characteristic and vibrational spectroscopic study were conducted and compared with experimental data to observe differences in response with relation to different force fields, chain length of the material for different shock intensities.

  14. Comparing Simulations of Lipid Bilayers to Scattering Data: The GROMOS 43A1-S3 Force Field

    E-print Network

    Nagle, John F.

    Comparing Simulations of Lipid Bilayers to Scattering Data: The GROMOS 43A1-S3 Force Field Anthony in SIMtoEXP.2 Distances from the bilayer center for the components and for DHH/2 were obtained manually by locating the peak in the profiles plotted in SIMtoEXP. The distances from the bilayer center of N (nitrogen

  15. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA

    PubMed Central

    Huang, Lei; Roux, Benoît

    2013-01-01

    Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out. PMID:24223528

  16. The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids.

    PubMed

    Sprenger, K G; Jaeger, Vance W; Pfaendtner, Jim

    2015-05-01

    We have applied molecular dynamics to calculate thermodynamic and transport properties of a set of 19 room-temperature ionic liquids. Since accurately simulating the thermophysical properties of solvents strongly depends upon the force field of choice, we tested the accuracy of the general AMBER force field, without refinement, for the case of ionic liquids. Electrostatic point charges were developed using ab initio calculations and a charge scaling factor of 0.8 to more accurately predict dynamic properties. The density, heat capacity, molar enthalpy of vaporization, self-diffusivity, and shear viscosity of the ionic liquids were computed and compared to experimentally available data, and good agreement across a wide range of cation and anion types was observed. Results show that, for a wide range of ionic liquids, the general AMBER force field, with no tuning of parameters, can reproduce a variety of thermodynamic and transport properties with similar accuracy to that of other published, often IL-specific, force fields. PMID:25853313

  17. Carbon fluxes forced by anticyclonic mesoscale eddies generated by islands at the subtropical NE Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Lasternas, S.; Piedeleu, M.; Sangrà, P.; Duarte, C. M.; Agustí, S.

    2012-08-01

    The carbon fluxes mediated by planktonic communities in two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) at the Canary Eddy Corridor were studied and compared with the dynamics in two far-field (FF) stations located outside the eddies. We observed favorable conditions and signs for upwelling at the center of CEs and for downwelling and mixing at the centers of AEs. CEs were characterized by higher nutrients concentration and highest chlorophyll a concentration, associated with highest microphytoplankton and diatoms abundance. AEs displayed similar chlorophyll a values and nutrients concentration (except highest ammonium concentration) to those of the FF stations and were characterized by increasing abundance of picophytoplankton and heterotrophic bacteria. While primary production was similar between the systems, the production of dissolved organic carbon (PDOC) was significantly higher at AEs. Phytoplankton cell mortality was lowest in CEs and we found higher cell mortality in AE than FF, despite similar chl a concentration. Environmental changes at the AEs presented significant prejudicial effects on the phytoplankton health as indicated by higher phytoplankton mortality (e.g. 60% of dead diatoms cells) and higher cell lysis rates observed at AEs than at two other systems. The adverse conditions associated to the early-stage anticyclonic systems, mainly triggered by active downwelling, resulted in higher consequent PDOC production, corresponding to forcing of the carbon flux to the dissolved pool and a weakness of the carbon pump.

  18. Decay Characteristics of Levitation Force of YBCO Bulk Exposed to AC Magnetic Field above NdFeB Guideway

    NASA Astrophysics Data System (ADS)

    Liu, Minxian; Lu, Yiyun; Wang, Suyu; Ma, Guangtong

    2011-04-01

    The superconducting maglev vehicle is one of the most promising applications of HTS bulks. In such a system, the nonuniformity of the magnetic field along the movement direction above the NdFeB guideway is inevitable due to the assembly error and inhomogeneity of the material property of the NdFeB magnet. So it is required to study the characteristics of levitation force of the bulks affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we will study the characteristics of the levitation force relaxation between the HTS bulk and the NdFeB guideway by an experiment in which AC external magnetic field generated by an electromagnet is used to simulate the time-varying external magnetic field caused by the inhomogeneity of the guideway. From the experimental results, it has found that the levitation force is decreasing with the application of the AC external magnetic field, and the decay increasing with the amplitude of the applied magnetic field and is almost independent of the frequency.

  19. Dark-field full-field optical coherence tomography.

    PubMed

    Auksorius, Egidijus; Boccara, A Claude

    2015-07-15

    Full-field optical coherence tomography (FF-OCT) provides en face images from deep in the tissue with high spatial resolution. Specular reflections, however, may reduce image contrast as it can be much stronger than the backscattered signal from a specimen. To this end, we demonstrate dark-field FF-OCT (d-FF-OCT) that can block specular reflections by the help of an opaque disk in the pupil-conjugated plane. The reference mirror is replaced by a blazed grating, which eliminates a walk-off between the sample and the reference beams on a camera that otherwise limits the imaging field-of-view (FOV). We show that d-FF-OCT can suppress specular reflections efficiently from the glass-specimen interface by at least two orders of magnitude and yield higher contrast images compared to the conventional FF-OCT. PMID:26176447

  20. The R.E.D. Tools: Advances in RESP and ESP charge derivation and force field library building

    PubMed Central

    Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

    2010-01-01

    Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure, because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, http://q4md-forcefieldtools.org/RED/) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed. PMID:20574571

  1. Nonlinear force-free magnetic field extrapolations: comparison of the Grad-Rubin and Wheatland-Sturrock-Roumeliotis algorithm

    E-print Network

    B. Inhester; T. Wiegelmann

    2008-01-23

    We compare the performance of two alternative algorithms which aim to construct a force-free magnetic field given suitable boundary conditions. For this comparison, we have implemented both algorithms on the same finite element grid which uses Whitney forms to describe the fields within the grid cells. The additional use of conjugate gradient and multigrid iterations result in quite effective codes. The Grad-Rubin and Wheatland-Sturrock-Roumeliotis algorithms both perform well for the reconstruction of a known analytic force-free field. For more arbitrary boundary conditions the Wheatland-Sturrock-Roumeliotis approach has some difficulties because it requires overdetermined boundary information which may include inconsistencies. The Grad-Rubin code on the other hand loses convergence for strong current densities. For the example we have investigated, however, the maximum possible current density seems to be not far from the limit beyond which a force free field cannot exist anymore for a given normal magnetic field intensity on the boundary.

  2. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    SciTech Connect

    Trément, Sébastien; Rousseau, Bernard; Schnell, Benoît; Petitjean, Laurent; Couty, Marc

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  3. Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials.

    PubMed

    Hagler, A T

    2015-12-01

    Computer simulations are increasingly prevalent, complementing experimental studies in all fields of biophysics, chemistry, and materials. Their utility, however, is critically dependent on the validity of the underlying force fields employed. In this Perspective we review the ability of quantum mechanics, and in particular analytical ab initio derivatives, to inform on the nature of intra- and intermolecular interactions. The power inherent in the exploitation of forces and second derivatives (Hessians) to derive force fields for a variety of compound types, including inorganic, organic, and biomolecules, is explored. We discuss the use of these quantities along with QM energies and geometries to determine force constants, including nonbond and electrostatic parameters, and to assess the functional form of the energy surface. The latter includes the optimal form of out-of-plane interactions and the necessity for anharmonicity, and terms to account for coupling between internals, to adequately represent the energy of intramolecular deformations. In addition, individual second derivatives of the energy with respect to selected interaction coordinates, such as interatomic distances or individual dihedral angles, have been shown to select out for the corresponding interactions, annihilating other interactions in the potential expression. Exploitation of these quantities allows one to probe the individual interaction and explore phenomena such as, for example, anisotropy of atom-atom nonbonded interactions, charge flux, or the functional form of isolated dihedral angles, e.g., a single dihedral X-C-C-Y about a tetrahedral C-C bond. PMID:26642978

  4. Realistic sampling of amino acid geometries for a multipolar polarizable force field.

    PubMed

    Hughes, Timothy J; Cardamone, Salvatore; Popelier, Paul L A

    2015-09-15

    The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X-ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF. PMID:26235784

  5. Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

    NASA Technical Reports Server (NTRS)

    Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

    2012-01-01

    Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

  6. A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation

    SciTech Connect

    Kirschner, Karl N.; Lins, Roberto D.; Maass, Astrid; Soares, Thereza A.

    2012-11-13

    Lipopolysaccharides (LPS) comprise the outermost layer of the Gram-negative bacteria cell envelope. Packed onto a lipid layer, the outer membrane displays remarkable physical?chemical differences compared to cell membranes. The carbohydrate-rich region confers a membrane asymmetry that underlies many biological processes such as endotoxicity, antibiotic resistance, and cell adhesion. Furthermore, unlike membrane proteins from other sources, integral outer-membrane proteins do not consist of transmembrane ? helices; instead they consist of antiparallel ?-barrels, which highlights the importance of the LPS membrane as a medium. In this work, we present an extension of the GLYCAM06 force field that has been specifically developed for LPS membranes using our Wolf2Pack program. This new set of parameters for lipopolysaccharide molecules expands the GLYCAM06 repertoire of monosaccharides to include phosphorylated N- and O-acetylglucosamine, 3-deoxy-D-manno-oct-2- ulosonic acid, L-glycero-D-manno-heptose and its O-carbamoylated variant, and N-alanine-D-galactosamine. A total of 1 µs of molecular dynamics simulations of the rough LPS membrane of Pseudomonas aeruginosa PA01 is used to showcase the added parameter set. The equilibration of the LPS membrane is shown to be signi!cantly slower compared to phospholipid membranes, on the order of 500 ns. It is further shown that water molecules penetrate the hydrocarbon region up to the terminal methyl groups, much deeper than commonly observed for phospholipid bilayers, and in agreement with neutron diffraction measurements. A comparison of simulated structural, dynamical, and electrostatic properties against corresponding experimentally available data shows that the present parameter set reproduces well the overall structure and the permeability of LPS membranes in the liquid-crystalline phase.

  7. Energetics and structures of fluoro- and chlorofluorocarbons in zeolites: Force field development and Monte Carlo simulations

    SciTech Connect

    Mellot, C.F.; Cheetham, A.K.

    1999-05-13

    Canonical Monte Carlo simulations on the adsorption of a series of fluoro-, chlorofluoro-, and hydrofluorocarbons (CF{sub 4}, CF{sub 3}Cl, CF{sub 2}Cl{sub 2}, CFCl{sub 3}, CHF{sub 3}) in siliceous Y and NaY zeolites have been performed and are compared with available calorimetric data on the same host-guest systems. A new force field for fluorocarbon-type molecules in zeolites has been developed, and the (N,V,T) simulations predict adsorption heats with good accuracy. Further insights into the key features of host-guest interactions are gleaned from the relative contributions of the short-range and electrostatic interactions to the total adsorption heats and the analysis of host-guest pair functions. In siliceous Y, host-guest interactions are driven primarily by F{hor_ellipsis}O{sub zeolite} and Cl{hor_ellipsis}O{sub zeolite} van der Waals interactions, and H{hor_ellipsis}O{sub zeolite} hydrogen bonding in the case of hydrogen-containing fluorocarbons. When the fluorocarbon is adsorbed in a cation-containing zeolite, such as NaY, additional F{hor_ellipsis}Na{sub zeolite} electrostatic interactions with Na cations of the supercage are clearly revealed and control the orientation of the sorbate molecules within the supercages. In addition, (N,V,T) simulations have enabled us to compare the behavior of CHF{sub 3} with that of CHCl{sub 3}. The heats of adsorption at zero loading are very similar, but the relative contributions of the short-range and long-range interactions are inverted between the two systems, with the electrostatic term dominating in the case of the fluorocarbon.

  8. The hypothalamic neuropeptide FF network is impaired in hypertensive patients

    PubMed Central

    Goncharuk, Valeri D; Buijs, Ruud M; Jhamandas, Jack H; Swaab, Dick F

    2014-01-01

    Background The human hypothalamus contains the neuropeptide FF (NPFF) neurochemical network. Animal experiments demonstrated that NPFF is implicated in the central cardiovascular regulation. We therefore studied expression of this peptide in the hypothalamus of individuals who suffered from essential hypertension (n = 8) and died suddenly due to acute myocardial infarction (AMI), and compared to that of healthy individuals (controls) (n = 6) who died abruptly due to mechanical trauma of the chest. Methods The frozen right part of the hypothalamus was cut coronally into serial sections of 20 ?m thickness, and each tenth section was stained immunohistochemically using antibody against NPFF. The central section through each hypothalamic nucleus was characterized by the highest intensity of NPFF immunostaining and thus was chosen for quantitative densitometry. Results In hypertensive patients, the area occupied by NPFF immunostained neuronal elements in the central sections through the suprachiasmatic nucleus (SCh), paraventricular hypothalamic nucleus (Pa), bed nucleus of the stria terminalis (BST), perinuclear zone (PNZ) of the supraoptic nucleus (SON), dorso- (DMH), ventromedial (VMH) nuclei, and perifornical nucleus (PeF) was dramatically decreased compared to controls, ranging about six times less in the VMH to 15 times less in the central part of the BST (BSTC). The NPFF innervation of both nonstained neuronal profiles and microvasculature was extremely poor in hypertensive patients compared to control. Conclusions The decreased NPFF expression in the hypothalamus of hypertensive patients might be a cause of impairment of its interaction with other neurochemical systems, and thereby might be involved in the pathogenesis of the disease. PMID:25161813

  9. Coupled energy-drift and force-balance equations for high-field hot-carrier transport

    SciTech Connect

    Huang, Danhong; Alsing, P.M.; Apostolova, T.; Cardimona, D.A.

    2005-05-15

    Coupled energy-drift and force-balance equations that contain a frictional force for the center-of-mass motion of electrons are derived for hot-electron transport under a strong dc electric field. The frictional force is found to be related to the net rate of phonon emission, which takes away the momentum of a phonon from an electron during each phonon-emission event. The net rate of phonon emission is determined by the Boltzmann scattering equation, which depends on the distribution of electrons interacting with phonons. The work done by the frictional force is included into the energy-drift equation for the electron-relative scattering motion and is found to increase the thermal energy of the electrons. The importance of the hot-electron effect in the energy-drift term under a strong dc field is demonstrated in reducing the field-dependent drift velocity and mobility. The Doppler shift in the energy conservation of scattering electrons interacting with impurities and phonons is found to lead to an anisotropic distribution of electrons in the momentum space along the field direction. The importance of this anisotropic distribution is demonstrated through a comparison with the isotropic energy-balance equation, from which we find that defining a state-independent electron temperature becomes impossible. To the leading order, the energy-drift equation is linearized with a distribution function by expanding it into a Fokker-Planck-type equation, along with the expansions of both the force-balance equation and the Boltzmann scattering equation for hot phonons.

  10. Guiding-centre transformation of the radiation-reaction force in a non-uniform magnetic field

    NASA Astrophysics Data System (ADS)

    Hirvijoki, E.; Decker, J.; Brizard, A. J.; Embréus, O.

    2015-10-01

    > In this paper, we present the guiding-centre transformation of the radiation-reaction force of a classical point charge travelling in a non-uniform magnetic field. The transformation is valid as long as the gyroradius of the charged particles is much smaller than the magnetic field non-uniformity length scale, so that the guiding-centre Lie-transform method is applicable. Elimination of the gyromotion time scale from the radiation-reaction force is obtained with the Poisson-bracket formalism originally introduced by Brizard (Phys. Plasmas, vol. 11, 2004, 4429-4438), where it was used to eliminate the fast gyromotion from the Fokker-Planck collision operator. The formalism presented here is applicable to the motion of charged particles in planetary magnetic fields as well as in magnetic confinement fusion plasmas, where the corresponding so-called synchrotron radiation can be detected. Applications of the guiding-centre radiation-reaction force include tracing of charged particle orbits in complex magnetic fields as well as the kinetic description of plasma when the loss of energy and momentum due to radiation plays an important role, e.g. for runaway-electron dynamics in tokamaks.

  11. Atomic Force Microscope Based Near-field Imaging for Probing Cell Surface Interactions 

    E-print Network

    Amini, Sina

    2013-03-26

    )-integrin constructs (acceptors) studied. In both techniques, the QD-modified microspheres were mounted on atomic force microscope (AFM) cantilevers, functionalized with fibronectin, and brought into contact with fluorescently-labeled HeLa or vascular smooth muscle...

  12. Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

    NASA Astrophysics Data System (ADS)

    Treweek, Benjamin C.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.

    2015-10-01

    Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.

  13. Evidence that filament fracture occurs in an ITER toroidal field conductor after cyclic Lorentz force loading in SULTAN

    NASA Astrophysics Data System (ADS)

    Sanabria, Carlos; Lee, Peter J.; Starch, William; Pong, Ian; Vostner, Alexander; Jewell, Matthew C.; Devred, Arnaud; Larbalestier, David C.

    2012-07-01

    We analyzed the ITER TFEU5 cable-in-conduit conductor (CICC) after the full SULTAN conductor qualification test in order to explore whether Lorentz force induced strand movement inside the CICC produces any fracture of the brittle Nb3Sn filaments. Metallographic image analysis was used to quantify the change in void fraction of each sub-cable (petal); strands move in the direction of the Lorentz force, increasing the void space on the low force side of the CICC and producing a densification on the high force side. Adjacent strand counting shows that local increases in void space result in lower local strand-strand support. Extensive metallographic sampling unambiguously confirms that Nb3Sn filament fracture occurred in the TFEU5 CICC, but the filament fracture was highly localized to strand sections with high local curvature (likely produced during cabling, where strands are pivoted around each other). More than 95% of the straighter strand sections were free of filament cracks, while less than 60% of the bent strand sections were crack free. The high concentration of filament fractures on the tensile side of the strand-strand pivot points indicates that these pivot points are responsible for the vast majority of filament fracture. Much lower crack densities were observed in CICC sections extracted from a lower, gradient-field region of the SULTAN-tested cable. We conclude that localized filament fracture is induced by high Lorentz forces during SULTAN testing of this prototype toroidal field CICC and that the strand sections with the most damage are located at the petal corners of the high field zone.

  14. Unsteady hydrodynamic forces acting on a robotic arm and its flow field: application to the crawl stroke.

    PubMed

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

    2014-04-11

    This study aims to clarify the mechanisms by which unsteady hydrodynamic forces act on the hand of a swimmer during a crawl stroke. Measurements were performed for a hand attached to a robotic arm with five degrees of freedom independently controlled by a computer. The computer was programmed so the hand and arm mimicked a human performing the stroke. We directly measured forces on the hand and pressure distributions around it at 200 Hz; flow fields underwater near the hand were obtained via 2D particle image velocimetry (PIV). The data revealed two mechanisms that generate unsteady forces during a crawl stroke. One is the unsteady lift force generated when hand movement changes direction during the stroke, leading to vortex shedding and bound vortex created around it. This bound vortex circulation results in a lift that contributes to the thrust. The other occurs when the hand moves linearly with a large angle of attack, creating a Kármán vortex street. This street alternatively sheds clockwise and counterclockwise vortices, resulting in a quasi-steady drag contributing to the thrust. We presume that professional swimmers benefit from both mechanisms. Further studies are necessary in which 3D flow fields are measured using a 3D PIV system and a human swimmer. PMID:24524992

  15. Thermal conductivity of carbon dioxide from non-equilibrium molecular dynamics: A systematic study of several common force fields

    NASA Astrophysics Data System (ADS)

    Trinh, Thuat T.; Vlugt, Thijs J. H.; Kjelstrup, Signe

    2014-10-01

    We report a systematic investigation of the thermal conductivity of various three-site models of carbon dioxide (CO2) using nonequilibrium molecular dynamics in the temperature range 300-1000 K and for pressures up to 200 MPa. A direct comparison with experimental data is made. Three popular CO2 force fields (MSM, EPM2, and TraPPE) and two flexible models (based on EPM2) were investigated. All rigid force fields accurately predict the equation of state for carbon dioxide for the given range of variables. They can also reproduce the thermal conductivity of CO2 at room temperature and predict a decrease of the thermal conductivity with increasing temperature. At high temperatures, the rigid models underestimate the thermal conductivity.

  16. PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

    PubMed

    Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

    2015-12-01

    Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins. PMID:26597989

  17. Unstable operations in the Bousfield-Kan spectral sequence for simplicial commutative FF?-algebras

    E-print Network

    Donovan, Michael Jack

    2015-01-01

    In this thesis we study the Bousfield-Kan spectral sequence (BKSS) in the Quillen model category sCom of simplicial commutative FF? -algebras. We develop a theory of unstable operations for this BKSS and relate these ...

  18. 78 FR 60306 - Aquatic Nuisance Species Task Force Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-01

    ...FXFR133609ANS09-FF09F14000-134] Aquatic Nuisance Species Task Force Meeting AGENCY...Service, announce a public meeting of the Aquatic Nuisance Species (ANS) Task Force...prevent introduction and dispersal of aquatic invasive species (AIS); to...

  19. Transferable force field for equilibrium and transport properties in linear, branched, and bifunctional amines I. Primary amines.

    PubMed

    Orozco, Gustavo A; Nieto-Draghi, Carlos; Mackie, Allan D; Lachet, Véronique

    2011-12-15

    A new anisotropic united atom (AUA4) force field is developed to predict the phase equilibrium and transport properties of different primary amines. The force field transferability was studied for an important set of molecules, including linear amines (methyl, ethyl, n-propyl, and n-hexylamine), branched amines (isopropyl and isobutylamine), and bifunctional amines (ethylenediamine, 1,3-propanediamine, and 1,5-pentanediamine). Monte Carlo simulations in the Gibbs ensemble were carried out to study thermodynamic properties such as equilibrium densities, vaporization enthalpies, and vapor pressures. Critical coordinates (critical density, critical temperature, and critical pressure) and normal boiling points were also calculated. The shear viscosity coefficients were studied for methyl, ethyl, and n-propylamine at different temperatures using molecular dynamics. Our results show a very good agreement with experimental values for thermodynamic properties and are an improvement on the models available in the literature, all of which are all-atom. Viscosity coefficients also show a good agreement compared with experimental data, demonstrating the transferability of our force field not only to predict thermodynamic properties but also to predict transport properties. PMID:22034922

  20. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes.

    PubMed

    MacDermaid, Christopher M; Kashyap, Hemant K; DeVane, Russell H; Shinoda, Wataru; Klauda, Jeffery B; Klein, Michael L; Fiorin, Giacomo

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes. PMID:26723629

  1. Specific features of the thermal electromotive force in Bi quantum wires in transverse magnetic and electric fields

    NASA Astrophysics Data System (ADS)

    Sinyavskii, E. P.; Solovenko, V. G.

    2014-11-01

    The thermal electromotive force (emf) in Bi quantum wires has been calculated in the model of potential in the form of a paraboloid of revolution in a uniform magnetic field H, which is normal to the axis of the studied nanostructure, and in a direct-current (dc) electric field E ? H. It has been shown that, with an increase in E, the thermal emf ?xx is described by a nonmonotonic function at different values of H. A physical interpretation of this behavior of ?xx as a function of E is proposed with account for the interaction between carriers and the rough surface of the nanowire.

  2. Empirical modeling of 3-D force-balanced plasma and magnetic field structures during substorm growth phase

    NASA Astrophysics Data System (ADS)

    Yue, Chao; Wang, Chih-Ping; Nishimura, Yukitoshi; Murphy, Kyle R.; Xing, Xiaoyan; Lyons, Larry; Henderson, Michael; Angelopoulos, Vassilis; Lui, A. T. Y.; Nagai, Tsugunobu

    2015-08-01

    Accurate evaluation of the physical processes during the substorm growth phase, including formation of field-aligned currents (FACs), isotropization by current sheet scattering, instabilities, and ionosphere-magnetosphere connection, relies on knowing the realistic three-dimensional (3-D) magnetic field configuration, which cannot be reliably provided by current available empirical models. We have established a 3-D substorm growth phase magnetic field model, which is uniquely constructed from empirical plasma sheet pressures under the constraint of force balance. We investigated the evolution of model pressure and magnetic field responding to increasing energy loading and their configurations under different solar wind dynamic pressure (PSW) and sunspot number. Our model reproduces the typical growth phase evolution signatures: plasma pressure increases, magnetic field lines become more stretched, current sheet becomes thinner, and the Region 2 FACs are enhanced. The model magnetic fields agree quantitatively well with observed fields. The magnetic field is substantially more stretched under higher PSW, while the dependence on sunspot number is nonlinear and less substantial. By applying our modeling to a substorm event, we found that (1) the equatorward movement of proton aurora during the growth phase is mainly due to continuous stretching of magnetic field lines, (2) the ballooning instability is more favorable during late growth phase around midnight tail where there is a localized plasma beta peak, and (3) the equatorial mapping of the breakup auroral arc is at X~-14 RE near midnight, coinciding with the location of the maximum growth rate for the ballooning instability.

  3. "Atypical" chronic wasting disease in PRNP genotype 225FF mule deer.

    PubMed

    Wolfe, Lisa L; Fox, Karen A; Miller, Michael W

    2014-07-01

    We compared mule deer (Odocoileus hemionus) of two different PRNP genotypes (225SS, 225FF) for susceptibility to chronic wasting disease (CWD) in the face of environmental exposure to infectivity. All three 225SS deer had immunohistochemistry (IHC)-positive tonsil biopsies by 710 days postexposure (dpe), developed classic clinical signs by 723-1,200 dpe, and showed gross and microscopic pathology, enzyme-linked immunosorbent assay (ELISA) results, and IHC staining typical of prion disease in mule deer. In contrast, although all three 225FF deer also became infected, the two individuals surviving >720 dpe had consistently negative biopsies, developed more-subtle clinical signs of CWD, and died 924 or 1,783 dpe. The 225FF deer were "suspect" by ELISA postmortem but showed negative or equivocal IHC staining of lymphoid tissues; both clinically affected 225FF deer had spongiform encephalopathy in the absence of IHC staining in the brain tissue. The experimental cases resembled three cases encountered among five additional captive 225FF deer that were not part of our experiment but also died from CWD. Aside from differences in clinical disease presentation and detection, 225FF mule deer also showed other, more-subtle, atypical traits that may help to explain the rarity of this genotype in natural populations, even in the presence of enzootic CWD. PMID:24807352

  4. Optical force on a discrete invisibility cloak in time-dependent fields

    SciTech Connect

    Chaumet, Patrick C.; Zolla, Frederic; Nicolet, Andre; Belkebir, Kamal; Rahmani, Adel

    2011-09-15

    We study, in time domain, the exchange of momentum between an electromagnetic pulse and a three-dimensional, discrete, spherical invisibility cloak. We find that a discrete cloak, initially at rest, would experience an electromagnetic force due to the pulse but would acquire zero net momentum and net displacement. On the other hand, we find that while the cloak may manage to conceal an object and shroud it from the electromagnetic forces associated with the pulse, the cloak itself can experience optomechanical stress on a scale much larger than the object would in the absence of the cloak. We also consider the effects of material dispersion and losses on the electromagnetic forces experienced by the cloak and show that they lead to a transfer of momentum from the pulse to the cloak.

  5. Suppression of magnetic levitation force in melt-textured YBa2Cu3O7-x superconductors by a transverse AC magnetic field

    NASA Astrophysics Data System (ADS)

    Rudnev, I. A.; Ermolaev, Yu S.

    2008-02-01

    We have studied experimentally the influence of transverse ac magnetic fields on the levitation force arising between a permanent NdFeB magnet and a bulk melt-textured HTSC YBCO superconducting sample. The axes of superconducting disc and cylindrical magnet were coinciding while the transverse ac magnetic field generated by resistive coil was directed parallel to surface of a disc i.e., perpendicular to the disc axis. We found that application of both impulse and alternative transverse magnetic fields results in suppression of the value of levitation force and its relaxation rate. Namely, the variable magnetic field with amplitude 12 mT, that approximately in 20 times is less than field of a constant magnet, causes suppression of force more than twice. Monotonous behavior of value of levitation force reduction with the increase in transverse magnetic field amplitude was observed. The possible origin of observed phenomenon is discussed.

  6. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

    PubMed

    Mobley, David L; Dumont, Elise; Chodera, John D; Dill, Ken A

    2007-03-01

    In molecular simulations with fixed-charge force fields, the choice of partial atomic charges influences numerous computed physical properties, including binding free energies. Many molecular mechanics force fields specify how nonbonded parameters should be determined, but various choices are often available for how these charges are to be determined for arbitrary small molecules. Here, we compute hydration free energies for a set of 44 small, neutral molecules in two different explicit water models (TIP3P and TIP4P-Ew) to examine the influence of charge model on agreement with experiment. Using the AMBER GAFF force field for nonbonded parameters, we test several different methods for obtaining partial atomic charges, including two fast methods exploiting semiempirical quantum calculations and methods deriving charges from the electrostatic potentials computed with several different levels of ab initio quantum calculations with and without a continuum reaction field treatment of solvent. We find that the best charge sets give a root-mean-square error from experiment of roughly 1 kcal/mol. Surprisingly, agreement with experimental hydration free energies does not increase substantially with increasing level of quantum theory, even when the quantum calculations are performed with a reaction field treatment to better model the aqueous phase. We also find that the semiempirical AM1-BCC method for computing charges works almost as well as any of the more computationally expensive ab initio methods and that the root-mean-square error reported here is similar to that for implicit solvent models reported in the literature. Further, we find that the discrepancy with experimental hydration free energies grows substantially with the polarity of the compound, as does its variation across theory levels. PMID:17291029

  7. Forces acting on a small particle in an acoustical field in a thermoviscous fluid

    E-print Network

    Karlsen, Jonas Tobias

    2015-01-01

    We present a theoretical analysis of the acoustic radiation force on a single small particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Our analysis places no restrictions on the length scales of the viscous and thermal boundary layer thicknesses $\\delta_\\mathrm{s}$ and $\\delta_\\mathrm{t}$ relative to the particle radius $a$, but it assumes the particle to be small in comparison to the acoustic wavelength $\\lambda$. This is the limit relevant to scattering of sound and ultrasound waves from micrometer-sized particles. For particles of size comparable to or smaller than the boundary layers, the thermoviscous theory leads to profound consequences for the acoustic radiation force. Not only do we predict forces orders of magnitude larger than expected from ideal-fluid theory, but for certain relevant choices of materials, we also find a sign change in the acoustic radiation force on different-sized but otherwise identical parti...

  8. Field measurements of interactions between furnaces and forced air distribution systems

    E-print Network

    to distribute this energy throughout the house (forced air ducts, hot water radiators, radiant panels etc This work was supported by the Assistant Secretary for Energy Efficiency and Renewable Energy of the U.S. Department of Energy, Office of Building Technologies, Existing Buildings Energy Research Program

  9. Forces acting on a small particle in an acoustical field in a thermoviscous fluid

    NASA Astrophysics Data System (ADS)

    Karlsen, Jonas T.; Bruus, Henrik

    2015-10-01

    We present a theoretical analysis of the acoustic radiation force on a single small spherical particle, either a thermoviscous fluid droplet or a thermoelastic solid particle, suspended in a viscous and heat-conducting fluid medium. Within the perturbation assumptions, our analysis places no restrictions on the length scales of the viscous and thermal boundary-layer thicknesses ?s and ?t relative to the particle radius a , but it assumes the particle to be small in comparison to the acoustic wavelength ? . This is the limit relevant to scattering of ultrasound waves from nanometer- and micrometer-sized particles. For particles of size comparable to or smaller than the boundary layers, the thermoviscous theory leads to profound consequences for the acoustic radiation force. Not only do we predict forces orders of magnitude larger than expected from ideal-fluid theory, but for certain relevant choices of materials, we also find a sign change in the acoustic radiation force on different-sized but otherwise identical particles. These findings lead to the concept of a particle-size-dependent acoustophoretic contrast factor, highly relevant to acoustic separation of microparticles in gases, as well as to handling of nanoparticles in lab-on-a-chip systems.

  10. A purely ab initio spectroscopic quality quartic force field for acetylene Jan M. L. Martin

    E-print Network

    Martin, Jan M.L.

    fundamentals for HCCH, HCCD, DCCD, H13 CCH, and H13 C13 CH with a mean absolute error of 1.3 cm 1 absolute error MAE of about 3 cm 1 . The starting point for these refinements was the older 1976 force does not obey cylindrical symmetry relationships for linear molecules, and therefore is not physical

  11. Self-force via $m$-mode regularization and 2+1D evolution: III. Gravitational field on Schwarzschild spacetime

    E-print Network

    Sam R. Dolan; Leor Barack

    2012-11-19

    This is the third in a series of papers aimed at developing a practical time-domain method for self-force calculations in Kerr spacetime. The key elements of the method are (i) removal of a singular part of the perturbation field with a suitable analytic "puncture", (ii) decomposition of the perturbation equations in azimuthal ($m$-)modes, taking advantage of the axial symmetry of the Kerr background, (iii) numerical evolution of the individual $m$-modes in 2+1-dimensions with a finite difference scheme, and (iv) reconstruction of the local self-force from the mode sum. Here we report a first implementation of the method to compute the gravitational self-force. We work in the Lorenz gauge, solving directly for the metric perturbation in 2+1-dimensions. The modes $m=0,1$ contain nonradiative pieces, whose time-domain evolution is hampered by certain gauge instabilities. We study this problem in detail and propose ways around it. In the current work we use the Schwarzschild geometry as a platform for development; in a forthcoming paper---the fourth in the series---we apply our method to the gravitational self-force in Kerr geometry.

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

    PubMed

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

    2011-07-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs. PMID:21609950

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

    PubMed Central

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

    2011-01-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs. PMID:21609950

  14. Observation of the orientation of membrane protein crystals grown in high magnetic force fields

    NASA Astrophysics Data System (ADS)

    Numoto, Nobutaka; Shimizu, Ken-ichi; Matsumoto, Kazuya; Miki, Kunio; Kita, Akiko

    2013-03-01

    Crystallization of membrane proteins in magnetic fields is thought to reveal the magnetic orientations of crystals, and is expected to enhance crystal quality for X-ray crystallographic analysis. The light-harvesting complex 2 (LH2) from a photosynthetic bacterium, Thermochromatium tepidum was crystallized in steep-gradient magnetic fields. The rod-shaped crystals of LH2 grown in the magnetic fields were oriented parallel to the magnetic field direction. An X-ray diffraction experiment indicated that the overall R value and crystal mosaicity are improved for the magnetically oriented crystal, and the helix bundles of LH2 were located parallel to the magnetic field direction in the crystal packing.

  15. Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A

    PubMed Central

    Davis, Joseph E.; Patel, Sandeep

    2009-01-01

    Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modelled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, headgroup orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation, since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties. PMID:19526999

  16. Electromagnetic Forces of High- T c Superconducting Coated Conductor Coils Subjected to Sinusoidal Traveling Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Li, Jing; Yen, Fei; Zheng, Shijun; Wang, Suyu

    2014-01-01

    In order to optimize the structure of high temperature superconducting coils for linear motor applications, three separate coils with different shapes made of Re-BCO coated conductor were studied: circular shaped single pancake, circular shaped double-pancake and racetrack shaped single-pancake. The thrust and vertical forces of the three coils above a conventional flat linear three-phases winding were investigated experimentally. With the aid of the experimentally obtained values, it was found that single-pancake coil in the shape of a racetrack was the best selection for a flat single-sided linear motor system. Studies were also made on the frequency characteristics of the vertical force of the racetrack shaped single-pancake coil.

  17. Analytic cubic and quartic force fields using density-functional theory

    SciTech Connect

    Ringholm, Magnus; Gao, Bin; Thorvaldsen, Andreas J.; Ruud, Kenneth; Jonsson, Dan; High Performance Computing Group, University of Tromsø—The Arctic University of Norway, 9037 Tromsø ; Bast, Radovan; Ekström, Ulf; Helgaker, Trygve

    2014-01-21

    We present the first analytic implementation of cubic and quartic force constants at the level of Kohn–Sham density-functional theory. The implementation is based on an open-ended formalism for the evaluation of energy derivatives in an atomic-orbital basis. The implementation relies on the availability of open-ended codes for evaluation of one- and two-electron integrals differentiated with respect to nuclear displacements as well as automatic differentiation of the exchange–correlation kernels. We use generalized second-order vibrational perturbation theory to calculate the fundamental frequencies of methane, ethane, benzene, and aniline, comparing B3LYP, BLYP, and Hartree–Fock results. The Hartree–Fock anharmonic corrections agree well with the B3LYP corrections when calculated at the B3LYP geometry and from B3LYP normal coordinates, suggesting that the inclusion of electron correlation is not essential for the reliable calculation of cubic and quartic force constants.

  18. Effect of self-consistent magnetic field on plasma sheet penetration to the inner magnetosphere under enhanced convection: RCM simulations combined with force-balance magnetic field solver

    NASA Astrophysics Data System (ADS)

    Gkioulidou, M.; Wang, C.; Lyons, L. R.; Wolf, R. A.

    2010-12-01

    Transport of plasma sheet particles into the inner magnetosphere is strongly affected by the penetration of the convection electric field, which is the result of the large-scale magnetosphere-ionosphere electromagnetic coupling. This transport, on the other hand, results in plasma heating and magnetic field stretching, which become very significant in the inner plasma sheet (inside 20 RE). We have previously run simulations with the Rice Convection Model (RCM) to investigate how the earthward penetration of convection electric field, and therefore plasma sheet population, depends on plasma sheet boundary conditions. Outer boundary conditions at r ~20 RE are a function of MLT and interplanetary conditions based on 11 years of Geotail data. In the previous simulations, Tsyganenko 96 magnetic field model (T96) was used so force balance between plasma pressure and magnetic fields was not maintained. We have now integrated the RCM with a magnetic field solver (Liu et al., 2006) to obtain the required force balance in the equatorial plane. We have run the self-consistent simulations under enhanced convection with different boundary conditions in which we kept different parameters (flux tube particle content, plasma pressure, plasma beta, or magnetic fields) at the outer boundary to be MLT-dependent but time independent. Different boundary conditions result in qualitatively similar plasma sheet profiles. The results show that magnetic field has a dawn dusk asymmetry with field lines being more stretched in the pre-midnight sector, due to relatively higher plasma pressure there. The asymmetry in the magnetic fields in turn affects the radial distance and MLT of plasma sheet penetration into the inner magnetosphere. In comparison with results using the T96, plasma transport under self-consistent magnetic field results in proton and electron plasma sheet inner edges that are located in higher latitudes, weaker pressure gradients, and more efficient shielding of the near-Earth convection electric field (since auroral conductance is also confined to higher latitudes). We are currently evaluating the simulated plasma sheet properties by comparing them with statistical results obtained from Geotail and THEMIS observations.

  19. Assessment of Standard Force Field Models against High-Quality ab initio Potential Curves for Prototypes of pi-pi, CH/pi, and SH/pi Interactions

    SciTech Connect

    Sumpter, Bobby G; Sherrill, David; Sinnokrot, Mutasem O; Marshall, Michael S.; Hohenstein, Edward G.; Walker, Ross; Gould, Ian R

    2009-01-01

    Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechani- cal potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH4 complex, and the benzene-H2S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions)are employed for the empirical force fields.

  20. The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

    NASA Astrophysics Data System (ADS)

    Liu, Minxian; Wang, Yan

    2012-01-01

    In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.