Deriving force field parameters for coordination complexes

DEFF Research Database (Denmark)

Norrby, Per-Ola; Brandt, Peter

2001-01-01

The process of deriving molecular mechanics force fields for coordination complexes is outlined. Force field basics are introduced with an emphasis on special requirements for metal complexes. The review is then focused on how to set up the initial model, define the target, refine the parameters......, and validate the final force field, Alternatives to force field derivation are discussed briefly....

Polarization effects in molecular mechanical force fields

Energy Technology Data Exchange (ETDEWEB)

Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

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. (topical review)

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

Science.gov (United States)

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

2014-09-16

involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

Near field plasmon and force microscopy

NARCIS (Netherlands)

de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

1995-01-01

A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the

Ehrenfest force in inhomogeneous magnetic field

International Nuclear Information System (INIS)

Sisakyan, A.N.; Shevchenko, O.Yu.; Samojlov, V.N.

2000-01-01

The Ehrenfest force in an inhomogeneous magnetic field is calculated. It is shown that there exist such (very rare) topologically nontrivial physical situations when the Gauss theorem in its classic formulation fails and, as a consequence, apart from the usual Lorentz force an additional, purely imaginary force acts on the charged particle. This force arises only in inhomogeneous magnetic fields of special configurations, has a purely quantum origin, and disappears in the classical limit

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

Science.gov (United States)

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

2016-01-21

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

Surface Forces Apparatus measurements of interactions between rough and reactive calcite surfaces.

Science.gov (United States)

Dziadkowiec, Joanna; Javadi, Shaghayegh; Bratvold, Jon Einar; Nilsen, Ola; Røyne, Anja

2018-05-28

Nm-range forces acting between calcite surfaces in water affect macroscopic properties of carbonate rocks and calcite-based granular materials, and are significantly influenced by calcite surface recrystallization. We suggest that the repulsive mechanical effects related to nm-scale surface recrystallization of calcite in water could be partially responsible for the observed decrease of cohesion in calcitic rocks saturated with water. Using the Surface Forces Apparatus (SFA), we simultaneously followed the calcite reactivity and measured the forces in water in two surface configurations: between two rough calcite surfaces (CC), or between rough calcite and a smooth mica surface (CM). We used nm-scale rough, polycrystalline calcite films prepared by Atomic Layer Deposition (ALD). We measured only repulsive forces in CC in CaCO 3 -saturated water, which was related to roughness and possibly to repulsive hydration effects. Adhesive or repulsive forces were measured in CM in CaCO 3 -saturated water depending on calcite roughness, and the adhesion was likely enhanced by electrostatic effects. The pull-off adhesive force in CM became stronger with time and this increase was correlated with a decrease of roughness at contacts, which parameter could be estimated from the measured force-distance curves. That suggested a progressive increase of real contact areas between the surfaces, caused by gradual pressure-driven deformation of calcite surface asperities during repeated loading-unloading cycles. Reactivity of calcite was affected by mass transport across nm to µm-thick gaps between the surfaces. Major roughening was observed only for the smoothest calcite films, where gaps between two opposing surfaces were nm-thick over µm-sized areas, and led to force of crystallization that could overcome confining pressures of the order of MPa. Any substantial roughening of calcite caused a significant increase of the repulsive mechanical force contribution.

Transition States from Empirical Force Fields

DEFF Research Database (Denmark)

Jensen, Frank; Norrby, Per-Ola

2003-01-01

This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...

Size-dependent reactivity of magnetite nanoparticles: a field-laboratory comparison

Science.gov (United States)

Swindle, Andrew L.; Elwood Madden, Andrew S.; Cozzarelli, Isabelle M.; Benamara, Mourad

2014-01-01

Logistic challenges make direct comparisons between laboratory- and field-based investigations into the size-dependent reactivity of nanomaterials difficult. This investigation sought to compare the size-dependent reactivity of nanoparticles in a field setting to a laboratory analog using the specific example of magnetite dissolution. Synthetic magnetite nanoparticles of three size intervals, ∼6 nm, ∼44 nm, and ∼90 nm were emplaced in the subsurface of the USGS research site at the Norman Landfill for up to 30 days using custom-made subsurface nanoparticle holders. Laboratory analog dissolution experiments were conducted using synthetic groundwater. Reaction products were analyzed via TEM and SEM and compared to initial particle characterizations. Field results indicated that an organic coating developed on the particle surfaces largely inhibiting reactivity. Limited dissolution occurred, with the amount of dissolution decreasing as particle size decreased. Conversely, the laboratory analogs without organics revealed greater dissolution of the smaller particles. These results showed that the presence of dissolved organics led to a nearly complete reversal in the size-dependent reactivity trends displayed between the field and laboratory experiments indicating that size-dependent trends observed in laboratory investigations may not be relevant in organic-rich natural systems.

Force-free field model of ball lightning

International Nuclear Information System (INIS)

Tsui, K.H.

2001-01-01

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

Near field plasmon and force microscopy

OpenAIRE

de Hollander, R.B.G.; van Hulst, N.F.; Kooyman, R.P.H.

1995-01-01

A scanning plasmon near field optical microscope (SPNM) is presented which combines a conventional far field surface plasmon microscope with a stand-alone atomic force microscope (AFM). Near field plasmon and force images are recorded simultaneously both with a lateral resolution limited by the probe size to about 20 nm. At variance to previous work, utilizing a scanning tunneling microscope (STM) with a metallic tip, a dielectric silicon-nitride tip is used in contact mode. This arrangement ...

Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

Science.gov (United States)

Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

2016-07-28

The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

Science.gov (United States)

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. Copyright © 2015 the American Physiological Society.

Harmonic force field for nitro compounds.

Science.gov (United States)

Bellido, Edson P; Seminario, Jorge M

2012-06-01

Molecular simulations leading to sensors for the detection of explosive compounds require force field parameters that can reproduce the mechanical and vibrational properties of energetic materials. We developed precise harmonic force fields for alanine polypeptides and glycine oligopeptides using the FUERZA procedure that uses the Hessian tensor (obtained from ab initio calculations) to calculate precise parameters. In this work, we used the same procedure to calculate generalized force field parameters of several nitro compounds. We found a linear relationship between force constant and bond distance. The average angle in the nitro compounds was 116°, excluding the 90° angle of the carbon atoms in the octanitrocubane. The calculated parameters permitted the accurate molecular modeling of nitro compounds containing many functional groups. Results were acceptable when compared with others obtained using methods that are specific for one type of molecule, and much better than others obtained using methods that are too general (these ignore the chemical effects of surrounding atoms on the bonding and therefore the bond strength, which affects the mechanical and vibrational properties of the whole molecule).

Induced forces in the gravitational field

International Nuclear Information System (INIS)

Voracek, P.

1979-01-01

In this paper the expression for the magnitude of the so-called induced force, acting on a mass particle, is deduced. The origin of this force is causally connected to the increase of the rest mass of the particle in the gravitational field. (orig.)

Controlling Casimir force via coherent driving field

Science.gov (United States)

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.

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

Science.gov (United States)

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. © 2015 Wiley Periodicals, Inc.

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

Science.gov (United States)

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

2012-02-14

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

Generation of spin motive force in a soliton lattice

International Nuclear Information System (INIS)

Ovchinnikov, A. S.; Sinitsyn, V. E.; Bostrem, I. G.; Kishine, J.

2013-01-01

The generation of a spin motive force in a chiral helimagnet due to the action of two crossed magnetic fields is considered. The cases of pulsed and periodic magnetic fields directed along the helical axis under a perpendicular dc field are analyzed. It is shown that, in the case of a pulsed field, the spin motive force is related to dissipation, whereas in a periodic field, there is a reactive component that is not related to damping processes.

Formation, characterization and dynamics of onion like carbon structures from nanodiamonds using reactive force-fields for electrical energy storage

Energy Technology Data Exchange (ETDEWEB)

Ganesh, Panchapakesan [ORNL; Kent, Paul R [ORNL; Mochalin, Vadym N [ORNL

2011-01-01

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.

Formation, characterization, and dynamics of onion-like carbon structures for electrical energy storage from nanodiamonds using reactive force fields

Energy Technology Data Exchange (ETDEWEB)

Ganesh, P. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Kent, P. R. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Mochalin, V. [Drexel Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering

2011-10-01

We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbonnanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbonnanostructure appears, with a shell-shell spacing of about ~3.4 Å for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large (~29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.

Force fields for silicas and aluminophosphates based on ab initio calculations

NARCIS (Netherlands)

Beest, van B.W.H.; Kramer, G.J.; Santen, van R.A.

1990-01-01

Authors address the problem of finding interat. force fields for silicas from ab initio calcns. on small clusters. The force field cannot be detd. from cluster data alone; incorporation of bulk-system information into the force field remains essential. Bearing this in mind, authors derive a force

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

Science.gov (United States)

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

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Preface: Special Topic: From Quantum Mechanics to Force Fields

Science.gov (United States)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

Force-field compensation in a manual tracking task.

Directory of Open Access Journals (Sweden)

Valentina Squeri

2010-06-01

Full Text Available 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.

Software Process Improvement Using Force Field Analysis ...

African Journals Online (AJOL)

An improvement plan is then drawn and implemented. This paper studied the state of Nigerian software development organizations based on selected attributes. Force field analysis is used to partition the factors obtained into driving and restraining forces. An attempt was made to improve the software development process ...

Force-free magnetic fields - The magneto-frictional method

Science.gov (United States)

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.

Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections

International Nuclear Information System (INIS)

Choe, G.S.; Cheng, C.Z.

2002-01-01

In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

Science.gov (United States)

Mehlenbacher, Randy D.; Kolbl, Rea; Lay, Alice; Dionne, Jennifer A.

2018-02-01

Cellular signalling is governed in large part by mechanical forces and electromagnetic fields. Mechanical forces play a critical role in cell differentiation, tissue organization and diseases such as cancer and heart disease; electrical fields are essential for intercellular communication, muscle contraction, neural signalling and sensory perception. Therefore, quantifying a biological system's forces and fields is crucial for understanding physiology and disease pathology and for developing medical tools for repair and recovery. This Review highlights advances in sensing mechanical forces and electrical fields in vivo, focusing on optical probes. The emergence of biocompatible optical probes, such as genetically encoded voltage indicators, molecular rotors, fluorescent dyes, semiconducting nanoparticles, plasmonic nanoparticles and lanthanide-doped upconverting nanoparticles, offers exciting opportunities to push the limits of spatial and temporal resolution, stability, multi-modality and stimuli sensitivity in bioimaging. We further discuss the materials design principles behind these probes and compare them across various metrics to facilitate sensor selection. Finally, we examine which advances are necessary to fully unravel the role of mechanical forces and electrical fields in vivo, such as the ability to probe the vectorial nature of forces, the development of combined force and field sensors, and the design of efficient optical actuators.

Martini Force Field Parameters for Glycolipids

NARCIS (Netherlands)

Lopez, Cesar A.; Sovova, Zofie; van Eerden, Floris J.; de Vries, Alex H.; Marrink, Siewert J.

We present an extension of the Martini coarse-grained force field to glycolipids. The glycolipids considered here are the glycoglycerolipids monogalactosyldiacylglycerol (MGDG), sulfoquinovosyldiacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), and phosphatidylinositol (PI) and its

Generalized force in classical field theory. [Euler-Lagrange equations

Energy Technology Data Exchange (ETDEWEB)

Krause, J [Universidad Central de Venezuela, Caracas

1976-02-01

The source strengths of the Euler-Lagrange equations, for a system of interacting fields, are heuristically interpreted as generalized forces. The canonical form of the energy-momentum tensor thus consistently appears, without recourse to space-time symmetry arguments. A concept of 'conservative' generalized force in classical field theory is also briefly discussed.

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

Science.gov (United States)

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

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.

Vibrations of a molecule in an external force field.

Science.gov (United States)

Okabayashi, Norio; Peronio, Angelo; Paulsson, Magnus; Arai, Toyoko; Giessibl, Franz J

2018-05-01

The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

Dynamics of solar magnetic fields. VI. Force-free magnetic fields and motions of magnetic foot-points

International Nuclear Information System (INIS)

Low, B.C.; Nakagawa, Y.

1975-01-01

A mathematical model is developed to consider the evolution of force-free magnetic fields in relation to the displacements of their foot-points. For a magnetic field depending on only two Cartesian coordinates and time, the problem reduces to solving a nonlinear elliptic partial differential equation. As illustration of the physical process, two specific examples of evolving force-free magnetic fields are examined in detail, one evolving with rising and the other with descending field lines. It is shown that these two contrasting behaviors of the field lines correspond to sheared motions of their foot-points of quite different characters. The physical implications of these two examples of evolving force-free magnetic fields are discussed. (auth)

Reactive diffusion and stresses in nanowires or nanorods

International Nuclear Information System (INIS)

Roussel, Manuel; Erdélyi, Zoltán; Schmitz, Guido

2017-01-01

Heterostructured nanowires are of prime interest in nowadays technology such as field-effect transistors, field emitters, batteries and solar cells. We consider their aging behavior and developed a model focusing on reactive diffusion in core-shell nanowires. A complete set of analytical equations is presented that takes into account thermodynamic driving forces, vacancy distribution, elastic stress and its plastic relaxation. This complete description of the reactive diffusion can be used in finite element simulations to investigate diffusion processes in various geometries. In order to show clearly the interplay between the cylindrical geometry, the reactive diffusion and the stresses developing in the nanowire, we investigate the formation of an intermetallic reaction product in various core-shell geometries. Emphasis is placed on showing how it is possible to control the kinetics of the reaction by applying an axial stress to the nanowires.

Perspective: Ab initio force field methods derived from quantum mechanics

Science.gov (United States)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

A new united atom force field for adsorption of alkenes in zeolites

NARCIS (Netherlands)

Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.

2008-01-01

A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we

Solitons in a random force field

International Nuclear Information System (INIS)

Bass, F.G.; Konotop, V.V.; Sinitsyn, Y.A.

1985-01-01

We study the dynamics of a soliton of the sine-Gordon equation in a random force field in the adiabatic approximation. We obtain an Einstein-Fokker equation and find the distribution function for the soliton parameters which we use to evaluate its statistical characteristics. We derive an equation for the averaged functions of the soliton parameters. We determine the limits of applicability of the delta-correlated in time random field approximation

Relativistic derivation of the ponderomotive force produced by two intense laser fields

International Nuclear Information System (INIS)

Stroscio, M.A.

1985-01-01

The ponderomotive force plays a fundamental role in the absorption of laser light on self-consistent plasma density profiles, in multiple-photon ionization, and in intense field electrodynamics. The relativistic corrections to the ponderomotive force of a transversely polarized electromagnetic wave lead to an approximately 20-percent reduction in the single particle ponderomotive force produced by a 10-γm 10 16 -W/cm 2 laser field. Recent experimental investigations are based on using two intense laser fields to produce desired lasermatter interactions. This paper presents the first derivation of the nonlinear relativistic ponderomotive force produced by two intense laser fields. The results demonstrate that relativistic ponderomotive forces are not additive

Improved Parameters for the Martini Coarse-Grained Protein Force Field

NARCIS (Netherlands)

de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew; Arnarez, Clement; Wassenaar, Tsjerk A.; Schafer, Lars V.; Periole, Xavier; Tieleman, D. Peter; Marrink, Siewert J.

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too

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

Science.gov (United States)

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

2012-01-01

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

Concurrent Validity of a Portable Force Plate Using Vertical Jump Force-Time Characteristics.

Science.gov (United States)

Lake, Jason; Mundy, Peter; Comfort, Paul; McMahon, John J; Suchomel, Timothy J; Carden, Patrick

2018-05-29

This study examined concurrent validity of countermovement vertical jump (CMJ) reactive strength index modified and force-time characteristics recorded using a one dimensional portable and laboratory force plate system. Twenty-eight men performed bilateral CMJs on two portable force plates placed on top of two in-ground force plates, both recording vertical ground reaction force at 1000 Hz. Time to take-off, jump height, reactive strength index modified, braking and propulsion impulse, mean net force, and duration were calculated from the vertical force from both force plate systems. Results from both systems were highly correlated (r≥.99). There were small (dbraking impulse, braking mean net force, propulsion impulse, and propulsion mean net force (psystem (95% CL: .9% to 2.5%), indicating very good agreement across all of the dependent variables. The largest limits of agreement belonged to jump height (2.1%), time to take-off (3.4%), and reactive strength index modified (3.8%). The portable force plate system provides a valid method of obtaining reactive strength measures, and several underpinning force-time variables, from unloaded CMJ and practitioners can use both force plates interchangeably.

Energy of Force-Free Magnetic Fields in Relation to Coronal Mass Ejections; TOPICAL

International Nuclear Information System (INIS)

G.S. Choe; C.Z. Cheng

2002-01-01

In typical observations of coronal mass ejections (CMEs), a magnetic structure of a helmet-shaped closed configuration bulges out and eventually opens up. However, a spontaneous transition between these field configurations has been regarded to be energetically impossible in force-free fields according to the Aly-Sturrock theorem. The theorem states that the maximum energy state of force-free fields with a given boundary normal field distribution is the open field. The theorem implicitly assumes the existence of the maximum energy state, which may not be taken for granted. In this study, we have constructed force-free fields containing tangential discontinuities in multiple flux systems. These force-free fields can be generated from a potential field by footpoint motions that do not conserve the boundary normal field distribution. Some of these force-free fields are found to have more magnetic energy than the corresponding open fields. The constructed force-free configurations are compared with observational features of CME-bearing active regions. Possible mechanisms of CMEs are also discussed

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

Science.gov (United States)

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

Ponderomotive force, magnetic fields and hydrodynamics of laser produced plasmas

International Nuclear Information System (INIS)

Bobin, J.-L.; Wee Woo; Degroot, J.-S.

1977-01-01

Nonlinear effects deeply change the structure of a laser driven plasma flow. For high intensities, the radiation pressure should be taken into account. It acts through a ponderomotive force proportional to the electron density and to the gradient of the mean electric field energy density of the incident wave. Static magnetic fields originate from a term in the ponderomotive force which includes radiation absorption and whose curl is non zero. The basic properties of the structure are determined analytically in the absence of thermal conductivity and magnetic fields: steep density gradient close to the cut-off density, shelf at lower densities. The conditions of a steady state regime are set up. The isothermal case is specially investigated. It is shown that the cavities which are created in a motionless plasma may disappear due to the onset of a flow. Regions in which electromagnetic forces arising from the static field compensate the ponderomotive force are determined. The subsequent effects on the flow itself are studied [fr

Energy buildup in sheared force-free magnetic fields

Science.gov (United States)

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.

Optical Near-field Interactions and Forces for Optoelectronic Devices

Science.gov (United States)

Kohoutek, John Michael

Throughout history, as a particle view of the universe began to take shape, scientists began to realize that these particles were attracted to each other and hence came up with theories, both analytical and empirical in nature, to explain their interaction. The interaction pair potential (empirical) and electromagnetics (analytical) theories, both help to explain not only the interaction between the basic constituents of matter, such as atoms and molecules, but also between macroscopic objects, such as two surfaces in close proximity. The electrostatic force, optical force, and Casimir force can be categorized as such forces. A surface plasmon (SP) is a collective motion of electrons generated by light at the interface between two mediums of opposite signs of dielectric susceptibility (e.g. metal and dielectric). Recently, surface plasmon resonance (SPR) has been exploited in many areas through the use of tiny antennas that work on similar principles as radio frequency (RF) antennas in optoelectronic devices. These antennas can produce a very high gradient in the electric field thereby leading to an optical force, similar in concept to the surface forces discussed above. The Atomic Force Microscope (AFM) was introduced in the 1980s at IBM. Here we report on its uses in measuring these aforementioned forces and fields, as well as actively modulating and manipulating multiple optoelectronic devices. We have shown that it is possible to change the far field radiation pattern of an optical antenna-integrated device through modification of the near-field of the device. This modification is possible through change of the local refractive index or reflectivity of the "hot spot" of the device, either mechanically or optically. Finally, we have shown how a mechanically active device can be used to detect light with high gain and low noise at room temperature. It is the aim of several of these integrated and future devices to be used for applications in molecular sensing

Machine learning of accurate energy-conserving molecular force fields

Science.gov (United States)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

Various aspects of magnetic field influence on forced convection

Directory of Open Access Journals (Sweden)

Pleskacz Lukasz

2016-01-01

Full Text Available Flows in the channels of various geometry can be found everywhere in industrial or daily life applications. They are used to deliver media to certain locations or they are the place where heat may be exchanged. For Authors both points of view are interesting. The enhancement methods for heat transfer during the forced convection are demanded due to a technological development and tendency to miniaturization. At the same time it is also worth to find mechanisms that would help to avoid negative effects like pressure losses or sedimentation in the channel flows. This paper shows and discuss various aspects of magnetic field influence on forced convection. A mathematical model consisted of the mass, momentum and energy conservation equations. In the momentum conservation equation magnetic force term was included. In order to calculate this magnetic force Biot-Savart’s law was utilized. Numerical analysis was performed with the usage of commonly applied software. However, userdefined functions were implemented. The results revealed that both temperature and velocity fields were influenced by the strong magnetic field.

Valence force fields and the lattice dynamics of beryllium oxide

International Nuclear Information System (INIS)

Ramani, R.; Mani, K.K.; Singh, R.P.

1976-01-01

The lattice dynamics of beryllium oxide have been studied using a rigid-ion model, with short-range forces represented by a valence force field. Various existing calculations on group-IV elements using such a field have been examined as a prelude to transference of force constants from diamond to beryllium oxide. The effects of ionicity on the force constants have been included in the form of scale factors. It is shown that no satisfactory fit to the long-wavelength data on BeO can be found with transferred force constants. However, adequate least-squares fits can be found both with four- and six-parameter valence force fields, the discrepancy with experiment being large only for one optical mode at the Brillouin-zone center. Dispersion curves along Δ and Σ are presented and are in fair agreement with experiment, deviations arising essentially from the quality of the fit to the long-wavelength data. The bond-bending interactions are found to play a significant role and arguments have been presented to show that the inclusion of further angle-angle interactions would yield a very satisfactory picture of the dynamics

Nonequilibrium forces between neutral atoms mediated by a quantum field

International Nuclear Information System (INIS)

Behunin, Ryan O.; Hu, Bei-Lok

2010-01-01

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

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

Science.gov (United States)

Best, Robert B; Hummer, Gerhard

2009-07-02

Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.

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

International Nuclear Information System (INIS)

Sorin Zaharia; Cheng, C.Z.

2002-01-01

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 (gradient) 2 P = (gradient) · (J x B) in the equatorial plane, and 1-D profiles on the Sun-Earth axis by integrating (gradient)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

Rapid parameterization of small molecules using the Force Field Toolkit.

Science.gov (United States)

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

2013-12-15

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

Relationships Between Countermovement Jump Ground Reaction Forces and Jump Height, Reactive Strength Index, and Jump Time.

Science.gov (United States)

Barker, Leland A; Harry, John R; Mercer, John A

2018-01-01

Barker, LA, Harry, JR, and Mercer, JA. Relationships between countermovement jump ground reaction forces and jump height, reactive strength index, and jump time. J Strength Cond Res 32(1): 248-254, 2018-The purpose of this study was to determine the relationship between ground reaction force (GRF) variables to jump height, jump time, and the reactive strength index (RSI). Twenty-six, Division-I, male, soccer players performed 3 maximum effort countermovement jumps (CMJs) on a dual-force platform system that measured 3-dimensional kinetic data. The trial producing peak jump height was used for analysis. Vertical GRF (Fz) variables were divided into unloading, eccentric, amortization, and concentric phases and correlated with jump height, RSI (RSI = jump height/jump time), and jump time (from start to takeoff). Significant correlations were observed between jump height and RSI, concentric kinetic energy, peak power, concentric work, and concentric displacement. Significant correlations were observed between RSI and jump time, peak power, unload Fz, eccentric work, eccentric rate of force development (RFD), amortization Fz, amortization time, second Fz peak, average concentric Fz, and concentric displacement. Significant correlations were observed between jump time and unload Fz, eccentric work, eccentric RFD, amortization Fz, amortization time, average concentric Fz, and concentric work. In conclusion, jump height correlated with variables derived from the concentric phase only (work, power, and displacement), whereas Fz variables from the unloading, eccentric, amortization, and concentric phases correlated highly with RSI and jump time. These observations demonstrate the importance of countermovement Fz characteristics for time-sensitive CMJ performance measures. Researchers and practitioners should include RSI and jump time with jump height to improve their assessment of jump performance.

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

Science.gov (United States)

Geng, Yanan; Wu, Weida

2014-05-01

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

Mapping the force field of a hydrogen-bonded assembly

Science.gov (United States)

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

2014-05-01

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

Nuclear Forces from Effective Field Theory

International Nuclear Information System (INIS)

Krebs, H.

2011-01-01

Chiral effective field theory allows for a systematic and model-independent derivation of the forces between nucleons in harmony with the symmetries of the quantum chromodynamics. After a brief review on the current status in the development of the chiral nuclear forces I will focus on the role of the Δ-resonance contributions in the nuclear dynamics.We find improvement in the convergence of the chiral expansion of the nuclear forces if we explicitly take into account the Δ-resonance degrees of freedom. The overall results for two-nucleon forces with and without explicit Δ-resonance degrees of freedom are remarkably similar. We discussed the long- and shorter-range N 3 LO contributions to chiral three-nucleon forces. No additional free parameters appear at this order. There are five different topology classes which contribute to the forces. Three of them describe long-range contributions which constitute the first systematic corrections to the leading 2π exchange that appear at N 2 LO. Another two contributions are of a shorter range and include, additionally to an exchange of pions, also one short-range contact interaction and all corresponding 1/m corrections. The requirement of renormalizability leads to unique expressions for N 3 LO contributions to the three-nucleon force (except for 1/m-corrections). We presented the complete N 2 LO analysis of the nuclear forces with explicit Δ-isobar degrees of freedom. Although the overall results in the isospin-conserving case are very similar in the Δ-less and Δ-full theories, we found a much better convergence in all peripheral partial waves once Δ-resonance is explicitly taken into account. The leading CSB contributions to nuclear forces are proportional to nucleon- and Δ-mass splittings. There appear strong cancellations between the two contributions which at leading order yield weaker V III potentials. This effect is, however, entirely compensated at subleading order such that the results in the theories

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

Energy Technology Data Exchange (ETDEWEB)

Kelley, Anne Myers [Chemistry and Chemical Biology, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States)

2016-06-07

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.

ReaxFF Reactive Force-Field Study of Molybdenum Disulfide (MoS2).

Science.gov (United States)

Ostadhossein, Alireza; Rahnamoun, Ali; Wang, Yuanxi; Zhao, Peng; Zhang, Sulin; Crespi, Vincent H; van Duin, Adri C T

2017-02-02

Two-dimensional layers of molybdenum disulfide, MoS 2 , have been recognized as promising materials for nanoelectronics due to their exceptional electronic and optical properties. Here we develop a new ReaxFF reactive potential that can accurately describe the thermodynamic and structural properties of MoS 2 sheets, guided by extensive density functional theory simulations. This potential is then applied to the formation energies of five different types of vacancies, various vacancy migration barriers, and the transition barrier between the semiconducting 2H and metallic 1T phases. The energetics of ripplocations, a recently observed defect in van der Waals layers, is examined, and the interplay between these defects and sulfur vacancies is studied. As strain engineering of MoS 2 sheets is an effective way to manipulate the sheets' electronic and optical properties, the new ReaxFF description can provide valuable insights into morphological changes that occur under various loading conditions and defect distributions, thus allowing one to tailor the electronic properties of these 2D crystals.

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

DEFF Research Database (Denmark)

Barthélemy, Dorothy; Alain, S; Grey, Michael James

2012-01-01

measured changes in motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) in the tibialis anterior (TA) muscle before, during, and after subjects adapted to a force field applied to the ankle joint during treadmill walking. When the force field assisted dorsiflexion during...... the swing phase of the step cycle, subjects adapted by decreasing TA EMG activity. In contrast, when the force field resisted dorsiflexion, they increased TA EMG activity. After the force field was removed, normal EMG activity gradually returned over the next 5 min of walking. TA MEPs elicited in the early...... be explained by changes in background TA EMG activity. These effects seemed specific to walking, as similar changes in TA MEP were not seen when seated subjects were tested during static dorsiflexion. These observations suggest that the corticospinal tract contributes to the adaptation of walking...

Topological and statistical properties of nonlinear force-free fields

Science.gov (United States)

Mangalam, A.; Prasad, A.

2018-01-01

We use our semi-analytic solution of the nonlinear force-free field equation to construct three-dimensional magnetic fields that are applicable to the solar corona and study their statistical properties for estimating the degree of braiding exhibited by these fields. We present a new formula for calculating the winding number and compare it with the formula for the crossing number. The comparison is shown for a toy model of two helices and for realistic cases of nonlinear force-free fields; conceptually the formulae are nearly the same but the resulting distributions calculated for a given topology can be different. We also calculate linkages, which are useful topological quantities that are independent measures of the contribution of magnetic braiding to the total free energy and relative helicity of the field. Finally, we derive new analytical bounds for the free energy and relative helicity for the field configurations in terms of the linking number. These bounds will be of utility in estimating the braided energy available for nano-flares or for eruptions.

Charm production and the confining force field

International Nuclear Information System (INIS)

Andersson, B.; Bengtsson, H.-U.; Gustafson, G.

1983-03-01

We show that charm production at SPS energies can be understood simply from O(α 2 sub (s)) QCD processes when combined with fragmentation of the colour fields stretched by the final state partons. The tension of the confining force field responsible for particle production is found to pull the charmed particles away from the reaction centre, giving rise to a harder x sub (F)-spectrum than would be expected from the bare QCD matrix elements. (Authors)

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview.

Science.gov (United States)

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

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

Energy Technology Data Exchange (ETDEWEB)

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes; Bonn, Mischa [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany); Sulpizi, Marialore, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de [Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz (Germany)

2016-08-14

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 (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} 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.

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

International Nuclear Information System (INIS)

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

2016-01-01

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 (O TMAO ) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O TMAO to mimic the O TMAO lone pairs and we migrate the negative charge on the O TMAO 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.

Dusty plasmas in a constant electric field: Role of the electron drag force

International Nuclear Information System (INIS)

Khrapak, S.A.; Morfill, G.E.

2004-01-01

We investigate the forces experienced by a microparticle immersed in a weakly ionized plasma with constant electric field. These are electric force and the forces associated with the momentum transfer from electrons and ions drifting in the field (electron and ion drag forces). It is shown that the effect of the electron drag, which is often neglected, can be substantial in a certain parameter range. Numerical calculation of the forces for a reasonable set of plasma parameters is performed to illustrate the importance of this effect

A note on the heritability of reactivity assessed at field tests for Danish Warmblood horses

DEFF Research Database (Denmark)

Rothmann, Janne; Christensen, Ole F.; Søndergaard, Eva

2014-01-01

Temperament traits in horses, especially reactivity, are an important trait in relation to human–horse accidents and the welfare of the horses. However, so far, temperament is often not included in many horse breeding programs. Most of the behavioral genetic studies in horses have been based on i......, a high standard error was untainted. Nevertheless, results suggested a genetic variation of reactivity when assessed at field tests, but further research is needed before reactivity can be incorporated as a selection criteria into a breeding program....

Van der Waals Forces and Photon-Less Effective Field Theory

International Nuclear Information System (INIS)

Arriola, E.R.

2011-01-01

In the ultra-cold regime Van der Waals forces between neutral atoms can be represented by short range effective interactions. We show that universal low energy scaling features of the underlying vdW long range force stemming from two photon exchange impose restrictions on an Effective Field Theory without explicit photons. The role of naively redundant operators, relevant to the definition of three body forces, is also analyzed. (author)

Dynamics of confined reactive water in smectite clay-zeolite composites.

Science.gov (United States)

Pitman, Michael C; van Duin, Adri C T

2012-02-15

The dynamics of water confined to mesoporous regions in minerals such as swelling clays and zeolites is fundamental to a wide range of resource management issues impacting many processes on a global scale, including radioactive waste containment, desalination, and enhanced oil recovery. Large-scale atomic models of freely diffusing multilayer smectite particles at low hydration confined in a silicalite cage are used to investigate water dynamics in the composite environment with the ReaxFF reactive force field over a temperature range of 300-647 K. The reactive capability of the force field enabled a range of relevant surface chemistry to emerge, including acid/base equilibria in the interlayer calcium hydrates and silanol formation on the edges of the clay and inner surface of the zeolite housing. After annealing, the resulting clay models exhibit both mono- and bilayer hydration structures. Clay surface hydration redistributed markedly and yielded to silicalite water loading. We find that the absolute rates and temperature dependence of water dynamics compare well to neutron scattering data and pulse field gradient measures from relevant samples of Ca-montmorillonite and silicalite, respectively. Within an atomistic, reactive context, our results distinguish water dynamics in the interlayer Ca(OH)(2)·nH(2)O environment from water flowing over the clay surface, and from water diffusing within silicalite. We find that the diffusion of water when complexed to Ca hydrates is considerably slower than freely diffusing water over the clay surface, and the reduced mobility is well described by a difference in the Arrhenius pre-exponential factor rather than a change in activation energy.

TET Offensive II Field Force Vietnam After Action Report 31 January - 18 February 1968

Science.gov (United States)

1968-03-01

and the 5th VC Division. V During this same period of time there were no majur shifts in ARVN forces . However III Corps shifted three...8217-".•: ’ ’SSIFJED U.S. ARMY. VIETNAM. II FIELD FORCE . TET OFFENSIVE II FIELD FORCE VIETNAM AFTER ACTION REPORT, 31 JANUARY-18 FEB- RUARY 1968...H FIELD FORCE VIETNAM AFTER ACTION REPORT 31 January-18 February 1968 RECORD K0- ! FlSjl fi-.-A-,>-•: it tT*\\ : *si h s» -wP Mr-, £< St

Finger-Shaped GelForce: Sensor for Measuring Surface Traction Fields for Robotic Hand.

Science.gov (United States)

Sato, K; Kamiyama, K; Kawakami, N; Tachi, S

2010-01-01

It is believed that the use of haptic sensors to measure the magnitude, direction, and distribution of a force will enable a robotic hand to perform dexterous operations. Therefore, we develop a new type of finger-shaped haptic sensor using GelForce technology. GelForce is a vision-based sensor that can be used to measure the distribution of force vectors, or surface traction fields. The simple structure of the GelForce enables us to develop a compact finger-shaped GelForce for the robotic hand. GelForce that is developed on the basis of an elastic theory can be used to calculate surface traction fields using a conversion equation. However, this conversion equation cannot be analytically solved when the elastic body of the sensor has a complicated shape such as the shape of a finger. Therefore, we propose an observational method and construct a prototype of the finger-shaped GelForce. By using this prototype, we evaluate the basic performance of the finger-shaped GelForce. Then, we conduct a field test by performing grasping operations using a robotic hand. The results of this test show that using the observational method, the finger-shaped GelForce can be successfully used in a robotic hand.

Radiation reaction force and unification of electromagnetic and gravitational fields

International Nuclear Information System (INIS)

Lo, C.Y.; Goldstein, G.R.; Napier, A.

1981-04-01

A unified theory of electromagnetic and gravitational fields should modify classical electrodynamics such that the radiation reaction force is accounted for. The analysis leads to a five-dimensional unified theory of five variables. The theory is supported by showing that, for the case of a charged particle moving in a constant magnetic field, the radiation reaction force is indeed included. Moreover, this example shows explicitly that physical changes are associated with the fifth variable. Thus, the notion of a physical five-dimensional space should be seriously taken into consideration

Systematic Parameterization of Lignin for the CHARMM Force Field

Energy Technology Data Exchange (ETDEWEB)

Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg; Crowley, Michael

2017-07-06

Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between

Secondary Structure of Rat and Human Amylin across Force Fields.

Directory of Open Access Journals (Sweden)

Kyle Quynn Hoffmann

Full Text Available 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

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

Directory of Open Access Journals (Sweden)

Anne eFocke

2013-07-01

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

Accurate van der Waals force field for gas adsorption in porous materials.

Science.gov (United States)

Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

2017-09-05

An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

International Nuclear Information System (INIS)

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

2016-01-01

An empirically parameterized intermolecular force field is developed for crystal structure modelling and prediction. The model is optimized for use with an atomic multipole description of electrostatic interactions. 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%

Nonequilibrium forces between atoms and dielectrics mediated by a quantum field

International Nuclear Information System (INIS)

Behunin, Ryan O.; Hu, Bei-Lok

2011-01-01

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

Modeling Enzymatic Transition States by Force Field Methods

DEFF Research Database (Denmark)

Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

2009-01-01

The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... of the TS geometry on the flexibility of the system has been probed by fixing layers of atoms around the active site and using increasingly larger nonbonded cutoffs. The variability over the 20 structures is found to decrease as the system is made more flexible. Relative energies have been calculated...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...

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

OpenAIRE

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

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...

Martini Coarse-Grained Force Field : Extension to DNA

NARCIS (Netherlands)

Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the

Martini Coarse-Grained Force Field : Extension to Carbohydrates

NARCIS (Netherlands)

Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

2009-01-01

We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

Artificial force fields for multi-agent simulations of maritime traffic and risk estimation

NARCIS (Netherlands)

Xiao, F.; Ligteringen, H.; Van Gulijk, C.; Ale, B.J.M.

2012-01-01

A probabilistic risk model is designed to estimate probabilities of collisions for shipping accidents in busy waterways. We propose a method based on multi-agent simulation that uses an artificial force field to model ship maneuvers. The artificial force field is calibrated by AIS data (Automatic

A mobile-mobile transport model for simulating reactive transport in connected heterogeneous fields

Science.gov (United States)

Lu, Chunhui; Wang, Zhiyuan; Zhao, Yue; Rathore, Saubhagya Singh; Huo, Jinge; Tang, Yuening; Liu, Ming; Gong, Rulan; Cirpka, Olaf A.; Luo, Jian

2018-05-01

Mobile-immobile transport models can be effective in reproducing heavily tailed breakthrough curves of concentration. However, such models may not adequately describe transport along multiple flow paths with intermediate velocity contrasts in connected fields. We propose using the mobile-mobile model for simulating subsurface flow and associated mixing-controlled reactive transport in connected fields. This model includes two local concentrations, one in the fast- and the other in the slow-flow domain, which predict both the concentration mean and variance. The normalized total concentration variance within the flux is found to be a non-monotonic function of the discharge ratio with a maximum concentration variance at intermediate values of the discharge ratio. We test the mobile-mobile model for mixing-controlled reactive transport with an instantaneous, irreversible bimolecular reaction in structured and connected random heterogeneous domains, and compare the performance of the mobile-mobile to the mobile-immobile model. The results indicate that the mobile-mobile model generally predicts the concentration breakthrough curves (BTCs) of the reactive compound better. Particularly, for cases of an elliptical inclusion with intermediate hydraulic-conductivity contrasts, where the travel-time distribution shows bimodal behavior, the prediction of both the BTCs and maximum product concentration is significantly improved. Our results exemplify that the conceptual model of two mobile domains with diffusive mass transfer in between is in general good for predicting mixing-controlled reactive transport, and particularly so in cases where the transfer in the low-conductivity zones is by slow advection rather than diffusion.

Building machine learning force fields for nanoclusters

Science.gov (United States)

Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro

2018-06-01

We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.

Equations of motion of a particle interacting with a scalar field

International Nuclear Information System (INIS)

Sato, N.K.

1984-01-01

The equations of motion of a particle (nucleon) interacting with a escalar (mesonic) field are derived by the energy momentum tensor moments method of Papapetrou. After a detailed study of the mesonic radiation field the expression of the reactive radiation force of the field upon the particle is established. (Author) [pt

A levitation force and magnetic field distribution measurement system in three dimensions

International Nuclear Information System (INIS)

Yang, W.M.; Chao, X.X.; Shu, Z.B.; Zhu, S.H.; Wu, X.L.; Bian, X.B.; Liu, P.

2006-01-01

A levitation force and magnetic field distribution measurement system in three dimension has been designed and constructed, which can be used for the levitation force measurement between a superconductor and a magnet, or magnet to magnet in three dimensions; and for the measurement of magnetic field distribution in three dimensions according to your need in space. It can also give out the dynamical changing result of magnetic field density with time during levitation force measurement. If we change the sensor of the detector of the measurement system, it also can be used for other kinds of measurement of physical properties. It is a good device for the measurement of magnetic properties of materials. In addition the device can also be used to work at carving in three dimensions

Self-consistent mean field forces in turbulent plasmas: Current and momentum relaxation

International Nuclear Information System (INIS)

Hegna, C.C.

1997-08-01

The properties of turbulent plasmas are described using the two-fluid equations. Under some modest assumptions, global constraints for the turbulent mean field forces that act on the ion and electron fluids are derived. These constraints imply a functional form for the parallel mean field forces in the Ohm's law and the momentum balance equation. These forms suggest that the fluctuations attempt to relax the plasma to a state where both the current and the bulk plasma momentum are aligned along the mean magnetic field with proportionality constants that are global constants. Observations of flow profile evolution during discrete dynamo activity in reversed field pinch experiments are interpreted

Sultan - forced flow, high field test facility

International Nuclear Information System (INIS)

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

1981-01-01

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

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

Science.gov (United States)

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

Science.gov (United States)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

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

Energy Technology Data Exchange (ETDEWEB)

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de [Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg (Germany); Kibies, Patrick; Frach, Roland; Kast, Stefan M., E-mail: stefan.kast@tu-dortmund.de [Physikalische Chemie III, Technische Universität Dortmund, 44227 Dortmund (Germany); Imoto, Sho, E-mail: sho.imoto@theochem.rub.de; Marx, Dominik [Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany); Suladze, Saba; Winter, Roland [Physikalische Chemie I, Technische Universität Dortmund, 44227 Dortmund (Germany)

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.

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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

2016-01-01

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.

Quantum mechanical force field for water with explicit electronic polarization.

Science.gov (United States)

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

2013-08-07

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

The growth of the concept of forces and fields

International Nuclear Information System (INIS)

Mukherji, Visvapriya

1979-01-01

The history and development of the concept of forces and fields in nature as was existing since two millenia ago to the ones that are being proposed and modified in the present day schools of field theorists have been traced. The concepts of Aristotle, Galileo, Democritus, Roemer, Newton, etc. which are considered classical in nature are outlined. The modern idea of field theories which owes its origin to the hypothesis propounded by Euler and the later developments by Laplace, Kelvin and Maxwell are described. Finally, Einstein's theory of relativity which projected a very novel interpretation of the gravitational field has also been explained in brief. Some of the hitherto unanswered questions in the field are also posed. (K.B.)

Calculation of the radiation force on a cylinder in a standing wave acoustic field

Energy Technology Data Exchange (ETDEWEB)

Haydock, David [Unilever R and D Colworth, Sharnbrook, Bedford MK44 1LQ (United Kingdom); Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

2005-04-15

We present a new calculation of the radiation force on a cylinder in a standing wave acoustic field. We use the formula to calculate the force on a cylinder which is free to move in the field and one which is fixed in space.

Calculation of the radiation force on a cylinder in a standing wave acoustic field

International Nuclear Information System (INIS)

Haydock, David

2005-01-01

We present a new calculation of the radiation force on a cylinder in a standing wave acoustic field. We use the formula to calculate the force on a cylinder which is free to move in the field and one which is fixed in space

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

Science.gov (United States)

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

2014-12-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Fan, Zhaochuan; Vlugt, Thijs J. H., E-mail: t.j.h.vlugt@tudelft.nl [Process and Energy Department, Delft University of Technology, Leeghwaterstraat 39, 2628 CB Delft,The Netherlands (Netherlands); Koster, Rik S.; Fang, Changming; Huis, Marijn A. van [Debye Institute for Nanomaterials Science and Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht (Netherlands); Wang, Shuaiwei [Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan 450006 (China); Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W. [Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands)

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.

Effects of Force Field Selection on the Computational Ranking of MOFs for CO2 Separations.

Science.gov (United States)

Dokur, Derya; Keskin, Seda

2018-02-14

Metal-organic frameworks (MOFs) have been considered as highly promising materials for adsorption-based CO 2 separations. The number of synthesized MOFs has been increasing very rapidly. High-throughput molecular simulations are very useful to screen large numbers of MOFs in order to identify the most promising adsorbents prior to extensive experimental studies. Results of molecular simulations depend on the force field used to define the interactions between gas molecules and MOFs. Choosing the appropriate force field for MOFs is essential to make reliable predictions about the materials' performance. In this work, we performed two sets of molecular simulations using the two widely used generic force fields, Dreiding and UFF, and obtained adsorption data of CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 mixtures in 100 different MOF structures. Using this adsorption data, several adsorbent evaluation metrics including selectivity, working capacity, sorbent selection parameter, and percent regenerability were computed for each MOF. MOFs were then ranked based on these evaluation metrics, and top performing materials were identified. We then examined the sensitivity of the MOF rankings to the force field type. Our results showed that although there are significant quantitative differences between some adsorbent evaluation metrics computed using different force fields, rankings of the top MOF adsorbents for CO 2 separations are generally similar: 8, 8, and 9 out of the top 10 most selective MOFs were found to be identical in the ranking for CO 2 /H 2 , CO 2 /N 2 , and CO 2 /CH 4 separations using Dreiding and UFF. We finally suggested a force field factor depending on the energy parameters of atoms present in the MOFs to quantify the robustness of the simulation results to the force field selection. This easily computable factor will be highly useful to determine whether the results are sensitive to the force field type or not prior to performing computationally demanding

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

Energy Technology Data Exchange (ETDEWEB)

Lerche, I. [Institut für Geowissenschaften, Naturwissenschaftliche Fakultät III, Martin-Luther Universität, D-06099 Halle (Germany); Low, B. C. [High Altitude Observatory, National Center for Atmospheric Research, Boulder, Colorado 80307 (United States)

2014-10-15

An axisymmetric force-free magnetic field B(r, θ) in spherical coordinates is defined by a function r sin θB{sub φ}=Q(A) relating its azimuthal component to its poloidal flux-function A. The power law r sin θB{sub φ}=aA|A|{sup 1/n}, n a positive constant, admits separable fields with A=(A{sub n}(θ))/(r{sup n}) , posing a nonlinear boundary-value problem for the constant parameter a as an eigenvalue and A{sub n}(θ) as its eigenfunction [B. C. Low and Y. Q Lou, Astrophys. J. 352, 343 (1990)]. A complete analysis is presented of the eigenvalue spectrum for a given n, providing a unified understanding of the eigenfunctions and the physical relationship between the field's degree of multi-polarity and rate of radial decay via the parameter n. These force-free fields, self-similar on spheres of constant r, have basic astrophysical applications. As explicit solutions they have, over the years, served as standard benchmarks for testing 3D numerical codes developed to compute general force-free fields in the solar corona. The study presented includes a set of illustrative multipolar field solutions to address the magnetohydrodynamics (MHD) issues underlying the observation that the solar corona has a statistical preference for negative and positive magnetic helicities in its northern and southern hemispheres, respectively; a hemispherical effect, unchanging as the Sun's global field reverses polarity in successive eleven-year cycles. Generalizing these force-free fields to the separable form B=(H(θ,φ))/(r{sup n+2}) promises field solutions of even richer topological varieties but allowing for φ-dependence greatly complicates the governing equations that have remained intractable. The axisymmetric results obtained are discussed in relation to this generalization and the Parker Magnetostatic Theorem. The axisymmetric solutions are mathematically related to a family of 3D time-dependent ideal MHD solutions for a polytropic fluid of index γ = 4

Force fields of charged particles in micro-nanofluidic preconcentration systems

Science.gov (United States)

Gong, Lingyan; Ouyang, Wei; Li, Zirui; Han, Jongyoon

2017-12-01

Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system. This letter studies the particle trapping phenomena that are not explainable in the 1D model through the calculation of the two-dimensional (2D) force fields. The trapping of charged particles is shown to significantly distort the electric field and fluid flow pattern, which in turn leads to the different trapping behaviors of particles of different sizes. The mechanisms behind the protrusions and instability of the focused band, which are important factors determining overall preconcentration efficiency, are revealed through analyzing the rotating fluxes of particles in the vicinity of the ion-selective membrane. The differences in the enrichment factors of differently sized particles are understood through the interplay between the electric force and convective fluid flow. These results provide insights into the electrokinetic concentration effect, which could facilitate the design and optimization of ICP-based preconcentration systems.

Self-consistent Optomechanical Dynamics and Radiation Forces in Thermal Light Fields

International Nuclear Information System (INIS)

Sonnleitner, M.

2014-01-01

We discuss two different aspects of the mechanical interaction between neutral matter and electromagnetic radiation.The first part addresses the complex dynamics of an elastic dielectric deformed by optical forces. To do so we use a one-dimensional model describing the medium by an array of beam splitters such that the interaction with the incident waves can be described with a transfer-matrix approach. Since the force on each individual beam splitter is known we thus obtain the correct volumetric force density inside the medium. Sending a light field through an initially homogeneous dielectric then results in density modulations which in turn alter the optical properties of this medium.The second part is concerned with mechanical light-effects on atoms in thermal radiation fields. At hand of a generic setup of an atom interacting with a hot sphere emitting blackbody radiation we show that the emerging gradient force may surpass gravity by several orders of magnitude. The strength of the repulsive scattering force strongly depends on the spectrum of the involved atoms and can be neglected in some setups. A special emphasis lies on possible implications on astrophysical scenarios where the interactions between heated dust and atoms, molecules or nanoparticles are of crucial interest. (author) [de

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

Science.gov (United States)

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

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

Science.gov (United States)

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

2015-01-01

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

Integrated Process Design and Control of Multi-element Reactive Distillation Processes

DEFF Research Database (Denmark)

Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

2016-01-01

In this work, integrated process design and control of reactive distillation processes involving multi-elements is presented. The reactive distillation column is designed using methods and tools which are similar in concept to non-reactive distillation design methods, such as driving force approach....... The methods employed in this work are based on equivalent element concept. This concept facilitates the representation of a multi-element reactive system as equivalent binary light and heavy key elements. First, the reactive distillation column is designed at the maximum driving force where through steady...

Electric field and dielectrophoretic force on a dielectric particle chain in a parallel-plate electrode system

International Nuclear Information System (INIS)

Techaumnat, B; Eua-arporn, B; Takuma, T

2004-01-01

This paper presents results of calculations of the electric field and dielectrophoretic force on a dielectric particle chain suspended in a host liquid lying between parallel-plate electrodes. The method of calculation is based on the method of multipole images using the multipole re-expansion technique. We have investigated the effect of the particle permittivity, the tilt angle (between the chain and the applied field) and the chain arrangement on the electric field and force. The results show that the electric field intensification rises in accordance with the increase in the ratio of the particle-to-liquid permittivity, Γ ε . The electric field at the contact point between the particles decreases with increasing tilt angle, while the maximal field at the contact point between the particles and the plate electrodes is almost unchanged. The maximal field can be approximated by a simple formula, which is a quadratic function of Γ ε . The dielectrophoretic force depends significantly on the distance from other particles or an electrode. However, for the tilt angles in this paper, the horizontal force on the upper particle of the chain always has the direction opposite to the shear direction. The maximal horizontal force of a chain varies proportional to (Γ ε - 1) 1.7 if the particles in the chain are still in contact with each other. The approximated force, based on the force on an isolated chain, has been compared with our calculation results. The comparison shows that no approximation model agrees well with our results throughout the range of permittivity ratios

Use the Protonmotive Force: Mitochondrial Uncoupling and Reactive Oxygen Species.

Science.gov (United States)

Berry, Brandon J; Trewin, Adam J; Amitrano, Andrea M; Kim, Minsoo; Wojtovich, Andrew P

2018-04-04

Mitochondrial respiration results in an electrochemical proton gradient, or protonmotive force (pmf), across the mitochondrial inner membrane. The pmf is a form of potential energy consisting of charge (∆ψ m ) and chemical (∆pH) components, that together drive ATP production. In a process called uncoupling, proton leak into the mitochondrial matrix independent of ATP production dissipates the pmf and energy is lost as heat. Other events can directly dissipate the pmf independent of ATP production as well, such as chemical exposure or mechanisms involving regulated mitochondrial membrane electrolyte transport. Uncoupling has defined roles in metabolic plasticity and can be linked through signal transduction to physiologic events. In the latter case, the pmf impacts mitochondrial reactive oxygen species (ROS) production. Although capable of molecular damage, ROS also have signaling properties that depend on the timing, location, and quantity of their production. In this review, we provide a general overview of mitochondrial ROS production, mechanisms of uncoupling, and how these work in tandem to affect physiology and pathologies, including obesity, cardiovascular disease, and immunity. Overall, we highlight that isolated bioenergetic models-mitochondria and cells-only partially recapitulate the complex link between the pmf and ROS signaling that occurs in vivo. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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

1995-01-01

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

ATK-ForceField: a new generation molecular dynamics software package

Science.gov (United States)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

On the absorbing force of magnetic fields acting on magnetic particle under magnetic particle examination

International Nuclear Information System (INIS)

Maeda, N.

1988-01-01

During the magnetic particle examination, magnetic particles near defects are deposited by an absorbing force of magnetic fields acting on the magnetic particles. Therefore, a quantitative determination of this absorbing force is a theoretical and experimental basis for solving various problems associated with magnetic particle examinations. The absorbing force is formulated based on a magnetic dipole model, and a measuring method of the absorbing force using magnetic fields formed around linear current is proposed. Measurements according to this method produced appropriate results, verifying the validation of the concept and the measuring method

Relationship of scattering phase shifts to special radiation force conditions for spheres in axisymmetric wave-fields.

Science.gov (United States)

Marston, Philip L; Zhang, Likun

2017-05-01

When investigating the radiation forces on spheres in complicated wave-fields, the interpretation of analytical results can be simplified by retaining the s-function notation and associated phase shifts imported into acoustics from quantum scattering theory. For situations in which dissipation is negligible, as taken to be the case in the present investigation, there is an additional simplification in that partial-wave phase shifts become real numbers that vanish when the partial-wave index becomes large and when the wave-number-sphere-radius product vanishes. By restricting attention to monopole and dipole phase shifts, transitions in the axial radiation force for axisymmetric wave-fields are found to be related to wave-field parameters for traveling and standing Bessel wave-fields by considering the ratio of the phase shifts. For traveling waves, the special force conditions concern negative forces while for standing waves, the special force conditions concern vanishing radiation forces. An intermediate step involves considering the functional dependence on phase shifts. An appendix gives an approximation for zero-force plane standing wave conditions. Connections with early investigations of acoustic levitation are mentioned and some complications associated with viscosity are briefly noted.

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

Science.gov (United States)

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

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

Vector field statistical analysis of kinematic and force trajectories.

Science.gov (United States)

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

2013-09-27

When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of 'non-directed' hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called 'statistical parametric mapping' (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems. © 2013 Published by Elsevier Ltd. All rights reserved.

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

International Nuclear Information System (INIS)

Weening, R. H.

2011-01-01

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

New approaches and solutions of the nonlinear force-free field

International Nuclear Information System (INIS)

Xie Baisong; Yin Xintao; Luo Xia

2006-01-01

New approaches to nonlinear force-free field equations are presented and new exact solutions are found analytically. Examples are given and some implications of the results to astrophysical solar plasmas as well as tokamak plasmas are discussed

Quantifying the Attractive Force Exerted on the Pinned Calcium Spiral Waves by Using the Adventive Field

International Nuclear Information System (INIS)

Qiu Kang; Tang Jun; Luo Jin-Ming; Ma Jun

2013-01-01

The cytosolic calcium system is inhomogenous because of the discrete and random distribution of ion channels on the ER membrane. It is well known that the spiral tip can be pinned by the heterogenous area, and the field can detach the spiral from the heterogeneity. We use the adventive field to counteract the attractive force exerting on the calcium spiral wave by the heterogeneity, then the strength of the adventive field is used to quantify the attractive force indirectly. Two factors determining the attractive force are studied. It is found that: (1) the attractive force sharply increases with size of the heterogeneity for small-size heterogeneity, whereas the force increases to a saturated value for large-size heterogeneity; (2) for large-size heterogeneity, the force almost remains constant unless the level of the heterogeneity vanishes, the force decreases to zero linearly and sharply, and for small-size heterogeneity, the force decreases successively with the level of the heterogeneity. Furthermore, it is found that the forces exist only when the spiral tip is very close to the heterogenous area. Our study may shed some light on the control or suppression of the calcium spiral wave

Coupled energy-drift and force-balance equations for high-field hot-carrier transport

International Nuclear Information System (INIS)

Huang, Danhong; Alsing, P.M.; Apostolova, T.; Cardimona, D.A.

2005-01-01

Coupled energy-drift and force-balance equations that contain a frictional force for the center-of-mass motion of electrons are derived for hot-electron transport under a strong dc electric field. The frictional force is found to be related to the net rate of phonon emission, which takes away the momentum of a phonon from an electron during each phonon-emission event. The net rate of phonon emission is determined by the Boltzmann scattering equation, which depends on the distribution of electrons interacting with phonons. The work done by the frictional force is included into the energy-drift equation for the electron-relative scattering motion and is found to increase the thermal energy of the electrons. The importance of the hot-electron effect in the energy-drift term under a strong dc field is demonstrated in reducing the field-dependent drift velocity and mobility. The Doppler shift in the energy conservation of scattering electrons interacting with impurities and phonons is found to lead to an anisotropic distribution of electrons in the momentum space along the field direction. The importance of this anisotropic distribution is demonstrated through a comparison with the isotropic energy-balance equation, from which we find that defining a state-independent electron temperature becomes impossible. To the leading order, the energy-drift equation is linearized with a distribution function by expanding it into a Fokker-Planck-type equation, along with the expansions of both the force-balance equation and the Boltzmann scattering equation for hot phonons

Reactive sites influence in PMMA oligomers reactivity: a DFT study

Science.gov (United States)

Paz, C. V.; Vásquez, S. R.; Flores, N.; García, L.; Rico, J. L.

2018-01-01

In this work, we present a theoretical study of methyl methacrylate (MMA) living anionic polymerization. The study was addressed to understanding two important experimental observations made for Michael Szwarc in 1956. The unexpected effect of reactive sites concentration in the propagation rate, and the self-killer behavior of MMA (deactivating of living anionic polymerization). The theoretical calculations were performed by density functional theory (DFT) to obtain the frontier molecular orbitals values. These values were used to calculate and analyze the chemical interaction descriptors in DFT-Koopmans’ theorem. As a result, it was observed that the longest chain-length species (related with low concentration of reactive sites) exhibit the highest reactivity (behavior associated with the increase of the propagation rate). The improvement in this reactivity was attributed to the crosslinking produced in the polymethyl methacrylate chains. Meanwhile, the self-killer behavior was associated with the intermolecular forces present in the reactive sites. This behavior was associated to an obstruction in solvation, since the active sites remained active through all propagation species. The theoretical results were in good agreement with the Szwarc experiments.

A bidirectional brain-machine interface algorithm that approximates arbitrary force-fields.

Directory of Open Access Journals (Sweden)

Alessandro Vato

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

Patterning in systems driven by nonlocal external forces.

Science.gov (United States)

Luneville, L; Mallick, K; Pontikis, V; Simeone, D

2016-11-01

This work focuses on systems displaying domain patterns resulting from competing external and internal dynamics. To this end, we introduce a Lyapunov functional capable of describing the steady states of systems subject to external forces, by adding nonlocal terms to the Landau Ginzburg free energy of the system. Thereby, we extend the existing methodology treating long-range order interactions, to the case of external nonlocal forces. By studying the quadratic term of this Lyapunov functional, we compute the phase diagram in the temperature versus external field and we determine all possible modulated phases (domain patterns) as a function of the external forces and the temperature. Finally, we investigate patterning in chemical reactive mixtures and binary mixtures under irradiation, and we show that the last case opens the path toward micro-structural engineering of materials.

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

Science.gov (United States)

Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

2017-12-01

We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

Science.gov (United States)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

Effects of lorentz force on flow fields of free burning arc and wall stabilized non-transferred arc

International Nuclear Information System (INIS)

Peng Yi; Huang Heji; Pan Wenxia

2013-01-01

The flow fields of two typical DC plasma arcs, namely the transferred free burning arc and the non-transferred arc were simulated by solving hydrodynamic equations and electromagnetic equations. The effects of the Lorentz force on the characteristics of the flow fields of these two typical DC plasma arcs were estimated. Results show that in the case of the free burning arc, the Lorentz force due to the current self-induced magnetic field has significant impact on the flow fields, as the self-induced magnetic compression is the main arc constraint mechanism. However, in the case of the non-transferred arc generated in a torch with long and narrow inter-electrode inserts and an abruptly expanded anode, the Lorentz force has limited impact on the flow fields of the plasma especially at the downstream of the inter-electrode inserts, compared with the strong wall constraints and relatively high aerodynamic force. This is because the ratio of the electromagnetic force to the aerodynamic force is only about 0.01 in this region. When the main consideration is outlet parameters of the wall stabilized non-transferred DC arc plasma generator, in order to improve the efficiency of the numerical simulation program, the Lorentz force could be neglected in the non-transferred arc in some cases. (authors)

Regularization of fields for self-force problems in curved spacetime: Foundations and a time-domain application

International Nuclear Information System (INIS)

Vega, Ian; Detweiler, Steven

2008-01-01

We propose an approach for the calculation of self-forces, energy fluxes and waveforms arising from moving point charges in curved spacetimes. As opposed to mode-sum schemes that regularize the self-force derived from the singular retarded field, this approach regularizes the retarded field itself. The singular part of the retarded field is first analytically identified and removed, yielding a finite, differentiable remainder from which the self-force is easily calculated. This regular remainder solves a wave equation which enjoys the benefit of having a nonsingular source. Solving this wave equation for the remainder completely avoids the calculation of the singular retarded field along with the attendant difficulties associated with numerically modeling a delta-function source. From this differentiable remainder one may compute the self-force, the energy flux, and also a waveform which reflects the effects of the self-force. As a test of principle, we implement this method using a 4th-order (1+1) code, and calculate the self-force for the simple case of a scalar charge moving in a circular orbit around a Schwarzschild black hole. We achieve agreement with frequency-domain results to ∼0.1% or better.

Reactivation of a dormant earthflow documented by field monitoring data

Science.gov (United States)

Berti, Matteo; Simoni, Alessandro

2017-04-01

Large, deep-seated earthflows are common in mountainous areas where clay soils or fine-grained weak rocks are dominant. Distinctive features of these landslides are the relatively slow movements and the complex style of activity, in which mass flow is accompanied by basal sliding along localized shear zones. Earthflows are subjected to periodic reactivations separated by long intervals of dormancy. Although the dynamics of earthflows is widely documented in the literature, field data on the reactivation process are almost absent because of the difficulty of catching the critical acceleration phase. We document the reactivation of a large, dormant earthflow that occurred in February 2014 in the Northern Apennines of Italy. The Montecchi earthflow is located about 50 km to the south of Bologna, on the left side of the Silla Valley. Slopes are mainly constituted by chaotic sedimentary melanges belonging to the Palombini Shale (lower Cretaceous-Cenomanian). The earthflow first reactivated in November 1994, after an apparently unexceptional precipitation of 95 mm over a week. Surface velocities reached the value of few meters per day during the failure, then the landslide slowed down. One month after the reactivation, the velocity reduced to 1.2 mm/day and five months later it was further decreased to 0.1-0.2 mm/day. In the following years, the landslide became dormant with residual movements in the order of few mm/month. A monitoring system was installed in July 2004 to investigate the slope response to rainfalls and the displacement rates of the landslide during the dormant phase. The monitoring system has been operational for more than 10 years by adapting the number, type, and location of monitoring sensors to the evolving landslide. The monitoring system was operational when, on the 10th of February 2014, the landslide reactivated again. At the time of the failure two monitored sections were operational in the source area (upper section) and in the central part

Magnetohydrodynamic Modeling of Solar Coronal Dynamics with an Initial Non-force-free Magnetic Field

Energy Technology Data Exchange (ETDEWEB)

Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay [Udaipur Solar Observatory, Physical Research Laboratory, Dewali, Bari Road, Udaipur-313001 (India)

2017-05-01

The magnetic fields in the solar corona are generally neither force-free nor axisymmetric and have complex dynamics that are difficult to characterize. Here we simulate the topological evolution of solar coronal magnetic field lines (MFLs) using a magnetohydrodynamic model. The simulation is initialized with a non-axisymmetric non-force-free magnetic field that best correlates with the observed vector magnetograms of solar active regions (ARs). To focus on these ideas, simulations are performed for the flaring AR 11283 noted for its complexity and well-documented dynamics. The simulated dynamics develops as the initial Lorentz force pushes the plasma and facilitates successive magnetic reconnections at the two X-type null lines present in the initial field. Importantly, the simulation allows for the spontaneous development of mass flow, unique among contemporary works, that preferentially reconnects field lines at one of the X-type null lines. Consequently, a flux rope consisting of low-lying twisted MFLs, which approximately traces the major polarity inversion line, undergoes an asymmetric monotonic rise. The rise is attributed to a reduction in the magnetic tension force at the region overlying the rope, resulting from the reconnection. A monotonic rise of the rope is in conformity with the standard scenario of flares. Importantly, the simulated dynamics leads to bifurcations of the flux rope, which, being akin to the observed filament bifurcation in AR 11283, establishes the appropriateness of the initial field in describing ARs.

Microscopic derivation of the force on a dielectric fluid in an electromagnetic field

International Nuclear Information System (INIS)

Lai, H.M.; Suen, W.M.; Young, K.

1982-01-01

The force acting on a Clausius-Mossotti fluid in an electromagnetic field is evaluated microscopically. Owing to the modification of the two-particle density by the electric field, an additional mechanical force Δf/sup( M/) is found. When this is added to the electrical force f/sup( E/), the total force in the static case becomes identical to that deduced macroscopically by Helmholtz. The analysis is extended to various time-dependent cases, and it is pointed out that Δf/sup( M/) essentially assumes its static value on time scales longer than T/sub c/, the relaxation time of the two-particle density, but is otherwise negligibly small. Thus Peierls's theory of the momentum of light is valid only for pulses much shorter than T/sub c/; the necessary correction due to Δf/sup( M/) in other cases is given and discussed

Scalar meson field and many-body forces. Chapter 23

International Nuclear Information System (INIS)

Nyman, E.M.

1979-01-01

In applications of field theory to the theory of the nuclear forces, one has frequently assumed that there is a scalar meson. It will then be responsible for most of the medium-range attraction between the nucleons. According to current ideas, however, it is possible to account for the medium-range attraction without an elementary sigma meson. This approach requires a careful treatment of the exchange of interacting pairs of π mesons, such as to include those ππ interactions which are responsible for the formation and decay of the sigma meson. Recently, the scalar field in the nuclear many-body problem has begun to receive more attention. There are two reasons for this change of philosophy. One reason is the discovery of neutron stars. In neutron stars, the nucleon number density can be much higher than in nuclei. One therefore wants to derive the equation of state from a relativistic many-body theory. This forces one to deal explicitly with a set of mesons, such that in the non-relativistic limit one recovers the one-boson-exchange potential. (Auth.)

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

NARCIS (Netherlands)

Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

2007-01-01

The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ

Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol

NARCIS (Netherlands)

Winger, Moritz; de Vries, Alex H.; van Gunsteren, Wilfred F.

2009-01-01

A molecular dynamics (MD) study of ,-dimethoxypolyethylene glycol has been carried out under various conditions with respect to solvent composition, ionic strength, chain length, force field and temperature. A previous MD study on a 15-mer of polyethyleneglycol (PEG) suggested a helical equilibrium

Efficient nonparametric n -body force fields from machine learning

Science.gov (United States)

Glielmo, Aldo; Zeni, Claudio; De Vita, Alessandro

2018-05-01

We provide a definition and explicit expressions for n -body Gaussian process (GP) kernels, which can learn any interatomic interaction occurring in a physical system, up to n -body contributions, for any value of n . The series is complete, as it can be shown that the "universal approximator" squared exponential kernel can be written as a sum of n -body kernels. These recipes enable the choice of optimally efficient force models for each target system, as confirmed by extensive testing on various materials. We furthermore describe how the n -body kernels can be "mapped" on equivalent representations that provide database-size-independent predictions and are thus crucially more efficient. We explicitly carry out this mapping procedure for the first nontrivial (three-body) kernel of the series, and we show that this reproduces the GP-predicted forces with meV /Å accuracy while being orders of magnitude faster. These results pave the way to using novel force models (here named "M-FFs") that are computationally as fast as their corresponding standard parametrized n -body force fields, while retaining the nonparametric character, the ease of training and validation, and the accuracy of the best recently proposed machine-learning potentials.

Force field inside the void in complex plasmas under microgravity conditions

International Nuclear Information System (INIS)

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

2005-01-01

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

Nonlinear gravitational self-force: Field outside a small body

Science.gov (United States)

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.

Laboratory and field scale demonstration of reactive barrier systems

International Nuclear Information System (INIS)

Dwyer, B.P.; Marozas, D.C.; Cantrell, K.; Stewart, W.

1996-10-01

In an effort to devise a cost efficient technology for remediation of uranium contaminated groundwater, the Department of Energy's Uranium Mill Tailings Remedial Action (DOE-UMTRA) Program through Sandia National Laboratories (SNL) fabricated a pilot scale research project utilizing reactive subsurface barriers at an UMTRA site in Durango, Colorado. A reactive subsurface barrier is produced by placing a reactant material (in this experiment, metallic iron) in the flow path of the contaminated groundwater. The reactive media then removes and/or transforms the contaminant(s) to regulatory acceptable levels. Experimental design and results are discussed with regard to other potential applications of reactive barrier remediation strategies at other sites with contaminated groundwater problems

Integrated Process Design and Control of Reactive Distillation Processes

DEFF Research Database (Denmark)

Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

2015-01-01

on the element concept, which is used to translate a system of compounds into elements. The operation of the reactive distillation column at the highest driving force and other candidate points is analyzed through analytical solution as well as rigorous open-loop and closed-loop simulations. By application...... of this approach, it is shown that designing the reactive distillation process at the maximum driving force results in an optimal design in terms of controllability and operability. It is verified that the reactive distillation design option is less sensitive to the disturbances in the feed at the highest driving...

Leveraging intellectual capital through Lewin's Force Field Analysis: The case of software development companies

Directory of Open Access Journals (Sweden)

Alexandru Capatina

2017-09-01

Full Text Available This article presents an original conceptual framework for the strategic management of intellectual capital assets in software development companies. The framework is based on Lewin's Force Field Analysis. The framework makes it possible to assess software company managers’ opinions regarding the way driving and restraining forces affect the pillars of intellectual capital. The capacity to adapt to change is vital for companies in knowledge-intensive industries. Accordingly, this study examined a sample of 74 Romanian software development companies. The aim was to help companies benefit from managing the driving and restraining forces acting upon the pillars of intellectual capital (human, structural, and relational. The effects of the driving forces, quantified by PathMaker software's Force Field Tool, were observed to be greater than the restraining forces for each pillar of intellectual capital. This paper contributes by showing the explanatory power of this framework. The framework thus offers a tool that helps managers drive change in their organizations through effective intellectual capital management. Furthermore, this article describes how to encourage the implementation of changes that create value for software development companies.

The Quantum Space Phase Transitions for Particles and Force Fields

Directory of Open Access Journals (Sweden)

Chung D.-Y.

2006-07-01

Full Text Available We introduce a phenomenological formalism in which the space structure is treated in terms of attachment space and detachment space. Attachment space attaches to an object, while detachment space detaches from the object. The combination of these spaces results in three quantum space phases: binary partition space, miscible space and binary lattice space. Binary lattice space consists of repetitive units of alternative attachment space and detachment space. In miscible space, attachment space is miscible to detachment space, and there is no separation between attachment space and detachment spaces. In binary partition space, detachment space and attachment space are in two separat continuous regions. The transition from wavefunction to the collapse of wavefuction under interference becomes the quantum space phase transition from binary lattice space to miscible space. At extremely conditions, the gauge boson force field undergoes a quantum space phase transition to a "hedge boson force field", consisting of a "vacuum" core surrounded by a hedge boson shell, like a bubble with boundary.

Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

Science.gov (United States)

Radosinski, Lukasz; Labus, Karolina

2017-10-05

Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.

Gravitomagnetic field of the universe and Coriolis force on the rotating Earth

International Nuclear Information System (INIS)

Veto, B

2011-01-01

The Machian effect of distant masses of the universe in the frame of reference of the rotating Earth is demonstrated using the gravitomagnetic approach of general relativity. This effect appears in the form of a gravitomagnetic Lorentz force acting on moving bodies on the Earth. The gravitomagnetic field of the universe-deduced from a simple model-exerts a gravitomagnetic Lorentz force on moving bodies, a force parallel to and with comparable strength to the Coriolis force observed on the rotating Earth. It seems after simple considerations that the Coriolis force happens to be the gravitomagnetic Lorentz force exerted by the mass of a black hole universe. The description of the phenomenon is simpler using the gravitomagnetic approach than the standard formulation of general relativity, so the method relying on gravitomagnetism is advisable in lectures intended for master's degree level physics students and advanced undergraduates.

The MARTINI force field : Coarse grained model for biomolecular simulations

NARCIS (Netherlands)

Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge; Tieleman, D. Peter; de Vries, Alex H.

2007-01-01

We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To

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

Science.gov (United States)

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

2016-03-05

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

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

Science.gov (United States)

Yao, Shuang; Zhang, Yang; Guan, Baiou

2015-08-01

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

A molecular mechanics (MM3(96)) force field for metal-amide complexes

International Nuclear Information System (INIS)

Hay, B.P.; Clement, O.; Sandrone, G.; Dixon, D.A.

1998-01-01

A molecular mechanics (MM3(96)) force field is reported for modeling metal complexes of amides in which the amide is coordinated through oxygen. This model uses a points-on-a-sphere approach which involves the parameterization of the Msingle bondO stretch, the Msingle bondO double-bond C bend, and the Msingle bondO double-bond Csingle bondX (X = C, H, N) torsion interactions. Relationships between force field parameters and metal ion properties (charge, ionic radius, and electronegativity) are presented that allow the application of this model to a wide range of metal ions. The model satisfactorily reproduces the structures of over fifty amide complexes with the alkaline earths, transition metals, lanthanides, and actinides

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

Full Text Available Abstract Background Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA, we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM and multiple empirical criteria based method (MECBM hybrided with different force fields. Results Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%. On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost. Conclusions By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.

Science.gov (United States)

Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D

2002-03-01

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.

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

International Nuclear Information System (INIS)

Jiang Chaowei; Feng Xueshang; Xiang Changqing

2012-01-01

Reliable measurements of the solar magnetic field are still restricted to the photosphere, and our present knowledge of the three-dimensional coronal magnetic field is largely based on extrapolations from photospheric magnetograms using physical models, e.g., the nonlinear force-free field (NLFFF) model that is usually adopted. Most of the currently available NLFFF codes have been developed with computational volume such as a Cartesian box or a spherical wedge, while a global full-sphere extrapolation is still under development. A high-performance global extrapolation code is in particular urgently needed considering that the Solar Dynamics Observatory can provide a full-disk magnetogram with resolution up to 4096 × 4096. In this work, we present a new parallelized code for global NLFFF extrapolation with the photosphere magnetogram as input. The method is based on the magnetohydrodynamics relaxation approach, the CESE-MHD numerical scheme, and a Yin-Yang spherical grid that is used to overcome the polar problems of the standard spherical grid. The code is validated by two full-sphere force-free solutions from Low and Lou's semi-analytic force-free field model. The code shows high accuracy and fast convergence, and can be ready for future practical application if combined with an adaptive mesh refinement technique.

Electronic forces as descriptors of nucleophilic and electrophilic regioselectivity and stereoselectivity.

Science.gov (United States)

Liu, Shubin; Rong, Chunying; Lu, Tian

2017-01-04

One of the main tasks of theoretical chemistry is to rationalize computational results with chemical insights. Key concepts of such nature include nucleophilicity, electrophilicity, regioselectivity, and stereoselectivity. While computational tools are available to predict barrier heights and other reactivity properties with acceptable accuracy, a conceptual framework to appreciate above quantities is still lacking. In this work, we introduce the electronic force as the fundamental driving force of chemical processes to understand and predict molecular reactivity. It has three components but only two are independent. These forces, electrostatic and steric, can be employed as reliable descriptors for nucleophilic and electrophilic regioselectivity and stereoselectivity. The advantages of using these forces to evaluate molecular reactivity are that electrophilic and nucleophilic attacks are featured by distinct characteristics in the electrostatic force and no knowledge of quantum effects included in the kinetic and exchange-correlation energies is required. Examples are provided to highlight the validity and general applicability of these reactivity descriptors. Possible applications in ambident reactivity, σ and π holes, frustrated Lewis pairs, and stereoselective reactions are also included in this work.

A Kirkwood-Buff derived force field for alkaline earth halide salts

Science.gov (United States)

Naleem, Nawavi; Bentenitis, Nikolaos; Smith, Paul E.

2018-06-01

The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX2), where M = Mg2+, Ca2+, Sr2+, Ba2+ and X = Cl-, Br-, I-, which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

A Non-Linear Force-Free Field Model for the Evolving Magnetic Structure of Solar Filaments

Science.gov (United States)

Mackay, Duncan H.; van Ballegooijen, A. A.

2009-12-01

In this paper the effect of a small magnetic element approaching the main body of a solar filament is considered through non-linear force-free field modeling. The filament is represented by a series of magnetic dips. Once the dips are calculated, a simple hydrostatic atmosphere model is applied to determine which structures have sufficient column mass depth to be visible in Hα. Two orientations of the bipole are considered, either parallel or anti-parallel to the overlying arcade. The magnetic polarity that lies closest to the filament is then advected towards the filament. Initially for both the dominant and minority polarity advected elements, right/left bearing barbs are produced for dextral/sinsitral filaments. The production of barbs due to dominant polarity elements is a new feature. In later stages the filament breaks into two dipped sections and takes a highly irregular, non-symmetrical form with multiple pillars. The two sections are connected by field lines with double dips even though the twist of the field is less than one turn. Reconnection is not found to play a key role in the break up of the filament. The non-linear force-free fields produce very different results to extrapolated linear-force free fields. For the cases considered here the linear force-free field does not produce the break up of the filament nor the production of barbs as a result of dominant polarity elements.

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

Energy Technology Data Exchange (ETDEWEB)

Huyer, S [Univ. of Colorado, Boulder, CO (US)

1993-04-01

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

A Basic Experiment on Two-Dimensional Force of HTSC-Bulk in DC Magnetic-Field

OpenAIRE

吉田, 欣二郎; 松田, 茂雄; 松本, 洋和

2000-01-01

High temperature superconducting (HTSC) bulk can levitate stably on a track which consists of permanent magnets of the same polarity. This is because HTSC-bulk has a pinning force which keeps from vertical displacement due to the weight. We have proposed a new LSM theory which is based on an idea of considering the pinning force as synchronizing force in using armature travelling-magnetic-field instead of permanent magnets. However, the lift force enough to levitate the vehicle on the ground ...

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

Science.gov (United States)

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

1994-01-01

It is known from computer calculations that if a force-free magnetic field configuration is stressed progressively by footpoint displacements, the configuration expands and approaches the open configuration with the same surface flux distribution and the energy of the field increases progressively. For configurations of translationalsymmetry, it has been found empirically that the energy tends asymptotically to a certain functional form. It is here shown that analysis of a simple model of the asymptotic form of force-free fields of translational symmetry leads to and therefore justifies this functional form. According to this model, the field evolves in a well-behaved manner with no indication of instability or loss of equilibrium.

Voltage equilibration for reactive atomistic simulations of electrochemical processes

International Nuclear Information System (INIS)

Onofrio, Nicolas; Strachan, Alejandro

2015-01-01

We introduce electrochemical dynamics with implicit degrees of freedom (EChemDID), a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and their effect on the self-consistent partial atomic charges used in reactive molecular dynamics. An additional variable assigned to each atom denotes the local potential in its vicinity and we use fictitious, but computationally convenient, dynamics to describe its equilibration within connected metallic structures on-the-fly during the molecular dynamics simulation. This local electrostatic potential is used to dynamically modify the atomic electronegativities used to compute partial atomic changes via charge equilibration. Validation tests show that the method provides an accurate description of the electric fields generated by the applied voltage and the driving force for electrochemical reactions. We demonstrate EChemDID via simulations of the operation of electrochemical metallization cells. The simulations predict the switching of the device between a high-resistance to a low-resistance state as a conductive metallic bridge is formed and resistive currents that can be compared with experimental measurements. In addition to applications in nanoelectronics, EChemDID could be useful to model electrochemical energy conversion devices

Reactive scattering theory for molecular transitions in time-dependent fields

International Nuclear Information System (INIS)

Peskin, U.; Miller, W.H.

1995-01-01

A new approach is introduced for computing probabilities of molecular transitions in time-dependent fields. The method is based on the stationary (t,t') representation of the Schroedinger equation and is shown to be equivalent to infinite order time-dependent perturbation theory. Bound-to-bound (i.e., photoexcitation) and bound-to-continuum (i.e., photoreaction) transitions are regarded as reactive collisions with the ''time coordinate'' as the reaction coordinate in an extended Hilbert space. A numerical method based on imposing absorbing boundary conditions for the time coordinate in a discrete variable representation framework is introduced. A single operation of the Green's operator provides all the state-specific transition probabilities as well as partial state-resolved (inclusive) reaction probabilities. Illustrative numerical applications are given for model systems

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

Science.gov (United States)

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

2016-04-12

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

Probing the Importance of Charge Flux in Force Field Modeling.

Science.gov (United States)

Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

2017-08-08

We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

How well do force fields capture the strength of salt bridges in proteins?

Directory of Open Access Journals (Sweden)

Mustapha Carab Ahmed

2018-06-01

Full Text Available Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1 to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

Vector electric field measurement via position-modulated Kelvin probe force microscopy

Science.gov (United States)

Dwyer, Ryan P.; Smieska, Louisa M.; Tirmzi, Ali Moeed; Marohn, John A.

2017-10-01

High-quality spatially resolved measurements of electric fields are critical to understanding charge injection, charge transport, and charge trapping in semiconducting materials. Here, we report a variation of frequency-modulated Kelvin probe force microscopy that enables spatially resolved measurements of the electric field. We measure electric field components along multiple directions simultaneously by employing position modulation and lock-in detection in addition to numeric differentiation of the surface potential. We demonstrate the technique by recording linescans of the in-plane electric field vector in the vicinity of a patch of trapped charge in a 2,7-diphenyl[1]benzothieno[3,2-b][1]benzothiophene (DPh-BTBT) organic field-effect transistor. This technique is simple to implement and should be especially useful for studying electric fields in spatially inhomogeneous samples like organic transistors and photovoltaic blends.

ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

Science.gov (United States)

Stolworthy, L D; Shirts, R B

1997-03-01

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

Simplified TiO2 force fields for studies of its interaction with biomolecules

Science.gov (United States)

Luan, Binquan; Huynh, Tien; Zhou, Ruhong

2015-06-01

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

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

Science.gov (United States)

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

2015-02-11

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

Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

DEFF Research Database (Denmark)

Voroshylova, I. V.; Chaban, V. V.

2014-01-01

Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

Dipole and quadrupole forces exerted on atoms in laser fields: The nonperturbative approach

International Nuclear Information System (INIS)

Sindelka, Milan; Moiseyev, Nimrod; Cederbaum, Lorenz S.

2006-01-01

Manipulation of cold atoms by lasers has so far been studied solely within the framework of the conventional dipole approximation, and the atom-light interaction has been treated using low order perturbation theory. Laser control of atomic motions has been ascribed exclusively to the corresponding light-induced dipole forces. In this work, we present a general theory to derive the potential experienced by an atom in a monochromatic laser field in a context analogous to the Born-Oppenheimer approximation for molecules in the field-free case. The formulation goes beyond the dipole approximation and gives rise to the field-atom coupling potential terms which so far have not been taken into consideration in theoretical or experimental studies. Contrary to conventional approaches, our method is based upon the many electron Floquet theory and remains valid also for high intensity laser fields (i.e., for a strongly nonperturbative atom-light interaction). As an illustration of the developed theory, we investigate the trapping of cold atoms in optical lattices. We find that for some atoms for specific laser parameters, despite the absence of the dipole force, the laser trapping is still possible due to the electric quadrupole forces. Namely, we show that by using realistic laser parameters one can form a quadrupole optical lattice which is sufficiently strong to trap Ca and Na atoms

Forces on a current-carrying wire in a magnetic field: the macro-micro connection

DEFF Research Database (Denmark)

Avelar Sotomaior Karam, Ricardo; Kneubil, Fabiana; Robilotta, Manoel

2017-01-01

The classic problem of determining the force on a current-carrying wire in a magnetic field is critically analysed. A common explanation found in many introductory textbooks is to represent the force on the wire as the sum of the forces on charge carriers. In this approach neither the nature...... of the forces involved nor their application points are fully discussed. In this paper we provide an alternative microscopic explanation that is suitable for introductory electromagnetism courses at university level. By considering the wire as a superposition of a positive and a negative cylindrical charge...

Structure reactivity relationships during N2O hydrogenation over Au-Ag alloys: A study by field emission techniques

Science.gov (United States)

Jacobs, Luc; Barroo, Cédric; Gilis, Natalia; Lambeets, Sten V.; Genty, Eric; Visart de Bocarmé, Thierry

2018-03-01

To make available atomic oxygen at the surface of a catalyst is the key step for oxidation reactions on Au-based catalysts. In this context, Au-Ag alloys catalysts exhibit promising properties for selective oxidation reactions of alcohols: low temperature activity and high selectivity. The presence of O(ads) and its effects on the catalytic reactivity is studied via the N2O dissociative adsorption and subsequent hydrogenation. Field emission techniques are particularly suited to study this reaction: Field Ion Microscopy (FIM) and Field Emission Microscopy (FEM) enable to image the extremity of sharp metallic tips, the size and morphology of which are close to those of one single catalytic particle. The reaction dynamics is studied in the 300-320 K temperature range and at a pressure of 3.5 × 10-3 Pa. The main results are a strong structure/reactivity relationship during N2O + H2 reaction over Au-8.8 at.%Ag model catalysts. Comparison of high-resolution FIM images of the clean sample and FEM images during reaction shows a sensitivity of the reaction to the local structure of the facets, independently of the used partial pressures of both N2O and H2. This suggests a localised dissociative adsorption step for N2O and H2 with the formation of a reactive interface around the {210} facets.

The Röntgen interaction and forces on dipoles in time-modulated optical fields

Science.gov (United States)

Sonnleitner, Matthias; Barnett, Stephen M.

2017-12-01

The Röntgen term is an often neglected contribution to the interaction between an atom and an electromagnetic field in the electric dipole approximation. In this work we discuss how this interaction term leads to a difference between the kinetic and canonical momentum of an atom which, in turn, leads to surprising radiation forces acting on the atom. We use a number of examples to explore the main features of this interaction, namely forces acting against the expected dipole force or accelerations perpendicular to the beam propagation axis.

Continuous micro-feeding of fine cohesive powders actuated by pulse inertia force and acoustic radiation force in ultrasonic standing wave field.

Science.gov (United States)

Wang, Hongcheng; Wu, Liqun; Zhang, Ting; Chen, Rangrang; Zhang, Linan

2018-07-10

Stable continuous micro-feeding of fine cohesive powders has recently gained importance in many fields. However, it remains a great challenge in practice because of the powder aggregate caused by interparticle cohesive forces in small capillaries. This paper describes a novel method of feeding fine cohesive powder actuated by a pulse inertia force and acoustic radiation force simultaneously in an ultrasonic standing wave field using a tapered glass nozzle. Nozzles with different outlet diameters are fabricated using glass via a heating process. A pulse inertia force is excited to drive powder movement to the outlet section of the nozzle in a consolidated columnar rod mode. An acoustic radiation force is generated to suspend the particles and make the rod break into large quantities of small agglomerates which impact each other randomly. So the aggregation phenomenon in the fluidization of cohesive powders can be eliminated. The suspended powder is discharged continuously from the nozzle orifice owing to the self-gravities and collisions between the inner particles. The micro-feeding rates can be controlled accurately and the minimum values for RespitoseSV003 and Granulac230 are 0.4 mg/s and 0.5 mg/s respectively. The relative standard deviations of all data points are below 0.12, which is considerably smaller than those of existing vibration feeders with small capillaries. Copyright © 2018 Elsevier B.V. All rights reserved.

A Chemo-Mechanical Model of Diffusion in Reactive Systems

Directory of Open Access Journals (Sweden)

Kerstin Weinberg

2018-02-01

Full Text Available The functional properties of multi-component materials are often determined by a rearrangement of their different phases and by chemical reactions of their components. In this contribution, a material model is presented which enables computational simulations and structural optimization of solid multi-component systems. Typical Systems of this kind are anodes in batteries, reactive polymer blends and propellants. The physical processes which are assumed to contribute to the microstructural evolution are: (i particle exchange and mechanical deformation; (ii spinodal decomposition and phase coarsening; (iii chemical reactions between the components; and (iv energetic forces associated with the elastic field of the solid. To illustrate the capability of the deduced coupled field model, three-dimensional Non-Uniform Rational Basis Spline (NURBS based finite element simulations of such multi-component structures are presented.

Reactive Strength Index: A Poor Indicator of Reactive Strength?

Science.gov (United States)

Healy, Robin; Kenny, Ian; Harrison, Drew

2017-11-28

The primary aim was to assess the relationships between reactive strength measures and associated kinematic and kinetic performance variables achieved during drop jumps. A secondary aim was to highlight issues with the use of reactive strength measures as performance indicators. Twenty eight national and international level sprinters, consisting of fourteen men and women, participated in this cross-sectional analysis. Athletes performed drop jumps from a 0.3 m box onto a force platform with dependent variables contact time (CT), landing time (TLand), push-off time (TPush), flight time (FT), jump height (JH), reactive strength index (RSI, calculated as JH / CT), reactive strength ratio (RSR, calculated as FT / CT) and vertical leg spring stiffness (Kvert) recorded. Pearson's correlation test found very high to near perfect relationships between RSI and RSR (r = 0.91 to 0.97), with mixed relationships found between RSI, RSR and the key performance variables, (Men: r = -0.86 to -0.71 between RSI/RSR and CT, r = 0.80 to 0.92 between RSI/RSR and JH; Women: r = -0.85 to -0.56 between RSR and CT, r = 0.71 between RSI and JH). This study demonstrates that the method of assessing reactive strength (RSI versus RSR) may be influenced by the performance strategies adopted i.e. whether an athlete achieves their best reactive strength scores via low CTs, high JHs or a combination. Coaches are advised to limit the variability in performance strategies by implementing upper and / or lower CT thresholds to accurately compare performances between individuals.

Effect of magnetic field and radiative condensation on the Jeans instability of dusty plasma with polarization force

International Nuclear Information System (INIS)

Prajapati, R.P.

2013-01-01

The Jeans instability of self-gravitating dusty plasma with polarization force is investigated considering the effects of magnetic field, dust temperature and radiative condensation. The condition of Jeans instability and expression of critical Jeans wave number are obtained which depend upon polarization force and dust temperature but these are unaffected by the presence of magnetic field. The radiative heat-loss functions also modify the Jeans condition of instability and expression of critical Jeans wave number. It is observed that the polarization force and ratio of radiative heat-loss functions have destabilizing while magnetic field and dust temperature have stabilizing influence on the growth rate of Jeans instability.

Field measurement of basal forces generated by erosive debris flows

Science.gov (United States)

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

Analysis of PM Magnetization Field Effects on the Unbalanced Magnetic Forces due to Rotor Eccentricity in BLDC Motors

Directory of Open Access Journals (Sweden)

S. Mahdiuon-Rad

2013-08-01

Full Text Available This paper investigates both static and dynamic eccentricities in single phase brushless DC (BLDC motors and analyzes the effect of the PM magnetization field on unbalanced magnetic forces acting on the rotor. Three common types of PM magnetization field patterns including radial, parallel and sinusoidal magnetizations are considered. In both static and dynamic eccentricities, harmonic components of the unbalanced magnetic forces on the rotor are extracted and analyzed. Based on simulation results, the magnetization fields that produce the lowest and highest unbalanced magnetic forces are determined in rotor eccentricity conditions.

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

Energy Technology Data Exchange (ETDEWEB)

Afanas' ev, A A; Rubinov, A N [B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, Minsk (Belarus); Gaida, L S; Guzatov, D V; Svistun, A Ch [Yanka Kupala State University of Grodno, Grodno (Belarus)

2015-10-31

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

Streamwise-body-force-model for rapid simulation combining internal and external flow fields

Directory of Open Access Journals (Sweden)

Cui Rong

2016-10-01

Full Text Available A streamwise-body-force-model (SBFM is developed and applied in the overall flow simulation for the distributed propulsion system, combining internal and external flow fields. In view of axial stage effects, fan or compressor effects could be simplified as body forces along the streamline. These body forces which are functions of local parameters could be added as source terms in Navier-Stokes equations to replace solid boundary conditions of blades and hubs. The validation of SBFM with uniform inlet and distortion inlet of compressors shows that pressure performance characteristics agree well with experimental data. A three-dimensional simulation of the integration configuration, via a blended wing body aircraft with a distributed propulsion system using the SBFM, has been completed. Lift coefficient and drag coefficient agree well with wind tunnel test results. Results show that to reach the goal of rapid integrated simulation combining internal and external flow fields, the computational fluid dynamics method based on SBFM is reasonable.

Characterizing the Potential for Injection-Induced Fault Reactivation Through Subsurface Structural Mapping and Stress Field Analysis, Wellington Field, Sumner County, Kansas

Science.gov (United States)

Schwab, Drew R.; Bidgoli, Tandis S.; Taylor, Michael H.

2017-12-01

Kansas, like other parts of the central U.S., has experienced a recent increase in seismicity. Correlation of these events with brine disposal operations suggests pore fluid pressure increases are reactivating preexisting faults, but rigorous evaluation at injection sites is lacking. Here we determine the suitability of CO2 injection into the Cambrian-Ordovician Arbuckle Group for long-term storage and into a Mississippian reservoir for enhanced oil recovery in Wellington Field, Sumner County, Kansas. To determine the potential for injection-induced earthquakes, we map subsurface faults and estimate in situ stresses, perform slip and dilation tendency analyses to identify well-oriented faults relative to the estimated stress field, and determine the pressure changes required to induce slip at reservoir and basement depths. Three-dimensional seismic reflection data reveal 12 near-vertical faults, mostly striking NNE, consistent with nodal planes from moment tensor solutions from recent earthquakes in the region. Most of the faults cut both reservoirs and several clearly penetrate the Precambrian basement. Drilling-induced fractures (N = 40) identified from image logs and inversion of earthquake moment tensor solutions (N = 65) indicate that the maximum horizontal stress is approximately EW. Slip tendency analysis indicates that faults striking <020° are stable under current reservoir conditions, whereas faults striking 020°-049° may be prone to reactivation with increasing pore fluid pressure. Although the proposed injection volume (40,000 t) is unlikely to reactive faults at reservoir depths, high-rate injection operations could reach pressures beyond the critical threshold for slip within the basement, as demonstrated by the large number of injection-induced earthquakes west of the study area.

Lienard-Wiechert field as covariant dynamics of electric lines of force

International Nuclear Information System (INIS)

Arutyunyan, S.G.

1989-01-01

The Lienard-Wiechert field of an arbitrarily moving charge is presented as a system of Lorentz-covariant moving electric lines of force. It is shown that the 4-vector describing these lines is written as a sum of the 4-vector of the charge and the isotropic 4-vector directed to the observation point. The motion of this 4-vector is described by the equation coinciding with the equation of motion for magnetic moment in external fields provided that the intrinsic magnetic moment is zero. By the system of lines that corresponds to the complete equation of magnetic moment in external fields the electromagnetic field is restored. It turned out that the spatial magnetic current proportional to the isotropic 4-vector directed to the observation point corresponds to this field. 8 refs

New Maids and Caretakers in Paris?: The Reactivation of Transnational Social Fields of Spanish Emigration Following the Economic Crisis

Directory of Open Access Journals (Sweden)

Laura Oso

2017-12-01

Full Text Available This article analyses the migration of Spanish women to France following the 2008 economic crisis, considering the reactivation of the transnational social fields that have been built up between the two countries over the years. It reveals how the recession has led to a renewal of the gender-based labour niches filled by women emigrating to Paris in the period between 1950 and 1970 (bonnes à tout faire or maid, domestic workers, caretakers and cleaners, stemming from the reactivation of transnational fields built up through social networks woven by the various migratory trends. It provides an insight into the way these transnational fields are linked to global production and reproduction chains in terms of the patriarchal reorganisation of the labour market and workforce. It concludes that the economic crisis has reinforced traditional social reproduction channels rooted in gender-based sources of employment.

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Adaptation of multi-joint balance coordination to whole body force fields

NARCIS (Netherlands)

Engelhart, Denise; Schouten, Alfred Christiaan; Pasma, Jantsje; Aarts, Ronald G.K.M.; Pasma, J.; Meskers, Carel; Maier, Andrea; van der Kooij, Herman

2014-01-01

Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how

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

Science.gov (United States)

2014-01-01

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

The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

International Nuclear Information System (INIS)

Liu Minxian; Wang Yan

2012-01-01

The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

The attenuation of the levitation force of HTS bulk exposed to AC magnetic field on the above NdFeB guideway

Energy Technology Data Exchange (ETDEWEB)

Liu Minxian, E-mail: liukey_sjtu@263.net [School of Computer Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010 (China); Wang Yan [Luoyang Institute of Science and Technology, Luoyang, Henan 471023 (China)

2012-01-15

The characteristic of the levitation force relaxation was studied by experiment. The levitation force is attenuated with the application of the AC external magnetic field. The decay increases with the amplitude of the A external magnetic field. The decay is almost independent of the frequency of AC field. In the present High Temperature Superconducting (HTS) maglev vehicle system, the air gaps between the adjacent permanent magnets make the magnetic fields above the NdFeB guideway non-uniform. So it is required to study the characteristics of levitation force of the HTS bulk affected by the non-uniform applied magnetic fields along the moving direction. In this paper, we have studied the characteristics of the levitation force relaxation by an experiment in which AC magnetic field generated by an electromagnet is used to simulate the time-varying magnetic field caused by the inhomogeneity of the NdFeB guideway. From the experiment results, it is found that the levitation force is attenuated with the application of the AC field, and the attenuation is increased with the amplitude of the AC field, but the attenuation is almost independent of the frequency the AC magnetic field.

Probing Field Distributions on Waveguide Structures with an Atomic Force/Photon Scanning Tunneling Microscope

NARCIS (Netherlands)

Borgonjen, E.G.; Borgonjen, E.G.; Moers, M.H.P.; Moers, M.H.P.; Ruiter, A.G.T.; van Hulst, N.F.

1995-01-01

A 'stand-alone' Photon Scanning Tunneling Microscope combined with an Atomic force Microscope, using a micro-fabricated silicon-nitride probe, is applied to the imaging of field distribution in integrated optical ridge waveguides. The electric field on the waveguide is locally probed by coupling to

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

Science.gov (United States)

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. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of Enlisted Force Retention Levels and Career Field Stability

Science.gov (United States)

2017-03-23

APPLICATION OF ENLISTED FORCE RETENTION LEVELS AND CAREER FIELD STABILITY THESIS Presented to the Faculty Department of Operational Sciences ...Fulfillment of the Requirements for the Degree of Master of Science in Operations Research Jamie T. Zimmermann, MS, BS Captain, USAF March 2017...Appendix B. The function proc lifetest is a nonparametric estimate of the survivor function using either the Kaplan-Meier method or the actuarial

Driving force of PCMI failure under reactivity initiated accident conditions and influence of hydrogen embrittlement on failure limit

International Nuclear Information System (INIS)

Tomiyasu, Kunihiko; Sugiyama, Tomoyuki; Nakamura, Takehiko; Fuketa, Toyoshi

2005-09-01

In order to clarify the driving force of PCMI (Pellet/Cladding Mechanical Interaction) failure on high burnup fuels and to investigate the influence of hydrogen embrittlement on failure limit under RIA (Reactivity Initiated Accident) conditions, RIA-simulation experiments were performed on fresh fuel rods in the NSRR (Nuclear Safety Research Reactor). The driving force of PCMI was restricted only to thermal expansion of pellet by using fresh UO 2 pellets. Fresh claddings were pre-hydrided to simulate hydrogen absorption of high burnup fuel rods. In seven experiments out of fourteen, test rods resulted in PCMI failure, which has been observed in the NSRR tests on high burnup PWR fuels, in terms of the transient behavior and the fracture configuration. This indicates that the driving force of PCMI failure is sufficiently explained with thermal expansion of pellet and a contribution of fission gas on it is small. A large number of incipient cracks were generated in the outer surface of the cladding even on non-failed fuel rods, and they stopped at the boundary between hydride rim, which was a hydride layer localized in the periphery of the cladding, and metallic layer. It suggests that the integrity of the metallic layer except for the hydride rim has particular importance for failure limit. Fuel enthalpy at failure correlates with the thickness of hydride rim, and tends to decrease with thicker hydride layer. (author)

Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

KAUST Repository

Lacoste, Deanna

2016-06-23

The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

Transfer functions of laminar premixed flames subjected to forcing by acoustic waves, AC electric fields, and non-thermal plasma discharges

KAUST Repository

Lacoste, Deanna; Xiong, Yuan; Moeck, Jonas P.; Chung, Suk-Ho; Roberts, William L.; Cha, Min

2016-01-01

The responses of laminar methane-air flames to forcing by acoustic waves, AC electric fields, and nanosecond repetitively pulsed (NRP) glow discharges are reported here. The experimental setup consists of an axisymmetric burner with a nozzle made from a quartz tube. Three different flame geometries have been studied: conical, M-shaped and V-shaped flames. A central stainless steel rod is used as a cathode for the electric field and plasma excitations. The acoustic forcing is obtained with a loudspeaker located at the bottom part of the burner. For forcing by AC electric fields, a metallic grid is placed above the rod and connected to an AC power supply. Plasma forcing is obtained by applying high-voltage pulses of 10-ns duration applied at 10 kHz, between the rod and an annular stainless steel ring, placed at the outlet of the quartz tube. The chemiluminescence of CH is used to determine the heat release rate fluctuations. For forcing by acoustic waves and plasma, the geometry of the flame plays a key role in the response of the combustion, while the flame shape does not affect the response of the combustion to electric field forcing. The flame response to acoustic forcing of about 10% of the incoming flow is similar to those obtained in the literature. The flames are found to be responsive to an AC electric field across the whole range of frequencies studied. A forcing mechanism, based on the generation of ionic wind, is proposed. The gain of the transfer function obtained for plasma forcing is found to be up to 5 times higher than for acoustic forcing. A possible mechanism of plasma forcing is introduced.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Stimulated Raman spectroscopy and nanoscopy of molecules using near field photon induced forces without resonant electronic enhancement gain

Energy Technology Data Exchange (ETDEWEB)

Tamma, Venkata Ananth [CaSTL Center, Department of Chemistry, University of California, Irvine, California 92697 (United States); Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu [Department of Electrical Engineering and Computer Science, 142 Engineering Tower, University of California, Irvine, California 92697 (United States); Nowak, Derek [Molecular Vista, Inc., 6840 Via Del Oro, San Jose, California 95119 (United States)

2016-06-06

We report on stimulated Raman spectroscopy and nanoscopy of molecules, excited without resonant electronic enhancement gain, and recorded using near field photon induced forces. Photon-induced interaction forces between the sharp metal coated silicon tip of an Atomic Force Microscope (AFM) and a sample resulting from stimulated Raman excitation were detected. We controlled the tip to sample spacing using the higher order flexural eigenmodes of the AFM cantilever, enabling the tip to come very close to the sample. As a result, the detection sensitivity was increased compared with previous work on Raman force microscopy. Raman vibrational spectra of azobenzene thiol and l-phenylalanine were measured and found to agree well with published results. Near-field force detection eliminates the need for far-field optical spectrometer detection. Recorded images show spatial resolution far below the optical diffraction limit. Further optimization and use of ultrafast pulsed lasers could push the detection sensitivity towards the single molecule limit.

Alkali aggregate reactivity in concrete structures in western Canada

International Nuclear Information System (INIS)

Morgan, D.R.; Empey, D.

1989-01-01

In several regions of Canada, particularly parts of Ontario, Quebec and the Maritime Provinces, research, testing and evaluation of aged concrete structures in the field has shown that alkali aggregate reactivity can give rise to pronounced concrete deterioration, particularly in hydraulic structures subjected to saturation or alternate wetting and drying such as locks, dams, canals, etc. Concrete deterioration is mainly caused by alkali-silica reactions and alkali-carbonate reactions, but a third type of deterioration involves slow/late expanding alkali-silicate/silica reactivity. The alkalies NaOH and KOH in the concrete pore solutions are mainly responsible for attack on expansive rocks and minerals in concrete. Methods for evaluating alkali-aggregate reaction potential in aggregates, and field and laboratory methods for detecting deterioration are discussed. Examples of alkali-aggregate reactions in structures is western Canada are detailed, including a water reservoir at Canadian Forces Base Chilliwack in British Columbia, the Oldman River diversion and flume, the Lundbreck Falls Bridge, and the St Mary's Reservoir spillway, all in southern Alberta. Mitigative measures include avoidance of use of suspect aggregates, but if this cannot be avoided it is recommended to keep the total alkalies in the concrete as low as possible and minimize opportunities for saturation of concrete by moisture. 16 refs., 19 figs., 1 tab

Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme

OpenAIRE

Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.

2005-01-01

The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.

Implications of confining force field structures in hard hadronic processes

International Nuclear Information System (INIS)

Bengtsson, H.-U.

1983-04-01

This thesis is centered on the study of confining force field structures in hard scattering processes. Perturbative QCD provides the means of calculating any process on the parton level, but to be able accurately to describe the actual outcome of an event, one still needs a phenomenological model for how quarks and gluons transform into observable hadrons. One such model is based on the assumption that the particles are produced by the confining fields stretched between the partons. The actual particle distributions will then depend on the topology of the confining fields. We have developed a Monte Carlo program to simulate complete events in hard scattering, and we use this to study the properties of the confining field in different trigger situations. We further look at the amount of hard processes that can be expected in experiments that trigger on transverse energy sum (calorimeter experiments). Finally, we investigate charm production within our model. (author)

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Science.gov (United States)

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.

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

Science.gov (United States)

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

2009-06-03

Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during

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

Directory of Open Access Journals (Sweden)

Bouyer Laurent J

2009-06-01

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

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

Science.gov (United States)

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

2009-01-01

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

Force field refinement from NMR scalar couplings

Energy Technology Data Exchange (ETDEWEB)

Huang Jing [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland); Meuwly, Markus, E-mail: m.meuwly@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

2012-03-02

Graphical abstract: We show that two classes of H-bonds are sufficient to quantitatively describe scalar NMR coupling constants in small proteins. Highlights: Black-Right-Pointing-Pointer We present force field refinements based on explicit MD simulations using scalar couplings across hydrogen bonds. Black-Right-Pointing-Pointer This leads to {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.03 Hz at best compared to experiment. Black-Right-Pointing-Pointer A classification of H-bonds according to secondary structure is not sufficiently robust. Black-Right-Pointing-Pointer Grouping H-bonds into two classes and reparametrization yields an RMSD of 0.07 Hz. Black-Right-Pointing-Pointer This is an improvement of 50. - Abstract: NMR observables contain valuable information about the protein dynamics sampling a high-dimensional potential energy surface. Depending on the observable, the dynamics is sensitive to different time-windows. Scalar coupling constants {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} reflect the pico- to nanosecond motions associated with the intermolecular hydrogen bond network. Including an explicit H-bond in the molecular mechanics with proton transfer (MMPT) potential allows us to reproduce experimentally determined {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings to within 0.02 Hz at best for ubiquitin and protein G. This is based on taking account of the chemically changing environment by grouping the H-bonds into up to seven classes. However, grouping them into two classes already reduces the RMSD between computed and observed {sup h3}J{sub NC{sup }{sup P}{sup r}{sup i}{sup m}{sup e}} couplings by almost 50%. Thus, using ensemble-averaged data with two classes of H-bonds leads to substantially improved scalar couplings from simulations with accurate force fields.

Improvement of a force field to model the edges of clay particles

International Nuclear Information System (INIS)

Pouvreau, Maxime

2016-01-01

The CLAYFF force field is widely used to model the interfaces of clay minerals - and related layered materials - with an aqueous phase. In the simulations, clay particles are typically represented by semi-infinite layers, i.e. only surfaces parallel to the layer plane (basal surfaces) are considered. This simplification is acceptable to a certain extent, but clay layers are really nano sized and terminated by lateral surfaces or edges. These surfaces can not only adsorb solvated species but are also subject to proton transfers, and all physico-chemical processes related to the aqueous phase acidity predominantly occur at the edges. By adding to the CLAYFF force field a Metal-O-H angle bending term whose parameters are correctly adjusted, the simulations of edge interfaces become possible.The parameters of Al-O-H and Mg-O-H terms were obtained from DFT calculations on bulk, basal surface and edge structural models of gibbsite Al(OH) 3 and brucite Mg(OH) 2 , whose layers can be considered as the backbones of clay minerals and related materials. In addition, the Si-O-H term was parametrized from an edge model of kaolinite Al 2 Si 2 O 5 (OH) 4 . Molecular dynamics simulations based on DFT and on CLAYFF with and without Metal-O-H term were performed. The modified force field clearly improves the description of hydroxylated surfaces: the orientation and the vibrational dynamics of the hydroxyl groups, the hydrogen bonding, and the coordination of metal atoms belonging to the edge are all closer to reality [fr

New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking.

Science.gov (United States)

Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B

2017-11-01

Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.

Influence of AC external magnetic field on guidance force relaxation between HTS bulk and NdFeB guideway

Energy Technology Data Exchange (ETDEWEB)

Zhang Longcai [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)], E-mail: zhlcai2000@163.com; Wang Suyu; Wang Jiasu; Zheng Jun [Applied Superconductivity Laboratory, P.O. Box 152, Southwest Jiaotong University, Chengdu, Sichuan 610031 (China)

2007-12-01

Superconducting maglev vehicle is one of the most promising applications of HTS bulks. In such a system, the HTS bulks are always exposed to time-varying external magnetic field, which is generated by the inhomogeneous surface magnetic field of the NdFeB guideway. So it is required to study whether the guidance force of the bulks is influenced by the inhomogeneity. In this paper, we studied the characteristics of the guidance force relaxation between the HTS bulk and the NdFeB guideway by an experiment in which AC external magnetic field generated by an electromagnet was used to simulate the time-varying external magnetic field caused by the inhomogeneity of the guideway. From the experiment results, it was found that the guidance force was decreased with the application of the AC external magnetic field, and the decay increased with the amplitude and was almost independent of the frequency.

A verification of quantum field theory – measurement of Casimir force

Indian Academy of Sciences (India)

journal of. Feb. & Mar. 2001 physics pp. 239–243. A verification of quantum field theory ... minum coated a sphere and flat plate using an atomic force microscope. ... where R is the radius of curvature of the spherical surface. The finite .... sured by AFM) of 60% Au/40% Pd, to form a nonreactive and conductive top layer. For.

A Model-Based Methodology for Integrated Design and Operation of Reactive Distillation Processes

DEFF Research Database (Denmark)

Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

2015-01-01

and resolved. A new approach isto tackle process intensification and controllability issues in an integrated manner, in the early stages of process design. This integrated and simultaneous synthesis approach provides optimal operation and moreefficient control of complex intensified systems that suffice...... calculation of reactive bubble points. For an energy-efficient design, the driving-forc eapproach (to determine the optimal feed location) for a reactive system has been employed. For both thereactive McCabe-Thiele and driving force method, vapor-liquid equilibrium data are based on elements. Thereactive...... system of compounds (methanol, isobutene and MTBE) to a binary system ofelements (elements A and B). For a binary element system, a simple reactive McCabe-Thiele-type method (to determine the number of reactive stages) has been used. The reactive equilibrium curve is constructed through sequential...

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Science.gov (United States)

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

Variably Saturated Flow and Multicomponent Biogeochemical Reactive Transport Modeling of a Uranium Bioremediation Field Experiment

International Nuclear Information System (INIS)

Yabusaki, Steven B.; Fang, Yilin; Williams, Kenneth H.; Murray, Christopher J.; Ward, Anderson L.; Dayvault, Richard; Waichler, Scott R.; Newcomer, Darrell R.; Spane, Frank A.; Long, Philip E.

2011-01-01

Field experiments at a former uranium mill tailings site have identified the potential for stimulating indigenous bacteria to catalyze the conversion of aqueous uranium in the +6 oxidation state to immobile solid-associated uranium in the +4 oxidation state. This effectively removes uranium from solution resulting in groundwater concentrations below actionable standards. Three-dimensional, coupled variably-saturated flow and biogeochemical reactive transport modeling of a 2008 in situ uranium bioremediation field experiment is used to better understand the interplay of transport rates and biogeochemical reaction rates that determine the location and magnitude of key reaction products. A comprehensive reaction network, developed largely through previous 1-D modeling studies, was used to simulate the impacts on uranium behavior of pulsed acetate amendment, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. A principal challenge is the mechanistic representation of biologically-mediated terminal electron acceptor process (TEAP) reactions whose products significantly alter geochemical controls on uranium mobility through increases in pH, alkalinity, exchangeable cations, and highly reactive reduction products. In general, these simulations of the 2008 Big Rusty acetate biostimulation field experiment in Rifle, Colorado confirmed previously identified behaviors including (1) initial dominance by iron reducing bacteria that concomitantly reduce aqueous U(VI), (2) sulfate reducing bacteria that become dominant after ∼30 days and outcompete iron reducers for the acetate electron donor, (3) continuing iron-reducer activity and U(VI) bioreduction during dominantly sulfate reducing conditions, and (4) lower apparent U(VI) removal from groundwater during dominantly sulfate reducing conditions. New knowledge on simultaneously active metal and sulfate reducers has been

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

Science.gov (United States)

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

2015-07-27

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

Steady state models for filamentary plasma structures associated with force free magnetic fields

International Nuclear Information System (INIS)

Marklund, G.

1978-05-01

This paper presents a model for filamentary plasma structures associated with force-free magnetic fields. A homogenous electric field parallel to the symmetry axis of the magnetic field is assumed. Under the influence of these fields, the plasma will drift radially inwards resulting in an accumulation of plasma in the central region. We assume recombination losses to keep the central plasma density at a finite value, and the recombined plasma i.e. the neutrals to diffuse radially outwards. Plasma density and some neutral gas density distributions for a steady state situation are calculated for various cases

The influence of inhomogeneous magnetic field over a NdFeB guideway on levitation force of the HTS bulk maglev system

Science.gov (United States)

Zhao, Lifeng; Deng, Jiangtao; Li, Linbo; Feng, Ning; Wei, Pu; Lei, Wei; Jiang, Jing; Wang, Xiqin; Zhang, Yong; Zhao, Yong

2018-04-01

Dynamic responses of high temperature superconducting bulk to inhomogeneous magnetic field distribution of permanent magnet guideway, as well as enlarged amplitude of magnetic field obtained by partially covering the permanent magnet guideway (PMG) with iron sheets in different thickness, are investigated. Experiments show that the instantaneous levitation force increases with the increase of the variation rate of magnetic field (dB/dt). Meanwhile, inhomogeneous magnetic field from PMG causes the decay of levitation force. The decay of levitation force almost increases linearly with the increase of alternating magnetic field amplitude. It should be very important for the application of high-speed maglev system.

Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

International Nuclear Information System (INIS)

Haydock, David

2005-01-01

We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important

Lattice Boltzmann simulations of the time-averaged forces on a cylinder in a sound field

Energy Technology Data Exchange (ETDEWEB)

Haydock, David [Unilever R and D Colworth, Sharnbrook, Bedford MK44 1LQ (United Kingdom); Department of Physics, Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom)

2005-04-15

We show that lattice Boltzmann simulations can be used to model the radiation force on an object in a standing wave acoustic field and comparisons are made to theoretical predictions. We show how viscous effects change the radiation force and predict the motion of a particle placed near a boundary where viscous effects are important.

Rigorous force field optimization principles based on statistical distance minimization

Energy Technology Data Exchange (ETDEWEB)

Vlcek, Lukas, E-mail: vlcekl1@ornl.gov [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States); Joint Institute for Computational Sciences, University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173 (United States); Chialvo, Ariel A. [Chemical Sciences Division, Geochemistry & Interfacial Sciences Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110 (United States)

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.

Atomic insight into tribochemical wear mechanism of silicon at the Si/SiO{sub 2} interface in aqueous environment: Molecular dynamics simulations using ReaxFF reactive force field

Energy Technology Data Exchange (ETDEWEB)

Wen, Jialin; Ma, Tianbao [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Zhang, Weiwei; Psofogiannakis, George; Duin, Adri C.T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, PA 16802 (United States); Chen, Lei; Qian, Linmao [Tribology Research Institute, Key Laboratory of Advanced Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031 (China); Hu, Yuanzhong [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China); Lu, Xinchun, E-mail: xclu@tsinghua.edu.cn [State Key Laboratory of Tribology, Tsinghua University, Beijing 100084 (China)

2016-12-30

Highlights: • New ReaxFF reactive force field was applied to simulate the tribochemical wear process at Si/SiO{sub 2} interface. • Wear of silicon atoms is due to the breaking of Si–O–Si bonds and Si–Si–O–Si bond chains on the Si substrate. • Interfacial bridge bonds play an important role during the tribochemical wear process. • Higher pressures applied to the silica phase can cause more Si atoms to be removed by forming more interfacial bridge bonds. • Water plays an opposing role in the wear process because of its both chemical and mechanical effects. - Abstract: In this work, the atomic mechanism of tribochemical wear of silicon at the Si/SiO{sub 2} interface in aqueous environment was investigated using ReaxFF molecular dynamics (MD) simulations. Two types of Si atom removal pathways were detected in the wear process. The first is caused by the destruction of stretched Si–O–Si bonds on the Si substrate surface and is assisted by the attachment of H atoms on the bridging oxygen atoms of the bonds. The other is caused by the rupture of Si–Si bonds in the stretched Si–Si–O–Si bond chains at the interface. Both pathways effectively remove Si atoms from the silicon surface via interfacial Si–O–Si bridge bonds. Our simulations also demonstrate that higher pressures applied to the silica phase can cause more Si atoms to be removed due to the formation of increased numbers of interfacial Si–O–Si bridge bonds. Besides, water plays a dual role in the wear mechanism, by oxidizing the Si substrate surface as well as by preventing the close contact of the surfaces. This work shows that the removal of Si atoms from the substrate is a result of both chemical reaction and mechanical effects and contributes to the understanding of tribochemical wear behavior in the microelectromechanical systems (MEMS) and Si chemical mechanical polishing (CMP) process.

High rate reactive sputtering in an opposed cathode closed-field unbalanced magnetron sputtering system

Science.gov (United States)

Sproul, William D.; Rudnik, Paul J.; Graham, Michael E.; Rohde, Suzanne L.

1990-01-01

Attention is given to an opposed cathode sputtering system constructed with the ability to coat parts with a size up to 15 cm in diameter and 30 cm in length. Initial trials with this system revealed very low substrate bias currents. When the AlNiCo magnets in the two opposed cathodes were arranged in a mirrored configuration, the plasma density at the substrate was low, and the substrate bias current density was less than 1 mA/sq cm. If the magnets were arranged in a closed-field configuration where the field lines from one set of magnets were coupled with the other set, the substrate bias current density was as high as 5.7 mA/sq cm when NdFeB magnets were used. In the closed-field configuration, the substrate bias current density was related to the magnetic field strength between the two cathodes and to the sputtering pressure. Hard well-adhered TiN coatings were reactively sputtered in the opposed cathode system in the closed-field configuration, but the mirrored configuration produced films with poor adhesion because of etching problems and low plasma density at the substrate.

Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

International Nuclear Information System (INIS)

Abdoli, A; Mirzaee, I; Purmahmod, N; Anvari, A

2008-01-01

Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s -1 at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A b and D c , have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications

Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

Science.gov (United States)

Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke

2015-06-25

Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

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

Science.gov (United States)

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

2013-03-21

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

Calculation of magnetic field and electromagnetic forces in MHD superconducting magnets

International Nuclear Information System (INIS)

Martinelli, G.; Morini, A.; Moisio, M.F.

1992-01-01

The realization of a superconducting prototype magnet for MHD energy conversion is under development in Italy. Electromechanical industries and University research groups are involved in the project. The paper deals with analytical methods developed at the Department of Electrical Engineering of Padova University for calculating magnetic field and electromagnetic forces in MHD superconducting magnets and utilized in the preliminary design of the prototype

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

Science.gov (United States)

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

Small strain multiphase-field model accounting for configurational forces and mechanical jump conditions

Science.gov (United States)

Schneider, Daniel; Schoof, Ephraim; Tschukin, Oleg; Reiter, Andreas; Herrmann, Christoph; Schwab, Felix; Selzer, Michael; Nestler, Britta

2018-03-01

Computational models based on the phase-field method have become an essential tool in material science and physics in order to investigate materials with complex microstructures. The models typically operate on a mesoscopic length scale resolving structural changes of the material and provide valuable information about the evolution of microstructures and mechanical property relations. For many interesting and important phenomena, such as martensitic phase transformation, mechanical driving forces play an important role in the evolution of microstructures. In order to investigate such physical processes, an accurate calculation of the stresses and the strain energy in the transition region is indispensable. We recall a multiphase-field elasticity model based on the force balance and the Hadamard jump condition at the interface. We show the quantitative characteristics of the model by comparing the stresses, strains and configurational forces with theoretical predictions in two-phase cases and with results from sharp interface calculations in a multiphase case. As an application, we choose the martensitic phase transformation process in multigrain systems and demonstrate the influence of the local homogenization scheme within the transition regions on the resulting microstructures.

Tuning the Mass of Chameleon Fields in Casimir Force Experiments

CERN Document Server

Brax, Ph; Davis, A C; Shaw, D J; Iannuzzi, D

2010-01-01

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.

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

Science.gov (United States)

Lee, M.W.; Meuwly, M.

2013-01-01

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

Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

Science.gov (United States)

Lee, Kuo Hao; Chen, Jianhan

2017-06-15

Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations.

Science.gov (United States)

Watts, Charles R; Gregory, Andrew; Frisbie, Cole; Lovas, Sándor

2018-03-01

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different. © 2017 Wiley Periodicals, Inc.

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

Energy Technology Data Exchange (ETDEWEB)

Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

2014-04-07

We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

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

Science.gov (United States)

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

2015-10-01

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

Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

International Nuclear Information System (INIS)

Zhang Longcai; Wang Suyu; Wang Jiasu

2009-01-01

Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

Suppression of guidance force decay of HTS bulk exposed to AC magnetic field perturbation in a maglev vehicle system

Energy Technology Data Exchange (ETDEWEB)

Zhang Longcai, E-mail: zhlcai2000@163.co [College of Air Traffic Management, Civil Aviation Flight University of China, Guanghan, Sichuan 618307 (China); Wang Suyu; Wang Jiasu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)

2009-07-01

Superconducting maglev vehicle was one of the most promising applications of HTS bulks. In such a system, the HTS bulks were always exposed to AC external magnetic field, which was generated by the inhomogeneous surface magnetic field of the NdFeB guideway. In our previous work, it was observed that the guidance force of the YBCO bulk over the NdFdB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In this paper, we adopted a method to suppress the decay by altering the field-cooled height of the bulk. From the experimental results, it was found that the decay rate of the guidance force was smaller at lower field-cooled height. So we could suppress the guidance force decay of HTS bulk exposed to AC external magnetic field perturbation in the maglev vehicle system by reducing the field-cooled height of the bulk. Furthermore, all the experimental results in this paper were explained based on Bean critical-state model.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

DEFF Research Database (Denmark)

Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

2017-01-01

of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base...

The scaled-charge additive force field for amino acid based ionic liquids

DEFF Research Database (Denmark)

Fileti, E. E.; Chaban, V. V.

2014-01-01

Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs...... comprising 1-ethyl-3-methylimidazolium cation and amino acid anions. The anions were obtained via deprotonation of carboxyl group. Specific cation-anion non-covalent interactions were taken into account by computing electrostatic potential for ion pairs. The van der Waals interactions were adopted from...

Determination of the viscous acoustic field for liquid drop positioning/forcing in an acoustic levitation chamber in microgravity

Science.gov (United States)

Lyell, Margaret J.

1992-01-01

The development of acoustic levitation systems has provided a technology with which to undertake droplet studies as well as do containerless processing experiments in a microgravity environment. Acoustic levitation chambers utilize radiation pressure forces to position/manipulate the drop. Oscillations can be induced via frequency modulation of the acoustic wave, with the modulated acoustic radiation vector acting as the driving force. To account for tangential as well as radial forcing, it is necessary that the viscous effects be included in the acoustic field. The method of composite expansions is employed in the determination of the acoustic field with viscous effects.

Calculation of electromagnetic fields and forces in coil systems of arbitrary geometry

International Nuclear Information System (INIS)

Sackett, S.J.

1975-01-01

A computer program, EFFI, is described which calculates the electric and magnetic fields due to an arbitrary spatial distribution of current-carrying circular loops, circular arcs, and straight lines. The electric field is assumed to arise solely from the time variation of the magnetic field, and the magnetic field due to the changing electric field is assumed to be negligible. In addition, the conductor bundle elements (loops, arcs, lines) are assumed to be absent. Electric and magnetic flux lines and magnetic forces and inductances are also calculated by the program. The algorithm used in the code, which is based on a combination of direct and numerical integration using the Biot-Savart law, is discussed. The methods used to maintain accuracy in calculating fields within the conductor bundle, in particular, are detailed. Several examples are then presented to illustrate the input and output features as well as the accuracy obtained and the running time required

Simulation of body force field effects on airfoil separation control and optimization of plasma actuator

Energy Technology Data Exchange (ETDEWEB)

Abdoli, A; Mirzaee, I; Purmahmod, N [Faculty of Engineering, Urmia University, Urmia (Iran, Islamic Republic of); Anvari, A [Department of Physics, Sharif University of Technology, Tehran (Iran, Islamic Republic of)], E-mail: ab.abdoli@gmail.com

2008-09-07

Among all active flow control methods, EHD, MHD and EMHD are the only methods which operate on the basis of body force induction on flow field. The EHD plasma actuator is the proper method which has been used in various flow control applications recently. In this paper, the effects of different body force fields on different domains have been studied for separation control on NACA 0021 and the results have been discussed. The airflow velocity has been assumed to be 35 m s{sup -1} at a post-stall angle of attack of 23 deg. Three different domains have been used around the airfoil to investigate body forces with different strengths and directions and those which give the best result in separation control have been obtained for each domain. It has been shown that the results could be used for optimizing the plasma actuator by manipulating its electrode configuration. Two non-dimensional numbers, A{sub b} and D{sub c}, have been obtained and validated by different applied body forces. These numbers have been defined for plasma actuators to show their efficiency in different applications.

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

Science.gov (United States)

Veto, B.

2011-01-01

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

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

Science.gov (United States)

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

2014-12-01

The goal of this research is to clarify the mechanism by which unsteady forces are generated during sculling by a skilled swimmer and thereby to contribute to improving propulsive techniques. We used particle image velocimetry (PIV) to acquire data on the kinematics of the hand during sculling, such as fluid forces and flow field. By investigating the correlations between these data, we expected to find a new propulsion mechanism. The experiment was performed in a flow-controlled water channel. The participant executed sculling motions to remain at a fixed position despite constant water flow. PIV was used to visualize the flow-field cross-section in the plane of hand motion. Moreover, the fluid forces acting on the hand were estimated from pressure distribution measurements performed on the hand and simultaneous three-dimensional motion analysis. By executing the sculling motion, a skilled swimmer produces large unsteady fluid forces when the leading-edge vortex occurs on the dorsal side of the hand and wake capture occurs on the palm side. By using a new approach, we observed interesting unsteady fluid phenomena similar to those of flying insects. The study indicates that it is essential for swimmers to fully exploit vortices. A better understanding of these phenomena might lead to an improvement in sculling techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

Xu, Dong; Zhang, Yang

2012-07-01

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

Zero mass field quantization and Kibble's long-range force criterion for the Goldstone theorem

International Nuclear Information System (INIS)

Wright, S.H.

1981-01-01

The central theme of the dissertation is an investigation of the long-range force criterion used by Kibble in his discussion of the Goldstone Theorem. This investigation is broken up into the following sections: I. Introduction. Spontaneous symmetry breaking, the Goldstone Theorem and the conditions under which it holds are discussed. II. Massless Wave Expansions. In order to make explicit calculations of the operator commutators used in applying Kibble's criterion, it is necessary to work out the operator expansions for a massless field. Unusual results are obtained which include operators corresponding to classical macroscopic field modes. III. The Kibble Criterion for Simple Models Exhibiting Spontaneously Broken Symmetries. The results of the previous section are applied to simple models with spontaneously broken symmetries, namely, the real scalar massless field and the Goldstone model without gauge coupling. IV. The Higgs Mechanism in Classical Field Theory. It is shown that the Higgs Mechanism has a simple interpretation in terms of classical field theory, namely, that it arises from a derivative coupling term between the Goldstone fields and the gauge fields. V. The Higgs Mechanism and Kibble's Criterion. This section draws together the material discussed in sections II to IV. Explicit calculations are made to evaluate Kibble's criterion on a Goldstone-Higgs type of model in the Coulomb gauge. It is found, as expected, that the criterion is not met, but not for reasons relating to the range of the mediating force. By referring to the findings of sections III and IV, it is concluded that the common denominator underlying both the Higgs Mechanism and the failure of Kibble's criterion is a structural aspect of the field equations: derivative coupling between fields

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

Science.gov (United States)

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

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

A. V. Sulimov

2017-01-01

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

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

Science.gov (United States)

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

2017-01-01

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

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

Science.gov (United States)

Schein, Perry; Ashcroft, Colby K; O'Dell, Dakota; Adam, Ian S; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David

2015-08-15

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

Resonance oscillations of nonreciprocal long-range van der Waals forces between atoms in electromagnetic fields

Science.gov (United States)

Sherkunov, Yury

2018-03-01

We study theoretically the van der Waals interaction between two atoms out of equilibrium with an isotropic electromagnetic field. We demonstrate that at large interatomic separations, the van der Waals forces are resonant, spatially oscillating, and nonreciprocal due to resonance absorption and emission of virtual photons. We suggest that the van der Waals forces can be controlled and manipulated by tuning the spectrum of artificially created random light.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

Science.gov (United States)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Moessbauer study of the fast magnetization reversal forced in permalloy and invar by an external rf magnetic field

International Nuclear Information System (INIS)

Kopcewicz, M.

1978-01-01

The effect of fast magnetization reversal leading to fast relaxation of the hyperfine field (collapse effect) forced by an external rf magnetic field is studied using the Moessbauer technique for permalloy and invar. The rf collapse and sideband effects are investigated as a function of external rf field, frequency, and intensity. The collapse of the hfs spectrum through unresolved hfs spectrum, triangular shape to a single line, as well as the formation of sidebands is observed. The rf collapse effect is attributed to the rf forced uniform rotation of internal magnetization which causes fast magnetization reversal leading to fast relaxation of the hyperfine field as a result of which the average field at the Moessbauer nuclei is reduced to zero. The difference of the magnetization reversal process in permalloy and invar are discussed. It is shown that the origin of collapse and sideband effects is totaly different: the collapse effect being of purely magnetic origin while the formation of sidebands is due to the rf induced mechanical vibrations of iron atoms within the sample. It is possible to damp sidebands without affecting the collapse effect. The results obtained show that the application of the rf field to ferromagnetic materials gives a unique possibility to force, simulate, and control the relaxation effects in ferromagnetic materials. (author)

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

Science.gov (United States)

Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

2012-01-10

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

Projection and nested force-gradient methods for quantum field theories

Energy Technology Data Exchange (ETDEWEB)

Shcherbakov, Dmitry

2017-07-26

For the Hybrid Monte Carlo algorithm (HMC), often used to study the fundamental quantum field theory of quarks and gluons, quantum chromodynamics (QCD), on the lattice, one is interested in efficient numerical time integration schemes which preserve geometric properties of the flow and are optimal in terms of computational costs per trajectory for a given acceptance rate. High order numerical methods allow the use of larger step sizes, but demand a larger computational effort per step; low order schemes do not require such large computational costs per step, but need more steps per trajectory. So there is a need to balance these opposing effects. In this work we introduce novel geometric numerical time integrators, namely, projection and nested force-gradient methods in order to improve the efficiency of the HMC algorithm in application to the problems of quantum field theories.

Methodology for Design and Analysis of Reactive Distillation Involving Multielement Systems

DEFF Research Database (Denmark)

Jantharasuk, Amnart; Gani, Rafiqul; Górak, Andrzej

2011-01-01

A new methodology for design and analysis of reactive distillation has been developed. In this work, the elementbased approach, coupled with a driving force diagram, has been extended and applied to the design of a reactive distillation column involving multielement (multicomponent) systems...... consisting of two components. Based on this methodology, an optimal design configuration is identified using the equivalent binary-element-driving force diagram. Two case studies of methyl acetate (MeOAc) synthesis and methyl-tert-butyl ether (MTBE) synthesis have been considered to demonstrate...... the successful applications of the methodology. Moreover, energy requirements for various column configurations corresponding to different feed locatio...

High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

Energy Technology Data Exchange (ETDEWEB)

Tian, Ye [Sanford-Burnham-Prebys Medical Discovery Institute (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham-Prebys Medical Discovery Institute (United States)

2017-01-15

Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

Air Force Officer Accession Planning: Addressing Key Gaps in Meeting Career Field Academic Degree Requirements for Nonrated Officers

Science.gov (United States)

2016-06-09

C O R P O R A T I O N Research Report Air Force Officer Accession Planning Addressing Key Gaps in Meeting Career Field Academic Degree Requirements...potential performance, and how to include these quality measures in the classification process. The research sponsor asked us to focus on academic ...Andrew P., and James K. Lowe, “Decision Support for the Career Field Selection Process at the US Air Force Academy,” European Journal of Operational

Contributions of primary and secondary biogenic VOC tototal OH reactivity during the CABINEX (Community Atmosphere-Biosphere INteractions Experiments-09 field campaign

Directory of Open Access Journals (Sweden)

S. Kim

2011-08-01

Full Text Available We present OH reactivity measurements using the comparative reactivity method with a branch enclosure technique for four different tree species (red oak, white pine, beech and red maple in the UMBS PROPHET tower footprint during the Community Atmosphere Biosphere INteraction EXperiment (CABINEX field campaign in July of 2009. Proton Transfer Reaction-Mass Spectrometry (PTR-MS was sequentially used as a detector for OH reactivity and BVOC concentrations including isoprene and monoterpenes (MT for enclosure air. Therefore, the measurement dataset contains both measured and calculated OH reactivity from well-known BVOC. The results indicate that isoprene and MT, and in one case a sesquiterpene, can account for the measured OH reactivity. Significant discrepancy between measured OH reactivity and calculated OH reactivity from isoprene and MT is found for the red maple enclosure dataset but it can be reconciled by adding reactivity from emission of a sesquiterpene, α-farnesene, detected by GC-MS. This leads us to conclude that no significant unknown BVOC emission contributed to ambient OH reactivity from these trees at least during the study period. However, this conclusion should be followed up by more comprehensive side-by-side intercomparison between measured and calculated OH reactivity and laboratory experiments with controlled temperature and light environments to verify effects of those essential parameters towards unknown/unmeasured reactive BVOC emissions. This conclusion leads us to explore the contribution towards ambient OH reactivity (the dominant OH sink in this ecosystem oxidation products such as hydroxyacetone, glyoxal, methylglyoxal and C4 and C5-hydroxycarbonyl using recently published isoprene oxidation mechanisms (Mainz Isoprene Mechanism II and Leuven Isoprene Mechanism. Evaluation of conventionally unmeasured first generation oxidation products of isoprene and their possible contribution to ambient missing OH reactivity

Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors.

Science.gov (United States)

Sundar, Vikram; Gelbwaser-Klimovsky, David; Aspuru-Guzik, Alán

2018-04-05

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Magnetic Field Equivalent Current Analysis-Based Radial Force Control for Bearingless Permanent Magnet Synchronous Motors

Directory of Open Access Journals (Sweden)

Huangqiu Zhu

2015-05-01

Full Text Available Bearingless permanent magnet synchronous motors (BPMSMs, with all advantages of permanent magnet motors (PMSMs and magnetic bearings, have become an important research direction in the bearingless motor field. To realize a stable suspension for the BPMSM, accurate decoupling control between the electromagnetic torque and radial suspension force is indispensable. In this paper, a concise and reliable analysis method based on a magnetic field equivalent current is presented. By this analysis method, the operation principle is analyzed theoretically, and the necessary conditions to produce a stable radial suspension force are confirmed. In addition, mathematical models of the torque and radial suspension force are established which is verified by the finite element analysis (FEA software ANSYS. Finally, an experimental prototype of a 2-4 poles surface-mounted BPMSM is tested with the customized control strategy. The simulation and experimental results have shown that the motor has good rotation and suspension performance, and validated the accuracy of the proposed analysis method and the feasibility of the control strategy.

Compatibility of the Chameleon-Field Model with Fifth-Force Experiments, Cosmology, and PVLAS and CAST Results

International Nuclear Information System (INIS)

Brax, Philippe; Bruck, Carsten van de; Davis, Anne-Christine

2007-01-01

We analyze the PVLAS results using a chameleon field whose properties depend on the environment. We find that, assuming a runaway bare potential V(φ) and a universal coupling to matter, the chameleon potential is such that the scalar field can act as dark energy. Moreover, the chameleon-field model is compatible with the CERN Axion Solar Telescope results, fifth-force experiments, and cosmology

Influence of AC external magnetic field perturbation on the guidance force of HTS bulk over a NdFeB guideway

International Nuclear Information System (INIS)

Zhang Longcai; Wang Jiasu; Wang Suyu; He Qingyong

2007-01-01

Superconducting maglev vehicle system requires that the surface magnetic field of the guideway is uniform along the forward direction. But in practice the surface magnetic field of the NdFeB permanent magnet guideway is not always immutable. So the HTS bulks in this case are exposed to AC external magnetic field, which may induce the energy loss in the bulk and influence the guidance force between the HTS bulks and the NdFeB guideway. In this paper, we experimentally studied the influence of the AC external magnetic field perturbation on the guidance force of a HTS bulk over the NdFeB guideway. The experimental results showed that the guidance force was influenced by the application of the AC external magnetic. The guidance fore hysteresis became more evident with the amplitude of the AC field and was independent of the frequency in the range 90-400 Hz. We attributed the reason to magnetic hysteresis loss in the superconductor

Influence of AC external magnetic field perturbation on the guidance force of HTS bulk over a NdFeB guideway

Energy Technology Data Exchange (ETDEWEB)

Zhang Longcai [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)]. E-mail: zhlcai2000@163.com; Wang Jiasu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China); Wang Suyu [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China); He Qingyong [Applied Superconductivity Laboratory, Southwest Jiaotong University, P.O. Box 152, Chengdu, Sichuan 610031 (China)

2007-08-01

Superconducting maglev vehicle system requires that the surface magnetic field of the guideway is uniform along the forward direction. But in practice the surface magnetic field of the NdFeB permanent magnet guideway is not always immutable. So the HTS bulks in this case are exposed to AC external magnetic field, which may induce the energy loss in the bulk and influence the guidance force between the HTS bulks and the NdFeB guideway. In this paper, we experimentally studied the influence of the AC external magnetic field perturbation on the guidance force of a HTS bulk over the NdFeB guideway. The experimental results showed that the guidance force was influenced by the application of the AC external magnetic. The guidance fore hysteresis became more evident with the amplitude of the AC field and was independent of the frequency in the range 90-400 Hz. We attributed the reason to magnetic hysteresis loss in the superconductor.

AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms.

Science.gov (United States)

Wu, Xiaojing; Clavaguera, Carine; Lagardère, Louis; Piquemal, Jean-Philip; de la Lande, Aurélien

2018-04-16

We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H 2 O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.

The reactivity of natural phenols

Energy Technology Data Exchange (ETDEWEB)

Denisov, Evgenii T; Denisova, Taisa G [Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)

2009-11-30

This review surveys physicochemical data of natural phenols published in recent years. The structures of some compounds of this class are given. A complete set of the dissociation energies of the O-H bonds for 71 natural phenols is presented. Kinetic characteristics of the reactions of peroxyl, alkyl and thiyl radicals with natural phenols, exchange reactions of phenoxyl radicals with phenols and reactions of phenoxyl radicals with lipids, hydroperoxides, cysteine and ascorbic acid are compiled and described systematically. The reactivity of phenols in radical reactions and the factors that determine the reactivity (the enthalpy of reaction, triplet repulsion, the electronegativities of atoms at the reaction centre, the presence of pi-electrons adjacent to the reaction centre, the radii of atoms at the reaction centre, steric hindrance, the force constants of the reacting bonds) are discussed. An important role of hydrogen bonding between surrounding molecules and the OH groups of natural phenols in decreasing their reactivities is noted.

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

Energy Technology Data Exchange (ETDEWEB)

Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2015-02-10

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

Active and reactive behaviour in human mobility: the influence of attraction points on pedestrians

Science.gov (United States)

Gutiérrez-Roig, M.; Sagarra, O.; Oltra, A.; Palmer, J. R. B.; Bartumeus, F.; Díaz-Guilera, A.; Perelló, J.

2016-07-01

Human mobility is becoming an accessible field of study, thanks to the progress and availability of tracking technologies as a common feature of smart phones. We describe an example of a scalable experiment exploiting these circumstances at a public, outdoor fair in Barcelona (Spain). Participants were tracked while wandering through an open space with activity stands attracting their attention. We develop a general modelling framework based on Langevin dynamics, which allows us to test the influence of two distinct types of ingredients on mobility: reactive or context-dependent factors, modelled by means of a force field generated by attraction points in a given spatial configuration and active or inherent factors, modelled from intrinsic movement patterns of the subjects. The additive and constructive framework model accounts for some observed features. Starting with the simplest model (purely random walkers) as a reference, we progressively introduce different ingredients such as persistence, memory and perceptual landscape, aiming to untangle active and reactive contributions and quantify their respective relevance. The proposed approach may help in anticipating the spatial distribution of citizens in alternative scenarios and in improving the design of public events based on a facts-based approach.

Active and reactive behaviour in human mobility: the influence of attraction points on pedestrians.

Science.gov (United States)

Gutiérrez-Roig, M; Sagarra, O; Oltra, A; Palmer, J R B; Bartumeus, F; Díaz-Guilera, A; Perelló, J

2016-07-01

Human mobility is becoming an accessible field of study, thanks to the progress and availability of tracking technologies as a common feature of smart phones. We describe an example of a scalable experiment exploiting these circumstances at a public, outdoor fair in Barcelona (Spain). Participants were tracked while wandering through an open space with activity stands attracting their attention. We develop a general modelling framework based on Langevin dynamics, which allows us to test the influence of two distinct types of ingredients on mobility: reactive or context-dependent factors, modelled by means of a force field generated by attraction points in a given spatial configuration and active or inherent factors, modelled from intrinsic movement patterns of the subjects. The additive and constructive framework model accounts for some observed features. Starting with the simplest model (purely random walkers) as a reference, we progressively introduce different ingredients such as persistence, memory and perceptual landscape, aiming to untangle active and reactive contributions and quantify their respective relevance. The proposed approach may help in anticipating the spatial distribution of citizens in alternative scenarios and in improving the design of public events based on a facts-based approach.

An automated analysis workflow for optimization of force-field parameters using neutron scattering data

Energy Technology Data Exchange (ETDEWEB)

Lynch, Vickie E.; Borreguero, Jose M. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Bhowmik, Debsindhu [Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Ganesh, Panchapakesan; Sumpter, Bobby G. [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Proffen, Thomas E. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Goswami, Monojoy, E-mail: goswamim@ornl.gov [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)

2017-07-01

Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.

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

Science.gov (United States)

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

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

Reactive solute transport in physically and chemically heterogeneous porous media with multimodal reactive mineral facies: the Lagrangian approach.

Science.gov (United States)

Soltanian, Mohamad Reza; Ritzi, Robert W; Dai, Zhenxue; Huang, Chao Cheng

2015-03-01

Physical and chemical heterogeneities have a large impact on reactive transport in porous media. Examples of heterogeneous attributes affecting reactive mass transport are the hydraulic conductivity (K), and the equilibrium sorption distribution coefficient (Kd). This paper uses the Deng et al. (2013) conceptual model for multimodal reactive mineral facies and a Lagrangian-based stochastic theory in order to analyze the reactive solute dispersion in three-dimensional anisotropic heterogeneous porous media with hierarchical organization of reactive minerals. An example based on real field data is used to illustrate the time evolution trends of reactive solute dispersion. The results show that the correlation between the hydraulic conductivity and the equilibrium sorption distribution coefficient does have a significant effect on reactive solute dispersion. The anisotropy ratio does not have a significant effect on reactive solute dispersion. Furthermore, through a sensitivity analysis we investigate the impact of changing the mean, variance, and integral scale of K and Kd on reactive solute dispersion. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Are current atomistic force fields accurate enough to study proteins in crowded environments?

Directory of Open Access Journals (Sweden)

Drazen Petrov

2014-05-01

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

Crystal structure prediction of flexible molecules using parallel genetic algorithms with a standard force field.

Science.gov (United States)

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

2009-10-01

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling crystal structures using a distributed parallel genetic algorithm and local energy minimization of the structures followed by the classifying, sorting, and archiving of the most relevant structures. Our results indicate that the method can consistently find the experimentally known crystal structures of flexible molecules, but the number of missing structures and poor ranking observed in some crystals show the need for further improvement of the potential. Copyright 2009 Wiley Periodicals, Inc.

On the Shape of Force-Free Field Lines in the Solar Corona

KAUST Repository

Prior, C.

2012-02-02

This paper studies the shape parameters of looped field lines in a linear force-free magnetic field. Loop structures with a sufficient amount of kinking are generally seen to form S or inverse S (Z) shapes in the corona (as viewed in projection). For a single field line, we can ask how much the field line is kinked (as measured by the writhe), and how much neighbouring flux twists about the line (as measured by the twist number). The magnetic helicity of a flux element surrounding the field line can be decomposed into these two quantities. We find that the twist helicity contribution dominates the writhe helicity contribution, for field lines of significant aspect ratio, even when their structure is highly kinked. These calculations shed light on some popular assumptions of the field. First, we show that the writhe of field lines of significant aspect ratio (the apex height divided by the footpoint width) can sometimes be of opposite sign to the helicity. Secondly, we demonstrate the possibility of field line structures which could be interpreted as Z-shaped, but which have a helicity value sign expected of an S-shaped structure. These results suggest that caution should be exercised in using two-dimensional images to draw conclusions on the helicity value of field lines and flux tubes. © 2012 Springer Science+Business Media B.V.

Simulation of a force on force exercise

International Nuclear Information System (INIS)

Terhune, R.; Van Slyke, D.; Sheppard, T.; Brandrup, M.

1988-01-01

The Security Exercise Evaluation System (SEES) is under development for use in planning Force on Force exercises and as an aid in post-exercise evaluation. This study is part of the development cycle where the simulation results are compared to field data to provide guidance for further development of the model. SEES is an event-driven stochastic computer program simulating individual movement and combat within an urban terrain environment. The simulator models the physics of movement, line of sight, and weapon effects. It relies on the controllers to provide all knowledge of security tactics, which are entered by the controllers during the simulation using interactive color graphic workstations. They are able to develop, modify and implement plans promptly as the simulator maintains real time. This paper reports on how SEES will be used to develop an intrusion plan, test the security response tactics and develop observer logistics. A Force on Force field exercise will then be executed to follow the plan with observations recorded. An analysis is made by first comparing the plan and events of the simulation with the field exercise, modifying the simulation plan to match the actual field exercise, and then running the simulation to develop a distribution of possible outcomes

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

Energy Technology Data Exchange (ETDEWEB)

MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

2015-12-28

The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

Dispersion Forces

CERN Document Server

Buhmann, Stefan Yoshi

2012-01-01

In this book, a modern unified theory of dispersion forces on atoms and bodies is presented which covers a broad range of advanced aspects and scenarios. Macroscopic quantum electrodynamics is shown to provide a powerful framework for dispersion forces which allows for discussing general properties like their non-additivity and the relation between microscopic and macroscopic interactions. It is demonstrated how the general results can be used to obtain dispersion forces on atoms in the presence of bodies of various shapes and materials. Starting with a brief recapitulation of volume I, this volume II deals especially with bodies of irregular shapes, universal scaling laws, dynamical forces on excited atoms, enhanced forces in cavity quantum electrodynamics, non-equilibrium forces in thermal environments and quantum friction. The book gives both the specialist and those new to the field a thorough overview over recent results in the field. It provides a toolbox for studying dispersion forces in various contex...

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

Directory of Open Access Journals (Sweden)

Jesús Sanz Maudes

2012-08-01

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

Reactivating dynamics for the susceptible-infected-susceptible model: a simple method to simulate the absorbing phase

Science.gov (United States)

Macedo-Filho, A.; Alves, G. A.; Costa Filho, R. N.; Alves, T. F. A.

2018-04-01

We investigated the susceptible-infected-susceptible model on a square lattice in the presence of a conjugated field based on recently proposed reactivating dynamics. Reactivating dynamics consists of reactivating the infection by adding one infected site, chosen randomly when the infection dies out, avoiding the dynamics being trapped in the absorbing state. We show that the reactivating dynamics can be interpreted as the usual dynamics performed in the presence of an effective conjugated field, named the reactivating field. The reactivating field scales as the inverse of the lattice number of vertices n, which vanishes at the thermodynamic limit and does not affect any scaling properties including ones related to the conjugated field.

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

International Nuclear Information System (INIS)

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

2011-01-01

This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and 19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

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

Science.gov (United States)

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

2011-01-01

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

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

Science.gov (United States)

Giulianotti, Richard; Robertson, Roland

2012-06-01

This paper provides a sociological model of the key transnational political and economic forces that are shaping the 'global football field'. The model draws upon, and significantly extends, the theory of the 'global field' developed previously by Robertson. The model features four quadrants, each of which contains a dominant operating principle, an 'elemental reference point', and an 'elemental theme'. The quadrants contain, first, neo-liberalism, associated with the individual and elite football clubs; second, neo-mercantilism, associated with nation-states and national football systems; third, international relations, associated with international governing bodies; and fourth, global civil society, associated with diverse institutions that pursue human development and/or social justice. We examine some of the interactions and tensions between the major institutional and ideological forces across the four quadrants. We conclude by examining how the weakest quadrant, featuring global civil society, may gain greater prominence within football. In broad terms, we argue that our four-fold model may be utilized to map and to examine other substantive research fields with reference to globalization. © London School of Economics and Political Science 2012.

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

Energy Technology Data Exchange (ETDEWEB)

Kawashima, K.

1976-01-01

The equations for calculating the acoustic field produced within a nonmagnetic metal by interaction of eddy currents with a static magnetic field were obtained on the assumptions (1) an ultrasonic wave is generated by the electromagentic force through classical and macroscopic phenomena; (2) the electric, magnetic, and elastic properties of the metal are linear, isotropic, and homogeneous throughout the metal, which occupies semi-infinite space; (3) the whole system is axially symmetric; and (4) eddy currents and elastic waves show a steady-state sinusoidal variation. The acoustic field produced by a specific electromagnetic ultrasonic transducer with axial symmetry was calculated numerically, and the results showed a well-defined ultrasonic wave beam, which was narrower than had been expected from the size of the transducer. (auth)

Influence of Complete Coriolis Force on the Dispersion Relation of Ocean Internal-wave in a Background Currents Field

Directory of Open Access Journals (Sweden)

Liu Yongjun

2015-01-01

Full Text Available In this thesis, the influence of complete Coriolis force (the model includes both the vertical and horizontal components of Coriolis force on the dispersion relation of ocean internal-wave under background currents field are studied, it is important to the study of ocean internal waves in density-stratified ocean. We start from the control equation of sea water movement in the background of the non-traditional approximation, and the vertical velocity solution is derived where buoyancy frequency N(z gradually varies with the ocean depth z. The results show that the influence of complete Coriolis force on the dispersion relation of ocean internal-wave under background currents field is obvious, and these results provide strong evidence for the understanding of dynamic process of density stratified ocean internal waves.

Atomic force and scanning near-field optical microscopy study of carbocyanine dye J-aggregates

Czech Academy of Sciences Publication Activity Database

Prokhorov, V.V.; Petrova, M.G.; Kovaleva, Natalia; Demikhov, E.I.

2014-01-01

Roč. 10, č. 5 (2014), s. 700-704 ISSN 1573-4137 Institutional support: RVO:68378271 Keywords : carbocyanine dye * elementary fibri * high-resolution atomic force microscopy * J-aggregate * probe microscopy * scanning near-field optical microscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.096, year: 2014

Investigations of Reactive Carbohydrates in Glycosidic Bond Formation and Degradation

DEFF Research Database (Denmark)

Heuckendorff, Mads

The overall objective of the research described in this thesis was to explore the field of glycosidic bond formation and degradation. In more detail, the objective was to do further research in the field of highly reactive glycosyl donors. New ways of making highly reactive donors were explored...

Reactive transport model and apparent Kd of Ni in the near field of a HLW repository in granite

Science.gov (United States)

Lu, Chuanhe; Samper, Javier; Luis Cormenzana, José; Ma, Hongyun; Montenegro, Luis; Ángel Cuñado, Miguel

2012-12-01

Current performance assessment models for radionuclide migration through the near field of high-level radioactive waste repositories often rely on the assumption of a constant Kd for sorption. The validity of such assumption is evaluated here with a reactive transport model for Ni2+ in the near field of a repository in granite. Model results show that Ni2+ sorbs mainly by surface complexation on weak sorption sites. The apparent Kd of Ni2+, Kda, depends on the concentration of dissolved Ni and pH and is constant only when the concentration of dissolved Ni is smaller than 10-6 mol/L. The results of the sensitivity runs show that Kda is sensitive to the water flux at the bentonite-granite interface, the effective diffusion of the bentonite and the concentration of weak sorption sites of the bentonite. The competition of other nuclides such as Cs+ on Ni2+ sorption is not important. Corrosion products, however, affect significantly the sorption of Ni2+ on the bentonite. The model with a constant Kd does not reproduce the release rates of Ni2+ from the bentonite into the granite. A model with a variable Kd which depends on the concentration of dissolved Ni2+ and pH may provide an acceptable surrogate of the multicomponent reactive transport model for the conditions of the repository considered in our model. Simulations using the Kd-approach were performed with GoldSim based on the interpolation in the pH and concentration table, while the reactive transport model simulations were performed with CORE2D which incorporates multisite surface complexation.

Construction of an accurate quartic force field by using generalised least-squares fitting and experimental design

International Nuclear Information System (INIS)

Carbonniere, Philippe; Begue, Didier; Dargelos, Alain; Pouchan, Claude

2004-01-01

In this work we present an attractive least-squares fitting procedure which allows for the calculation of a quartic force field by jointly using energy, gradient, and Hessian data, obtained from electronic wave function calculations on a suitably chosen grid of points. We use the experimental design to select the grid points: a 'simplex-sum' of Box and Behnken grid was chosen for its efficiency and accuracy. We illustrate the numerical implementations of the method by using the energy and gradient data for H 2 O and H 2 CO. The B3LYP/cc-pVTZ quartic force field performed from 11 and 44 simplex-sum configurations shows excellent agreement in comparison to the classical 44 and 168 energy calculations

Force-free fields in the vicinity of a Reissner-Nordstroem black hole

International Nuclear Information System (INIS)

Evangelidis, E.

1978-01-01

The behaviour of a force-free field has been studied in a Reissner-Nordstroem metric. An expansion in tensor harmonics of even-odd parity reduced the radial equations in a differential equation of the Sturm-Liouville system which was solved asymptotically in a conveniently defined space coordinate. Further, it has been possible to regularize the singular behaviour of the Reissner-Nordstroem metric at the event horizon and the modified metric to be given explicitly. (Auth.)

Chemical stability and in chemico reactivity of 24 fragrance ingredients of concern for skin sensitization risk assessment.

Science.gov (United States)

Avonto, Cristina; Wang, Mei; Chittiboyina, Amar G; Vukmanovic, Stanislav; Khan, Ikhlas A

2018-02-01

Twenty-four pure fragrance ingredients have been identified as potential concern for skin sensitization. Several of these compounds are chemically unstable and convert into reactive species upon exposure to air or light. In the present work, a systematic investigation of the correlation between chemical stability and reactivity has been undertaken. The compounds were subjected to forced photodegradation for three months and the chemical changes were studied with GC-MS. At the end of the stability study, two-thirds of the samples were found to be unstable. The generation of chemically reactive species was investigated using the in chemico HTS-DCYA assay. Eleven and fourteen compounds were chemically reactive before and after three months, respectively. A significant increase in reactivity upon degradation was found for isoeugenol, linalool, limonene, lyral, citronellol and geraniol; in the same conditions, the reactivity of hydroxycitronellal decreased. The non-reactive compounds α-isomethyl ionone, benzyl alcohol, amyl cinnamal and farnesol became reactive after photo-oxidative degradation. Overall, forced degradation resulted in four non-reactive fragrance compounds to display in chemico thiol reactivity, while ten out of 24 compounds remained inactive. Chemical degradation does not necessarily occur with generation of reactive species. Non-chemical activation may be involved for the 10 stable unreactive compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interrupted orthodontic force results in less root resorption than continuous force in human premolars as measured by microcomputed tomography.

Science.gov (United States)

Sawicka, Monika; Bedini, Rossella; Wierzbicki, Piotr M; Pameijer, Cornelis H

2014-01-01

Root resorption is an undesirable but very frequently occurring sequel of orthodontic treatment. The aim of this study was to compare root resorption caused by either continuous (CF) or interrupted (IF) orthodontic force. The study was performed on human subjects on 30 first upper and lower premolars scheduled for extraction for orthodontic reasons. During four weeks before extraction 12 teeth were subjected to either CF or IF. The force was generated by a segmental titanium-molybdenum alloy cantilever spring that was activated in buccal direction. Initially a force of 60 CentiNewton was used in both CF and IF groups, the force in the former, however, was reactivated every week for 4 weeks. There was no reactivation of force in the IF group after initial application. A morphometric analysis of root resorption was performed by microcomputed tomography and the extent of tooth movement was measured on stone casts. Furthermore, a Tartarate-Resistant Acidic Phosphatase activity (TRAP), the marker enzyme of osteoclasts and cementoclasts, was determined by histochemical method. The Mann-Whitney U test was used to compare the difference in measured parameters between treatment and control tooth groups. The number of resorption craters was significantly higher and their average volume almost twice as large in the CF compared to the IF group (p root structure as opposed to continuous force while the same tooth movement was achieved.

Electrochemical force microscopy

Energy Technology Data Exchange (ETDEWEB)

Kalinin, Sergei V.; Jesse, Stephen; Collins, Liam F.; Rodriguez, Brian J.

2017-01-10

A system and method for electrochemical force microscopy are provided. The system and method are based on a multidimensional detection scheme that is sensitive to forces experienced by a biased electrode in a solution. The multidimensional approach allows separation of fast processes, such as double layer charging, and charge relaxation, and slow processes, such as diffusion and faradaic reactions, as well as capturing the bias dependence of the response. The time-resolved and bias measurements can also allow probing both linear (small bias range) and non-linear (large bias range) electrochemical regimes and potentially the de-convolution of charge dynamics and diffusion processes from steric effects and electrochemical reactivity.

An electric field in a gravitational field

International Nuclear Information System (INIS)

Harpaz, Amos

2005-01-01

The behaviour of an electric field in a gravitational field is analysed. It is found that due to the mass (energy) of the electric field, it is subjected to gravity and it falls in the gravitational field. This fall curves the electric field, a stress force (a reaction force) is created, and the interaction of this reaction force with the static charge gives rise to the creation of radiation

On the use of quartic force fields in variational calculations

Science.gov (United States)

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.

Baryonic forces and hyperons in nuclear matter from SU(3) chiral effective field theory

Energy Technology Data Exchange (ETDEWEB)

Petschauer, Stefan Karl

2016-02-12

In this work the baryon-baryon interaction is studied at next-to-leading order in SU(3) chiral effective field theory and applied to hyperon-nucleon scattering. The properties of hyperons in isospin-symmetric as well as asymmetric nuclear matter are calculated within the Bruecker-Hartree-Fock formalism. Moreover, the leading three-baryon interaction is derived and its low-energy constants are estimated from decuplet intermediate states. We conclude, that chiral effective field theory is a well-suited tool to describe the baryonic forces.

Recent Progress in Molecular Simulation of Aqueous Electrolytes: Force Fields, Chemical Potentials and Solubility.

Czech Academy of Sciences Publication Activity Database

Nezbeda, Ivo; Moučka, F.; Smith, W.R.

2016-01-01

Roč. 114, č. 11 (2016), s. 1665-1690 ISSN 0026-8976 R&D Projects: GA ČR GA15-19542S Grant - others:NSERC(CA) OGP1041 Institutional support: RVO:67985858 Keywords : force fields * chemical potentials * aqueous electrolytes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.870, year: 2016

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

Science.gov (United States)

Miller, Mark S.; Lay, Wesley K.

2016-01-01

Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide. PMID:27052117

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

International Nuclear Information System (INIS)

Morante, S.; Rossi, G.C.

2017-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)

2017-02-15

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

Feedforward compensation for novel dynamics depends on force field orientation but is similar for the left and right arms.

Science.gov (United States)

Reuter, Eva-Maria; Cunnington, Ross; Mattingley, Jason B; Riek, Stephan; Carroll, Timothy J

2016-11-01

There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153-167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. Copyright © 2016 the American Physiological Society.

Systematic Integrated Process Design and Control of Reactive Distillation Processes Involving Multi-elements

DEFF Research Database (Denmark)

Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

2016-01-01

driving force approach. Next, through analytical, steady-state and closed-loop dynamic analysis it is verified that the control structure, disturbance rejection and energy requirement of the reactive distillation column is better than any other operation point that is not at the maximum driving force...

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

International Nuclear Information System (INIS)

Zhang, X. M.; Zhang, M.; Su, J. T.

2017-01-01

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such as limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.

Reactive oxygen species and fatigue-induced prolonged low-frequency force depression in skeletal muscle fibres of rats, mice and SOD2 overexpressing mice.

Science.gov (United States)

Bruton, Joseph D; Place, Nicolas; Yamada, Takashi; Silva, José P; Andrade, Francisco H; Dahlstedt, Anders J; Zhang, Shi-Jin; Katz, Abram; Larsson, Nils-Göran; Westerblad, Håkan

2008-01-01

Skeletal muscle often shows a delayed force recovery after fatiguing stimulation, especially at low stimulation frequencies. In this study we focus on the role of reactive oxygen species (ROS) in this fatigue-induced prolonged low-frequency force depression. Intact, single muscle fibres were dissected from flexor digitorum brevis (FDB) muscles of rats and wild-type and superoxide dismutase 2 (SOD2) overexpressing mice. Force and myoplasmic free [Ca(2+)] ([Ca(2+)](i)) were measured. Fibres were stimulated at different frequencies before and 30 min after fatigue induced by repeated tetani. The results show a marked force decrease at low stimulation frequencies 30 min after fatiguing stimulation in all fibres. This decrease was associated with reduced tetanic [Ca(2+)](i) in wild-type mouse fibres, whereas rat fibres and mouse SOD2 overexpressing fibres instead displayed a decreased myofibrillar Ca(2+) sensitivity. The SOD activity was approximately 50% lower in wild-type mouse than in rat FDB muscles. Myoplasmic ROS increased during repeated tetanic stimulation in rat fibres but not in wild-type mouse fibres. The decreased Ca(2+) sensitivity in rat fibres could be partially reversed by application of the reducing agent dithiothreitol, whereas the decrease in tetanic [Ca(2+)](i) in wild-type mouse fibres was not affected by dithiothreitol or the antioxidant N-acetylcysteine. In conclusion, we describe two different causes of fatigue-induced prolonged low-frequency force depression, which correlate to differences in SOD activity and ROS metabolism. These findings may have clinical implications since ROS-mediated impairments in myofibrillar function can be counteracted by reductants and antioxidants, whereas changes in SR Ca(2+) handling appear more resistant to interventions.

Reactive dispersive contaminant transport in coastal aquifers: Numerical simulation of a reactive Henry problem

KAUST Repository

Nick, H.M.

2013-02-01

The reactive mixing between seawater and terrestrial water in coastal aquifers influences the water quality of submarine groundwater discharge. While these waters come into contact at the seawater groundwater interface by density driven flow, their chemical components dilute and react through dispersion. A larger interface and wider mixing zone may provide favorable conditions for the natural attenuation of contaminant plumes. It has been claimed that the extent of this mixing is controlled by both, porous media properties and flow conditions. In this study, the interplay between dispersion and reactive processes in coastal aquifers is investigated by means of numerical experiments. Particularly, the impact of dispersion coefficients, the velocity field induced by density driven flow and chemical component reactivities on reactive transport in such aquifers is studied. To do this, a hybrid finite-element finite-volume method and a reactive simulator are coupled, and model accuracy and applicability are assessed. A simple redox reaction is considered to describe the degradation of a contaminant which requires mixing of the contaminated groundwater and the seawater containing the terminal electron acceptor. The resulting degradation is observed for different scenarios considering different magnitudes of dispersion and chemical reactivity. Three reactive transport regimes are found: reaction controlled, reaction-dispersion controlled and dispersion controlled. Computational results suggest that the chemical components\\' reactivity as well as dispersion coefficients play a significant role on controlling reactive mixing zones and extent of contaminant removal in coastal aquifers. Further, our results confirm that the dilution index is a better alternative to the second central spatial moment of a plume to describe the mixing of reactive solutes in coastal aquifers. © 2012 Elsevier B.V.

Influence of grain size and upper critical magnetic field on global pinning force of bronze-processed Nb/sub 3/Sn compound

International Nuclear Information System (INIS)

Ochiai, S.; Osamura, K.

1986-01-01

In order to know the dependency of global pinning force of Nb/sub 3/Sn compound on grain size and upper critical magnetic field, the global pinning force was measured at 3-15 T using bronze-processed multifilamentary composites. The grain size and upper critical magnetic field were varied by two types of annealing treatment: one is the isothermal annealing at 873, 973 and 1073 K up to 1730 ks and another is the two-stage annealing (low temperature annealing to form fine grains at 873 K for 1730 ks + high temperature annealing to raise upper critical magnetic field at 1073 K up to 18 ks). In the case of isothermal annealing treatment, both of grain size and upper critical magnetic field increased with increasing annealing temperature and time except for the annealing treatments at high temperature for prolonged times. In the case of two-stage annealing, both of them increased with second stage annealing time. The increase in grain size led to decrease in the pinning force but the increase in upper critical magnetic field to increase in it. From the analysis of the present data based on the Suenaga's speculation concerning with the density of pinning site and the Kramer's equation, it was suggested that the pinning force is, to a first approximation, proportional to the product of inverse grain size and (1-h)/sup 2/h/sup 1/2/ where h is the reduced magnetic field

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

Energy Technology Data Exchange (ETDEWEB)

Sun, Jiajia [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Shi, Zongqian, E-mail: zqshi@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Jia, Shenli [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an, Shaanxi Province 710049 (China); Zhang, Pengbo [Department of Anesthesiology, Second Affiliated Hospital of Xi’an Jiaotong University School of Medicine, No.157 West 5 Road, Xi’an, Shaanxi Province 710004 (China)

2017-04-01

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

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

Science.gov (United States)

2016-01-01

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

Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes

DEFF Research Database (Denmark)

Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus

2015-01-01

The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical...

Relationships between Isometric Force-Time Characteristics and Dynamic Performance

Directory of Open Access Journals (Sweden)

Thomas Dos’Santos

2017-09-01

Full Text Available The purpose of this study was to explore the relationships between isometric mid-thigh pull (IMTP force-time characteristics (peak force and time-specific force vales (100–250 ms and dynamic performance and compare dynamic performance between stronger and weaker athletes. Forty-three athletes from different sports (rowing, soccer, bicycle motocross, and hockey performed three trials of the squat jump (SJ, countermovement jump (CMJ, and IMTP, and performed a one repetition maximum power clean (PC. Reactive strength index modified (RSImod was also calculated from the CMJ. Statistically significant large correlations between IMTP force-time characteristics and PC (ρ = 0.569–0.674, p < 0.001, and moderate correlations between IMTP force-time characteristics (excluding force at 100 ms and RSImod (ρ = 0.389–0.449, p = 0.013–0.050 were observed. Only force at 250 ms demonstrated a statistically significant moderate correlation with CMJ height (ρ = 0.346, p = 0.016 and no statistically significant associations were observed between IMTP force-time characteristics and SJ height. Stronger athletes (top 10 demonstrated statistically significantly greater CMJ heights, RSImods, and PCs (p ≤ 0.004, g = 1.32–1.89 compared to weaker (bottom 10 athletes, but no differences in SJ height were observed (p = 0.871, g = 0.06. These findings highlight that the ability to apply rapidly high levels of force in short time intervals is integral for PC, CMJ height, and reactive strength.

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer’s peptides

Energy Technology Data Exchange (ETDEWEB)

Tran, Thanh Thuy; Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr; Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

2016-05-28

Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ{sub 16−22} and Aβ{sub 37−42} of the full length Aβ{sub 1−42} Alzheimer’s peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ{sub 16−22} dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ{sub 16−22} and the dimer and trimer of Aβ{sub 37−42}. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ{sub 16−22} decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ{sub 37−42} decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

DEFF Research Database (Denmark)

Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

2004-01-01

of the (gg, gt and tg) rotamers of methyl alpha-D-glucopyranoside and methyl alpha-D-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol. respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error...

Confinement of plasma along shaped open magnetic fields from the centrifugal force of supersonic plasma rotation.

Science.gov (United States)

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

2010-08-20

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

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

Science.gov (United States)

Pavlova, Anna; Parks, Jerry M; Gumbart, James C

2018-02-13

Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co 3+ , Co 2+ , and Co 1+ , and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.

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

National Research Council Canada - National Science Library

Bunte, Steven

2000-01-01

To investigate the mechanical and other condensed phase properties of energetic materials using atomistic simulation techniques, the COMPASS force field has been expanded to include high-energy nitro functional groups...

On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters.

Science.gov (United States)

Bachmann, Stephan J; Lin, Zhixiong; Stafforst, Thorsten; van Gunsteren, Wilfred F; Dolenc, Jožica

2014-01-14

The technique of one-step perturbation to explore the relation between particular force-field parameters on the one hand and particular properties of a biomolecular system on the other hand from one or a few molecular dynamics simulations is applied to investigate the dependence of the free enthalpy of dimer formation and of crystal dissolution of a self-complementary fragment (H-CGTACG-NH2) of peptide nucleic acid, PNA, a mimic of DNA. The simulations show that PNA dimer formation in aqueous solution is favored by a decrease in the base charges with respect to values of the GROMOS 45A4 force field, while it is disfavored by a decrease in the backbone charges. In contrast, crystal dissolution of the PNA dimer is favored by a decrease in base charges, while a variation of backbone charges has a minor effect on this free enthalpy change. These opposite effects in a crystalline versus aqueous solution environment can be understood from the different water contents for these systems and have consequences for biomolecular force-field development.

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

Science.gov (United States)

Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

2013-10-08

We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

Development of a tuned interfacial force field parameter set for the simulation of protein adsorption to silica glass.

Science.gov (United States)

Snyder, James A; Abramyan, Tigran; Yancey, Jeremy A; Thyparambil, Aby A; Wei, Yang; Stuart, Steven J; Latour, Robert A

2012-12-01

Adsorption free energies for eight host-guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5-9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.

Post Audit of a Field Scale Reactive Transport Model of Uranium at a Former Mill Site

Science.gov (United States)

Curtis, G. P.

2015-12-01

Reactive transport of hexavalent uranium (U(VI)) in a shallow alluvial aquifer at a former uranium mill tailings site near Naturita CO has been monitored for nearly 30 years by the US Department of Energy and the US Geological Survey. Groundwater at the site has high concentrations of chloride, alkalinity and U(VI) as a owing to ore processing at the site from 1941 to 1974. We previously calibrated a multicomponent reactive transport model to data collected at the site from 1986 to 2001. A two dimensional nonreactive transport model used a uniform hydraulic conductivity which was estimated from observed chloride concentrations and tritium helium age dates. A reactive transport model for the 2km long site was developed by including an equilibrium U(VI) surface complexation model calibrated to laboratory data and calcite equilibrium. The calibrated model reproduced both nonreactive tracers as well as the observed U(VI), pH and alkalinity. Forward simulations for the period 2002-2015 conducted with the calibrated model predict significantly faster natural attenuation of U(VI) concentrations than has been observed by the persistent high U(VI) concentrations at the site. Alternative modeling approaches are being evaluating evaluated using recent data to determine if the persistence can be explained by multirate mass transfer models developed from experimental observations at the column scale(~0.2m), the laboratory tank scale (~2m), the field tracer test scale (~1-4m) or geophysical observation scale (~1-5m). Results of this comparison should provide insight into the persistence of U(VI) plumes and improved management options.

Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

Science.gov (United States)

Heinen, Jurn; Burtch, Nicholas C; Walton, Krista S; Fonseca Guerra, Célia; Dubbeldam, David

2016-12-12

For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Systematic Integrated Process Design and Control of Binary Element Reactive Distillation Processes

DEFF Research Database (Denmark)

Mansouri, Seyed Soheil; Sales-Cruz, Mauricio; Huusom, Jakob Kjøbsted

2016-01-01

In this work, integrated process design and control of reactive distillation processes is considered through a computer-aided framework. First, a set of simple design methods for reactive distillation column that are similar in concept to non-reactive distillation design methods are extended...... to design-control of reactive distillation columns. These methods are based on the element concept where the reacting system of compounds is represented as elements. When only two elements are needed to represent the reacting system of more than two compounds, a binary element system is identified....... It is shown that the same design-control principles that apply to a non-reacting binary system of compounds are also valid for a reactive binary system of elements for distillation columns. Application of this framework shows that designing the reactive distillation process at the maximum driving force...

NONLINEAR FORCE-FREE MAGNETIC FIELD FITTING TO CORONAL LOOPS WITH AND WITHOUT STEREOSCOPY

International Nuclear Information System (INIS)

Aschwanden, Markus J.

2013-01-01

We developed a new nonlinear force-free magnetic field (NLFFF) forward-fitting algorithm based on an analytical approximation of force-free and divergence-free NLFFF solutions, which requires as input a line-of-sight magnetogram and traced two-dimensional (2D) loop coordinates of coronal loops only, in contrast to stereoscopically triangulated three-dimensional loop coordinates used in previous studies. Test results of simulated magnetic configurations and from four active regions observed with STEREO demonstrate that NLFFF solutions can be fitted with equal accuracy with or without stereoscopy, which relinquishes the necessity of STEREO data for magnetic modeling of active regions (on the solar disk). The 2D loop tracing method achieves a 2D misalignment of μ 2 = 2.°7 ± 1.°3 between the model field lines and observed loops, and an accuracy of ≈1.0% for the magnetic energy or free magnetic energy ratio. The three times higher spatial resolution of TRACE or SDO/AIA (compared with STEREO) also yields a proportionally smaller misalignment angle between model fit and observations. Visual/manual loop tracings are found to produce more accurate magnetic model fits than automated tracing algorithms. The computation time of the new forward-fitting code amounts to a few minutes per active region.

Toward Structure Prediction for Short Peptides Using the Improved SAAP Force Field Parameters

Directory of Open Access Journals (Sweden)

Kenichi Dedachi

2013-01-01

Full Text Available Based on the observation that Ramachandran-type potential energy surfaces of single amino acid units in water are in good agreement with statistical structures of the corresponding amino acid residues in proteins, we recently developed a new all-atom force field called SAAP, in which the total energy function for a polypeptide is expressed basically as a sum of single amino acid potentials and electrostatic and Lennard-Jones potentials between the amino acid units. In this study, the SAAP force field (SAAPFF parameters were improved, and classical canonical Monte Carlo (MC simulation was carried out for short peptide models, that is, Met-enkephalin and chignolin, at 300 K in an implicit water model. Diverse structures were reasonably obtained for Met-enkephalin, while three folded structures, one of which corresponds to a native-like structure with three native hydrogen bonds, were obtained for chignolin. The results suggested that the SAAP-MC method is useful for conformational sampling for the short peptides. A protocol of SAAP-MC simulation followed by structural clustering and examination of the obtained structures by ab initio calculation or simply by the number of the hydrogen bonds (or the hardness was demonstrated to be an effective strategy toward structure prediction for short peptide molecules.

A Simple Model of Fields Including the Strong or Nuclear Force and a Cosmological Speculation

Directory of Open Access Journals (Sweden)

David L. Spencer

2016-10-01

Full Text Available Reexamining the assumptions underlying the General Theory of Relativity and calling an object's gravitational field its inertia, and acceleration simply resistance to that inertia, yields a simple field model where the potential (kinetic energy of a particle at rest is its capacity to move itself when its inertial field becomes imbalanced. The model then attributes electromagnetic and strong forces to the effects of changes in basic particle shape. Following up on the model's assumption that the relative intensity of a particle's gravitational field is always inversely related to its perceived volume and assuming that all black holes spin, may create the possibility of a cosmic rebound where a final spinning black hole ends with a new Big Bang.

Ionization induced by strong electromagnetic field in low dimensional systems bound by short range forces

Energy Technology Data Exchange (ETDEWEB)

Eminov, P.A., E-mail: peminov@mail.ru [Moscow State University of Instrument Engineering and Computer Sciences, 20 Stromynka Street, Moscow 2107996 (Russian Federation); National Research University Higher School of Economics, 3/12 Bolshoy Trekhsvyatskiy pereulok, Moscow 109028 (Russian Federation)

2013-10-01

Ionization processes for a two dimensional quantum dot subjected to combined electrostatic and alternating electric fields of the same direction are studied using quantum mechanical methods. We derive analytical equations for the ionization probability in dependence on characteristic parameters of the system for both extreme cases of a constant electric field and of a linearly polarized electromagnetic wave. The ionization probabilities for a superposition of dc and low frequency ac electric fields of the same direction are calculated. The impulse distribution of ionization probability for a system bound by short range forces is found for a superposition of constant and alternating fields. The total probability for this process per unit of time is derived within exponential accuracy. For the first time the influence of alternating electric field on electron tunneling probability induced by an electrostatic field is studied taking into account the pre-exponential term.

Three-dimensional computation of magnetic fields and Lorentz forces of an LHC dipole magnet

International Nuclear Information System (INIS)

Daum, C.; Avest, D. ter

1989-07-01

Magnetic fields and Lorentz forces of an LHC dipole magnet are calculated using the method of image currents to represent the effect of the iron shield. The calculation is performed for coils of finite length using a parametrization for coil heads of constant perimeter. A comparison with calculations based on POISSON and TOSCA is made. (author). 5 refs.; 31 figs.; 6 tabs

Source evaluation report phase 2 investigation: Limited field investigation. Final report: United States Air Force Environmental Restoration Program, Eielson Air Force Base, Alaska

Energy Technology Data Exchange (ETDEWEB)

1994-10-01

This report describes the limited field investigation work done to address issues and answer unresolved questions regarding a collection of potential contaminant sources at Eielson Air Force Base (AFB), near Fairbanks, Alaska. These sources were listed in the Eielson AFB Federal Facility Agreement supporting the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) cleanup of the base. The limited field investigation began in 1993 to resolve all remaining technical issues and provide the data and analysis required to evaluate the environmental hazard associated with these sites. The objective of the limited field investigation was to allow the remedial project managers to sort each site into one of three categories: requiring remedial investigation/feasibility study, requiring interim removal action, or requiring no further remedial action.

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

Science.gov (United States)

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

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

Science.gov (United States)

Mason, Elisa

1999-01-01

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

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

DEFF Research Database (Denmark)

Rossi, G.; Monticelli, L.; Puisto, S. R.

2011-01-01

We hereby introduce a new hybrid thermodynamic-structural approach to the coarse-graining of polymers. The new model is developed within the framework of the MARTINI force-field (Marrink et al., J. Phys. Chem. B, 2007, 111, 7812), which uses mainly thermodynamic properties as targets...... of microseconds. Finally, we tested our model in dilute conditions. The collapse of the polymer chains in a bad solvent and the swelling in a good solvent could be reproduced....

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

Science.gov (United States)

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

The evolution of the temperature field during cavity collapse in liquid nitromethane. Part II: reactive case

Science.gov (United States)

Michael, L.; Nikiforakis, N.

2018-02-01

two- and three-dimensional simulations to examine the change in topology, temperatures, and reactive strength of the hot spots by the third dimension. It is apparent that belated ignition times can be avoided by the use of three-dimensional simulations. The effect of the chemical reactions on the topology and strength of the hot spots in the timescales considered is also studied, in a comparison between inert and reactive simulations where maximum temperature fields and their growth rates are examined.

A Multiposture Locomotor Training Device with Force-Field Control

Directory of Open Access Journals (Sweden)

Jianfeng Sui

2014-11-01

Full Text Available This paper introduces a multiposture locomotor training device (MPLTD with a closed-loop control scheme based on joint angle feedback, which is able to overcome various difficulties resulting from mechanical vibration and the weight of trainer to achieve higher accuracy trajectory. By introducing the force-field control scheme used in the closed-loop control, the device can obtain the active-constrained mode including the passive one. The MPLTD is mainly composed of three systems: posture adjusting and weight support system, lower limb exoskeleton system, and control system, of which the lower limb exoskeleton system mainly includes the indifferent equilibrium mechanism with two degrees of freedom (DOF and the driving torque is calculated by the Lagrangian function. In addition, a series of experiments, the weight support and the trajectory accuracy experiment, demonstrate a good performance of mechanical structure and the closed-loop control.

Different forces

CERN Multimedia

1982-01-01

The different forces, together with a pictorial analogy of how the exchange of particles works. The table lists the relative strength of the couplings, the quanta associated with the force fields and the bodies or phenomena in which they have a dominant role.

Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

International Nuclear Information System (INIS)

Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; Gunsteren, W. F. van

2004-01-01

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, 3 J NHα and 3 J αβ coupling constants, and 1 5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone 3 J HNα -coupling constants and 1 H- 1 5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain 3 J αβ -coupling constants and 1 H- 1 5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result

Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas

International Nuclear Information System (INIS)

Ebihara, Ken-ichi; Watanabe, Tadashi

2000-10-01

The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)

Combining an Elastic Network With a Coarse-Grained Molecular Force Field : Structure, Dynamics, and Intermolecular Recognition

NARCIS (Netherlands)

Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan; Ceruso, Marco A.

Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this

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

Energy Technology Data Exchange (ETDEWEB)

Mulcahy, T.M.; Hull, J.R.; Almer, J.D. (Argonne National Lab., IL (United States)); Rossing, T.D. (Northern Illinois Univ., De Kalb, IL (United States))

1992-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Mulcahy, T.M.; Hull, J.R.; Almer, J.D. [Argonne National Lab., IL (United States); Rossing, T.D. [Northern Illinois Univ., De Kalb, IL (United States)

1992-04-01

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

On a role of the Bsub(z) component of interplanetary magnetic field in a force balance in the day time magnetopause

International Nuclear Information System (INIS)

Kuznetsova, T.V.

1980-01-01

The role of interplanetary magnetic field (IMF) in the force balance in the day time magnetopause is discussed. The effect of the circular DR-current on the balance of pressures in the magnetopause is taken into account in the calculations. It is shown that IMF plays a significant role in the balance of forces in the day time magnetopause. The ratio of magnetic pressure to the thermal pressure of solar wind in subsolar point is k=0.5. The field observed in magnetosphere near the neutral line is lower by the value of transition region field. All the conclusions are obtained for Bsub(z) [ru

Differential reactivity of immune sera from human vaccinees with field strains of eastern equine encephalitis virus.

Science.gov (United States)

Strizki, J M; Repik, P M

1995-11-01

Eastern equine encephalitis (EEE) virus is a mosquito-borne alphavirus that can produce a severe and often fatal acute encephalitis in humans, with significant neurologic sequelae in survivors. Due to the serious nature of the disease, an investigational inactivated EEE vaccine (PE-6) is available to individuals at risk for infection. Both serologic and recent molecular analyses of EEE viruses have demonstrated marked differences between the two antigenic varieties of EEE virus, designated North American (NA) and South American (SA). In view of these findings, we have examined the reactivity of sera from three individuals immunized with the EEE vaccine, derived from an NA isolate, with field strains of EEE virus. Anti-EEE serum antibodies from vaccinees reacted strongly in Western blot assays with both of the envelope (E1 and E2) glycoproteins of each NA strain examined, while reactivities with the glycoproteins of SA strains were substantially weaker and variable and dependent upon both the immune response of the vaccinee and the virus isolate assayed. Most striking was the modest to virtual lack of reactivity with the E2 protein of SA strains. Antigenic differences among the glycoproteins of EEE viruses were not as pronounced in immunoprecipitation analysis. Most significantly, although human immune sera displayed high neutralizing titers against each of the NA isolates examined, only negligible neutralizing titers were obtained against SA isolates. These data suggest that immunized individuals would mount an effective antibody response against infection with NA strains of EEE virus, but that further investigation is clearly warranted to fully assess the protective capability of the vaccine against infection with SA strains.

An atomistic fingerprint algorithm for learning ab initio molecular force fields

Science.gov (United States)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Recent advances toward a general purpose linear-scaling quantum force field.

Science.gov (United States)

Giese, Timothy J; Huang, Ming; Chen, Haoyuan; York, Darrin M

2014-09-16

Conspectus There is need in the molecular simulation community to develop new quantum mechanical (QM) methods that can be routinely applied to the simulation of large molecular systems in complex, heterogeneous condensed phase environments. Although conventional methods, such as the hybrid quantum mechanical/molecular mechanical (QM/MM) method, are adequate for many problems, there remain other applications that demand a fully quantum mechanical approach. QM methods are generally required in applications that involve changes in electronic structure, such as when chemical bond formation or cleavage occurs, when molecules respond to one another through polarization or charge transfer, or when matter interacts with electromagnetic fields. A full QM treatment, rather than QM/MM, is necessary when these features present themselves over a wide spatial range that, in some cases, may span the entire system. Specific examples include the study of catalytic events that involve delocalized changes in chemical bonds, charge transfer, or extensive polarization of the macromolecular environment; drug discovery applications, where the wide range of nonstandard residues and protonation states are challenging to model with purely empirical MM force fields; and the interpretation of spectroscopic observables. Unfortunately, the enormous computational cost of conventional QM methods limit their practical application to small systems. Linear-scaling electronic structure methods (LSQMs) make possible the calculation of large systems but are still too computationally intensive to be applied with the degree of configurational sampling often required to make meaningful comparison with experiment. In this work, we present advances in the development of a quantum mechanical force field (QMFF) suitable for application to biological macromolecules and condensed phase simulations. QMFFs leverage the benefits provided by the LSQM and QM/MM approaches to produce a fully QM method that is able to

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

Science.gov (United States)

Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

2018-03-01

Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

The effect of magnet size on the levitation force and attractive force of single-domain YBCO bulk superconductors

International Nuclear Information System (INIS)

Yang, W M; Chao, X X; Bian, X B; Liu, P; Feng, Y; Zhang, P X; Zhou, L

2003-01-01

The levitation forces between a single-domain YBCO bulk and several magnets of different sizes have been measured at 77 K to investigate the effect of the magnet size on the levitation force. It is found that the levitation force reaches a largest (peak) value when the size of the magnet approaches that of the superconductor when the other conditions are fixed. The absolute maximum attractive force (in the field-cooled state) increases with the increasing of the magnet size, and is saturated when the magnet size approaches that of the superconductor. The maximum attractive force in the field-cooled (FC) state is much higher than that of the maximum attractive force in the zero field-cooled (ZFC) state. The results indicate that the effects of magnetic field distribution on the levitation force have to be considered during the designing and manufacturing of superconducting devices

Dip-Pen Nanolithography on (Bio)Reactive Monolayer and Block-Copolymer Platforms: Deposition of Lines of Single Macromolecules

NARCIS (Netherlands)

Salazar, Ramon B.; Shovsky, A.; Schönherr, Holger; Vancso, Gyula J.

2006-01-01

The application of atomic force microscopy (AFM) tip-mediated molecular transfer (dip-pen nanolithography or DPN) to fabricate nanopatterned (bio)reactive platforms based on dendrimers on reactive self-assembled monolayer (SAM) and polymer thin films is discussed. The transfer of high-molar-mass

A force-based protein biochip

Science.gov (United States)

Blank, K.; Mai, T.; Gilbert, I.; Schiffmann, S.; Rankl, J.; Zivin, R.; Tackney, C.; Nicolaus, T.; Spinnler, K.; Oesterhelt, F.; Benoit, M.; Clausen-Schaumann, H.; Gaub, H. E.

2003-09-01

A parallel assay for the quantification of single-molecule binding forces was developed based on differential unbinding force measurements where ligand-receptor interactions are compared with the unzipping forces of DNA hybrids. Using the DNA zippers as molecular force sensors, the efficient discrimination between specific and nonspecific interactions was demonstrated for small molecules binding to specific receptors, as well as for protein-protein interactions on protein arrays. Finally, an antibody sandwich assay with different capture antibodies on one chip surface and with the detection antibodies linked to a congruent surface via the DNA zippers was used to capture and quantify a recombinant hepatitis C antigen from solution. In this case, the DNA zippers enable not only discrimination between specific and nonspecific binding, but also allow for the local application of detection antibodies, thereby eliminating false-positive results caused by cross-reactive antibodies and nonspecific binding.

Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

Energy Technology Data Exchange (ETDEWEB)

Wang Zunjing; Deserno, Markus, E-mail: zwang@cmu.ed, E-mail: deserno@andrew.cmu.ed [Department of Physics, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213 (United States)

2010-09-15

We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field

International Nuclear Information System (INIS)

Wang Zunjing; Deserno, Markus

2010-01-01

We study the lipid and phase transferability of our recently developed systematically coarse-grained solvent-free membrane model. The force field was explicitly parameterized to describe a fluid 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer at 310 K with correct structure and area per lipid, while gaining at least three orders of magnitude in computational efficiency (see Wang and Deserno 2010 J. Phys. Chem. B 114 11207-20). Here, we show that exchanging CG tails, without any subsequent re-parameterization, creates reliable models of 1,2-dioleoylphosphatidylcholine (DOPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipids in terms of structure and area per lipid. Furthermore, all CG lipids undergo a liquid-gel transition upon cooling, with characteristics like those observed in experiments and all-atom simulations during phase transformation. These studies suggest a promising transferability of our force field parameters to different lipid species and thermodynamic state points, properties that are a prerequisite for even more complex systems, such as mixtures.

StringForce

DEFF Research Database (Denmark)

Barendregt, Wolmet; Börjesson, Peter; Eriksson, Eva

2017-01-01

In this paper, we present the forced collaborative interaction game StringForce. StringForce is developed for a special education context to support training of collaboration skills, using readily available technologies and avoiding the creation of a "mobile bubble". In order to play String......Force two or four physically collocated tablets are required. These tablets are connected to form one large shared game area. The game can only be played by collaborating. StringForce extends previous work, both technologically and regarding social-emotional training. We believe String......Force to be an interesting demo for the IDC community, as it intertwines several relevant research fields, such as mobile interaction and collaborative gaming in the special education context....

Volume pinning force and upper critical field of irradiated Nb3Sn

International Nuclear Information System (INIS)

Maier, P.; Seibt, E.

1981-01-01

Irradiation by neutrons and ions in A15 superconductors (Nb 3 Sn, V 3 Ga) exerts a stronger influence on the pinning behavior than in nonordered alloys (NbTi). In this work it is shown for deuteron irradiated Nb 3 /Sn wires prepared by the bronze process that the dose curve of the volume pinning force P/sub V/ can be conveniently described by a sum of two terms, due to the grain boundary pinning and to the radiation pinning, respectively. After deduction of the contribution by the radiation-induced pinning centers, good agreement is obtained between the measured P/sub V/ values and those calculated using the upper critical field B/sub c/2 and the transition temperature T/sub c/ on the basis of the irradiation fluence. The use of a theoretical relationship between B/sub c/2 and T/sub c/ is supported by measured values. Application to multifilamentary superconductors with high current carrying capabilities simplifies the calculation of P/sub V/, since the radiation induced volume pinning force can be neglected

New arrangements in force in the field of transport

CERN Multimedia

Tom Wegelius

2006-01-01

Please take note of the following information concerning new arrangements in force in the field of transport: China: Regulations applying to wooden packaging materials as of 1st January 2006 As scheduled, China introduced standard ISPM No. 15 on 1st January 2006. This was officially confirmed in a letter from the Federal Minister for Consumer Protection, Food and Agriculture. Henceforth, China will apply the same conditions to the importation of wooden packaging materials as various other countries, including the United States, Mexico and Brazil. This means that items shipped to China in wooden packaging will no longer need to be accompanied by a certificate relating to the protection of plant species or other phytosanitary documents (such as heat treatment certificates). However, a guarantee that the wooden packaging complies with standard ISPM No. 15 will be required. Phase II of US regulations concerning wooden packaging material Phase II of regulations concerning the importation of wooden packaging ma...

Role of tip chemical reactivity on atom manipulation process in dynamic force microscopy

Czech Academy of Sciences Publication Activity Database

Sugimoto, Y.; Yurtsever, A.; Abe, M.; Morita, S.; Ondráček, Martin; Pou, P.; Perez, R.; Jelínek, Pavel

2013-01-01

Roč. 7, č. 8 (2013), s. 7370-7376 ISSN 1936-0851 R&D Projects: GA ČR(CZ) GPP204/11/P578 Grant - others:GA AV ČR(CZ) M100101207 Institutional support: RVO:68378271 Keywords : noncontact atomic force microscopy * atomic manipulation * force spectroscopy * chemical interaction force * DFT simulations * nudged elastic band Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 12.033, year: 2013 http://pubs.acs.org/doi/abs/10.1021/nn403097p

Electromagnetic force support for thermonuclear device

International Nuclear Information System (INIS)

Sugimoto, Makoto; Yoshida, Kiyoshi; Tachikawa, Nobuo; Omori, Junji.

1992-01-01

The device of the present invention certainly supports electromagnetic force exerted on toroidal magnetic field coils. That is, a pair of support members are disposed being abutted against each other between toroidal magnetic field coils disposed radially in the torus direction of a vacuum vessel. Both of the support members are connected under an insulative state by way of an insulative structural portion having an insulation key. In addition, each of the support members and each of the toroidal magnetic field coils are connected by electromagnetic force support portions having a metal taper key and a metal spacer and supporting the electromagnetic force. With such a constitution, the electromagnetic force exerted on the toroidal magnetic field coils is supported by the electromagnetic force support portion having the metal taper key and the metal spacer. As a result, stable electromagnetic force support can be attained. Further, since the insulative structural portion has the insulation key, it can be assembled easily. (I.S.)

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

Science.gov (United States)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

Effect of simulated resistance, fleeing, and use of force on standardized field sobriety testing.

Science.gov (United States)

Ho, Jeffrey; Dawes, Donald; Nystrom, Paul; Moore, Johanna; Steinberg, Lila; Tilton, Annemarie; Miner, James

2015-07-01

When a law enforcement officer (LEO) stops a suspect believed to be operating (a vehicle) while impaired (OWI), the suspect may resist or flee, and the LEO may respond with force. The suspect may then undergo a Standardized Field Sobriety Test (SFST) to gauge impairment. It is not known whether resistance, fleeing, or actions of force can create an inaccurate SFST result. We examined the effect of resistance, fleeing, and force on the SFST. Human volunteers were prospectively randomized to have a SFST before and after one of five scenarios: (1) five-second conducted electrical weapon exposure; (2) 100-yard (91.4 m) sprint; (3) 45-second physical fight; (4) police dog bite with protective gear; and (5) Oleoresin Capsicum spray to the face with eyes shielded. The SFST was administered and graded by a qualified LEO. After the SFST, the volunteer entered their scenario and was then administered another SFST. Data were analyzed using descriptive statistics. SFST performance was compared before and after using chi-square tests. Fifty-seven subjects enrolled. Three received a single-point penalty during one component of the three-component SFST pre-scenario. No subject received a penalty point in any components of the SFST post-scenario (p = 0.08). This is the first human study to examine the effects of physical resistance, flight, and use of force on the SFST result. We did not detect a difference in the performance of subjects taking the SFST before and after exposure to resistance, flight, or a simulated use of force. © Australian Council for Educational Research 2014.

Nietzsche et les paradoxes de la force

Directory of Open Access Journals (Sweden)

Arnaud François

2011-06-01

Full Text Available According to this paper, the Nietzschean notion of force actually consists of a number of paradoxes, which I seek to formulate through the philosophical problems they pose. These paradoxes revolve around this fundamental paradox: on the one hand, force is able to rise and fall, but precisely how could such an increase and such a decrease be designed, as far as only what is given once for all can accept quantitative determinations? I come to draw two methods to answer this question (contrariety between two positive forces, reactivity of one force against the other, which suggest two ways of posing the biological and medical problems today, related to the notions of health and disease, in the scope of which Nietzsche has encountered it.

Assessing Reactive Strength Measures in Jumping and Hopping Using the Optojump™ System

Directory of Open Access Journals (Sweden)

Healy Robin

2016-12-01

Full Text Available The aim of this study was to assess the concurrent validity of the Optojump™ system (Microgate, Bolzano, Italy versus a force platform in the estimation of temporal and reactive strength measures. In two separate investigations, twenty physically active males performed double-leg and single-leg drop jumps from a box height of 0.3 m and a 10 s vertical bilateral hopping test. Contact time, flight time and total time (the sum of contact and flight time were concurrently assessed during single and double-leg drop jumps and during hopping. Jump height, the reactive strength index and the reactive strength ratio were also calculated from contact time and flight time. Despite intraclass correlation coefficients (ICCs for all variables being close to 1 (ICC > 0.975, a significant overestimation was found in contact time (0.005 ± 0.002 s and underestimations in flight time (0.005 ± 0.003 s, the reactive strength index (0.04 ± 0.02 m·s-1 and the reactive strength ratio (0.07 ± 0.04. Overestimations in contact time and underestimations in flight time were attributed to the physical design of the Optojump™ system as the transmitter and receiver units were positioned 0.003 m above the floor level. The Optojump™ demonstrated excellent overall temporal validity with no differences found between systems for total time. Coaches are advised to be consistent with the instrumentation used to assess athletes, however, in the case of comparison between reactive strength values collected with the Optojump™ and values collected with a force platform, regression equations are provided.

Laser radiation forces in laser-produced plasmas

International Nuclear Information System (INIS)

Stamper, J.A.

1975-01-01

There are two contributions to laser radiation forces acting on the electrons. Transfer of momentum from the fields to the electrons results in a field pressure contribution and occurs whenever there is absorption or reflection. The quiver pressure contribution, associated with electron quiver motion, is due to inhomogeneous fields inducing momentum transfer within the electron system. It is shown that the ponderomotive force with force density, (epsilon-1)/8πdel 2 >, does not include the field contribution and does not lead to a general description of macroscopic processes. A theory is discussed which does give a general macroscopic description (absorption, reflection, refraction, and magnetic field generation) and which reduces to the ponderomotive force for purely sinusoidal fields in a neutral, homogeneous, nonabsorbing plasma

Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

Science.gov (United States)

1996-03-01

differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide.

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH 2 ). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD 3 CD in H 2 O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

Magnetic field effects on the vestibular system: calculation of the pressure on the cupula due to ionic current-induced Lorentz force

International Nuclear Information System (INIS)

Antunes, A; Glover, P M; Li, Y; Mian, O S; Day, B L

2012-01-01

Large static magnetic fields may be employed in magnetic resonance imaging (MRI). At high magnetic field strengths (usually from about 3 T and above) it is possible for humans to perceive a number of effects. One such effect is mild vertigo. Recently, Roberts et al (2011 Current Biology 21 1635–40) proposed a Lorentz-force mechanism resulting from the ionic currents occurring naturally in the endolymph of the vestibular system. In the present work a more detailed calculation of the forces and resulting pressures in the vestibular system is carried out using a numerical model. Firstly, realistic 3D finite element conductivity and fluid maps of the utricle and a single semi-circular canal containing the current sources (dark cells) and sinks (hair cells) of the utricle and ampulla were constructed. Secondly, the electrical current densities in the fluid are calculated. Thirdly, the developed Lorentz force is used directly in the Navier–Stokes equation and the trans-cupular pressure is computed. Since the driving force field is relatively large in comparison with the advective acceleration, we demonstrate that it is possible to perform an approximation in the Navier–Stokes equations that reduces the problem to solving a simpler Poisson equation. This simplification allows rapid and easy calculation for many different directions of applied magnetic field. At 7 T a maximum cupula pressure difference of 1.6 mPa was calculated for the combined ampullar (0.7 µA) and utricular (3.31 µA) distributed current sources, assuming a hair-cell resting current of 100 pA per unit. These pressure values are up to an order of magnitude lower than those proposed by Roberts et al using a simplistic model and calculation, and are in good agreement with the estimated pressure values for nystagmus velocities in caloric experiments. This modeling work supports the hypothesis that the Lorentz force mechanism is a significant contributor to the perception of magnetic field induced

Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide

Science.gov (United States)

Iwaoka, Michio; Suzuki, Toshiki; Shoji, Yuya; Dedachi, Kenichi; Shimosato, Taku; Minezaki, Toshiya; Hojo, Hironobu; Onuki, Hiroyuki; Hirota, Hiroshi

2017-12-01

Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2). For chignolin, REMC/SAAP3D simulation correctly produced native β-turn structures, whose minimal all-atom root-mean-square deviation value measured from the native NMR structure (except for H) was 1.2 Å, at 300 K in implicit water, along with misfolded β-hairpin structures with unpacked aromatic side chains of Tyr2 and Trp9. Similar results were obtained for chignolin analog [G1Y,G10Y], which folded more tightly to the native β-turn structure than chignolin did. For C-peptide, on the other hand, the α-helix content was larger than the β content on average, suggesting a significant helix-forming propensity. When the imidazole side chain of His12 was protonated (i.e., [His12Hip]), the α content became larger. These observations as well as the representative structures obtained by clustering analysis were in reasonable agreement not only with the structures of C-peptide that were determined in this study by NMR in 30% CD3CD in H2O at 298 K but also with the experimental and theoretical behaviors having been reported for protonated C-peptide. Thus, accuracy of the SAAP force field was improved by applying three-dimensional main-chain parameters, supporting prominent importance of SAAP for peptide conformations.

An alternative approach to the management of reactive metals: tolerant cementitious systems

International Nuclear Information System (INIS)

Swift, P.; Cox, J.; Wise, M.; McKinney, J.; Rhodes, C.

2015-01-01

In recent years research has focused on preventing or minimising corrosion of reactive metals to ensure long-term waste package integrity. An alternative approach to the encapsulation of reactive metals is being explored. The approach will identify a cementitious-based encapsulating material that will allow corrosion of reactive metals to occur in a controlled and predictable manner, rather than seeking to limit or prevent the corrosion, whilst retaining waste package integrity. A low strength grout will be developed that will be 'tolerant' to the expansive forces generated by the corrosion products of reactive metals. Novel cementitious systems (e.g. foamed cements, rubber composite cements, cenosphere composite cements, lime mortars, bentonite cements etc.) that may be tolerant to potentially expansive waste products, such as reactive metals will be considered and assessed in a series of small-scale preliminary trials (compressive strength, porosity, permeability, pore solution pH, etc.)

Relativistic equation of the orbit of a particle in a arbitrary central force field

International Nuclear Information System (INIS)

Aaron, Francisc D.

2005-01-01

The equation of the orbit of a relativistic particle moving in an arbitrary central force field is derived. Straightforward generalizations of well-known first and second order differential equations are given. It is pointed out that the relativistic equation of the orbit has the same form as in the non-relativistic case, the only changes consisting in the appearance of additional terms proportional to 1/c 2 in both potential and total energies. (author)

Study of vapour phase dynamics with nitrogen boiling in the field of centrifugal forces

International Nuclear Information System (INIS)

Levchenko, N.M.; Kolod'ko, I.M.

1987-01-01

The vapour phase dynamics during film boiling of liquid nitrogen on horizontal wire in the field of centrifugal forces has been studied experimentally in a wide range of overloads(1 ≤ η ≤ 375) and heat fluxes (q kp2 ≤ q ≤ 4q kpi ). The available data confirmed and the theoretical relationships suggested make it possible to calculate the hydrodynamic film boiling parameters (wave length, bubble departure diameter and frequency) for other liquids

An inverse method for determining the interaction force between the probe and sample using scanning near-field optical microscopy

International Nuclear Information System (INIS)

Chang, Win-Jin; Fang, Te-Hua

2006-01-01

This study proposes a means for calculating the interaction force during the scanning process using a scanning near-field optical microscope (SNOM) probe. The determination of the interaction force in the scanning system is regarded as an inverse vibration problem. The conjugate gradient method is applied to treat the inverse problem using available displacement measurements. The results show that the conjugate gradient method is less sensitive to measurement errors and prior information on the functional form of quality was not required. Furthermore, the initial guesses for the interaction force can be arbitrarily chosen for the iteration process

Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

Energy Technology Data Exchange (ETDEWEB)

Soares, T. A. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Daura, X. [Universitat Autonoma de Barcelona, InstitucioCatalana de Recerca i Estudis Avancats and Institut de Biotecnologia i Biomedicina (Spain); Oostenbrink, C. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Smith, L. J. [University of Oxford, Oxford Centre for Molecular Sciences, Central Chemistry Laboratory (United Kingdom); Gunsteren, W. F. van [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland)], E-mail: wfvgn@igc.phys.chem.ethz.ch

2004-12-15

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone {sup 3}J{sub HN{alpha}}-coupling constants and {sup 1}H- {sup 1}5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain {sup 3}J{sub {alpha}}{sub {beta}}-coupling constants and {sup 1}H- {sup 1}5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the

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

Science.gov (United States)

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

2016-10-21

Local field potential (LFP) signals recorded by intracortical microelectrodes implanted in primary motor cortex can be used as a high informative input for decoding of motor functions. Recent studies show that different kinematic parameters such as position and velocity can be inferred from multiple LFP signals as precisely as spiking activities, however, continuous decoding of the force magnitude from the LFP signals in freely moving animals has remained an open problem. Here, we trained three rats to press a force sensor for getting a drop of water as a reward. A 16-channel micro-wire array was implanted in the primary motor cortex of each trained rat, and obtained LFP signals were used for decoding of the continuous values recorded by the force sensor. Average coefficient of correlation and the coefficient of determination between decoded and actual force signals were r = 0.66 and R 2  = 0.42, respectively. We found that LFP signal on gamma frequency bands (30-120 Hz) had the most contribution in the trained decoding model. This study suggests the feasibility of using low number of LFP channels for the continuous force decoding in freely moving animals resembling BMI systems in real life applications.

Entropy Generation in Natural Convection Under an Evanescent Magnetic Field

International Nuclear Information System (INIS)

Magherbi, Mourad; El Jery, Atef; Ben Brahim, Ammar

2009-01-01

We numerically study the effect of an externally-evanescent magnetic field on total entropy generation in conducting and non-reactive fluid enclosed in a square cavity. The horizontal walls of the enclosure are assumed to be insulated while the vertical walls are kept isothermal. A control volume finite element method is used to solve the conservation equations at Prandtl number of 0.71. The values of relaxation time of the magnetic field are chosen, so that the Lorentz force acts only in the transient state of entropy generation in natural convection. The total entropy generation was calculated for fixed value of irreversibility distribution ratio, different relaxation time varying from 0 to 1/5 and Grashof number equal to 10 5

Magnus force in superfluids and superconductors

International Nuclear Information System (INIS)

Sonin, E.B.

1997-01-01

The forces on the vortex, transverse to its velocity, are considered. In addition to the superfluid Magnus force from the condensate (superfluid component), there are transverse forces from thermal quasiparticles and external fields violating the Galilean invariance. The forces between quasiparticles and the vortex originate from interference of quasiparticles with trajectories on the left and on the right from the vortex like similar forces for electrons interacting with the thin magnetic-flux tube (the Aharonov-Bohm effect). These forces are derived for phonons from the equations of superfluid hydrodynamics, and for BCS quasiparticles from the Bogolyubov endash de Gennes equations. The effect of external fields breaking Galilean invariance is analyzed for vortices in the two-dimensional Josephson junction array. The symmetry analysis of the classical equations for the array shows that the total transverse force on the vortex vanishes. Therefore the Hall effect which is linear in the transverse force is absent also. This means that the Magnus force from the superfluid component exactly cancels with the transverse force from the external fields. The results of other approaches are also brought together for discussion. copyright 1997 The American Physical Society

Lorentz force actuation of a heated atomic force microscope cantilever.

Science.gov (United States)

Lee, Byeonghee; Prater, Craig B; King, William P

2012-02-10

We report Lorentz force-induced actuation of a silicon microcantilever having an integrated resistive heater. Oscillating current through the cantilever interacts with the magnetic field around a NdFeB permanent magnet and induces a Lorentz force that deflects the cantilever. The same current induces cantilever heating. With AC currents as low as 0.2 mA, the cantilever can be oscillated as much as 80 nm at resonance with a DC temperature rise of less than 5 °C. By comparison, the AC temperature variation leads to a thermomechanical oscillation that is about 1000 times smaller than the Lorentz deflection at the cantilever resonance. The cantilever position in the nonuniform magnetic field affects the Lorentz force-induced deflection, with the magnetic field parallel to the cantilever having the largest effect on cantilever actuation. We demonstrate how the cantilever actuation can be used for imaging, and for measuring the local material softening temperature by sensing the contact resonance shift.

The outflows accelerated by the magnetic fields and radiation force of accretion disks

Energy Technology Data Exchange (ETDEWEB)

Cao, Xinwu, E-mail: cxw@shao.ac.cn [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, Shanghai, 200030 (China)

2014-03-01

The inner region of a luminous accretion disk is radiation-pressure-dominated. We estimate the surface temperature of a radiation-pressure-dominated accretion disk, Θ=c{sub s}{sup 2}/r{sup 2}Ω{sub K}{sup 2}≪(H/r){sup 2}, which is significantly lower than that of a gas-pressure-dominated disk, Θ ∼ (H/r){sup 2}. This means that the outflow can be launched magnetically from the photosphere of the radiation-pressure-dominated disk only if the effective potential barrier along the magnetic field line is extremely shallow or no potential barrier is present. For the latter case, the slow sonic point in the outflow will probably be in the disk, which leads to a slow circular dense flow above the disk. This implies that hot gas (probably in the corona) is necessary for launching an outflow from the radiation-pressure-dominated disk, which provides a natural explanation for the observational evidence that the relativistic jets are related to hot plasma in some X-ray binaries and active galactic nuclei. We investigate the outflows accelerated from the hot corona above the disk by the magnetic field and radiation force of the accretion disk. We find that with the help of the radiation force, the mass loss rate in the outflow is high, which leads to a slow outflow. This may be why the jets in radio-loud narrow-line Seyfert galaxies are in general mildly relativistic compared with those in blazars.

Operation of a scanning near field optical microscope in reflection in combination with a scanning force microscope

NARCIS (Netherlands)

van Hulst, N.F.; Moers, M.H.P.; Moers, M.H.P.; Noordman, O.F.J.; Noordman, O.F.J.; Faulkner, T.; Segerink, Franciscus B.; van der Werf, Kees; de Grooth, B.G.; Bölger, B.; Bölger, B.

1992-01-01

Images obtained with a scanning near field optical microscope (SNOM) operating in reflection are presented. We have obtained the first results with a SiN tip as optical probe. The instrument is simultaneously operated as a scanning force microscope (SFM). Moreover, the instrument incorporates an

Characterizing the potential for fault reactivation related to CO2 injection through subsurface structural mapping and stress field analysis, Wellington Field, Sumner County, KS

Science.gov (United States)

Schwab, D.; Bidgoli, T.; Taylor, M. H.

2015-12-01

South-central Kansas has experienced an unprecedented increase in seismic activity since 2013. The spatial and temporal relationship of the seismicity with brine disposal operations has renewed interest in the role of fluids in fault reactivation. This study focuses on determining the suitability of CO2 injection into a Cambro-Ordovician reservoir for long-term storage and a Mississippian reservoir for enhanced oil recovery in Wellington Field, Sumner County, Kansas. Our approach for determining the potential for induced seismicity has been to (1) map subsurface faults and estimate in-situ stresses, (2) perform slip and dilation tendency analysis to identify optimally-oriented faults relative to the estimated stress field, and (3) monitor surface deformation through cGPS data and InSAR imaging. Through the use of 3D seismic reflection data, 60 near vertical, NNE-striking faults have been identified. The faults range in length from 140-410 m and have vertical separations of 3-32m. A number of faults appear to be restricted to shallow intervals, while others clearly cut the top basement reflector. Drilling-induced tensile fractures (N=78) identified from image logs and inversion of earthquake focal mechanism solutions (N=54) are consistent with the maximum horizontal stress (SHmax) oriented ~E-W. Both strike-slip and normal-slip fault plane solutions for earthquakes near the study area suggest that SHmax and Sv may be similar in magnitude. Estimates of stress magnitudes using step rate tests (Shmin = 2666 psi), density logs (Sv = 5308 psi), and calculations from wells with drilling induced tensile fractures (SHmax = 4547-6655 psi) are determined at the gauge depth of 4869ft. Preliminary slip and dilation tendency analysis indicates that faults striking 0°-20° are stable, whereas faults striking 26°-44° may have a moderate risk for reactivation with increasing pore-fluid pressure.

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

Directory of Open Access Journals (Sweden)

R. Hedayati

2018-03-01

Full Text Available Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of “action-at-a-distance” metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson’s ratios as a way of making “action-at-a-distance” metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable robotics and exosuits.

Coupled force-balance and particle-occupation rate equations for high-field electron transport

International Nuclear Information System (INIS)

Lei, X. L.

2008-01-01

It is pointed out that in the framework of balance-equation approach, the coupled force-balance and particle-occupation rate equations can be used as a complete set of equations to determine the high-field transport of semiconductors in both strong and weak electron-electron interaction limits. We call to attention that the occupation rate equation conserves the total particle number and maintains the energy balance of the relative electron system, and there is no need to introduce any other term in it. The addition of an energy-drift term in the particle-occupation rate equation [Phys. Rev. B 71, 195205 (2005)] is physically inadequate for the violation of the total particle-number conservation and the energy balance. It may lead to a substantial unphysical increase of the total particle number by the application of a dc electric field

Mind as a force field: comments on a new interactionistic hypothesis.

Science.gov (United States)

Lindahl, B I; Arhem, P

1994-11-07

The survival and development of consciousness in biological evolution call for an explanation. An interactionistic mind-brain theory seems to have the greatest explanatory value in this context. An interpretation of an interactionistic hypothesis, recently proposed by Karl Popper, is discussed both theoretically and based on recent experimental data. In the interpretation, the distinction between the conscious mind and the brain is seen as a division into what is subjective and what is objective, and not as an ontological distinction between something immaterial and something material. The interactionistic hypothesis is based on similarities between minds and physical forces. The conscious mind is understood to interact with randomly spontaneous spatio-temporal patterns of action potentials through an electromagnetic field. Consequences and suggestions for future studies are discussed.

Research on a novel axial-flux magnetic-field-modulated brushless double-rotor machine with low axial force and high efficiency

Directory of Open Access Journals (Sweden)

Chengde Tong

2017-05-01

Full Text Available The axial-flux magnetic-field-modulated brushless double-rotor machine (MFM-BDRM is a possible alternative as a power-split device for hybrid electric vehicles (HEVs. However, the existence of large axial force may lead to assembly problems and rich inner air-gap harmonics could result in high PM loss and low efficiency. This paper proposes a novel axial-flux MFM-BDRM with improved PM rotor structure. 2-D analytical method to predict the magnetic-field distribution of the proposed MFM-BDRM is developed and the design procedure of the proposed machine is illustrated. The impact of key geometrical parameters on axial force and torque is investigated. To evaluate the advantage of the proposed machine, a comparison is made with a conventional one with respect to electromagnetic performances. Results show that the proposed machine is effective in reducing PM eddy loss and axial force by 60% and 35%, respectively.

Understrength Air Force Officer Career Fields. A Force Management Approach

Science.gov (United States)

2005-01-01

LtCol John Crown (DPSA). In addition, we had very helpful interviews with Mr. Vaughan Blackstone (DPAPP) and Mr. Dennis Miller (DPPAO). Also at...problems in managing personnel assignments. First, there is a high " tax " for special-duty jobs that requires them to place personnel officers into...targeted year-groups populated above the ideal force- structure line (called TOPLINE), in the run up to the RIF of 1992, the desire to avoid or

Evolution of wave turbulence under "gusty" forcing.

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Annenkov, S Y; Shrira, V I

2011-09-09

We consider nonlinear evolution of a random wave field under gusty forcing, fluctuating around a constant mean. Here the classical wave turbulence theory that assumes a proximity to stationarity is not applicable. We show by direct numerical simulation that the self-similarity of wave field evolution survives under fluctuating forcing. The wave field statistical characteristics averaged over fluctuations of forcing evolve as if there were a certain constant "effective wind." The results justify the use of the kinetic equations with forcing averaged over gusts as a good first approximation.

Review of Abiotic Degradation of Chlorinated Solvents by Reactive Iron Minerals

Science.gov (United States)

Abiotic degradation of chlorinated solvents by reactive iron minerals such as iron sulfides, magnetite, green rust, and other Fe(II)-containing minerals has been observed in both laboratory and field conditions. These reactive iron minerals typically form under iron and sulfate ...

Construction of force-free fields which have toroidal surfaces about a given surface

International Nuclear Information System (INIS)

Bouligand, G.

1983-05-01

A study of two-fields (B vector, rotB vector) of conservative flux which admits a family of toroidal surfaces of parameter phi on a domain limited by a given surface S, suggests their construction by a Cauchy-Arzela method of step by step. Taking into account the Newcomb condition this method is consistent with force-free magnetic fields and with helical equilibria with scalar pressure. The method supposes that B vector is of class C 1 . This construction makes use of the remarkable property of the field B vector to be the surface gradient of a generating multivalued function Q on a closed surface. Consequently, the initial surface will be given with its normal metric coefficient K; that is to say, B vector admits a family F of homotopic surfaces on a infinitesimal domain about S, an element of F. From this, the periodic part of Q is a solution of a Beltrami equation for the flux conservation of which numerical resolution is envisaged. The study of these fields is made in a biorthogonal system of coordinates. The coeffficients of the two fundamental metric forms of magnetic surfaces vary with phi and are interrelated by a sixth order differential system of equations which gives their variation [fr

Acoustic forcing of a liquid drop

Science.gov (United States)

Lyell, M. J.

1992-01-01

The development of systems such as acoustic levitation chambers will allow for the positioning and manipulation of material samples (drops) in a microgravity environment. This provides the capability for fundamental studies in droplet dynamics as well as containerless processing work. Such systems use acoustic radiation pressure forces to position or to further manipulate (e.g., oscillate) the sample. The primary objective was to determine the effect of a viscous acoustic field/tangential radiation pressure forcing on drop oscillations. To this end, the viscous acoustic field is determined. Modified (forced) hydrodynamic field equations which result from a consistent perturbation expansion scheme are solved. This is done in the separate cases of an unmodulated and a modulated acoustic field. The effect of the tangential radiation stress on the hydrodynamic field (drop oscillations) is found to manifest as a correction to the velocity field in a sublayer region near the drop/host interface. Moreover, the forcing due to the radiation pressure vector at the interface is modified by inclusion of tangential stresses.

The Electromotive Force in Different Reference Frames

Science.gov (United States)

Adler, Charles L.

2018-05-01

The electromotive force (EMF) is the work per unit charge around a wire loop caused by a time-varying magnetic flux threading the loop. It is due to a force moving the charges around the loop. This is true whether the change in flux is due to the wire loop being stationary and the field changing in time, or the loop moving through a spatially varying field. In the first case, we say that the time-varying magnetic field induces an electric field that provides the force; in the second, we say that the force is due to the magnetic field acting on the charges in the moving loop. The theory of relativity states that both viewpoints must be equivalent, but it is sometimes difficult to harmonize them.

Adaptation to delayed force perturbations in reaching movements.

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Noa Levy

Full Text Available Adaptation to deterministic force perturbations during reaching movements was extensively studied in the last few decades. Here, we use this methodology to explore the ability of the brain to adapt to a delayed velocity-dependent force field. Two groups of subjects preformed a standard reaching experiment under a velocity dependent force field. The force was either immediately proportional to the current velocity (Control or lagged it by 50 ms (Test. The results demonstrate clear adaptation to the delayed force perturbations. Deviations from a straight line during catch trials were shifted in time compared to post-adaptation to a non-delayed velocity dependent field (Control, indicating expectation to the delayed force field. Adaptation to force fields is considered to be a process in which the motor system predicts the forces to be expected based on the state that a limb will assume in response to motor commands. This study demonstrates for the first time that the temporal window of this prediction needs not to be fixed. This is relevant to the ability of the adaptive mechanisms to compensate for variability in the transmission of information across the sensory-motor system.

Nonlinear nonresonant forces by radio-frequency waves in plasmas

International Nuclear Information System (INIS)

Gao Zhe; Fisch, Nathaniel J.; Qin, Hong; Myra, J. R.

2007-01-01

Nonresonant forces by applied rf waves in plasmas are analyzed. Along the background dc magnetic field, the force arises from the gradient of the ponderomotive potential. Only when the dc magnetic field is straight, however, is this parallel force completely consistent with that from the single particle picture, where the ponderomotive force depends on the gradients of rf fields only. Across the dc magnetic field, besides the ponderomotive force from the particle picture, additional Reynolds stress and polarization stress contribute to the total force. For waves with frequency much lower than the cyclotron frequency, the perpendicular forces from the particle and fluid pictures can have opposite signs. In plasmas with a symmetry angle (e.g., toroidal systems), nonresonant forces cannot drive net flow or current in the flux surface, but the radial force may influence macroscopic behavior of plasma. Moreover, nonresonant forces may drive flow or current in linear plasmas or in a localized region of toroidal plasmas

Structural and reactivity models for copper oxygenases: cooperative effects and novel reactivities.

Science.gov (United States)

Serrano-Plana, Joan; Garcia-Bosch, Isaac; Company, Anna; Costas, Miquel

2015-08-18

Dioxygen is widely used in nature as oxidant. Nature itself has served as inspiration to use O2 in chemical synthesis. However, the use of dioxygen as an oxidant is not straightforward. Its triplet ground-state electronic structure makes it unreactive toward most organic substrates. In natural systems, metalloenzymes activate O2 by reducing it to more reactive peroxide (O2(2-)) or superoxide (O2(-)) forms. Over the years, the development of model systems containing transition metals has become a convenient tool for unravelling O2-activation mechanistic aspects and reproducing the oxidative activity of enzymes. Several copper-based systems have been developed within this area. Tyrosinase is a copper-based O2-activating enzyme, whose structure and reactivity have been widely studied, and that serves as a paradigm for O2 activation at a dimetal site. It contains a dicopper center in its active site, and it catalyzes the regioselective ortho-hydroxylation of phenols to catechols and further oxidation to quinones. This represents an important step in melanin biosynthesis and it is mediated by a dicopper(II) side-on peroxo intermediate species. In the present accounts, our research in the field of copper models for oxygen activation is collected. We have developed m-xylyl linked dicopper systems that mimick structural and reactivity aspects of tyrosinase. Synergistic cooperation of the two copper(I) centers results in O2 binding and formation of bis(μ-oxo)dicopper(III) cores. These in turn bind and ortho-hydroxylate phenolates via an electrophilic attack of the oxo ligand over the arene. Interestingly the bis(μ-oxo)dicopper(III) cores can also engage in ortho-hydroxylation-defluorination of deprotonated 2-fluorophenols, substrates that are well-known enzyme inhibitors. Analysis of Cu2O2 species with different binding modes show that only the bis(μ-oxo)dicopper(III) cores can mediate the reaction. Finally, the use of unsymmetric systems for oxygen activation is a field

DOE Task Force meeting on Electrical Breakdown of Insulating Ceramics in a High Radiation Field

International Nuclear Information System (INIS)

Green, P.H.