Science.gov

Sample records for force field ff

  1. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.

    PubMed

    Ye, Wei; Ji, Dingjue; Wang, Wei; Luo, Ray; Chen, Hai-Feng

    2015-05-26

    Over 40% of eukaryotic proteomic sequences have been predicted to be intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) and confirmed to be associated with many diseases. However, widely used force fields cannot well reproduce the conformers of IDPs. Previously the ff99IDPs force field was released to simulate IDPs with CMAP energy corrections for the eight disorder-promoting residues. In order to further confirm the performance of ff99IDPs, three representative IDP systems (arginine-rich HIV-1 Rev, aspartic proteinase inhibitor IA3, and α-synuclein) were used to test and evaluate the simulation results. The results show that for free disordered proteins, the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements and better than those from ff99SBildn. Thus, ff99IDPs can sample more clusters of disordered conformers than ff99SBildn. For structural proteins, both ff99IDPs and ff99SBildn can well reproduce the conformations. In general, ff99IDPs can successfully be used to simulate the conformations of IDPs and IDRs in both bound and free states. However, relative errors could still be found at the boundaries of ordered residues scattered in long disorder-promoting sequences. Therefore, polarizable force fields might be one of the possible ways to further improve the performance on IDPs. PMID:25919886

  2. eReaxFF: A Pseudoclassical Treatment of Explicit Electrons within Reactive Force Field Simulations.

    PubMed

    Islam, Md Mahbubul; Kolesov, Grigory; Verstraelen, Toon; Kaxiras, Efthimios; van Duin, Adri C T

    2016-08-01

    We present a computational tool, eReaxFF, for simulating explicit electrons within the framework of the standard ReaxFF reactive force field method. We treat electrons explicitly in a pseudoclassical manner that enables simulation several orders of magnitude faster than quantum chemistry (QC) methods, while retaining the ReaxFF transferability. We delineate here the fundamental concepts of the eReaxFF method and the integration of the Atom-condensed Kohn-Sham DFT approximated to second order (ACKS2) charge calculation scheme into the eReaxFF. We trained our force field to capture electron affinities (EA) of various species. As a proof-of-principle, we performed a set of molecular dynamics (MD) simulations with an explicit electron model for representative hydrocarbon radicals. We establish a good qualitative agreement of EAs of various species with experimental data, and MD simulations with eReaxFF agree well with the corresponding Ehrenfest dynamics simulations. The standard ReaxFF parameters available in the literature are transferrable to the eReaxFF method. The computationally economic eReaxFF method will be a useful tool for studying large-scale chemical and physical systems with explicit electrons as an alternative to computationally demanding QC methods. PMID:27399177

  3. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

    PubMed

    Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

    2014-01-14

    The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development. PMID:26579910

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

    PubMed Central

    Vanommeslaeghe, K.; MacKerell, A. D.

    2012-01-01

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

  5. The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation

    PubMed Central

    Spasic, Aleksandar; Serafini, John; Mathews, David H.

    2012-01-01

    The ability of the Amber ff99 force field to predict relative free energies of RNA helix formation was investigated. The test systems were three hexaloop RNA hairpins with identical loops and varying stems. The potential of mean force of stretching the hairpins from the native state to an extended conformation was calculated with umbrella sampling. Because the hairpins have identical loop sequence, the differences in free energy changes are only from the stem composition. The Amber ff99 force field was able to correctly predict the order of stabilities of the hairpins, although the magnitude of the free energy change is larger than that determined by optical melting experiments. The two measurements cannot be compared directly because the unfolded state in the optical melting experiments is a random coil, while the end state in the umbrella sampling simulations was an elongated chain. The calculations can be compared to reference data by using a thermodynamic cycle. By applying the thermodynamic cycle to the transitions between the hairpins using simulations and nearest neighbor data, agreement was found to be within the sampling error of simulations, thus demonstrating that ff99 force field is able to accurately predict relative free energies of RNA helix formation. PMID:23112748

  6. 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 α-helical and β-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

  7. 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 α-helical and β-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

  8. Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

    PubMed

    Zheng, Mo; Li, Xiaoxia; Guo, Li

    2013-04-01

    Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. PMID:23454611

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

    NASA Astrophysics Data System (ADS)

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

    2005-07-01

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

  10. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    PubMed

    Müller, Julian; Hartke, Bernd

    2016-08-01

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach. PMID:27415976

  11. 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

  12. The ReaxFF reactive force-field: Development, applications, and future directions

    DOE PAGESBeta

    Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; Kylasa, Sudhir; Zheng, Yuanzia; Shin, Yun Kyung; Junkermeier, Chad; Engel-Herbert, Roman; Janik, Michael J.; Aktulga, Hasan Metin; et al

    2016-03-04

    The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

  13. 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

  14. ReaxFF Reactive Force-Field Modeling of the Triple-Phase Boundary in a Solid Oxide Fuel Cell.

    PubMed

    Merinov, Boris V; Mueller, Jonathan E; van Duin, Adri C T; An, Qi; Goddard, William A

    2014-11-20

    In our study, the Ni/YSZ ReaxFF reactive force field was developed by combining the YSZ and Ni/C/H descriptions. ReaxFF reactive molecular dynamics (RMD) were applied to model chemical reactions, diffusion, and other physicochemical processes at the fuel/Ni/YSZ interface. The ReaxFF RMD simulations were performed on the H2/Ni/YSZ and C4H10/Ni/YSZ triple-phase boundary (TPB) systems at 1250 and 2000 K, respectively. The simulations indicate amorphization of the Ni surface, partial decohesion (delamination) at the interface, and coking, which have indeed all been observed experimentally. They also allowed us to derive the mechanism of the butane conversion at the Ni/YSZ interface. Many steps of this mechanism are similar to the pyrolysis of butane. The products obtained in our simulations are the same as those in experiment, which indicates that the developed ReaxFF potential properly describes complex physicochemical processes, such as the oxide-ion diffusion, fuel conversion, water formation reaction, coking, and delamination, occurring at the TPB and can be recommended for further computational studies of the fuel/electrode/electrolyte interfaces in a SOFC. PMID:26276491

  15. 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

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

    PubMed

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

    2012-12-21

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

  17. 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

  18. Improved ReaxFF force field parameters for Au-S-C-H systems.

    PubMed

    Bae, Gyun-Tack; Aikens, Christine M

    2013-10-10

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

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

    PubMed Central

    2014-01-01

    We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

  20. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

    PubMed

    Debiec, Karl T; Cerutti, David S; Baker, Lewis R; Gronenborn, Angela M; Case, David A; Chong, Lillian T

    2016-08-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides-all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  1. Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

    PubMed Central

    2016-01-01

    We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

  2. QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

    PubMed

    Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

    2015-05-15

    QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. PMID:25740170

  3. 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.

  4. 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

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

    PubMed

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

    2010-09-01

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

  6. Study of ice cluster impacts on amorphous silica using the ReaxFF reactive force field molecular dynamics simulation method

    NASA Astrophysics Data System (ADS)

    Rahnamoun, A.; van Duin, A. C. T.

    2016-03-01

    We study the dynamics of the collisions between amorphous silica structures and amorphous and crystal ice clusters with impact velocities of 1 km/s, 4 km/s, and 7 km/s using the ReaxFF reactive molecular dynamics simulation method. The initial ice clusters consist of 150 water molecules for the amorphous ice cluster and 128 water molecules for the crystal ice cluster. The ice clusters are collided on the surface of amorphous fully oxidized and suboxide silica. These simulations show that at 1 km/s impact velocities, all the ice clusters accumulate on the surface and at 4 km/s and 7 km/s impact velocities, some of the ice cluster molecules bounce back from the surface. At 4 km/s and 7 km/s impact velocities, few of the water molecules dissociations are observed. The effect of the second ice cluster impacts on the surfaces which are fully covered with ice, on the mass loss/accumulation is studied. These studies show that at 1 km/s impacts, the entire ice cluster accumulates on the surface at both first and second ice impacts. At higher impact velocities, some ice molecules which after the first ice impacts have been attached to the surface will separate from the surface after the second ice impacts at 7 km/s impact velocity. For the 4 km/s ice cluster impact, ice accumulation is observed for the crystal ice cluster impacts and ice separation is observed for the amorphous ice impacts. Observing the temperatures of the ice clusters during the collisions indicates that the possibility of electron excitement at impact velocities less than 10 km/s is minimal and ReaxFF reactive molecular dynamics simulation can predict the chemistry of these hypervelocity impacts. However, at impact velocities close to 10 km/s the average temperature of the impacting ice clusters increase to about 2000 K, with individual molecules occasionally reaching temperatures of over 8000 K and thus it will be prudent to consider the concept of electron excitation at these higher impact velocities

  7. 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.

  8. 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

  9. Development of a ReaxFF reactive force field for Si/Ge/H systems and application to atomic hydrogen bombardment of Si, Ge, and SiGe (100) surfaces

    NASA Astrophysics Data System (ADS)

    Psofogiannakis, George; van Duin, Adri C. T.

    2016-04-01

    A new reactive force field was developed for use in molecular dynamics simulations of chemical systems composed of silicon (Si), germanium (Ge), and hydrogen (H) with the ReaxFF code. The development incorporated Ge into the ReaxFF family of reactive potentials by fitting against a diverse training set of DFT data that pertain to Si/Ge/H bonding environments. The predictive capacity of the force field was manifested in molecular dynamics simulations of the H atom bombardment of the (100) surface of c-Si, c-Ge, and c-SiGe crystalline solid slabs in order to simulate the effects of the H-plasma semiconductor cleaning process in the near-surface region. Phenomena related to surface and subsurface H adsorption, H2 generation, and surface etching were described and compared in relation to material composition and the kinetic energy of the impinging atoms.

  10. Atomic Insight into the Lithium Storage and Diffusion Mechanism of SiO2/Al2O3 Electrodes of Lithium Ion Batteries: ReaxFF Reactive Force Field Modeling.

    PubMed

    Ostadhossein, Alireza; Kim, Sung-Yup; Cubuk, Ekin D; Qi, Yue; van Duin, Adri C T

    2016-04-01

    Atomically deposited layers of SiO2 and Al2O3 have been recognized as promising coating materials to buffer the volumetric expansion and capacity retention upon the chemo-mechanical cycling of the nanostructured silicon- (Si-) based electrodes. Furthermore, silica (SiO2) is known as a promising candidate for the anode of next-generation lithium ion batteries (LIBs) due to its superior specific charge capacity and low discharge potential similar to Si anodes. In order to describe Li-transport in mixed silica/alumina/silicon systems we developed a ReaxFF potential for Li-Si-O-Al interactions. Using this potential, a series of hybrid grand canonical Monte Carlo (GCMC) and molecular dynamic (MD) simulations were carried out to probe the lithiation behavior of silica structures. The Li transport through both crystalline and amorphous silica was evaluated using the newly optimized force field. The anisotropic diffusivity of Li in crystalline silica cases is demonstrated. The ReaxFF diffusion study also verifies the transferability of the new force field from crystalline to amorphous phases. Our simulation results indicates the capability of the developed force field to examine the energetics and kinetics of lithiation as well as Li transportation within the crystalline/amorphous silica and alumina phases and provide a fundamental understanding on the lithiation reactions involved in the Si electrodes covered by silica/alumina coating layers. PMID:26978039

  11. 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

  12. The Early Universe f2 FF Model of Primordial Magnetic Field at Natural Inflation

    NASA Astrophysics Data System (ADS)

    Almuhammad, Anwar; Lopez-Mobilia, Rafael

    2015-04-01

    We study the simple gauge invariant model f2 FF as a way to generate primordial magnetic fields (PMF) in Natural Inflation (NI). We compute both magnetic and electric spectra generated by the f2 FF model in NI for different values of model parameters and find that both de Sitter and power law expansion lead to the same results at sufficiently large number of e-foldings, as expected. We also find that the necessary scale invariance property of the PMF cannot be obtained in NI in first order of slow roll limits under the constraints derived from the recent BICEP2 results. Furthermore, if these constraints are relaxed to achieve scale invariance, then the model suffers from backreaction problems for almost all values of model parameters. We show that there is a narrow range of the height of the potential Λ around Λmin ~ 0 . 00460MPl and of the commoving wave number k around kmin ~ 5 . 5 ×10-4 , at which the problem of backreaction might be avoided. The value of Λmin lies within the range of Λ compatible with the BICEP2 results. However, the relatively short range of k presents a serious challenge to the viability of this model.

  13. Force field dependence of riboswitch dynamics.

    PubMed

    Hanke, Christian A; Gohlke, Holger

    2015-01-01

    Riboswitches are noncoding regulatory elements that control gene expression in response to the presence of metabolites, which bind to the aptamer domain. Metabolite binding appears to occur through a combination of conformational selection and induced fit mechanism. This demands to characterize the structural dynamics of the apo state of aptamer domains. In principle, molecular dynamics (MD) simulations can give insights at the atomistic level into the dynamics of the aptamer domain. However, it is unclear to what extent contemporary force fields can bias such insights. Here, we show that the Amber force field ff99 yields the best agreement with detailed experimental observations on differences in the structural dynamics of wild type and mutant aptamer domains of the guanine-sensing riboswitch (Gsw), including a pronounced influence of Mg2+. In contrast, applying ff99 with parmbsc0 and parmχOL modifications (denoted ff10) results in strongly damped motions and overly stable tertiary loop-loop interactions. These results are based on 58 MD simulations with an aggregate simulation time>11 μs, careful modeling of Mg2+ ions, and thorough statistical testing. Our results suggest that the moderate stabilization of the χ-anti region in ff10 can have an unwanted damping effect on functionally relevant structural dynamics of marginally stable RNA systems. This suggestion is supported by crystal structure analyses of Gsw aptamer domains that reveal χ torsions with high-anti values in the most mobile regions. We expect that future RNA force field development will benefit from considering marginally stable RNA systems and optimization toward good representations of dynamics in addition to structural characteristics. PMID:25726465

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

    PubMed

    Jaramillo-Botero, Andres; Naserifar, Saber; Goddard, William A

    2014-04-01

    First-principles-based force fields prepared from large quantum mechanical data sets are now the norm in predictive molecular dynamics simulations for complex chemical processes, as opposed to force fields fitted solely from phenomenological data. In principle, the former allow improved accuracy and transferability over a wider range of molecular compositions, interactions, and environmental conditions unexplored by experiments. That is, assuming they have been optimally prepared from a diverse training set. The trade-off has been force field engines that are functionally complex, with a large number of nonbonded and bonded analytical forms that give rise to rather large parameter search spaces. To address this problem, we have developed GARFfield (genetic algorithm-based reactive force field optimizer method), a hybrid multiobjective Pareto-optimal parameter development scheme based on genetic algorithms, hill-climbing routines and conjugate-gradient minimization. To demonstrate the capabilities of GARFfield we use it to develop two very different force fields: (1) the ReaxFF reactive force field for modeling the adiabatic reactive dynamics of silicon carbide growth from an methyltrichlorosilane precursor and (2) the SiC electron force field with effective core pseudopotentials for modeling nonadiabatic dynamic phenomena with highly excited electronic states. The flexible and open architecture of GARFfield enables efficient and fast parallel optimization of parameters from quantum mechanical data sets for demanding applications like ReaxFF, electronic fast forward (or electron force field), and others including atomistic reactive charge-optimized many-body interatomic potentials, Morse, and coarse-grain force fields. PMID:26580361

  15. 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.

  16. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

    PubMed

    Maier, James A; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E; Simmerling, Carlos

    2015-08-11

    Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements. PMID:26574453

  17. Primordial magnetic fields in the f2FF model in large field inflation under de Sitter and power law expansion

    NASA Astrophysics Data System (ADS)

    AlMuhammad, A. S.; Lopez-Mobilia, R.

    2016-03-01

    We use the f2FF model to study the generation of primordial magnetic fields (PMF) in the context of large field inflation (LFI), described by the potential, V ˜ M φp. We compute the magnetic and electric spectra for all possible values of the model parameters under de Sitter and power law expansion. We show that scale invariant PMF are not obtained in LFI to first order in the slow roll approximation, if we impose the constraint V(φ=0)˜ 0. Alternatively, if these constraints are relaxed, the scale invariant PMF can be generated. The associated electric field energy can fall below the energy density of inflation, ρInf for the ranges of comoving wavenumbers, k > 8 × 10-7 Mpc-1 and k > 4 × 10-6 Mpc-1 in de Sitter and power law (PL) expansion. Further, it can drop below ρInf on the ranges, e-foldings N > 51, p<1.66, p >2.03, l_0 > 3 × 105 MPl-1 (H_i < 3.3 × 10-6 MPl), and M > 2.8 × 10-3 MPl. All of the above ranges fit with the observational constraints.

  18. Carbohydrate force fields

    PubMed Central

    Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.

    2014-01-01

    Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813

  19. 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)

  20. Multifactorial global search algorithm in the problem of optimizing a reactive force field

    NASA Astrophysics Data System (ADS)

    Stepanova, M. M.; Shefov, K. S.; Slavyanov, S. Yu.

    2016-04-01

    We present a new multifactorial global search algorithm ( MGSA) and check the operability of the algorithm on the Michalewicz and Rastrigin functions. We discuss the choice of an objective function and additional search criteria in the context of the problem of reactive force field ( ReaxFF) optimization and study the ranking of the ReaxFF parameters together with their impact on the objective function.

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

    SciTech Connect

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

    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.

  2. Force-Field Parameter Fitter

    Energy Science and Technology Software Center (ESTSC)

    2015-05-27

    ParFit is a flexible and extendable framework and library of classes for fitting force-field parameters to data from high-level ab-initio calculations on the basis of deterministic and stochastic algorithms. Currently, the code is fitting MM3 and Merck force-field parameters but could easily extend to other force-field types.

  3. Force field dependent solution properties of glycine oligomers

    PubMed Central

    Drake, Justin A.

    2015-01-01

    Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

  4. Force field-dependent solution properties of glycine oligomers.

    PubMed

    Drake, Justin A; Pettitt, B Montgomery

    2015-06-30

    Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly(3) and Gly(10) in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly(3) and Gly(10) were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

  5. 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.

  6. Development of the CHARMM Force Field for Lipids

    PubMed Central

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

    2011-01-01

    The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990’s to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed. PMID:21760975

  7. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    PubMed

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  8. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields

    PubMed Central

    Vitalini, F.; Noé, F.; Keller, B.G.

    2016-01-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

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

    SciTech Connect

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

    2007-11-01

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

  10. Polarizable Force Field with a σ-Hole for Liquid and Aqueous Bromomethane.

    PubMed

    Adluri, Archita N S; Murphy, Jennifer N; Tozer, Tiffany; Rowley, Christopher N

    2015-10-22

    Bromomethane (CH3Br) is an acutely toxic environmental pollutant that contributes to ozone depletion. Molecular simulation could be a valuable tool for studying its partitioning and transport in the environment if an accurate molecular model was available. The generalized Amber force field (GAFF), OPLS (optimized potentials for liquid simulations) force field, and CHARMM general force field (CGenFF) were tested for their ability to model the physical properties of liquid bromomethane. The OPLS force field was in fairly good agreement with experiment, while CGenFF and GAFF were significantly in error. The Br Lennard-Jones parameters of the GAFF and CGenFF models were reparameterized, but their radial distribution functions still have significant deviations from those calculated by ab initio molecular dynamics (AIMD). A Drude polarizable force field for bromomethane was parametrized with an off-center positively charged site to represent the C-Br σ-hole. This model is in good agreement with the bulk physical properties and the AIMD RDFs. The modest solubility of bromomethane was reproduced by this model, with dispersion interactions being the dominant water-solute interaction. The water-solute electrostatic interactions are a smaller factor in solubility. This model predicts bromomethane to have a 13 kJ mol(-1) surface excess potential at the water-vapor interface. PMID:26419599

  11. Coarse graining of force fields for metal-organic frameworks.

    PubMed

    Dürholt, Johannes P; Galvelis, Raimondas; Schmid, Rochus

    2016-03-14

    We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference. On the example of the copper paddle-wheel based HKUST-1, a maximally coarse grained model, using a single bead for each three and four coordinated vertex, was developed as a proof of concept. By adding non-bonded interactions with a modified Buckingham potential, the resulting MOF-FF-CGNB is able to predict local deformation energies of the building blocks as well as bulk properties like the tbovs.pto energy difference or elastic constants in a semi-quantitative way. As expected, the negative thermal expansion of HKUST-1 is not reproduced by the maximally coarse grained model. At the expense of atomic resolution, substantially larger systems (up to tens of nanometers in size) can be simulated with respect to structural and mechanical properties, bridging the gap to the mesoscale. As an example the deformation of the [111] surface of HKUST-1 by a "tip" could be computed without artifacts from periodic images. PMID:26732756

  12. Atomistic force field for pyridinium-based ionic liquids: reliable transport properties.

    PubMed

    Voroshylova, Iuliia V; Chaban, Vitaly V

    2014-09-11

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cation-anion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove that three parameters per interaction site (atom diameter, depth of potential well, point electrostatic charge) provide a sufficient basis to predict thermodynamics (heat of vaporization, density), structure (radial distributions), and transport (diffusion, viscosity, conductivity) of ILs at room conditions and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia Lopes-Pádua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids. PMID:25144141

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

    NASA Astrophysics Data System (ADS)

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

    2006-07-01

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

  14. 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.

  15. 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.

  16. Force field development and simulations of senior dialkyl sulfoxides.

    PubMed

    Chaban, Vitaly V

    2016-04-21

    Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations. The additive pairwise force field (FF) for EMSO and DESO was proposed for the first time, preserving explicit compatibility with their most known homologue, DMSO. The simulations reveal similar structures and thermodynamic properties of DMSO, DESO and EMSO. However, the transport properties are significantly different: DESO and DMSO are less mobile and an order of magnitude more viscous. Furthermore, dipole reorientation in DESO and EMSO occurs ca. 2-4 times slower than in DMSO at room temperature. This observation favors applications of higher sulfoxides as cryoprotectants and provides a microscopic interpretation of the earlier experimental data. PMID:27031577

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

    NASA Astrophysics Data System (ADS)

    Bai, Xue-Ning; Spitkovsky, Anatoly

    2010-06-01

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

  18. Improved Force Field Parameters Lead to a Better Description of RNA Structure.

    PubMed

    Bergonzo, Christina; Cheatham, Thomas E

    2015-09-01

    We compare the performance of two different RNA force fields in four water models in simulating the conformational ensembles r(GACC) and r(CCCC). With the increased sampling facilitated by multidimensional replica exchange molecular dynamics (M-REMD), populations are compared to NMR data to evaluate force field reliability. The combination of AMBER ff12 with vdW(bb) modifications and the OPC water model produces results in quantitative agreement with the NMR ensemble that have eluded us to date. PMID:26575892

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

    PubMed Central

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

    2014-01-01

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

  20. Conformational dynamics of two natively unfolded fragment peptides: Comparison of the AMBER and CHARMM force fields

    PubMed Central

    Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D.; Shen, Jana

    2015-01-01

    Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly-used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states and dynamics of intrinsically disordered proteins. In this work we compare the three commonly-used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NT9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions. PMID:26020564

  1. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

    PubMed

    Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana

    2015-06-25

    Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions. PMID:26020564

  2. Improving an all-atom force field.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-01

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

  3. A molecular mechanics force field for lignin

    SciTech Connect

    Petridis, Loukas; Smith, Jeremy C

    2009-02-01

    A CHARMM molecular mechanics force field for lignin is derived. Parameterization is based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by the examination of methoxybenzene:water interactions. Dihedral parameters are optimized by fitting to critical rotational potentials and bonded parameters are obtained by optimizing vibrational frequencies and normal modes. Finally, the force field is validated by performing a molecular dynamics simulation of a crystal of a lignin fragment molecule and comparing simulation-derived structural features with experimental results. Together with the existing force field for polysaccharides, this lignin force field will enable full simulations of lignocellulose.

  4. Polarization effects in molecular mechanical force fields.

    PubMed

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

    2009-08-19

    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

  5. 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

  6. Reactive Force Field for Liquid Hydrazoic Acid with Applications to Detonation Chemistry

    NASA Astrophysics Data System (ADS)

    Furman, David; Dubnikova, Faina; van Duin, Adri; Zeiri, Yehuda; Kosloff, Ronnie

    The development of a reactive force field (ReaxFF formalism) for Hydrazoic acid (HN3), a highly sensitive liquid energetic material, is reported. The force field accurately reproduces results of density functional theory (DFT) calculations. The quality and performance of the force field are examined by detailed comparison with DFT calculations related to uni, bi and trimolecular thermal decomposition routes. Reactive molecular dynamics (RMD) simulations are performed to reveal the initial chemical events governing the detonation chemistry of liquid HN3. The outcome of these simulations compares very well with recent results of tight-binding DFT molecular dynamics and thermodynamic calculations. Based on our RMD simulations, predictions were made for the activation energies and volumes in a broad range of temperatures and initial material compressions. Work Supported by The Center of Excellence for Explosives Detection, Mitigation and Response, Department of Homeland Security.

  7. Force Field Development for Lipid Membrane Simulations.

    PubMed

    Lyubartsev, Alexander P; Rabinovich, Alexander L

    2016-10-01

    With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26766518

  8. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations.

    PubMed

    Grimme, Stefan

    2014-10-14

    A black-box type procedure is presented for the generation of molecule-specific, classical potential energy functions (force-field, FF) solely from quantum mechanically (QM) computed input data. The approach can treat covalently bound molecules and noncovalent complexes with almost arbitrary structure. The necessary QM information consists of the equilibrium structure and the corresponding Hessian matrix, atomic partial charges, and covalent bond orders. The FF fit is performed automatically without any further input and yields a specific (nontransferable) potential which very closely resembles the QM reference potential near the equilibrium. The resulting atomistic, fully flexible FF is anharmonic and allows smooth dissociation of covalent bonds into atoms. A newly proposed force-constant-bond-energy relation with little empiricism provides reasonably accurate (about 5-10% error) atomization energies for almost arbitrary diatomic and polyatomic molecules. Intra- and intermolecular noncovalent interactions are treated by using well established and accurate D3 dispersion coefficients, CM5 charges from small basis set QM calculations, and a new interatomic repulsion potential. Particular attention has been paid to the construction of the torsion potentials which are partially obtained from automatic QM-tight-binding calculations for model systems. Detailed benchmarks are presented for conformational energies, atomization energies, vibrational frequencies, gas phase structures of organic molecules, and transition metal complexes. Comparisons to results from standard FF or semiempirical methods reveal very good accuracy of the new potential. While further studies are necessary to validate the approach, the initial results suggest QMDFF as a routine tool for the computation of a wide range of properties and systems (e.g., for molecular dynamics of isolated molecules, explicit solvation, self-solvation (melting) or even for molecular crystals) in particular when standard

  9. 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, α-helices, and β-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 α-helix and β-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 β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-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

  10. 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, α-helices, and β-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 α-helix and β-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 β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-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

  11. 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, α-helices, and β-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 α-helix and β-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 β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-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

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

    PubMed

    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, α-helices, and β-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 α-helix and β-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 β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-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

  13. Static and dynamical Meissner force fields

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  14. The force field for imidazolium-based ionic liquids: Novel anions with polar residues

    NASA Astrophysics Data System (ADS)

    Fileti, Eudes Eterno; Chaban, Vitaly V.

    2015-07-01

    Many molecules can be converted into ions via relatively simple procedures. These ions can be combined into ionic liquids (ILs). 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. All anions were obtained via deprotonation of carboxyl group in analogy with acetate anion. We account for peculiar interactions between the anion and the cation by fitting electrostatic potential for an ion pair, in contrast to isolated ions. Furthermore, we account for hydrogen bonds obtained via electronic structure consideration. The developed model fosters computational investigation of ionic liquids.

  15. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

    PubMed

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

    2012-12-01

    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

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

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-15

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

  17. 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.

  18. Three-Dimensional Force Field Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schwarz, Alexander; Hölscher, Hendrik; Langkat, S. M.; Wiesendanger, R.

    2003-12-01

    A method is presented that utilizes the frequency modulation technique in ultra-high vacuum to measure the tip-sample force field in all three dimensions with atomic resolution. It is based on a systematic procedure to record frequency shift versus distance curves. After their conversion into the tip-surface potential landscape the complete force field in all three dimensions can be calculated. Experimental results obtained in the non-contact regime on NiO(001) with an iron-coated silicon tip are presented to demonstrate that interatomic vertical and lateral forces can be determined and assigned to specific sites within the surface unit cell.

  19. Lipid14: The Amber Lipid Force Field.

    PubMed

    Dickson, Callum J; Madej, Benjamin D; Skjevik, Age A; Betz, Robin M; Teigen, Knut; Gould, Ian R; Walker, Ross C

    2014-02-11

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

  20. Controlling Casimir force via coherent driving field

    NASA Astrophysics Data System (ADS)

    Ahmad, Rashid; Abbas, Muqaddar; Ahmad, Iftikhar; Qamar, Sajid

    2016-04-01

    A four level atom-field configuration is used to investigate the coherent control of Casimir force between two identical plates made up of chiral atomic media and separated by vacuum of width d. The electromagnetic chirality-induced negative refraction is obtained via atomic coherence. The behavior of Casimir force is investigated using Casimir-Lifshitz formula. It is noticed that Casimir force can be switched from repulsive to attractive and vice versa via coherent control of the driving field. This switching feature provides new possibilities of using the repulsive Casimir force in the development of new emerging technologies, such as, micro-electro-mechanical and nano-electro-mechanical systems, i.e., MEMS and NEMS, respectively.

  1. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields.

    PubMed

    Zgarbová, Marie; Rosnik, Andreana M; Luque, F Javier; Curutchet, Carles; Jurečka, Petr

    2015-09-30

    Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary. PMID:26224547

  2. 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

  3. 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

  4. Parametric Study of ReaxFF Simulation Parameters for Molecular Dynamics Modeling of Reactive Carbon Gases.

    PubMed

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

    2012-09-11

    The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions. PMID:26605713

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

    PubMed Central

    Peters, Martin B.; Yang, Yue; Wang, Bing; Füsti-Molnár, László; Weaver, Michael N.; Merz, Kenneth M.

    2010-01-01

    Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262–8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement. PMID:20856692

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  7. Reactive force field development for magnesium chloride hydrates and its application for seasonal heat storage.

    PubMed

    Pathak, Amar Deep; Nedea, Silvia; van Duin, Adri C T; Zondag, Herbert; Rindt, Camilo; Smeulders, David

    2016-06-21

    MgCl2 hydrates are considered as high-potential candidates for seasonal heat storage materials. These materials have high storage capacity and fast dehydration kinetics. However, as a side reaction to dehydration, hydrolysis may occur. Hydrolysis is an irreversible reaction, which produces HCl gas thus affecting the durability of heat storage systems. In this study, we present the parameterization of a reactive force field (ReaxFF) for MgCl2 hydrates to study the dehydration and hydrolysis kinetics of MgCl2·H2O and MgCl2·2H2O. The ReaxFF parameters have been derived by training against quantum mechanics data obtained from Density Functional Theory (DFT) calculations consisting of bond dissociation curves, angle bending curves, reaction enthalpies, and equation of state. A single-parameter search algorithm in combination with a Metropolis Monte Carlo algorithm is successfully used for this ReaxFF parameterization. The newly developed force field is validated by examining the elastic properties of MgCl2 hydrates and the proton transfer reaction barrier, which is important for the hydrolysis reaction. The bulk moduli of MgCl2·H2O and MgCl2·2H2O obtained from ReaxFF are in close agreement with the bulk moduli obtained from DFT. A barrier of 20.24 kcal mol(-1) for the proton transfer in MgCl2·2H2O is obtained, which is in good agreement with the barrier (19.55 kcal mol(-1)) obtained from DFT. Molecular dynamics simulations using the newly developed ReaxFF on 2D-periodic slabs of MgCl2·H2O and MgCl2·2H2O show that the dehydration rate increases more rapidly with temperature in MgCl2·H2O than in MgCl2·2H2O, in the temperature range 300-500 K. The onset temperature of HCl formation, a crucial design parameter in seasonal heat storage systems, is observed at 340 K for MgCl2·H2O, which is in agreement with experiments. The HCl formation is not observed for MgCl2·2H2O. The diffusion coefficient of H2O through MgCl2·H2O is lower than through MgCl2·2H2O, and can

  8. Sultan - forced flow, high field test facility

    SciTech Connect

    Horvath, I.; Vecsey, G.; Weymuth, P.; Zellweger, J.

    1981-09-01

    Three European laboratories: CNEN (Frascati, I) ECN (Petten, NL) and SIN (Villigen, CH) decided to coordinate their development efforts and to install a common high field forced flow test facility at Villigen Switzerland. The test facility SULTAN (Supraleiter Testanlage) is presently under construction. As a first step, an 8T/1m bore solenoid with cryogenic periphery will be ready in 1981. The cryogenic system, data acquisition system and power supplies which are contributed by SIN are described. Experimental feasibilities, including cooling, and instrumentation are reviewed. Progress of components and facility construction is described. Planned extension of the background field up to 12T by insert coils is outlined. 5 refs.

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

    PubMed

    Grubišić, Sonja; Brancato, Giuseppe; Pedone, Alfonso; Barone, Vincenzo

    2012-11-28

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

  10. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.

    PubMed

    Fluitt, Aaron M; de Pablo, Juan J

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation. PMID:26331258

  11. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    SciTech Connect

    Fluitt, Aaron M.; de Pablo, Juan J.

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  12. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    PubMed Central

    Fluitt, Aaron M.; de Pablo, Juan J.

    2015-01-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB∗, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation. PMID:26331258

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

    PubMed

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

    2014-09-25

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

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  16. 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.

  17. 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.

  18. 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 β-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

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

    PubMed

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

    2014-08-01

    A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I-NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H2O, formamide, and imidazole molecular fragments and their complexes with the Mg(2+) cation. Reference data obtained from ab initio calculations using an auc-cc-pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available. PMID:24965869

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

    PubMed Central

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

    2013-01-01

    Fixed-charge empirical force fields have been developed and widely used over the past three decades for all-atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. While this is generally suitable for single-phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. While nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual-force-field approach (Dual-FF) to address this problem and implemented it in the CHARMM simulation package. This Dual-FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intra-phase interactions and a separate set to represent inter-phase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intra-phase and inter-phase molecular behavior to be accurately and efficiently modeled in the same simulation. PMID:22488548

  2. Electromagnetic unification of matter and force fields

    NASA Astrophysics Data System (ADS)

    John, Sarah

    2004-05-01

    Special relativity and quantum mechanics are descriptive of electromagnetic propagation in waveguides, with mass analogous to the cutoff frequency of a waveguide mode [S.John, Bull.Am.Phys.Soc. vol.39,no.2,1254 (1994)]. It is further postulated herein that all spin 1/2 matter (necessarily massive) and spin 1 force fields have their origin in the electromagnetic fields E and B. This concept is not new. Majorana, among others have obtained electromagnetic representations of Dirac-like equations valid for the zero-mass case. Here, the spinor representation of the Maxwell equations, as given by Sallhofer, is extended to oscillatory fields with propagation constant m to obtain, in the absence of charge and current densities, the coupled equation (M. hatp + β E)ψ = 0 , where M = diag[ M σ, M^* σ ] , β = offdiag[I,I] , ψ ^ = i ^dag ( σ. B0 ( p), σ. E_0(p)), and M=m+ip, with the energy-mass relation given by E^2 = M M . Further, it is shown that the interaction term of QED is a direct consequence of including the sources and currents of Maxwell equations. Qualitative field patterns for spin 1/2 and spin 1 states, such as the electron, neutrino, magnetic monopole, quarks, photon, and massive gauge bosons are suggested.

  3. Cosmic Ray Acceleration in Force Free Fields

    NASA Astrophysics Data System (ADS)

    Colgate, Stirling; Li, Hui; Kronberg, Philipp

    2002-11-01

    Galactic, extragalactic, and cluster magnetic fields are in apparent pressure equilibrium with the in-fall pressure of matter from the external medium, IGM, onto the Galaxies and clusters, and from the voids onto the galaxy sheets, (walls), implying fields of 5 , 0.5, & 20 μG respectively. Equipartition or minimum energy, implies β_CR=n_CRm_pc^2/(B^2/8π)˜= 1. The total energy in field and CRs is then ˜= 10^55 ergs Galactic and ˜= 4 ot 10^60 ergs per galaxy in the IGM and less within clusters, e.g., radio lobes, synchrotron "glow" in the IGM (Kronberg), and the UHECRs spectrum, Γ =-2.6. CRs escape from the Galaxy to the IGM, τ˜=10^7y, and similarly from the walls to the voids, ˜=10^8y, less than the GZK cut-off time provided B_galaxy>B_IGM>B_voids. The free energy of black hole formation, The Los Alamos model, is just sufficient. The lack of shocks at the boundaries of over pressured radio lobes and the need for high acceleration efficiency suggests eE_allel˜= eη_reconJ_allel, acceleration by reconnection of these force-free fields.

  4. Reactive Force Field Study of Li/C Systems for Electrical Energy Storage.

    PubMed

    Raju, Muralikrishna; Ganesh, P; Kent, Paul R C; van Duin, Adri C T

    2015-05-12

    Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li-C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphite with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. This is a key step toward modeling of realistic carbon materials for energy applications. PMID:26574418

  5. A reactive force field study of Li/C systems for electrical energy storage

    DOE PAGESBeta

    Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; van Duin, Adri C.T.

    2015-04-02

    Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less

  6. A reactive force field study of Li/C systems for electrical energy storage

    SciTech Connect

    Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; van Duin, Adri C.T.

    2015-04-02

    Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphite with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.

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

    DOE PAGESBeta

    Beste, Ariana

    2014-10-06

    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.

  9. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field.

    PubMed

    Yang, Longhua; Skjevik, Åge A; Han Du, Wen-Ge; Noodleman, Louis; Walker, Ross C; Götz, Andreas W

    2016-09-01

    Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies. PMID:27547799

  10. 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…

  11. Motor imagery facilitates force field learning.

    PubMed

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

    2011-06-13

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

  12. 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.)

  13. 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.

  14. Brief: Field measurements of casing tension forces

    SciTech Connect

    Quigley, M.S.; Lewis, D.B.; Boswell, R.S.

    1995-02-01

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

  15. TOPICAL REVIEW: Polarization effects in molecular mechanical force fields

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

    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.

  16. 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.

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

    PubMed

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

    2013-05-30

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

  18. Ponderomotive Force in the Presence of Electric Fields

    NASA Technical Reports Server (NTRS)

    Khazanov, G. V.; Krivorutsky, E. N.

    2013-01-01

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

  19. Comparison of Cellulose Ib Simulations with Three Carbohydrate Force Fields

    SciTech Connect

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

    2012-02-14

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

  20. PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS

    PubMed Central

    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

    2015-01-01

    We present parmbsc1, a new force-field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (~140 μs) covering most of the DNA structural space. Parmbsc1 provides high quality results in diverse systems, solving problems of previous force-fields. Parmbsc1 aims to be a reference force-field for the study of DNA in the next decade. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/. PMID:26569599

  1. The interoperability force in the ERP field

    NASA Astrophysics Data System (ADS)

    Boza, Andrés; Cuenca, Llanos; Poler, Raúl; Michaelides, Zenon

    2015-04-01

    Enterprise resource planning (ERP) systems participate in interoperability projects and this participation sometimes leads to new proposals for the ERP field. The aim of this paper is to identify the role that interoperability plays in the evolution of ERP systems. To go about this, ERP systems have been first identified within interoperability frameworks. Second, the initiatives in the ERP field driven by interoperability requirements have been identified from two perspectives: technological and business. The ERP field is evolving from classical ERP as information system integrators to a new generation of fully interoperable ERP. Interoperability is changing the way of running business, and ERP systems are changing to adapt to the current stream of interoperability.

  2. 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.

  3. Vibrational spectrum and force field of dimethyldimethoxysilane

    SciTech Connect

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

    1986-01-01

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

  4. 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

  5. Mitigated-force carriage for high magnetic field environments

    SciTech Connect

    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.

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

    DOEpatents

    Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.

    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.

  7. 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.

  8. Force field parameter estimation of functional perfluoropolyether lubricants

    SciTech Connect

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

    2011-01-01

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

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

  10. 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.

  11. 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.

  12. Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants

    SciTech Connect

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

    2011-01-01

    The head disk interface in hard disk drive can be considered one of the hierarchical multiscale systems, which require the hybridization of multiscale modeling methods with coarse-graining procedure. However, the fundamental force field parameters are required to enable the coarse-graining procedure from atomistic/molecular scale to mesoscale models .In this paper, we investigate beyond molecular level and perform ab-initio calculations to obtain the force field parameters. Intramolecular force field parameters for the Zdol and Ztetraolwere 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.

  13. Comparing molecular dynamics force fields in the essential subspace.

    PubMed

    Martín-García, Fernando; Papaleo, Elena; Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2015-01-01

    The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178

  14. Force-Field Compensation in a Manual Tracking Task

    PubMed Central

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

    2010-01-01

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

  15. 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.

  16. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

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

  17. 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

  18. Force-free magnetic fields - The magneto-frictional method

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  19. 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.

  20. Imaging Nanoscale Electromagnetic Near-Field Distributions Using Optical Forces.

    PubMed

    Huang, Fei; Tamma, Venkata Ananth; Mardy, Zahra; Burdett, Jonathan; Wickramasinghe, H Kumar

    2015-01-01

    We demonstrate the application of Atomic Force Microscopy (AFM) for mapping optical near-fields with nanometer resolution, limited only by the AFM probe geometry. By detecting the optical force between a gold coated AFM probe and its image dipole on a glass substrate, we profile the electric field distributions of tightly focused laser beams with different polarizations. The experimentally recorded focal force maps agree well with theoretical predictions based on a dipole-dipole interaction model. We experimentally estimate the aspect ratio of the apex of gold coated AFM probe using only optical forces. We also show that the optical force between a sharp gold coated AFM probe and a spherical gold nanoparticle of radius 15 nm, is indicative of the electric field distribution between the two interacting particles. Photo Induced Force Microscopy (PIFM) allows for background free, thermal noise limited mechanical imaging of optical phenomenon over wide range of wavelengths from Visible to RF with detection sensitivity limited only by AFM performance. PMID:26073331

  1. 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.

  2. Toroidal linear force-free magnetic fields with axial symmetry

    NASA Astrophysics Data System (ADS)

    Vandas, M.; Romashets, E.

    2016-01-01

    Aims: Interplanetary magnetic flux ropes are often described as linear force-free fields. To account for their curvature, toroidal configurations must be used. The aim is to find an analytic description of a linear force-free magnetic field of the toroidal geometry in which the cross section of flux ropes can be controlled. Methods: The solution is found as a superposition of fields given by linear force-free cylinders tangential to a generating toroid. The cylindrical field is expressed in a series of terms that are not all cylindrically symmetric. Results: We found the general form of a toroidal linear force-free magnetic field. The field is azimuthally symmetric with respect to the torus axis. It depends on a set of coefficients that enables controlling the flux rope shape (cross section) to some extent. By varying the coefficients, flux ropes with circular and elliptic cross sections were constructed. Numerical comparison suggests that the simple analytic formula for calculating the helicity in toroidal flux ropes of the circular cross section can be used for flux ropes with elliptic cross sections if the minor radius in the formula is set to the geometric mean of the semi-axes of the elliptic cross section.

  3. 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.

  4. An implicit divalent counterion force field for RNA molecular dynamics

    NASA Astrophysics Data System (ADS)

    Henke, Paul S.; Mak, Chi H.

    2016-03-01

    How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

  5. Additive CHARMM force field for naturally occurring modified ribonucleotides.

    PubMed

    Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D; Nilsson, Lennart

    2016-04-15

    More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. PMID:26841080

  6. Additive CHARMM force field for naturally occurring modified ribonucleotides

    PubMed Central

    Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D.

    2016-01-01

    More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26841080

  7. 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

  8. 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

  9. Simulation of Forces between Humid Amorphous Silica Surfaces: A Comparison of Empirical Atomistic Force Fields

    PubMed Central

    2012-01-01

    Atmospheric humidity strongly influences the interactions between dry granular particles in process containers. To reduce the energy loss in industrial production processes caused by particle agglomeration, a basic understanding of the dependence of particle interactions on humidity is necessary. Hence, in this study, molecular dynamic simulations were carried out to calculate the adhesion between silica surfaces in the presence of adsorbed water. For a realistic description, the choice of force field is crucial. Because of their frequent use and transferability to biochemical systems, the Clay and CWCA force fields were investigated with respect to their ability to describe the water–silica interface in comparison to the more advanced Reax force field, ab initio calculations, and experiments. PMID:23378869

  10. Scattered field generation and optical forces in transformation optics

    NASA Astrophysics Data System (ADS)

    Novitsky, A. V.

    2016-04-01

    In this paper we develop an approach for making various scattered electromagnetic fields on the transformation-optics ground. To do so, we use the a special coordinate transformation from the a vacuum virtual space to physical space, which changes the boundary of the scattering device upon transformation. We explore this approach for small scatterers compared with radiation wavelength, which allows us to predict the arbitrarily directed optical forces. Obtaining scattered fields and optical forces can be useful in nano-optics and optical micromanipulation.

  11. 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).

  12. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    SciTech Connect

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L.; MacKerell, Alexander D.; Klauda, Jeffery B.; Im, Wonpil

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

  13. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    PubMed Central

    2015-01-01

    Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules. PMID:26631602

  14. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    DOE PAGESBeta

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; et al

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

  15. Mitigated-force carriage for high magnetic field environments

    DOEpatents

    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. Water clusters in an argon matrix: infrared spectra from molecular dynamics simulations with a self-consistent charge density functional-based tight binding/force-field potential.

    PubMed

    Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand

    2015-03-19

    The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ∼340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the

  17. 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.

  18. Force field development from first principles for materials design

    NASA Astrophysics Data System (ADS)

    Chan, Maria; Kinaci, Alper; Narayanan, Badri; Sen, Fatih; Gray, Stephen; Davis, Michael; Sankaranaryanan, Subramanian

    2015-03-01

    The ability to perform accurate calculations efficiently is crucial for computational materials design. In this talk, we will discuss a stream-lined approach to force field development using first principles density functional theory training data and machine learning algorithms. We will also discuss the validation of this approach on precious metal nanoparticles.

  19. An improved generalized AMBER force field (GAFF) for urea.

    PubMed

    Ozpinar, Gül Altinbaş; Peukert, Wolfgang; Clark, Timothy

    2010-09-01

    We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data. PMID:20162312

  20. 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...

  1. Frequency-dependent force fields for QMMM calculations.

    PubMed

    Harczuk, Ignat; Vahtras, Olav; Ågren, Hans

    2015-03-28

    We outline the construction of frequency-dependent polarizable force fields. The force fields are derived from analytic response theory for different frequencies using a generalization of the LoProp algorithm giving a decomposition of a molecular dynamical polarizability to localized atomic dynamical polarizabilities. These force fields can enter in a variety of applications - we focus on two such applications in this work: firstly, they can be incorporated in a physical, straightforward, way for current existing methods that use polarizable embeddings, and we can show, for the first time, the effect of the frequency dispersion within the classical environment of a quantum mechanics-molecular mechanics (QMMM) method. Our methodology is here evaluated for some test cases comprising water clusters and organic residues. Secondly, together with a modified Silberstein-Applequist procedure for interacting inducible point-dipoles, these frequency-dependent polarizable force fields can be used for a classical determination of frequency-dependent cluster polarizabilities. We evaluate this methodology by comparing with the corresponding results obtained from quantum mechanics or QMMM where the absolute mean [small alpha, Greek, macron] is determined with respect to the size of the QM and MM parts of the total system. PMID:25714984

  2. Symmetrization of the AMBER and CHARMM force fields.

    PubMed

    Małolepsza, Edyta; Strodel, Birgit; Khalili, Mey; Trygubenko, Semen; Fejer, Szilard N; Wales, David J

    2010-05-01

    The AMBER and CHARMM force fields are analyzed from the viewpoint of the permutational symmetry of the potential for feasible exchanges of identical atoms and chemical groups in amino and nucleic acids. In each case, we propose schemes for symmetrizing the potentials, which greatly facilitate the bookkeeping associated with constructing kinetic transition networks via geometry optimization. PMID:20082393

  3. Generating distributed forcing fields for spatial hydrologic modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spatial hydrologic modeling requires the development of distributed forcing fields of weather and precipitation. This is particularly difficult in mountainous regions of the western US, where measurement sites are limited and the landscape is dominated by complex terrain and variations in vegetatio...

  4. The effect of gravitational tidal forces on renormalized quantum fields

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.; Shore, Graham M.

    2012-02-01

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

  5. GLYCAM06: a generalizable biomolecular force field. Carbohydrates.

    PubMed

    Kirschner, Karl N; Yongye, Austin B; Tschampel, Sarah M; González-Outeiriño, Jorge; Daniels, Charlisa R; Foley, B Lachele; Woods, Robert J

    2008-03-01

    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 alpha- and beta-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

  6. 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 α- and β-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

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

    PubMed

    Moučka, 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

  8. 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

  9. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616

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

    SciTech Connect

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

    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.

  11. Grafted polyelectrolyte in strong electric field under load: Field-regulated force and chain contraction

    NASA Astrophysics Data System (ADS)

    Brilliantov, N. V.; Seidel, C.

    2012-01-01

    The response of grafted polyelectrolytes to electrostatic field that favors adsorption is studied theoretically and by means of molecular dynamics (MD). Applying to the free chain end a constant force which counteracts adsorption, we analyze the size of the desorbed part as a function of force and electric field. Simulations with different loads, corresponding to linear, nonlinear and Hertzian springs, applied to the free end have been also performed to explore the generation of mechanical force by electric field. The MD results are in good agreement with the predictions of theory.

  12. 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.

  13. 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

  14. FF/C SCRUBBER DEMONSTRATION ON A SECONDARY METALS RECOVERY FURNACE

    EPA Science Inventory

    The paper describes a flux force/condensation (FF/C) scrubbing system that was built to control particulate emissions from a secondary metals recovery furnace. Total mass penetration and fractional penetration measurements were made under several different operating modes. The pe...

  15. Optical field and attractive force at the subwavelength slit.

    PubMed

    Shapiro, David; Nies, Daniel; Belai, Oleg; Wurm, Matthias; Nesterov, Vladimir

    2016-07-11

    In recent works, a novel light-induced attractive force was predicted between two metal plates. This force arises by the interaction of surface plasmons which are excited at the metal when a transverse magnetic mode propagates through a subwavelength slit between two metal bodies. In this paper, the analytical and numerical calculations of this magnetic field are presented for the perfect metal and for gold. The amplitude and the phase transient curves between the known limiting cases of narrow and wide slits compared to the wavelength are found. The curve is shown to oscillate due to the emergence of new waveguide modes. The analytic solution for the perfect metal is in agreement with the computation for gold by means of the finite element method. The simple asymptotic formula for the light-induced attractive force is found in the limit of a narrow slit. PMID:27410865

  16. An assessment of the anharmonic force fields of the halogen cyanides

    NASA Astrophysics Data System (ADS)

    Lacy, M.

    Anharmonic force fields in the ϱ representation (ϱ = Я/ r) have been calculated using the matrix diagonalization technique. A simple model force field and comparison method are used to assess the force fields currently available for these molecules. From this analysis, the potential surfaces defined by the present force fields are estimated to be within 2-5% of the actual molecular potential.

  17. Nonlinear Force-Free Field Extrapolation of NOAA AR 0696

    NASA Astrophysics Data System (ADS)

    Thalmann, J. K.; Wiegelmann, T.

    2007-12-01

    We investigate the 3D coronal magnetic field structure of NOAA AR 0696 in the period of November 09-11, 2004, before and after an X2.5 flare (occurring around 02:13 UT on November 10, 2004). The coronal magnetic field dominates the structure of the solar corona and consequently plays a key role for the understanding of the initiation of flares. The most accurate presently available method to derive the coronal magnetic field is currently the nonlinear force-free field extrapolation from measurements of the photospheric magnetic field vector. These vector-magnetograms were processed from stokes I, Q, U, and V measurements of the Big Bear Solar Observatory and extrapolated into the corona with the nonlinear force-free optimization code developed by Wiegelmann (2004). We analyze the corresponding time series of coronal equilibria regarding topology changes of the 3D coronal magnetic field during the flare. Furthermore, quantities such as the temporal evolution of the magnetic energy and helicity are computed.

  18. Mapping the force field of a hydrogen-bonded assembly

    PubMed Central

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

    2014-01-01

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

  19. Direct computation of parameters for accurate polarizable force fields

    SciTech Connect

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

    2014-11-21

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

  20. Efficient parametrization of complex molecule-surface force fields.

    PubMed

    Gao, David Z; Federici Canova, Filippo; Watkins, Matthew B; Shluger, Alexander L

    2015-06-15

    We present an efficient scheme for parametrizing complex molecule-surface force fields from ab initio data. The cost of producing a sufficient fitting library is mitigated using a 2D periodic embedded slab model made possible by the quantum mechanics/molecular mechanics scheme in CP2K. These results were then used in conjunction with genetic algorithm (GA) methods to optimize the large parameter sets needed to describe such systems. The derived potentials are able to well reproduce adsorption geometries and adsorption energies calculated using density functional theory. Finally, we discuss the challenges in creating a sufficient fitting library, determining whether or not the GA optimization has completed, and the transferability of such force fields to similar molecules. PMID:25891018

  1. A Maximum-Likelihood Approach to Force-Field Calibration.

    PubMed

    Zaborowski, Bartłomiej; Jagieła, Dawid; Czaplewski, Cezary; Hałabis, Anna; Lewandowska, Agnieszka; Żmudzińska, Wioletta; Ołdziej, Stanisław; Karczyńska, Agnieszka; Omieczynski, Christian; Wirecki, Tomasz; Liwo, Adam

    2015-09-28

    A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental conformations, calculated with the current energy function. Because the theoretical distribution is given in the form of the simulated conformations only, the contributions from all of the simulated conformations, with Gaussian weights in the distances from a given experimental conformation, are added to give the contribution to the target function from this conformation. In contrast to earlier methods for force-field calibration, the approach does not suffer from the arbitrariness of dividing the decoy set into native-like and non-native structures; however, if such a division is made instead of using Gaussian weights, application of the maximum-likelihood method results in the well-known energy-gap maximization. The computational procedure consists of cycles of decoy generation and maximum-likelihood-function optimization, which are iterated until convergence is reached. The method was tested with Gaussian distributions and then applied to the physics-based coarse-grained UNRES force field for proteins. The NMR structures of the tryptophan cage, a small α-helical protein, determined at three temperatures (T = 280, 305, and 313 K) by Hałabis et al. ( J. Phys. Chem. B 2012 , 116 , 6898 - 6907 ), were used. Multiplexed replica-exchange molecular dynamics was used to generate the decoys. The iterative procedure exhibited steady convergence. Three variants of optimization were tried: optimization of the energy-term weights alone and use of the experimental ensemble of the folded protein only at T = 280 K (run 1); optimization of the energy-term weights and use of experimental ensembles at all three temperatures (run 2

  2. Force-field parameters for beryllium complexes in amorphous layers.

    PubMed

    Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander

    2016-09-01

    Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data. Graphical Abstract Beryllium complexes in amorphous layersᅟ. PMID:27550375

  3. Tuning the mass of chameleon fields in Casimir force experiments.

    PubMed

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

    2010-06-18

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

  4. Quantum mechanical force field for water with explicit electronic polarization

    SciTech Connect

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

    2013-08-07

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

  5. Quantum mechanical force field for water with explicit electronic polarization

    PubMed Central

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

    2013-01-01

    A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 106 self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

  6. 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

  7. Force-free magnetic fields - Generating functions and footpoint displacements

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard; Verma, Ritu

    1991-01-01

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

  8. 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

  9. 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.

  10. 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

  11. Weber's gravitational force as static weak field approximation

    NASA Astrophysics Data System (ADS)

    Tiandho, Yuant

    2016-02-01

    Weber's gravitational force (WGF) is one of gravitational model that can accommodate a non-static system because it depends not only on the distance but also on the velocity and the acceleration. Unlike Newton's law of gravitation, WGF can predict the anomalous of Mercury and gravitational bending of light near massive object very well. Then, some researchers use WGF as an alternative model of gravitation and propose a new mechanics theory namely the relational mechanics theory. However, currently we have known that the theory of general relativity which proposed by Einstein can explain gravity with very accurate. Through the static weak field approximation for the non-relativistic object, we also have known that the theory of general relativity will reduce to Newton's law of gravity. In this work, we expand the static weak field approximation that compatible with relativistic object and we obtain a force equation which correspond to WGF. Therefore, WGF is more precise than Newton's gravitational law. The static-weak gravitational field that we used is a solution of the Einstein's equation in the vacuum that satisfy the linear field approximation. The expression of WGF with ξ = 1 and satisfy the requirement of energy conservation are obtained after resolving the geodesic equation. By this result, we can conclude that WGF can be derived from the general relativity.

  12. Force field measurements within the exclusion zone of water.

    PubMed

    Chen, Chi-Shuo; Chung, Wei-Ju; Hsu, Ian C; Wu, Chien-Ming; Chin, Wei-Chun

    2012-01-01

    Water molecules play critical roles in many biological functions, such as protein dynamics, enzymatic activities, and cellular responses. Previous nuclear magnetic resonance and neutron scattering studies have shown that water molecules bind to specific sites on surfaces and form localized clusters. However, most current experimental techniques cannot measure dynamic behaviors of ordered water molecules on cell-size (10 μm) scale. Recently, the long-distance effect of structured water has been demonstrated by Pollack and his colleagues. Namely, there is a structured water layer near the hydrophilic surface that can exclude solutes (Zheng et al, Adv Colloid Interface Sci 127:19-27, 2006; Pollack 2006, Adv Colloid Interface Sci 103:173-196, 2003). The repelling forces of water clusters inside this exclusion region are investigated in this study. With a laser tweezers system, we found the existence of an unexpected force fields inside the solute-free exclusion zone near a Nafion surface. Our results suggest that the water clusters could transduce mechanical signals on the micrometer range within the exclusion zone. This unexpected inhomogeneous force field near the hydrophilic surface would provide a new insight into cellular activities, leading to a potential new physical chemistry mechanism for cell biology. PMID:23277674

  13. Coarse-grained force field; general folding theory

    PubMed Central

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

    2012-01-01

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

  14. Comparison of force fields on the basis of various model approaches--how to design the best model for the [CnMIM][NTf2] family of ionic liquids.

    PubMed

    Köddermann, Thorsten; Reith, Dirk; Ludwig, Ralf

    2013-10-01

    In this contribution, we present two new united-atom force fields (UA-FFs) for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [C(n)MIM][NTf(2)] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient-based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all-atom force field (AA-FF) for [C(n)MIM][NTf(2)] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem- 2007, 8, 2464), the new force fields were derived to fit experimental densities, self-diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C(2)MIM][NTf(2)]. In the manual force field, the alkyl chains of the cation and the CF3 groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA-FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA-FFs are slightly superior for speed-up reasons. The UA-FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization. PMID

  15. 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.

  16. 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

  17. Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

    PubMed Central

    Savelyev, Alexey; MacKerell, Alexander D.

    2015-01-01

    In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

  18. Sodium Chloride, NaCl/ϵ: New Force Field.

    PubMed

    Fuentes-Azcatl, Raúl; Barbosa, Marcia C

    2016-03-10

    A new computational model for sodium chloride, the NaCl/ϵ, is proposed. The force field employed 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 parametrization is obtained by fitting the density of the crystal and the density and the dielectric constant of the mixture of the salt with water at a diluted solution. Our model shows good agreement with the experimental values for the density and for the surface tension of 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/ϵ together with the water TIP4P/ϵ models provide a good approximation for studying electrolyte solutions. PMID:26890321

  19. Rigorous force field optimization principles based on statistical distance minimization

    SciTech Connect

    Vlcek, Lukas; Chialvo, Ariel A.

    2015-10-14

    We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. We exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of the approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.

  20. Deformation field of the soft substrate induced by capillary force

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  1. 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.

  2. 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

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

    DOE PAGESBeta

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

    2014-12-18

    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. In this research, we perform molecular dynamics (MD) simulations using the reactive force field (ReaxFF) to characterize the lithiation process of c-SiNWs. Our calculations showmore » 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. In conclusion, 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.« less

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

    SciTech Connect

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

    2014-12-18

    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. In this research, 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. In conclusion, 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.

  5. Coastal Downscaling Experiments: Can CESM Fields Successfully Force Regional Coastal Ocean Simulations with Strong Freshwater Forcing?

    NASA Astrophysics Data System (ADS)

    MacCready, P.; Bryan, F.; Tseng, Y. H.; Whitney, M. M.

    2014-12-01

    The coastal ocean accounts for about half of the global fish harvest, but is poorly resolved in global climate models (a one-degree grid barely sees the continental shelf). Moreover, coastal ocean circulation is strongly modified by river freshwater sources, often coming from estuarine systems that are completely unresolved in the coarse grid. River freshwater input in CESM is added in a practical but ad hoc way, by imposing a surface salinity sink over a region of the ocean approximating the plume area of a given river. Here we present results from a series of model experiments using a high-resolution (1.5 km) ROMS model of the NE Pacific, including the Columbia River and the inland waters of Puget Sound. The base model does multi-year hindcasts using the best available sources of atmospheric (MM5/WRF), ocean (NCOM), river (USGS), and tidal forcing. It has been heavily validated against observations of all sorts, and performs well, so it is an ideal test bed for downscaling experiments. The model framework also does biogeochemistry, including oxygen, and carbon chemistry is being added to make forecasts of Ocean Acidification.This high-resolution ROMS model is systematically run in downscaling experiments for the year 2005 with combinations of CESM forcing (CAM, POP, and rivers) swapped in. Skill is calculated using observations. It is found that the runs with CESM forcing generally retain much of the skill of the base model. A compact metric of response to freshwater forcing is used, which is the mechanical energy required to destratify a shallow coastal volume. This, along with the average temperature and salinity of the volume, are used to characterize and compare runs, including the original CESM-POP fields. Finally the model is run with projected CESM simulation forcing at the end of 21st century based on a set of RCP scenarios, and the compact metrics are used to quantify differences from 2005.

  6. Nonlinear gravitational self-force: Field outside a small body

    NASA Astrophysics Data System (ADS)

    Pound, Adam

    2012-10-01

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

  7. 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

  8. 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

    2016-01-14

    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 α-iron (ferrite), Fe3C (cementite), and ferrite-cementite interfaces with a vacancy cluster. We also investigate the growth of nanovoids in α-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

  9. The Anharmonic Force Field of BeH2 Revisited

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  10. Micro-gravity: current distributions creating a uniform force field

    NASA Astrophysics Data System (ADS)

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

    2001-02-01

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

  11. On the use of quartic force fields in variational calculations

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we 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 describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. 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.

  12. 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.

  13. 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

    , 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

  14. 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

  15. Automated conformational energy fitting for force-field development

    PubMed Central

    Guvench, Olgun; MacKerell, Alexander D.

    2010-01-01

    We present a general conformational-energy fitting procedure based on Monte Carlo simulated annealing (MCSA) for application in the development of molecular mechanics force fields. Starting with a target potential energy surface and an unparameterized molecular mechanics potential energy surface, an optimized set of either dihedral or grid-based correction map (CMAP) parameters is produced that minimizes the root mean squared error (RMSE) between the parameterized and targeted energies. The fitting is done using an MCSA search in parameter space and consistently converges to the same RMSE irrespective of the randomized parameters used to seed the search. Any number of dihedral parameters can be simultaneously parameterized, allowing for fitting to multi-dimensional potential energy scans. Fitting options for dihedral parameters include non-uniform weighting of the target data, constraining multiple optimized parameters to the same value, constraining parameters to be no greater than a user-specified maximum value, including all or only a subset of multiplicities defining the dihedral Fourier series, and optimization of phase angles in addition to force constants. The dihedral parameter fitting algorithm’s performance is characterized through multi-dimensional fitting of cyclohexane, tetrahydropyran, and hexopyranose monosaccharide energetics, with the latter case having a 30-dimensional parameter space. The CMAP fitting is applied in the context of polypeptides, and is used to develop a parameterization that simultaneously captures the φ, ψ energetics of the alanine dipeptide and the alanine tetrapeptide. Because the dihedral energy term is common to many force fields, we have implemented the dihedral-fitting algorithm in the portable Python scripting language and have made it freely available as Supplementary Material. PMID:18458967

  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. Unified Field Theory and Force Formulas of Interactions

    NASA Astrophysics Data System (ADS)

    Ma, Tian; Wang, Shouhong

    2013-04-01

    The main objective of this talk is to drive a unified field model coupling four interactions, based on the principle of interaction dynamics (PID) and the principle of representation invariance (PID). Intuitively, PID takes the variation of the action functional under energy-momentum conservation constraint. PRI requires that physical laws be independent of representations of the gauge groups. One important outcome of this unified field model is a natural duality between the interacting fields (g, A, W^a, S^k), corresponding to graviton, photon, intermediate vector bosons W^± and Z and gluons, and the adjoint bosonic fields (φ,, ^aw, ^ks). This duality predicts two Higgs particles of similar mass with one due to weak interaction and the other due to strong interaction. PID and PRI can be applied directly to individual interactions, leading to 1) modified Einstein equations, giving rise to a unified theory for dark matter and dark energy, 2) three levels of strong interaction potentials for quark, nucleon/hadron, and atom respectively, and 3) a weak interaction potential. These potential/force formulas offer a clear mechanism for both quark confinement and asymptotic freedom.

  18. Adaptation and generalization in acceleration dependent force fields

    PubMed Central

    Hwang, Eun Jung; Smith, Maurice A.; Shadmehr, Reza

    2005-01-01

    Any passive rigid inertial object that we hold in our hand, e.g., a tennis racquet, imposes a field of forces on the arm that depends on limb position, velocity, and acceleration. A fundamental characteristic of this field is that the forces due to acceleration and velocity are linearly separable in the intrinsic coordinates of the limb. In order to learn such dynamics with a collection of basis elements, a control system would generalize correctly and therefore perform optimally if the basis elements that were sensitive to limb velocity were not sensitive to acceleration, and vice versa. However, in the mammalian nervous system proprioceptive sensors like muscle spindles encode a nonlinear combination of all components of limb state, with sensitivity to velocity dominating sensitivity to acceleration. Therefore, limb state in the space of proprioception is not linearly separable despite the fact that this separation is a desirable property of control systems that form models of inertial objects. In building internal models of limb dynamics, does the brain use a representation that is optimal for control of inertial objects, or a representation that is closely tied to how peripheral sensors measure limb state? Here we show that in humans, patterns of generalization of reaching movements in acceleration dependent fields are strongly inconsistent with basis elements that are optimized for control of inertial objects. Unlike a robot controller that models the dynamics of the natural world and represents velocity and acceleration independently, internal models of dynamics that people learn appear to be rooted in the properties of proprioception, nonlinearly responding to the pattern of muscle activation and representing velocity more strongly than acceleration. PMID:16292640

  19. Towards a force field based on density fitting

    PubMed Central

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

    2007-01-01

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

  20. 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...

  1. 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.

  2. The harmonic force field and rz structure of HNCO

    NASA Astrophysics Data System (ADS)

    Fusina, Luciano; Mills, Ian M.

    1981-04-01

    The presently available microwave, millimeter wave, and far-infrared data of five isotopic species of isocyanic acid, namely, HNCO, H 15NCO, HN 13CO, HNC 18O, and DNCO, have been used to obtain improved values of the ground-state rotational constants, the five quartic distortion constants, and some higher-order distortion constants in the IrS reduced Hamiltonian of Watson. The appropriate planarity relation among the quartic centrifugal distortion constants has been imposed in the fitting procedure. The general harmonic force field of isocyanic acid has been determined using all existing data, and assuming a trans bent equilibrium geometry of the molecule with an NCO angle of 170°. Finally an rz structure has been obtained using the Az, Bz, and Cz rotational constants of five isotopic species. The bending of the NCO chain is found to be 8° in the trans configuration.

  3. 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).

  4. Derivation of a Molecular Mechanics Force Field for Cholesterol

    SciTech Connect

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

    2004-01-01

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

  5. 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.

  6. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

    PubMed Central

    Vanommeslaeghe, K.

    2014-01-01

    Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274

  7. 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, MI

  8. The Space Structure, Force Fields and Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Krasnoholovets, Volodymyr; Chung, Ding-Yu

    2006-06-01

    It is proposed that the cosmic digital code consists of 1 and 0 for an attachment space and a detachment space, respectively. The attachment space attaches to an object, while the detachment space detaches from the object. The cosmic digital code relates to the reduction of > 4D space-time into 4D space-time and the derivation of the space structure. Through the detachment space, > 4D space-time is sliced into infinitely many 4D slices surrounding the 4D core attachment space. The space structurally is a partition space, or a lattice space. The lattice space consists of repetitive units of alternative attachment space and detachment space and provides for a coherent wave function and gauge force fields, while the partition space consists of separated continuous phases of attachment space and detachment space providing the space structure for the collapse of wave function and the permanent detachment or attachment of gauge bosons. Thus, the wave function and gauge bosons become pure physical fields. The mechanism for the emergence of the space structure is varying dimension numbers, ensuring the metric for the slicing of > 4D space-time.

  9. Critical Casimir forces in the presence of random surface fields

    NASA Astrophysics Data System (ADS)

    Maciołek, A.; Vasilyev, O.; Dotsenko, V.; Dietrich, S.

    2015-03-01

    We study critical Casimir forces (CCFs) fC for films of thickness L which in the three-dimensional bulk belong to the Ising universality class and which are exposed to random surface fields (RSFs) on both surfaces. We consider the case in which, in the absence of RSFs, the surfaces of the film belong to the surface universality class of the so-called ordinary transition. We carry out a finite-size scaling analysis and show that for weak disorder, CCFs still exhibit scaling, acquiring a random field scaling variable w that is zero for pure systems. We confirm these analytic predictions by Monte Carlo (MC) simulations. Moreover, our MC data show that fC varies as fC(w →0 ) -fC(w =0 ) ˜w2 . Asymptotically, for large L , w scales as w ˜L-0.26→0 , indicating that this type of disorder is an irrelevant perturbation of the ordinary surface universality class. However, for thin films such that w ≃1 , we find that the presence of RSFs with vanishing mean value increases significantly the strength of CCFs, as compared to systems without them, and it shifts the extremum of the scaling function of fC toward lower temperatures. But fC remains attractive.

  10. Lorentz force electrical impedance tomography using magnetic field measurements

    NASA Astrophysics Data System (ADS)

    Zengin, Reyhan; Güneri Gençer, Nevzat

    2016-08-01

    In this study, magnetic field measurement technique is investigated to image the electrical conductivity properties of biological tissues using Lorentz forces. This technique is based on electrical current induction using ultrasound together with an applied static magnetic field. The magnetic field intensity generated due to induced currents is measured using two coil configurations, namely, a rectangular loop coil and a novel xy coil pair. A time-varying voltage is picked-up and recorded while the acoustic wave propagates along its path. The forward problem of this imaging modality is defined as calculation of the pick-up voltages due to a given acoustic excitation and known body properties. Firstly, the feasibility of the proposed technique is investigated analytically. The basic field equations governing the behaviour of time-varying electromagnetic fields are presented. Secondly, the general formulation of the partial differential equations for the scalar and magnetic vector potentials are derived. To investigate the feasibility of this technique, numerical studies are conducted using a finite element method based software. To sense the pick-up voltages a novel coil configuration (xy coil pairs) is proposed. Two-dimensional numerical geometry with a 16-element linear phased array (LPA) ultrasonic transducer (1 MHz) and a conductive body (breast fat) with five tumorous tissues is modeled. The static magnetic field is assumed to be 4 Tesla. To understand the performance of the imaging system, the sensitivity matrix is analyzed. The sensitivity matrix is obtained for two different locations of LPA transducer with eleven steering angles from -{{25}\\circ} to {{25}\\circ} at intervals of {{5}\\circ} . The characteristics of the imaging system are shown with the singular value decomposition (SVD) of the sensitivity matrix. The images are reconstructed with the truncated SVD algorithm. The signal-to-noise ratio in measurements is assumed 80 dB. Simulation studies

  11. Lorentz force electrical impedance tomography using magnetic field measurements.

    PubMed

    Zengin, Reyhan; Gençer, Nevzat Güneri

    2016-08-21

    In this study, magnetic field measurement technique is investigated to image the electrical conductivity properties of biological tissues using Lorentz forces. This technique is based on electrical current induction using ultrasound together with an applied static magnetic field. The magnetic field intensity generated due to induced currents is measured using two coil configurations, namely, a rectangular loop coil and a novel xy coil pair. A time-varying voltage is picked-up and recorded while the acoustic wave propagates along its path. The forward problem of this imaging modality is defined as calculation of the pick-up voltages due to a given acoustic excitation and known body properties. Firstly, the feasibility of the proposed technique is investigated analytically. The basic field equations governing the behaviour of time-varying electromagnetic fields are presented. Secondly, the general formulation of the partial differential equations for the scalar and magnetic vector potentials are derived. To investigate the feasibility of this technique, numerical studies are conducted using a finite element method based software. To sense the pick-up voltages a novel coil configuration (xy coil pairs) is proposed. Two-dimensional numerical geometry with a 16-element linear phased array (LPA) ultrasonic transducer (1 MHz) and a conductive body (breast fat) with five tumorous tissues is modeled. The static magnetic field is assumed to be 4 Tesla. To understand the performance of the imaging system, the sensitivity matrix is analyzed. The sensitivity matrix is obtained for two different locations of LPA transducer with eleven steering angles from [Formula: see text] to [Formula: see text] at intervals of [Formula: see text]. The characteristics of the imaging system are shown with the singular value decomposition (SVD) of the sensitivity matrix. The images are reconstructed with the truncated SVD algorithm. The signal-to-noise ratio in measurements is assumed 80 d

  12. Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding.

    PubMed

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

    2011-05-10

    The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two β-peptides which show different dominant folds, i.e., a 314-helix and a hairpin, using three different force fields, i.e., GROMOS 45A3, 53A6, and 54A7. The 54A7 force field stabilizes both folds, and the agreement of the simulated NOE atom-atom distances with the experimental NMR data is slightly improved when using the 54A7 force field, while the agreement of the (3)J couplings with experimental results remains essentially unchanged when varying the force field. The 54A7 force field developed to improve the stability of α-helical structures in proteins can thus be safely used in simulations of β-peptides. PMID:26610119

  13. 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

  14. Development of a ReaxFF potential for Ag/Zn/O and application to Ag deposition on ZnO

    NASA Astrophysics Data System (ADS)

    Lloyd, A.; Cornil, D.; van Duin, A. C. T.; van Duin, D.; Smith, R.; Kenny, S. D.; Cornil, J.; Beljonne, D.

    2016-03-01

    A new empirical potential has been derived to model an Ag-Zn-O system. Additional parameters have been included into the reactive force field (ReaxFF) parameter set established for ZnO to describe the interaction between Ag and ZnO for use in molecular dynamics (MD) simulations. The reactive force field parameters have been fitted to density functional theory (DFT) calculations performed on both bulk crystal and surface structures. ReaxFF accurately reproduces the equations of state determined for silver, silver zinc alloy and silver oxide crystals via DFT. It also compares well to DFT binding energies and works of separation for Ag on a ZnO surface. The potential was then used to model single point Ag deposition on polar (000 1 bar) and non-polar (10 1 bar0) orientations of a ZnO wurtzite substrate, at different energies. Simulation results then predict that maximum Ag adsorption on a ZnO surface requires deposition energies of ≤ 10 eV.

  15. Novel concepts in near-field optics: from magnetic near-field to optical forces

    NASA Astrophysics Data System (ADS)

    Yang, Honghua

    Driven by the progress in nanotechnology, imaging and spectroscopy tools with nanometer spatial resolution are needed for in situ material characterizations. Near-field optics provides a unique way to selectively excite and detect elementary electronic and vibrational interactions at the nanometer scale, through interactions of light with matter in the near-field region. This dissertation discusses the development and applications of near-field optical imaging techniques, including plasmonic material characterization, optical spectral nano-imaging and magnetic field detection using scattering-type scanning near-field optical microscopy (s-SNOM), and exploring new modalities of optical spectroscopy based on optical gradient force detection. Firstly, the optical dielectric functions of one of the most common plasmonic materials---silver is measured with ellipsometry, and analyzed with the Drude model over a broad spectral range from visible to mid-infrared. This work was motivated by the conflicting results of previous measurements, and the need for accurate values for a wide range of applications of silver in plasmonics, optical antennas, and metamaterials. This measurement provides a reference for dielectric functions of silver used in metamaterials, plasmonics, and nanophotonics. Secondly, I implemented an infrared s-SNOM instrument for spectroscopic nano-imaging at both room temperature and low temperature. As one of the first cryogenic s-SNOM instruments, the novel design concept and key specifications are discussed. Initial low-temperature and high-temperature performances of the instrument are examined by imaging of optical conductivity of vanadium oxides (VO2 and V2O 3) across their phase transitions. The spectroscopic imaging capability is demonstrated on chemical vibrational resonances of Poly(methyl methacrylate) (PMMA) and other samples. The third part of this dissertation explores imaging of optical magnetic fields. As a proof-of-principle, the magnetic

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

    PubMed

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

    2015-01-15

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

  17. Shock-induced decomposition of high energy materials: A ReaxFF molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Tiwari, Subodh; Mishra, Ankit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    Atomistic simulations of shock-induced detonation provide critical information about high-energy (HE) materials such as sensitivity, crystallographic anisotropy, detonation velocity, and reaction pathways. However, first principles methods are unable to handle systems large enough to describe shock appropriately. We report reactive-force-field ReaxFF simulations of shock-induced decomposition of 1, 3, 5-triamino-2, 3, 6-trinitrobenzene (TATB) and 1,1-diamino 2-2-dinitroethane (FOX-7) crystal. A flyer acts as mechanical stimuli to introduce a shock, which in turn initiated chemical reactions. Our simulation showed a shock speed of 9.8 km/s and 8.23 km/s for TATB and FOX-7, respectively. Reactivity analysis proves that FOX-7 is more reactive than TATB. Chemical reaction pathways analysis revealed similar pathways for the formation of N2 and H2O in both TATB and FOX-7. However, abundance of NH3 formation is specific to FOX-7. Large clusters formed during the reactions also shows different compositions between TATB and FOX-7. Carbon soot formation is much more pronounced in TATB. Overall, this study provides a detailed comparison between shock induced reaction pathway between FOX-7 and TATB. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555.

  18. Automation of AMOEBA polarizable force field parameterization for small molecules

    PubMed Central

    Wu, Johnny C.; Chattree, Gaurav

    2012-01-01

    A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database. PMID:22505837

  19. Searching the Force Field Electrostatic Multipole Parameter Space.

    PubMed

    Jakobsen, Sofie; Jensen, Frank

    2016-04-12

    We show by tensor decomposition analyses that the molecular electrostatic potential for amino acid peptide models has an effective rank less than twice the number of atoms. This rank indicates the number of parameters that can be derived from the electrostatic potential in a statistically significant way. Using this as a guideline, we investigate different strategies for deriving a reduced set of atomic charges, dipoles, and quadrupoles capable of reproducing the reference electrostatic potential with a low error. A full combinatorial search of selected parameter subspaces for N-methylacetamide and a cysteine peptide model indicates that there are many different parameter sets capable of providing errors close to that of the global minimum. Among the different reduced multipole parameter sets that have low errors, there is consensus that atoms involved in π-bonding require higher order multipole moments. The possible correlation between multipole parameters is investigated by exhaustive searches of combinations of up to four parameters distributed in all possible ways on all possible atomic sites. These analyses show that there is no advantage in considering combinations of multipoles compared to a simple approach where the importance of each multipole moment is evaluated sequentially. When combined with possible weighting factors related to the computational efficiency of each type of multipole moment, this may provide a systematic strategy for determining a computational efficient representation of the electrostatic component in force field calculations. PMID:26925529

  20. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

    PubMed Central

    2014-01-01

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

  1. The FoldX web server: an online force field

    PubMed Central

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

    2005-01-01

    FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at . The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed. PMID:15980494

  2. Force field independent metal parameters using a nonbonded dummy model.

    PubMed

    Duarte, Fernanda; Bauer, Paul; Barrozo, Alexandre; Amrein, Beat Anton; Purg, Miha; Aqvist, Johan; Kamerlin, Shina Caroline Lynn

    2014-04-24

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn(2+), Zn(2+), Mg(2+), and Ca(2+), as well as providing new parameters for Ni(2+), Co(2+), and Fe(2+). In all the cases, we are able to reproduce both M(2+)-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers. PMID:24670003

  3. Force Fields for Carbohydrate-Divalent Cation Interactions.

    PubMed

    Chen, Hsieh; Cox, Jason R; Panagiotopoulos, Athanassios Z

    2016-06-16

    We report molecular dynamics simulations to study intermolecular interactions for carbohydrate-divalent cation complexes. We observed that common force fields from literature with standard Lorentz-Berthelot combining rules are unable to reproduce the experimental stability constants for model carbohydrate monomer (α-d-Allopyranose) and alkali earth metal cation (Mg(2+), Ca(2+), Sr(2+), or Ba(2+)) complexes. A modified combining rule with rescaled effective cross-interaction radius between cations and the hydroxyl oxygens on the carbohydrates was introduced to reproduce the experimental stability constants, which the preferential carbohydrate-cation complexing structures through the ax-eq-ax sequence of O-1, O-2, and O-3 on α-d-Allopyranose were also observed. The effective radius scaling factor obtained from (α-d-Allopyranose)-Ca(2+) complexes was directly transferrable to the similar six-membered ring (α-d-Ribopyranose)-Ca(2+) complexes; however, reparameterization for the scaling factor may be necessary for the five-membered ring (α-d-Ribofuranose)-Ca(2+) complexes. PMID:27210229

  4. Forced Field Extrapolation of the Magnetic Structure of the Hα fibrils in the Solar Chromosphere

    NASA Astrophysics Data System (ADS)

    Xiaoshuai, Zhu; Huaning, Wang; Zhanle, Du; Han, He

    2016-07-01

    We present a careful assessment of forced field extrapolation using the Solar Dynamics Observatory/Helioseismic and Magnetic Imager magnetogram. We use several metrics to check the convergence property. The extrapolated field lines below 3600 km appear to be aligned with most of the Hα fibrils observed by the New Vacuum Solar Telescope. In the region where magnetic energy is far larger than potential energy, the field lines computed by forced field extrapolation are still consistent with the patterns of Hα fibrils while the nonlinear force-free field results show a large misalignment. The horizontal average of the lorentz force ratio shows that the forced region where the force-free assumption fails can reach heights of 1400–1800 km. The non-force-free state of the chromosphere is also confirmed based on recent radiation magnetohydrodynamics simulations.

  5. 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.

  6. 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)

  7. Power counting for nuclear forces in chiral effective field theory

    NASA Astrophysics Data System (ADS)

    Long, Bingwei

    2016-02-01

    The present note summarizes the discourse on power counting issues of chiral nuclear forces, with an emphasis on renormalization-group invariance. Given its introductory nature, I will lean toward narrating a coherent point of view on the concepts, rather than covering comprehensively the development of chiral nuclear forces in different approaches.

  8. 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

  9. A turbulent nonisothermal jet in an Archimedean force field

    NASA Astrophysics Data System (ADS)

    Elemasov, V. E.; Glebov, G. A.; Kozlov, A. P.

    An integral method for calculating a vertical nonisothermal jet is presented which allows for the effects of Archimedean forces and nonisothermality. The method can be extended to the calculation of axisymmetric and plane jets in a slipstream and also to the case of jets issuing into a medium of a different concentration. It is shown that the consideration of Archimedean forces and nonisothermality results in a better agreement between calculations and experimental data.

  10. Cell Separation by Non-Inertial Force Fields in Microfluidic Systems

    PubMed Central

    Tsutsui, Hideaki; Ho, Chih-Ming

    2009-01-01

    Cell and microparticle separation in microfluidic systems has recently gained significant attention in sample preparations for biological and chemical studies. Microfluidic separation is typically achieved by applying differential forces on the target particles to guide them into different paths. This paper reviews basic concepts and novel designs of such microfluidic separators with emphasis on the use of non-inertial force fields, including dielectrophoretic force, optical gradient force, magnetic force, and acoustic primary radiation force. Comparisons of separation performances with discussions on physiological effects and instrumentation issues toward point-of-care devices are provided as references for choosing appropriate separation methods for various applications. PMID:20046897

  11. Quantum field theory of the Casimir force for graphene

    NASA Astrophysics Data System (ADS)

    Klimchitskaya, G. L.

    2016-01-01

    We present theoretical description of the Casimir interaction in graphene systems which is based on the Lifshitz theory of dispersion forces and the formalism of the polarization tensor in (2+1)-dimensional space-time. The representation for the polarization tensor of graphene allowing the analytic continuation to the whole plane of complex frequencies is given. This representation is used to obtain simple asymptotic expressions for the reflection coefficients at all Matsubara frequencies and to investigate the origin of large thermal effect in the Casimir force for graphene. The developed theory is shown to be in a good agreement with the experimental data on measuring the gradient of the Casimir force between a Au-coated sphere and a graphene-coated substrate. The possibility to observe the thermal effect for graphene due to a minor modification of the already existing experimental setup is demonstrated.

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

    SciTech Connect

    Li, Y.C.; Zhang, N.C.

    1994-12-31

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

  13. Axial acoustic radiation force on a sphere in Gaussian field

    SciTech Connect

    Wu, Rongrong; Liu, Xiaozhou Gong, Xiufen

    2015-10-28

    Based on the finite series method, the acoustical radiation force resulting from a Gaussian beam incident on a spherical object is investigated analytically. When the position of the particles deviating from the center of the beam, the Gaussian beam is expanded as a spherical function at the center of the particles and the expanded coefficients of the Gaussian beam is calculated. The analytical expression of the acoustic radiation force on spherical particles deviating from the Gaussian beam center is deduced. The acoustic radiation force affected by the acoustic frequency and the offset distance from the Gaussian beam center is investigated. Results have been presented for Gaussian beams with different wavelengths and it has been shown that the interaction of a Gaussian beam with a sphere can result in attractive axial force under specific operational conditions. Results indicate the capability of manipulating and separating spherical spheres based on their mechanical and acoustical properties, the results provided here may provide a theoretical basis for development of single-beam acoustical tweezers.

  14. 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.

  15. Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory

    NASA Astrophysics Data System (ADS)

    McDaniel, Jesse G.; Schmidt, J. R.

    2016-05-01

    Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.

  16. Next-Generation Force Fields from Symmetry-Adapted Perturbation Theory.

    PubMed

    McDaniel, Jesse G; Schmidt, J R

    2016-05-27

    Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT. PMID:27070322

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

    SciTech Connect

    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.

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

    PubMed Central

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

    2014-01-01

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

  19. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy. PMID:27230942

  20. 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.

  1. Generation of mechanical force by grafted polyelectrolytes in an electric field

    NASA Astrophysics Data System (ADS)

    Brilliantov, N. V.; Budkov, Yu. A.; Seidel, C.

    2016-03-01

    We study theoretically and by means of molecular dynamics (MD) simulations the generation of mechanical force by grafted polyelectrolytes in an external electric field, which favors its adsorption on the grafting plane. The force arises in deformable bodies linked to the free end of the chain. Varying the field, one controls the length of the nonadsorbed part of the chain and hence the deformation of the target body, i.e., the arising force too. We consider target bodies with a linear force-deformation relation and with a Hertzian one. While the first relation models a coiled Gaussian chain, the second one describes the force response of a squeezed colloidal particle. The theoretical dependences of generated force and compression of the target body on an applied field agree very well with the results of MD simulations. The analyzed phenomenon may play an important role in future nanomachinery, e.g., it may be used to design nanovices to fix nanosized objects.

  2. 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.

  3. Superdiffusion to normal diffusion: particle motion in three-dimensional force-free magnetic fields

    NASA Astrophysics Data System (ADS)

    Holguin, F.; Ram, A. K.; Krishnamurthy, V.; Dasgupta, B.

    2015-11-01

    Magnetic fields in regions of low plasma pressure and large currents, such as in interstellar space and gaseous nebulae, are force-free as the Lorentz force vanishes. The Arnold-Beltrami-Childress (ABC) field is an example of a three-dimensional, force-free, helical magnetic field. The field lines form complex and varied structures in space that are a mix of regular and chaotic lines of force. Charged particles moving in the region of chaotic field lines exhibit anomalous superdiffusion. The sine field, or the Archontis field, is a special case of ABC field with the cosine terms left out. The lines of force of a sine field are completely chaotic in space. However, the diffusion of particles in the sine field is normal. The time evolution of an ensemble of particles can be divided into three domains. For short times, the motion is essentially ballistic. For intermediate times, the motion is characterized by a decay of the velocity autocorrelation function. For longer times, the particles undergo diffusion. We present results on the diffusion of field lines, and of particles, in the ABC and sine fields. In particular, the transition from superdiffusion to normal diffusion is discussed.

  4. 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.

  5. Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

    NASA Astrophysics Data System (ADS)

    Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, Nadine J.; Ondráček, Martin; van der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel

    2016-05-01

    How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.

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

    PubMed Central

    Stockinger, Christian; Focke, Anne; Stein, Thorsten

    2014-01-01

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

  7. 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.

  8. 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), 106μm(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.

  9. 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 α-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

  10. Comparison of three empirical force fields for phonon calculations in CdSe quantum dots

    NASA Astrophysics Data System (ADS)

    Kelley, Anne Myers

    2016-06-01

    Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ˜2.8 and ˜5.2 nm (˜410 and ˜2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies for the strongly Raman-active "longitudinal optical" phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.

  11. Hierarchical atom type definitions and extensible all-atom force fields.

    PubMed

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. PMID:26537332

  12. 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 α. 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 α 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Luo, Yuan; Yobas, Levent

    2014-09-01

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

  15. 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.

  16. Assessing the Current State of Amber Force Field Modifications for DNA.

    PubMed

    Galindo-Murillo, Rodrigo; Robertson, James C; Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr; Cheatham, Thomas E

    2016-08-01

    The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew-Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to

  17. Tailoring the Optical Dipole Force for Molecules by Field-Induced Alignment

    NASA Astrophysics Data System (ADS)

    Purcell, S. M.; Barker, P. F.

    2009-10-01

    We report on the ability to tailor the optical dipole force for molecules by tuning their effective polarizability with strong field alignment using polarized fields. We have measured a difference of 20% in the dipole force on cold CS2 molecules when changing from linear to near-circular polarization using peak field intensities of 5.7×1011Wcm-2. A variation in the focal length with laser polarization of a molecular-optical lens formed by a single focused laser beam was also measured. This provides a new way of modifying this force for many molecules.

  18. Free-molecule heat transfer in a conservative force field between parallel surfaces

    NASA Astrophysics Data System (ADS)

    Hardt, Steffen

    2016-05-01

    The heat flux between parallel surfaces is computed analytically assuming that heat is transferred by particles moving ballistically under the influence of a conservative force field. Particle reflection at the surfaces is governed by a Maxwell-type boundary condition. It is found that the force field can give rise to a substantial reduction, but also to an enhancement of the heat flux, depending on the ratio of the temperatures at the two surfaces. The influence of the accommodation coefficients is studied. An asymmetry introduced by the force field and/or the boundary conditions at the two surfaces causes a significant heat-flux rectification, characteristic for a thermal diode.

  19. An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

    An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858

  20. Assessing the Current State of Amber Force Field Modifications for DNA

    PubMed Central

    2016-01-01

    The utility of molecular dynamics (MD) simulations to model biomolecular structure, dynamics, and interactions has witnessed enormous advances in recent years due to the availability of optimized MD software and access to significant computational power, including GPU multicore computing engines and other specialized hardware. This has led researchers to routinely extend conformational sampling times to the microsecond level and beyond. The extended sampling time has allowed the community not only to converge conformational ensembles through complete sampling but also to discover deficiencies and overcome problems with the force fields. Accuracy of the force fields is a key component, along with sampling, toward being able to generate accurate and stable structures of biopolymers. The Amber force field for nucleic acids has been used extensively since the 1990s, and multiple artifacts have been discovered, corrected, and reassessed by different research groups. We present a direct comparison of two of the most recent and state-of-the-art Amber force field modifications, bsc1 and OL15, that focus on accurate modeling of double-stranded DNA. After extensive MD simulations with five test cases and two different water models, we conclude that both modifications are a remarkable improvement over the previous bsc0 force field. Both force field modifications show better agreement when compared to experimental structures. To ensure convergence, the Drew–Dickerson dodecamer (DDD) system was simulated using 100 independent MD simulations, each extended to at least 10 μs, and the independent MD simulations were concatenated into a single 1 ms long trajectory for each combination of force field and water model. This is significantly beyond the time scale needed to converge the conformational ensemble of the internal portions of a DNA helix absent internal base pair opening. Considering all of the simulations discussed in the current work, the MD simulations performed to

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

    NASA Astrophysics Data System (ADS)

    Knoop, Claas; Fritsching, Udo

    2013-10-01

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

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

    NASA Technical Reports Server (NTRS)

    Yang, Wei-Hong

    1987-01-01

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

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

    PubMed

    Martín Pendás, A; 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. PMID:23039579

  4. 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

  5. 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...

  6. 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.

  7. Magnetic field dependence of magnetic domains in Co doped Mn2Sb using magnetic force microscopy

    NASA Astrophysics Data System (ADS)

    Singh, Vikram; Saha, Pampi; Kushwaha, Pallavi; Thamizhavel, A.; Rawat, Rajeev

    2016-05-01

    Magnetic domains in the ferrimagnetic state of Co doped Mn2Sb single crystal has been visualized using Magnetic Force Microscopy. It shows fractal like domain structure. With the application of magnetic field, single domain state is achieved around 2000 Oe. The MFM images collected during field increasing and decreasing cycles show different morphology for same field value.

  8. On gravity, other forces in nature and the creation of mass particles and force fields in the universe

    NASA Astrophysics Data System (ADS)

    Sujak, Peter

    2014-03-01

    This work derives the relation between the Planck constant and currently valid Einstein's gravitational constant h / c = κ = 8 πG /c4 = 2 . 13 - 2 . 21 ×10-42 . The relation between the Planck constant and Newton's gravitational, between the Planck constant and 1 Coulomb and 1 Henry is deduced. This work establishes that the Planck constant represents the density of momentum of the void space in the Universe, and momentum of a photon p = h / λ represents the compression of this density, and that the momentum of the photon p = h /λo inevitably equals internal momentum of created proton by ppi = h /λo =mp c . In this work, we state that through generating mass particles, by compressing the density of momentum of the vacuum into a photon and bring this photon to stop, we concurrently generate a gravitational field of these particles. The value of momentum of the gravitational field on the surface of the proton is equal in size, but reversely oriented to the value of the internal momentum of the proton in explicit direction as ppi / π = h /λo =mp c / π . This work proves that gravitational force has its opposite force in the internal momentum of atomic particles of matter. This work maintains that the essence of the composition of all mass matter, as well as force fields in its vicinity, are created in full by the compression of the momentum of the void space in the universe.

  9. Force-Field Induced Bias in the Structure of Aβ21-30: 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 β, the Aβ21-30, 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 β 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 Aβ21-30 peptide. PMID:26629886

  10. Forced magnetic reconnection and field penetration of an externally applied rotating helical magnetic field in the TEXTOR tokamak.

    PubMed

    Kikuchi, Y; de Bock, M F M; Finken, K H; Jakubowski, M; Jaspers, R; Koslowski, H R; Kraemer-Flecken, A; Lehnen, M; Liang, Y; Matsunaga, G; Reiser, D; Wolf, R C; Zimmermann, O

    2006-08-25

    The magnetic field penetration process into a magnetized plasma is of basic interest both for plasma physics and astrophysics. In this context special measurements on the field penetration and field amplification are performed by a Hall probe on the dynamic ergodic divertor (DED) on the TEXTOR tokamak and the data are interpreted by a two-fluid plasma model. It is observed that the growth of the forced magnetic reconnection by the rotating DED field is accompanied by a change of the plasma fluid rotation. The differential rotation frequency between the DED field and the plasma plays an important role in the process of the excitation of tearing modes. The momentum input from the rotating DED field to the plasma is interpreted by both a ponderomotive force at the rational surface and a radial electric field modified by an edge ergodization. PMID:17026312

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  12. A new force field including charge directionality for TMAO in aqueous solution

    NASA Astrophysics Data System (ADS)

    Usui, Kota; Nagata, Yuki; Hunger, Johannes; Bonn, Mischa; Sulpizi, Marialore

    2016-08-01

    We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (OTMAO) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around OTMAO to mimic the OTMAO lone pairs and we migrate the negative charge on the OTMAO to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

  13. Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields

    NASA Astrophysics Data System (ADS)

    Wei, Caiyi; Mei, Ye; Zhang, Dawei

    2010-07-01

    Molecular dynamics studies of 5CITEP binding with HIV-1 integrase (IN) are presented using both polarized and nonpolarized force fields. When nonpolarized force field is used, the ligand drifts away from the original binding site. However, this depressing behavior can be curbed by introducing electronic polarization effect into the force field that stabilizes the protein structure and keeps the ligand in the binding pocket. Moreover, simulation under polarized force field gives a binding energy of -4.85 kcal/mol which is in excellent agreement with the experimental Δ G of -4.38 kcal/mol. The results demonstrate the importance of intra-protein electronic polarization in stabilizing the binding complex of IN-5CITEP and accurately predicting the binding energy.

  14. 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.

  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

  16. 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.

  17. The magnification of SN 1997ff, the farthest known supernova

    SciTech Connect

    Benitez, Narciso; Riess, Adam; Nugent, Peter; Dickinson, Mark; Chornock, Ryan; Filippenko, Alexei V.

    2002-09-03

    With a redshift of z {approx} 1.7, SN 1997ff is the most distant type Ia supernova discovered so far. This SN is close to several bright, z = 0.6-0.9 galaxies, and we consider the effects of lensing by those objects on the magnitude of SN 1997ff. We estimate their velocity dispersions using the Tully-Fisher and Faber-Jackson relations corrected for evolution effects, and calculate, applying the multiple-plane lensing formalism, that SN 1997ff is magnified by 0.34{+-}0.12 mag. Due to the spatial configuration of the foreground galaxies, the shear from individual lenses partially cancels out,and the total distortion induced on the host galaxy is considerably smaller than that produced by a single lens having the same magnification. After correction for lensing, the revised distance to SN 1997ff is m-M = 45.49 {+-} 0.34 mag, which improves the agreement with the {Omega}{sub M} = 0.35, {Omega}{Lambda} = 0.65 cosmology expected from lower-redshift SNe Ia, and is inconsistent at the {approx} 3 sigma confidence level with a uniform gray dust model or a simple evolution model.

  18. The ReaxFF method - new applications and developments

    NASA Astrophysics Data System (ADS)

    van Duin, Adri

    The ReaxFF method provides a highly transferable simulation method for atomistic scale simulations on chemical reactions at the nanosecond and nanometer scale. It combines concepts of bond-order based potentials with a polarizable charge distribution. Since it initial development for hydrocarbons in 2001, we have found that this concept is transferable to applications to elements all across the periodic table, including all first row elements, metals, ceramics and ionic materials. For all these elements and associated materials we have demonstrated that ReaxFF can reproduce quantum mechanics-based structures, reaction energies and reaction barriers with reasonable accuracy, enabling the method to predict reaction kinetics in complicated, multi-material environments at a relatively modest computational expense. This presentation will describe the current concepts of the ReaxFF method, the current status of the various ReaxFF codes, including parallel implementations and recently developed hybrid Grand Canonical Monte Carlo options - which significantly increase its application areas. Also, we will present and overview of recent applications to a range of materials of increasing complexity, with a focus on applications to combustion, biomaterials, batteries, tribology and catalysis.

  19. 8. Elevation of west side of FF. Coal came from ...

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

    8. Elevation of west side of FF. Coal came from GG (breaker) to bins at top from which it dropped down in to ball mills and then sent it by conveyor to bunkers. Looking east - Rouge Steel Company, 3001 Miller Road, Dearborn, MI

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

    PubMed

    Zhang, Chaoyang; Wen, Yushi; Xue, Xianggui

    2014-08-13

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

  1. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  2. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    PubMed Central

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  3. 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.

  4. Influence of mechanical force field on the electromechanical stability of dielectric elastomers

    NASA Astrophysics Data System (ADS)

    Liu, Yanju; Liu, Liwu; Leng, Jinsong

    2009-12-01

    Arbitrary free energy functions, as is proposed by Zhao and Suo, can be applied to analyze the electromechanical stability of the dielectric elastomer. To study the electromechanical stability of mechanical force field placed on dielectric elastomer, variable free energy functions are applied to analyze the mechanical performance of dielectric elastomer. The relation among critical nominal electric field, critical real electric field, nominal stress and mechanical force field is derived, which agrees well with the experimental results. Such a result is capable of understanding better the stability conditions of dielectric elastomers and furthermore guiding the design and manufacture of sensors and actuators based on dielectric elastomers.

  5. Influence of mechanical force field on the electromechanical stability of dielectric elastomers

    NASA Astrophysics Data System (ADS)

    Liu, Yanju; Liu, Liwu; Leng, Jinsong

    2010-03-01

    Arbitrary free energy functions, as is proposed by Zhao and Suo, can be applied to analyze the electromechanical stability of the dielectric elastomer. To study the electromechanical stability of mechanical force field placed on dielectric elastomer, variable free energy functions are applied to analyze the mechanical performance of dielectric elastomer. The relation among critical nominal electric field, critical real electric field, nominal stress and mechanical force field is derived, which agrees well with the experimental results. Such a result is capable of understanding better the stability conditions of dielectric elastomers and furthermore guiding the design and manufacture of sensors and actuators based on dielectric elastomers.

  6. 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.

  7. Submolecular features of epitaxially grown PTCDA on Cu(111) analyzed by force field spectroscopy.

    PubMed

    Braun, D-A; Weiner, D; Such, B; Fuchs, H; Schirmeisen, A

    2009-07-01

    Submolecular features of epitaxially grown 3,4,9,10-perylenetetra-carboxylic-dianhydride (PTCDA) on Cu(111) are resolved in non-contact atomic force microscopy topography scans in ultrahigh vacuum. While molecules in the first layer above the Cu substrate are depicted as featureless ovals, the second layer molecules show an intramolecular structure with a height corrugation of up to 40 pm. Force field spectroscopy experiments with submolecular resolution show that the tip-molecule forces differ significantly on the first and second layer molecules. Possible contributions to these force differences from mechanical deformations of the molecules as well as the internal charge density distribution are discussed. PMID:19509447

  8. 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.

  9. Fractal growth in the presence of a surface force field

    NASA Astrophysics Data System (ADS)

    Carlier, F.; Brion, E.; Akulin, V. M.

    2012-05-01

    We numerically simulate the dynamics of atomic clusters aggregation deposited on a surface interacting with the growing island. We make use of the well-known DLA model but replace the underlying diffusion equation by the Smoluchowski equation which results in a drifted DLA model and anisotropic jump probabilities. The shape of the structures resulting from their aggregation-limited random walk is affected by the presence of a Laplacian potential due to, for instance, the surface stress field. We characterize the morphologies we obtain by their Hausdorff fractal dimension as well as the so-called external fractal dimension. We compare our results to previously published experimental results for antimony and silver clusters deposited onto graphite surface.

  10. Mie scattering and optical forces from evanescent fields: a complex-angle approach.

    PubMed

    Bekshaev, Aleksandr Y; Bliokh, Konstantin Y; Nori, Franco

    2013-03-25

    Mie theory is one of the main tools describing scattering of propagating electromagnetic waves by spherical particles. Evanescent optical fields are also scattered by particles and exert radiation forces which can be used for optical near-field manipulations. We show that the Mie theory can be naturally adopted for the scattering of evanescent waves via rotation of its standard solutions by a complex angle. This offers a simple and powerful tool for calculations of the scattered fields and radiation forces. Comparison with other, more cumbersome, approaches shows perfect agreement, thereby validating our theory. As examples of its application, we calculate angular distributions of the scattered far-field irradiance and radiation forces acting on dielectric and conducting particles immersed in an evanescent field. PMID:23546090

  11. 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

  12. 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

  13. 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

  14. Fluctuation-Induced Interactions in external magnetic fields: Casimir force and Radiative Heat Transfer

    NASA Astrophysics Data System (ADS)

    Esquivel-Sirvent, Raul

    Thermally induced electromagnetic fields give rise to the Casimir force and the near field heat transfer between two bodies separated by a gap. These phenomena are described by Rytova's theory of fluctuating electromagnetic fields and both the Casimir force and the near field heat transfer depend on the local dielectric function of the bodies. In this work we present a theoretical calculation on the modulation of fluctuation-induced interactions in the presence of an external magnetic field. The system consists of two parallel plates separated by a gap d. Each plate is isotropic and has a local dielectric function. Applying an external magnetic field parallel to the plates, in the so called Voigt configuration, the plates become anisotropic. In particular, we consider plates of InSb. For the Casimir force the two plates are kept at the same temperature and the external field reduces the magnitude of the force. Similarly if the two plates are kept at different temperature the near field radiative heat transfer is modulated by the magnitude of the external magnetic field. The results are extended to semiconducting quantum wells. In both cases, the excitation of magnetoplasmons provides an explanation for the observed effect.

  15. Relativistic mean field model based on realistic nuclear forces

    SciTech Connect

    Hirose, S.; Serra, M.; Ring, P.; Otsuka, T.; Akaishi, Y.

    2007-02-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed

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

    2014-08-01

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

  18. Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

    PubMed

    Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

    2016-04-14

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures - while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields. PMID:27083705

  19. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

    PubMed

    Lupyan, Dmitry; Abramov, Yuriy A; Sherman, Woody

    2012-11-01

    The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130 small molecules from the CSD containing an intramolecular sulfur-oxygen distance less than the sum of their van der Waals (vdW) radii. Close S···O distances are observed in several important medicinal chemistry motifs (e.g. a carbonyl oxygen connected by a carbon or nitrogen linker to a sulfur) and are not treated well with existing parameters in the MMFFs or OPLS_2005 force fields, resulting in suboptimal geometries and energetics. In this work, we develop modified parameters for the OPLS_2005 force field to better treat this specific interaction in order to generate conformations close to those found in the CSD structures. We use a combination of refitting a force field torsional parameter, adding a specific atom pair vdW term, and attenuating the electrostatic interactions to obtain an improvement in the accuracy of geometry minimizations and conformational searches for these molecules. Specifically, in a conformational search 58 % of the cases produced a conformation less than 0.25 Å from the CSD crystal conformation with the modified OPLS force field parameters developed in this work. In contrast, 25 and 37 % produced a conformation less than 0.25 Å with the MMFFs and OPLS_2005 force fields, respectively. As an application of the new parameters, we generated conformations for the tyrosine kinase inhibitor axitinib (trade name Inlyta) that could be correctly repacked into three observed polymorphic structures, which was not possible with conformations generated using MMFFs or OPLS_2005. The improved parameters can be mapped directly onto physical characteristics of the systems that are treated inadequately with the molecular mechanics force fields used in this study and potentially other force fields as well. PMID:23053737

  20. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.

    PubMed

    Zheng, Suqing; Tang, Qing; He, Jian; Du, Shiyu; Xu, Shaofang; Wang, Chaojie; Xu, Yong; Lin, Fu

    2016-04-25

    Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools. PMID:26998926

  1. Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    NASA Astrophysics Data System (ADS)

    Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M.

    2016-04-01

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures - while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  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. 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 ...

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  5. Mechanical response of all-MoS2 single-layer heterostructures: a ReaxFF investigation.

    PubMed

    Mortazavi, Bohayra; Ostadhossein, Alireza; Rabczuk, Timon; van Duin, Adri C T

    2016-09-14

    Molybdenum disulfide (MoS2) is a highly attractive 2D material due to its interesting electronic properties. Recent experimental advances confirm the possibility of further tuning the electronic properties of MoS2 through the fabrication of single-layer heterostructures consisting of semiconducting (2H) and metallic (1T) MoS2 phases. Nonetheless, despite significant technological and scientific interest, there is currently limited information concerning the mechanical properties of these heterostructure systems. This investigation aims at extending our understanding of the mechanical properties of all-MoS2 single-layer structures at room temperature. This goal was achieved by performing extensive classical molecular dynamics simulations using a recently developed ReaxFF force field. We first studied the direction dependent mechanical properties of defect-free 2H and 1T phases. Our modelling results for pristine 2H MoS2 were found to be in good agreement with the experimental tests and first-principles theoretical predictions. We also discuss the mechanical response of 2H/1T single layer heterostructures. Our reactive molecular dynamics results suggest all-MoS2 heterostructures as suitable candidates for providing a strong and flexible material with tuneable electronic properties. PMID:27510638

  6. 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.

  7. Surface Catalysis Modeling of Air-SiO2 Systems Under Hypersonic Conditions Using ReaxFF MD Simulation

    NASA Astrophysics Data System (ADS)

    Norman, Paul; Schwartzentruber, Tom; Cozmuta, Ioana

    2009-11-01

    The high-speed entry of a blunt body into Earth's atmosphere brings about the dissociation of diatomic nitrogen and oxygen molecules via the shockwave formed in front of the body. Through surface catalysis, these dissociated atoms can recombine on the heat shield of the body, increasing its overall heating. The goal of this project is to study surface catalysis on amorphous silicon-dioxide (SiO2), a significant component in the reusable thermal protection system used on the Space Shuttle. Specifically, our objective is to determine the rates of recombination of monatomic N and O for the range of temperatures and pressures experienced by a heat shield during Earth re-entry. Additionally, we aim to determine the rates of specific reaction mechanisms on a SiO2 surface, including adsorption, desorption, surface diffusion, and various recombination processes. This is accomplished by performing large reactive molecular dynamics simulations using the ReaxFF force field, which naturally allows bond formation/breaking to occur during the course of a molecular dynamics simulation. Several methods for speeding up the equilibration and collection of rates for low-pressure gas-surface systems (typical of re-entry conditions) where events become infrequent will also be discussed.

  8. Evaluation of Representations and Response Models for Polarizable Force Fields

    PubMed Central

    2016-01-01

    For classical simulations of condensed-phase systems, such as organic liquids and biomolecules, to achieve high accuracy, they will probably need to incorporate an accurate, efficient model of conformation-dependent electronic polarization. Thus, it is of interest to understand what determines the accuracy of a polarizable electrostatics model. This study approaches this problem by breaking polarization models down into two main components: the representation of electronic polarization and the response model used for mapping from an inducing field to the polarization within the chosen representation. Among the most common polarization representations are redistribution of atom-centered charges, such as those used in the fluctuating charge model, and atom-centered point dipoles, such as those used in a number of different polarization models. Each of these representations has been combined with one or more response models. The response model of fluctuating charge, for example, is based on the idea of electronegativity equalization in the context of changing electrostatic potentials (ESPs), whereas point-dipole representations typically use a response model based on point polarizabilities whose induced dipoles are computed based on interaction with other charges and dipoles. Here, we decouple polarization representations from their typical response models to analyze the strengths and weaknesses of various polarization approximations. First, we compare the maximal possible accuracies achievable by the charge redistribution and point-dipole model representations, by testing their ability to replicate quantum mechanical (QM) ESPs around small molecules polarized by external inducing charges. Perhaps not surprisingly, the atom-centered dipole model can yield higher accuracy. Next, we test two of the most commonly used response functions used for the point-dipole representations, self-consistent and direct (or first-order) inducible point polarizabilities, where the

  9. Modeling of Centrifugal Force Field and the Effect on Filling and Solidification in Centrifugal Casting

    NASA Astrophysics Data System (ADS)

    Sheng, Wenbin; Ma, Chunxue; Gu, Wanli

    2011-06-01

    Based on the steady flow in a tube, a mathematical model has been established for the consideration of centrifuging force field by combining the equations of continuity, conservation of momentum and general energy. Effects of centrifugal field on the filling and solidification are modeled by two accessional terms: centrifugal force and Chorios force. In addition, the transfer of heat by convection is considered to achieve a coupling calculation of velocity field and temperature field. The solution of pressure item is avoided by introducing the stream function ψ(x,y) and the eddy function ξ(x,y). Corresponding difference formats for the simultaneous equations of centrifugal filling, the accessional terms and the solidifying latent heat have been established by the finite difference technique. Furthermore, the centrifugal filling and solidification processes in a horizontal tube are summarized to interpret the mechanism by which internal defects are formed in centrifugal castings.

  10. 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.

  11. 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

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

    PubMed Central

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

    2009-01-01

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

  13. The rate of separation of magnetic lines of force in a random magnetic field.

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.

    1973-01-01

    The mixing of magnetic lines of force, as represented by their rate of separation, as a function of distance along the magnetic field, is considered with emphasis on neighboring lines of force. This effect is particularly important in understanding the transport of charged particles perpendicular to the average magnetic field. The calculation is carried out in the approximation that the separation changes by an amount small compared with the correlation scale normal to the field, in a distance along the field of a few correlation scales. It is found that the rate of separation is very sensitive to the precise form of the power spectrum. Application to the interplanetary and interstellar magnetic fields is discussed, and it is shown that in some cases field lines, much closer together than the correlation scale, separate at a rate which is effectively as rapid as if they were many correlation lengths apart.

  14. 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.

  15. Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

    PubMed

    Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

    2016-03-14

    We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability. PMID:26979693

  16. Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids.

    PubMed

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

    2014-06-26

    The development of AMOEBA (a multipolar polarizable force field) for imidazolium based ionic liquids is presented. Our parametrization method follows the AMOEBA procedure and introduces the use of QM intermolecular total interactions as well as QM energy decomposition analysis (EDA) to fit individual interaction energy components. The distributed multipoles for the cation and anions have been derived using both the Gaussian distributed multipole analysis (GDMA) and Gaussian electrostatic model-distributed multipole (GEM-DM) methods.1 The intermolecular interactions of a 1,3-dimethylimidazolium [dmim(+)] cation with various anions, including fluoride [F(-)], chloride [Cl(-)], nitrate [NO(3)(-)], and tetraflorouborate [BF(4)(-)], were studied using quantum chemistry calculations at the MP2/6-311G(d,p) level of theory. Energy decomposition analysis was performed for each pair using the restricted variational space decomposition approach (RVS) at the HF/6-311G(d,p) level. The new force field was validated by running a series of molecular dynamic (MD) simulations and by analyzing thermodynamic and structural properties of these systems. A number of thermodynamic properties obtained from MD simulations were compared with available experimental data. The ionic liquid structure reproduced using the AMOEBA force field is also compared with the data from neutron diffraction experiment and other MD simulations. Employing GEM-DM force fields resulted in a good agreement on liquid densities ρ, enthalpies of vaporization ΔH(vap), and diffusion coefficients D(±) in comparison with conventional force fields. PMID:24901255

  17. Parameterization and optimization of the menthol force field for molecular dynamics simulations.

    PubMed

    Jasik, Mateusz; Szefczyk, Borys

    2016-10-01

    Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field. PMID:27604277

  18. Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

    PubMed Central

    Hapala, Prokop; Švec, Martin; Stetsovych, Oleksandr; van der Heijden, Nadine J.; Ondráček, Martin; van der Lit, Joost; Mutombo, Pingo; Swart, Ingmar; Jelínek, Pavel

    2016-01-01

    How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution. PMID:27230940

  19. The Sensitivity of Simulated Ocean Biogeochemistry to Forcing Fields Derived from NCEP and MERRA Reanalysis Products

    NASA Technical Reports Server (NTRS)

    Gregg, Watson; Casey, Nancy

    2010-01-01

    Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in addition to aerosol and cloud information which is derived from satellite data). The question posed here is, does the choice of reanalysis products make a difference in the representation of ocean biology and biogeochemistry? NOBM was forced by NCEP and MERRA reanalysis products for the period 2002-2009. We find that in 2009 global distributions and abundances of biological variables (total chlorophyll and nutrients) and carbon (dissolved inorganic and organic carbon and surface pCO2) were similar between the two different forcing fields. Global statistical comparisons with satellite and in situ data also showed negligible differences.

  20. Targeting glioblastoma via intranasal administration of Ff bacteriophages

    PubMed Central

    Dor-On, Eyal; Solomon, Beka

    2015-01-01

    Bacteriophages (phages) are ubiquitous viruses that control the growth and diversity of bacteria. Although they have no tropism to mammalian cells, accumulated evidence suggests that phages are not neutral to the mammalian macro-host and can promote immunomodulatory and anti-tumorigenic activities. Here we demonstrate that Ff phages that do not display any proteins or peptides could inhibit the growth of subcutaneous glioblastoma tumors in mice and that this activity is mediated in part by lipopolysaccharide molecules attached to their virion. Using the intranasal route, a non-invasive approach to deliver therapeutics directly to the CNS, we further show that phages rapidly accumulate in the brains of mice and could attenuate progression of orthotopic glioblastoma. Taken together, this study provides new insight into phages non-bacterial activities and demonstrates the feasibility of delivering Ff phages intranasally to treat brain malignancies. PMID:26074908

  1. 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.

  2. Quasi-static evolution of sheared force-free fields and the solar flare problem

    NASA Technical Reports Server (NTRS)

    Aly, J. J.

    1985-01-01

    Some new results are given showing the possible evolution of a two-dimensional force-free field in the half-space z greater than 0 toward an open field. This evolution is driven by shearing motions applied to the feet of the field lines on the boundary z = 0. The consequences of these results for a model of the two-ribbon solar flare are discussed.

  3. 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

  4. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-nmr Force Field

    PubMed Central

    Li, Shuxiang; Andrews, Casey T.; Frembgen-Kesner, Tamara; Miller, Mark S.; Siemonsma, Stephen L.; Collingsworth, Timothy D.; Rockafellow, Isaac T.; Ngo, Nguyet Anh; Campbell, Brady A.; Brown, Reid F.; Guo, Chengxuan; Schrodt, Michael; Liu, Yu-Tsan; Elcock, Adrian H.

    2015-01-01

    Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. 3Jhnhα coupling constants and δhα chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average 3Jhnhα and δhα values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring. PMID:26579777

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

    DOEpatents

    Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.

    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.

  6. 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.

  7. Centrifugal and electric field forces dual-pumping CD-like microfluidic platform for biomedical separation.

    PubMed

    Wang, Gou-Jen; Hsu, Wen-Haw; Chang, Yau-Zin; Yang, Hsiharng

    2004-03-01

    In this article, we propose a versatile CD-like multi-channel electrophoresis-based biomedical separation system that is driven by the interactive forces between the centrifugal force and the electric field force. The centrifugal force control of this system is realized through the velocity control of a DC servo motor, while the electric field is governed through the concentric conducting circuits, which are suitably designed and fabricated by sputtering on metal mask method, and can be adjusted to provide multi-stage voltages. Experimental results demonstrate that the electro-osmotic flow (EOF) effect can be effectively reduced when the electric field force and centrifugal force are in the opposite direction. Benefits from this are that the electrophoresis separation time can be prolonged and the length of the microfluidic channels can be shortened; therefore, more effective separation efficiency can be obtained. Moreover, other advantages, such as lower joule-heat generation, low-chemistry reaction, and no variation on the ion concentration during processes, make this biomedical separation system more useful. PMID:15307444

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  10. Magnetic field sensor based on the Ampere's force using dual-polarization DBR fiber laser

    NASA Astrophysics Data System (ADS)

    Yao, Shuang; Zhang, Yang; Guan, Baiou

    2015-08-01

    A novel magnetic field sensor using distributed Bragg reflector (DBR) fiber laser by Ampere's force effect is proposed and experimentally demonstrated. The key sensing element, that is the dual-polarization DBR fiber laser, is fixed on the middle part of two copper plates which carry the current. Ampere's force is applied onto the coppers due to an external magnetic field generated by a DC solenoid. Thus, the lateral force from the coppers is converted to a corresponding beat frequency signal shift produced by the DBR laser. The electric current sensing is also realized by the same configuration and same principle simultaneously in an intuitive manner. Good agreement between the theory calculation and the experimental results is obtained, which shows a good linearity. This sensor's sensitivity to the magnetic field and to the electric current finally reaches ~258.92 kHz/mT and ~1.08727 MHz/A, respectively.

  11. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    PubMed

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-01

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. PMID:26493154

  12. 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).

  13. 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

  14. A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Bergh, Magnus; Caleman, Carl

    2016-01-01

    Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.

  15. Development of a True Transition State Force Field from Quantum Mechanical Calculations.

    PubMed

    Madarász, Ádám; Berta, Dénes; Paton, Robert S

    2016-04-12

    Transition state force fields (TSFF) treated the TS structure as an artificial minimum on the potential energy surface in the past decades. The necessary parameters were developed either manually or by the Quantum-to-molecular mechanics method (Q2MM). In contrast with these approaches, here we propose to model the TS structures as genuine saddle points at the molecular mechanics level. Different methods were tested on small model systems of general chemical reactions such as protonation, nucleophilic attack, and substitution, and the new procedure led to more accurate models than the Q2MM-type parametrization. To demonstrate the practicality of our approach, transferrable parameters have been developed for Mo-catalyzed olefin metathesis using quantum mechanical properties as reference data. Based on the proposed strategy, any force field can be extended with true transition state force field (TTSFF) parameters, and they can be readily applied in several molecular mechanics programs as well. PMID:26925858

  16. Mapping of force fields in a capacitively driven radiofrequency plasma discharge

    NASA Astrophysics Data System (ADS)

    Dropmann, Michael; Chen, M.; Sabo, H.; Laufer, R.; Herdrich, G.; Matthews, L. S.; Hyde, T. W.

    2016-08-01

    > In this paper a method is described that allows mapping of the forces acting on dust particles in a GEC reference cell. Monodisperse particles are dropped into the plasma environment and their trajectories are tracked using a high-speed camera system to determine local accelerations and respective forces. Collecting data from a large number of particle drops allows the identification of three-dimensional vector fields for the acting forces. The procedure is described and multiple examples in which the method has been applied are given. These examples include a simple plasma sheath, plasmas perturbed by a horizontal and vertical dipole magnet, an array of multiple magnets mimicking the fields found at a lunar swirl, and the fields inside a glass box used for particle confinement. Further applicability in other plasma environments will be discussed shortly.

  17. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

    PubMed Central

    Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.

    2015-01-01

    Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208

  18. 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

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

    PubMed

    Iwata, Natsumi; Kishimoto, Yasuaki

    2014-01-24

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

  20. 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.

  1. Refinement of the application of the GROMOS 54A7 force field to β-peptides.

    PubMed

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2013-12-15

    In this study, a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, a right-handed 2.7(10/12)-helix and a left-handed 3(14)-helix, is simulated using different GROMOS force-field parameter sets. When applying the recently developed GROMOS 54A7 force field, a significant destabilization effect on the 2.7(10/12)-helix of the peptide is observed, and the agreement with the experimental NOE distance bounds is much worse compared with the ones using previous versions of the GROMOS force field. This led us to investigate the free enthalpy difference between the two helices as a function of a variation of different subsets of force-field parameters. Both long time molecular dynamics simulations and one-step perturbation predictions suggest that the disagreement with the experimental NMR data when using the 54A7 force field is caused by the use for β-peptides of the new backbone φ-/ψ-torsional-angle energy terms introduced in this force field which were based on conformational fitting of backbone φ/ψ angles for a large set of proteins. This means that these parameters of backbone φ- and ψ-torsional-angle terms should not be applied to non-α-peptides such as β-peptides. This modified assignment of torsional-angle energy terms and parameters is denoted as 54A7_β. It corrects the wrong description of the conformational ensemble of the hexa-β-peptide obtained using the previous assignment and yields as good agreement with NMR data for other β-peptides that adopt a single helical or a hairpin fold. PMID:24122968

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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 t2, 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 tα, where α > 1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics, both of magnetic

  3. 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 α}, where α > 1, and is weakly dependent on the energy of the particles. These super-diffusive characteristics

  4. 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

  5. Transferability of coarse-grained force field for nCB liquid crystal systems.

    PubMed

    Zhang, Jianguo; Guo, Hongxia

    2014-05-01

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

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

    SciTech Connect

    Zhu, X. S.; Wang, H. N.; Du, Z. L.; Fan, Y. L.

    2013-05-10

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

  7. 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

  8. 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.

  9. Measurement of GHz range magnetic field distribution near a coplanar waveguide using a beating field-type magnetic force microscope

    NASA Astrophysics Data System (ADS)

    Endo, Y.; Fukushima, M.; Arai, K.; Yanagi, K.; Shimada, Y.; Yamaguchi, M.

    2014-05-01

    This paper describes the measurement of microscopic radio frequency (RF) field distribution with a magnetic force microscope (MFM) tip exploring the beat signal from a coplanar waveguide (CPW) with a signal line as fine as 5 μm and a ground line of 50 μm. To produce a beating field in close proximity to the CPW, two RF currents with slightly different frequencies are supplied, where one is the signal current with a fixed frequency of 1.1 GHz and the other is the reference. The reference is adjusted to produce a beat with a frequency near the cantilever mechanical resonance frequency. Thus, the mechanical resonance of the cantilever excited by the beat field includes information about the 1.1 GHz field distribution from the CPW signal current. Detection of a beating field with a MFM tip can provide very high resolutions of the RF field distribution in the proximity of RF circuit component.

  10. Unified boundary conditions and Casimir forces for fields with arbitrary spin

    NASA Astrophysics Data System (ADS)

    Bennett, Robert; Stokes, Adam

    The electromagnetic Casimir effect is well-known and has been extensively studied for the last half-century. This attractive force between parallel plates arises from the imposition of boundary conditions upon the fluctuating spin-1 photon field, so a natural further question is wether fields of different spin can cause similar forces when confined in the same way. However, so far it has not been clear what the appropriate boundary conditions for physically-confined spinor fields may be. Here we present work that generalises the physically well-motivated electromagnetic boundary conditions to fields of arbitrary spin, thus arriving at physically reasonable boundary conditions and Casimir forces for a selection of interesting fields. For example, the so-called `bag model' boundary conditions from nuclear physics emerge from our generalised boundary condition as a special case, as do the linearised gravity boundary conditions suggested in a remarkable recent proposal concerning possible measurement of gravitonic Casimir forces. Supported by the UK Engineering and Physical Sciences Research Council (EPSRC).

  11. Equilibrium of magnetic fields with arbitrary interweaving of the lines of force. II - Discontinuities in the field

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1986-01-01

    The surfaces of discontinuity (SDs) identified by Parker (1986) in the torsion of a force-free magnetic field in an infinitely conducting fluid contained betweeen two fixed boundary planes are characterized analytically. It is shown that field discontinuities (current sheets) occur whenever an SD terminates within the fluid or intersects with another SD, that intersections occur in most cases, and that the resulting current sheets are responsible for most field dissipation in highly conducting fluids. The astrophysical implications of these findings and a number of unresolved problems are discussed.

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

    SciTech Connect

    Thalmann, J. K.; Tiwari, S. K.; Wiegelmann, T.

    2013-05-20

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

  13. 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, θ) in spherical coordinates is defined by a function r sin θ B φ = Q ( A ) relating its azimuthal component to its poloidal flux-function A. The power law r sin θ B φ = a A | A | 1/ n, n a positive constant, admits separable fields with A = An/(θ)rn, posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and An(θ) 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/(θ ,φ)rn+2 promises field solutions of even richer topological varieties but allowing for φ-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 γ = 4/3 as discussed in the Appendix.

  14. Changes in tibiofemoral contact forces during running in response to in-field gait retraining.

    PubMed

    Willy, Richard W; Meardon, Stacey A; Schmidt, André; Blaylock, Nathan R; Hadding, Scott A; Willson, John D

    2016-09-01

    We evaluated the efficacy of an in-field gait retraining programme using mobile biofeedback to reduce cumulative and peak tibiofemoral loads during running. Thirty runners were randomised to either a retraining group or control group. Retrainers were asked to increase their step rate by 7.5% over preferred in response to real-time feedback provided by a wrist mounted running computer for 8 routine in-field runs. An inverse dynamics driven musculoskeletal model estimated total and medial tibiofemoral joint compartment contact forces. Peak and impulse per step total tibiofemoral contact forces were immediately reduced by 7.6% and 10.6%, respectively (P < 0.001). Similarly, medial tibiofemoral compartment peak and impulse per step tibiofemoral contact forces were reduced by 8.2% and 10.6%, respectively (P < 0.001). Interestingly, no changes were found in knee adduction moment measures. Post gait retraining, reductions in medial tibiofemoral compartment peak and impulse per step tibiofemoral contact force were still present (P < 0.01). At the 1-month post-retraining follow-up, these reductions remained (P < 0.05). With these per stance reductions in tibiofemoral contact forces in mind, cumulative tibiofemoral contact forces did not change due to the estimated increase in number of steps to run 1 km. PMID:26679058

  15. Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

    SciTech Connect

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger

    2015-11-20

    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. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.

  16. Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

    DOE PAGESBeta

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger

    2015-11-20

    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 goldmore » 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. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.« less

  17. 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

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    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.

  20. 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.

  1. 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.

  2. Scalar field self-force effects on orbits about a Schwarzschild black hole

    SciTech Connect

    Diaz-Rivera, Luz Maria; Whiting, Bernard F.; Detweiler, Steven; Messaritaki, Eirini

    2004-12-15

    For a particle of mass {mu} and scalar charge q, we compute the effects of the scalar field self-force upon circular orbits, upon slightly eccentric orbits and upon the innermost stable circular orbit (ISCO) of a Schwarzschild black hole of mass m. For circular orbits the self-force is outward and causes the angular frequency at a given radius to decrease. For slightly eccentric orbits the self-force decreases the rate of the precession of the orbit. The effect of the self-force moves the radius of the innermost stable circular orbit inward by 0.122 701xq{sup 2}/{mu}, and it increases the angular frequency of the ISCO by the fraction 0.029 165 7xq{sup 2}/{mu}m.

  3. Force field inside the void in complex plasmas under microgravity conditions

    SciTech Connect

    Kretschmer, M.; Khrapak, S.A.; Zhdanov, S.K.; Thomas, H.M.; Morfill, G.E.; Fortov, V.E.; Lipaev, A.M.; Molotkov, V.I.; Ivanov, A.I.; Turin, M.V.

    2005-05-01

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

  4. 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.

  5. Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics.

    PubMed

    Poger, David; Mark, Alan E

    2012-11-13

    The sensitivity of the structure and dynamics of a fully hydrated pure bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in molecular dynamics simulations to changes in force-field and simulation parameters has been assessed. Three related force fields (the Gromos 54A7 force field, a Gromos 53A6-derived parameter set and a variant of the Berger parameters) in combination with either particle-mesh Ewald (PME) or a reaction field (RF) were compared. Structural properties such as the area per lipid, carbon-deuterium order parameters, electron density profile and bilayer thicknesses, are reproduced by all the parameter sets within the uncertainty of the available experimental data. However, there are clear differences in the ordering of the glycerol backbone and choline headgroup, and the orientation of the headgroup dipole. In some cases, the degree of ordering was reminiscent of a liquid-ordered phase. It is also shown that, although the lateral diffusion of the lipids in the plane of the bilayer is often used to validate lipid force fields, because of the uncertainty in the experimental measurements and the fact that the lateral diffusion is dependent on the choice of the simulation conditions, it should not be employed as a measure of quality. Finally, the simulations show that the effect of small changes in force-field parameters on the structure and dynamics of a bilayer is more significant than the treatment of the long-range electrostatic interactions using RF or PME. Overall, the Gromos 54A7 best reproduced the range of experimental data examined. PMID:26605633

  6. 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.

  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 β 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. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields.

    PubMed

    Kratz, Eric G; Walker, Alice R; Lagardère, Louis; Lipparini, Filippo; Piquemal, Jean-Philip; Andrés Cisneros, G

    2016-04-30

    We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc. PMID:26781073

  9. The spectroscopic constants and anharmonic force field of AgSH: An ab initio study.

    PubMed

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Zhu, Ziliang

    2016-07-01

    The equilibrium structure, spectroscopy constants, and anharmonic force field of silver hydrosulfide (AgSH) have been calculated at B3P86, B3PW91 and MP2 methods employing two basis sets, TZP and QZP, respectively. The calculated geometries, ground state rotational constants, harmonic vibrational wave numbers, and quartic and sextic centrifugal distortion constants are compared with the available experimental and theoretical data. The equilibrium rotational constants, fundamental frequencies, anharmonic constants, and vibration-rotation interaction constants, Coriolis coupling constants, cubic and quartic force constants are predicted. The calculated results show that the MP2/TZP results are in good agreement with experiment observation and are also an advisable choice to study the anharmonic force field of AgSH. PMID:27085293

  10. The spectroscopic constants and anharmonic force field of AgSH: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Zhu, Ziliang

    2016-07-01

    The equilibrium structure, spectroscopy constants, and anharmonic force field of silver hydrosulfide (AgSH) have been calculated at B3P86, B3PW91 and MP2 methods employing two basis sets, TZP and QZP, respectively. The calculated geometries, ground state rotational constants, harmonic vibrational wave numbers, and quartic and sextic centrifugal distortion constants are compared with the available experimental and theoretical data. The equilibrium rotational constants, fundamental frequencies, anharmonic constants, and vibration-rotation interaction constants, Coriolis coupling constants, cubic and quartic force constants are predicted. The calculated results show that the MP2/TZP results are in good agreement with experiment observation and are also an advisable choice to study the anharmonic force field of AgSH.

  11. Active control of sound fields in elastic cylinders by multi-control forces

    NASA Technical Reports Server (NTRS)

    Jones, J. D.; Fuller, C. R.

    1987-01-01

    An unstiffened cylindrical model was used to study the control of sound transmission into aircraft cabins by the use of multi-control forces applied directly to the cylinder wall. External acoustic monopoles were located on each side of the cylinder to approximate the propeller noise source. This allowed the study of a dual control system utilizing multi-control forces in conjunction with synchrophasing of the twin acoustic monopole sources. For acoustic resonant conditions within the cavity, a spatially averaged noise reduction of approximately 30 dB was achieved using the active control system for both in-phase and out-of-phase monopoles; however, effective reduction of the sound field was dependent upon judiciously positioning the control forces for optimal control of the sound field.

  12. 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.

  13. 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

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

    PubMed Central

    2013-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Mareš, Jiří; 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.

  16. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

    PubMed

    Harder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K; Knight, Jennifer L; Kaus, Joseph W; Cerutti, David S; Krilov, Goran; Jorgensen, William L; Abel, Robert; Friesner, Richard A

    2016-01-12

    The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field. PMID:26584231

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  19. An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates.

    PubMed

    Sibaev, M; Crittenden, D L

    2016-06-01

    In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm(-1) in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/. PMID:27276945

  20. Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

    PubMed

    Robertson, Michael J; Tirado-Rives, Julian; Jorgensen, William L

    2015-07-14

    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 φ, ψ, χ1, and χ2 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

  1. Toward a Broadly Applicable Force Field for d(6)-Piano Stool Complexes.

    PubMed

    Schmid, Maurus H; Ward, Thomas R; Meuwly, Markus

    2013-05-14

    Three-legged piano stool complexes are prototypical organometallic complexes relevant to a wide range of chemically relevant questions. Force field parametrization of transition-metal complexes is difficult and underdeveloped, and metal-specific force fields and software are required. Here we report our efforts to derive parameters for the conventional CHARMM and the Valbond-CHARMM force fields for d(6)-piano stool complexes. In Valbond-CHARMM, the usual angular term is replaced with hybrid orbital strength functions. These functions describe the energy not only of distorted bond angles around the minimum but also at very large distortions. Structure optimizations led to a good agreement between the calculated force field and the X-ray structures. They were comparable to RMSDs obtained between X-ray and DFT structures. In addition, and contrary to treating the systems with DFT, molecular dynamics simulations on the multiple nanosecond time scale are possible and allow to compute meaningful structural and energetic observables. Explicit solvent simulations of the complexes in methanol and water allow to determine the solvent distribution around the complexes. The parametrization presented here will be a useful starting point for dynamics investigations of catalysts in structurally more demanding environments. PMID:26583724

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

    PubMed

    Lee, Myung Won; Meuwly, Markus

    2013-12-14

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

  3. 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.

  4. 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.

  5. 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…

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

    ERIC Educational Resources Information Center

    Mason, Elisa

    1999-01-01

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

  7. Self-force of a scalar field for circular orbits about a Schwarzschild black hole

    NASA Astrophysics Data System (ADS)

    Detweiler, Steven; Messaritaki, Eirini; Whiting, Bernard F.

    2003-05-01

    The foundations are laid for the numerical computation of the actual worldline for a particle orbiting a black hole and emitting gravitational waves. The essential practicalities of this computation are illustrated here for a scalar particle of infinitesimal size and small but finite scalar charge. This particle deviates from a geodesic because it interacts with its own retarded field ψret. A recently introduced Green’s function GS precisely determines the singular part ψS of the retarded field. This part exerts no force on the particle. The remainder of the field ψR=ψret-ψS is a vacuum solution of the field equation and is entirely responsible for the self-force. A particular, locally inertial coordinate system is used to determine an expansion of ψS in the vicinity of the particle. For a particle in a circular orbit in the Schwarzschild geometry, the mode-sum decomposition of the difference between ψret and the dominant terms in the expansion of ψS provide a mode-sum decomposition of an approximation for ψR from which the self-force is obtained. When more terms are included in the expansion, the approximation for ψR is increasingly differentiable, and the mode sum for the self-force converges more rapidly.

  8. 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.

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

    SciTech Connect

    Guo, Y.; Ding, M. D.; Liu, Y.; Sun, X. D.; DeRosa, M. L.; Wiegelmann, T.

    2012-11-20

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

  10. 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.

  11. Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

    PubMed

    Lay, Wesley K; Miller, Mark S; Elcock, Adrian H

    2016-04-12

    GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields. PMID:26967542

  12. Dynamic structure and cluster formation in confined nanofluids under the action of an external force field

    NASA Astrophysics Data System (ADS)

    Ben-Abdallah, Philippe

    2006-10-01

    The dynamic structure and the formation of clusters in nanoparticle colloidal solutions (nanofluids) confined between two parallel walls and submitted to the action of an external force field is studied by extensive Brownian-dynamics simulations. The self-correlation of individual particles and the time correlation between distinct particles are analyzed by calculating the density-density time correlation (van Hove) function. It is shown that the self-diffusion is reduced by the external force field while the lifetime of collective modes of nanoparticles (i.e., natural phonons) is significantly enhanced by this force. We demonstrate that this result is related to disorder-order transitions in the nanoparticle spatial distribution under perturbation. Interestingly, we highlight that the interaction forces mediated by the walls act like repulsive interparticle forces. They tend to increase the structural disorder and to lower the lifetime of collective modes. Our results suggest that the heat transport properties of nanofluids could be actively controlled in nanometer-size systems.

  13. 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

  14. 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

  15. Can an isotropic plasma pressure distribution be in force balance with the T96 model field?

    NASA Astrophysics Data System (ADS)

    Zaharia, Sorin; Cheng, C. Z.

    2003-11-01

    In this paper we investigate how close the gradient force of an isotropic pressure distribution P can be in force balance with the magnetic (Lorentz) force in the T96 empirical model. The study leads to the conclusion that no isotropic pressure can be found in exact force balance with the magnetic field of the quiet time T96 model. The conclusion is derived from several analyses: (1) computing the loop integral of J × B from the model along a closed contour in the equatorial plane (the integral should vanish if J × B = ∇P); (2) obtaining one-dimensional profiles for P on the Sun-Earth axis by integrating ∇P = J × B and comparing them with observations; and (3) decomposing J × B into gradient-free and curl-free terms (the former term would be zero in an exact equilibrium) and subsequently computing the two terms by solving a Poisson-like equation with constraints. Possible physical reasons for our finding that no P exists such that J × B = ∇P include small mass flows as well as nonisotropic (and possibly even nongyrotropic) terms in the magnetospheric pressure tensor. While the lack of exact force balance with isotropic P will probably be not too serious for many situations, for some physical applications, such as the computation of Birkeland currents using the Vasyliunas relation, care must be exercised if one uses the model field in conjunction with isotropic pressure. Finally, we discuss possible ways of computing magnetospheric configurations in exact force balance with isotropic P by using empirical model fields as a starting point.

  16. Field-driven crossover from attractive-to-repulsive Casimir-like force in smectic films.

    PubMed

    de Oliveira, I N; Lyra, M L

    2004-11-01

    External fields have a profound effect on the fluctuations of strongly correlated fluids, such as a liquid crystal. Within a harmonic functional integral approach, we compute the fluctuation-induced force between the surfaces of a smectic liquid-crystal film under the presence of an ordering field. In particular, we show that for asymmetrically anchored films, the thermal Casimir interaction energy can be collapsed into a universal form crossing over from a repulsive to an attractive interaction as the film thickness is increased. We discuss the possible relevance of this field effect in nematic-smectic wetting transitions. PMID:15600581

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

    SciTech Connect

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

    1996-03-01

    Electron holography is applied for the study of the leakage field of thin-film ferromagnetic tips used as probes in magnetic force microscopy. We used commercially available pyramidal tips covered on one face with a thin NiCo film, which were then placed in a high external magnetic field directed along the pyramid axis. Good agreement between simulated and experimental electron phase difference maps allows to measure the local flux from the ferromagnetic tips and therefore to evaluate the perturbation induced by the microprobe stray field on the sample area. {copyright} {ital 1996 American Institute of Physics.}

  18. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    PubMed

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments. PMID:22247593

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

    SciTech Connect

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

    2012-01-01

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

  20. Optical forces on a Rayleigh dielectric particle in a patterned near-field landscape

    NASA Astrophysics Data System (ADS)

    Zelenina, Anna; Quidant, Romain; Petrov, Dmitri; Badenes, Goncal

    2005-07-01

    The trapping of micro-objects by optical radiation forces, so-called optical tweezers, has become widely used in physical, chemical and biological experiments where accurate and non-invasive manipulation is required. Recent advances in beam shaping render it possible for instance to rotate or to dynamically manipulate independently several elements. Today, one of the remaining challenges of conventional optical tweezers is the direct manipulation of systems with sizes belonging to the sub-wavelength or Rayleigh regime. Indeed, the diffraction limit prevents in that case from achieving a commensurable trapping volume and thus does not allow for minimizing the fluctuations in position of the trapped object due to its strong Brownian motion. In order to overcome this limitation, it has been proposed to use evanescent fields instead of the usual propagating fields. Recent advances in optics of noble metal nano-structures have recently provided new configurations to achieve nano-optical tweezers. Especially, tightly localized modes resulting from the coupling between resonant noble metal nanostructures may offer the gradient forces able to trap and manipulate Rayleigh objects. In this work, we calculate the radiation forces exerted on a nanometric dielectric sphere when exposed to a patterned optical near-field landscape at an interface decorated with resonant gold nanostructures. By comparing their magnitude with other forces that affect the movement of the particle, we discuss the practical ability of our configuration for multiple parallel optical manipulation.

  1. 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.

  2. 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.

  3. Effects of external force fields on peptide self-assembly and biomimetic silica synthesis

    NASA Astrophysics Data System (ADS)

    Yu, Jun; Wang, Qinrong; Zhang, Xin

    2014-08-01

    This study investigated the influence of physical parameters on the dynamic self-assembly of short peptide amphiphiles (A6K and V6K) and the peptide-mediated silica morphologies by applying external force fields (electric and flow fields). Diverse self-assembled structures (nanofibers, nanorods, or lamellar stacks) can be obtained depending on field intensities and molecular architectures. Although the trend in the structural transitions observed from the electrostatic stimulation differed from that obtained in flow field, the common features indicate that the formed structures exhibit a higher extent of end-to-end merging or lateral association. These self-assembled peptide-based nanostructures then were used as organic templates to tailor silica deposition. It was found that the application of flow fields can stably produce fibril morphology. However, in the case of electric fields, different silica structures were obtained by using different systems. The silica morphologies directed by V6K peptide were transformed from fibrils to plate-like structures, and A6K peptide produced fibril silica materials. The difference may be attributed to different biomimetic conditions, including external forces, solubility of hydrophobic blocks, and intensity of peptide-silicate interactions. This understanding of the mechanism by which external fields affect the self-assembled amphiphilic peptide nanostructures and the silicification process allows us to manipulate the role of short amphiphilic peptides in silica formation in vitro.

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

    NASA Astrophysics Data System (ADS)

    Jenke, Martin Günter; Santschi, Christian; Hoffmann, Patrik

    2008-02-01

    Accurate simultaneous measurements on the topography and electrostatic force field of 500nm pitch interdigitated electrodes embedded in a thin SiO2 layer in a plane perpendicular to the orientation of the electrodes are shown for the first time. A static force distance curve (FDC) based method has been developed, which allows a lateral and vertical resolution of 25 and 2nm, respectively. The measured force field distribution remains stable as result of the well controlled fabrication procedure of Pt cantilever tips that allows thousands of FDC measurements. A numerical model is established as well which demonstrates good agreement with the experimental results.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Fano resonance of the ultrasensitve optical force excited by Gaussian evanescent field

    NASA Astrophysics Data System (ADS)

    Yang, Yang; Li, Jiafang; Li, Zhi-Yuan

    2015-07-01

    In this paper, we study the angle-dependent Fano-like optical force spectra of plasmonic Ag nanoparticles, which exhibit extraordinary transformation from Lorentzian resonance to Fano resonance when excited by a Gaussian evanescent wave. We systematically analyze the behavior of this asymmetric scattering induced optical force under different conditions and find that this Fano interference-induced force is ultrasensitive to the excitation wavelength, incident angle and particle size, as well as the core-shell configuration, which could be useful for wavelength- and angle-dependent size-selective optical manipulation. The origin of this Fano resonance is further identified as the interference between the two adjacent-order multipolar plasmonic modes excited in the Ag particle under the excitation of an inhomogeneously distributed evanescent field.

  11. A coarse-grain force field for RDX: Density dependent and energy conserving

    NASA Astrophysics Data System (ADS)

    Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.

    2016-03-01

    We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.

  12. 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

  13. Relating GRACE terrestrial water storage variations to global fields of atmospheric forcing

    NASA Astrophysics Data System (ADS)

    Humphrey, Vincent; Gudmundsson, Lukas; Isabelle Seneviratne, Sonia

    2015-04-01

    Synoptic, seasonal and inter-annual fluctuations in atmospheric dynamics all influence terrestrial water storage, with impacts on ecosystems functions, human activities and land-climate interactions. Here we explore to which degree atmospheric variables can explain GRACE estimates of terrestrial water storage on different time scales. Since 2012, the most recent GRACE gravity field solutions (Release 05) can be used to monitor global changes in terrestrial water storage with an unprecedented level of accuracy over more than a decade. In addition, the release of associated gridded and post-processed products facilitates comparisons with other global datasets such as land surface model outputs or satellite observations. We investigate how decadal trends, inter-annual fluctuations as well as monthly anomalies of the seasonal cycle of terrestrial water storage can be related to fields of atmospheric forcing, including e.g. precipitation and temperature as estimated in global reanalysis products using statistical techniques. In the majority of the locations with high signal to noise ratio, both short and long-term fluctuations of total terrestrial water storage can be reconstructed to a large degree based on available atmospheric forcing. However, in some locations atmospheric forcing alone is not sufficient to explain the total change in water storage, suggesting strong influence of other processes. Within that framework, the question of an amplification or attenuation of atmospheric forcing through land-surface feedbacks and changes in long term water storage is discussed, also with respect to uncertainties and potential systematic biases in the results.

  14. 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

  15. 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

  16. Development and implementation of configurational forces based constitutive phase field models for shape memory alloys

    NASA Astrophysics Data System (ADS)

    Agboola, Babatunde Omogbolahan

    Continuum thermodynamic constitutive phase field models are developed to simulate the rate dependent, thermomechanical response and precipitate formation in shape memory alloys (SMAs). The two models are based on the application of the balance of configurational forces, a scalar order parameter (a phase field) and atomic concentration to extend standard continuum thermodynamics approach. Constitutive field equations that capture the kinetics of solid-solid martensitic phase transition in SMA and the diffusion mediated precipitate formation in an elastic solid are developed. The coupled set of thermodynamically consistent field equations results from balance of configuration forces, balance of linear momentum, balance of energy and balance of atomic species mass. The field equations capture the kinetics of phase transition, deformation and elastic wave, heat transfer and atomic diffusion respectively. The first model is thermomechanical and is used to simulate the macroscopic response of SMA such as pseudoelasticity; transformation induced pseudo-creep, stress relaxation as well as the effect of cooling rate on mechanical and thermally induced phase transformation of SMA. The second model couples diffusion with elasticity to simulate growth and coarsening of precipitate and experimentally observed concentration depletion near the precipitates Results of the simulations of the macroscopic SMA response are in very good agreement with experimental observation. Simulations suggest that rate dependent and complex thermomechanical response of SMA are due to the interaction of an inherent time scale ( as well as length scale) of phase transformation, introduced through the balance of configurational forces, with other time scales. This work contributes to improved SMA modeling, scientific understanding and design. In particular, for aerospace application under stringent requirement and severe environmental conditions. Contribution of fundamental use of balance of

  17. 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, θ) in spherical coordinates is defined by a function r sin θB{sub φ}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r sin θB{sub φ}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(θ))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(θ) 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(θ,φ))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for φ-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 γ = 4/3 as

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

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

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

    PubMed

    Özpınar, Gül Altınbaş; Beierlein, Frank R; Peukert, Wolfgang; Zahn, Dirk; Clark, Timothy

    2012-08-01

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

  20. Accurate Structure Prediction and Conformational Analysis of Cyclic Peptides with Residue-Specific Force Fields.

    PubMed

    Geng, Hao; Jiang, Fan; Wu, Yun-Dong

    2016-05-19

    Cyclic peptides (CPs) are promising candidates for drugs, chemical biology tools, and self-assembling nanomaterials. However, the development of reliable and accurate computational methods for their structure prediction has been challenging. Here, 20 all-trans CPs of 5-12 residues selected from Cambridge Structure Database have been simulated using replica-exchange molecular dynamics with four different force fields. Our recently developed residue-specific force fields RSFF1 and RSFF2 can correctly identify the crystal-like conformations of more than half CPs as the most populated conformation. The RSFF2 performs the best, which consistently predicts the crystal structures of 17 out of 20 CPs with rmsd < 1.1 Å. We also compared the backbone (ϕ, ψ) sampling of residues in CPs with those in short linear peptides and in globular proteins. In general, unlike linear peptides, CPs have local conformational free energies and entropies quite similar to globular proteins. PMID:27128113

  1. Surface Tension of Organic Liquids Using the OPLS/AA Force Field.

    PubMed

    Zubillaga, Rafael A; Labastida, Ariana; Cruz, Bibiana; Martínez, Juan Carlos; Sánchez, Enrique; Alejandre, José

    2013-03-12

    Molecular dynamics simulations are performed to obtain the surface tension of 61 organic liquids using the OPLS/AA (all-atom optimized potential for liquid simulations). The force field parameters are the same as those recently used (Caleman et al. J. Chem. Theory Comput.2012, 8, 61) to determine several thermodynamic properties of 146 organic liquids. The correct evaluation of surface tension using slab simulations of liquids requires one to properly take into account the long-range interactions (Trukhymchuk and Alejandre J. Chem. Phys.1999, 111, 8510). In addition, the liquid density from slab simulations has to be the same as that obtained in liquid simulations at constant temperature and pressure. The new results of surface tensions from this work improve those reported by Caleman et al. The OPLS/AA force field gives good surface tensions compared with experimental data for most of the systems studied in this work, although it was developed to simulate liquids. PMID:26587622

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  3. General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides.

    PubMed

    Torsello, Mauro; Pimenta, Antonio C; Wolters, Lando P; Moreira, Irina S; Orian, Laura; Polimeno, Antonino

    2016-06-30

    The General AMBER Force Field (GAFF) has been extended to describe a series of selenium and tellurium diphenyl dichalcogenides. These compounds, besides being eco-friendly catalysts for numerous oxidations in organic chemistry, display peroxidase activity, i.e., can reduce hydrogen peroxide and harmful organic hydroperoxides to water/alcohols and as such are very promising antioxidant drugs. The novel GAFF parameters are tested in MD simulations in different solvents and the (77)Se NMR chemical shift of diphenyl diselenide is computed using structures extracted from MD snapshots and found in nice agreement with the measured value in CDCl3. The whole computational protocol is described in detail and integrated with in-house code to allow easy derivation of the force field parameters for analogous compounds as well as for Se/Te organocompounds in general. PMID:27267296

  4. Effects of neutrals on internal forces and thermal conduction of a plasma in a magnetic field

    NASA Astrophysics Data System (ADS)

    Hirano, K.

    1984-08-01

    Using the Chapman-Enskog approximation the Boltzmann equation was solved to obtain friction and thermal forces appearing between ions and their parent atoms remaining in a plasma. The heat fluxes due to thermal conduction through ions and atoms were also evaluated. Charge transfer and the elastic scattering assuming the Sutherland potential were adopted as the basic collision process between ions and atoms. It was demonstrated that thermal force on neutrals always pushes them toward higher temperature region across a strong magnetic field but colder place along the field lines if the temperature is higher than 25 eV. A very small amount of neutrals, e.g., 1 ppm to the ion density, is found to be enough for neutrals transfering even much larger heat flux than the one by ion thermal conduction loss at a fusion temperature.

  5. 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.

  6. Thermodynamic and Transport Properties of H2O + NaCl from Polarizable Force Fields.

    PubMed

    Jiang, Hao; Mester, Zoltan; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2015-08-11

    Molecular dynamics and Monte Carlo simulations were performed to obtain thermodynamic and transport properties of the binary H2O + NaCl system using the polarizable force fields of Kiss and Baranyai ( J. Chem. Phys. 2013 , 138 , 204507 and 2014 , 141 , 114501 ). In particular, liquid densities, electrolyte and crystal chemical potentials of NaCl, salt solubilities, mean ionic activity coefficients, vapor pressures, vapor-liquid interfacial tensions, and viscosities were obtained as functions of temperature, pressure, and salt concentration. We compared the performance of the polarizable force fields against fixed-point-charge (nonpolarizable) models. Most of the properties of interest are better represented by the polarizable models, which also remain physically realistic at elevated temperatures. PMID:26574461

  7. A study of the force-field equation for the propagation of galactic cosmic rays

    NASA Technical Reports Server (NTRS)

    Gleeson, L. J.; Urch, I. H.

    1973-01-01

    A new development is given of the solution of the equation of the force-field approximation for the propagation of galactic cosmic rays in the interplanetary region. It leads to simpler methods for determining the force-field parameters. A method is given for determining the separable diffusion coefficient from observations of galactic electron spectrum and near-earth electron spectra; it is shown that this diffusion coefficient is not unique but may have a periodic-like dependence upon rigidity; and the method is used to obtain diffusion coefficients for 1965 and 1968. Approximate formulae relating small changes in intensity and diffusion coefficient are developed and some applications of these noted; in one it is shown that the form of, and changes in, diffusion coefficient deduced previously for a neutron monitor event during June-September 1969 are unnecessarily constrained and therefore probably not correct.

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

    PubMed Central

    2015-01-01

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

  9. On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields.

    PubMed

    Antila, Hanne S; Salonen, Emppu

    2015-04-15

    The Thole induced point dipole model is combined with three different point charge fitting methods, Merz-Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self-consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4-10%. PMID:25753482

  10. 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

  11. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    SciTech Connect

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-12-31

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  12. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-12-01

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  13. 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

  14. Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

    PubMed Central

    2016-01-01

    Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

  15. 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

  16. Polarizable Water Model for the Coarse-Grained MARTINI Force Field

    PubMed Central

    Sengupta, Durba; Marrink, Siewert J.

    2010-01-01

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

  17. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.

    PubMed

    Li, Hui; Ngo, Van; Da Silva, Mauricio Chagas; Salahub, Dennis R; Callahan, Karen; Roux, Benoît; Noskov, Sergei Yu

    2015-07-23

    Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K(+), Na(+), Ca(2+), and Cl(-)) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca(2+) binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

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

    PubMed Central

    Zhu, Xiao; MacKerell, Alexander D.

    2010-01-01

    Condensed-phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over non-polarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Towards development of a polarizable force field for biological molecules, parameters for a series of sulfur-containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 non-polarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur-containing molecules including cysteine and methionine residues in proteins. PMID:20575015

  19. SEISMIC PERFORMANCE OF RC BRIDGE COLUMNS UNDER VARYING AXIAL FORCE DUE TO NEAR-FIELD VERTICAL GROUND MOTIONS

    NASA Astrophysics Data System (ADS)

    Matsuzaki, Hiroshi; Kumagai, Yuji; Kawashima, Kazuhiko

    Recently, high acceleration and high frequency near-field vertical ground motions were recorded at several sites. The extreme vertical ground motions can induce high frequency varying axial force which develop even tensile force in reinforced concrete bridge columns. Cyclic loading experiments of RC columns were conducted to clarify the seismic performance of RC bridge columns under near-field vertical ground motions. It is shown that core concrete is crushed extensively due to varying axial force after longitudinal bars buckle.

  20. A new force field for molecular dynamics studies of Li + and Na +-nafion

    NASA Astrophysics Data System (ADS)

    Soolo, Endel; Liivat, Anti; Kasemägi, Heiki; Tamm, Tarmo; Brandell, Daniel; Aabloo, Alvo

    2008-03-01

    Nafion is widely known as one of the most popular membrane materials for low temperature fuel cell applications. However, the particular exchange membrane material properties make it also valuable for other applications. One of the electroactive polymer (EAP) subclasses, ionic polymer metal composites (IPMC) commonly exploits Nafion as the ion exchange polymer membrane. The ion conducting properties of Nafion are extremely important for IPMCs. Although, ion conductivity depends strongly on the structural properties of the polymer matrix, there has been very little insight at the atomistic level. Molecular dynamics simulations are one of the possibilities to study the ion conduction mechanism at atomistic level. So far, the simulation results have been rather contradictory and very much dependent from the force fields and polymer matrix setup used. In the present work, new force field parameters for Li + and Na + - nafion based on DFT calculations are presented. The developed potentials and the force field were tested by molecular dynamics simulations. It can be concluded that Li + and Na + ions are coordinated to different Nafion side-chain terminal group (SO 3 -) oxygens and to very few water molecules. One cation is coordinated to three different side-chains. Oxygens of SO 3 groups and cations form complicated multi-header systems. In the equilibrium state, no cations dissociated from side chains were found.

  1. Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.

    PubMed

    Bradshaw, Richard T; Essex, Jonathan W

    2016-08-01

    Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies. PMID:27341007

  2. Validating lipid force fields against experimental data: Progress, challenges and perspectives.

    PubMed

    Poger, David; Caron, Bertrand; Mark, Alan E

    2016-07-01

    Biological membranes display a great diversity in lipid composition and lateral structure that is crucial in a variety of cellular functions. Simulations of membranes have contributed significantly to the understanding of the properties, functions and behaviour of membranes and membrane-protein assemblies. This success relies on the ability of the force field used to describe lipid-lipid and lipid-environment interactions accurately, reproducibly and realistically. In this review, we present some recent progress in lipid force-field development and validation strategies. In particular, we highlight how a range of properties obtained from various experimental techniques on lipid bilayers and membranes, can be used to assess the quality of a force field. We discuss the limitations and assumptions that are inherent to both computational and experimental approaches and how these can influence the comparison between simulations and experimental data. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26850737

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

    PubMed Central

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

    2012-01-01

    Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

  4. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics.

    PubMed

    Gil-Ley, Alejandro; Bottaro, Sandro; Bussi, Giovanni

    2016-06-14

    The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement. PMID:27153317

  5. 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

  6. Development of a force field for zeolitic imidazolate framework-8 with structural flexibility.

    PubMed

    Hu, Zhongqiao; Zhang, Liling; Jiang, Jianwen

    2012-06-28

    A force field is developed for zeolitic imidazolate framework-8 (ZIF-8) with structural flexibility by combining quantum chemical calculations and classical Amber force field. The predicted crystalline properties of ZIF-8 (lattice constants, bond lengths, angles, dihedrals, and x-ray diffraction patterns) agree well with experimental results. A structural transition from crystalline to amorphous as found in experiment is observed. The mechanical properties of ZIF-8 are also described fairly well by the force field, particularly the Young's modulus predicted matches perfectly with measured value. Furthermore, the heat capacity of ZIF-8 as a typical thermophysical property is predicted and close to experimental data available for other metal-organic frameworks. It is revealed the structural flexibility of ZIF-8 exerts a significant effect on gas diffusion. In rigid ZIF-8, no diffusive behavior is observed for CH(4) within the simulation time scale of current study. With the structural flexibility, however, the predicted diffusivities of CH(4) and CO(2) are close to reported data in the literature. The density distributions and free energy profiles of CH(4) and CO(2) in the pore of ZIF-8 are estimated to analyze the mechanism of gas diffusion. PMID:22755595

  7. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    PubMed Central

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

    Using quantum mechanical studies and liquid phase simulations, the AMOEBA force field for dimethylphosphate (DMP) ion and trimethylphosphate (TMP) has been developed. Based on 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 accounting of chemical environments. 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 liquid TMP by comparing simulated density and heat of vaporization values with experimental data. Structural insight obtained from MD simulations indicates liquid TMP is stabilized by both nonpolar-nonpolar contacts and hydrogen bonding. The current study is an important step towards developing the AMOEBA model for nucleic acids. PMID:26574325

  9. Dielectrophoretic forces and potentials induced on pairs of cells in an electric field.

    PubMed Central

    Foster, K R; Sowers, A E

    1995-01-01

    A combined numerical/experimental study is reported of the membrane potentials and dielectrophoretically induced forces between cells, membrane pressures, and velocity of attraction of cells under the influence of an electric field. This study was designed to explore electrical and mechanical effects produced by a field on cells in close proximity or undergoing electrically induced fusion. Laplace's equation for pairs of membrane-covered spheres in close proximity was solved numerically by the boundary element method, and the electrically induced forces on the cells and between cells were obtained by evaluating the Maxwell stress tensor. The velocity of approach of erythrocyte ghosts or fused ghosts in a 60-Hz field of 6 V/mm was measured experimentally, and the data were interpreted by using Batchelor's theory for hydrodynamic interaction of hard spheres. The numerical results show clearly the origin of the dielectrophoretic pressures and forces in fused and unfused cells and the effects of a nearby cell on the induced membrane potentials. The experimental results agree well with predictions based on the simple electrical model of the cell. The analysis shows the strong effect of hydrodynamic interactions between the cells in determining their velocity of approach. PMID:8519978

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

    PubMed Central

    Xie, Wangshen; Gao, Jiali

    2008-01-01

    An electronic structure-based polarization method, called the X-POL potential, has been described for the purpose of constructing an empirical force field for modeling polypeptides. In the X-POL potential, the internal, bonded interactions are fully represented by an electronic structure theory augmented with some empirical torsional terms. Non-bonded interactions are modeled by an iterative, combined quantum mechanical and molecular mechanical method, in which the molecular mechanical partial charges are derived from the molecular wave functions of the individual fragments. In this paper, the feasibility of such an electronic structure force field is illustrated by small model compounds. A method has been developed for separating a polypeptide chain into peptide units and its parameterization procedure in the X-POL potential is documented and tested on glycine dipeptide. We envision that the next generation of force fields for biomolecular polymer simulations will be developed based on electronic structure theory, which can adequately define and treat many-body polarization and charge delocalization effects. PMID:18985172

  11. 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

  12. 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.

  13. 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

  14. 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

  15. Development of an improved molecular dynamics force field for surface-adsorption simulations of molybdenum disulfide

    NASA Astrophysics Data System (ADS)

    Leuty, Gary; Berry, Rajiv; Muratore, Christopher; Varshney, Vikas; Turner, Heath

    Transition metal dichalcogenides (TMDs) such as molybdenum disulfide (MoS2) have garnered significant interest in recent years. With a layered structure similar to graphene, TMDs also have an intrinsic band gap. This band gap makes them an attractive alternative to graphene in many applications. MoS2 in particular has received attention due to the placement and tenability of its band gap, via functionalization, mechanical manipulation or physisorption. The latter of these is of interest in biosensor devices. Such applications are dependent on understanding physisorption on the MoS2 surface at the molecular level. This can be difficult experimentally but is possible via computer simulation techniques such as molecular dynamics (MD) simulations. MD simulations, however, require a force field accurate to the process modeled. Such a force field must correctly describe non-bonded interactions between substrate layers and between the surface and adsorbates. The force fields we are aware of have focused on intra-layer covalent bonding for structural and vibrational analysis. This work seeks to develop, through DFT and MD simulations with experimental characterization of surface adsorption, a more accurate parameterization for non-bonded interactions for MoS2.

  16. 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 μs 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

  17. 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 μs 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

  18. What Do Effective Field Theories Tell Us About the Nuclear Force?

    NASA Astrophysics Data System (ADS)

    Friar, J. L.

    2003-10-01

    Potentials are the tools that traditional nuclear physics uses to calculate bound states and reaction rates. First-generation potentials (developed more than a decade ago) used many different mechanisms to motivate shapes and strengths, while their fits to nucleon-nucleon scattering data were indifferent. Second-generation potentials, whose fits to data range from good to excellent, were constructed within the past decade using the same motivations. Accurate third-generation potentials are now being developed using the language and techniques of chiral perturbation theory, which is an effective field theory based on the symmetries of QCD. The philosophy of such effective field theories has made a large impact on the way I view nuclear potentials. Power counting, for example, uses the scales of strongly interacting systems to provide a systematic and concise organizational scheme that subsumes both two-nucleon and three-nucleon potentials. Although this new development has led to a rapid advance in our understanding of nuclear forces (especially in isospin violation), much of this work mirrors traditional approaches. Many of the techniques usually associated with field theory (such as regularization and renormalization, for example) also have direct analogues in more traditional approaches to constructing potentials. Examples of nuclear-force mechanisms and their associated scales will be discussed throughout the talk, together with my appreciation of how well we understand the nuclear force.

  19. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics

    PubMed Central

    2016-01-01

    The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the α and ζ backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement. PMID:27153317

  20. GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates.

    PubMed

    Pol-Fachin, Laercio; Rusu, Victor H; Verli, Hugo; Lins, Roberto D

    2012-11-13

    An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules. PMID:26605624

  1. General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

    PubMed Central

    2016-01-01

    Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge–charge function previously reported (PiquemalJ.-P.; J. Phys. Chem. A2003, 107, 1035326313624) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (ParkerT. M.; J. Chem. Phys.2014, 140, 09410624606352). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields. PMID:26413036

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

    PubMed Central

    Schyman, Patric; Jorgensen, William L.

    2013-01-01

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

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

    SciTech Connect

    Zhang, Xiaoguang; Pantelides, Sokrates T.

    2009-01-01

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

  4. PARTICULATE CONTROL HIGHLIGHTS: FLUX FORCE/CONDENSATION WET SCRUBBING

    EPA Science Inventory

    The report gives highlights of EPA's flux force/condensation (FF/C) program, a system that involves the use of water vapor condensation effects to enhance fine particle collection. FF/C scrubbing offers significant cost advantages over conventional control equipment for a large n...

  5. STUDY OF HORIZONTAL-SPRAY FLUX FORCE/CONDENSATION SCRUBBER

    EPA Science Inventory

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

  6. 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.

  7. 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.

  8. Orbital motion in generalized static fields of FELs accounting for axial magnetic field, beam forces, undulator and external focusing

    SciTech Connect

    Papadichev, V.A.

    1995-12-31

    Various types of undulators with or without axial magnetic field are used in FELs. Supplementary beam focusing can be applied by wedging, inclining or profiling pole faces of plan undulators or superposing external focusing magnetic fields in addition to undulator own focusing. Space-charge forces influence significantly particle motion in high-current, low-energy electron beams. Finally, one can use simultaneously two or more different undulators for some specific purpose: more efficient and selective higher harmonics generation, changing polarization types and direction, gain enhancement in double-period undulator etc. All these cases can be treated by solving the generalized equations of transverse orbital motion in a linear approximation, which is widely used for orbit calculation, gives sufficient accuracy for practical purposes and allows to consider many variants and optimize the chosen one. The undulator field is described as a field of two plane undulators with mutually orthogonal fields and an arbitrary axial (phase) shift between them. Various values of the phase shift correspond to right- or left-handed helical undulators, plane undulator of different polarization etc. The general formulae are reduced to forms that allow easier examination of particular cases: planar or helical undulator combined with axial magnetic field or without it, gyroresonance, limiting beam current, polarization etc.

  9. 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.

  10. Generation of Seed Magnetic Field Around First Stars: Effects of Radiation Force

    NASA Astrophysics Data System (ADS)

    Ando, Masashi; Doi, Kentaro; Susa, Hajime

    2010-06-01

    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 (~10-15 G for first stars, ~10-11 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 lsim10-19 G. This seed magnetic field will not affect subsequent star formation in the neighborhood of first stars.

  11. A Multi-scale Thermomechanical-Solidification Model to Simulate the Transient Force Field Deforming an Aluminum 6061 Semisolid Weld

    NASA Astrophysics Data System (ADS)

    Zareie Rajani, H. R.; Phillion, A. B.

    2015-08-01

    Formation of hot cracks is strongly affected by the transient force field acting on the semisolid weld-base metal interface. This paper presents a model that numerically simulates such a transient force field as a function of welding parameters. The model consists of two modules: (1) By means of a granular model of solidification, the microstructure of the semisolid area within the weld is reconstructed in three dimensions; (2) Since the transient force field is developed through the mechanical interaction between the semisolid weld and its base metal, the mechanical response of the base metal to the solidification of the weld is then simulated through finite element analysis. The results show that changing welding parameters and welding constraints varies the transient force field. Based on the obtained force fields, a qualitative study is also conducted to predict the susceptibility of various welds to hot cracking.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

    This paper reports the results of an experimental investigation on a two-dimensional (2-D) wing undergoing symmetric simple harmonic flapping motion. The purpose of this investigation is to study how flapping frequency (or Reynolds number) and angular amplitude affect aerodynamic force generation and the associated flow field during flapping for Reynolds number ( Re) ranging from 663 to 2652, and angular amplitudes ( α A) of 30°, 45° and 60°. Our results support the findings of earlier studies that fluid inertia and leading edge vortices play dominant roles in the generation of aerodynamic forces. More importantly, time-resolved force coefficients during flapping are found to be more sensitive to changes in α A than in Re. In fact, a subtle change in α A may lead to considerable changes in the lift and drag coefficients, and there appears to be an optimal mean lift coefficient left( {overline {C_{{text{l}}} } } right) around α A = 45°, at least for the range of flow parameters considered here. This optimal condition coincides with the development a reverse Karman Vortex street in the wake, which has a higher jet stream than a vortex dipole at α A = 30° and a neutral wake structure at α A = 60°. Although Re has less effect on temporal force coefficients and the associated wake structures, increasing Re tends to equalize mean lift coefficients (and also mean drag coefficients) during downstroke and upstroke, thus suggesting an increasing symmetry in the mean force generation between these strokes. Although the current study deals with a 2-D hovering motion only, the unique force characteristics observed here, particularly their strong dependence on α A, may also occur in a three-dimensional hovering motion, and flying insects may well have taken advantage of these characteristics to help them to stay aloft and maneuver.

  14. Torque-consistent 3D force balance and optimization of non-resonant fields in tokamaks

    NASA Astrophysics Data System (ADS)

    Park, Jong-Kyu

    2015-11-01

    A non-axisymmetric magnetic perturbation in tokamaks breaks the toroidal symmetry and produces toroidal torque, which is well known as neoclassical toroidal viscosity (NTV) effects. Although NTV torque is second order, it is the first-order change in the pressure anisotropy that drives currents associated with local torques and thereby modifies the field penetration in force balance. The force operator becomes non-Hermitian, but can be directly solved using parallel, toroidal, and radial force balance, leading to a modified Euler-Lagrange equation. The general perturbed equilibrium code (GPEC), which has been successfully developed to solve the modified Euler-Lagrange equation, gives the torque-consistent 3D force balance as well as self-consistent NTV torque. The self-shielding of the torque becomes apparent in the solutions in high β, which was implied in recent MARS-K applications. Furthermore, the full response matrix including the torque in GPEC provides a new and systematic way of optimizing torque and non-resonant fields. Recently the optimization of 3D fields for torque has been actively studied using the stellarator optimizing tools, but the efficiency and accuracy can be greatly improved by directly incorporating the torque response matrix. There are salient features uncovered by response with the torque, as the response can become invisible in amplitudes but only significant in toroidal phase shift. A perturbation in backward helicity is an example, in which NTV can be induced substantially but quietly without measurable response in amplitudes. A number of other GPEC applications will also be discussed, including the multi-mode responses in high- β tokamak plasmas and the new non-axisymmetric control coil (NCC) design in NSTX-U. This work was supported by DOE Contract DE-AC02-09CH11466.

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

    PubMed Central

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

    2014-01-01

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

  16. Automatic measurement of water levels within the 300-FF-5 boundary

    SciTech Connect

    Campbell, M.D.; Newcomer, D.R.

    1992-04-01

    A network of pressure transducers with dataloggers and radio transceivers was designed to monitor water levels in 42 wells within the CERCLA 300-FF-5 boundary in the 300 Area at the Hanford Site. Automatic datalogging, radio retrieval, and computer processing provide hourly measurements that appear precise within {plus_minus}0.02 ft at a cost expected to be less than $1 each compared with $9 each for steel-tape measurements made manually. Laboratory and field results both confirm that precision is half of that originally specified. This report is intended as a reference to be used in operating and maintaining the monitoring system. The report includes water-level measurements from the first eight wells monitored.

  17. Automatic measurement of water levels within the 300-FF-5 boundary

    SciTech Connect

    Campbell, M.D.; Newcomer, D.R.

    1992-04-01

    A network of pressure transducers with dataloggers and radio transceivers was designed to monitor water levels in 42 wells within the CERCLA 300-FF-5 boundary in the 300 Area at the Hanford Site. Automatic datalogging, radio retrieval, and computer processing provide hourly measurements that appear precise within {plus minus}0.02 ft at a cost expected to be less than $1 each compared with $9 each for steel-tape measurements made manually. Laboratory and field results both confirm that precision is half of that originally specified. This report is intended as a reference to be used in operating and maintaining the monitoring system. The report includes water-level measurements from the first eight wells monitored.

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

    NASA Astrophysics Data System (ADS)

    Buta, R.; Block, D. L.

    2001-05-01

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

  19. Intraplate Stress Field in Brazil Using Focal Mechanisms: Regional and Local Patterns: Examples of Regional Forces Controlling the Stress Field

    NASA Astrophysics Data System (ADS)

    Dias, F. L.; Assumpcao, M.

    2014-12-01

    The knowledge of stress field is fundamental not only to understand driving forces and plate deformation but also in the study of intraplate seismicity. In Brazil, the stress field has been determined mainly using focal mechanisms and a breakout data and in-situ measurements. However, the stress field still is poorly known in Brazil. We show a recent compilation of focal mechanism determined in Brazil (Fig 1). The focal mechanisms of some recent earthquakes (magnitude lower than 5 mb) were studied using waveform modeling. We stacked the record of several teleseismic stations (> 30°) with a good signal/noise ratio and we grouped then according to distance and azimuth. With the focal mechanisms available in literature and those obtained in this work, we were able to identify some patterns: the central region shows compressional pattern (E-W SHmax), which is predicted by regional theoretical models ( Coblentz & Richardson, 1996 and the TD0 model of Lithgow & Bertelloni, 2004). This compression is mainly due to the interaction of tectonic plate forces. Meanwhile in the Amazon region, we find an indication of SHMax oriented in the SE-NW direction, probably caused by the Caribbean plate interaction (Meijer, 1995) and Amazon Fan, we have flexural stresses caused by sedimentary load with is in agreement with local theoretical models (Watts et al., 2009) . In northern coastal region, the compression rotates following the coastline, which indicates an important local component related to spreading effects at the continental/oceanic transition (Assumpção, 1998). We determine the focal mechanism of several events in Brazil using different techniques according to the available data. The major difficulty is to determine focal mechanism of low magnitudes events (< 5.0 mb) using distant or few seismograph stations. We find examples of stress perturbati