Science.gov

Sample records for non-inertial force fields

  1. Explaining as Mediated Action: An Analysis of Pre-Service Teachers' Account of Forces of Inertia in Non-Inertial Frames of Reference

    ERIC Educational Resources Information Center

    de Pereira, Alexsandro Pereira; Lima Junior, Paulo; Rodrigues, Renato Felix

    2016-01-01

    Explaining is one of the most important everyday practices in science education. In this article, we examine how scientific explanations could serve as cultural tools for members of a group of pre-service physics teachers. Specifically, we aim at their use of explanations about forces of inertia in non-inertial frames of reference. A basic…

  2. The error of L5/S1 joint moment calculation in a body-centered non-inertial reference frame when the fictitious force is ignored.

    PubMed

    Xu, Xu; Faber, Gert S; Kingma, Idsart; Chang, Chien-Chi; Hsiang, Simon M

    2013-07-26

    In ergonomics studies, linked segment models are commonly used for estimating dynamic L5/S1 joint moments during lifting tasks. The kinematics data input to these models are with respect to an arbitrary stationary reference frame. However, a body-centered reference frame, which is defined using the position and the orientation of human body segments, is sometimes used to conveniently identify the location of the load relative to the body. When a body-centered reference frame is moving with the body, it is a non-inertial reference frame and fictitious force exists. Directly applying a linked segment model to the kinematics data with respect to a body-centered non-inertial reference frame will ignore the effect of this fictitious force and introduce errors during L5/S1 moment estimation. In the current study, various lifting tasks were performed in the laboratory environment. The L5/S1 joint moments during the lifting tasks were calculated by a linked segment model with respect to a stationary reference frame and to a body-centered non-inertial reference frame. The results indicate that applying a linked segment model with respect to a body-centered non-inertial reference frame will result in overestimating the peak L5/S1 joint moments of the coronal plane, sagittal plane, and transverse plane during lifting tasks by 78%, 2%, and 59% on average, respectively. The instant when the peak moment occurred was delayed by 0.13, 0.03, and 0.09s on average, correspondingly for the three planes. The root-mean-square errors of the L5/S1 joint moment for the three planes are 21Nm, 19Nm, and 9Nm, correspondingly.

  3. Explaining as Mediated Action. An Analysis of Pre-service Teachers' Account of Forces of Inertia in Non-inertial Frames of Reference

    NASA Astrophysics Data System (ADS)

    de Pereira, Alexsandro Pereira; Lima Junior, Paulo; Rodrigues, Renato Felix

    2016-05-01

    Explaining is one of the most important everyday practices in science education. In this article, we examine how scientific explanations could serve as cultural tools for members of a group of pre-service physics teachers. Specifically, we aim at their use of explanations about forces of inertia in non-inertial frames of reference. A basic assumption of our study is that explanatory tools (e.g., typical explanations learned) shape the ways we think and speak about the world. Drawing on the theory of mediated action, analysis illustrates three major claims on scientific explanations: (1) explaining is an act of actively responding to explanations presented by others (and not only to evidence itself); (2) the actual experience of explaining involves the enactment of power and authority; (3) resistance (not acknowledging an explanation as one's own) might be a constitutive part of learning how to explain (hence, teachers could approach scientific explanation in a less dogmatic way). These assertions expand the possibilities of dialogue between studies of scientific explanations and the social sciences. Implications for science teaching and research in science education are presented.

  4. Spin transport in non-inertial frame

    NASA Astrophysics Data System (ADS)

    Chowdhury, Debashree; Basu, B.

    2014-09-01

    The influence of acceleration and rotation on spintronic applications is theoretically investigated. In our formulation, considering a Dirac particle in a non-inertial frame, different spin related aspects are studied. The spin current appearing due to the inertial spin-orbit coupling (SOC) is enhanced by the interband mixing of the conduction and valence band states. Importantly, one can achieve a large spin current through the k → . p → method in this non-inertial frame. Furthermore, apart from the inertial SOC term due to acceleration, for a particular choice of the rotation frequency, a new kind of SOC term can be obtained from the spin rotation coupling (SRC). This new kind of SOC is of Dresselhaus type and controllable through the rotation frequency. In the field of spintronic applications, utilizing the inertial SOC and SRC induced SOC term, theoretical proposals for the inertial spin filter, inertial spin galvanic effect are demonstrated. Finally, one can tune the spin relaxation time in semiconductors by tuning the non-inertial parameters.

  5. Physics of Non-Inertial Reference Frames

    SciTech Connect

    Kamalov, Timur F.

    2010-12-22

    Physics of non-inertial reference frames is a generalizing of Newton's laws to any reference frames. It is the system of general axioms for classical and quantum mechanics. The first, Kinematics Principle reads: the kinematic state of a body free of forces conserves and equal in absolute value to an invariant of the observer's reference frame. The second, Dynamics Principle extended Newton's second law to non-inertial reference frames and also contains additional variables there are higher derivatives of coordinates. Dynamics Principle reads: a force induces a change in the kinematic state of the body and is proportional to the rate of its change. It is mean that if the kinematic invariant of the reference frame is n-th derivative with respect the time, then the dynamics of a body being affected by the force F is described by the 2n-th differential equation. The third, Statics Principle reads: the sum of all forces acting a body at rest is equal to zero.

  6. Non-inertial calibration of vibratory gyroscopes

    NASA Technical Reports Server (NTRS)

    Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor)

    2003-01-01

    The electrostatic elements already present in a vibratory gyroscope are used to simulate the Coriolis forces. An artificial electrostatic rotation signal is added to the closed-loop force rebalance system. Because the Coriolis force is at the same frequency as the artificial electrostatic force, the simulated force may be introduced into the system to perform an inertial test on MEMS vibratory gyroscopes without the use of a rotation table.

  7. Turbulence Modeling in Non-Inertial Frames of Reference,

    DTIC Science & Technology

    1988-03-01

    40-R193 962 TURBULENCE MODELING IN NON-INERTIAL FRAMES OF REFERENCE 1Iii (U) INSTITUTE FOR COMPUTER APLICATIONS IN SCIENCE AND ENGINERIN C G MPEZIALE...0ICASE r TURBULENCE MODELING IN NON-INE&TIAL ~ FRANKS OF REFERENCE D1C SELECD Charles G. Spezial* APR0 81D Contract No. NASI-18107 March 1988 Vr oum

  8. Turbulence modeling in non-inertial frames of reference

    NASA Technical Reports Server (NTRS)

    Speziale, Charles G.

    1988-01-01

    The effect of an arbitrary change of frame on the structure of turbulence models is examined from a fundamental theoretical standpoint. It is proven, as a rigorous consequence of the Navier-Stokes equations, that turbulence models must be form invariant under arbitrary translational accelerations of the reference frame and should only be affected by rotations through the intrinsic mean vorticity. A direct application of the invariance property along with the Taylor-Proudman Theorem, material frame-indifference in the limit of two-dimensional turbulence and Rapid Distortion Theory is shown to yield powerful constraints on the allowable form of turbulence models. Most of the commonly used turbulence models are demonstrated to be in serious violation of these constraints and consequently are inconsistent with the Navier-Stokes equations in non-inertial frames. Alternative models with improved non-inertial properties are developed and some simple applications to rotating turbulent flows are considered.

  9. Force-Field Parameter Fitter

    SciTech Connect

    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.

  10. NEW APPROACHES: The importance of non-inertial reference systems in some problems of translational dynamics

    NASA Astrophysics Data System (ADS)

    Casanova, R.; Mendialdua, J.

    1997-11-01

    The importance of using non-inertial reference systems in some problems of translational dynamics is addressed. For this, a problem is presented with its detailed solution. Typical misconceptions and preconceptions of students in this subject are discussed.

  11. Dynamic properties of force fields

    NASA Astrophysics Data System (ADS)

    Vitalini, F.; Mey, A. S. J. S.; Noé, F.; Keller, B. G.

    2015-02-01

    Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.

  12. Contrasting Classical and Quantum Vacuum States in Non-inertial Frames

    NASA Astrophysics Data System (ADS)

    Boyer, Timothy H.

    2013-08-01

    Classical electron theory with classical electromagnetic zero-point radiation (stochastic electrodynamics) is the classical theory which most closely approximates quantum electrodynamics. Indeed, in inertial frames, there is a general connection between classical field theories with classical zero-point radiation and quantum field theories. However, this connection does not extend to noninertial frames where the time parameter is not a geodesic coordinate. Quantum field theory applies the canonical quantization procedure (depending on the local time coordinate) to a mirror-walled box, and, in general, each non-inertial coordinate frame has its own vacuum state. In particular, there is a distinction between the "Minkowski vacuum" for a box at rest in an inertial frame and a "Rindler vacuum" for an accelerating box which has fixed spatial coordinates in an (accelerating) Rindler frame. In complete contrast, the spectrum of random classical zero-point radiation is based upon symmetry principles of relativistic spacetime; in empty space, the correlation functions depend upon only the geodesic separations (and their coordinate derivatives) between the spacetime points. The behavior of classical zero-point radiation in a noninertial frame is found by tensor transformations and still depends only upon the geodesic separations, now expressed in the non-inertial coordinates. It makes no difference whether a box of classical zero-point radiation is gradually or suddenly set into uniform acceleration; the radiation in the interior retains the same correlation function except for small end-point (Casimir) corrections. Thus in classical theory where zero-point radiation is defined in terms of geodesic separations, there is nothing physically comparable to the quantum distinction between the Minkowski and Rindler vacuum states. It is also noted that relativistic classical systems with internal potential energy must be spatially extended and can not be point systems. The

  13. The relativistic blackbody spectrum in inertial and non-inertial reference frames

    NASA Astrophysics Data System (ADS)

    Lee, Jeffrey S.; Cleaver, Gerald B.

    2017-04-01

    By invoking inverse temperature as a van Kampen-Israel future-directed timelike 4-vector, this paper derives the Relativistic Blackbody Spectrum, the Relativistic Wien's Displacement Law, and the Relativistic Stefan-Boltzmann Law in inertial and non-inertial reference frames.

  14. 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

  15. On the Effects of Curvature on the Confinement of a Neutral Particle to a Quantum Dot Induced by Non-inertial Effects

    NASA Astrophysics Data System (ADS)

    Bakke, K.

    2012-03-01

    We discuss the influence of a linear topological defect on the bound states of a non-relativistic neutral particle with permanent magnetic dipole moment in two distinct cases: In the first case, we consider a Fermi-Walker reference frame for the observers and show how non-inertial effects yield bound states analogous to having a neutral particle subject to the Tan-Inkson model for a quantum dot (W.-C. Tan, J.C. Inkson, Semicond. Sci. Technol. 11:1635, 1996); in the second case, we consider the action of a constant force and obtain the energy levels of the bound states.

  16. The task of the relativistic oscillator in a non-inertial frame of reference

    NASA Astrophysics Data System (ADS)

    Perepelkin, E. E.; Sadovnikov, B. I.; Inozemtseva, N. G.

    2016-09-01

    The relativistic theory is one of the most difficult parts of theoretical physics to understand by high school students and scientists alike. In this paper, the important aspects from this theory are considered. The case of the non-inertial reference frame in which the space-time interval was presented for the Lorentz-like transformations, and the condition by which the transition to the inertial reference frame takes place, is shown.

  17. Quantum correlations of helicity entangled states in non-inertial frames beyond single mode approximation

    SciTech Connect

    Harsij, Zeynab Mirza, Behrouz

    2014-12-15

    A helicity entangled tripartite state is considered in which the degree of entanglement is preserved in non-inertial frames. It is shown that Quantum Entanglement remains observer independent. As another measure of quantum correlation, Quantum Discord has been investigated. It is explicitly shown that acceleration has no effect on the degree of quantum correlation for the bipartite and tripartite helicity entangled states. Geometric Quantum Discord as a Hilbert–Schmidt distance is computed for helicity entangled states. It is shown that living in non-inertial frames does not make any influence on this distance, either. In addition, the analysis has been extended beyond single mode approximation to show that acceleration does not have any impact on the quantum features in the limit beyond the single mode. As an interesting result, while the density matrix depends on the right and left Unruh modes, the Negativity as a measure of Quantum Entanglement remains constant. Also, Quantum Discord does not change beyond single mode approximation. - Highlights: • The helicity entangled states here are observer independent in non-inertial frames. • It is explicitly shown that Quantum Discord for these states is observer independent. • Geometric Quantum Discord is also not affected by acceleration increase. • Extending to beyond single mode does not change the degree of entanglement. • Beyond single mode approximation the degree of Quantum Discord is also preserved.

  18. 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.

  19. 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.

  20. Force fields for classical molecular dynamics.

    PubMed

    Monticelli, Luca; Tieleman, D Peter

    2013-01-01

    In this chapter we review the basic features and the principles underlying molecular mechanics force fields commonly used in molecular modeling of biological macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.

  1. Enhancement of multipartite entanglement in an open system under non-inertial frames

    NASA Astrophysics Data System (ADS)

    Sun, Wen-Yang; Wang, Dong; Yang, Jie; Ye, Liu

    2017-04-01

    In this paper, multipartite entanglement enhancement in an open system under non-inertial frames via local non-unitary operations is explored. Explicitly, we investigate an available methodology to enhance tripartite entanglement of X-state, when the systems suffer from amplitude damping (AD) noise and one subsystem is under non-inertial frames. As an illustration, we consider three cases (one subsystem or multi-subsystem suffers from decoherence) by using local non-unitary operations, and the corresponding entanglement behaviors are revealed. It turns out that the local non-unitary operation can enhance entanglement to some degree. The Unruh effect and decoherence will influence the tripartite entanglement. However, the impact of Unruh effect on tripartite entanglement is weaker than that of decoherence. In addition, we obtain an interesting result: One can estimate and probe the decoherence strength (AD noise) in accordance with the change of local non-unitary operation strength and genuinely multipartite entanglement variation. Therefore, our work may be beneficial to explore the dynamic behavior of tripartite entanglement in open systems under relativity frame.

  2. Lipid14: The Amber Lipid Force Field

    PubMed Central

    2015-01-01

    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

  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. Neutrino interaction with background matter in a non-inertial frame

    NASA Astrophysics Data System (ADS)

    Dvornikov, Maxim

    2015-07-01

    We study Dirac neutrinos propagating in rotating background matter. First we derive the Dirac equation for a single massive neutrino in the non-inertial frame, where matter is at rest. This equation is written in the effective curved spacetime corresponding to the co-rotating frame. We find the exact solution of the Dirac equation. The neutrino energy levels for ultrarelativistic particles are obtained. Then we discuss several neutrino mass eigenstates, with a nonzero mixing between them, interacting with rotating background matter. We derive the effective Schrödinger equation governing neutrino flavor oscillations in rotating matter. The new resonance condition for neutrino oscillations is obtained. We also examine the correction to the resonance condition caused by the matter rotation.

  5. Entanglement concentration for two-mode Gaussian states in non-inertial frames

    NASA Astrophysics Data System (ADS)

    Di Noia, Maurizio; Giraldi, Filippo; Petruccione, Francesco

    2017-04-01

    Entanglement creation and concentration by means of a beam splitter (BS) is analysed for a generic two-mode bipartite Gaussian state in a relativistic framework. The total correlations, the purity and the entanglement in terms of logarithmic negativity are analytically studied for observers in an inertial state and in a non-inertial state of uniform acceleration. The dependence of entanglement on the BS transmissivity due to the Unruh effect is analysed in the case when one or both observers undergo uniform acceleration. Due to the Unruh effect, depending on the initial Gaussian state parameters and observed accelerations, the best condition for entanglement generation limited to the two modes of the observers in their regions is not always a balanced beam splitter, as it is for the inertial case.

  6. New aspects in force field calculations

    NASA Astrophysics Data System (ADS)

    Mink, J.

    A literature survey of more than 500 recently published papers suggest that experimental force field computations dominate (˜400 papers) but an ever-increasing number (˜75 papers) report on results of quantum chemical calculations, of which 46 are ab initio calculations. A user friendly and time-saving complete program system containing eleven subprograms capable of calculating vibrational frequencies, potential energy distributions, mean square amplitudes, Cartesian displacement of the atoms and refining the initial set of force constants is described. Results of complete force field studies of mercuriomethanes, C(HgX) 4 (X = F, Cl, Br, I, CN and CH 3) are discussed. The CHg and HgX stretching force constants are considerably lower than in related compounds of CH 3HgX, suggesting some interaction between mercury atoms. The "non-bonded" Hg…Hg bond order is around 0.15. A new normal-coordinate treatment using rigid body approximation for π-complexes has been suggested. The metal-ethylene skeletal force constants are calculated for Zeise-type chloride and bromide anions.

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

    PubMed

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

    2014-04-08

    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.

  8. Field study on moving force identification

    NASA Astrophysics Data System (ADS)

    Chan, Hung-tin Tommy; Yung, Tak H.; Law, S. S.

    2001-08-01

    A field measurement to validate a moving force identification method was carried out on an existing prestressed concrete highway bridge with a span length of 28 m. The test bridge is located at Ma Tau Wai, Kowloon, Hong Kong. A heavy 2-axle truck with known axle loads was used as a control vehicle. Besides the control vehicle, axle load data of in-service vehicles were also collected. The bridge responses acquired for the identification were indirectly measured using strain gauges. Results show that dynamic axle loads induced from both control and in-service vehicles can be identified indicating the method is valid for identification of moving forces.

  9. 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

    2014-08-05

    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.

  10. 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.

  11. Ab initio based polarizable force field parametrization

    NASA Astrophysics Data System (ADS)

    Masia, Marco

    2008-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

    Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field (GAFF) for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes.

  13. 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…

  14. LESSONS LEARNED, HEADQUARTERS, I FIELD FORCE VIETNAM ARTILLERY

    DTIC Science & Technology

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

  15. Reactive Force Fields via Explicit Valency

    NASA Astrophysics Data System (ADS)

    Kale, Seyit

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

  16. 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.)

  17. 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.

  18. Friction forces arising from fluctuating thermal fields

    NASA Astrophysics Data System (ADS)

    Zurita-Sánchez, Jorge R.; Greffet, Jean-Jacques; Novotny, Lukas

    2004-02-01

    We calculate the damping of a classical oscillator induced by the electromagnetic field generated by thermally fluctuating currents in the environment. The fluctuation-dissipation theorem is applied to derive the linear-velocity damping coefficient γ. It turns out that γ is the result of fourth-order correlation functions. The theory is applied to a particle oscillating parallel to a flat substrate and numerical values for γ are evaluated for particle and substrate materials made of silver and glass. We find that losses are much higher for dielectric materials than for metals because of the higher resistivity. We predict that measurements performed on metal films are strongly affected by the underlying dielectric substrate and we show that our theory reproduces existing theoretical results in the nonretarded limit. The theory provides an explanation for the observed distance-dependent damping in shear-force microscopy and it gives guidance for future experiments. Also, the theory should be of importance for the design of nanoscale mechanical systems and for understanding the trade-offs of miniaturization.

  19. 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.

  20. Understrength Air Force Officer Career Fields. A Force Management Approach

    DTIC Science & Technology

    2005-01-01

    communications, and computers; intelligence, surveillance, and reconnaissance CFM career field manager CGO company-grade officer CMDB Consolidated Manpower...this report were drawn from two data sources. The first is the Consolidated Manpower Data Base ( CMDB ), which is the collection of Unit Manpower

  1. 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.

  2. Motor force field learning influences visual processing of target motion.

    PubMed

    Brown, Liana E; Wilson, Elizabeth T; Goodale, Melvyn A; Gribble, Paul L

    2007-09-12

    There are reciprocal connections between visual and motor areas of the cerebral cortex. Although recent studies have provided intriguing new insights, in comparison with volume of research on the visual control of movement, relatively little is known about how movement influences vision. The motor system is perfectly suited to learn about environmental forces. Does environmental force information, learned by the motor system, influence visual processing? Here, we show that learning to compensate for a force applied to the hand influenced how participants predicted target motion for interception. Ss trained in one of three constant force fields by making reaching movements while holding a robotic manipulandum. The robot applied forces in a null [null force field (NFF)], leftward [leftward force field (LFF)], or [rightward force field (RFF)] direction. Training was followed immediately with an interception task. The target accelerated from left to right and Ss's task was to stab it. When viewing time was optimal for prediction, the RFF group initiated their responses earlier and hit more targets, and the LFF group initiated their responses later and hit fewer targets, than the NFF group. In follow-up experiments, we show that motor learning is necessary, and we rule out the possibility that explicit force direction information drives how Ss altered their predictions of visual motion. Environmental force information, acquired by motor learning, influenced how the motion of nearby visual targets was predicted.

  3. 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.

  4. Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

    PubMed

    Matthews, James F; Beckham, Gregg T; Bergenstråhle-Wohlert, Malin; Brady, John W; Himmel, Michael E; Crowley, Michael 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 Iβ 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 Iβ 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.

  5. Comparison of generic force fields for packing of concave molecules

    NASA Astrophysics Data System (ADS)

    Del Regno, Annalaura; Siperstein, Flor R.

    2014-09-01

    Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.

  6. Approximate photochemical dynamics of azobenzene with reactive force fields

    SciTech Connect

    Li, Yan; Hartke, Bernd

    2013-12-14

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

  7. Approximate photochemical dynamics of azobenzene with reactive force fields

    NASA Astrophysics Data System (ADS)

    Li, Yan; Hartke, Bernd

    2013-12-01

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

  8. Infiltration of fibrous preform in the centrifugal force field

    SciTech Connect

    Nishida, Yoshinori; Shirayanagi, Itaru; Sakai, Yoshibumi; Tozawa, Yasuhisa

    1994-12-31

    The pressure to infiltrate molten aluminum into alumina short fiber preform was generated by centrifugal force, and the start pressure for the infiltration was measured. The fundamental equation of infiltration phenomenon was derived from the equation of the conservation of momentum of fluid flow in the porous media in the centrifugal force field. One-dimensional solution of the equation was obtained to discuss the characteristics of fluid flow in a centrifugal force field. It was made clear that centrifugal force is effective as a motive force to infiltrate molten metal into fibrous preform, the pressure distribution of molten metal in the preform is different from that predicted by D`Arcy`s law and the infiltration is enhanced by centrifugal force.

  9. 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.

  10. Radiation from an Accelerated Point Charge and Non-Inertial Observers

    ERIC Educational Resources Information Center

    Leonov, A. B.

    2012-01-01

    It is known that observers comoving with a uniformly accelerated point charge detect the electromagnetic field of a charge as a static electric field. We show that one can find a similar family of observers, which detect the field of a charge as a static electric field, in the general case of arbitrary point-charge motion. We find the velocities…

  11. 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.

  12. Science in a Box. Magnets III: Force Fields.

    ERIC Educational Resources Information Center

    Learning, 1992

    1992-01-01

    Presents ideas to help elementary school educators teach their students about magnetic force fields by observing how iron filings line up around magnets. The article lists materials needed and offers a student page with suggested student activities. (SM)

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

    PubMed

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

    2010-09-01

    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.

  14. 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.

  15. Force Structure Matters: The US Field Artillery in Operational Art

    DTIC Science & Technology

    2015-05-23

    YYYY) 23-05-2015 2. REPORT TYPE Master’s Thesis 3. DATES COVERED (From - To) June 2014 – May 2015 4. TITLE AND SUBTITLE Force Structure Matters...organizational structure of the US Field Artillery. Defining key terminology within the fires capability requirement generates an understanding of the type ...Force Structure Matters: The US Field Artillery in Operational Art A Monograph by MAJ Alex A. Aquino United States Army

  16. 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.

  17. 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.

  18. Measuring the complete force field of an optical trap.

    PubMed

    Jahnel, Marcus; Behrndt, Martin; Jannasch, Anita; Schäffer, Erik; Grill, Stephan W

    2011-04-01

    The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. An improved OPLS-AA force field for carbohydrates.

    PubMed

    Kony, D; Damm, W; Stoll, S; Van Gunsteren, W F

    2002-11-30

    This work describes an improved version of the original OPLS-all atom (OPLS-AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio-derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS-AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D-glucose, D-mannose, and D-galactose, as well as of the methyl-pyranosides of D-glucose, D-mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS-AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of alpha-D-glucose and alpha-D-galactose the ratios for the three different conformations of the hydroxymethylene group and the average (3)J(H,H) coupling constants are derived and compared to experimental values. The results obtained for OPLS-AA-SEI force field are in good agreement with experiment whereas the properties derived for the OPLS-AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS-AA-SEI force field will allow simulating larger carbohydrates or

  4. 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

  5. Operational Art in I Field Force, 1965 to 1967

    DTIC Science & Technology

    2012-10-17

    border infiltration, gain and maintain control over the rice production, and separate the enemy from the population of South Vietnam , I Field Force...Force found in Vietnam and the current and future environment for the U.S. military. The U.S. will likely see conflicts that produce hybrid warfare...days of the Vietnam War. The monograph does not answer how or why the U.S. and her allies failed to save a competent South Vietnam ; rather, this study

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

    PubMed Central

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

    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

  7. 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

  8. Parametrization of macrolide antibiotics using the force field toolkit.

    PubMed

    Pavlova, Anna; Gumbart, James C

    2015-10-15

    Macrolides are an important class of antibiotics that target the bacterial ribosome. Computer simulations of macrolides are limited as specific force field parameters have not been previously developed for them. Here, we determine CHARMM-compatible force field parameters for erythromycin, azithromycin, and telithromycin, using the force field toolkit (ffTK) plugin in VMD. Because of their large size, novel approaches for parametrizing them had to be developed. Two methods for determining partial atomic charges, from interactions with TIP3P water and from the electrostatic potential, as well as several approaches for fitting the dihedral parameters were tested. The performance of the different parameter sets was evaluated by molecular dynamics simulations of the macrolides in ribosome, with a distinct improvement in maintenance of key interactions observed after refinement of the initial parameters. Based on the results of the macrolide tests, recommended procedures for parametrizing very large molecules using ffTK are given.

  9. 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.

  10. 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.

  11. 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

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

    PubMed Central

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

    2013-01-01

    We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36–155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides. PMID:23997693

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

    PubMed

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

    2013-08-13

    We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ1) for all amino acids with a CMAP correction term. The CMAP potential in PRIMO is optimized based on the new CHARMM C36 CMAP. The resulting optimized force field has been applied in MD simulations of several proteins of 36-155 amino acids and shown that the root-mean-squared-deviation of the average structure from the corresponding crystallographic structure varies between 1.80 and 4.03 Å. PRIMO is shown to fold several small peptides to their native-like structures from extended conformations. These results suggest the applicability of the PRIMO force field in the study of protein structures in aqueous solution, structure predictions as well as ab initio folding of small peptides.

  14. Acoustic Force Density Acting on Inhomogeneous Fluids in Acoustic Fields

    NASA Astrophysics Data System (ADS)

    Karlsen, Jonas T.; Augustsson, Per; Bruus, Henrik

    2016-09-01

    We present a theory for the acoustic force density acting on inhomogeneous fluids in acoustic fields on time scales that are slow compared to the acoustic oscillation period. The acoustic force density depends on gradients in the density and compressibility of the fluid. For microfluidic systems, the theory predicts a relocation of the inhomogeneities into stable field-dependent configurations, which are qualitatively different from the horizontally layered configurations due to gravity. Experimental validation is obtained by confocal imaging of aqueous solutions in a glass-silicon microchip.

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Moriarty, Philip

    2014-03-01

    Hydrogen-bonding underpins the structure, properties, and dynamics of a vast array of systems spanning a wide variety of scientific fields. From the striking complexity of the phase diagram of H2O and the elegance of base pair interactions in DNA, to the directionality inherent in supramolecular self-assembly at surfaces, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the H-bond, including the magnitude of the force and binding energy, force constant, and decay length associated with the interaction, have been vigorously debated for many decades. I will discuss how dynamic force microscopy (DFM) using a qPlus sensor can quantitatively map the tip-sample force-field for naphthalene tetracarboxylic diimide (NTCDI) molecules hydrogen-bonded in 2D assemblies. A comparison of experimental images and force spectra with their simulated counterparts from density functional theory calculations shows that image contrast due to intermolecular hydrogen bonds arises fundamentally from charge density depletion due to strong tip-sample interactions. Interpretation of DFM images of hydrogen bonds 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.

  17. Mitigated-force carriage for high magnetic field environments

    SciTech Connect

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

    2014-05-20

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

  18. Bioventing Field Initiative at Keesler Air Force Base, Mississippi

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at Keesler AFB, Mississippi, as part of the Bioventing Field initiative for the U.S. Air Force Center...and installation of bioventing systems. Each site at the base is discussed individually, followed by a description of site activities at the...background area. The purpose of this Bioventing Field initiative is to measure the soil gas permeability and microbial activity at a contaminated site in

  19. Introduction of periodic boundary conditions into UNRES force field.

    PubMed

    Sieradzan, Adam K

    2015-05-05

    In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the ββα hetero tetramer 1 protein system.

  20. Energy buildup in sheared force-free magnetic fields

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard; Low, Boon C.

    1992-01-01

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

  1. A Survey of Snakebite Knowledge among Field Forces in China

    PubMed Central

    Chen, Chulin; Gui, Li; Kan, Ting; Li, Shuang; Qiu, Chen

    2016-01-01

    Background: A snakebite is a neglected extrinsic injury associated with high morbidity and global mortality. Members of Chinese field forces are at high risk of snakebites, and their perception and knowledge of snakebites are unknown. The aim of this study is to assess perception and knowledge of snakebites in field forces in southeast China; Methods: A cross-sectional questionnaire-based survey was conducted in July 2016. A total of 216 field force members participated in this study; Results: A total of 10.3% had experienced snakebites and 86.4% rated their demands for knowledge about snakebite as “high”. No significant correlation between the actual and perceived snakebite knowledge status was detected (κ = 0.0237, p = 0.3852). Ineffective and harmful traditional first-aid methods, such as the application of tourniquets, sucking the venom out of the wound, and making local incisions, were used by more than three quarters of the respondents. However, pressure immobilization bandages were applied by only 17.3% of members. The proportion of responses for each question was not significantly different among the respondents when considering separate demographic groups; Conclusions: Snakebite knowledge among Chinese field force members is inadequate and in some cases misleading, when focusing on manifestation, prevention, and first-aid. A pragmatic, intensive educational scheme should be undertaken in at-risk populations. PMID:28035960

  2. 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...

  3. A polarizable ellipsoidal force field for halogen bonds.

    PubMed

    Du, Likai; Gao, Jun; Bi, Fuzhen; Wang, Lili; Liu, Chengbu

    2013-09-05

    The anisotropic effects and short-range quantum effects are essential characters in the formation of halogen bonds. Since there are an array of applications of halogen bonds and much difficulty in modeling them in classical force fields, the current research reports solely the polarizable ellipsoidal force field (PEff) for halogen bonds. The anisotropic charge distribution was represented with the combination of a negative charged sphere and a positively charged ellipsoid. The polarization energy was incorporated by the induced dipole model. The resulting force field is "physically motivated," which includes separate, explicit terms to account for the electrostatic, repulsion/dispersion, and polarization interaction. Furthermore, it is largely compatible with existing, standard simulation packages. The fitted parameters are transferable and compatible with the general AMBER force field. This PEff model could correctly reproduces the potential energy surface of halogen bonds at MP2 level. Finally, the prediction of the halogen bond properties of human Cathepsin L (hcatL) has been found to be in excellent qualitative agreement with the cocrystal structures.

  4. Bioventing Field Initiative at Robins Air Force Base, Georgia

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at three sites at Robins Air Force Base (AFB), Georgia, as part of the Bioventing Field initiative for...respiration test, and installation of a bioventing system. The specific objectives of this task are described in the following section. The test sites at the

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

    DTIC Science & Technology

    2012-07-01

    communities upon establishment of the Force Support officer career field. With the 38F career field merger and creation of the FSS, officers previously...section. As the development of a competency model typically entails significant investments of time and money , one should ideally first define the...potential workforce management and assignment shortcomings. Dues (2011) utilized a simulation tool to determine how dynamic endogenous and exogenous

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Non-Markovian Brownian motion in a magnetic field and time-dependent force fields

    NASA Astrophysics Data System (ADS)

    Hidalgo-Gonzalez, J. C.; Jiménez-Aquino, J. I.; Romero-Bastida, M.

    2016-11-01

    This work focuses on the derivation of the velocity and phase-space generalized Fokker-Planck equations for a Brownian charged particle embedded in a memory thermal bath and under the action of force fields: a constant magnetic field and arbitrary time-dependent force fields. To achieve the aforementioned goal we use a Gaussian but non-Markovian generalized Langevin equation with an arbitrary friction memory kernel. In a similar way, the generalized diffusion equation in the zero inertia limit is also derived. Additionally we show, in the absence of the time-dependent external forces, that, if the fluctuation-dissipation relation of the second kind is valid, then the generalized Langevin dynamics associated with the charged particle reaches a stationary state in the large-time limit. The consistency of our theoretical results is also verified when they are compared with those derived in the absence of the force fields and in the Markovian case.

  11. Vehicle-track interaction at high frequencies - Modelling of a flexible rotating wheelset in non-inertial reference frames

    NASA Astrophysics Data System (ADS)

    Guiral, A.; Alonso, A.; Giménez, J. G.

    2015-10-01

    Vehicle-track interaction in the mid- and high-frequency range has become an important issue for rolling-stock manufacturers, railway operators and administrations. Previous modelling approaches have been focused on the development of flexible wheelset-track systems based on the assumption that the unsprung masses are decoupled from the high-frequency dynamic behaviour of carbody and bogies. In this respect, the available flexible wheelset models account for gyroscopic and inertial effects due to the main rotation but are, in general, developed from the viewpoint of inertial spaces and consequently restricted to the study of tangent layouts. The aim of this paper is to present the formulation of a flexible rotating wheelset derived within the framework of a non-inertial vehicle moving reference frame. This brings a double advantage; on the one hand, the formulation is not restricted to tangent tracks, but is also suitable for the study of transition curves and curve negotiation. On the other hand, the use of a vehicle moving reference frame allows the introduction of the hypothesis of small displacement for the degrees of freedom of the wheelset. This hypothesis is not applied to the pitch angle, as it is associated with the main axis of rotation. In addition, unlike previous flexible wheelset models that only consider the rotation around the main axis, all the degrees of freedom will be considered when developing the dynamic equations of motion. Results for the proposed model will be presented and the influence of the inertial and gyroscopic terms not taken into account in previous derived formulations will be evaluated.

  12. 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

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

    PubMed

    Geng, Yanan; Wu, Weida

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    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.

  15. 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

  16. 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.

  17. 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.

  18. Four-nucleon force in chiral effective field theory

    SciTech Connect

    Evgeny Epelbaum

    2005-10-25

    We derive the leading contribution to the four--nucleon force within the framework of chiral effective field theory. It is governed by the exchange of pions and the lowest--order nucleon--nucleon contact interaction and includes effects due to the nonlinear pion--nucleon couplings and the pion self interactions constrained by the chiral symmetry of QCD. The resulting 4NF does not contain any unknown parameters and can be tested in future few--and many--nucleon studies.

  19. 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

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

    PubMed

    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(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across

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

    PubMed

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

    2016-01-01

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

  2. Accurate Force Field Development for Modeling Conjugated Polymers.

    PubMed

    DuBay, Kateri H; Hall, Michelle Lynn; Hughes, Thomas F; Wu, Chuanjie; Reichman, David R; Friesner, Richard A

    2012-11-13

    The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.

  3. 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

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

    DOE PAGES

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; ...

    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

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

    SciTech Connect

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

    2008-03-15

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

  6. 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

  7. 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.

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

    PubMed Central

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

    2013-01-01

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

  9. New force field on modeling intrinsically disordered proteins.

    PubMed

    Wang, Wei; Ye, Wei; Jiang, Cheng; Luo, Ray; Chen, Hai-Feng

    2014-09-01

    Intrinsically disordered proteins or intrinsically disordered protein regions comprise a large portion of eukaryotic proteomes (between 35% and 51%). These intrinsically disordered proteins were found to link with cancer and various other diseases. However, widely used additive force field parameter sets are insufficient in quantifying the structural properties of intrinsically disordered proteins. Therefore, we explored to a systematic correction of a base additive force field parameter set (chosen as Amber ff99SBildn) to correct the biases that was first demonstrated in simulations with the base parameter set. Specifically, the φ/ψ distributions of disorder-promoting residues were systematically corrected with the CMAP method. Our simulations show that the CMAP corrected Amber parameter set, termed ff99IDPs, improves the φ/ψ distributions of the disorder-promoting residues with respect to the benchmark data of intrinsically disordered protein structures, with root mean-squared percentage deviation less than 0.15% between the simulation and the benchmark. Our further validation shows that the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements for two tested IDPs, MeV NTAIL , and p53. The predicted residue dipolar couplings also show high correlation with experimental data. Interestingly, our simulations show that ff99IDPs can still be used to model the ordered state when the intrinsically disordered proteins are in complex, in contrast to ff99SBildn that can be applied well only to the ordered complex structures. These findings confirm that the newly proposed Amber ff99IDPs parameter set provides a reasonable tool in further studies of intrinsically disordered protein structures. In addition, our study also shows the importance of considering intrinsically disordered protein structures in general-purposed force field developments for both additive and non-additive models.

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

    PubMed Central

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

    2008-01-01

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

  11. Development of accurate force fields for the simulation of biomineralization.

    PubMed

    Raiteri, Paolo; Demichelis, Raffaella; Gale, Julian D

    2013-01-01

    The existence of an accurate force field (FF) model that reproduces the free-energy landscape is a key prerequisite for the simulation of biomineralization. Here, the stages in the development of such a model are discussed including the quality of the water model, the thermodynamics of polymorphism, and the free energies of solvation for the relevant species. The reliability of FFs can then be benchmarked against quantities such as the free energy of ion pairing in solution, the solubility product, and the structure of the mineral-water interface.

  12. 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.

  13. Transferability of coarse-grained force fields: The polymer case

    NASA Astrophysics Data System (ADS)

    Carbone, Paola; Varzaneh, Hossein Ali Karimi; Chen, Xiaoyu; Müller-Plathe, Florian

    2008-02-01

    A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at

  14. 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.

  15. Study of Elastin Sequences with Solvent Induced Force Field

    NASA Astrophysics Data System (ADS)

    Arkin, Handan

    Conformational structures of two common repeat motifs Val1-Pro2-Gly3-Val4-Gly5 and Gly1-Leu2-Gly3-Gly4 of tropoelastin are investigated by using the multicanonical simulation procedure with solvation effects included energy force field. The effects of solvation energy term on the conformations are determined by analyzing Ramachandran plots. By minimizing the energy structures along the trajectory, the thermodynamically most stable low-energy microstates of the molecule in aqueous solution are determined and the root mean square deviations of these structures with respect to the global minimum are calculated.

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

    PubMed Central

    Li, Jicun; Wang, Feng

    2015-01-01

    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. PMID:26590540

  17. 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.

  18. 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...

  19. 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

  20. A quantum mechanical polarizable force field for biomolecular interactions

    PubMed Central

    Donchev, A. G.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, O. V.; Tarasov, V. I.

    2005-01-01

    We introduce a quantum mechanical polarizable force field (QMPFF) fitted solely to QM data at the MP2/aTZ(-hp) level. Atomic charge density is modeled by point-charge nuclei and floating exponentially shaped electron clouds. The functional form of interaction energy parallels quantum mechanics by including electrostatic, exchange, induction, and dispersion terms. Separate fitting of each term to the counterpart calculated from high-quality QM data ensures high transferability of QMPFF parameters to different molecular environments, as well as accurate fit to a broad range of experimental data in both gas and liquid phases. QMPFF, which is much more efficient than ab initio QM, is optimized for the accurate simulation of biomolecular systems and the design of drugs. PMID:15911753

  1. An accurate ab initio quartic force field for ammonia

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  2. Systematic procedure to parametrize force fields for molecular fluids.

    PubMed

    Salas, Frank José; Méndez-Maldonado, G Arlette; Núñez-Rojas, Edgar; Aguilar-Pineda, Gabriel Eloy; Domínguez, Hector; Alejandre, José

    2015-02-10

    A new strategy to develop force fields for molecular fluids is presented. The intermolecular parameters are fitted to reproduce experimental values of target properties at ambient conditions and also the critical temperature. The partial charges are chosen to match the dielectric constant. The Lennard-Jones parameters, εii and σii, are fitted to reproduce the surface tension at the vapor-liquid interface and the liquid density, respectively. The choice of those properties allows obtaining systematically the final parameters using a small number of simulations. It is shown that the use of surface tension as a target property is better than the choice of heat of vaporization. The method is applied to molecules, from all atoms to a coarse-grained level, such as pyridine, dichloromethane, methanol, and 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) at different temperatures and pressures. The heat of vaporization, radial distribution functions, and self-diffusion coeficient are also calculated.

  3. The anharmonic force field and equilibrium molecular structure of ketene

    NASA Astrophysics Data System (ADS)

    East, Allan L. L.; Allen, Wesley D.; Klippenstein, Stephen J.

    1995-06-01

    A comprehensive anharmonic vibrational analysis of isotopic ketenes has been performed on the basis of a complete ab initio quartic force field constructed by means of second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles and doubles (CCSD) approach, augmented for structural optimizations by a contribution for connected triple excitations [CCSD(T)]. The atomic-orbital basis sets of the study entailed C,O(10s6p/5s4p) and H(6s/4s) spaces multiply polarized in the valence region to give QZ(2d,2p) and QZ(2d1f,2p1d) sets. An iterative anharmonic vibrational refinement of a limited set of quadratic scaling parameters on 27 fundamentals of H2CCO, HDCCO, D2CCO, and H2C13CO generates a final quartic force field which reproduces the empirical νi data with an average absolute error of only 1.1 cm-1. This force field yields a complete and self-consistent set of Coriolis (ζij), vibrational anharmonic (χij), vibration-rotation interaction (αi), and quartic and sextic centrifugal distortion constants, providing a critical assessment of the assorted spectroscopic constants determined over many years and also facilitating future computations of vibrational state densities for detailed tests of unimolecular dissociation theories. The harmonic frequencies ascertained for H2CCO (in cm-1), with associated anharmonicities in parentheses, are ω1(a1)=3202.2(-129.2), ω2(a1)=2197.2(-44.4), ω3(a1)=1415.2(-25.9), ω4(a1)=1146.0(-29.7), ω5(b1)=581.9(+7.1), ω6(b1)=502.6(+26.3), ω7(b2)=3308.2(-141.3), ω8(b2)=996.0(-17.9), and ω9(b2)=433.6(+5.0). The large positive anharmonicity for the ν6(b1) C=C=O bending mode, which is principally a Coriolis effect, warrants continued investigation. Explicit first-order treatments of the strong Fermi interactions within the (ν4,2ν5,ν5+ν6,2ν6) manifold reveal resonance shifts for ν4(H2CCO, HDCCO, D2CCO) of (-12.1, -10.0, +12.2) cm-1, in order. The experimental assignments for this Fermi tetrad are confirmed to

  4. Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

    PubMed Central

    2015-01-01

    Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron–sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein–water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance. PMID:24955078

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

    PubMed

    Behme, G; Hesjedal, T

    2001-07-01

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

  6. 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).

  7. The Bonding Forces In Liquid Metals And Ultrasonic Field Action

    SciTech Connect

    Moraru, Luminita; Murariu, Gabriel

    2007-04-23

    The understanding of the liquid metals properties is still imperfect. Assuming that the liquids are isotropic and show some elasticity properties, there are no physical reasons for rejecting the applicability of the fundamental ideas of the Debye theory to the description of the properties of liquid state. The approach is intended to relate the temperature Debye to the intensity of bonding forces between neighboring atoms and, in turn, to correlate this with the high power ultrasonic field action.In order to highlight the effect of the ultrasonic wave on the Debye temperature values, the experiments were carried out under similar conditions both with and without sonication. The relationship between the Debye temperature for both liquid and solid state is {theta}{sub D}{sup solid} / {theta}{sub D}{sup liquid} = 0.85.

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

    PubMed

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

    2009-01-28

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

  9. 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

  10. 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.

  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. 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

  13. Effects of Hall electric fields on the saturation of forced antiparallel magnetic field merging

    NASA Astrophysics Data System (ADS)

    Dorelli, John C.

    2003-08-01

    The role of Hall electric fields in flux pile-up antiparallel magnetic field merging is addressed. Analytical solutions of the resistive Hall magnetohydrodynamics (Hall-MHD) equations are obtained, describing stagnation point flows in a thin current sheet. The stagnation point flow solutions explain a number of interesting effects observed in two-dimensional resistive Hall-MHD simulations of forced magnetic reconnection. In particular, when Hall electric fields are important within the current sheet, less pile-up of magnetic energy is required upstream of the current sheet to support a given reconnection electric field. Fast electron flows transport magnetic flux into the diffusion layer without requiring a compensating drop in plasma pressure upstream of the current sheet. The maximum flux pile-up merging rate allowed by the external plasma pressure becomes independent of the Lundquist number, scaling like the square root of the ratio of the ion inertial length to the spatial scale of the stagnation point flow. Thus, Hall electric fields provide a possible solution to the problem of flux pile-up saturation in two-dimensional, resistive MHD models of forced magnetic reconnection.

  14. A universal and ultrasensitive vectorial nanomechanical sensor for imaging 2D force fields

    NASA Astrophysics Data System (ADS)

    de Lépinay, Laure Mercier; Pigeau, Benjamin; Besga, Benjamin; Vincent, Pascal; Poncharal, Philippe; Arcizet, Olivier

    2016-10-01

    The miniaturization of force probes into nanomechanical oscillators enables ultrasensitive investigations of forces on dimensions smaller than their characteristic length scales. It also unravels the vectorial character of the force field and how its topology impacts the measurement. Here we present an ultrasensitive method for imaging two-dimensional vectorial force fields by optomechanically following the bidimensional Brownian motion of a singly clamped nanowire. This approach relies on angular and spectral tomography of its quasi-frequency-degenerated transverse mechanical polarizations: immersing the nanoresonator in a vectorial force field not only shifts its eigenfrequencies but also rotates the orientation of the eigenmodes, as a nanocompass. This universal method is employed to map a tunable electrostatic force field whose spatial gradients can even dominate the intrinsic nanowire properties. Enabling vectorial force field imaging with demonstrated sensitivities of attonewton variations over the nanoprobe Brownian trajectory will have a strong impact on scientific exploration at the nanoscale.

  15. Fast docking using the CHARMM force field with EADock DSS.

    PubMed

    Grosdidier, Aurélien; Zoete, Vincent; Michielin, Olivier

    2011-07-30

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-07-23

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

  18. Investigation of Acoustic Fields Generated by Eddy Currents Using an Atomic Force Microscope (Postprint)

    DTIC Science & Technology

    2012-08-01

    AFRL-RX-WP-JA-2014-0230 INVESTIGATION OF ACOUSTIC FIELDS GENERATED BY EDDY CURRENTS USING AN ATOMIC FORCE MICROSCOPE (POSTPRINT) V...Institute of Physics AIR FORCE RESEARCH LABORATORY MATERIALS AND MANUFACTURING DIRECTORATE WRIGHT-PATTERSON AIR FORCE BASE, OH 45433-7750 AIR... FORCE MATERIEL COMMAND UNITED STATES AIR FORCE NOTICE AND SIGNATURE PAGE Using Government drawings, specifications, or other data included in

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

    SciTech Connect

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

    2015-10-31

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

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

    PubMed

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

    2013-01-01

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

  1. Rapid changes in corticospinal excitability during force field adaptation of human walking.

    PubMed

    Barthélemy, D; Alain, S; Grey, M J; Nielsen, J B; Bouyer, L J

    2012-03-01

    Force field adaptation of locomotor muscle activity is one way of studying the ability of the motor control networks in the brain and spinal cord to adapt in a flexible way to changes in the environment. Here, we investigate whether the corticospinal tract is involved in this adaptation. We measured changes in motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) in the tibialis anterior (TA) muscle before, during, and after subjects adapted to a force field applied to the ankle joint during treadmill walking. When the force field assisted dorsiflexion during the swing phase of the step cycle, subjects adapted by decreasing TA EMG activity. In contrast, when the force field resisted dorsiflexion, they increased TA EMG activity. After the force field was removed, normal EMG activity gradually returned over the next 5 min of walking. TA MEPs elicited in the early swing phase of the step cycle were smaller during adaptation to the assistive force field and larger during adaptation to the resistive force field. When elicited 5 min after the force field was removed, MEPs returned to their original values. The changes in TA MEPs were larger than what could be explained by changes in background TA EMG activity. These effects seemed specific to walking, as similar changes in TA MEP were not seen when seated subjects were tested during static dorsiflexion. These observations suggest that the corticospinal tract contributes to the adaptation of walking to an external force field.

  2. Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  3. Accurate Quartic Force Fields and Vibrational Frequencies for HCN and HNC

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  4. 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.

  5. 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.

  6. Force field development with GOMC, a fast new Monte Carlo molecular simulation code

    NASA Astrophysics Data System (ADS)

    Mick, Jason Richard

    In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. A viable non-axisymmetric non-force-free field to represent solar active regions

    NASA Astrophysics Data System (ADS)

    Prasad, A.; Bhattacharyya, R.

    2016-11-01

    A combination of analytical calculations and vectormagnetogram data is utilized to develop a non-axisymmetric non-force-free magnetic field and assess its viability in describing solar active regions. For that purpose, we construct a local spherical shell where a planar surface, tangential to the inner sphere, represents a Cartesian cutout of an active region. The magnetic field defined on the surface is then correlated with magnetograms. The analysis finds that the non-axisymmetric non-force-free magnetic field, obtained by a superposition of two linear-force-free fields, correlates reasonably well with magnetograms.

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

    PubMed

    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.

  14. Shear force control for a terahertz near field microscope.

    PubMed

    Buersgens, F; Acuna, G; Lang, C H; Potrebic, S I; Manus, S; Kersting, R

    2007-11-01

    We report on the advancement of apertureless terahertz microscopy by active shear force control of the scanning probe. Extreme subwavelength spatial resolution and a maximized image contrast are achieved by maintaining a tip-surface distance of about 20 nm. The constant distance between scanning tip and surface results in terahertz images that mirror the dielectric permittivity of the surface.

  15. 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.

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

    PubMed

    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.

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

    PubMed Central

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

    1997-01-01

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

  18. 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.

  19. 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)

  20. A multidimensional pendulum in a nonconservative force field under the presence of linear damping

    NASA Astrophysics Data System (ADS)

    Shamolin, M. V.

    2016-09-01

    A nonconservative force field in the dynamics of a multidimensional solid is constructed according to the results from the dynamics of real solids occurring in the force field of the action of the medium. In this case, it becomes possible to generalize the equations of motion of a multidimensional solid in a similarly constructed field of forces and to obtain a complete list of, generally speaking, transcendental first integrals expressed through a finite combination of elementary functions. In the study, the integrability in elementary functions is shown for the simultaneous equations of motion of a dynamically symmetric fixed multidimensional solid under the action of a nonconservative pair of forces in the presence of the linear damping moment (the additional dependence of the force field on the tensor of angular velocity of the solid).

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

    SciTech Connect

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

    2010-02-10

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

  2. 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.

  3. Highly focused conical optical field for Pico-Newton scale force sensing

    NASA Astrophysics Data System (ADS)

    Deng, Hongchang; Yuan, Libo

    2014-05-01

    We propose a highly focused conical optical filed generated by cone-frustum-shaped annular core fiber tip for Pico- Newton scale force sensing. We show that there are stable three-dimensional trap-points for Rayleigh particles in the main lobe and every ring of such field with Bessel-like profile. And the transverse trapping forces are much greater (almost 30 times) than their corresponding longitudinal radiation forces so that a particle trapped by highly focused conical beam is only sensitive for disturbing force in longitudinal direction. Force sensitivities in longitudinal direction and the detection range are also discussed.

  4. 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.

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

    PubMed

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

    2013-05-15

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

  6. Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme.

    PubMed

    Zhang, Lin; Bai, Shu; Sun, Yan

    2011-06-01

    Modeling, especially the force field, is crucial for the accuracy of molecular dynamics (MD) simulations. In order for more accurate description of adsorption and desorption behaviors of lysozyme in hydrophobic charge induction chromatography (HCIC), the Martini coarse-grained (CG) force field has been modified based on the statistical analysis and comparison of an all-atom (AA) force field, GROMOS96 43A1, and the Martini force field. The parameters describing the protein-adsorbent interactions have been adjusted to avoid too strong and unrealistic adsorption of lysozyme on the agarose matrix and HCIC ligands. It is found that the adsorption and desorption behaviors monitored using the modified Martini force field and MD simulation are consistent with previous simulation results with 46-bead β-barrel model protein. Repeated adjustment of both protein position and orientation is necessary to generate enough contacts for a stable adsorption. After reducing the pH in the mobile phase, the lysozyme-ligand electrostatic repulsion leads to protein desorption. In the adsorption process, little conformational transition of lysozyme is observed due to its stable structure, which is in line with previous experimental observations. So, it is concluded that after appropriate modification, the Martini force field can be used to examine the HCIC process of lysozyme. The modification strategy has thus extended the applicability of the Martini force field to protein chromatography, and it is expected to facilitate studies of exploring the molecular details in adsorption chromatography of proteins.

  7. 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.

  8. 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.

  9. Particles with nonlinear electric response: Suppressing van der Waals forces by an external field

    NASA Astrophysics Data System (ADS)

    Soo, Heino; Dean, David S.; Krüger, Matthias

    2017-01-01

    We study the classical thermal component of Casimir, or van der Waals, forces between point particles with highly anharmonic dipole Hamiltonians when they are subjected to an external electric field. Using a model for which the individual dipole moments saturate in a strong field (a model that mimics the charges in a neutral, perfectly conducting sphere), we find that the resulting Casimir force depends strongly on the strength of the field, as demonstrated by analytical results. For a certain angle between the external field and center-to-center axis, the fluctuation force can be tuned and suppressed to arbitrarily small values. We compare the forces between these particles with those between particles with harmonic Hamiltonians and also provide a simple formula for asymptotically large external fields, which we expect to be generally valid for the case of saturating dipole moments.

  10. 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.

  11. 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

    2016-08-09

    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

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

    PubMed Central

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

    2013-01-01

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

  13. Structural evolution of nucleobase clusters using force field models and density functional theory

    NASA Astrophysics Data System (ADS)

    Chiriki, Siva; Dagar, Anuradha; Bulusu, Satya S.

    2015-08-01

    We report global minima for all nucleobase clusters (nucleobase)n, with 2 ≤ n ≤ 4. The global minima are predicted using force field based global optimization methods followed by local optimizations using the dispersion corrected DFT method. In this study, we use both non-polarizable (OPLS-AA) and polarizable (AMOEBA) force fields for global optimization. Here we emphasize on the reliability of AMOEBA force field used for predicting accurate global minima of nucleobase clusters. The average deviation in binding energies using AMOEBA is 3 kcal/mol from the DFT while the average deviation using OPLS-AA is 8 kcal/mol from DFT.

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

    NASA Astrophysics Data System (ADS)

    Rosenthal, Eran

    2004-12-01

    I use the recently developed massive field approach to calculate the scalar self-force on a static particle in a Schwarzschild spacetime. In this approach the scalar self-force is obtained from the difference between the (massless) scalar field, and an auxiliary massive scalar field combined with a certain limiting process. By applying this approach to a static particle in Schwarzschild I show that the scalar self-force vanishes in this case. This result conforms with a previous analysis [A. G. Wiseman, Phys. Rev. D612000084014].

  15. Forced Magnetic Reconnection and Field Penetration of an Externally Applied Rotating Helical Magnetic Field in the TEXTOR Tokamak

    SciTech Connect

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

    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.

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

    PubMed

    Martín Pendás, A; Hernández-Trujillo, J

    2012-10-07

    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.

  17. Predator Force Structure Changes at Indian Springs Air Force Auxiliary Field, Nevada Environmental Assessment

    DTIC Science & Technology

    2003-07-01

    the North Las Vegas Library (Main Branch), the Indian Springs Library, and online at www.cevp.com and www.nellis.af.mil. A Notice of Availability...USGS (U.S. Geological Survey). 2001. Online Table of Seismic Hazards. http://geohazards.cr.usgs.gov/eq/faults/fsrpage11.html Predator Force...Sincerely, __ ~~~-~ Heather K. Elliott Nevada State Clearinghouse/ SPOC NEVADA STATE CLEARINGHOUSE Department of Administration Budget and Planning

  18. Decoding gripping force based on local field potentials recorded from subthalamic nucleus in humans.

    PubMed

    Tan, Huiling; Pogosyan, Alek; Ashkan, Keyoumars; Green, Alexander L; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Hariz, Marwan; Brown, Peter

    2016-11-18

    The basal ganglia are known to be involved in the planning, execution and control of gripping force and movement vigour. Here we aim to define the nature of the basal ganglia control signal for force and to decode gripping force based on local field potential (LFP) activities recorded from the subthalamic nucleus (STN) in patients with deep brain stimulation (DBS) electrodes. We found that STN LFP activities in the gamma (55-90 Hz) and beta (13-30m Hz) bands were most informative about gripping force, and that a first order dynamic linear model with these STN LFP features as inputs can be used to decode the temporal profile of gripping force. Our results enhance the understanding of how the basal ganglia control gripping force, and also suggest that deep brain LFPs could potentially be used to decode movement parameters related to force and movement vigour for the development of advanced human-machine interfaces.

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

    ERIC Educational Resources Information Center

    Hakel, Milton D.; And Others

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

  20. 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.

  1. Force-Field Prediction of Materials Properties in Metal-Organic Frameworks

    PubMed Central

    2016-01-01

    In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can be observed when looking at properties sensitive to framework vibrational modes. This observation is more pronounced upon the introduction of framework charges. PMID:28008758

  2. 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.

  3. Energetics of infinite homopolypeptide chains: a new look at commonly used force fields.

    PubMed

    Penev, Evgeni; Ireta, Joel; Shea, Joan-Emma

    2008-06-05

    We present a novel method for comparing the long-range part of force fields in the presence of a maximally cooperative network of nonbonded interactions. The method is based on mapping the potential energy surface of an infinite polypeptide chain in the gas phase by using cylindrical coordinates (the twist and pitch) as geometry descriptors. We apply our method to an infinite polyalanine chain and consider the AMBER99, AMBER99SB, CHARMM27, and OPLS-AA/L fixed partial-charge force fields and the protein-specific version of the AMOEBA polarizable force field. Results from our analysis are compared to those obtained from high-level density-functional theory (DFT) calculations. We find that all force fields produce stronger stabilization of the helical conformations as compared to DFT, with only AMBER99/AMBER99SB satisfactorily reproducing all three helical conformations (pi, alpha, and 3(10)).

  4. Water properties from first principles: Simulations by a general-purpose quantum mechanical polarizable force field

    PubMed Central

    Donchev, A. G.; Galkin, N. G.; Illarionov, A. A.; Khoruzhii, O. V.; Olevanov, M. A.; Ozrin, V. D.; Subbotin, M. V.; Tarasov, V. I.

    2006-01-01

    We have recently introduced a quantum mechanical polarizable force field (QMPFF) fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here, we present an improved form of the force field, QMPFF2, and apply it to simulations of liquid water. The results of the simulations show excellent agreement with a variety of experimental thermodynamic and structural data, as good or better than that provided by specialized water potentials. In particular, QMPFF2 is the only ab initio force field to accurately reproduce the anomalous temperature dependence of water density to our knowledge. The ability of the same force field to successfully simulate the properties of both organic molecules and water suggests it will be useful for simulations of proteins and protein–ligand interactions in the aqueous environment. PMID:16723394

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

    PubMed

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

    2013-09-30

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

  6. 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.

  7. Blunt force cranial trauma in the Cambodian killing fields.

    PubMed

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

    2006-09-01

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

  8. Topological constraints and the existence of force-free fields

    NASA Technical Reports Server (NTRS)

    Antiochos, S. K.

    1986-01-01

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

  9. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.

    PubMed

    Malde, Alpeshkumar K; Zuo, Le; Breeze, Matthew; Stroet, Martin; Poger, David; Nair, Pramod C; Oostenbrink, Chris; Mark, Alan E

    2011-12-13

    The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.

  10. 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

  11. 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.

  12. MATCH: an atom-typing toolset for molecular mechanics force fields.

    PubMed

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

    2012-01-15

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

  13. 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...

  14. 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

  15. 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.

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

    SciTech Connect

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

    2010-01-15

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

  17. 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%.

  18. 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.

  19. First principles derived, transferable force fields for CO2 adsorption in Na-exchanged cationic zeolites.

    PubMed

    Fang, Hanjun; Kamakoti, Preeti; Ravikovitch, Peter I; Aronson, Matthew; Paur, Charanjit; Sholl, David S

    2013-08-21

    The development of accurate force fields is vital for predicting adsorption in porous materials. Previously, we introduced a first principles-based transferable force field for CO2 adsorption in siliceous zeolites (Fang et al., J. Phys. Chem. C, 2012, 116, 10692). In this study, we extend our approach to CO2 adsorption in cationic zeolites which possess more complex structures. Na-exchanged zeolites are chosen for demonstrating the approach. These methods account for several structural complexities including Al distribution, cation positions and cation mobility, all of which are important for predicting adsorption. The simulation results are validated with high-resolution experimental measurements of isotherms and microcalorimetric heats of adsorption on well-characterized materials. The choice of first-principles method has a significant influence on the ability of force fields to accurately describe CO2-zeolite interactions. The PBE-D2 derived force field, which performed well for CO2 adsorption in siliceous zeolites, does not do so for Na-exchanged zeolites; the PBE-D2 method overestimates CO2 adsorption energies on multi-cation sites that are common in cationic zeolites with low Si/Al ratios. In contrast, a force field derived from the DFT/CC method performed well. Agreement was obtained between simulation and experiment not only for LTA-4A on which the force field fitting is based, but for other two common adsorbents, NaX and NaY.

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

    PubMed

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

    2015-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

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

    2014-12-28

    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.

  3. Gramicidin A channel as a test ground for molecular dynamics force fields.

    PubMed

    Allen, Toby W; Baştuğ, Turgut; Kuyucak, Serdar; Chung, Shin-Ho

    2003-04-01

    We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K(+) ion is calculated along the channel axis using the umbrella sampling method. Calculations are performed using two of the most common force fields in MD simulations: CHARMM and GROMACS. Both force fields lead to large central barriers for K(+) ion permeation, that are substantially higher than those deduced from the physiological data by inverse methods. In long MD simulations lasting over 60 ns, several ions are observed to enter the binding site but none of them crossed the channel despite the presence of a large driving field. The present results, taken together with many earlier studies, highlights the shortcomings of the standard force fields used in MD simulations of ion channels and calls for construction of more appropriate force fields for this purpose.

  4. 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

  5. Quantum force of nanomagnets loosely fastened to the matrix in a magnetic field gradient

    NASA Astrophysics Data System (ADS)

    Kim, Gwang-Hee

    2016-11-01

    We study nanomagnets that exhibit quantum forces, but are not firmly fixed to the substrate. The Hamiltonian of a rotating spin system is derived in the presence of a microwave field and a transverse field gradient, and analytic expressions for the forces are obtained. We show that the period of the oscillating force depends upon the coupling constant of the system to the matrix and the total angular momentum, and we discuss the conditions under which they can be observed within the framework of experimentally controllable parameters.

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

    PubMed

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

    2012-01-01

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

  7. MAGNETIC HELICITY OF SELF-SIMILAR AXISYMMETRIC FORCE-FREE FIELDS

    SciTech Connect

    Zhang Mei; Flyer, Natasha; Low, Boon Chye

    2012-08-10

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

  8. 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.

  9. 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.

  10. 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

  11. 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

    2014-08-07

    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.

  12. Vibrational spectroscopy and the development of new force fields for biological molecules.

    PubMed

    Gerber, R B; Chaban, G M; Gregurick, S K; Brauer, B

    2003-03-01

    The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy.

  13. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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 ...

  1. Interim Report for Bioventing Field Initiative at Westover Air Force Base, Massachusetts

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at Westover Air Force Base (AFB), Massachusetts, as part of the Bioventing Field Initiative for the...respiration test, and installation of bioventing systems. The specific objectives of this Bioventing Field Initiative are described in the following section

  2. Bioventing Field Initiative at Galena and Campion Air Force Stations, Alaska

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at Galena Air Force Station (AFS) and Campion AFS, Alaska, as part of the Bioventing Field Initiative...air permeability test, in situ respiration tests, and installation of bioventing systems. The specific objectives of this Bioventing Field Initiative

  3. 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.

  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. Observation of the Field, Current and Force Distributions in an Optimized Superconducting Levitation with Translational Symmetry

    NASA Astrophysics Data System (ADS)

    Ye, Chang-Qing; Ma, Guang-Tong; Liu, Kun; Wang, Jia-Su

    2017-01-01

    The superconducting levitation realized by immersing the high-temperature superconductors (HTSs) into nonuniform magnetic field is deemed promising in a wide range of industrial applications such as maglev transportation and kinetic energy storage. Using a well-established electromagnetic model to mathematically describe the HTS, we have developed an efficient scheme that is capable of intelligently and globally optimizing the permanent magnet guideway (PMG) with single or multiple HTSs levitated above for the maglev transportation applications. With maximizing the levitation force as the principal objective, we optimized the dimensions of a Halbach-derived PMG to observe how the field, current and force distribute inside the HTSs when the optimized situation is achieved. Using a pristine PMG as a reference, we have analyzed the critical issues for enhancing the levitation force through comparing the field, current and force distributions between the optimized and pristine PMGs. It was also found that the optimized dimensions of the PMG are highly dependent upon the levitated HTS. Moreover, the guidance force is not always contradictory to the levitation force and may also be enhanced when the levitation force is prescribed to be the principle objective, depending on the configuration of levitation system and lateral displacement.

  6. 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.

  7. A novel elastic force-field to influence mediolateral foot placement during walking.

    PubMed

    Nyberg, Elizabeth; Broadway, Jordan; Finetto, Christian; Dean, Jesse

    2016-12-01

    Bipedal gait can be stabilized through mechanically-appropriate mediolateral foot placement, although this strategy is disrupted in a subset of neurologically injured individuals with balance deficits. The goal of the present work was to develop a device to influence mediolateral foot placement during treadmill walking. We created a novel force-field using a combination of passive elasticity and active control; wires in series with extension springs run parallel to the treadmill belts and can be rapidly repositioned to exert mediolateral forces on the legs of users. This mechanical structure creates a channel-like force landscape that resists displacements of each leg away from its prescribed mediolateral position, producing near-linear effective mediolateral stiffness. The depth of these force-field channels can be predictably controlled by manipulating extension spring initial tension. In human testing, we found that the force-field can effectively "get-out-of-the-way" when desired, closely following the mediolateral leg trajectory with a delay of approximately 110 ms. The force-field can also encourage users to adjust their mediolateral foot placement in order to walk with either narrower or wider steps, without interfering with forward gait progression. Future work will test whether this novel device can help retrain a stable gait pattern in clinical populations.

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

    PubMed

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

    2014-11-11

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

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

    PubMed Central

    2015-01-01

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

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

    SciTech Connect

    Sorin Zaharia; C.Z. Cheng

    2002-06-18

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

  11. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.

    PubMed

    Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

    2015-07-01

    Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

  12. 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.

  13. 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.

  14. Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

    NASA Astrophysics Data System (ADS)

    Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

    2004-12-01

    Secondary-structure forming tendencies are examined for six well-known protein force fields: AMBER94, AMBER96, AMBER99, CHARMM22, OPLS-AA/L, and GROMOS96. We performed generalized-ensemble molecular dynamics simulations of two peptides. One of these peptides is C-peptide of ribonuclease A, and the other is the C-terminal fragment from the B1 domain of streptococcal protein G. The former is known to form α-helix structure and the latter β-hairpin structure by experiments. The simulation results revealed significant differences of the secondary-structure forming tendencies among the force fields. Of the six force fields, the results of AMBER99 and CHARMM22 were in accord with experiments for C-peptide. For G-peptide, on the other hand, the results of OPLS-AA/L and GROMOS96 were most consistent with experiments. Therefore, further improvements on the force fields are necessary for studying the protein folding problem from the first principles, in which a single force field can be used for all cases.

  15. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

    NASA Astrophysics Data System (ADS)

    Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

    2015-07-01

    Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

  16. Force-field parameterization of the galactic cosmic ray spectrum: Validation for Forbush decreases

    NASA Astrophysics Data System (ADS)

    Usoskin, I. G.; Kovaltsov, G. A.; Adriani, O.; Barbarino, G. C.; Bazilevskaya, G. A.; Bellotti, R.; Boezio, M.; Bogomolov, E. A.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bruno, A.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; De Donato, C.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A. M.; Karelin, A. V.; Koldashov, S. V.; Koldobskiy, S.; Krutkov, S. Y.; Kvashnin, A. N.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A. G.; Menn, W.; Mergé, M.; Mikhailov, V. V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Pizzolotto, C.; Ricci, M.; Ricciarini, S. B.; Rossetto, L.; Sarkar, R.; Scotti, V.; Simon, M.; Sparvoli, R.; Spillantini, P.; Stozhkov, Y. I.; Vacchi, A.; Vannuccini, E.; Vasilyev, G. I.; Voronov, S. A.; Yurkin, Y. T.; Zampa, G.; Zampa, N.; Zverev, V. G.

    2015-06-01

    A useful parametrization of the energy spectrum of galactic cosmic rays (GCR) near Earth is offered by the so-called force-field model which describes the shape of the entire spectrum with a single parameter, the modulation potential. While the usefulness of the force-field approximation has been confirmed for regular periods of solar modulation, it was not tested explicitly for disturbed periods, when GCR are locally modulated by strong interplanetary transients. Here we use direct measurements of protons and α -particles performed by the PAMELA space-borne instrument during December 2006, including a major Forbush decrease, in order to directly test the validity of the force-field parameterization. We conclude that (1) The force-field parametrization works very well in describing the energy spectra of protons and α -particles directly measured by PAMELA outside the Earths atmosphere; (2) The energy spectrum of GCR can be well parameterized by the force-field model also during a strong Forbush decrease; (3) The estimate of the GCR modulation parameter, obtained using data from the world-wide neutron monitor network, is in good agreement with the spectra directly measured by PAMELA during the studied interval. This result is obtained on the basis of a single event analysis, more events need to be analyzed.

  17. First-Principles, Physically Motivated Force Field for the Ionic Liquid [BMIM][BF4].

    PubMed

    Choi, Eunsong; McDaniel, Jesse G; Schmidt, J R; Yethiraj, Arun

    2014-08-07

    Molecular simulations play an important role in establishing structure-property relations in complex fluids such as room-temperature ionic liquids. Classical force fields are the starting point when large systems or long times are of interest. These force fields must be not only accurate but also transferable. In this work, we report a physically motivated force field for the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) based on symmetry-adapted perturbation theory. The predictions (from molecular dynamics simulations) of the liquid density, enthalpy of vaporization, diffusion coefficients, viscosity, and conductivity are in excellent agreement with experiment, with no adjustable parameters. The explicit energy decomposition inherent in the force field enables a quantitative analysis of the important physical interactions in these systems. We find that polarization is crucial and there is little evidence of charge transfer. We also argue that the often used procedure of scaling down charges in molecular simulations of ionic liquids is unphysical for [BMIM][BF4]. Because all intermolecular interactions in the force field are parametrized from first-principles, we anticipate good transferability to other ionic liquid systems and physical conditions.

  18. Molecular simulations of imidazolium-based tricyanomethanide ionic liquids using an optimized classical force field.

    PubMed

    Vergadou, Niki; Androulaki, Eleni; Hill, Jörg-Rüdiger; Economou, Ioannis G

    2016-03-07

    Imidazolium-based ionic liquids (ILs) incorporating the tricyanomethanide ([TCM(-)]) anion are studied using an optimized classical force field. These ILs are very promising candidates for use in a wide range of cutting-edge technologies and, to our knowledge, it is the first time that this IL family is subject to a molecular simulation study with the use of a classical atomistic force field. The [C4mim(+)][TCM(-)] ionic liquid at 298.15 K and at atmospheric pressure was used as the basis for force field optimization which primarily involved the determination of the Lennard-Jones parameters of [TCM(-)] and the implementation of three quantum mechanical schemes for the calculation of the partial charge distribution and the identification of the appropriate scaling factor for the reduction of the total ionic charge. The optimized force field was validated by performing simulations of the 1-alkyl-3-methylimidazolium tricyanomethanide ([Cnmim(+)][TCM(-)], n = 2, 4, 6, and 8) IL family at various temperatures. The results for density, self-diffusivity and viscosity are in very good agreement with the available experimental data for all ILs verifying that the force field reliably reproduces the behaviour of the imidazolium-based [TCM(-)] IL family in a wide temperature range. Furthermore, a detailed analysis of the microscopic structure and the complex dynamic behaviour of the ILs under study was performed.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Sensing dipole fields at atomic steps with combined scanning tunneling and force microscopy.

    PubMed

    Park, Jeong Young; Sacha, G M; Enachescu, M; Ogletree, D F; Ribeiro, R A; Canfield, P C; Jenks, C J; Thiel, P A; Sáenz, J J; Salmeron, M

    2005-09-23

    The electric field of dipoles localized at the atomic steps of metal surfaces due to the Smoluchowski effect were measured from the electrostatic force exerted on the biased tip of a scanning tunneling microscope. By varying the tip-sample bias the contribution of the step dipole was separated from changes in the force due to van der Waals and polarization forces. Combined with electrostatic calculations, the method was used to determine the local dipole moment in steps of different heights on Au(111) and on the twofold surface of an Al-Ni-Co decagonal quasicrystal.

  6. 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

  7. 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

  8. The 'Arm Force Field' method to predict manual arm strength based on only hand location and force direction.

    PubMed

    La Delfa, Nicholas J; Potvin, Jim R

    2017-03-01

    This paper describes the development of a novel method (termed the 'Arm Force Field' or 'AFF') to predict manual arm strength (MAS) for a wide range of body orientations, hand locations and any force direction. This method used an artificial neural network (ANN) to predict the effects of hand location and force direction on MAS, and included a method to estimate the contribution of the arm's weight to the predicted strength. The AFF method predicted the MAS values very well (r(2) = 0.97, RMSD = 5.2 N, n = 456) and maintained good generalizability with external test data (r(2) = 0.842, RMSD = 13.1 N, n = 80). The AFF can be readily integrated within any DHM ergonomics software, and appears to be a more robust, reliable and valid method of estimating the strength capabilities of the arm, when compared to current approaches.

  9. Preprocessing of Hinode/SOT Vector Magnetograms for Nonlinear Force-Free Coronal Magnetic Field Modeling

    NASA Astrophysics Data System (ADS)

    Wiegelmann, T.; Thalmann, J. K.; Schrijver, C. J.; De Rosa, M. L.; Metcalf, T. R.

    2008-09-01

    The solar magnetic field is key to understanding the physical processes in the solar atmosphere. Nonlinear force-free codes have been shown to be useful in extrapolating the coronal field from underlying vector boundary data (for an overview see Schrijver et al. (2006)). However, we can only measure the magnetic field vector routinely with high accuracy in the photosphere with, e.g., Hinode/SOT, and unfortunately these data do not fulfill the force-free consistency condition as defined by Aly (1989). We must therefore apply some transformations to these data before nonlinear force-free extrapolation codes can be legitimately applied. To this end, we have developed a minimization procedure that uses the measured photospheric field vectors as input to approximate a more chromospheric like field (The method was dubbed preprocessing. See Wiegelmann et al. (2006) for details). The procedure includes force-free consistency integrals and spatial smoothing. The method has been intensively tested with model active regions (see Metcalf et al. 2008) and been applied to several ground based vector magnetogram data before. Here we apply the preprocessing program to photospheric magnetic field measurements with the Hinode/SOT instrument.

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

    NASA Astrophysics Data System (ADS)

    He, Han; Wang, Huaning

    2008-05-01

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

  11. 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.

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

    PubMed

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

    2015-06-22

    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.

  13. Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical Bayesian models.

    PubMed

    Wu, Stephen; Angelikopoulos, Panagiotis; Tauriello, Gerardo; Papadimitriou, Costas; Koumoutsakos, Petros

    2016-12-28

    We propose a hierarchical Bayesian framework to systematically integrate heterogeneous data for the calibration of force fields in Molecular Dynamics (MD) simulations. Our approach enables the fusion of diverse experimental data sets of the physico-chemical properties of a system at different thermodynamic conditions. We demonstrate the value of this framework for the robust calibration of MD force-fields for water using experimental data of its diffusivity, radial distribution function, and density. In order to address the high computational cost associated with the hierarchical Bayesian models, we develop a novel surrogate model based on the empirical interpolation method. Further computational savings are achieved by implementing a highly parallel transitional Markov chain Monte Carlo technique. The present method bypasses possible subjective weightings of the experimental data in identifying MD force-field parameters.

  14. 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

  15. 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.

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

    PubMed

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

    2015-09-24

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

  17. Force field parametrization by weak coupling. Re-engineering SPC water

    NASA Astrophysics Data System (ADS)

    Berweger, Christian D.; van Gunsteren, Wilfred F.; Müller-Plathe, Florian

    1995-01-01

    A recently developed scheme for the automatic adjustment of force field parameters to experimentally observed properties is applied to the simple-point-charge (SPC) water model. The refinement procedure is based on a first-order coupling of a force-field parameter (say, an atomic charge) to the deviation of a calculated bulk liquid property (e.g. the heat of vaporization) from its ideal value. I.e. the method is very similar in spirit to the weak-coupling scheme used to implement constant-temperature or constant-pressure molecular dynamics. With the method we have refined the charges and the Lennard-Jones diameter of the SPC water model at several state points of high temperature and high pressure. We also have studied how these force-field parameters have to be reoptimized as the cutoff distance is varied.

  18. 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).

  19. The SPASIBA force field of model compounds related to lipids of biomembranes

    NASA Astrophysics Data System (ADS)

    Chhiba, M.; Vergoten, G.

    1996-10-01

    The vibrational spectroscopic force field SPASIBA (Spectroscopic Potential Algorithm for SImulating Biomolecular conformational Adaptability), which has been shown to exhibit unique properties over the whole molecular potential energy surface rather than in the vicinity of minima (as current force fields do), has been developed for a series of model compounds related to the lipid component of biological membranes. The structures, relative energies and vibrational spectra of several phosphate anions, acetylcholine cations, phosphorylcholine and some of their deuterated analogs have been investigated in detail. In particular, the root mean square deviation of 11 cm -1 between the observed and the calculated vibrational frequency lends some confidence to the expectation that this force field will give meaningful results when used in molecular dynamics simulations.

  20. 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.

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

    PubMed

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

    2016-03-05

    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.

  2. 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.

  3. Use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields.

    PubMed

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

    2014-06-19

    The predictive power of biomolecular simulation critically depends on the quality of the force field or molecular model used and on the extent of conformational sampling that can be achieved. Both issues are addressed. First, it is shown that widely used force fields for simulation of proteins in aqueous solution appear to have rather different propensities to stabilize or destabilize α-, π-, and 3(10)- helical structures, which is an important feature of a biomolecular force field due to the omni-presence of such secondary structure in proteins. Second, the relative stability of secondary structure elements in proteins can only be computationally determined through so-called free-energy calculations, the accuracy of which critically depends on the extent of configurational sampling. It is shown that the method of enveloping distribution sampling is a very efficient method to extensively sample different parts of configurational space.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Iwata, Natsumi; Kishimoto, Yasuaki

    2014-01-01

    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.

  6. 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.

  7. 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.

  8. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

    PubMed

    Kührová, Petra; Best, Robert B; Bottaro, Sandro; Bussi, Giovanni; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel

    2016-09-13

    The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.

  9. 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

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

    PubMed

    Vanommeslaeghe, K; MacKerell, A D

    2012-12-21

    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/ .

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

    PubMed

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

    2015-04-15

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

  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. Reparameterization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

    PubMed

    Miller, Mark S; Lay, Wesley Kayser; Li, Shuxiang; Hacker, William Charles; An, Jiadi; Ren, Jianlan; Elcock, Adrian Hamilton

    2017-03-15

    There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparameterize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models. In general, for both the amino acids and the small molecules, the tested force fields produce computed osmotic coefficients that are lower than experiment; this is indicative of excessively favorable solute-solute interactions. The sole exception to this general trend is provided by GROMOS54a7 when applied to amino acids: in this case, the computed osmotic coefficients are consistently too high. Importantly, we show that all of the force fields tested can be made to accurately reproduce the experimental osmotic coefficients of the amino acids when minor modifications - some previously reported by others and some that are new to this study - are made to the van der Waals interactions of the charged terminal groups. Special care is required, however, when simulating Proline with a number of the force fields, and a hydroxyl-group specific modification is required in order to correct Serine and Threonine when simulated with AMBER ff99SB-ILDN. Interestingly, an alternative parameterization of the van der Waals interactions in the latter force field, proposed by the Nerenberg and Head-Gordon groups, is shown to immediately produce osmotic coefficients that are in excellent agreement with experiment. Overall, this study reinforces the idea that osmotic coefficient measurements can be used to identify general shortcomings in commonly used force fields' descriptions of solute-solute interactions, and further demonstrates that modifications to van der

  14. 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

  15. 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

  16. 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.

  17. Carbonic anhydrase binding site parameterization in OPLS-AA force field.

    PubMed

    Bernadat, Guillaume; Supuran, Claudiu T; Iorga, Bogdan I

    2013-03-15

    The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH(-) forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes.

  18. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.

    PubMed

    Shivakumar, Devleena; Harder, Edward; Damm, Wolfgang; Friesner, Richard A; Sherman, Woody

    2012-08-14

    Explicit solvent molecular dynamics free energy perturbation simulations were performed to predict absolute solvation free energies of 239 diverse small molecules. We use OPLS2.0, the next generation OPLS force field, and compare the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI. OPLS2.0 produces the best correlation with experimental data (R(2) = 0.95, slope = 0.96) and the lowest average unsigned errors (0.7 kcal/mol). Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements.

  19. 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.

  20. 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.

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

    PubMed

    Milek, Theodor; Meyer, Bernd; Zahn, Dirk

    2013-10-14

    We report on the development of force-field parameters for accurately modeling lithium and hydroxide ions in ethanol in solution. Based on quantum calculations of small molecular clusters mimicking the solvent structure of individual ions as well as the solvated LiOH dimer, significant improvements of off-the-shelf force-fields are obtained. The quality of our model is demonstrated by comparison to ab initio molecular dynamics of the bulk solution and to experimental data available for ethanol/water mixtures.

  2. 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

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

    SciTech Connect

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-07-15

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

  4. Field and material stresses predict observable surface forces in optical and electrostatic manipulation

    NASA Astrophysics Data System (ADS)

    Kemp, Brandon A.; Sheppard, Cheyenne J.

    2016-09-01

    The momentum of light in media has been one of the most debated topics in physics over the past one hundred years. Originally a theoretical debate over the electrodynamics of moving media, practical applications have emerged over the past few decades due to interest in optical manipulation and nanotechnology. Resolution of the debate identifies a kinetic momentum as the momentum of the fields responsible for center of mass translations and a canonical momentum related to the coupled field and material system. The optical momentum resolution has been considered incomplete because it did not uniquely identify the full stress-energy-momentum (SEM) tensor of the field-kinetic subsystem. A consequence of this partial resolution is that the field-kinetic momentum could be described by three of the leading formulations found in the literature. The Abraham, Einstein-Laub, and Chu SEM tensors share the field-kinetic momentum, but their SEM tensors differ resulting in competing force densities. We can show now that the Abraham and Einstein-Laub formulations are invalid since their SEM tensors are not frame invariant, whereas the Chu SEM tensor satisfies relativistic principles as the field-kinetic formulation. However, a number of reports indicate that the force distribution in matter may not accurately represent experimental observations. In this correspondence, we show that the field-kinetic SEM tensor can be used along with the corresponding material subsystem to accurately predict experimental force and stress distributions. We model experimental examples from optical and static manipulation of particles and fluids.

  5. 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

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

    DOE PAGES

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; ...

    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

  7. 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.

  8. Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin.

    PubMed

    Han, Sanghwa

    2008-12-12

    Estimation of structural perturbation induced by S-nitrosation is important to understand the mode of cellular signal transduction mediated by nitric oxide. Crystal structures of S-nitrosated proteins have been solved only for a few cases, however, so that molecular dynamics simulation may provide an alternative tool for probing structural perturbation. In this study AMBER-99 force field parameters for S-nitrosocysteine were developed and applied to molecular dynamics simulations of S-nitrosated thioredoxin. Geometry optimization at the level of HF/6-31G * was followed by a restrained electrostatic potential charge-fitting to obtain the atomic charges of S-nitrosocysteine. Force constants for bonds and angles were obtained from generalized AMBER force field. Torsional force constants for CC-SN and CS-NO were determined by fitting the torsional profiles obtained from geometry optimization with those from molecular mechanical energy minimization. Finally molecular dynamics simulations were performed with theses parameters on oxidized and reduced thioredoxin with and without S-nitrosocysteine. In all cases the root-mean-square deviations of alpha-carbons yielded well-behaved trajectories. The CC-SH dihedral angle which fluctuated severely during the simulation became quiet upon S-nitrosation. In conclusion the force field parameters developed in this study for S-nitrosocysteine appear to be suitable for molecular dynamics simulations of S-nitrosated proteins.

  9. 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.

  10. Radiation force on a spherical object in the field of a focused cylindrical transducer.

    PubMed

    Chen, X; Apfel, R E

    1997-05-01

    An exact solution of the radiation force on a spherical object, when positioned on the acoustic axis of a cylindrical transducer, is provided. The solution is valid for any type of sphere of any size. The radiation force function allows the calibration of high-frequency focused ultrasound fields from radiation force measurements and expands the utility of the elastic sphere radiometer developed by Dunn et al. [Acustica 38, 58-61 (1977)]. Numeral results reveal an oscillatory behavior of the radiation force function for small spheres near the transducer surface and this behavior may present an opportunity for particle sorting based on the mechanical properties of the particle and other types of manipulation.

  11. 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.

  12. 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.

  13. Decoding gripping force based on local field potentials recorded from subthalamic nucleus in humans

    PubMed Central

    Tan, Huiling; Pogosyan, Alek; Ashkan, Keyoumars; Green, Alexander L; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Hariz, Marwan; Brown, Peter

    2016-01-01

    The basal ganglia are known to be involved in the planning, execution and control of gripping force and movement vigour. Here we aim to define the nature of the basal ganglia control signal for force and to decode gripping force based on local field potential (LFP) activities recorded from the subthalamic nucleus (STN) in patients with deep brain stimulation (DBS) electrodes. We found that STN LFP activities in the gamma (55–90 Hz) and beta (13–30m Hz) bands were most informative about gripping force, and that a first order dynamic linear model with these STN LFP features as inputs can be used to decode the temporal profile of gripping force. Our results enhance the understanding of how the basal ganglia control gripping force, and also suggest that deep brain LFPs could potentially be used to decode movement parameters related to force and movement vigour for the development of advanced human-machine interfaces. DOI: http://dx.doi.org/10.7554/eLife.19089.001 PMID:27855780

  14. 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.

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

    PubMed

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

    2014-02-01

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

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

    PubMed

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

    2016-07-05

    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.

  17. 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

  18. 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.

  19. Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

    PubMed

    Bell, David R; Qi, Rui; Jing, Zhifeng; Xiang, Jin Yu; Mejias, Christopher; Schnieders, Michael J; Ponder, Jay W; Ren, Pengyu

    2016-11-09

    Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

  20. 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…

  1. CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety.

    PubMed

    Ramos Sasselli, I; Ulijn, R V; Tuttle, T

    2016-02-14

    Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail. Molecular dynamic simulations using the CHARMM force field have been applied to a wide variety of peptide-based systems to obtain molecular level details of processes that are inaccessible with experimental techniques. However, this force field does not include parameters for the aromatic moieties which dictate the self-assembly of these systems. The standard CHARMM force field parameterization protocol uses hydrophilic interactions for the non-bonding parameters evaluation. However, to effectively reproduce the self-assembling behaviour of these molecules, the balance between the hydrophilic and hydrophobic nature of the molecule is essential. In this work, a modified parameterization protocol for the CHARMM force field for these aromatic moieties is presented. This protocol is applied for the specific case of the Fmoc moiety. The resulting set of parameters satisfies the conformational and interactions analysis and is able to reproduce experimental results such as the Fmoc-S-OMe water/octanol partition free energy and the self-assembly of Fmoc-S-OH and Fmoc-Y-OH into spherical micelles and fibres, respectively, while also providing detailed information on the mechanism of these processes. The effectiveness of the parameters for the Fmoc moiety validates the protocol as a robust approach to paramterise this class of compounds.

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

    PubMed

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

    2015-07-14

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

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

    PubMed

    Ferrando, Nicolas; Lachet, Véronique; Boutin, Anne

    2012-03-15

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

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

    NASA Astrophysics Data System (ADS)

    Mulcahy, T. M.; Hull, J. R.; Almer, J. D.; Rossing, T. D.

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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    PubMed

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

    2011-09-15

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

  10. Study of electric fields parallel to the magnetic lines of force using artificially injected energetic electrons

    NASA Technical Reports Server (NTRS)

    Wilhelm, K.; Bernstein, W.; Whalen, B. A.

    1980-01-01

    Electron beam experiments using rocket-borne instrumentation will be discussed. The observations indicate that reflections of energetic electrons may occur at possible electric field configurations parallel to the direction of the magnetic lines of force in an altitude range of several thousand kilometers above the ionosphere.

  11. 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.

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

    PubMed

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

    2013-11-12

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

  13. 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.

  14. 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…

  15. A new force field of formamide and the effect of the dielectric constant on miscibility.

    PubMed

    de la Luz, Alexander Pérez; Méndez-Maldonado, G Arlette; Núñez-Rojas, Edgar; Bresme, Fernando; Alejandre, José

    2015-06-09

    Current force fields underestimate significantly the dielectric constant of formamide at standard conditions. We present a derivation of an accurate potential for formamide, with a functional form based on the OPLS/AA force field. Our procedure follows the approach introduced by Salas et al. ( J. Chem. Theory Comput. 2015 , 11 , 683 - 693 ) that relies on ab initio calculations and molecular dynamics simulations. We consider several strategies to derive the atomic charges of formamide. We find that the inclusion of polarization effects in the quantum mechanical computations is essential to obtain reliable force fields. By varying the atomic charges and the Lennard-Jones parameters describing the dispersion interactions in the OPLS/AA force field, we derive an optimum set of parameters that provides accurate results for the dielectric constant, surface tension, and bulk density of liquid formamide in a wide range of thermodynamic states. We test the transferability of our parameters to investigate liquid/liquid mixtures. We have chosen as case study an equimolar mixture of formamide and hexan-2-one. This mixture involves two fluids with very different polar characteristics, namely, large differences in their dielectric constants and their performance as solvents. The new potential predicts a liquid/liquid phase separation, in good agreement with experimental data, and highlights the importance of the correct parametrization of the pure liquid phases to investigate liquid mixtures. Finally, we examine the microscopic origin of the observed inmiscibility between formamide and hexa-2-one.

  16. Interim Report for Bioventing Field Initiative at Robins Air Force Base, Georgia

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at Robins Air Force Base (AFB), Georgia, as part of the Bioventing Field Initiative for the U.S. Air...soil gas survey, air permeability test, in situ respiration tests, and installation of bioventing systems. The specific objectives of this task are described in the following section.

  17. Interim Report for Bioventing Field Initiative at Site UST 173, Robins Air Force Base, Georgia

    DTIC Science & Technology

    2007-11-02

    This report describes the activities conducted at Robins Air Force Base (AFB), Georgia, Site UST 173 as part of the Bioventing Field Initiative for...which includes a soil gas survey, air permeability test, in situ respiration tests, and installation of bioventing systems. The specific objectives of this task are described in the following section.

  18. Why the OPLS-AA force field cannot produce the β-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field?

    PubMed

    Cao, Zanxia; Liu, Lei; Wang, Jihua

    2011-12-01

    The optimal combination of force field and water model is an essential problem that is able to increase molecular dynamics simulation quality for different types of proteins and peptides. In this work, an attempt has been made to explore the problem by studying H1 peptide using four different models based on different force fields, water models and electrostatic schemes. The driving force for H1 peptide conformation transition and the reason why the OPLS-AA force field cannot produce the β-hairpin structure of H1 peptide in solution while the GROMOS 43A1 force field can do were investigated by temperature replica exchange molecular dynamics simulation (T-REMD). The simulation using the GROMOS 43A1 force field preferred to adopt a β-hairpin structure, which was in good agreement with the several other simulations and the experimental evidences. However, the simulation using the OPLS-AA force field has a significant difference from the simulations with the GROMOS 43A1 force field simulation. The results show that the driving force in H1 peptide conformation transition is solvent exposure of its hydrophobic residues. However, the subtle balances between residue-residue interactions and residue-solvent interaction are disrupted by using the OPLS-AA force field, which induced the reduction in the number of residue-residue contact. Similar solvent exposure of the hydrophobic residues is observed for all the conformations sampled using the OPLS-AA force field. For H1 peptide which exhibits large solvent exposure of the hydrophobic residues, the GROMOS 43A1 force field with the SPC water model can provide more accurate results.

  19. 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.

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

    DOE PAGES

    Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; ...

    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

  1. 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.

  2. 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.

  3. Calculation of force fields of chromium, molybdenum and tungsten hexafluorides and dioxodifluorides by means of the Tikchonov regularization method

    NASA Astrophysics Data System (ADS)

    Kochikov, I. V.; Yagola, A. G.; Kuramshina, G. M.; Kovba, V. M.; Pentin, Yu. A.

    Force fields and mean amplitudes of vibration of chromium, molybdenum and tungsten hexafluorides and dioxodifluorides are calculated using Tikchonov's regularization method and are compared with those for oxotetrafluorides.

  4. 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

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

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  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.

    PubMed

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

    2015-10-28

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  9. 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.

  10. 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.

  11. Molecular dynamics simulation of tri-n-butyl-phosphate liquid: a force field comparative study.

    PubMed

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

    2012-01-12

    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 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.

  12. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

    PubMed

    Duke, Robert E; Starovoytov, Oleg N; Piquemal, Jean-Philip; Cisneros, G Andrés

    2014-04-08

    GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed.

  13. 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.

  14. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Morante, S.; Rossi, G. C.

    2017-02-01

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg-Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann-Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  15. Ground-water resources of the Holloman Air Force Base well field area, 1967, New Mexico

    USGS Publications Warehouse

    Ballance, W.C.; Mattick, Robert E.

    1976-01-01

    Water consumption at Holloman Air Force Base (HAFB), N. Mex., reached an all time high in 1964 and 1965. Further increases in withdrawal without expansion of pumping facilities will hasten the chemical deterioration of the ground water pumped from the well fields. Saline water in the well-field area is present on the north and west sides of the potable-water area and in a thin shallow zone that overlies the potable-water sands in part of the potable-water area. The latter source is affecting quality of the water produced from most wells. The saturated thickness of material underlying the Boles well field ranges from about 3 ,500 feet in the western part of the field to about 1,200 feet in the eastern part of the field. In the Douglass and San Andres well fields, the saturated thickness ranges from 3,500 feet to about 300 feet. Expansion of the Boles and San Andres well fields to the east and southeast would move the center of pumping away from the highly saline water to the north and west. This would eliminate overpumping of the present wells that has resulted from the expanded facilities at Holloman Air Force Base. (Woodard-USGS)

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

    PubMed

    Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

    2010-05-11

    A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

  17. Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?

    PubMed

    Siwy, Christopher M; Lockhart, Christopher; Klimov, Dmitri K

    2017-01-01

    By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the

  18. Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

    PubMed Central

    Siwy, Christopher M.

    2017-01-01

    By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the

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

    PubMed

    Xu, Dong; Zhang, Yang

    2012-07-01

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

  20. 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.

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

    USGS Publications Warehouse

    Geist, E.L.

    1996-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Behunin, Ryan O.; Hu, Bei-Lok

    2011-07-01

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

  3. Zinc oxide nanorod field effect transistor for long-time cellular force measurement

    PubMed Central

    Zong, Xianli; Zhu, Rong

    2017-01-01

    Mechanical forces generated by cells are known to influence a vast range of cellular functions ranging from receptor signaling and transcription to differentiation and proliferation. We report a novel measurement approach using zinc oxide nanorods as a peeping transducer to monitor dynamic mechanical behavior of cellular traction on surrounding substrate. We develop a ZnO nanorod field effect transistor (FET) as an ultrasensitive force sensor to realize long-time, unstained, and in-situ detection of cell cycle phases, including attachment, spread, and mitosis. Excellent biocompatibility and ultra-sensitivity of the biomechanical measurement is ensured by coating a parylene film on the FET sensor as a concealment, which provides complete electronic isolation between the sensor and cell. With unique features of ultra-sensitivity, label-free, easy handling, and good biocompatibility, the force sensor allows feasible for tracking cellular dynamics in physiological contexts and understanding their contribution to biological processes. PMID:28272551

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Aschwanden, M. J.

    2013-12-01

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

  6. 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.

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

    PubMed Central

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

    2012-01-01

    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

  8. All-Optical Chirality-Sensitive Sorting via Reversible Lateral Forces in Interference Fields.

    PubMed

    Zhang, Tianhang; Mahdy, Mahdy Rahman Chowdhury; Liu, Yongmin; Teng, Jing Hua; Lim, Chwee Teck; Wang, Zheng; Qiu, Cheng-Wei

    2017-04-05

    Separating substances by their chirality faces great challenges as well as opportunities in chemistry and biology. In this study, we propose an all-optical solution for passive sorting of chiral objects using chirality-dependent lateral optical forces induced by judiciously interfered fields. First, we investigate the optical forces when the chiral objects are situated in the interference field formed by two plane waves with arbitrary polarization states. When the plane waves are either linearly or circularly polarized, nonzero lateral forces are found at the particle's trapping positions, making such sideways motions observable. Although the lateral forces have different magnitudes on particles with different chirality, their directions are the same for opposite handedness particles, rendering it difficult to separate the chiral particles. We further solve the sorting problem by investigating more complicated polarization states. Finally, we achieve the chiral-selective separation by illuminating only one beam toward the chiral substance situated at an interface between two media, taking advantage of the native interference between the incident and reflective beams at the interface. Our study provides a robust and insightful approach to sort chiral substances and biomolecules with plausible optical setups.

  9. 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.

  10. 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.

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

    PubMed

    Baykara, Mehmet Z; Dagdeviren, Omur E; Schwendemann, Todd C; Mönig, Harry; Altman, Eric I; Schwarz, Udo D

    2012-01-01

    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.

  12. 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.

  13. Continuous Force Decoding from Local Field Potentials of the Primary Motor Cortex in Freely Moving Rats

    PubMed Central

    Khorasani, Abed; Heydari Beni, Nargess; Shalchyan, Vahid; Daliri, Mohammad Reza

    2016-01-01

    Local field potential (LFP) signals recorded by intracortical microelectrodes implanted in primary motor cortex can be used as a high informative input for decoding of motor functions. Recent studies show that different kinematic parameters such as position and velocity can be inferred from multiple LFP signals as precisely as spiking activities, however, continuous decoding of the force magnitude from the LFP signals in freely moving animals has remained an open problem. Here, we trained three rats to press a force sensor for getting a drop of water as a reward. A 16-channel micro-wire array was implanted in the primary motor cortex of each trained rat, and obtained LFP signals were used for decoding of the continuous values recorded by the force sensor. Average coefficient of correlation and the coefficient of determination between decoded and actual force signals were r = 0.66 and R2 = 0.42, respectively. We found that LFP signal on gamma frequency bands (30–120 Hz) had the most contribution in the trained decoding model. This study suggests the feasibility of using low number of LFP channels for the continuous force decoding in freely moving animals resembling BMI systems in real life applications. PMID:27767063

  14. Calculating forces on thin flat plates with incomplete vorticity-field data

    NASA Astrophysics Data System (ADS)

    Limacher, Eric; Morton, Chris; Wood, David

    2016-11-01

    Optical experimental techniques such as particle image velocimetry (PIV) permit detailed quantification of velocities in the wakes of bluff bodies. Patterns in the wake development are significant to force generation, but it is not trivial to quantitatively relate changes in the wake to changes in measured forces. Key difficulties in this regard include: (i) accurate quantification of velocities close to the body, and (ii) the effect of missing velocity or vorticity data in regions where optical access is obscured. In the present work, we consider force formulations based on the vorticity field, wherein mathematical manipulation eliminates the need for accurate near-body velocity information. Attention is restricted to nominally two dimensional problems, namely (i) a linearly accelerating flat plate, investigated using PIV in a water tunnel, and (ii) a pitching plate in a freestream flow, as investigated numerically by Wang & Eldredge (2013). The effect of missing vorticity data on the pressure side of the plate has a significant impact on the calculation of force for the pitching plate test case. Fortunately, if the vorticity on the pressure side remains confined to a thin boundary layer, simple corrections can be applied to recover a force estimate.

  15. Minimum radiation force target size for power measurements in focused ultrasonic fields with circular symmetry.

    PubMed

    Beissner, K

    2010-12-01

    The time-averaged ultrasonic power emitted by medical ultrasonic equipment is mostly measured using a radiation force balance, and the question of the necessary target size is of practical importance. The question is answered here by calculations based on a Rayleigh integral algorithm for fields from circular, focusing transducers. This case occurs particularly in the field of high-intensity therapeutic ultrasound. The calculation yields the necessary size of an absorbing target so that the radiation force is 98% of that exerted on an absorber of infinite lateral size, and this as a function of the transducer-to-target distance, of the transducer radius in comparison with the wavelength and of the focus (half-)angle. Several distributions of the transducer vibration amplitude are considered. The Rayleigh integral strictly applies only to planar transducers, but among the amplitude distributions there is also one that allows the simulation of the spherically curved transducer type often found in practice.

  16. 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.

  17. Development of a ReaxFF Reactive Force Field for the Pt-Ni Alloy Catalyst.

    PubMed

    Shin, Yun Kyung; Gai, Lili; Raman, Sumathy; van Duin, Adri C T

    2016-10-03

    We developed the ReaxFF force field for Pt/Ni/C/H/O interactions, specifically targeted for heterogeneous catalysis application of the Pt-Ni alloy. The force field is trained using the DFT data for equations of state of Pt3Ni, PtNi3 and PtNi alloys, the surface energy of the PtxNi1-x(111) (x = 0.67-0.83), and binding energies of various atomic and molecular species (O, H, C, CH, CH2, CH3, CO, OH, and H2O) on these surfaces. The ReaxFF force field shows a Pt surface segregation at x ≥ 0.67 for the (111) surface and x ≥ 0.62 for the (100) surface in vacuum. In addition, from the investigation of the preferential alloy component of the adsorbates, it is expected that H and CH3 on the alloy surface to induce a segregation of Pt whereas the oxidation intermediates and products such as C, O, OH, H2O, CO, CH, and CH2 are found to induce Ni segregation. The relative order of binding strengths among adsorbates is a function of alloy composition and the force field is trained to describe the trend observed in DFT calculations, namely, H2 < H2O < CH3 ≈ O2 ≈ CO < OH < CH2 < C ≈ CH on Pt8Ni4, H2 < H2O < CO < O2 ≈ CH3 < OH < CH2 < CH < C on Pt9Ni3, and H2 < H2O < O2 < CO < CH3 < OH < CH2 < C ≈ CH on Pt10Ni2. Using this force field, we performed the grand-canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations for a Pt3Ni slab and a truncated cuboctahedral nanoparticle terminated by (111) and (100) faces, to examine the surface segregation trend under different gas environments. It is found that Pt segregates to the alloy surface when the surface is exposed to vacuum and/or H2 environment while Ni segregates under the O2 environment. These results suggest that the Pt/Ni alloy force field can be successfully used for the preparation of Pt-Ni nanobimetallic catalysts structure using GCMC and run MD simulations to investigate its role and the catalytic chemistry in catalytic oxidation, dehydrogenation and coupling reactions. The current Pt/Ni force field

  18. 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.

  19. The force-field derivation and application of explosive/additive interfaces

    NASA Astrophysics Data System (ADS)

    Long, Yao; Chen, Jun

    2016-10-01

    The inter-molecular force-field across RDX/(paraffin, fluoropolymer) interfaces are derived from first-principles calculated energies under the GGA+vdW functional. Based on the force-field, the polycrystal structures of mixture explosives are obtained, and a set of thermodynamic properties are calculated, including the elastic constants, thermal expansion coefficient, heat capacity, isothermal curve and the Hugoniot curve. The results are in good agreement with the available experiments, and provide a reasonable prediction about the properties of plastic bonded explosives. We find that the thermal expansion coefficient of a multi-component explosive is not only determined by the properties of the components, but is also affected by the thermal stress at the explosive/additive interfaces.

  20. Achieved slime flotation in centrifugal force field by float-hydrocyclone

    SciTech Connect

    Guode Xuzhanxian; Gaozhenshen Songzhiwei

    1997-12-31

    Based on the theory of intensifying flotation in a centrifugal force field, float-hydrocyclone (FH) is developed, which is a new type of equipment for slime flotation and consists of an air bubble generator and the cylindrical section of a hydrocyclone. The combination of pulp and air bubbles is fed into the FH tangentially at a high speed to effect the separation of slime in the centrifugal force field. It offers many advantages over mechanically agitated flotation cells. Commercial test results show that slime, especially fine slime, can be perfectly floated in the FH with rapid flotation and fine froth size. The quality and quantity of concentrate and tailings can be adjusted conveniently within a certain range according to different requirements.

  1. CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.

    PubMed

    Qi, Yifei; Ingólfsson, Helgi I; Cheng, Xi; Lee, Jumin; Marrink, Siewert J; Im, Wonpil

    2015-09-08

    Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.

  2. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7

    PubMed Central

    Kutov, D. C.; Sulimov, V. B.

    2017-01-01

    Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated. PMID:28191015

  3. Parameterization of classical force fields in the context of high pressure calculations

    NASA Astrophysics Data System (ADS)

    Yanciw, Brandon; Perkins, Jeffery; Wiebe, Brandon; Spooner, Jacob; Weinberg, Noham

    2013-06-01

    Activation volumes and volume profiles of chemical reactions are concepts widely used in high pressure reaction kinetics. We have recently shown that these quantities can be calculated using molecular dynamics (MD) simulations with accuracy comparable to that of the experiment. The major challenge in performing such calculations comes from the fact that standard MD force fields are parameterized for stable species and, therefore, are not directly usable for transient points along the reaction coordinate. We propose a consistent scheme of parameterization for such species based on fitting force field potentials to quantum mechanical deformation energies, and show that MD simulations with these parameters produce molar volumes of quality comparable to that of OPLS and the experiment.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  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. 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

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

    PubMed

    Bristow, Jessica K; Tiana, Davide; Walsh, Aron

    2014-10-14

    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.

  11. Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7.

    PubMed

    Sulimov, A V; Kutov, D C; Katkova, E V; Sulimov, V B

    2017-01-01

    Results of the combined use of the classical force field and the recent quantum chemical PM7 method for docking are presented. Initially the gridless docking of a flexible low molecular weight ligand into the rigid target protein is performed with the energy function calculated in the MMFF94 force field with implicit water solvent in the PCM model. Among several hundred thousand local minima, which are found in the docking procedure, about eight thousand lowest energy minima are chosen and then energies of these minima are recalculated with the recent quantum chemical semiempirical PM7 method. This procedure is applied to 16 test complexes with different proteins and ligands. For almost all test complexes such energy recalculation results in the global energy minimum configuration corresponding to the ligand pose near the native ligand position in the crystalized protein-ligand complex. A significant improvement of the ligand positioning accuracy comparing with MMFF94 energy calculations is demonstrated.

  12. CHARMM force field parameters for 2'-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs.

    PubMed

    Yu, Yue; Fursule, Ishan A; Mills, Landon C; Englert, Derek L; Berron, Brad J; Payne, Christina M

    2017-03-01

    2'-Hydroxybiphenyl-2-sulfinate (HBPS) desulfinase (DszB) catalyzes the cleavage of the carbon-sulfur bond from HBPS in the final step of microbial 4S pathway desulfurization reactions. DszB is notable for its substrate specificity and exhibits product inhibition, both of which hinder the overall 4S pathway turnover rate. To understand the molecular-level contributions to substrate and inhibitor binding to DszB, we plan to perform molecular dynamic simulations bound to an array of naphthenic molecules and biphenyl analogues of HBPS. However, many of the small molecules we are interested in are not included in standard force field packages, and thus, we must first produce accurate molecular mechanics force fields. Here, we develop and validate CHARMM-compatible force field parameters for the HBPS substrate, the 2-hydroxybiphenyl product, and potential inhibitors including: 2,2'-biphenol, 2-biphenyl carboxylic acid, 1,8-naphthosultam, and 1,8-naphthosultone. The selected molecules represent biphenyl compounds having both a single and double functional group and the planar naphthenic molecule class, all likely present in the oil-rich environment surrounding DszB-producing microorganisms. The Force Field Toolkit (ffTK) in VMD was used to optimize charge, bond distance, angle, and dihedral parameters. Optimized geometries were determined from quantum mechanical calculations. Molecular simulations of the molecules in explicit and implicit water solutions were conducted to assess the abilities of optimized parameters to recapitulate optimized geometries. Calculated infrared (IR) spectra were obtained and compared with experimental IR spectra for validation of the optimized MM parameters.

  13. 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

  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. Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal.

    PubMed

    Hu, Zhongqiao; Jiang, Jianwen

    2010-01-30

    Different biomolecular force fields (OPLS-AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the C(a) atoms of lysozymes are about 0.1 to 0.2 nm from OPLS-AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B-factors, whereas OPLS-AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten-fold slower than in bulk phase. The directional and average water diffusivities from OPLS-AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS-AA and AMBER03 predict larger hydrophilic solvent-accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS-AA for lysozyme and the Kirkwood-Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution.

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

    PubMed Central

    2015-01-01

    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

  17. Determining force field parameters using a physically based equation of state.

    PubMed

    van Westen, Thijs; Vlugt, Thijs J H; Gross, Joachim

    2011-06-23

    Force field parameters used in classical molecular simulations can be estimated from quantum mechanical calculations or spectroscopic measurements. This especially applies to bonded interactions such as bond-stretching, bond-bending, and torsional interactions. However, it is difficult and computational expensive to obtain accurate parameters describing the nonbonded van der Waals interactions from quantum mechanics. In many studies, these parameters are adjusted to reproduce experimental data, such as vapor-liquid equilibria (VLE) data. Adjusting these force field parameters to VLE data is currently a cumbersome and computationally expensive task. The reason is that the result of a calculation of the vapor-liquid equilibria depends on the van der Waals interactions of all atom types in the system, therefore requiring many time-consuming iterations. In this work, we use an analytical equation of state, the perturbed chain statistical associating fluid theory (PC-SAFT), to predict the results of molecular simulations for VLE. The analytical PC-SAFT equation of state is used to approximate the objective function f(p) as a function of the array of force field parameters p. The objective function is here for example defined as the deviations of vapor pressure, enthalpy of vaporization and liquid density data, with respect to experimental data. The parameters are optimized using the analytical PC-SAFT equation of state, which is orders of magnitude quicker to calculate than molecular simulation. The solution is an excellent approximation of the real objective function, so that the resulting method requires only very few molecular simulation runs to converge. The method is here illustrated by optimizing transferable Lennard-Jones parameters for the n-alkane series. Optimizing four force field parameters p = (ε(CH(2))(CH(2)), ε(CH(3))(CH(3)), σ(CH(2))(CH(2)), σ(CH(3))(CH(3))) we obtain excellent agreement of coexisting densities, vapor pressure and caloric properties

  18. Measurement of the Abraham force and its predicted QED corrections in crossed electric and magnetic fields.

    PubMed

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

    2011-10-21

    We report the observation by a new method of mechanical momentum transferred to gas phase atoms and molecules upon application of crossed oscillating electric and static magnetic fields. We identify this momentum as the microscopic analogue of the classical Abraham force. Two QED predictions of additional magnetoelectrically induced mechanical momentum are addressed. One of them is experimentally refuted; the other is found to be currently below our experimental detection.

  19. Plastic Changes in Hand Proprioception Following Force-Field Motor Learning

    PubMed Central

    Anguera, Joaquin A.

    2010-01-01

    Motor neurophysiologists are placing greater emphasis on sensory feedback processing than ever before. In line with this shift, a recent article by Ostry and colleagues provided timely new evidence that force-field motor learning influences not only motor output, but also proprioceptive sense. In this Neuro Forum, the merits and limitations of Ostry and colleagues are explored in the context of recent work on proprioceptive function, including several recent studies from this journal. PMID:20610787

  20. Plastic changes in hand proprioception following force-field motor learning.

    PubMed

    Goble, Daniel J; Anguera, Joaquin A

    2010-09-01

    Motor neurophysiologists are placing greater emphasis on sensory feedback processing than ever before. In line with this shift, a recent article by Ostry and colleagues provided timely new evidence that force-field motor learning influences not only motor output, but also proprioceptive sense. In this Neuro Forum, the merits and limitations of Ostry and colleagues are explored in the context of recent work on proprioceptive function, including several recent studies from this journal.

  1. Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction

    DTIC Science & Technology

    2008-07-29

    Coarse- 5a. CONTRACT NUMBER FA9550-07-C-0159 Grained Force Fields for Ionic Liquid Property Prediction 5b. GRANT NUMBER 5c. PROGRAM ELEMENT ...constant element for the N-C-N ring angle is punched to be ~3 Hartree/rad2, with several off-diagonal couplings of the same magnitude. This may be...for the study of materials that exhibit non-linear optical properties or for materials that contain transition metals, lanthanides, and actinides

  2. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble.

    PubMed

    Coimbra, João T S; Sousa, Sérgio F; Fernandes, Pedro A; Rangel, Maria; Ramos, Maria J

    2014-01-01

    The AMBER family of force fields is one of the most commonly used alternatives to describe proteins and drug-like molecules in molecular dynamics simulations. However, the absence of a specific set of parameters for lipids has been limiting the widespread application of this force field in biomembrane simulations, including membrane protein simulations and drug-membrane simulations. Here, we report the systematic parameterization of 12 common lipid types consistent with the General Amber Force Field (GAFF), with charge-parameters determined with RESP at the HF/6-31G(d) level of theory, to be consistent with AMBER. The accuracy of the scheme was evaluated by comparing predicted and experimental values for structural lipid properties in MD simulations in an NPT ensemble with explicit solvent in 100:100 bilayer systems. Globally, a consistent agreement with experimental reference data on membrane structures was achieved for some lipid types when using the typical MD conditions normally employed when handling membrane proteins and drug-membrane simulations (a tensionless NPT ensemble, 310 K), without the application of any of the constraints often used in other biomembrane simulations (such as the surface tension and the total simulation box area). The present set of parameters and the universal approach used in the parameterization of all the lipid types described here, as well as the consistency with the AMBER force field family, together with the tensionless NPT ensemble used, opens the door to systematic studies combining lipid components with small drug-like molecules or membrane proteins and show the potential of GAFF in dealing with biomembranes.

  3. 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.

  4. Developing multisite empirical force field models for Pt(II) and cisplatin.

    PubMed

    Cvitkovic, John P; Kaminski, George A

    2017-01-30

    We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.

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

    PubMed

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

    2005-02-10

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

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

    NASA Astrophysics Data System (ADS)

    Durmaz, Vedat

    2015-03-01

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

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

    SciTech Connect

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

    1988-10-15

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

  8. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

    PubMed

    He, Xibing; Lopes, Pedro E M; Mackerell, Alexander D

    2013-10-01

    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 resulting 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.

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

    PubMed

    Schyman, Patric; Jorgensen, William L

    2013-02-07

    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 (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), 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.

  10. Optimization of the OPLS-AA Force Field for Long Hydrocarbons.

    PubMed

    Siu, Shirley W I; Pluhackova, Kristyna; Böckmann, Rainer A

    2012-04-10

    The all-atom optimized potentials for liquid simulations (OPLS-AA) force field is a popular force field for simulating biomolecules. However, the current OPLS parameters for hydrocarbons developed using short alkanes cannot reproduce the liquid properties of long alkanes in molecular dynamics simulations. Therefore, the extension of OPLS-AA to (phospho)lipid molecules required for the study of biological membranes was hampered in the past. Here, we optimized the OPLS-AA force field for both short and long hydrocarbons. Following the framework of the OPLS-AA parametrization, we refined the torsional parameters for hydrocarbons by fitting to the gas-phase ab initio energy profiles calculated at the accurate MP2/aug-cc-pVTZ theory level. Additionally, the depth of the Lennard-Jones potential for methylene hydrogen atoms was adjusted to reproduce the densities and the heats of vaporization of alkanes and alkenes of different lengths. Optimization of partial charges finally allowed to reproduce the gel-to-liquid-phase transition temperature for pentadecane and solvation free energies. It is shown that the optimized parameter set (L-OPLS) yields improved hydrocarbon diffusion coefficients, viscosities, and gauche-trans ratios. Moreover, its applicability for lipid bilayer simulations is shown for a GMO bilayer in its liquid-crystalline phase.

  11. A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.

    PubMed

    Malloci, Giuliano; Vargiu, Attilio Vittorio; Serra, Giovanni; Bosin, Andrea; Ruggerone, Paolo; Ceccarelli, Matteo

    2015-08-03

    We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors). For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties) is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

  12. Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74

    PubMed Central

    2017-01-01

    The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach. PMID:28286598

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

    PubMed

    Wang, Qiantao; Rackers, Joshua A; He, Chenfeng; Qi, Rui; Narth, Christophe; Lagardere, Louis; Gresh, Nohad; Ponder, Jay W; Piquemal, Jean-Philip; Ren, Pengyu

    2015-06-09

    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 (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) 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 (Parker T. M.; J. Chem. Phys.2014, 140, 094106). 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.

  14. Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74.

    PubMed

    Becker, Tim M; Heinen, Jurn; Dubbeldam, David; Lin, Li-Chiang; Vlugt, Thijs J H

    2017-03-02

    The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach.

  15. A New Coarse-Grained Force Field for Membrane-Peptide Simulations.

    PubMed

    Wu, Zhe; Cui, Qiang; Yethiraj, Arun

    2011-11-08

    We present a new coarse-grained (CG) model for simulations of lipids and peptides. The model follows the same topology and parametrization strategy as the MARTINI force field but is based on our recently developed big multipole water (BMW) model for water (J. Phys. Chem. B2010, 114, 10524-10529). The new BMW-MARTINI force field reproduces many fundamental membrane properties and also yields improved energetics (when compared to the original MARTINI force-field) for the interactions between charged amino acids with lipid membranes, especially at the membrane-water interface. A stable attachment of cationic peptides (e.g., Arg8) to the membrane surface is predicted, consistent with experiment and in contrast to the MARTINI model. The model predicts electroporation when there is a charge imbalance across the lipid bilayer, an improvement over the original MARTINI. Moreover, the pore formed during electroporation is toroidal in nature, similar to the prediction of atomistic simulations but distinct from results of polarizable MARTINI for small charge imbalances. The simulations emphasize the importance of a reasonable description of the electrostatic properties of water in CG simulations. The BMW-MARTINI model is particularly suitable for describing interactions between highly charged peptides with lipid membranes, which is crucial to the study of antimicrobial peptides, cell penetrating peptides, and other proteins/peptides involved in the remodeling of biomembranes.

  16. Optimized atomistic force fields for aqueous solutions of Magnesium and Calcium Chloride: Analysis, achievements and limitations

    NASA Astrophysics Data System (ADS)

    Elfgen, Roman; Hülsmann, Marco; Krämer, Andreas; Köddermann, Thorsten; Kirschner, Karl N.; Reith, Dirk

    2016-10-01

    Molecular simulations are an important tool in the study of aqueous salt solutions. To predict the physical properties accurately and reliably, the molecular models must be tailored to reproduce experimental data. In this work, a combination of recent global and local optimization tools is used to derive force fields for MgCl2 (aq) and CaCl2 (aq). The molecular models for the ions are based on a Lennard-Jones (LJ) potential with a superimposed point charge. The LJ parameters are adjusted to reproduce the bulk density and shear viscosity of the different solutions at 1 bar and temperatures of 293.15, 303.15, and 318.15 K. It is shown that the σ-value of chloride consistently has the strongest influence on the system properties. The optimized force field for MgCl2 (aq) provides both properties in good agreement with the experimental data over a wide range of salt concentrations. For CaCl2 (aq), a compromise was made between the bulk density and shear viscosity, since reproducing the two properties requires two different choices of the LJ parameters. This is demonstrated by studying metamodels of the simulated data, which are generated to visualize the correlation between the parameters and observables by using projection plots. Consequently, in order to derive a transferable force field, an error of ˜3% on the bulk density has to be tolerated to yield the shear viscosity in satisfactory agreement with experimental data.

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

    PubMed

    Bradshaw, Richard T; Essex, Jonathan W

    2016-08-09

    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.

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

    PubMed Central

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

    2004-01-01

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

  19. CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes

    PubMed Central

    Mayaan, Evelyn; Moser, Adam; MacKerell, Alexander D.; York, Darrin M.

    2010-01-01

    Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg2+ and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from the CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges and Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the non-standard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects. PMID:17186477

  20. 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.

  1. 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.

  2. 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

  3. The force analysis for superparamagnetic nanoparticles-based gene delivery in an oscillating magnetic field

    NASA Astrophysics Data System (ADS)

    Sun, Jiajia; Shi, Zongqian; Jia, Shenli; Zhang, Pengbo

    2017-04-01

    Due to the peculiar magnetic properties and the ability to function in cell-level biological interaction, superparamagnetic nanoparticles (SMNP) have been being the attractive carrier for gene delivery. The superparamagnetic nanoparticles with surface-bound gene vector can be attracted to the surface of cells by the Kelvin force provided by external magnetic field. In this article, the influence of the oscillating magnetic field on the characteristics of magnetofection is studied in terms of the magnetophoretic velocity. The magnetic field of a cylindrical permanent magnet is calculated by equivalent current source (ECS) method, and the Kelvin force is derived by using the effective moment method. The results show that the static magnetic field accelerates the sedimentation of the particles, and drives the particles inward towards the axis of the magnet. Based on the investigation of the magnetophoretic velocity of the particle under horizontally oscillating magnetic field, an oscillating velocity within the amplitude of the magnet oscillation is observed. Furthermore, simulation results indicate that the oscillating amplitude plays an important role in regulating the active region, where the particles may present oscillating motion. The analysis of the magnetophoretic velocity gives us an insight into the physical mechanism of the magnetofection. It's also helpful to the optimal design of the magnetofection system.

  4. 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.

  5. Embedding Circular Force-Free Flux Ropes in Potential Magnetic Fields

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  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. Effect of Noise and Flow Field Resolution on the Evaluation of Fluid Dynamic Forces on Bodies Using only the Velocity Field and its Derivatives

    NASA Astrophysics Data System (ADS)

    Breda, Maria Cecilia; Krueger, Paul S.

    2010-11-01

    Determining unsteady fluid dynamic forces on bodies using only measurements of the velocity field and its derivatives is essential in many investigations, including studies of freely swimming or flying animals. In this project, all terms in a control-volume force equation utilizing only the velocity field and its derivatives discussed by Noca et al. (J. Fluids Struct., 13, 551 - 578) will be analyzed with regard to the influence of flow field noise and resolution to determine which terms dominate the error in the computed force and which factor has the greatest effect on the error. Using analytical and computational flow fields for which the lift and drag forces are known, irregularities found in real experimental results including noise and reduced spatial/temporal resolution will be added to assess their effect on the computed forces. Results for several canonical flows will be presented.

  8. 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

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

    NASA Astrophysics Data System (ADS)

    Dontsov, Egor V.; Guzina, Bojan B.

    2012-10-01

    The focus of this study is the sustained body force (the so-called acoustic radiation force) in homogeneous tissue-like solids generated by an elevated-intensity, focused ultrasound field (Mach number=O(10-3)) in situations when the latter is modulated by a low-frequency signal. This intermediate-asymptotics problem, which bears relevance to a number of emerging biomedical applications, is characterized by a number of small (but non-vanishing) parameters including the Mach number, the ratio between the modulation and ultrasound frequency, the ratio of the shear to bulk modulus, and the dimensionless attenuation coefficient. On approximating the response of soft tissues as that of a nonlinear viscoelastic solid with heat conduction, the featured second-order problem is tackled via a scaling paradigm wherein the transverse coordinates are scaled by the width of the focal region, while the axial and temporal coordinate are each split into a "fast" and "slow" component with the twin aim of: (i) canceling the linear terms from the field equations governing the propagation of elevated-intensity ultrasound, and (ii) accounting for the effect of ultrasound modulation. In the context of the focused ultrasound analyses, the key feature of the proposed study revolves around the dual-time-scale treatment of the temporal variable, which allows one to parse out the contribution of ultrasound and its modulation in the nonlinear solution. In this way the acoustic radiation force (ARF), giving rise to the mean tissue motion, is exacted by computing the "fast" time average of the germane field equations. A comparison with the existing theory reveals a number of key features that are brought to light by the new formulation, including the contributions to the ARF of ultrasound modulation and thermal expansion, as well as the precise role of constitutive nonlinearities in generating the sustained body force in tissue-like solids by a focused ultrasound beam.

  10. Analytic Properties of Force-free Jets in the Kerr Spacetime. III. Uniform Field Solution

    NASA Astrophysics Data System (ADS)

    Pan, Zhen; Yu, Cong; Huang, Lei

    2017-02-01

    The structure of the steady axisymmetric force-free magnetosphere of a Kerr black hole (BH) is governed by a second-order partial differential equation of A ϕ depending on two “free” functions {{Ω }}({A}φ ) and I({A}φ ), where A ϕ is the ϕ component of the vector potential of the electromagnetic field, Ω is the angular velocity of the magnetic field lines, and I is the poloidal electric current. In this paper, we investigate the solution uniqueness. Taking the asymptotically uniform field as an example, analytic studies imply that there are infinitely many solutions approaching the uniform field at infinity, while only a unique one is found in general relativistic magnetohydrodynamic simulations. To settle the disagreement, we reinvestigate the structure of the governing equation and numerically solve it with given constraint and boundary conditions. We find that the constraint condition (field lines smoothly crossing the light surface) and boundary conditions at the horizon and at infinity are connected via radiation conditions at horizon and at infinity, rather than being independent. With appropriate constraint and boundary conditions, we numerically solve the governing equation and find a unique solution. Contrary to naive expectations, our numerical solution yields a discontinuity in the angular velocity of the field lines and a current sheet along the last field line crossing the event horizon. We also briefly discuss the applicability of the perturbation approach to solving the governing equation.

  11. Nanophotonic force microscopy: Characterizing particle–surface interactions using near-field photonics

    DOE PAGES

    Schein, Perry; Kang, Pilgyu; O’Dell, Dakota; ...

    2015-01-27

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

  12. Nanophotonic force microscopy: Characterizing particle–surface interactions using near-field photonics

    SciTech Connect

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

    2015-01-27

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

  13. 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.

  14. Conformal field theory of critical Casimir forces between surfaces with alternating boundary conditions in two dimensions

    NASA Astrophysics Data System (ADS)

    Dubail, J.; Santachiara, R.; Emig, T.

    2017-03-01

    Systems as diverse as binary mixtures and inclusions in biological membranes, and many more, can be described effectively by interacting spins. When the critical fluctuations in these systems are constrained by boundary conditions, critical Casimir forces (CCF) emerge. Here we analyze CCF between boundaries with alternating boundary conditions in two dimensions, employing conformal field theory (CFT). After presenting the concept of boundary changing operators, we specifically consider two different boundary configurations for a strip of critical Ising spins: (I) alternating equi-sized domains of up and down spins on both sides of the strip, with a possible lateral shift, and (II) alternating domains of up and down spins of different size on one side and homogeneously fixed spins on the other side of the strip. Asymptotic results for the CCF at small and large distances are derived. We introduce a novel modified Szegö formula for determinants of real antisymmetric block Toeplitz matrices to obtain the exact CCF and the corresponding scaling functions at all distances. We demonstrate the existence of a surface renormalization group flow between universal force amplitudes of different magnitude and sign. The Casimir force can vanish at a stable equilibrium position that can be controlled by parameters of the boundary conditions. Lateral Casimir forces assume a universal simple cosine form at large separations.

  15. ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins.

    PubMed

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

    2017-01-01

    Intrinsically disordered proteins are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These intrinsically disordered proteins are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27, are insufficient in sampling the conformational characters of intrinsically disordered proteins. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of intrinsically disordered proteins. Further test suggests that the calculated secondary chemical shifts under ff14IDPs are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs is a robust model for improving the conformation sampling of intrinsically disordered proteins.

  16. Theoretical study of spectroscopic constants and anharmonic force field of SiF2.

    PubMed

    Li, Jing; Wang, Meishan; Yang, Chuanlu; Ma, Meizhong; Tong, Dianmin

    2015-05-01

    The equilibrium structure, spectroscopy constants, and anharmonic force field of SiF2 have been investigated at MP2, B3LYP, and B3PW91 levels of theory employing two basis sets cc-pVQZ and cc-pVTZ, respectively. The obtained equilibrium geometries, rotational constants, fundamental vibrational wave numbers, and centrifugal distortion constants are compared with the available experimental data or the previous theoretical values. The MP2/cc-pVQZ results of SiF2 are in excellent agreement with the available experimental data and afford a marked improvement over B3LYP/cc-pVQZ and B3PW91/cc-pVQZ in the calculation of spectroscopic constants and force constants of SiF2. The basis set enhancement beyond cc-pVQZ does not lead to a major improvement so that the cc-pVQZ basis set is sufficient for SiF2. The MP2/cc-pVQZ results may provide useful data for the spectroscopic experiment studies of SiF2. The used DFT method is also an advisable choice to study anharmonic force field of SiF2.

  17. A simulation study of poly(ethylene glycol) in ionic liquids using a physically motivated ab initio force-field

    NASA Astrophysics Data System (ADS)

    Choi, Eunsong; McDaniel, Jesse G.; Schmidt, J. R.; Yethiraj, Arun

    2014-03-01

    The behavior of poly(ethylene glycol) (PEG) in imidazolium-based ionic liquids (ILs) is studied from molecular dynamics simulations using a new physically motivated force-field. The new force-field accounts for various fundamental intermolecular interactions such as electrostatics, induction, exchange, and dispersion in separate terms where the parameters are derived from ab initio, symmetry adapted perturbation theory (SAPT). The crucial point about the new force-field when compared to other existing force-fields is that it is developed free from empirical parameterization; this is a great advantage particularly for the systems like polymer/IL solutions where experimental data are scarce. We first validate the force-field for neat ILs and neat PEG. Then the force-field is applied to the mixture of the two and the final results are compared with available experiments and simulation results using the OPLS-AA force-field. This work is supported by the National Science Foundation under Grant No. CHE-1111835.

  18. Active control of structurally-coupled sound fields in elastic cylinders by vibrational force inputs

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

    Active control of structurally-coupled sound fields in elastic cylinders is analytically and experimentally studied. The primary (noise) field in the cylinder model is generated by the coupled dynamic response of the shell under loading by a single exterior acoustic source. Control of the interior sound field is achieved by applying vibrational force inputs directly to the shell wall. Action of the point controllers serve to increase the input impedance of select structural modes of the shell which are well-coupled to the interior acoustic cavity, thus substantially reducing sound transmission into the cavity. Spatially-averaged noise reductions in excess of 30 dB are demonstrated for acoustic resonant conditions within the cavity. Twin controller configurations are presented which demonstrate the ability to independently control orthogonal modes of the interior acoustic space. Benefits and drawbacks of this new methodology for noise control are discussed and clearly demonstrated.

  19. Nonlinear force-free field extrapolation of the coronal magnetic field using the data obtained by the Hinode satellite

    NASA Astrophysics Data System (ADS)

    He, Han; Wang, Huaning; Yan, Yihua

    2011-01-01

    The Hinode satellite can obtain high-quality photospheric vector magnetograms of solar active regions and the simultaneous coronal loop images in soft X-ray and extreme ultraviolet (EUV) bands. In this paper, we continue the work of He and Wang (2008) and apply the newly developed upward boundary integration computational scheme for the nonlinear force-free field (NLFFF) extrapolation of the coronal magnetic field to the photospheric vector magnetograms acquired by the Spectro-Polarimeter of the Solar Optical Telescope aboard Hinode. Three time series vector magnetograms of the same solar active region, NOAA 10930, are selected for the NLFFF extrapolations, which were observed within the time interval of 26 h during 10-11 December 2006 when the active region crossed the central area of the Sun's disk. Parallel computation of the NLFFF extrapolation code was realized through OpenMP multithreaded, shared memory parallelism and Fortran 95 programming language for the extrapolation calculations. The comparison between the extrapolated field lines and the coronal loop images obtained by the X-Ray Telescope and the EUV Imaging Spectrometer of Hinode shows that, in the central area of the active region, the field line configurations generally agree with the coronal images, and the orientations of the field lines basically coincide with the coronal loop observations for all three successive magnetograms. This result supports the NLFFF model being used for tracing the time series evolution of the 3-D coronal magnetic structures as the responses of the quasi-equilibrium solar atmosphere to the vector magnetic field changes in the photosphere.

  20. Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

    PubMed

    Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

    2016-11-09

    First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol(-1). For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol(-1) and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol(-1)) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol(-1)). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

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

    PubMed

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

    2011-12-16

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

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

    NASA Astrophysics Data System (ADS)

    Coles, Jonathan P.; Masella, Michel

    2015-01-01

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

  3. Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Kim, S. H.; Hashi, S.; Ishiyama, K.

    2011-01-01

    This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

  4. Second Law Violations by Means of a Stratification of Temperature Due to Force Fields

    NASA Astrophysics Data System (ADS)

    Trupp, Andreas

    2002-11-01

    In 1868 J.C. Maxwell proved that a perpetual motion machine of the second kind would become possible, if the equilibrium temperature in a vertical column of gas subject to gravity were a function of height. However, Maxwell had claimed that the temperature had to be the same at all points of the column. So did Boltzmann. Their opponent was Loschmidt. He claimed that the equilibrium temperature declined with height, and that a perpetual motion machine of the second kind operating by means of such column was compatible with the second law of thermodynamics. Extending the general idea behind Loschmidt's concept to other force fields, gravity can be replaced by molecular forces acting on molecules that try to escape from the surface of a liquid into the vapor space. Experiments proving the difference of temperature between the liquid and the vapor phase were conducted in the 19th century already.

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

    PubMed Central

    Anwar, Muhammad Nabeel

    2013-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  8. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

    NASA Astrophysics Data System (ADS)

    Wang, Hao; Yang, Weitao

    2016-06-01

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

  9. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

    PubMed

    Wang, Hao; Yang, Weitao

    2016-06-14

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

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

    SciTech Connect

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

    2014-08-01

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

  12. Perspectives on the simulation of protein–surface interactions using empirical force field methods

    PubMed Central

    Latour, Robert A.

    2014-01-01

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

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

    PubMed

    Giulianotti, Richard; Robertson, Roland

    2012-06-01

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

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

    PubMed

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

    2015-06-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Rational design of ion force fields based on thermodynamic solvation properties

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H3O+) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the

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

    PubMed

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

    2016-03-01

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

  18. Force field analysis suggests a lowering of diffusion barriers in atomic manipulation due to presence of STM tip.

    PubMed

    Emmrich, Matthias; Schneiderbauer, Maximilian; Huber, Ferdinand; Weymouth, Alfred J; Okabayashi, Norio; Giessibl, Franz J

    2015-04-10

    We study the physics of atomic manipulation of CO on a Cu(111) surface by combined scanning tunneling microscopy and atomic force microscopy at liquid helium temperatures. In atomic manipulation, an adsorbed atom or molecule is arranged on the surface using the interaction of the adsorbate with substrate and tip. While previous experiments are consistent with a linear superposition model of tip and substrate forces, we find that the force threshold depends on the force field of the tip. Here, we use carbon monoxide front atom identification (COFI) to characterize the tip's force field. Tips that show COFI profiles with an attractive center can manipulate CO in any direction while tips with a repulsive center can only manipulate in certain directions. The force thresholds are independent of bias voltage in a range from 1 to 10 mV and independent of temperature in a range of 4.5 to 7.5 K.

  19. Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field

    PubMed Central

    Click, Timothy H.; Kaminski, George A.

    2009-01-01

    We have extended our previous studies of calculating acidity constants for the acidic residues found in the turkey ovomucoid third domain protein (OMTKY3) by determining the relative pKa values for the basic residues (Lys13, Arg21, Lys29, Lys34, His52, and Lys55). A polarizable force field (PFF) was employed. The values of the pKa were found by direct comparison of energies of solvated protonated and deprotonated forms of the protein. Poisson Boltzmann (PBF) and Generalized Born (SGB) continuum solvation models represent the hydration, and a non-polarizable fixed-charges OPLS-AA force field was used for comparison. Our results indicate that (i) the pKa values of the basic residues can be found in close agreement with the experimental values when a PFF is used in conjunction with the PBF solvation model, (ii) it is sufficient to take into the account only the residues which are in close proximity (hydrogen bonded) to the residue in question, and (iii) The PBF solvation model is superior to the SGB solvation model for these pKa calculations. The average error with the PBF/PFF model is only 0.7 pH units, compared with 2.2 and 6.1 units for the PBF/OPLS and SGB/OPLS, respectively. The maximum deviation of the PBF/PFF results from the experimental values is 1.7 pH units compared with 6.0 pH units for the PBF/OPLS. Moreover, the best results were obtained while using an advanced non-polar energy calculation scheme. The overall conclusion is that this methodology and force field are suitable for accurate assessment of pKa shifts for both acidic basic protein residues. PMID:19432439

  20. Genetic algorithm optimization of point charges in force field development: challenges and insights.

    PubMed

    Ivanov, Maxim V; Talipov, Marat R; Timerghazin, Qadir K

    2015-02-26

    Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA approach for the least-squares MEP point charge fitting, and show that the GA optimizations suffer from a magnified version of the classical buried atom effect, producing highly scattered yet correlated solutions. This effect can be understood in terms of the linearly independent, natural coordinates of the MEP fitting problem defined by the eigenvectors of the least-squares sum Hessian matrix, which are also equivalent to the eigenvectors of the covariance matrix evaluated for the scattered GA solutions. GAs quickly converge with respect to the high-curvature coordinates defined by the eigenvectors related to the leading terms of the multipole expansion, but have difficulty converging with respect to the low-curvature coordinates that mostly depend on the buried atom charges. The performance of the evolutionary techniques dramatically improves when the point charge optimization is performed using the Hessian or covariance matrix eigenvectors, an approach with a significant potential for the evolutionary optimization of the fixed-charge biomolecular force fields.

  1. Exploring solvent effects upon the Menshutkin reaction using a polarizable force field.

    PubMed

    Acevedo, Orlando; Jorgensen, William L

    2010-07-01

    The energetics of the Menshutkin reaction between triethylamine and ethyl iodide have been computed using B3LYP and MP2 with the LANL2DZ, LANL2DZd, SVP, MIDI!, 6-311G(d,p), and aug-cc-PVTZ basis sets. Small- and large-core energy-consistent relativistic pseudopotentials were employed. Solvent effect corrections were computed from QM/MM Monte Carlo simulations utilizing free-energy perturbation theory, PDDG/PM3, and both a nonpolarizable OPLS and polarizable OPLS-AAP force field. The B3LYP/MIDI! theory level provided the best DeltaG(++) values with a mean absolute error (MAE) of 4.9 kcal/mol from experiment in cyclohexane, CCl(4), THF, DMSO, acetonitrile, water, and methanol. However, the relative rates in cyclohexane, and to a certain extent CCl(4), were determined to be greatly underestimated when using the nonpolarizable OPLS force field. An overall reduction in the MAE to 3.1 kcal/mol using B3LYP/MIDI!/OPLS-AAP demonstrated the need for a fully polarizable force field when computing solvent effects for highly dipolar transition structures in low-dielectric media. The MAEs obtained with PDDG/PM3/OPLS and OPLS-AAP of 5.3 and 3.8 kcal/mol, respectively, provided comparable results to B3LYP at a fraction of the computational resources. The large rate accelerations observed in the reaction were correlated to an increased stabilization of the emerging charge separation at the transition state via favorable solute-solvent interactions.

  2. Predicting the thermodynamic properties of gold nanoparticles using different force fields

    NASA Astrophysics Data System (ADS)

    Park, Yongjin

    The objective of this research was to learn how to predict the thermodynamic properties of gold nanoparticles using computational tools. The lowest energy structures of gold nanoparticles of various sizes were determined and thermodynamic properties such as the free energy (F), internal energy (U), entropy (S), and specific heat (Cv) of the gold nanoparticles were investigated using a fully-atomistic Monte Carlo simulation method that utilizes a modified Wang-Landau algorithm. Eight well-known force fields for metallic systems were employed to model gold nanoparticles: the Lennard-Jones potential (LJ), the Lennard-Jones potential with Heinz's parameterization (LJH), the Gupta potential, the Sutton-Chen potential (SC), the Sutton-Chen potential with Pawluk's parameterization for small clusters (SCP), the Quantum Sutton-Chen potential (Q-SC), the Embedded Atom Method (EAM) by Cai and Ye, and the empirical potential for gold proposed by Olivier and coworkers (POT). Subsequently, we explored the accuracy of each force field in the description of the thermodynamic behavior of gold nanoparticles. The thermodynamic properties of gold nanoparticles were computed from the Density of States which was obtained as a result of the Monte Carlo simulation. Afterwards, the melting point of gold nanoparticles was determined from the behavior of the calculated thermodynamic properties and was compared with theory, experimental observations and other simulation results. The force fields employed predicted melting points of gold nanoparticles over a wide range of temperatures. A thorough comparison with the available experimental observations showed that the Quantum Sutton-Chen potential (Q-SC) correctly described the melting behavior of gold nanoparticles with sizes smaller than 1.3 nanometers.

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  5. Magneto-frictional Modeling of Coronal Nonlinear Force-free Fields. II. Application to Observations

    NASA Astrophysics Data System (ADS)

    Guo, Y.; Xia, C.; Keppens, R.

    2016-09-01

    A magneto-frictional module has been implemented and tested in the Message Passing Interface Adaptive Mesh Refinement Versatile Advection Code (MPI-AMRVAC) in the first paper of this series. Here, we apply the magneto-frictional method to observations to demonstrate its applicability in both Cartesian and spherical coordinates, and in uniform and block-adaptive octree grids. We first reconstruct a nonlinear force-free field (NLFFF) on a uniform grid of 1803 cells in Cartesian coordinates, with boundary conditions provided by the vector magnetic field observed by the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) at 06:00 UT on 2010 November 11 in active region NOAA 11123. The reconstructed NLFFF successfully reproduces the sheared and twisted field lines and magnetic null points. Next, we adopt a three-level block-adaptive grid to model the same active region with a higher spatial resolution on the bottom boundary and a coarser treatment of regions higher up. The force-free and divergence-free metrics obtained are comparable to the run with a uniform grid, and the reconstructed field topology is also very similar. Finally, a group of active regions, including NOAA 11401, 11402, 11405, and 11407, observed at 03:00 UT on 2012 January 23 by SDO/HMI is modeled with a five-level block-adaptive grid in spherical coordinates, where we reach a local resolution of 0\\buildrel{\\circ}\\over{.} 06 pixel-1 in an area of 790 Mm × 604 Mm. Local high spatial resolution and a large field of view in NLFFF modeling can be achieved simultaneously in parallel and block-adaptive magneto-frictional relaxations.

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

    PubMed

    Faccioli, P; a Beccara, S

    2016-01-01

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

  7. Dynamics of ions in a water drop using the AMOEBA polarizable force field

    NASA Astrophysics Data System (ADS)

    Thaunay, Florian; Ohanessian, Gilles; Clavaguéra, Carine

    2017-03-01

    Various ions carrying a charge from -2 to +3 were confined in a drop of 100 water molecules as a way to model coordination properties inside the cluster and at the interface. The behavior of the ions has been followed by molecular dynamics with the AMOEBA polarizable force field. Multiply charged ions and small singly charged ions are found to lie inside the droplet, while bigger monovalent ions sit near the surface. The results provide a coherent picture of average structural properties as well as residence times for which a general trend is proposed, especially for the anions.

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

    SciTech Connect

    Turner, L.R.

    1996-05-01

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

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

    SciTech Connect

    Turner, L.R.

    1997-03-01

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

  10. Determination of the electrostatic lever arm of carbon nanotube field effect transistors using Kelvin force microscopy

    NASA Astrophysics Data System (ADS)

    Brunel, David; Deresmes, Dominique; Mélin, Thierry

    2009-06-01

    We use Kelvin force microscopy (KFM) to study the electrostatic properties of single-walled carbon nanotube field effect transistor devices (CNTFETs) with backgate geometry at room temperature. We show that KFM maps recorded as a function of the device backgate polarization enable a complete phenomenological determination of the averaging effects associated with the KFM probe side capacitances, and thus, to obtain KFM measurements with quantitative character. The value of the electrostatic lever arm of the CNTFET is determined from KFM measurements and found in agreement with transport measurements based on Coulomb blockade.

  11. In-situ bioventing: Two US EPA and Air Force sponsored field studies

    SciTech Connect

    Sayles, G.D.; Hinchee, R.E.; Brenner, R.C.; Vogel, C.M.; Miller, R.N.

    1992-01-01

    Bioventing is the process of delivering oxygen by forced air movement through organically contaminated unsaturated soils in order to stimulate in situ biodegradation in an otherwise oxygen-limited environment. The paper is a report on progress of two ongoing bioventing field studies involving JP-4 jet fuel contamination. The first investigation, at Eielson AFB near Fairbanks, Alaska, is a study of bioventing in shallow soils and cold climates in conjunction with an evaluation of soil warming techniques. The second study, at Hill AFB near Salt Lake City, Utah, is examining bioventing of large volumes of soil and determining biodegradation and volatilization rates as a function of air injection rate.

  12. Role of external magnetic field and current closure in the force balance mechanism of a magnetically stabilized plasma torch

    NASA Astrophysics Data System (ADS)

    G, Ravi; Goyal, Vidhi

    2012-10-01

    Experimental investigations on the role of applied external magnetic field and return current closure in the force balance mechanism of a plasma torch are reported. The plasma torch is of low power and has wall, gas and magnetic stabilization mechanisms incorporated in it. Gas flow is divided into two parts: axial-central and peripheral-shroud, applied magnetic field is axial and return current is co-axial. Results indicate that application of large external magnetic field gives rise to not only J x B force but also, coupled with gas flow, to a new drag-cum-centrifugal force that acts on the plasma arc root and column. The magnetic field also plays a role in the return current closure dynamics and thus in the overall force balance mechanism. This in turn affects the electro-thermal efficiency of the plasma torch. Detailed experimental results, analytical calculations and physical model representing the processes will be presented and discussed.

  13. Mapping near-field environments of plasmonic and 2D materials with photo-induced force imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Tumkur, Thejaswi U.; Doiron, Chloe; Yang, Xiao; Li, Bo; Swearer, Dayne F.; Cerjan, Benjamin W.; Nordlander, Peter; Halas, Naomi J.; Ajayan, Pulickel M.; Ringe, Emilie; Thomann, Isabell

    2016-09-01

    We demonstrate the ability to map photo-induced gradient forces in materials, using a setup akin to atomic force microscopy. This technique allows for the simultaneous characterization of topographical features and optical near-fields in materials, with a high spatio-temporal resolution. We show that the near-field gradient forces can be translated onto electric fields, enabling the mapping of plasmonic hot-spots in gold nanostructures, and the resolution of sub-10 nm features in photocatalytic materials. We further show that the dispersion-sensitive nature of near-field gradient forces can be used to image and distinguish atomically thin layers of 2-D materials, with high contrast.

  14. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

    PubMed

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

    2013-05-30

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

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

    PubMed Central

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

    2013-01-01

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

  16. On the radiation force fields of fractional-order acoustic vortices

    NASA Astrophysics Data System (ADS)

    Hong, Z. Y.; Zhang, J.; Drinkwater, B. W.

    2015-04-01

    Here we report the creation and observation of acoustic vortices of fractional order. Whilst integer orders are known to produce axisymmetric acoustic fields, fractional orders are shown to break this symmetry and produce a vast array of unexplored field patterns, typically exhibiting multiple closely spaced phase singularities. Here, fractional acoustic vortices are created by emitting ultrasonic waves from an annular array of sources using multiple ramps of phase delay around its circumference. Acoustic radiation force patterns, including multiple concentration points, short straight lines, triangles, squares and discontinuous circles are simulated and experimentally observed. The fractional acoustic vortex leading to two closely spaced phase singularities is used to trap, and by controlling the order, reversibly manipulate two microparticles to a proximity of 0.3 acoustic wavelengths.

  17. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor

    PubMed Central

    Dennis, John Ojur; Ahmad, Farooq; Khir, M. Haris Bin Md; Hamid, Nor Hisham Bin

    2015-01-01

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT. PMID:26225972

  18. Gravitational forces in the Randall-Sundrum model with a scalar stabilizing field

    NASA Astrophysics Data System (ADS)

    Arnowitt, R.; Dent, J.

    2007-03-01

    We consider the problem of gravitational forces between point particles on the branes in a five-dimensional (5D) Randall-Sundrum model with two branes (at y1 and y2) and S1/Z2 symmetry of the fifth dimension. The matter on the branes is viewed as a perturbation on the vacuum metric and treated to linear order. In a previous work [R. Arnowitt and J. Dent, Phys. Rev. D 71, 124024 (2005).PRVDAQ0556-282110.1103/PhysRevD.71.124024] it was seen that the trace of the transverse part of the 4D metric on the TeV brane, fT(y2), contributed a Newtonian potential enhanced by e2βy2≅1032 and thus produced gross disagreement with the experiment. In this work we include a scalar stabilizing field ϕ and solve the coupled Einstein and scalar equations to leading order for the case where ϕ02/M53 is small and the vacuum field ϕ0(y) is a decreasing function of y. fT then grows a mass factor e-μr where, however, μ is suppressed from its natural value, O(MPl), by an exponential factor e-(1+λb)βy2, λb>0. Thus agreement with the experiment depends on the interplay between the enhancing and decaying exponentials. Current data eliminates a significant part of the parameter space, and the Randall-Sundrum model will be sensitive to any improvements on the tests of the Newtonian force law at smaller distances. An example of coupling of the ϕ field to the Higgs field is examined and found to generally produce very small effects.

  19. Field investigation source area ST58 old Quartermaster service station, Eielson Air Force Base, Alaska

    SciTech Connect

    Liikala, T.L.; Evans, J.C.

    1995-01-01

    Source area ST58 is the site of the old Quartermaster service station at Eielson Air Force Base, Alaska. The source area is one of several Source Evaluation Report sites being investigated by Pacific Northwest Laboratory for the US Air Force as candidates for no further remedial action, interim removal action, or a remedial investigation/feasibility study under a Federal Facilities Agreement. The purpose of this work was to characterize source area ST58 and excavate the most contaminated soils for use in composting treatability studies. A field investigation was conducted to determine the nature and extent of soil contamination. The field investigation entailed a records search; grid node location, surface geophysical, and soil gas surveys; and test pit soil sampling. Soil excavation followed based on the results of the field investigation. The site was backfilled with clean soil. Results from this work indicate close spatial correlation between screening instruments, used during the field investigation and soil excavation, and laboratory analyses. Gasoline was identified as the main subsurface contaminant based on the soil gas surveys and test pit soil sampling. A center of contamination was located near the northcentral portion of the source area, and a center was located in the northwestern comer. The contamination typically occurred near or below a former soil horizon probably as a result of surface spills and leaks from discontinuities and/or breaks in the underground piping. Piping locations were delineated during the surface geophysical surveys and corresponded very well to unscaled drawings of the site. The high subsurface concentrations of gasoline detected in the northwestern comer of the source area probably reflect ground-water contamination and/or possibly floating product.

  20. Optical Characterization of Lorentz Force Based CMOS-MEMS Magnetic Field Sensor.

    PubMed

    Dennis, John Ojur; Ahmad, Farooq; Khir, M Haris Bin Md; Bin Hamid, Nor Hisham

    2015-07-27

    Magnetic field sensors are becoming an essential part of everyday life due to the improvements in their sensitivities and resolutions, while at the same time they have become compact, smaller in size and economical. In the work presented herein a Lorentz force based CMOS-MEMS magnetic field sensor is designed, fabricated and optically characterized. The sensor is fabricated by using CMOS thin layers and dry post micromachining is used to release the device structure and finally the sensor chip is packaged in DIP. The sensor consists of a shuttle which is designed to resonate in the lateral direction (first mode of resonance). In the presence of an external magnetic field, the Lorentz force actuates the shuttle in the lateral direction and the amplitude of resonance is measured using an optical method. The differential change in the amplitude of the resonating shuttle shows the strength of the external magnetic field. The resonance frequency of the shuttle is determined to be 8164 Hz experimentally and from the resonance curve, the quality factor and damping ratio are obtained. In an open environment, the quality factor and damping ratio are found to be 51.34 and 0.00973 respectively. The sensitivity of the sensor is determined in static mode to be 0.034 µm/mT when a current of 10 mA passes through the shuttle, while it is found to be higher at resonance with a value of 1.35 µm/mT at 8 mA current. Finally, the resolution of the sensor is found to be 370.37 µT.

  1. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations.

    PubMed

    Graen, Timo; Hoefling, Martin; Grubmüller, Helmut

    2014-12-09

    Recent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized π-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories.

  2. Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

    PubMed

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

    2014-06-26

    Traditional protein force fields use one set of parameters for most of the 20 amino acids (AAs), allowing transferability of the parameters. However, a significant shortcoming is the difficulty to fit the Ramachandran plots of all AA residues simultaneously, affecting the accuracy of the force field. In this Feature Article, we report a new strategy for protein force field parametrization. Backbone and side-chain conformational distributions of all 20 AA residues obtained from protein coil library were used as the target data. The dihedral angle (torsion) potentials and some local nonbonded (1-4/1-5/1-6) interactions in OPLS-AA/L force field were modified such that the target data can be excellently reproduced by molecular dynamics simulations of dipeptides (blocked AAs) in explicit water, resulting in a new force field with AA-specific parameters, RSFF1. An efficient free energy decomposition approach was developed to separate the corrections on ϕ and ψ from the two-dimensional Ramachandran plots. RSFF1 is shown to reproduce the experimental NMR (3)J-coupling constants of AA dipeptides better than other force fields. It has a good balance between α-helical and β-sheet secondary structures. It can successfully fold a set of α-helix proteins (Trp-cage and Homeodomain) and β-hairpins (Trpzip-2, GB1 hairpin), which cannot be consistently stabilized by other state-of-the-art force fields. Interestingly, the RSFF1 force field systematically overestimates the melting temperature (and the stability of native state) of these peptides/proteins. It has a potential application in the simulation of protein folding and protein structure refinement.

  3. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field

    DTIC Science & Technology

    2000-11-01

    Lennard - Jones 9-6 function for the van der Waals (vdW) term and a Coulombic term for an electrostatic interaction. To validate the force field, molecular mechanics calculations and molecular dynamics simulations have been made on a variety of molecules containing the nitrate ester functionality. Using this force field, excellent agreement has been obtained between the calculated and experimental values for molecular structures, vibrational frequencies, liquid densities, heats of vaporization, crystal structure, mechanical properties and lattice

  4. Velocity measurements and concentration field visualizations in copper electrolysis under the influence of Lorentz forces and buoyancy

    NASA Astrophysics Data System (ADS)

    Weier, T.; Cierpka, C.; Huller, J.; Gerbeth, G.

    2006-12-01

    Velocity measurements and shadowgraph visualizations for copper electrolysis under the influence of a magnetic field are reported. Experiments in a rectangular cell show the expected strong correlation between flow features and limiting current density. The flow can be understood as driven by the interplay of Lorentz force and buoyancy. For a cylindrical cell with only slightly non-parallel electric and magnetic field lines, the presence and importance of the Lorentz force is demonstrated by velocity measurements. Figs 6, Refs 13.

  5. Prediction of SAMPL3 Host-Guest Binding Affinities: Evaluating the Accuracy of Generalized Force-Fields

    PubMed Central

    Muddana, Hari S.; Gilson, Michael K.

    2012-01-01

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

  6. Near-field Light Scattering Techniques for Measuring Nanoparticle-Surface Interaction Energies and Forces

    PubMed Central

    O'Dell, Dakota; Adam, Ian S.; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David

    2015-01-01

    Nanoparticles are quickly becoming commonplace in many commercial and industrial products, ranging from cosmetics to pharmaceuticals to medical diagnostics. Predicting the stability of the engineered nanoparticles within these products a priori remains an important and difficult challenge. Here we describe our techniques for measuring the mechanical interactions between nanoparticles and surfaces using near-field light scattering. Particle-surface interfacial forces are measured by optically “pushing” a particle against a reference surface and observing its motion using scattered near-field light. Unlike atomic force microscopy, this technique is not limited by thermal noise, but instead takes advantage of it. The integrated waveguide and microfluidic architecture allow for high-throughput measurements of about 1000 particles per hour. We characterize the reproducibility of and experimental uncertainty in the measurements made using the NanoTweezer surface instrument. We report surface interaction studies on gold nanoparticles with 50 nm diameters, smaller than previously reported in the literature using similar techniques. PMID:26855473

  7. A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols.

    PubMed

    Visscher, Koen M; Vosmeer, C Ruben; Luirink, Rosa A; Geerke, Daan P

    2017-03-30

    In this work, parameters are optimized for a charge-on-spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico-chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed-phase polarizabilities, and starting from the non-polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure-liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure-liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen-bonding and non-hydrogen-bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.

  8. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.

    PubMed

    Mohamed, Noor Asidah; Bradshaw, Richard T; Essex, Jonathan W

    2016-12-15

    The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field. Although AMOEBA results give mean errors close to "chemical accuracy," GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non-potential-specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  9. A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons.

    PubMed

    Szklarczyk, Oliwia M; Bachmann, Stephan J; van Gunsteren, Wilfred F

    2014-04-15

    Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge-on-spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united-atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self-diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force-field parameters for CH2, CH3, and CH4 moieties.

  10. A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

    PubMed

    Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P

    2016-02-13

    We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

  11. Advances in RNA molecular dynamics: a simulator's guide to RNA force fields.

    PubMed

    Vangaveti, Sweta; Ranganathan, Srivathsan V; Chen, Alan A

    2017-03-01

    Molecular simulations have become an essential tool for biochemical research. When they work properly, they are able to provide invaluable interpretations of experimental results and ultimately provide novel, experimentally testable predictions. Unfortunately, not all simulation models are created equal, and with inaccurate models it becomes unclear what is a bona fide prediction versus a simulation artifact. RNA models are still in their infancy compared to the many robust protein models that are widely in use, and for that reason the number of RNA force field revisions in recent years has been rapidly increasing. As there is no universally accepted 'best' RNA force field at the current time, RNA simulators must decide which one is most suited to their purposes, cognizant of its essential assumptions and their inherent strengths and weaknesses. Hopefully, armed with a better understanding of what goes inside the simulation 'black box,' RNA biochemists can devise novel experiments and provide crucial thermodynamic and structural data that will guide the development and testing of improved RNA models. WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396 For further resources related to this article, please visit the WIREs website.

  12. Point Defects in Carbon Nanotubes: ab initio and Force-Fields Based Simulations

    NASA Astrophysics Data System (ADS)

    Kroes, Jaap; Pietrucci, Fabio; Curioni, Alessandro; Andreoni, Wanda

    2014-03-01

    We present an extended investigation of point defects in carbon nanotubes (CNTs) and their effects on mechanical and electronic properties. This study is based on large-scale calculations using DFT with exchange and correlation functionals of the GGA - including empirical corrections for van-der-Waals interactions - and of the hybrid type. Additional simulations using classical interatomic potentials allow us to obtain a critical comparison between the outcome of DFT and force-fields. The CNT models adopted have a range of sizes and chiralities. In particular, (i) our simulations of oxygen chemisorption revealed a tendency to clustering and the existence of kinetic traps (epoxides), which explain STS data; (ii) the extension to oxygen isovalent species on CNTs and other graphitic surfaces has suggested a simple predictive model for the chemisorption pattern. Moreover, (iii) our analysis shows an intrinsic difficulty of available force fields to account for the energetics of vacancies and adsorption site preferences. Additional results aiming at characterizing the interaction of nitrogen oxides (NOx) with the CNT surface will also be presented. Work supported by SNSF Nano-Tera.ch and CSCS.

  13. A New Charge Model in The Valence Force Field Model for Phonon Calculations

    NASA Astrophysics Data System (ADS)

    Barrett, Christopher; Wang, Lin-Wang

    2013-03-01

    The classical ball and spring Valence Force Field model is useful to determine the elastic relaxation of thousand-atom nanosystems. We have also used it to calculate the phonon spectra of nanosystems. However, we found that the conventional point charge model in the Valence Force Field model can cause artificial instability in nanostructures. In this talk, we will present a new charge model which represents the electron cloud feature of the Born charge in a real crystal. More specifically, we have two opposite-signed point charges assigned to each atom, one at its real position, another at a position determined by its neighbor atoms. This innovation allows both electrostatic charges and Born charges to be accurately represented while retaining extreme efficiency. This customized VFF method is developed to be fittable to the results of density functional theory (DFT) calculation. We will present the results of CdSe bulk, surface, and nanowire calculations and compare them with the equivalent ab-initio calculations, for both in their accuracies and their costs. This work is supported by U.S. Department of Energy BES, Office of Science, under Contract No. DE-AC02-05CH11231.

  14. Field dependence of magnetic blocking temperature: Analog tests using coercive force data

    NASA Astrophysics Data System (ADS)

    Dunlop, David J.

    1982-02-01

    The field dependence of blocking temperature TB and the temperature dependence of coercive force Hc are shown to be analogous functions. Coercive force data, obtained routinely with standard equipment, can therefore be used in analog tests of theories of thermoremanent magnetization (TRM). Analog Hc data reported in this paper for single-domain and small multidomain magnetite dispersions and a variety of rocks are matched equally well by Néel's (1949) theory of thermally activated magnetization changes or Néel's (1955) theory of field-induced domain wall displacements. The temperature dependence of domain wall pinning is a crucial unknown in the wall displacement model, allowing considerable latitude in curve fitting. If the thermal activation model is assumed, reasonable values are found for the volume activated in a single magnetization reversal or wall jump in the fine- and medium-grained rocks tested. Additional independent evidence from hysteresis and microscopic examination is necessary, however, to choose between the competing TRM models in individual cases.

  15. Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides.

    PubMed

    Kahn, Kalju; Bruice, Thomas C

    2002-07-30

    The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.

  16. Development of glycyl radical parameters for the OPLS-AA/L force field.

    PubMed

    Komáromi, István; Owen, Michael C; Murphy, Richard F; Lovas, Sándor

    2008-09-01

    On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.

  17. Force field-based conformational searches: efficiency and performance for peptide receptor complexes

    NASA Astrophysics Data System (ADS)

    Grebner, Christoph; Niebling, Stephan; Schmuck, Carsten; Schlücker, Sebastian; Engels, Bernd

    2013-09-01

    Conformational search using force field methods on complex biomolecular systems is a key factor in understanding molecular and structural properties. The reliability of such investigations strongly depends on the efficiency of the conformational search algorithm as well as the accuracy of the employed force field. In the present work we compared the performance of two different approaches: the Monte-Carlo multiple minimum/low mode sampling (MCMM/LM), in combination with the OPLS2005 (MCMM/LM//OPLS2005), and Tabu-Search combined with Basin Hopping (TS/BH), employing the original OPLS-AA implementation proposed by Jorgensen (TS/BH//OPLS-AA). We investigated their performance in locating energetically low-lying structures and the efficiency in scanning the conformational phase space of non-covalently bonded complexes. As test systems we employed complexes of the artificial peptide receptor CBS-KKF with four different tetrapeptide ligands. The reliability and the accuracy of both approaches were examined by re-optimising all low-energy structures employing density functional theory with empirical dispersion correction in combination with triple zeta basis sets. Solvent effects were mimicked by a continuum solvent model. In all the four-test systems, the TS/BH//OPLS-AA approach yielded structures that are much lower in energy after the DFT optimisation. Additionally, it provided many low-lying structures that were not identified by the MCMM/LM//OPLS2005 approach.

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

    PubMed

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

    2014-05-01

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

  19. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

    PubMed Central

    2016-01-01

    Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643

  20. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

    PubMed Central

    Mohamed, Noor Asidah; Bradshaw, Richard T.

    2016-01-01

    The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27757978

  1. Directly resolving particles in an electric field: local charge, force, torque, and applications

    NASA Astrophysics Data System (ADS)

    Liu, Qianlong

    2011-11-01

    Prosperetti's seminal Physalis method for fluid flows with suspended particles is extended to electric fields to directly resolve finite-sized particles and to investigate accurately the mutual fluid-particle, particle-particle, and particle-boundary interactions. The method can be used for uncharged/charged dielectrics, uncharged/charged conductors, conductors with specified voltage, and general weak and strong discontinuous interface conditions. These interface conditions can be in terms of field variable, its gradients, and surface integration which has not been addesed by other numerical methods. In addition, for the first time, we rigorously derive the force and torque on the finite-sized particles resulting from the interactions between harmonics. The method, for the first time, directly resolves the particles with accurate local charge distribution, force, and torque on the particles, making many applications in engineering, mechanics, physics, chemistry, and biology possible, such as heterogeneous materials, microfluidics, electrophotography, electric double layer capacitors, and microstructures of nanodispersions. The efficiency of the method is demonstrated with up to one hundred thousand 3D particles, which suggests that the method can be used for many important engineering applications of broad interest. This research is supported by the Department of Energy under funding for an EFRC (the HeteroFoaM Center), grant no. DE-SC0001061.

  2. General Force-Field Parametrization Scheme for Molecular Dynamics Simulations of Conjugated Materials in Solution

    PubMed Central

    2016-01-01

    We describe a general scheme to obtain force-field parameters for classical molecular dynamics simulations of conjugated polymers. We identify a computationally inexpensive methodology for calculation of accurate intermonomer dihedral potentials and partial charges. Our findings indicate that the use of a two-step methodology of geometry optimization and single-point energy calculations using DFT methods produces potentials which compare favorably to high level theory calculation. We also report the effects of varying the conjugated backbone length and alkyl side-chain lengths on the dihedral profiles and partial charge distributions and determine the existence of converged lengths above which convergence is achieved in the force-field parameter sets. We thus determine which calculations are required for accurate parametrization and the scope of a given parameter set for variations to a given molecule. We perform simulations of long oligomers of dioctylfluorene and hexylthiophene in explicit solvent and find peristence lengths and end-length distributions consistent with experimental values. PMID:27397762

  3. Systematic refinement of Canongia Lopes-Pádua force field for pyrrolidinium-based ionic liquids.

    PubMed

    Chaban, Vitaly V; Voroshylova, Iuliia V

    2015-05-21

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. While Canongia Lopes-Pádua (CL&P) FF provides good to excellent thermodynamics and structure of pure room-temperature ionic liquids (RTILs), it suffers from drastically and systematically underestimated ionic motion. This occurs due to neglected partial electron transfer from the anion to the cation, resulting in unphysically small simulated self-diffusion and conductivity and high shear viscosities. We report a systematic refinement of the CL&P FF for six pyrrolidinium-based RTILs (1-N-butyl-1-methylpyrrolidinium dicyanamide, triflate, bis(fluorosulfonyl)imide, bis(trifluoromethanesulfonyl)imide, tetrafluoroborate, chloride). The elaborated procedure accounts for specific cation-anion interactions in the liquid phase. Once these interactions are described effectively, experimentally determined transport properties can be reproduced with an acceptable accuracy. Together with the original CL&P parameters, our force field fosters computational investigation of ionic liquids. In addition, the reported results shed more light on the chemical nature of cation-anion binding in various families of RTILs.

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

    PubMed Central

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

    2008-01-01

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

  5. Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

    SciTech Connect

    Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; Schwegler, Eric; Berkowitz, Max L.

    2016-05-27

    To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers became adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.

  6. Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

    DOE PAGES

    Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; ...

    2016-05-27

    To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers becamemore » adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.« less

  7. Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

    PubMed Central

    2015-01-01

    Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

  8. Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field.

    PubMed

    Boulanger, Eliot; Thiel, Walter

    2014-04-08

    The polarization of the environment can influence the results from hybrid quantum mechanical/molecular mechanical (QM/MM) simulations of enzymatic reactions. In this article, we address several technical aspects in the development of polarizable QM/MM embedding using the Drude Oscillator (DO) force field. We propose a stable and converging update of the DO polarization state for geometry optimizations and a suitable treatment of the QM/MM-DO boundary when the QM and MM regions are separated by cutting through a covalent bond. We assess the performance of our approach by computing binding energies and geometries of three selected complexes relevant to biomolecular modeling, namely the water trimer, the N-methylacetamide dimer, and the cationic bis(benzene)sodium sandwich complex. Using a recently published MM-DO force field for proteins, we evaluate the effect of MM polarization on the QM/MM energy profiles of the enzymatic reactions catalyzed by chorismate mutase and by p-hydroxybenzoate hydroxylase. We find that inclusion of MM polarization affects the computed barriers by about 10%.

  9. Development of a united-atom force field for 1-ethyl-3-methylimidazolium tetracyanoborate ionic liquid

    NASA Astrophysics Data System (ADS)

    Koller, Thomas; Ramos, Javier; Garrido, Nuno M.; Fröba, Andreas P.; Economou, Ioannis G.

    2012-06-01

    Three united-atom (UA) force fields are presented for the ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, abbreviated as [EMIM]+[B(CN)4]-. The atomistic charges were calculated based on the restrained electrostatic potential (RESP) of the isolated ions (abbreviated as force field 1, FF-1) and the ensemble averaged RESP (EA-RESP) method from the most stable ion pair configurations obtained by MP2/6-31G*+ calculations (abbreviated as FF-2 and FF-3). Non-electrostatic parameters for both ions were taken from the literature and Lennard-Jones parameters for the [B(CN)4]- anion were fitted in two different ways to reproduce the experimental liquid density. Molecular dynamics (MD) simulations were performed over a wide temperature range to identify the effect of the electrostatic and non-electrostatic potential on the liquid density and on transport properties such as self-diffusion coefficient and viscosity. Predicted liquid densities for the three parameter sets deviate less than 0.5% from experimental data. The molecular mobility with FF-2 and FF-3 using reduced charge sets is appreciably faster than that obtained with FF-1. FF-3 presents a refined non-electrostatic potential that leads to a notable improvement in both transport properties when compared to experimental data.

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

    PubMed Central

    Baker, Christopher M.; Best, Robert B.

    2013-01-01

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

  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. Theoretical study on the structures, force field, and vibrational spectra of cyclooctatetraene and cyclooctatetraene- d8

    NASA Astrophysics Data System (ADS)

    Zhou, Xuefeng; Liu, Ruifeng; Pulay, Peter

    1993-07-01

    The structures and force field of 1,3,5,7-cyclooctatetraene (COT) have been studied using ab initio theory at the SCF level with the 4-21G basis set. The quadratic force field of the D2 d structure obtained by systematic scaling of the ab initio force constants successfully reproduces the observed frequencies of COT and COT- d8 with a mean deviation of less than 10 cm -1 for non-CH stretching modes. On the basis of the calculated results, assignments of the fundamental vibrations are examined. The normal mode υ 5 is reassigned to a weak band at 758 cm -1 in the Raman spectrum of COT and to a weak band at 591 cm -1 in the Raman spectrum of COT- d8. The calculations favor the assignment of υ 26 given by Lippincott et al. [J. Am. Chem. Soc. 73, 3370 (1951)] over the revised assignment of Perec [Spectrochim. Acta 47A, 799 (1991)]. The calculations also furnish reliable prediction for the inactive A2 fundamentals of COT and COT- d8. The fundamental frequencies and IR and Raman intensities of 13CC 7H 8, which constitutes about 9% of COT in natural abundance, are also calculated. Only ν 10 (calculated at 908 cm -1) of the formal inactive A2 modes has appreciable Raman intensity (0.23 Å 4/amu). A spectral feature due to this fundametal is identified in the liquid Raman spectrum of Tabacik and Blaise [C. R. Acad. Sci. Ser. II 303, 539 (1986)] as a weak peak at 908 cm -1.

  13. Scalar field self-force effects on a particle orbiting a Reissner-Nordström black hole

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Carvalho, Gabriel G.; Geralico, Andrea

    2016-12-01

    Scalar field self-force effects on a scalar charge orbiting a Reissner-Nordström black hole are investigated. The scalar wave equation is solved analytically in a post-Newtonian framework, and the solution is used to compute the self-field (up to 7.5 post-Newtonian order) as well as the components of the self-force at the particle's location. The energy fluxes radiated to infinity and down the hole are also evaluated. Comparison with previous numerical results in the Schwarzschild case shows a reasonable agreement in both strong field and weak field regimes.

  14. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    NASA Astrophysics Data System (ADS)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical

  15. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

    PubMed

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie; Aspuru-Guzik, Alán; Kleinekathöfer, Ulrich

    2015-08-06

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna-Matthews-Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbital (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CH