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Sample records for non-inertial force fields

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

    PubMed Central

    Tsutsui, Hideaki; Ho, Chih-Ming

    2009-01-01

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

  2. Thermal bath of Dirac field in non-inertial frames

    NASA Astrophysics Data System (ADS)

    Zhang, Anwei

    2016-07-01

    The properties of inertial Dirac thermal bath viewed from the perspective of a uniformly accelerated observer is investigated. Using the single-mode approximation, we obtain the expression of the thermal reduced density matrix, which is constructed by the effective partition function in another way compared with the case of scalar field. We deduce the spectrum of particles and antiparticles seen by Rob and antiRob, respectively. It is found that the fermionic thermal bath will suppress the appearance of Unruh particles.

  3. 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…

  4. Non-Maximal Tripartite Entanglement Degradation of Dirac and Scalar Fields in Non-Inertial Frames

    NASA Astrophysics Data System (ADS)

    Salman, Khan; Niaz, Ali Khan; M. K., Khan

    2014-03-01

    The π-tangle is used to study the behavior of entanglement of a nonmaximal tripartite state of both Dirac and scalar fields in accelerated frame. For Dirac fields, the degree of degradation with acceleration of both one-tangle of accelerated observer and π-tangle, for the same initial entanglement, is different by just interchanging the values of probability amplitudes. A fraction of both one-tangles and the π-tangle always survives for any choice of acceleration and the degree of initial entanglement. For scalar field, the one-tangle of accelerated observer depends on the choice of values of probability amplitudes and it vanishes in the range of infinite acceleration, whereas for π-tangle this is not always true. The dependence of π-tangle on probability amplitudes varies with acceleration. In the lower range of acceleration, its behavior changes by switching between the values of probability amplitudes and for larger values of acceleration this dependence on probability amplitudes vanishes. Interestingly, unlike bipartite entanglement, the degradation of π-tangle against acceleration in the case of scalar fields is slower than for Dirac fields.

  5. 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.

  6. Physics of Non-Inertial Reference Frames

    NASA Astrophysics Data System (ADS)

    Kamalov, Timur F.

    2010-12-01

    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.

  7. 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.

  8. Non-Inertial Quantization: Truth or Illusion?

    NASA Astrophysics Data System (ADS)

    Cruz, S. Cruz y.; Mielnik, B.

    2016-03-01

    The quantum Hamiltonians in non inertial frames, while proper to describe the time evolution, might give a false information about the radiation of physical systems. The formal peculiarities observed for the uniformly rotating and accelerating frames might be caused by an excess of verbal approaches in the present day quantum theories.

  9. Carbohydrate force fields

    PubMed Central

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

    2014-01-01

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

  10. Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations

    SciTech Connect

    Klink, W.H.; Wickramasekara, S.

    2013-09-15

    This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle as well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is presented. •The Galilei group is generalized to infinite dimensional Galilean line group. •Loop prolongations of Galilean line group contain central extensions of Galilei group. •Unitary representations of the loops are constructed. •These representations lead to terms in the Hamiltonian corresponding to fictitious forces, including centrifugal and Coriolis

  11. 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.

  12. Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations

    NASA Astrophysics Data System (ADS)

    Klink, W. H.; Wickramasekara, S.

    2013-09-01

    This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle as well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics.

  13. Exploiting the wall-induced non-inertial lift in electrokinetic flow for a continuous particle separation by size.

    PubMed

    Lu, Xinyu; Hsu, Jyh-Ping; Xuan, Xiangchun

    2015-01-01

    Separating particles from a heterogeneous mixture is important and necessary in many engineering and biomedical applications. Electrokinetic flow-based continuous particle separation has thus far been realized primarily by the use of particle dielectrophoresis induced in constricted and/or curved microchannels. We develop in this work a new electrokinetic method that exploits the wall-induced non-inertial lift in a straight uniform microchannel to continuously separate particles by intrinsic properties (e.g., size and surface charge). Such an electrically originated lift force arises from the asymmetric electric field distribution around a particle nearby a planar dielectric wall. We demonstrate this method through separating both a binary and ternary mixture of dispersed polystyrene microspheres by size in a T-shaped microchannel. A semi-analytical model is also developed to simulate and understand the particle separation process. The predicted particle trajectories in the entire microchannel agree reasonably well with the experimental measurements. PMID:25521509

  14. Force-Field Parameter Fitter

    Energy Science and Technology Software Center (ESTSC)

    2015-05-27

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

  15. 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.

  16. Non-inertial Frames in Special and General Relativity

    NASA Astrophysics Data System (ADS)

    Lusanna, Luca

    A theory of global non-inertial frames in special relativity is developed by taking into account relativistic metrology and by avoiding the coordinate singularities of the rotating disk and of Fermi coordinates. Then this theory is used in general relativity for the treatment of globally hyperbolic, asymptotically Minkowskian space-times solution of Einstein's equations. Also some comments on the problem of dark matter, connecting it to the relativistic metrology used in astrophysics, are made.

  17. Are OPERA neutrinos faster than light because of non-inertial reference frames?

    NASA Astrophysics Data System (ADS)

    Germanà, C.

    2012-02-01

    Context. Recent results from the OPERA experiment reported a neutrino beam traveling faster than light. The challenging experiment measured the neutrino time of flight (TOF) over a baseline from the CERN to the Gran Sasso site, concluding that the neutrino beam arrives ~60 ns earlier than a light ray would do. Because the result, if confirmed, has an enormous impact on science, it might be worth double-checking the time definitions with respect to the non-inertial system in which the neutrino travel time was measured. An observer with a clock measuring the proper time τ free of non-inertial effects is the one located at the solar system barycenter (SSB). Aims: Potential problems in the OPERA data analysis connected with the definition of the reference frame and time synchronization are emphasized. We aim to investigate the synchronization of non-inertial clocks on Earth by relating this time to the proper time of an inertial observer at SSB. Methods: The Tempo2 software was used to time-stamp events observed on the geoid with respect to the SSB inertial observer time. Results: Neutrino results from OPERA might carry the fingerprint of non-inertial effects because they are timed by terrestrial clocks. The CERN-Gran Sasso clock synchronization is accomplished by applying corrections that depend on special and general relativistic time dilation effects at the clocks, depending on the position of the clocks in the solar system gravitational well. As a consequence, TOF distributions are centered on values shorter by tens of nanoseconds than expected, integrating over a period from April to December, longer if otherwise. It is worth remarking that the OPERA runs have always been carried out from April/May to November. Conclusions: If the analysis by Tempo2 holds for the OPERA experiment, the excellent measurement by the OPERA collaboration will turn into a proof of the general relativity theory in a weak field approximation. The analysis presented here is falsifiable

  18. Improving an all-atom force field.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-01

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

  19. A molecular mechanics force field for lignin

    SciTech Connect

    Petridis, Loukas; Smith, Jeremy C

    2009-02-01

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

  20. Polarization effects in molecular mechanical force fields

    PubMed Central

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

    2014-01-01

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

  1. Polarization effects in molecular mechanical force fields.

    PubMed

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

    2009-08-19

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

  2. Entanglement dynamics of non-inertial observers in a correlated environment

    NASA Astrophysics Data System (ADS)

    Ramzan, M.

    2013-01-01

    Effect of decoherence and correlated noise on the entanglement of X-type state of the Dirac fields in the non-inertial frame is investigated. A two qubit X-state is considered to be shared between the partners where Alice is in inertial frame and Rob in an accelerated frame. The concurrence is used to quantify the entanglement of the X-state system influenced by time correlated amplitude damping, depolarizing and bit flip channels. It is seen that amplitude damping and bit flip channels heavily influence the entanglement of the system as compared to the depolarizing channel. It is found possible to avoid entanglement sudden death (ESD) for all the channels under consideration for μ > 0.75 for any type of initial state. No ESD behaviour is seen for depolarizing channel in the presence of correlated noise for entire range of decoherence parameter p and Rob's acceleration r. It is also seen that the effect of environment is much stronger than that of acceleration of the accelerated partner. Furthermore, it is investigated that correlated noise compensates the loss of entanglement caused by the Unruh effect.

  3. Force Field Development for Lipid Membrane Simulations.

    PubMed

    Lyubartsev, Alexander P; Rabinovich, Alexander L

    2016-10-01

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

  4. 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.

  5. Three-Dimensional Force Field Spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2003-12-01

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

  6. Lipid14: The Amber Lipid Force Field.

    PubMed

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

    2014-02-11

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

  7. Controlling Casimir force via coherent driving field

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. 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

  9. 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.

  10. 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.

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

    PubMed

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

    2014-04-01

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

  12. Sultan - forced flow, high field test facility

    SciTech Connect

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

    1981-09-01

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

  13. Eddy-current non-inertial displacement sensing for underwater infrasound measurements.

    PubMed

    Donskoy, Dimitri M; Cray, Benjamin A

    2011-06-01

    A non-inertial sensing approach for an Acoustic Vector Sensor (AVS), which utilizes eddy-current displacement sensors and operates well at Ultra-Low Frequencies (ULF), is described here. In the past, most ULF measurements (from mHertz to approximately 10 Hertz) have been conducted using heavy geophones or seismometers that must be installed on the seafloor; these sensors are not suitable for water column measurements. Currently, there are no readily available compact and affordable underwater AVS that operate within this frequency region. Test results have confirmed the validity of the proposed eddy-current AVS design and have demonstrated high acoustic sensitivity. PMID:21682361

  14. Force field dependence of riboswitch dynamics.

    PubMed

    Hanke, Christian A; Gohlke, Holger

    2015-01-01

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

  15. Representation-free description of light-pulse atom interferometry including non-inertial effects

    NASA Astrophysics Data System (ADS)

    Kleinert, Stephan; Kajari, Endre; Roura, Albert; Schleich, Wolfgang P.

    2015-12-01

    Light-pulse atom interferometers rely on the wave nature of matter and its manipulation with coherent laser pulses. They are used for precise gravimetry and inertial sensing as well as for accurate measurements of fundamental constants. Reaching higher precision requires longer interferometer times which are naturally encountered in microgravity environments such as drop-tower facilities, sounding rockets and dedicated satellite missions aiming at fundamental quantum physics in space. In all those cases, it is necessary to consider arbitrary trajectories and varying orientations of the interferometer set-up in non-inertial frames of reference. Here we provide a versatile representation-free description of atom interferometry entirely based on operator algebra to address this general situation. We show how to analytically determine the phase shift as well as the visibility of interferometers with an arbitrary number of pulses including the effects of local gravitational accelerations, gravity gradients, the rotation of the lasers and non-inertial frames of reference. Our method conveniently unifies previous results and facilitates the investigation of novel interferometer geometries.

  16. Conformal field theory of critical Casimir forces

    NASA Astrophysics Data System (ADS)

    Emig, Thorsten; Bimonte, Giuseppe; Kardar, Mehran

    2015-03-01

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

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

    PubMed

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

    2014-08-01

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

  18. Transferable force field for alcohols and polyalcohols.

    PubMed

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

    2009-04-30

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

  19. Cosmic Ray Acceleration in Force Free Fields

    NASA Astrophysics Data System (ADS)

    Colgate, Stirling; Li, Hui; Kronberg, Philipp

    2002-11-01

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

  20. Electromagnetic unification of matter and force fields

    NASA Astrophysics Data System (ADS)

    John, Sarah

    2004-05-01

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

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

    PubMed Central

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

    2010-01-01

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

  2. 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…

  3. Motor imagery facilitates force field learning.

    PubMed

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

    2011-06-13

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

  4. 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.)

  5. 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.

  6. Brief: Field measurements of casing tension forces

    SciTech Connect

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

    1995-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

  8. Lorentz Body Force Induced by Traveling Magnetic Fields

    NASA Technical Reports Server (NTRS)

    Volz, M. P.; Mazuruk, K.

    2003-01-01

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

  9. 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.

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

    SciTech Connect

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

    2012-02-14

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

  11. 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)

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

    PubMed Central

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

    2015-01-01

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

  13. 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.

  14. 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.

  15. Vibrational spectrum and force field of dimethyldimethoxysilane

    SciTech Connect

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

    1986-01-01

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

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

    SciTech Connect

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

    2007-06-14

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

  17. 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.

  18. 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.

  19. 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.

  20. Force field parameter estimation of functional perfluoropolyether lubricants

    SciTech Connect

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

    2011-01-01

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

  1. Force Field Parameter Estimation of Functional Perfluoropolyether Lubricants

    SciTech Connect

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

    2011-01-01

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

  2. 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.

  3. 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.

  4. 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.

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

    PubMed

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

    2015-01-01

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

  6. 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

  7. Visualization of Force Fields in Protein Structure Prediction

    SciTech Connect

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

    2005-04-26

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

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

    PubMed

    Neumann, Marcus A

    2008-08-14

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

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

    PubMed

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

    2014-09-01

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

  10. 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

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

    PubMed

    Drake, Justin A; Pettitt, B Montgomery

    2015-06-30

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

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Vandas, M.; Romashets, E.

    2016-01-01

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

  15. Force-free field model of ball lightning

    NASA Astrophysics Data System (ADS)

    Tsui, K. H.

    2001-03-01

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

  16. 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

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

    PubMed

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

    2015-10-01

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Henke, Paul S.; Mak, Chi H.

    2016-03-01

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

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

    PubMed

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

    2016-04-15

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

  1. 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

  2. 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

  3. Scattered field generation and optical forces in transformation optics

    NASA Astrophysics Data System (ADS)

    Novitsky, A. V.

    2016-04-01

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

  4. Mitigated-force carriage for high magnetic field environments

    DOEpatents

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

    2014-05-20

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

  5. 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.

  6. Generating distributed forcing fields for spatial hydrologic modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Force field development from first principles for materials design

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2010-09-01

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

  9. 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...

  10. Symmetrization of the AMBER and CHARMM force fields.

    PubMed

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

    2010-05-01

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

  11. Frequency-dependent force fields for QMMM calculations.

    PubMed

    Harczuk, Ignat; Vahtras, Olav; Ågren, Hans

    2015-03-28

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

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

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.; Shore, Graham M.

    2012-02-01

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

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

    PubMed

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

    2008-03-01

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

  14. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates

    PubMed Central

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

    2015-01-01

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

  15. 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…

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

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

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

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

    PubMed

    Do, Hainam; Troisi, Alessandro

    2015-10-14

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Brilliantov, N. V.; Seidel, C.

    2012-01-01

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

  20. 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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Lacy, M.

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

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

    PubMed

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

    2016-07-11

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

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

    NASA Astrophysics Data System (ADS)

    Thalmann, J. K.; Wiegelmann, T.

    2007-12-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. 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.

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

    PubMed

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

    2015-06-15

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

  8. 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

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

    PubMed

    Emelyanova, Svetlana; Chashchikhin, Vladimir; Bagaturyants, Alexander

    2016-09-01

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

  10. 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

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

    SciTech Connect

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

    2013-08-07

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

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

    PubMed

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

    2010-06-18

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

  13. Current Status of the AMOEBA Polarizable Force Field

    PubMed Central

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

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Wolfson, Richard; Verma, Ritu

    1991-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Rembeczki, Szabolcs

    High field magnets have many important applications in different areas of research, in the power industry and also for military purposes. For example, high field magnets are particularly useful in: material sciences, high energy physics, plasma physics (as fusion magnets), high power applications (as energy storage devices), and space applications (in propulsion systems). One of the main issues with high-field magnets is the presence of very large electromagnetic stresses that must be counteracted and therefore require heavy support structures. In superconducting magnets, the problems caused by Lorentz forces are further complicated by the fact that superconductors for high field applications are pressure sensitive. The current carrying capacity is greatly reduced under stress and strain (especially in the case of Nb 3Sn and the new high temperature superconductors) so the reduction of the acting forces is of even greater importance. Different force-reduced magnet concepts have been studied in the past, both numerical and analytical methods have been used to solve this problem. The developed concepts are based on such complex winding geometries that the realization and manufacturing of such coils is extremely difficult and these concepts are mainly of theoretical interest. In the presented research, a novel concept for force-reduced magnets has been developed and analyzed which is easy to realize and therefore is of practical interest. The analysis has been performed with a new methodology, which does not require the time consuming finite element calculations. The developed computer models describe the 3-dimensional winding configuration by sets of filaments (filamentary approximation). This approach is much faster than finite element analysis and therefore allows rapid optimization of concepts. The method has been extensively tested on geometries of force-reduced solenoids where even analytical solutions exist. As a further cross check, the developed computer

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    DOE PAGESBeta

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

    2015-07-29

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

  20. 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

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

    PubMed

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

    2013-02-12

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

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

    NASA Astrophysics Data System (ADS)

    Tiandho, Yuant

    2016-02-01

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

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

    PubMed

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

    2012-01-01

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

  4. Coarse-grained force field; general folding theory

    PubMed Central

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

    2012-01-01

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

  5. 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

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

    PubMed

    Fuentes-Azcatl, Raúl; Barbosa, Marcia C

    2016-03-10

    A new computational model for sodium chloride, the NaCl/ϵ, is proposed. The force field employed for the description of the NaCl is based on a set of radial particle-particle pair potentials involving Lennard-Jones (LJ) and Coulombic forces. The parametrization is obtained by fitting the density of the crystal and the density and the dielectric constant of the mixture of the salt with water at a diluted solution. Our model shows good agreement with the experimental values for the density and for the surface tension of the pure system, and for the density, the viscosity, the diffusion, and the dielectric constant for the mixture with water at various molal concentrations. The NaCl/ϵ together with the water TIP4P/ϵ models provide a good approximation for studying electrolyte solutions. PMID:26890321

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Li, Jicun; Wang, Feng

    2015-11-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Pound, Adam

    2012-10-01

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

  12. 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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

    Quartic force fields (QFFs) have been shown to be one of the most effective ways to efficiently compute vibrational frequencies for small molecules. In this letter we discuss how the simple-internal or bond-length bond-angle (BLBA) coordinates can be transformed into Morse-cosine (-sine) coordinates which produce potential energy surfaces from QFFs that possess proper limiting behavior and can describe the vibrational (or rovibrational) energy levels of an arbitrary molecular system to 5 cm-1 or better compared to experiment. We investigate parameter scaling in the Morse coordinate, symmetry considerations, and examples of transformed QFFs making use of the MULTIMODE, TROVE, and VTET variational vibrational methods.

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

    PubMed

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

    2016-03-14

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

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

    PubMed Central

    McAliley, James H.; Bruce, David A.

    2011-01-01

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

  18. Automated conformational energy fitting for force-field development

    PubMed Central

    Guvench, Olgun; MacKerell, Alexander D.

    2010-01-01

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

  19. Unified Field Theory and Force Formulas of Interactions

    NASA Astrophysics Data System (ADS)

    Ma, Tian; Wang, Shouhong

    2013-04-01

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

  20. Towards a force field based on density fitting

    PubMed Central

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

    2007-01-01

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

  1. Adaptation and generalization in acceleration dependent force fields

    PubMed Central

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

    2005-01-01

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

  2. 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...

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

    PubMed

    Chaban, Vitaly V

    2016-04-21

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

  4. The harmonic force field and rz structure of HNCO

    NASA Astrophysics Data System (ADS)

    Fusina, Luciano; Mills, Ian M.

    1981-04-01

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

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

    SciTech Connect

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

    2007-03-01

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

  6. Derivation of a Molecular Mechanics Force Field for Cholesterol

    SciTech Connect

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

    2004-01-01

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

  7. 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).

  8. Development of the CHARMM Force Field for Lipids

    PubMed Central

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

    2011-01-01

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

  9. 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.

  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. 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

  12. The Space Structure, Force Fields and Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Krasnoholovets, Volodymyr; Chung, Ding-Yu

    2006-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  14. 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

  15. 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

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

    PubMed

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

    2011-05-10

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

  17. 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

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

    PubMed

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

    2015-01-15

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

  19. Searching the Force Field Electrostatic Multipole Parameter Space.

    PubMed

    Jakobsen, Sofie; Jensen, Frank

    2016-04-12

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

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

    PubMed Central

    2014-01-01

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

  1. The FoldX web server: an online force field

    PubMed Central

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

    2005-01-01

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

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

    PubMed Central

    Wu, Johnny C.; Chattree, Gaurav

    2012-01-01

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

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

    PubMed

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

    2014-04-24

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

  4. Force Fields for Carbohydrate-Divalent Cation Interactions.

    PubMed

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

    2016-06-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  6. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Long, Bingwei

    2016-02-01

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

  8. A turbulent nonisothermal jet in an Archimedean force field

    NASA Astrophysics Data System (ADS)

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

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

  9. Dirac Field, Gravity, Inertial Effects, and Computer Algebra

    NASA Astrophysics Data System (ADS)

    Vulcanov, Dumitru N.; Cotăescu, Ion I.

    The article presents some new results obtained for the non-relativistic approximation of the Dirac equation in a non-inertial reference frame — rotated and accelerated — and in Schwarzschild gravitational field. These results are obtained with new routines of algebraic programming in REDUCE + EXCALC language for the Dirac equation in a non-inertial reference frame and after three successive Foldy-Wouthuysen transformations.

  10. Quantum field theory of the Casimir force for graphene

    NASA Astrophysics Data System (ADS)

    Klimchitskaya, G. L.

    2016-01-01

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

  11. 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.

  12. 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.

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

    PubMed

    McDaniel, Jesse G; Schmidt, J R

    2016-05-27

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  16. 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

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

    PubMed

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

    2016-06-21

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

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    PubMed Central

    Stockinger, Christian; Focke, Anne; Stein, Thorsten

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kelley, Anne Myers

    2016-06-01

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

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

    PubMed

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

    2015-11-10

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

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

    PubMed

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

    2016-03-15

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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2001-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Luo, Yuan; Yobas, Levent

    2014-09-01

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

  11. 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.

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

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Hardt, Steffen

    2016-05-01

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

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

    PubMed

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

    2016-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

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

    PubMed Central

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Knoop, Claas; Fritsching, Udo

    2013-10-01

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

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

    NASA Technical Reports Server (NTRS)

    Yang, Wei-Hong

    1987-01-01

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

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

    PubMed

    Martín Pendás, A; Hernández-Trujillo, J

    2012-10-01

    The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density. PMID:23039579

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

    PubMed

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

    2015-03-17

    Molecular simulations have had a transformative impact on chemists' understanding of the structure and dynamics of molecular systems. Simulations can both explain and predict chemical phenomena, and they provide a unique bridge between the microscopic and macroscopic regimes. The input for such simulations is the intermolecular interactions, which then determine the forces on the constituent atoms and therefore the time evolution and equilibrium properties of the system. However, in practice, accuracy and reliability are often limited by the fidelity of the description of those very same interactions, most typically embodied approximately in mathematical form in what are known as force fields. Force fields most often utilize conceptually simple functional forms that have been parametrized to reproduce existing experimental gas phase or bulk data. Yet, reliance on empirical parametrization can sometimes introduce limitations with respect to novel chemical systems or uncontrolled errors when moving to temperatures, pressures, or environments that differ from those for which they were developed. Alternatively, it is possible to develop force fields entirely from first principles, using accurate electronic structure calculations to determine the intermolecular interactions. This introduces a new set of challenges, including the transferability of the resulting force field to related chemical systems. In response, we recently developed an alternative approach to develop force fields entirely from first-principles electronic structure calculations based on intermolecular perturbation theory. Making use of an energy decomposition analysis ensures, by construction, that the resulting force fields contain the correct balance of the various components of intermolecular interaction (exchange repulsion, electrostatics, induction, and dispersion), each treated by a functional form that reflects the underlying physics. We therefore refer to the resulting force fields as

  1. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Sujak, Peter

    2014-03-01

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

  4. Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.

    PubMed

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

    2015-12-28

    In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide. PMID:26629886

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

    PubMed

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

    2006-08-25

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Wei, Caiyi; Mei, Ye; Zhang, Dawei

    2010-07-01

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

  9. 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.

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

    PubMed

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  12. 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

  13. 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.

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

    PubMed

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

    2015-06-25

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

  15. 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

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

    PubMed

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

    2016-08-01

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

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

    Liu, Yanju; Liu, Liwu; Leng, Jinsong

    2009-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Liu, Yanju; Liu, Liwu; Leng, Jinsong

    2010-03-01

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

  1. 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.

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

    PubMed

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

    2009-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1988-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

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

    PubMed

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

    2013-03-25

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

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

    PubMed

    Müller, Julian; Hartke, Bernd

    2016-08-01

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

  7. 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

  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. PMID:25020237

  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. PMID:24874104

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

    NASA Astrophysics Data System (ADS)

    Esquivel-Sirvent, Raul

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

  11. Relativistic mean field model based on realistic nuclear forces

    SciTech Connect

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

    2007-02-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2016-04-14

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

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

    PubMed

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

    2014-10-14

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

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

    PubMed

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

    2012-11-01

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

  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. PMID:26998926

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  20. 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.

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

    EPA Science Inventory

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

  2. 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.

  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. 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.

  5. 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

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

    SciTech Connect

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

    2012-05-09

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

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

    PubMed

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

    2013-07-26

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

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

    PubMed Central

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

    2009-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.

    1973-01-01

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

  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.