Consistent force fields for saccharides

DEFF Research Database (Denmark)

Rasmussen, Kjeld

1999-01-01

Consistent force fields for carbohydrates were hitherto developed by extensive optimization ofpotential energy function parameters on experimental data and on ab initio results. A wide range of experimental data is used: internal structures obtained from gas phase electron diffraction and from x......-anomeric effects are accounted for without addition of specific terms. The work is done in the framework of the Consistent Force Field which originatedin Israel and was further developed in Denmark. The actual methods and strategies employed havebeen described previously. Extensive testing of the force field...

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)

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.

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

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

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

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

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.

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.

Combination Rules for Morse-Based van der Waals Force Fields.

Science.gov (United States)

Yang, Li; Sun, Lei; Deng, Wei-Qiao

2018-02-15

In traditional force fields (FFs), van der Waals interactions have been usually described by the Lennard-Jones potentials. Conventional combination rules for the parameters of van der Waals (VDW) cross-termed interactions were developed for the Lennard-Jones based FFs. Here, we report that the Morse potentials were a better function to describe VDW interactions calculated by highly precise quantum mechanics methods. A new set of combination rules was developed for Morse-based FFs, in which VDW interactions were described by Morse potentials. The new set of combination rules has been verified by comparing the second virial coefficients of 11 noble gas mixtures. For all of the mixed binaries considered in this work, the combination rules work very well and are superior to all three other existing sets of combination rules reported in the literature. We further used the Morse-based FF by using the combination rules to simulate the adsorption isotherms of CH 4 at 298 K in four covalent-organic frameworks (COFs). The overall agreement is great, which supports the further applications of this new set of combination rules in more realistic simulation systems.

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...

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-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

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.

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....

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 ...

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

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.

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

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.

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

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.

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).

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...

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.

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.

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

Energy Technology Data Exchange (ETDEWEB)

Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117, 7491 Trondheim (Norway)

2015-11-14

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

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.

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.

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.

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.

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.

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

Science.gov (United States)

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

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

Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

Science.gov (United States)

Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

2015-01-01

Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

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

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

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

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.

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

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

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

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.

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.

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

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples

Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges

Directory of Open Access Journals (Sweden)

Agustín Leobardo Herrera-May

2016-08-01

Full Text Available Microelectromechanical systems (MEMS resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases.

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.

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.

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)

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.

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 ...

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

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

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

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.

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/ .

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.

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.

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.

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

OpenAIRE

Lemkul, Justin A.; Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base...

Vortex network community based reduced-order force model

Science.gov (United States)

Gopalakrishnan Meena, Muralikrishnan; Nair, Aditya; Taira, Kunihiko

2017-11-01

We characterize the vortical wake interactions by utilizing network theory and cluster-based approaches, and develop a data-inspired unsteady force model. In the present work, the vortical interaction network is defined by nodes representing vortical elements and the edges quantified by induced velocity measures amongst the vortices. The full vorticity field is reduced to a finite number of vortical clusters based on network community detection algorithm, which serves as a basis for a skeleton network that captures the essence of the wake dynamics. We use this reduced representation of the wake to develop a data-inspired reduced-order force model that can predict unsteady fluid forces on the body. The overall formulation is demonstrated for laminar flows around canonical bluff body wake and stalled flow over an airfoil. We also show the robustness of the present network-based model against noisy data, which motivates applications towards turbulent flows and experimental measurements. Supported by the National Science Foundation (Grant 1632003).

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

Information driving force and its application in agent-based modeling

Science.gov (United States)

Chen, Ting-Ting; Zheng, Bo; Li, Yan; Jiang, Xiong-Fei

2018-04-01

Exploring the scientific impact of online big-data has attracted much attention of researchers from different fields in recent years. Complex financial systems are typical open systems profoundly influenced by the external information. Based on the large-scale data in the public media and stock markets, we first define an information driving force, and analyze how it affects the complex financial system. The information driving force is observed to be asymmetric in the bull and bear market states. As an application, we then propose an agent-based model driven by the information driving force. Especially, all the key parameters are determined from the empirical analysis rather than from statistical fitting of the simulation results. With our model, both the stationary properties and non-stationary dynamic behaviors are simulated. Considering the mean-field effect of the external information, we also propose a few-body model to simulate the financial market in the laboratory.

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.

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.

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

Science.gov (United States)

Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

2009-02-17

A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

Environmental Assessment for the National Museum of the United States Air Force Addition, Wright-Patterson Air Force Base, Ohio

Science.gov (United States)

2013-02-01

AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) United States Air Force 88th...Air Base Wing Wright-Patterson Air Force Base, Ohio 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES...visitors nationwide and from foreign countries. Softball and soccer fields are located adjacent to the Museum grounds and are operated by the 88 Air

External Force Estimation for Teleoperation Based on Proprioceptive Sensors

Directory of Open Access Journals (Sweden)

Enrique del Sol

2014-03-01

Full Text Available This paper establishes an approach to external force estimation for telerobotic control in radioactive environments by the use of an identified manipulator model and pressure sensors, without employing a force/torque sensor. The advantages of - and need for - force feedback have been well-established in the field of telerobotics, where electrical and back-drivable manipulators have traditionally been used. This research proposes a methodology employing hydraulic robots for telerobotics tasks based on a model identification scheme. Comparative results of a force sensor and the proposed approach using a hydraulic telemanipulator are presented under different conditions. This approach not only presents a cost effective solution but also a methodology for force estimation in radioactive environments, where the dose rates limit the use of electronic devices such as sensing equipment.

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.

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.

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.

Enhanced Particle Swarm Optimization Algorithm: Efficient Training of ReaxFF Reactive Force Fields.

Science.gov (United States)

Furman, David; Carmeli, Benny; Zeiri, Yehuda; Kosloff, Ronnie

2018-05-04

Particle swarm optimization is a powerful metaheuristic population-based global optimization algorithm. However, when applied to non-separable objective functions its performance on multimodal landscapes is significantly degraded. Here we show that a significant improvement in the search quality and efficiency on multimodal functions can be achieved by enhancing the basic rotation-invariant particle swarm optimization algorithm with isotropic Gaussian mutation operators. The new algorithm demonstrates a superior performance across several nonlinear, multimodal benchmark functions compared to the rotation-invariant Particle Swam Optimization (PSO) algorithm and the well-established simulated annealing and sequential one-parameter parabolic interpolation methods. A search for the optimal set of parameters for the dispersion interaction model in ReaxFF-lg reactive force field is carried out with respect to accurate DFT-TS calculations. The resulting optimized force field accurately describes the equations of state of several high-energy molecular crystals where such interactions are of crucial importance. The improved algorithm also presents a better performance compared to a Genetic Algorithm optimization method in the optimization of a ReaxFF-lg correction model parameters. The computational framework is implemented in a standalone C++ code that allows a straightforward development of ReaxFF reactive force fields.

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

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

[Environmental investigation of ground water contamination at Wright-Patterson Air Force Base, Ohio]. Volume 5, Field Investigation report

Energy Technology Data Exchange (ETDEWEB)

1992-03-01

An environmental investigation of ground water conditions has been undertaken at Wright-Patterson Air Force Base (WPAFB), Ohio to obtain data to assist in the evaluation of a potential removal action to prevent, to the extent practicable, migration of the contaminated ground water across Base boundaries. Field investigations were limited to the central section of the southwestern boundary of Area C and the Springfield Pike boundary of Area B. Further, the study was limited to a maximum depth of 150 feet below grade. Three primary activities of the field investigation were: (1) installation of 22 monitoring wells, (2) collection and analysis of ground water from 71 locations, (3) measurement of ground water elevations at 69 locations. Volatile organic compounds including trichloroethylene, perchloroethylene, and/or vinyl chloride were detected in concentrations exceeding Maximum Contaminant Levels (MCL) at three locations within the Area C investigation area. Ground water at the Springfield Pike boundary of Area B occurs in two primary units, separated by a thicker-than-expected clay layers. One well within Area B was determined to exceed the MCL for trichloroethylene.

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.

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)

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.

A ferrofluid based artificial tactile sensor with magnetic field control

Energy Technology Data Exchange (ETDEWEB)

Volkova, T.I., E-mail: tatiana.volkova@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany); Böhm, V., E-mail: valter.boehm@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany); Naletova, V.A., E-mail: naletova@imec.msu.ru [Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Kaufhold, T., E-mail: tobias.kaufhold@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany); Becker, F., E-mail: felix.becker@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany); Zeidis, I., E-mail: igor.zeidis@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany); Zimmermann, K., E-mail: klaus.zimmermann@tu-ilmenau.de [Technical Mechanics Group, Faculty of Mechanical Engineering, Technische Universität Ilmenau, Ilmenau D-98684 (Germany)

2017-06-01

The paper deals with a tactile sensor inspired by biological hairs of mammals. The working principle is based on the effect of the magnetic force exerted on a paramagnetic body submerged into a ferrofluid volume under the influence of a nonuniform magnetic field. The deflection of the sensor's rod caused by external mechanical stimuli may be unambiguously identified by the distortion of the magnetic field, which occurs due to the motion of the attached body in the ferrofluid. The magnetic force acting on the body is evaluated experimentally and theoretically for the nonuniform magnetic field of a permanent magnet. The controlled oscillations of the rod are realised by applying a nonuniform magnetic field of periodically altering direction. - Highlights: • A design approach of a tactile sensor inspired by special mammalian hairs is presented. • The working principle is based on magnetic properties of a ferrofluid in magnetic fields. • The magnetic force acting on a body submerged into a ferrofluid volume is evaluated. • External mechanical stimuli may be identified by the distortion of the magnetic field. • The controlled whisking-like oscillations of the sensor's rod are realised experimentally.

A ferrofluid based artificial tactile sensor with magnetic field control

International Nuclear Information System (INIS)

Volkova, T.I.; Böhm, V.; Naletova, V.A.; Kaufhold, T.; Becker, F.; Zeidis, I.; Zimmermann, K.

2017-01-01

The paper deals with a tactile sensor inspired by biological hairs of mammals. The working principle is based on the effect of the magnetic force exerted on a paramagnetic body submerged into a ferrofluid volume under the influence of a nonuniform magnetic field. The deflection of the sensor's rod caused by external mechanical stimuli may be unambiguously identified by the distortion of the magnetic field, which occurs due to the motion of the attached body in the ferrofluid. The magnetic force acting on the body is evaluated experimentally and theoretically for the nonuniform magnetic field of a permanent magnet. The controlled oscillations of the rod are realised by applying a nonuniform magnetic field of periodically altering direction. - Highlights: • A design approach of a tactile sensor inspired by special mammalian hairs is presented. • The working principle is based on magnetic properties of a ferrofluid in magnetic fields. • The magnetic force acting on a body submerged into a ferrofluid volume is evaluated. • External mechanical stimuli may be identified by the distortion of the magnetic field. • The controlled whisking-like oscillations of the sensor's rod are realised experimentally.

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.

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

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)

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

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

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.

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)

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

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

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.

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

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...

Development of a reactive force field for iron-oxyhydroxide systems.

Science.gov (United States)

Aryanpour, Masoud; van Duin, Adri C T; Kubicki, James D

2010-06-03

We adopt a classical force field methodology, ReaxFF, which is able to reproduce chemical reactions, and train its parameters for the thermodynamics of iron oxides as well as energetics of a few iron redox reactions. Two parametrizations are developed, and their results are compared with quantum calculations or experimental measurements. In addition to training, two test cases are considered: the lattice parameters of a selected set of iron minerals, and the molecular dynamics simulation of a model for alpha-FeOOH (goethite)-water interaction. Reliability and limitations of the developed force fields in predicting structure and energetics are discussed.

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.

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

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

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.

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

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.

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.

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 impact of previous knee injury on force plate and field-based measures of balance.

Science.gov (United States)

Baltich, Jennifer; Whittaker, Jackie; Von Tscharner, Vinzenz; Nettel-Aguirre, Alberto; Nigg, Benno M; Emery, Carolyn

2015-10-01

Individuals with post-traumatic osteoarthritis demonstrate increased sway during quiet stance. The prospective association between balance and disease onset is unknown. Improved understanding of balance in the period between joint injury and disease onset could inform secondary prevention strategies to prevent or delay the disease. This study examines the association between youth sport-related knee injury and balance, 3-10years post-injury. Participants included 50 individuals (ages 15-26years) with a sport-related intra-articular knee injury sustained 3-10years previously and 50 uninjured age-, sex- and sport-matched controls. Force-plate measures during single-limb stance (center-of-pressure 95% ellipse-area, path length, excursion, entropic half-life) and field-based balance scores (triple single-leg hop, star-excursion, unipedal dynamic balance) were collected. Descriptive statistics (mean within-pair difference; 95% confidence intervals) were used to compare groups. Linear regression (adjusted for injury history) was used to assess the relationship between ellipse-area and field-based scores. Injured participants on average demonstrated greater medio-lateral excursion [mean within-pair difference (95% confidence interval); 2.8mm (1.0, 4.5)], more regular medio-lateral position [10ms (2, 18)], and shorter triple single-leg hop distances [-30.9% (-8.1, -53.7)] than controls, while no between group differences existed for the remaining outcomes. After taking into consideration injury history, triple single leg hop scores demonstrated a linear association with ellipse area (β=0.52, 95% confidence interval 0.01, 1.01). On average the injured participants adjusted their position less frequently and demonstrated a larger magnitude of movement during single-limb stance compared to controls. These findings support the evaluation of balance outcomes in the period between knee injury and post-traumatic osteoarthritis onset. Copyright © 2015 Elsevier Ltd. All rights

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.

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.

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…

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.

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.

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

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

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.

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

Environmental Assessment for the Construction of a Photovoltaic Solar Array at Laughlin Air Force Base, Texas

Science.gov (United States)

2011-10-01

Softball Field FAMCamp Golf Course Club House Tennis Court GENERAL PLAN Update | Laughlin Air Force Base, Texas 4-9 CoMPonEnT PLAns Legend[ FIGuRE 4-3...Golf Course, FAMCamp RV Park, several baseball/ softball fields, a paintball field, an outdoor skeet shooting range, a multi-sport track and field

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.

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.

(Environmental investigation of ground water contamination at Wright-Patterson Air Force Base, Ohio)

Energy Technology Data Exchange (ETDEWEB)

1991-10-01

This report presents information concerning field procedures employed during the monitoring, well construction, well purging, sampling, and well logging at the Wright-Patterson Air Force Base. Activities were conducted in an effort to evaluate ground water contamination.

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.

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.

2017 Annual Terrestrial Sampling Plan for Sandia National Laboratories/New Mexico on Kirtland Air Force Base

Energy Technology Data Exchange (ETDEWEB)

Griffith, Stacy R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-02-01

The 2017 Annual Terrestrial Sampling Plan for Sandia National Laboratories/New Mexico on Kirtland Air Force Base has been prepared in accordance with the “Letter of Agreement Between Department of Energy, National Nuclear Security Administration, Sandia Field Office (DOE/NNSA/SFO) and 377th Air Base Wing (ABW), Kirtland Air Force Base (KAFB) for Terrestrial Sampling” (signed January 2017), Sandia National Laboratories, New Mexico (SNL/NM). The Letter of Agreement requires submittal of an annual terrestrial sampling plan.

2018 Annual Terrestrial Sampling Plan for Sandia National Laboratories/New Mexico on Kirtland Air Force Base.

Energy Technology Data Exchange (ETDEWEB)

Griffith, Stacy R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2018-01-01

The 2018 Annual Terrestrial Sampling Plan for Sandia National Laboratories/New Mexico on Kirtland Air Force Base has been prepared in accordance with the “Letter of Agreement Between Department of Energy, National Nuclear Security Administration, Sandia Field Office (DOE/NNSA/SFO) and 377th Air Base Wing (ABW), Kirtland Air Force Base (KAFB) for Terrestrial Sampling” (signed January 2017), Sandia National Laboratories, New Mexico (SNL/NM). The Letter of Agreement requires submittal of an annual terrestrial sampling plan.

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.

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.

Accurate fluid force measurement based on control surface integration

Science.gov (United States)

Lentink, David

2018-01-01

Nonintrusive 3D fluid force measurements are still challenging to conduct accurately for freely moving animals, vehicles, and deforming objects. Two techniques, 3D particle image velocimetry (PIV) and a new technique, the aerodynamic force platform (AFP), address this. Both rely on the control volume integral for momentum; whereas PIV requires numerical integration of flow fields, the AFP performs the integration mechanically based on rigid walls that form the control surface. The accuracy of both PIV and AFP measurements based on the control surface integration is thought to hinge on determining the unsteady body force associated with the acceleration of the volume of displaced fluid. Here, I introduce a set of non-dimensional error ratios to show which fluid and body parameters make the error negligible. The unsteady body force is insignificant in all conditions where the average density of the body is much greater than the density of the fluid, e.g., in gas. Whenever a strongly deforming body experiences significant buoyancy and acceleration, the error is significant. Remarkably, this error can be entirely corrected for with an exact factor provided that the body has a sufficiently homogenous density or acceleration distribution, which is common in liquids. The correction factor for omitting the unsteady body force, {{{ {ρ f}} {1 - {ρ f} ( {{ρ b}+{ρ f}} )}.{( {{{{ρ }}b}+{ρ f}} )}}} , depends only on the fluid, {ρ f}, and body, {{ρ }}b, density. Whereas these straightforward solutions work even at the liquid-gas interface in a significant number of cases, they do not work for generalized bodies undergoing buoyancy in combination with appreciable body density inhomogeneity, volume change (PIV), or volume rate-of-change (PIV and AFP). In these less common cases, the 3D body shape needs to be measured and resolved in time and space to estimate the unsteady body force. The analysis shows that accounting for the unsteady body force is straightforward to non

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

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

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.

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

Basing the US Air Force Special Operations Forces.

Science.gov (United States)

1986-12-01

Headquarters Military Airlift Command (Hq MAC/XONP), Scott AFB, IL, July 8, 1986. 2. Daskin , Mark S. " A Maximum Expected Covering Location Model: Formulation...7942 m~ I SAIR F ORME S ECI L PE DO S CHOOL’ 1 OF EMNIEERINO A E KCRAUS DEC 66 RFIT/OOLOS/MN-6 IUCLRS SIFIE F.’G1F/OI L Ehhmhmmhhhhhhl smomhmhmhhum...Ap a . %Ř ~ ,~, ~~%9~ q%%~ * % . i %%~ . ~* - out; ’-ILE Copy / AFIT/GOR/OS/86D-6 II BASING THE US AIR FORCE SPECIAL OPERATIONS FORCES THESIS Mark E

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.

Ocean Wave Simulation Based on Wind Field.

Directory of Open Access Journals (Sweden)

Zhongyi Li

Full Text Available Ocean wave simulation has a wide range of applications in movies, video games and training systems. Wind force is the main energy resource for generating ocean waves, which are the result of the interaction between wind and the ocean surface. While numerous methods to handle simulating oceans and other fluid phenomena have undergone rapid development during the past years in the field of computer graphic, few of them consider to construct ocean surface height field from the perspective of wind force driving ocean waves. We introduce wind force to the construction of the ocean surface height field through applying wind field data and wind-driven wave particles. Continual and realistic ocean waves result from the overlap of wind-driven wave particles, and a strategy was proposed to control these discrete wave particles and simulate an endless ocean surface. The results showed that the new method is capable of obtaining a realistic ocean scene under the influence of wind fields at real time rates.

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

Reciprocity-based experimental determination of dynamic forces and moments: A feasibility study

Science.gov (United States)

Ver, Istvan L.; Howe, Michael S.

1994-01-01

BBN Systems and Technologies has been tasked by the Georgia Tech Research Center to carry Task Assignment No. 7 for the NASA Langley Research Center to explore the feasibility of 'In-Situ Experimental Evaluation of the Source Strength of Complex Vibration Sources Utilizing Reciprocity.' The task was carried out under NASA Contract No. NAS1-19061. In flight it is not feasible to connect the vibration sources to their mounting points on the fuselage through force gauges to measure dynamic forces and moments directly. However, it is possible to measure the interior sound field or vibration response caused by these structureborne sound sources at many locations and invoke principle of reciprocity to predict the dynamic forces and moments. The work carried out in the framework of Task 7 was directed to explore the feasibility of reciprocity-based measurements of vibration forces and moments.

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

Gas adsorption in Mg-porphyrin-based porous organic frameworks: A computational simulation by first-principles derived force field.

Science.gov (United States)

Pang, Yujia; Li, Wenliang; Zhang, Jingping

2017-09-15

A novel type of porous organic frameworks, based on Mg-porphyrin, with diamond-like topology, named POF-Mgs is computationally designed, and the gas uptakes of CO 2 , H 2 , N 2 , and H 2 O in POF-Mgs are investigated by Grand canonical Monte Carlo simulations based on first-principles derived force fields (FF). The FF, which describes the interactions between POF-Mgs and gases, are fitted by dispersion corrected double-hybrid density functional theory, B2PLYP-D3. The good agreement between the obtained FF and the first-principle energies data confirms the reliability of the FF. Furthermore our simulation shows the presence of a small amount of H 2 O (≤ 0.01 kPa) does not much affect the adsorption quantity of CO 2 , but the presence of higher partial pressure of H 2 O (≥ 0.1 kPa) results in the CO 2 adsorption decrease significantly. The good performance of POF-Mgs in the simulation inspires us to design novel porous materials experimentally for gas adsorption and purification. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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.

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

Enhancement of force patterns classification based on Gaussian distributions.

Science.gov (United States)

Ertelt, Thomas; Solomonovs, Ilja; Gronwald, Thomas

2018-01-23

Description of the patterns of ground reaction force is a standard method in areas such as medicine, biomechanics and robotics. The fundamental parameter is the time course of the force, which is classified visually in particular in the field of clinical diagnostics. Here, the knowledge and experience of the diagnostician is relevant for its assessment. For an objective and valid discrimination of the ground reaction force pattern, a generic method, especially in the medical field, is absolutely necessary to describe the qualities of the time-course. The aim of the presented method was to combine the approaches of two existing procedures from the fields of machine learning and the Gauss approximation in order to take advantages of both methods for the classification of ground reaction force patterns. The current limitations of both methods could be eliminated by an overarching method. Twenty-nine male athletes from different sports were examined. Each participant was given the task of performing a one-legged stopping maneuver on a force plate from the maximum possible starting speed. The individual time course of the ground reaction force of each subject was registered and approximated on the basis of eight Gaussian distributions. The descriptive coefficients were then classified using Bayesian regulated neural networks. The different sports served as the distinguishing feature. Although the athletes were all given the same task, all sports referred to a different quality in the time course of ground reaction force. Meanwhile within each sport, the athletes were homogeneous. With an overall prediction (R = 0.938) all subjects/sports were classified correctly with 94.29% accuracy. The combination of the two methods: the mathematical description of the time course of ground reaction forces on the basis of Gaussian distributions and their classification by means of Bayesian regulated neural networks, seems an adequate and promising method to discriminate the

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.

Design Methodology for Magnetic Field-Based Soft Tri-Axis Tactile Sensors.

Science.gov (United States)

Wang, Hongbo; de Boer, Greg; Kow, Junwai; Alazmani, Ali; Ghajari, Mazdak; Hewson, Robert; Culmer, Peter

2016-08-24

Tactile sensors are essential if robots are to safely interact with the external world and to dexterously manipulate objects. Current tactile sensors have limitations restricting their use, notably being too fragile or having limited performance. Magnetic field-based soft tactile sensors offer a potential improvement, being durable, low cost, accurate and high bandwidth, but they are relatively undeveloped because of the complexities involved in design and calibration. This paper presents a general design methodology for magnetic field-based three-axis soft tactile sensors, enabling researchers to easily develop specific tactile sensors for a variety of applications. All aspects (design, fabrication, calibration and evaluation) of the development of tri-axis soft tactile sensors are presented and discussed. A moving least square approach is used to decouple and convert the magnetic field signal to force output to eliminate non-linearity and cross-talk effects. A case study of a tactile sensor prototype, MagOne, was developed. This achieved a resolution of 1.42 mN in normal force measurement (0.71 mN in shear force), good output repeatability and has a maximum hysteresis error of 3.4%. These results outperform comparable sensors reported previously, highlighting the efficacy of our methodology for sensor design.

Eielson Air Force Base OU-1 baseline risk assessment

International Nuclear Information System (INIS)

Jarvis, M.T.; Jarvis, T.T.; Van Houten, N.C.; Lewis, R.E.

1993-09-01

This Baseline Risk Assessment report is the second volume in a set of three volumes for operable Unit 1 (OU-1). The companion documents contain the Remedial Investigation and the Feasibility Study. Operable Unit 1 (OU-1) is one of several groups of hazardous waste sites located at Eielson Air Force Base (AFB) near Fairbanks, Alaska. The operable units at Eielson are typically characterized by petroleum, oil, lubricant/solvent contamination, and by the presence of organics floating at the water table. In 1989 and 1990, firms under contract to the Air Force conducted field studies to gather information about the extent of chemical contamination in soil, groundwater, and soil air pore space (soil gas) at the site. This report documents the results of a baseline risk assessment, which uses the 1989 and 1991 site characterization database to quantify the potential human health risk associated with past Base industrial activities in the vicinity of OU-1. Background data collected in 1992 were also used in the preparation of this report

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.

Hanscom Air Force Base

Data.gov (United States)

Federal Laboratory Consortium — MIT Lincoln Laboratory occupies 75 acres (20 acres of which are MIT property) on the eastern perimeter of Hanscom Air Force Base, which is at the nexus of Lexington,...

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.

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.

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

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.

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

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.

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.

Research on the comparison of performance-based concept and force-based concept

Science.gov (United States)

Wu, Zeyu; Wang, Dongwei

2011-03-01

There are two ideologies about structure design: force-based concept and performance-based concept. Generally, if the structure operates during elastic stage, the two philosophies usually attain the same results. But beyond that stage, the shortage of force-based method is exposed, and the merit of performance-based is displayed. Pros and cons of each strategy are listed herein, and then which structure is best suitable to each method analyzed. At last, a real structure is evaluated by adaptive pushover method to verify that performance-based method is better than force-based method.

Stability Analysis and Variational Integrator for Real-Time Formation Based on Potential Field

Directory of Open Access Journals (Sweden)

Shengqing Yang

2014-01-01

Full Text Available This paper investigates a framework of real-time formation of autonomous vehicles by using potential field and variational integrator. Real-time formation requires vehicles to have coordinated motion and efficient computation. Interactions described by potential field can meet the former requirement which results in a nonlinear system. Stability analysis of such nonlinear system is difficult. Our methodology of stability analysis is discussed in error dynamic system. Transformation of coordinates from inertial frame to body frame can help the stability analysis focus on the structure instead of particular coordinates. Then, the Jacobian of reduced system can be calculated. It can be proved that the formation is stable at the equilibrium point of error dynamic system with the effect of damping force. For consideration of calculation, variational integrator is introduced. It is equivalent to solving algebraic equations. Forced Euler-Lagrange equation in discrete expression is used to construct a forced variational integrator for vehicles in potential field and obstacle environment. By applying forced variational integrator on computation of vehicles' motion, real-time formation of vehicles in obstacle environment can be implemented. Algorithm based on forced variational integrator is designed for a leader-follower formation.

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.

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.

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.

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.

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.

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.

Athermalization in atomic force microscope based force spectroscopy using matched microstructure coupling.

Science.gov (United States)

Torun, H; Finkler, O; Degertekin, F L

2009-07-01

The authors describe a method for athermalization in atomic force microscope (AFM) based force spectroscopy applications using microstructures that thermomechanically match the AFM probes. The method uses a setup where the AFM probe is coupled with the matched structure and the displacements of both structures are read out simultaneously. The matched structure displaces with the AFM probe as temperature changes, thus the force applied to the sample can be kept constant without the need for a separate feedback loop for thermal drift compensation, and the differential signal can be used to cancel the shift in zero-force level of the AFM.

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.

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.

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.

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.

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.

[Environmental investigation of ground water contamination at Wright- Patterson Air Force Base, Ohio]. Volume 4, Health and Safety Plan (HSP); Phase 1, Task 4 Field Investigation report: Draft

Energy Technology Data Exchange (ETDEWEB)

1991-10-01

This Health and Safety Plan (HSP) was developed for the Environmental Investigation of Ground-water Contamination Investigation at Wright-Patterson Air Force Base near Dayton, Ohio, based on the projected scope of work for the Phase 1, Task 4 Field Investigation. The HSP describes hazards that may be encountered during the investigation, assesses the hazards, and indicates what type of personal protective equipment is to be used for each task performed. The HSP also addresses the medical monitoring program, decontamination procedures, air monitoring, training, site control, accident prevention, and emergency response.

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...

Robot Training With Vector Fields Based on Stroke Survivors' Individual Movement Statistics.

Science.gov (United States)

Wright, Zachary A; Lazzaro, Emily; Thielbar, Kelly O; Patton, James L; Huang, Felix C

2018-02-01

The wide variation in upper extremity motor impairments among stroke survivors necessitates more intelligent methods of customized therapy. However, current strategies for characterizing individual motor impairments are limited by the use of traditional clinical assessments (e.g., Fugl-Meyer) and simple engineering metrics (e.g., goal-directed performance). Our overall approach is to statistically identify the range of volitional movement capabilities, and then apply a robot-applied force vector field intervention that encourages under-expressed movements. We investigated whether explorative training with such customized force fields would improve stroke survivors' (n = 11) movement patterns in comparison to a control group that trained without forces (n = 11). Force and control groups increased Fugl-Meyer UE scores (average of 1.0 and 1.1, respectively), which is not considered clinically meaningful. Interestingly, participants from both groups demonstrated dramatic increases in their range of velocity during exploration following only six days of training (average increase of 166.4% and 153.7% for the Force and Control group, respectively). While both groups showed evidence of improvement, we also found evidence that customized forces affected learning in a systematic way. When customized forces were active, we observed broader distributions of velocity that were not present in the controls. Second, we found that these changes led to specific changes in unassisted motion. In addition, while the shape of movement distributions changed significantly for both groups, detailed analysis of the velocity distributions revealed that customized forces promoted a greater proportion of favorable changes. Taken together, these results provide encouraging evidence that patient-specific force fields based on individuals' movement statistics can be used to create new movement patterns and shape them in a customized manner. To the best of our knowledge, this paper is the first

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.

[Environmental investigation of ground water contamination at Wright-Patterson Air Force Base, Ohio]. Volume 3, Appendix A, Draft standard operating procedures and elements: Sampling and Analysis Plan (SAP): Phase 1, Task 4, Field Investigation, Draft

Energy Technology Data Exchange (ETDEWEB)

1991-10-01

This report presents information concerning field procedures employed during the monitoring, well construction, well purging, sampling, and well logging at the Wright-Patterson Air Force Base. Activities were conducted in an effort to evaluate ground water contamination.

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

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)

Phase-resolved fluid dynamic forces of a flapping foil energy harvester based on PIV measurements

Science.gov (United States)

Liburdy, James

2017-11-01

Two-dimensional particle image velocimetry measurements are performed in a wind tunnel to evaluate the spatial and temporal fluid dynamic forces acting on a flapping foil operating in the energy harvesting regime. Experiments are conducted at reduced frequencies (k = fc/U) of 0.05 - 0.2, pitching angle of, and heaving amplitude of A / c = 0.6. The phase-averaged pressure field is obtained by integrating the pressure Poisson equation. Fluid dynamic forces are then obtained through the integral momentum equation. Results are compared with a simple force model based on the concept of flow impulse. These results help to show the detailed force distributions, their transient nature and aide in understanding the impact of the fluid flow structures that contribute to the power production.

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

Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

DEFF Research Database (Denmark)

Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter

2013-01-01

In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously rep...

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

Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

International Nuclear Information System (INIS)

Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

2011-01-01

In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

Transitioning from Faculty-Led Lecture to Student-Centered Field Learning Facilitated by Near-Peer Mentors: Preliminary Findings from the GeoFORCE/ STEMFORCE Program.

Science.gov (United States)

Berry, M.; Wright, V. D.; Ellins, K. K.; Browder, M. G. J.; Castillo, R.; Kotowski, A. J.; Libarkin, J. C.; Lu, J.; Maredia, N.; Butler, N.

2017-12-01

GeoFORCE Texas, a geology-based outreach program in the Jackson School of Geosciences, offers weeklong summer geology field based courses to secondary students from minority-serving high schools in Texas and the Bahamas. Students transitioning from eighth to ninth grade are recruited into the program and ideally remain in GeoFORCE for four years. The program aims to empower underrepresented students by exposing them to experiences intended to inspire them to pursue geoscience or other STEM careers. Since the program's inception in 2005, GeoFORCE Texas has relied on a mix of classroom lectures delivered by a geoscience faculty member and time in the field. Early research findings from a National Science Foundation-sponsored GeoPaths-IMPACT project are influencing the evolution of field instruction away from the faculty-led lecture model to student-centered learning that may improve students' grasp of key geological concepts. The eleventh and twelfth grade programs are shifting towards this strategy. Each trip is facilitated by a seven-person team comprised of a geoscience graduate student, master teachers, four undergraduate geology students, and preservice teachers. Members of the instructional team reflected the racial, ethnic, and cultural diversity that the geoscience strives to achieve; all are excellent role models for GeoFORCE students. The outcome of the most recent Central Texas twelfth grade trip, which used a student-centered, project-based approach, was especially noteworthy. Each group was given a topic to apply to what they saw in the field, such as fluvial systems, cultural significance, or geohazards, etc., and present in any manner in front of peers and a panel of geoscience experts. Students used the latest presentation technology available to them (e.g. Prezi, iMovies) and sketches and site notes from field stops. The final presentations were clear, informative, and entertaining. It can be concluded that the students were more engaged with the

An Optimization-Based Impedance Approach for Robot Force Regulation with Prescribed Force Limits

Directory of Open Access Journals (Sweden)

R. de J. Portillo-Vélez

2015-01-01

Full Text Available An optimization based approach for the regulation of excessive or insufficient forces at the end-effector level is introduced. The objective is to minimize the interaction force error at the robot end effector, while constraining undesired interaction forces. To that end, a dynamic optimization problem (DOP is formulated considering a dynamic robot impedance model. Penalty functions are considered in the DOP to handle the constraints on the interaction force. The optimization problem is online solved through the gradient flow approach. Convergence properties are presented and the stability is drawn when the force limits are considered in the analysis. The effectiveness of our proposal is validated via experimental results for a robotic grasping task.

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

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

Science.gov (United States)

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-01

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

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

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)

Cell force mapping using a double-sided micropillar array based on the moiré fringe method

Science.gov (United States)

Zhang, F.; Anderson, S.; Zheng, X.; Roberts, E.; Qiu, Y.; Liao, R.; Zhang, X.

2014-07-01

The mapping of traction forces is crucial to understanding the means by which cells regulate their behavior and physiological function to adapt to and communicate with their local microenvironment. To this end, polymeric micropillar arrays have been used for measuring cell traction force. However, the small scale of the micropillar deflections induced by cell traction forces results in highly inefficient force analyses using conventional optical approaches; in many cases, cell forces may be below the limits of detection achieved using conventional microscopy. To address these limitations, the moiré phenomenon has been leveraged as a visualization tool for cell force mapping due to its inherent magnification effect and capacity for whole-field force measurements. This Letter reports an optomechanical cell force sensor, namely, a double-sided micropillar array (DMPA) made of poly(dimethylsiloxane), on which one side is employed to support cultured living cells while the opposing side serves as a reference pattern for generating moiré patterns. The distance between the two sides, which is a crucial parameter influencing moiré pattern contrast, is predetermined during fabrication using theoretical calculations based on the Talbot effect that aim to optimize contrast. Herein, double-sided micropillar arrays were validated by mapping mouse embryo fibroblast contraction forces and the resulting force maps compared to conventional microscopy image analyses as the reference standard. The DMPA-based approach precludes the requirement for aligning two independent periodic substrates, improves moiré contrast, and enables efficient moiré pattern generation. Furthermore, the double-sided structure readily allows for the integration of moiré-based cell force mapping into microfabricated cell culture environments or lab-on-a-chip devices.

B-spline tight frame based force matching method

Science.gov (United States)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

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.

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.

US Air Force Base Observations

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Hourly observations taken by U.S. Air Force personnel at bases in the United States and around the world. Foreign observations concentrated in the Middle East and...

Adaptation to delayed force perturbations in reaching movements.

Directory of Open Access Journals (Sweden)

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.

Development of a shear-force scanning near-field cathodoluminescence microscope for characterization of nanostructures' optical properties.

Science.gov (United States)

Bercu, N B; Troyon, M; Molinari, M

2016-09-01

An original scanning near-field cathodoluminescence microscope for nanostructure characterization has been developed and successfully tested. By using a bimorph piezoelectric stack both as actuator and detector, the developed setup constitutes a real improvement compared to previously reported SEM-based solutions. The technique combines a scanning probe and a scanning electron microscope in order to simultaneously offer near-field cathodoluminescence and topographic images of the sample. Share-force topography and cathodoluminescence measurements on GaN, SiC and ZnO nanostructures using the developed setup are presented showing a nanometric resolution in both topography and cathodoluminescence images with increased sensitivity compared to classical luminescence techniques. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Operable Unit 1 remedial investigation report, Eielson Air Force Base, Alaska

International Nuclear Information System (INIS)

Gilmore, T.J.; Fruland, R.M.; Liikala, T.L.

1994-06-01

This remedial investigation report for operable Unit 1 (OU-1) at Eielson Air Force Base presents data, calculations, and conclusions as to the nature and extent of surface and subsurface contamination at the eight source areas that make up OU-1. The information is based on the 1993 field investigation result and previous investigations. This report is the first in a set of three for OU-1. The other reports are the baseline risk assessment and feasibility study. The information in these reports will lead to a Record of Decision that will guide and conclude the environmental restoration effort for OU-1 at Eielson Air Force Base. The primary contaminants of concern include fuels and fuel-related contaminants (diesel; benzene, toluene, ethylbenzene, and xylene; total petroleum hydrocarbon; polycyclic aromatic hydrocarbons), maintenance-related solvents and cleaners (volatile chlorinated hydrocarbons such as trichloroothylene), polychlorinated biphenyls, and dichlorodiphenyltrichloroethane (DDT). The origins of contaminants of concern include leaks from storage tanks, drums and piping, and spills. Ongoing operations and past sitewide practices also contribute to contaminants of concern at OU-1 source areas. These include spraying mixed oil and solvent wastes on unpaved roads and aerial spraying of DDT

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

Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring

DEFF Research Database (Denmark)

Lanzarotti, Esteban; Marcatili, Paolo; Nielsen, Morten

2018-01-01

Interactions of T cell receptors (TCR) to peptides in complex with MHC (p:MHC) are key features that mediate cellular immune responses. While MHC binding is required for a peptide to be presented to T cells, not all MHC binders are immunogenic. The interaction of a TCR to the p:MHC complex holds...... terms. Building a benchmark of TCR:p:MHC complexes where epitopes and non-epitopes are modelled using state-of-the-art molecular modelling tools, scoring p:MHC to a given TCR using force-fields, optimized in a cross-validation setup to evaluate TCR inter atomic interactions involved with each p:MHC, we...... and model the TCR:p:MHC complex structure. In summary, we conclude that it is possible to identify the TCR cognate target among different candidate peptides by using a force-field based model, and believe this works could lay the foundation for future work within prediction of TCR:p:MHC interactions....

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.

Different elution modes and field programming in gravitational field-flow fractionation. III. Field programming by flow-rate gradient generated by a programmable pump.

Science.gov (United States)

Plocková, J; Chmelík, J

2001-05-25

Gravitational field-flow fractionation (GFFF) utilizes the Earth's gravitational field as an external force that causes the settlement of particles towards the channel accumulation wall. Hydrodynamic lift forces oppose this action by elevating particles away from the channel accumulation wall. These two counteracting forces enable modulation of the resulting force field acting on particles in GFFF. In this work, force-field programming based on modulating the magnitude of hydrodynamic lift forces was implemented via changes of flow-rate, which was accomplished by a programmable pump. Several flow-rate gradients (step gradients, linear gradients, parabolic, and combined gradients) were tested and evaluated as tools for optimization of the separation of a silica gel particle mixture. The influence of increasing amount of sample injected on the peak resolution under flow-rate gradient conditions was also investigated. This is the first time that flow-rate gradients have been implemented for programming of the resulting force field acting on particles in GFFF.

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.

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.

A Miniaturized Force Sensor Based on Hair-Like Flexible Magnetized Cylinders Deposited Over a Giant Magnetoresistive Sensor

KAUST Repository

Ribeiro, Pedro

2017-06-13

The detection of force with higher resolution than observed in humans (similar to 1 mN) is of great interest for emerging technologies, especially surgical robots, since this level of resolution could allow these devices to operate in extremely sensitive environments without harming these. In this paper, we present a force sensor fabricated with a miniaturized footprint (9 mm(2)), based on the detection of the magnetic field generated by magnetized flexible pillars over a giant magnetoresistive sensor. When these flexible pillars deflect due to external loads, the stray field emitted by these will change, thus varying the GMR sensor resistance. A sensor with an array of five pillars with 200 mu m diameter and 1 mm height was fabricated, achieving a 0 to 26 mN measurement range and capable of detecting a minimum force feature of 630 mu N. A simulation model to predict the distribution of magnetic field generated by the flexible pillars on the sensitive area of the GMR sensor in function of the applied force was developed and validated against the experimental results reported in this paper. The sensor was finally tested as a texture classification system, with the ability of differentiating between four distinct surfaces varying between 0 and 162 mu m root mean square surface roughness.

A Miniaturized Force Sensor Based on Hair-Like Flexible Magnetized Cylinders Deposited Over a Giant Magnetoresistive Sensor

KAUST Repository

Ribeiro, Pedro; Khan, Mohammed Asadullah; Alfadhel, Ahmed; Kosel, Jü rgen; Franco, Fernando; Cardoso, Susana; Bernardino, Alexandre; Santos-Victor, Jose; Jamone, Lorenzo

2017-01-01

The detection of force with higher resolution than observed in humans (similar to 1 mN) is of great interest for emerging technologies, especially surgical robots, since this level of resolution could allow these devices to operate in extremely sensitive environments without harming these. In this paper, we present a force sensor fabricated with a miniaturized footprint (9 mm(2)), based on the detection of the magnetic field generated by magnetized flexible pillars over a giant magnetoresistive sensor. When these flexible pillars deflect due to external loads, the stray field emitted by these will change, thus varying the GMR sensor resistance. A sensor with an array of five pillars with 200 mu m diameter and 1 mm height was fabricated, achieving a 0 to 26 mN measurement range and capable of detecting a minimum force feature of 630 mu N. A simulation model to predict the distribution of magnetic field generated by the flexible pillars on the sensitive area of the GMR sensor in function of the applied force was developed and validated against the experimental results reported in this paper. The sensor was finally tested as a texture classification system, with the ability of differentiating between four distinct surfaces varying between 0 and 162 mu m root mean square surface roughness.

Physical driving force of actomyosin motility based on the hydration effect.

Science.gov (United States)

Suzuki, Makoto; Mogami, George; Ohsugi, Hideyuki; Watanabe, Takahiro; Matubayasi, Nobuyuki

2017-12-01

We propose a driving force hypothesis based on previous thermodynamics, kinetics and structural data as well as additional experiments and calculations presented here on water-related phenomena in the actomyosin systems. Although Szent-Györgyi pointed out the importance of water in muscle contraction in 1951, few studies have focused on the water science of muscle because of the difficulty of analyzing hydration properties of the muscle proteins, actin, and myosin. The thermodynamics and energetics of muscle contraction are linked to the water-mediated regulation of protein-ligand and protein-protein interactions along with structural changes in protein molecules. In this study, we assume the following two points: (1) the periodic electric field distribution along an actin filament (F-actin) is unidirectionally modified upon binding of myosin subfragment 1 (M or myosin S1) with ADP and inorganic phosphate Pi (M.ADP.Pi complex) and (2) the solvation free energy of myosin S1 depends on the external electric field strength and the solvation free energy of myosin S1 in close proximity to F-actin can become the potential force to drive myosin S1 along F-actin. The first assumption is supported by integration of experimental reports. The second assumption is supported by model calculations utilizing molecular dynamics (MD) simulation to determine solvation free energies of a small organic molecule and two small proteins. MD simulations utilize the energy representation method (ER) and the roughly proportional relationship between the solvation free energy and the solvent-accessible surface area (SASA) of the protein. The estimated driving force acting on myosin S1 is as high as several piconewtons (pN), which is consistent with the experimentally observed force. © 2017 Wiley Periodicals, Inc.

Resonant Magnetic Field Sensors Based On MEMS Technology

Directory of Open Access Journals (Sweden)

Elías Manjarrez

2009-09-01

Full Text Available Microelectromechanical systems (MEMS technology allows the integration of magnetic field sensors with electronic components, which presents important advantages such as small size, light weight, minimum power consumption, low cost, better sensitivity and high resolution. We present a discussion and review of resonant magnetic field sensors based on MEMS technology. In practice, these sensors exploit the Lorentz force in order to detect external magnetic fields through the displacement of resonant structures, which are measured with optical, capacitive, and piezoresistive sensing techniques. From these, the optical sensing presents immunity to electromagnetic interference (EMI and reduces the read-out electronic complexity. Moreover, piezoresistive sensing requires an easy fabrication process as well as a standard packaging. A description of the operation mechanisms, advantages and drawbacks of each sensor is considered. MEMS magnetic field sensors are a potential alternative for numerous applications, including the automotive industry, military, medical, telecommunications, oceanographic, spatial, and environment science. In addition, future markets will need the development of several sensors on a single chip for measuring different parameters such as the magnetic field, pressure, temperature and acceleration.

Resonant Magnetic Field Sensors Based On MEMS Technology

Science.gov (United States)

Herrera-May, Agustín L.; Aguilera-Cortés, Luz A.; García-Ramírez, Pedro J.; Manjarrez, Elías

2009-01-01

Microelectromechanical systems (MEMS) technology allows the integration of magnetic field sensors with electronic components, which presents important advantages such as small size, light weight, minimum power consumption, low cost, better sensitivity and high resolution. We present a discussion and review of resonant magnetic field sensors based on MEMS technology. In practice, these sensors exploit the Lorentz force in order to detect external magnetic fields through the displacement of resonant structures, which are measured with optical, capacitive, and piezoresistive sensing techniques. From these, the optical sensing presents immunity to electromagnetic interference (EMI) and reduces the read-out electronic complexity. Moreover, piezoresistive sensing requires an easy fabrication process as well as a standard packaging. A description of the operation mechanisms, advantages and drawbacks of each sensor is considered. MEMS magnetic field sensors are a potential alternative for numerous applications, including the automotive industry, military, medical, telecommunications, oceanographic, spatial, and environment science. In addition, future markets will need the development of several sensors on a single chip for measuring different parameters such as the magnetic field, pressure, temperature and acceleration. PMID:22408480

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.

A comparison between highly resolved S-component observations and model calculations using force-free magnetic field extrapolations

International Nuclear Information System (INIS)

Seehafer, N.; Hildebrandt, J.; Krueger, A.; Akhmedov, Sh.; Gel'frejkh, G.B.

1983-01-01

Extensive model calculations of solar radio emission features were presented for the complex of solar active regions Hale No 16862, 16863, and 16864 on May 27, 1980 using force-free extrapolated magnetic fields with constant α and a treatment of radiative transfer of S-component emission. The photospheric magnetic field data were taken from magnetographic measurements whereas the required height distribution of temperature and electron density have been adopted from semi-empirical sunspot models based on recent X-, EUV-, optical, and radio observations. In contrast to the simpler magnetic field structure used in other studies, the complex source structure of the S-component emission is clearly represented by other characteristics. The results of the calculations are compared with the observations of the WRST (6 cm) and RATAN-600 (3.2 cm). (author)

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.

(Environmental investigation of ground water contamination at Wright- Patterson Air Force Base, Ohio)

Energy Technology Data Exchange (ETDEWEB)

1991-10-01

This Health and Safety Plan (HSP) was developed for the Environmental Investigation of Ground-water Contamination Investigation at Wright-Patterson Air Force Base near Dayton, Ohio, based on the projected scope of work for the Phase 1, Task 4 Field Investigation. The HSP describes hazards that may be encountered during the investigation, assesses the hazards, and indicates what type of personal protective equipment is to be used for each task performed. The HSP also addresses the medical monitoring program, decontamination procedures, air monitoring, training, site control, accident prevention, and emergency response.

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.

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

Numerical evaluation of guidance force decay of HTS bulk exposed to AC magnetic field over a NdFeB guideway

Energy Technology Data Exchange (ETDEWEB)

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

2007-12-01

The guidance force of the YBCO bulk over a NdFeB guideway used in the high-temperature superconducting maglev vehicle system was decayed by the application of the AC external magnetic field. In our previous work, we explained that the decay was due to the temperature rise of the HTS bulk caused by AC losses. In this paper, we adopted an analytic model to evaluate the decay of the critical current density of the bulk. And based on the analytic results and the Bean critical-state model, we calculated the guidance force as a function of times. Compared with the experimental results, the calculation results have almost the same trend and can qualitatively reveal the characteristics of guidance force of HTS bulk in this situation. Therefore, the guidance force decay of HTS bulk in the maglev vehicle system can be evaluated simply by this numerical method.

Optical force rectifiers based on PT-symmetric metasurfaces

Science.gov (United States)

Alaee, Rasoul; Gurlek, Burak; Christensen, Johan; Kadic, Muamer

2018-05-01

We introduce here the concept of optical force rectifier based on parity-time symmetric metasurfaces. Directly linked to the properties of non-Hermitian systems engineered by balanced loss and gain constituents, we show that light can exert asymmetric pulling or pushing forces on metasurfaces depending on the direction of the impinging light. This generates a complete force rectification in the vicinity of the exceptional point. Our findings have the potential to spark the design of applications in optical manipulation where the forces, strictly speaking, act unidirectionally.

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.

Structural study of Na2O-B2O3-SiO2 glasses from molecular simulations using a polarizable force field.

Science.gov (United States)

Pacaud, Fabien; Delaye, Jean-Marc; Charpentier, Thibault; Cormier, Laurent; Salanne, Mathieu

2017-10-28

Sodium borosilicate glasses Na 2 O-B 2 O 3 -SiO 2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO 4 and BO 4 (B IV ) and triangular BO 3 (B III ). One of the salient features of these compounds is the change of the B III /B IV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of B III /B IV with respect to the composition and the temperature.

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.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

Science.gov (United States)

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

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.

Capital Improvement Program Environmental Assessment, Dyess Air Force Base, Texas

Science.gov (United States)

2010-09-01

Counsel • Air Force Office of Special Investigations • Air Force Audit Agency • Boeing Aerospace Operations Inc . • Defense Security Service...this corresponds to a factor of 10 in relative sound energy (Bolt, Beranek, and Meuman, Inc . 1973). Table 4-1 shows the dBA scale of commons...configuration for the B-47. Intact -Interior shop upgraded for Nike Hercules in 1961. 5020 Field Maintenance Hangar Large Aircraft Maintenance Dock

Ponderomotive force near cyclotron resonance

Energy Technology Data Exchange (ETDEWEB)

Kono, Mitsuo; Sanuki, Heiji

1987-01-01

The ponderomotive force, which is involved in the excitation of macroscopic behaviors of plasma caused by wave motion, plays an important role in various non-linear wave motion phenomena. In the present study, equations for the pondermotive force for plasma in a uniform magnetic field is derived using a renormalization theory which is based on the Vlasov equation. It is shown that the pondermotive force, which diverges at the cyclotron resonence point according to adiabatic approximation, can be expressed by a non-divergent equation by taking into account the instability of the cyclotron orbit due to high-order scattering caused by a wave. This is related with chaotic particle behaviors near cyclotron resonance, where the pondermotive force is small and the diffusion process prevails. It is assumed here that the amplitude of the high-frequency electric field is not large and that the broadening of cyclotron levels is smaller than the distance between the levels. A global chaos will be created if the amplitude of the electric field becomes greater to allow the broadening to exceed the distance between the levels. (Nogami, K.).

Circuit Design of Surface Acoustic Wave Based Micro Force Sensor

Directory of Open Access Journals (Sweden)

Yuanyuan Li

2014-01-01

Full Text Available Pressure sensors are commonly used in industrial production and mechanical system. However, resistance strain, piezoresistive sensor, and ceramic capacitive pressure sensors possess limitations, especially in micro force measurement. A surface acoustic wave (SAW based micro force sensor is designed in this paper, which is based on the theories of wavelet transform, SAW detection, and pierce oscillator circuits. Using lithium niobate as the basal material, a mathematical model is established to analyze the frequency, and a peripheral circuit is designed to measure the micro force. The SAW based micro force sensor is tested to show the reasonable design of detection circuit and the stability of frequency and amplitude.

All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

Science.gov (United States)

Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

2013-10-31

A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row).

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.

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.

Dielectrophoresis-magnetophoresis force driven magnetic nanoparticle movement in transformer oil based magnetic fluids.

Science.gov (United States)

Lee, Jong-Chul; Lee, Sangyoup

2013-09-01

Magnetic fluid is a stable colloidal mixture contained magnetic nanoparticles coated with a surfactant. Recently, it was found that the fluid has properties to increase heat transfer and dielectric characteristics due to the added magnetic nanoparticles in transformer oils. The magnetic nanoparticles in the fluid experience an electrical force directed toward the place of maximum electric field strength when the electric field is applied. And when the external magnetic field is applied, the magnetic nanoparticles form long chains oriented along the direction of the field. The behaviors of magnetic nanoparticles in both the fields must play an important role in changing the heat transfer and dielectric characteristics of the fluids. In this study, we visualized the movement of magnetic nanoparticles influenced by both the fields applied in-situ. It was found that the magnetic nanoparticles travel in the region near the electrode by the electric field and form long chains along the field direction by the magnetic field. It can be inferred that the movement of magnetic nanoparticles appears by both the fields, and the breakdown voltage of transformer oil based magnetic fluids might be influenced according to the dispersion of magnetic nanoparticles.

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…

Novel nonlinear knowledge-based mean force potentials based on machine learning.

Science.gov (United States)

Dong, Qiwen; Zhou, Shuigeng

2011-01-01

The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge-based

Improved tests of extra-dimensional physics and thermal quantum field theory from new Casimir force measurements

International Nuclear Information System (INIS)

Decca, R.S.; Fischbach, E.; Klimchitskaya, G.L.; Mostepanenko, V.M.; Krause, D.E.; Lopez, D.

2003-01-01

We report new constraints on extra-dimensional models and other physics beyond the standard model based on measurements of the Casimir force between two dissimilar metals for separations in the range 0.2-1.2 μm. The Casimir force between a Au-coated sphere and a Cu-coated plate of a microelectromechanical torsional oscillator was measured statically with an absolute error of 0.3 pN. In addition, the Casimir pressure between two parallel plates was determined dynamically with an absolute error of ≅0.6 mPa. Within the limits of experimental and theoretical errors, the results are in agreement with a theory that takes into account the finite conductivity and roughness of the two metals. The level of agreement between experiment and theory was then used to set limits on the predictions of extra-dimensional physics and thermal quantum field theory. It is shown that two theoretical approaches to the thermal Casimir force which predict effects linear in temperature are ruled out by these experiments. Finally, constraints on Yukawa corrections to Newton's law of gravity are strengthened by more than an order of magnitude in the range 56-330 nm

Analysis of the Usage of Magnetic Force-directed Approach and Visual Techniques for Interactive Context-based Drawing of Multi-attributed Graphs

Directory of Open Access Journals (Sweden)

Zabiniako Vitaly

2014-12-01

Full Text Available In this article, the authors perform an analysis in order to assess adaptation of magnetic force-directed algorithms for context-based information extraction from multi-attributed graphs during visualization sessions. Theoretic standings behind magnetic force-directed approach are stated together with review on how particular features of respective algorithms in combination with appropriate visual techniques are especially suitable for improved processing and presenting of knowledge that is captured in form of graphs. The complexity of retrieving multi-attributed information within the proposed approach is handled with dedicated tools, such as selective attraction of nodes to MFE (Magnetic Force Emitter based on search criteria, localization of POI (Point of Interest regions, graph node anchoring, etc. Implicit compatibility of aforementioned tools with interactive nature of data exploration is distinguished. Description of case study, based on bibliometric network analysis is given, which is followed by the review of existing related works in this field. Conclusions are made and further studies in the field of visualization of multi-attributed graphs are defined.

Estimation of Handgrip Force from SEMG Based on Wavelet Scale Selection.

Science.gov (United States)

Wang, Kai; Zhang, Xianmin; Ota, Jun; Huang, Yanjiang

2018-02-24

This paper proposes a nonlinear correlation-based wavelet scale selection technology to select the effective wavelet scales for the estimation of handgrip force from surface electromyograms (SEMG). The SEMG signal corresponding to gripping force was collected from extensor and flexor forearm muscles during the force-varying analysis task. We performed a computational sensitivity analysis on the initial nonlinear SEMG-handgrip force model. To explore the nonlinear correlation between ten wavelet scales and handgrip force, a large-scale iteration based on the Monte Carlo simulation was conducted. To choose a suitable combination of scales, we proposed a rule to combine wavelet scales based on the sensitivity of each scale and selected the appropriate combination of wavelet scales based on sequence combination analysis (SCA). The results of SCA indicated that the scale combination VI is suitable for estimating force from the extensors and the combination V is suitable for the flexors. The proposed method was compared to two former methods through prolonged static and force-varying contraction tasks. The experiment results showed that the root mean square errors derived by the proposed method for both static and force-varying contraction tasks were less than 20%. The accuracy and robustness of the handgrip force derived by the proposed method is better than that obtained by the former methods.

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.

Crack growth in the creep region: criteria based on material forces

International Nuclear Information System (INIS)

Roche, R.L.

1984-12-01

Meaning of C* concept is discussed. It is shown that this concept is only a global approach of material force rate concept. The field of Csub(i)sup(*) (material force rate densities) is more representative of creep crack growth than C* integral. As application corrected expressions of C* are proposed for non isothermal cases, strain hardening creep and effect of material elasticity

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.

Science.gov (United States)

Verbaro, Daniel; Ghosh, Indrajit; Nau, Werner M; Schweitzer-Stenner, Reinhard

2010-12-30

overestimated distance between terminal carbonyl groups. In order to more accurately account for the experimental data, we changed the distribution parameters based on results recently obtained for the alanine-based tripeptides. The final model, which satisfactorily reproduced amide I' profiles, J-coupling constant, and the end-to-end distance of A(5)W, reinforces alanine's high structural preference for polyproline II. Our results suggest that distributions obtained from MD simulations suggesting a statistical coil-like distribution for alanine are still based on insufficiently accurate force fields.

History of wildland fires on Vandenberg Air Force Base, California

Science.gov (United States)

Hickson, Diana E.

1988-01-01

The fire history of the past 50 years for Vandenberg AFB, California was determined using aerial photography, field investigation, and historical and current written records. This constitutes a record of the vegetation age classes for the entire base. The location, cause, and fuel type for sixty fires from this time period were determined. The fires were mapped and entered into a geographic infomation system (GIS) for Vandenberg. Fire history maps derived from this GIS were printed at 1:9600 scale and are on deposit at the Vandenberg Environmental Task Force Office. Although some ecologically significant plant communities on Vandenberg are adapted to fire, no natural fire frequency could be determined, since only one fire possibly caused by lightning occurred in the area now within the base since 1937. Observations made during this study suggest that burning may encourage the invasion of exotic species into chaparral, in particular Burton Mesa or sandhill chaparral, an unusual and geographically limited form of chaparral found on the base.

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.

Estimation of Prestress Force Distribution in Multi-Strand System of Prestressed Concrete Structures Using Field Data Measured by Electromagnetic Sensor.

Science.gov (United States)

Cho, Keunhee; Cho, Jeong-Rae; Kim, Sung Tae; Park, Sung Yong; Kim, Young-Jin; Park, Young-Hwan

2016-08-18

The recently developed smart strand can be used to measure the prestress force in the prestressed concrete (PSC) structure from the construction stage to the in-service stage. The higher cost of the smart strand compared to the conventional strand renders it unaffordable to replace all the strands by smart strands, and results in the application of only a limited number of smart strands in the PSC structure. However, the prestress forces developed in the strands of the multi-strand system frequently adopted in PSC structures differ from each other, which means that the prestress force in the multi-strand system cannot be obtained by simple proportional scaling using the measurement of the smart strand. Therefore, this study examines the prestress force distribution in the multi-strand system to find the correlation between the prestress force measured by the smart strand and the prestress force distribution in the multi-strand system. To that goal, the prestress force distribution was measured using electromagnetic sensors for various factors of the multi-strand system adopted on site in the fabrication of actual PSC girders. The results verified the possibility to assume normal distribution for the prestress force distribution per anchor head, and a method computing the mean and standard deviation defining the normal distribution is proposed. This paper presents a meaningful finding by proposing an estimation method of the prestress force based upon field-measured data of the prestress force distribution in the multi-strand system of actual PSC structures.

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.

Environmental Assessment: General Plan-Based Environmental Impact Analysis Process, Laughlin Air Force Base

Science.gov (United States)

2007-05-01

BASED ENVIROMENTAL IMPACT ANALYSIS PROCESS LAUGHLIN AIR FORCE BASE, TEXAS AGENCY: 47th Flying Training Wing (FTW), Laughlin Air Force Base (AFB), Texas...m3 micrograms per cubic meter US United States USACE United States Army Corp of Engineers USC United States Code USCB United States Census Bureau...effects and annoyance in that very few flight operations and ground engine runs occur between 2200 hours and 0700 hours. BMPs include restricting the

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.

High-field transport of electrons and radiative effects using coupled force-balance and Fokker-Planck equations beyond the relaxation-time approximation

International Nuclear Information System (INIS)

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

2004-01-01

The dynamics of a many-electron system under both dc and infrared fields is separated into a center-of-mass and a relative motion. The first-order force-balance equation is employed for the slow center-of-mass motion of electrons, and the Fokker-Planck equation is used for the ultrafast relative scattering motion of degenerate electrons. This approach allows us to include the anisotropic energy-relaxation process which has been neglected in the energy-balance equation in the past. It also leads us to include the anisotropic coupling to the incident infrared field with different polarizations. Based on this model, the transport of electrons is explored under strong dc and infrared fields by going beyond the relaxation-time approximation. The anisotropic dependence of the electron distribution function on the parallel and perpendicular kinetic energies of electrons is displayed with respect to the dc field direction, and the effect of anisotropic coupling to an incident infrared field with polarizations parallel and perpendicular to the applied dc electric field is shown. The heating of electrons is more accurately described beyond the energy-balance equation with the inclusion of an anisotropic coupling to the infrared field. The drift velocity of electrons is found to increase with the amplitude of the infrared field due to a suppressed momentum-relaxation process (or frictional force) under parallel polarization but decreases with the amplitude due to an enhanced momentum-relaxation process under perpendicular polarization

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)

Investigation on stresses of superconductors under pulsed magnetic fields based on multiphysics model

International Nuclear Information System (INIS)

Yang, Xiaobin; Li, Xiuhong; He, Yafeng; Wang, Xiaojun; Xu, Bo

2017-01-01

Highlights: • The differential equation including temperature and magnetic field was derived for a long cylindrical superconductor. • Thermal stress and electromagnetic stress were studied at the same time under pulse field magnetizing. • The distributions of the magnetic field, the temperature and stresses are studied and compared for two pulse fields of the different duration. • The Role thermal stress and electromagnetic stress play in the process of pulse field magnetizing is discussed. - Abstract: A multiphysics model for the numerical computation of stresses, trapped field and temperature distribution of a infinite long superconducting cylinder is proposed, based on which the stresses, including the thermal stresses and mechanical stresses due to Lorentz force, and trapped fields in the superconductor subjected to pulsed magnetic fields are analyzed. By comparing the results under pulsed magnetic fields with different pulse durations, it is found that the both the mechanical stress due to the electromagnetic force and the thermal stress due to temperature gradient contribute to the total stress level in the superconductor. For pulsed magnetic field with short durations, the thermal stress is the dominant contribution to the total stress, because the heat generated by AC-loss builds up significant temperature gradient in such short durations. However, for a pulsed field with a long duration the gradient of temperature and flux, as well as the maximal tensile stress, are much smaller. And the results of this paper is meaningful for the design and manufacture of superconducting permanent magnets.

Investigation on stresses of superconductors under pulsed magnetic fields based on multiphysics model

Energy Technology Data Exchange (ETDEWEB)

Yang, Xiaobin, E-mail: yangxb@lzu.edu.cn; Li, Xiuhong; He, Yafeng; Wang, Xiaojun; Xu, Bo

2017-04-15

Highlights: • The differential equation including temperature and magnetic field was derived for a long cylindrical superconductor. • Thermal stress and electromagnetic stress were studied at the same time under pulse field magnetizing. • The distributions of the magnetic field, the temperature and stresses are studied and compared for two pulse fields of the different duration. • The Role thermal stress and electromagnetic stress play in the process of pulse field magnetizing is discussed. - Abstract: A multiphysics model for the numerical computation of stresses, trapped field and temperature distribution of a infinite long superconducting cylinder is proposed, based on which the stresses, including the thermal stresses and mechanical stresses due to Lorentz force, and trapped fields in the superconductor subjected to pulsed magnetic fields are analyzed. By comparing the results under pulsed magnetic fields with different pulse durations, it is found that the both the mechanical stress due to the electromagnetic force and the thermal stress due to temperature gradient contribute to the total stress level in the superconductor. For pulsed magnetic field with short durations, the thermal stress is the dominant contribution to the total stress, because the heat generated by AC-loss builds up significant temperature gradient in such short durations. However, for a pulsed field with a long duration the gradient of temperature and flux, as well as the maximal tensile stress, are much smaller. And the results of this paper is meaningful for the design and manufacture of superconducting permanent magnets.

Numerical analysis of the in-well vapor-stripping system demonstration at Edwards Air Force Base

International Nuclear Information System (INIS)

White, M.D.; Gilmore, T.J.

1996-10-01

Numerical simulations, with the Subsurface Transport Over Multiple Phases (STOMP) simulator, were applied to the field demonstration of an in-well vapor-stripping system at Edwards Air Force Base (AFB), near Mojave, California. The demonstration field site on the Edwards AFB was previously contaminated from traversing groundwater that was contained a varied composition of volatile organic compounds (VOCs), which primarily includes trichloroethylene (TCE). Contaminant TCE originated from surface basin that had been used to collect runoff during the cleaning of experimental rocket powered planes in the 1960s and 1970s. This report documents those simulations and associated numerical analyses. A companion report documents the in- well vapor-stripping demonstration from a field perspective

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.

Electromagnetic-based force sensor for Structural Health Monitoring(SHM)

International Nuclear Information System (INIS)

Choi, Man Yong; Park, Hae Won; Park, Jeong Hak; Sam, R.

2002-01-01

The demand for maintenance of structural health and safety to acceptable standards poses challenges for research and development of effective technologies for monitoring and measurement of parameters governing safety and health of structures. In this work, an electromagnetic based sensor has been investigated and developed for measuring force in pre-stressed steel cables and tendons. The change in magnetic permeability of a material caused by mechanical stress is exploited to measure force in the material. The sensor consists of a pair of sensing coils and a pair of reference coils. The sensing coils are wound around a stressed material while the reference pair are wound on a dummy specimen of same material as that under stress. When sensing and reference primary coils are excited by same current simultaneously, both the stressed and dummy materials are equally magnetized by the magnetic field generated by the current, and voltage is induced in the sensing and reference secondary coils. The induced voltage in each secondary coil is dependent on a number of factors including the magnetic permeability of its core which is a function of the core magnetizing current, temperature and stress/load. By suitably arranging the sensing and reference coils electro-magnetically, the effects of temperature and magnetizing current on the permeability of a stressed material can be eliminated in the output voltage of the sensor. The output voltage is a function of only the mechanical load in the stressed material, and can be calibrated for determination of force in pre-stressed materials

Magnetic force microscopy : Quantitative issues in biomaterials

NARCIS (Netherlands)

Passeri, D.; Dong, C.; Reggente, M.; Angeloni, L.; Barteri, M.; Scaramuzzo, F.A.; De Angelis, F.; Marinelli, F.; Antonelli, F.; Rinaldi, F.; Marianecci, C.; Carafa, M.; Sorbo, A.; Sordi, D.; Arends, I.W.C.E.; Rossi, M.

2014-01-01

Magnetic force microscopy (MFM) is an atomic force microscopy (AFM) based technique in which an AFM tip with a magnetic coating is used to probe local magnetic fields with the typical AFM spatial resolution, thus allowing one to acquire images reflecting the local magnetic properties of the samples

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

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.

GeoFORCE Alaska: Four-Year Field Program Brings Rural Alaskan High School Students into the STEM Pipeline

Science.gov (United States)

Fowell, S. J.; Rittgers, A.; Stephens, L.; Hutchinson, S.; Peters, H.; Snow, E.; Wartes, D.

2016-12-01

GeoFORCE Alaska is a four-year, field-based, summer geoscience program designed to raise graduation rates in rural Alaskan high schools, encourage participants to pursue college degrees, and increase the diversity of Alaska's technical workforce. Residents of predominantly Alaska Native villages holding degrees in science, technology, engineering, or math (STEM) bring valuable perspectives to decisions regarding management of cultural and natural resources. However, between 2010 and 2015 the average dropout rate for students in grades 7-12 was 8.5% per year in the North Slope School District and 7% per year in the Northwest Arctic School District. 2015 graduation rates were 70% and 75%, respectively. Statewide statistics highlight the challenge for Alaska Native students. During the 2014-2015 school year alone 37.6% of Alaska Native students dropped out of Alaskan public schools. At the college level, Alaska Native students are underrepresented in University of Alaska Fairbanks (UAF) science departments. Launched in 2012 by UAF in partnership with the longstanding University of Texas at Austin program, GeoFORCE applies the cohort model, leading the same group of high school students on geological field academies during four consecutive summers. Through a combination of active learning, teamwork, and hands-on projects at spectacular geological locations, students gain academic skills and confidence that facilitate high school and college success. To date, GeoFORCE Alaska has recruited two cohorts. 78% of these students identify as Alaska Native, reflecting community demographics. The inaugural cohort of 18 students from the North Slope Borough completed the Fourth-Year Academy in summer 2015. 94% of these students graduated from high school, at least 72% plan to attend college, and 33% will major in geoscience. A second cohort of 34 rising 9th and 10th graders entered the program in 2016. At the request of corporate sponsors, this cohort was recruited from both the

Magnetic field concentration using ferromagnetic material to propel a wireless power transfer based micro-robot

Directory of Open Access Journals (Sweden)

Dongwook Kim

2018-05-01

Full Text Available In this paper, we propose a novel coil structure, using a ferromagnetic material which concentrates the magnetic field, as the propulsion system of a wireless power transfer (WPT based micro-robot. This structure uses an incident magnetic field to induce current during wireless power transfer, to generate a Lorentz force. To prevent net cancelation of the Lorentz force in the load coil, ferrite films were applied to one side of the coil segment. The demonstrated simplicity and effectiveness of the proposed micro-robot showed its suitability for applications. Simulation and experimental results confirmed a velocity of 1.02 mm/s with 6 mW power transfer capacity for the 3 mm sized micro-robot.

Magnetic field concentration using ferromagnetic material to propel a wireless power transfer based micro-robot

Science.gov (United States)

Kim, Dongwook; Park, Bumjin; Park, Jaehyoung; Park, Hyun Ho; Ahn, Seungyoung

2018-05-01

In this paper, we propose a novel coil structure, using a ferromagnetic material which concentrates the magnetic field, as the propulsion system of a wireless power transfer (WPT) based micro-robot. This structure uses an incident magnetic field to induce current during wireless power transfer, to generate a Lorentz force. To prevent net cancelation of the Lorentz force in the load coil, ferrite films were applied to one side of the coil segment. The demonstrated simplicity and effectiveness of the proposed micro-robot showed its suitability for applications. Simulation and experimental results confirmed a velocity of 1.02 mm/s with 6 mW power transfer capacity for the 3 mm sized micro-robot.

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.

Grip Force and 3D Push-Pull Force Estimation Based on sEMG and GRNN

Directory of Open Access Journals (Sweden)

Changcheng Wu

2017-06-01

Full Text Available The estimation of the grip force and the 3D push-pull force (push and pull force in the three dimension space from the electromyogram (EMG signal is of great importance in the dexterous control of the EMG prosthetic hand. In this paper, an action force estimation method which is based on the eight channels of the surface EMG (sEMG and the Generalized Regression Neural Network (GRNN is proposed to meet the requirements of the force control of the intelligent EMG prosthetic hand. Firstly, the experimental platform, the acquisition of the sEMG, the feature extraction of the sEMG and the construction of GRNN are described. Then, the multi-channels of the sEMG when the hand is moving are captured by the EMG sensors attached on eight different positions of the arm skin surface. Meanwhile, a grip force sensor and a three dimension force sensor are adopted to measure the output force of the human's hand. The characteristic matrix of the sEMG and the force signals are used to construct the GRNN. The mean absolute value and the root mean square of the estimation errors, the correlation coefficients between the actual force and the estimated force are employed to assess the accuracy of the estimation. Analysis of variance (ANOVA is also employed to test the difference of the force estimation. The experiments are implemented to verify the effectiveness of the proposed estimation method and the results show that the output force of the human's hand can be correctly estimated by using sEMG and GRNN method.

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Science.gov (United States)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Moving force identification based on redundant concatenated dictionary and weighted l1-norm regularization

Science.gov (United States)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin; Chen, Ze-Peng; Luo, Wen-Feng

2018-01-01

Moving force identification (MFI) is an important inverse problem in the field of bridge structural health monitoring (SHM). Reasonable signal structures of moving forces are rarely considered in the existing MFI methods. Interaction forces are complex because they contain both slowly-varying harmonic and impact signals due to bridge vibration and bumps on a bridge deck, respectively. Therefore, the interaction forces are usually hard to be expressed completely and sparsely by using a single basis function set. Based on the redundant concatenated dictionary and weighted l1-norm regularization method, a hybrid method is proposed for MFI in this study. The redundant dictionary consists of both trigonometric functions and rectangular functions used for matching the harmonic and impact signal features of unknown moving forces. The weighted l1-norm regularization method is introduced for formulation of MFI equation, so that the signal features of moving forces can be accurately extracted. The fast iterative shrinkage-thresholding algorithm (FISTA) is used for solving the MFI problem. The optimal regularization parameter is appropriately chosen by the Bayesian information criterion (BIC) method. In order to assess the accuracy and the feasibility of the proposed method, a simply-supported beam bridge subjected to a moving force is taken as an example for numerical simulations. Finally, a series of experimental studies on MFI of a steel beam are performed in laboratory. Both numerical and experimental results show that the proposed method can accurately identify the moving forces with a strong robustness, and it has a better performance than the Tikhonov regularization method. Some related issues are discussed as well.

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.

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

Directory of Open Access Journals (Sweden)

Longhua Yang

2016-09-01

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

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.

Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy.

Science.gov (United States)

Walder, Robert; Van Patten, William J; Adhikari, Ayush; Perkins, Thomas T

2018-01-23

Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.

Ground-Based Midcourse Defense (GMD) Initial Defensive Operations Capability (IDOC) at Vandenberg Air Force Base Environmental Assessment

Science.gov (United States)

2003-08-28

Zielinski , EDAW, Inc., concerning utilities supply and demand for Vandenberg Air Force Base, 1 August. Rush, P., 2002. Personal communication between...Pernell W. Rush, Technical Sergeant, Water Utilities/Water Treatment NCO, USAF 30th CES/CEOIU, Vandenberg Air Force Base, and James E. Zielinski ... Dave Savinsky, Environmental Consultant, 30 CES/CEVC, Vandenberg Air Force Base, on the Preliminary Draft Ground-Based Midcourse Defense (GMD

Measurement model and calibration experiment of over-constrained parallel six-dimensional force sensor based on stiffness characteristics analysis

International Nuclear Information System (INIS)

Niu, Zhi; Zhao, Yanzhi; Zhao, Tieshi; Cao, Yachao; Liu, Menghua

2017-01-01

An over-constrained, parallel six-dimensional force sensor has various advantages, including its ability to bear heavy loads and provide redundant force measurement information. These advantages render the sensor valuable in important applications in the field of aerospace (space docking tests, etc). The stiffness of each component in the over-constrained structure has a considerable influence on the internal force distribution of the structure. Thus, the measurement model changes when the measurement branches of the sensor are under tensile or compressive force. This study establishes a general measurement model for an over-constrained parallel six-dimensional force sensor considering the different branch tensions and compression stiffness values. Numerical calculations and analyses are performed using practical examples. Based on the parallel mechanism, an over-constrained, orthogonal structure is proposed for a six-dimensional force sensor. Hence, a prototype is designed and developed, and a calibration experiment is conducted. The measurement accuracy of the sensor is improved based on the measurement model under different branch tensions and compression stiffness values. Moreover, the largest class I error is reduced from 5.81 to 2.23% full scale (FS), and the largest class II error is reduced from 3.425 to 1.871% FS. (paper)

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.

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

Final Nellis Air Force Base Capital Improvements Program Environmental Assessment

Science.gov (United States)

2013-08-01

pathology, radiology, dietetic and nutritional medicine, medical benefits and information. The 99th Security Forces Squadron provides flight-line...parking lots RKMF070024 Construct Soccer Field Parking Lot Roads/parking lots RKMF110155 Construct Solar Lighting At Hospital Track Recreation

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.

Hybrid Force Control Based on ICMAC for an Astronaut Rehabilitative Training Robot

Directory of Open Access Journals (Sweden)

Lixun Zhang

2012-08-01

Full Text Available A novel Astronaut Rehabilitative Training Robot (ART based on a cable-driven mechanism is represented in this paper. ART, a typical passive force servo system, can help astronauts to bench press in a microgravity environment. The purpose of this paper is to design controllers to eliminate the surplus force caused by an astronaut's active movements. Based on the dynamics modelling of the cable-driven unit, a hybrid force controller based on improved credit assignment CMAC (ICMAC is presented. A planning method for the cable tension is proposed so that the dynamic load produced by the ART can realistically simulate the gravity and inertial force of the barbell in a gravity environment. Finally, MATLAB simulation results of the man-machine cooperation system are provided in order to verify the effectiveness of the proposed control strategy. The simulation results show that the hybrid control method based on the structure invariance principle can inhibit the surplus force and that ICMAC can improve the dynamic performance of the passive force servo system. Furthermore, the hybrid force controller based on ICMAC can ensure the stability of the system.

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

Electric field responsive origami structures using electrostriction-based active materials

Science.gov (United States)

Ahmed, Saad; Arrojado, Erika; Sigamani, Nirmal; Ounaies, Zoubeida

2015-04-01

The objective of origami engineering is to combine origami principles with advanced materials to yield active origami shapes, which fold and unfold in response to external stimuli. We are investigating the use of P(VDF-TrFE-CTFE), a relaxor ferroelectric terpolymer, to realize origami-inspired folding and unfolding of structures and to actuate so-called action origami structures. To accomplish these two objectives, we have explored different approaches to the P(VDF-TrFECTFE) polymer actuator construction, ranging from unimorph to multilayered stacks. Electromechanical characterization of the terpolymer-based actuators is conducted with a focus on free strain, force-displacement and blocked force. Moreover dynamic thickness strains of P(VDF-TrFE-CTFE) terpolymer at different frequencies ranging from 0.1Hz to 10Hz is also measured. Quantifying the performance of terpolymer-based actuators is important to the design of action origami structures. Following these studies, action origami prototypes based on catapult, flapping butterfly wings and barking fox are actuated and characterization of these prototypes are conducted by studying impact of various parameters such as electric field magnitude and frequency, number of active layers, and actuator dimensions.

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...

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.

Reptiles and Amphibians of Fairchild Air Force Base, WA

Science.gov (United States)

2013-05-10

Reptiles and Amphibians of Fairchild Air Force Base, WA C on st ru ct io n E n gi n ee ri n g R es ea rc...online library at http://acwc.sdp.sirsi.net/client/default. ERDC/CERL TR-13-5 May 2013 Reptiles and Amphibians of Fairchild Air Force Base, WA...Washington, DC 20314-1000 ERDC/CERL TR-13-5 ii Abstract Many reptile and amphibian (collectively termed “herpetofauna”) populations are declining at

The analysis of cable forces based on natural frequency

Science.gov (United States)

Suangga, Made; Hidayat, Irpan; Juliastuti; Bontan, Darwin Julius

2017-12-01

A cable is a flexible structural member that is effective at resisting tensile forces. Cables are used in a variety of structures that employ their unique characteristics to create efficient design tension members. The condition of the cable forces in the cable supported structure is an important indication of judging whether the structure is in good condition. Several methods have been developed to measure on site cable forces. Vibration technique using correlation between natural frequency and cable forces is a simple method to determine in situ cable forces, however the method need accurate information on the boundary condition, cable mass, and cable length. The natural frequency of the cable is determined using FFT (Fast Fourier Transform) Technique to the acceleration record of the cable. Based on the natural frequency obtained, the cable forces then can be determine by analytical or by finite element program. This research is focus on the vibration techniques to determine the cable forces, to understand the physical parameter effect of the cable and also modelling techniques to the natural frequency and cable forces.

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

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

Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

Directory of Open Access Journals (Sweden)

Lihang Feng

Full Text Available Wheel force transducer (WFT, which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range.

Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

Science.gov (United States)

Feng, Lihang; Lin, Guoyu; Zhang, Weigong; Dai, Dong

2015-01-01

Wheel force transducer (WFT), which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range.

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.)

Applications of Molecular Dynamics, Monte Carlo and Metadynamics Simulations Using ReaxFF Reactive Force Fields to Fluid/Solid Interfaces

Science.gov (United States)

Raju, Muralikrishna

The interaction of dense fluids (water, polar organic solvents, room temperature ionic liquids, etc.) with solid substrates controls many chemical processes encountered in nature and industry. The key features of fluid-solid interfaces (FSIs) are the high mobility and often reactivity of the fluid phase, and the structural control provided by the solid phase. In this dissertation we apply molecular modeling methods to study FSIs in the following systems: 1. Dissociation of water on titania surfaces. We studied the adsorption and dissociation of water at 300 K on the following TiO2 surfaces: anatase (101), (100), (112), (001) and rutile (110) at various water coverages, using a recently developed ReaxFF reactive force field. The molecular and dissociative adsorption configurations predicted by ReaxFF for various water coverages agree with previous theoretical studies and experiment. 2. Mechanisms of Oriented Attachment in TiO2 nanocrystals. Oriented attachment (OA) of nanocrystals is now widely recognized as a key process in the solution-phase growth of hierarchical nanostructures. However, the microscopic origins of OA remain unclear. Using the same ReaxFF Ti/O/H reactive force field employed in the previous study, we perform molecular dynamics simulations to study the aggregation of various titanium dioxide (anatase) nanocrystals in vacuum and humid environments. 3. Li interactions in carbon based materials. Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length/time-scales and Li-ion concentrations. In this study we describe development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon based materials using atomistic simulations. We develop force-field parameters for Li-C systems using van

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

Force Characteristics Analysis for Linear Machine with DC Field Excitations

Directory of Open Access Journals (Sweden)

A/L Krishna Preshant

2018-01-01

Full Text Available In urban regions and particularly in developing countries such as Malaysia with its ever-growing transport sector, there is the need for energy efficient systems. In urban railway systems there is a requirement of frequent braking and start/stop motion, and energy is lost during these processes. To improve the issues of the conventional braking systems, particularly in Japan, they have introduced linear induction motor techniques. The drawbacks of this method, however, is the use of permanent magnets, which not only increase the weight of the entire system but also increases magnetic cogging. Hence an alternative is required which uses the same principles as Magnetic-Levitation but using a magnet-less system. Therefore, the objective of this research is to propose an electromagnetic rail brake system and to analyze the effect of replacing permanent magnets with a magnet-less braking systems to produce a significant amount of brake thrust as compared with the permanent magnet system. The modeling and performance analysis of the model is done using Finite Element Analysis (FEA. The mechanical aspects of the model are designed on Solidworks and then imported to JMAG Software to proceed with the electro-magnetic analysis of the model. There are 3 models developed: Base Model (steel, Permanent Magnet (PM Model and DC Coil Model. The performance of the proposed 2D models developed is evaluated in terms of average force produced and motor constant square density. By comparing the values for the 3 models for the same case of 9A current supplied for a 0.1mm/s moving velocity, the base model, permanent magnet model and DC coil model produced an average force of 7.78 N, 7.55 N, and 8.34 N respectively, however, with increase in DC current supplied to the DC coil model, the average force produced is increased to 13.32 N. Thus, the advantage of the DC coil (magnet-less model, is, that the force produced can be controlled by varying the number of turns in the

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

PC-based digital feedback control for scanning force microscope

International Nuclear Information System (INIS)

Mohd Ashhar Khalid

2002-01-01

In the past, most digital feedback implementation for scanned-probe microscope were based on a digital signal processor (DSP). At present DSP plug-in card with the input-output interface module is still expensive compared to a fast pentium PC motherboard. For a magnetic force microscope (MFM) digital feedback has an advantage where the magnetic signal can be easily separated from the topographic signal. In this paper, a simple low-cost PC-based digital feedback and imaging system for Scanning Force Microscope (SFM) is presented. (Author)

Hybrid Force Control Based on ICMAC for an Astronaut Rehabilitative Training Robot

OpenAIRE

Lixun Zhang; Yupeng Zou; Lan Wang; Xinping Pei

2012-01-01

A novel Astronaut Rehabilitative Training Robot (ART) based on a cable‐driven mechanism is represented in this paper. ART, a typical passive force servo system, can help astronauts to bench press in a microgravity environment. The purpose of this paper is to design controllers to eliminate the surplus force caused by an astronaut’s active movements. Based on the dynamics modelling of the cable‐driven unit, a hybrid force controller based on improved credit assignment CMAC (ICMAC) is presented...

Data Driven, Force Based Interaction for Quadrotors

Science.gov (United States)

McKinnon, Christopher D.

Quadrotors are small and agile, and are becoming more capable for their compact size. They are expected perform a wide variety of tasks including inspection, physical interaction, and formation flight. In all of these tasks, the quadrotors can come into close proximity with infrastructure or other quadrotors, and may experience significant external forces and torques. Reacting properly in each case is essential to completing the task safely and effectively. In this thesis, we develop an algorithm, based on the Unscented Kalman Filter, to estimate such forces and torques without making assumptions about the source of the forces and torques. We then show in experiment how the proposed estimation algorithm can be used in conjunction with controls and machine learning to choose the appropriate actions in a wide variety of tasks including detecting downwash, tracking the wind induced by a fan, and detecting proximity to the wall.

Transversal light forces in semiconductors

CERN Document Server

Lindberg, M

2003-01-01

The transversal light force is a well established effect in atomic and molecular systems that are exposed to spatially inhomogeneous light fields. In this paper it is shown theoretically that in an excited semiconductor, containing an electron-hole plasma or excitons, a similar light force exists, if the semiconductor is exposed to an ultrashort spatially inhomogeneous light field. The analysis is based on the equations of motion for the Wigner distribution functions of charge carrier populations and interband polarizations. The results show that, while the light force on the electron-hole plasma or the excitons does exist, its effects on the kinetic behaviour of the electron-hole plasma or the excitons are different compared to the situation in an atomic or molecular system. A detailed analysis presented here traces this difference back to the principal differences between atoms and molecules on the one hand and electron-hole plasmas or excitons on the other hand.

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

Science.gov (United States)

Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary

2018-03-01

A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.

High-resolution distributed-feedback fiber laser dc magnetometer based on the Lorentzian force

International Nuclear Information System (INIS)

Cranch, G A; Flockhart, G M H; Kirkendall, C K

2009-01-01

A low-frequency magnetic field sensor, based on a current-carrying beam driven by the Lorentzian force, is described. The amplitude of the oscillation is measured by a distributed-feedback fiber laser strain sensor attached to the beam. The transduction mechanism of the sensor is derived analytically using conventional beam theory, which is shown to accurately predict the responsivity of a prototype sensor. Excellent linearity and negligible hysteresis are demonstrated. Noise sources in the fiber laser strain sensor are described and thermo-mechanical noise in the transducer is estimated. The prototype sensor achieves a magnetic field resolution of 5 nT Hz for 25 mA of current, which is shown to be close to the predicted thermo-mechanical noise limit of the sensor. The current is supplied optically through a separate optical fiber yielding an electrically passive sensor head

Note: Design of FPGA based system identification module with application to atomic force microscopy

Science.gov (United States)

Ghosal, Sayan; Pradhan, Sourav; Salapaka, Murti

2018-05-01

The science of system identification is widely utilized in modeling input-output relationships of diverse systems. In this article, we report field programmable gate array (FPGA) based implementation of a real-time system identification algorithm which employs forgetting factors and bias compensation techniques. The FPGA module is employed to estimate the mechanical properties of surfaces of materials at the nano-scale with an atomic force microscope (AFM). The FPGA module is user friendly which can be interfaced with commercially available AFMs. Extensive simulation and experimental results validate the design.

(Environmental investigation of ground water contamination at Wright-Patterson Air Force Base, Ohio)

Energy Technology Data Exchange (ETDEWEB)

1992-03-01

An environmental investigation of ground water conditions has been undertaken at Wright-Patterson Air Force Base (WPAFB), Ohio to obtain data to assist in the evaluation of a potential removal action to prevent, to the extent practicable, migration of the contaminated ground water across Base boundaries. Field investigations were limited to the central section of the southwestern boundary of Area C and the Springfield Pike boundary of Area B. Further, the study was limited to a maximum depth of 150 feet below grade. Three primary activities of the field investigation were: (1) installation of 22 monitoring wells, (2) collection and analysis of ground water from 71 locations, (3) measurement of ground water elevations at 69 locations. Volatile organic compounds including trichloroethylene, perchloroethylene, and/or vinyl chloride were detected in concentrations exceeding Maximum Contaminant Levels (MCL) at three locations within the Area C investigation area. Ground water at the Springfield Pike boundary of Area B occurs in two primary units, separated by a thicker-than-expected clay layers. One well within Area B was determined to exceed the MCL for trichloroethylene.

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...

Ratchet baryogenesis and an analogy with the forced pendulum

Science.gov (United States)

Bamba, Kazuharu; Barrie, Neil D.; Sugamoto, Akio; Takeuchi, Tatsu; Yamashita, Kimiko

2018-06-01

A new scenario of baryogenesis via the ratchet mechanism is proposed based on an analogy with the forced pendulum. The oscillation of the inflaton field during the reheating epoch after inflation plays the role of the driving force, while the phase 𝜃 of a scalar baryon field (a complex scalar field with baryon number) plays the role of the angle of the pendulum. When the inflaton is coupled to the scalar baryon, the behavior of the phase 𝜃 can be analogous to that of the angle of the forced pendulum. If the oscillation of the driving force is adjusted to the pendulum’s motion, a directed rotation of the pendulum is obtained with a nonvanishing value of 𝜃˙, which models successful baryogenesis since 𝜃˙ is proportional to the baryon number density. Similar ratchet models which lead to directed motion have been used in the study of molecular motors in biology. There, the driving force is supplied by chemical reactions, while in our scenario this role is played by the inflaton during the reheating epoch.

A resonant force sensor based on ionic polymer metal composites

International Nuclear Information System (INIS)

Bonomo, Claudia; Fortuna, Luigi; Giannone, Pietro; Graziani, Salvatore; Strazzeri, Salvatore

2008-01-01

In this paper a novel force sensor, based on ionic polymer metal composites (IPMCs), is presented. The system has DC sensing capabilities and is able to work in the range of a few millinewtons. IPMCs are emerging materials used to realize motion actuators and sensors. An IPMC strip is activated in a beam fixed/simply-supported configuration. The beam is tightened at the simply-supported end by a force. This influences the natural resonant frequency of the beam; the value of the resonant frequency is used in the proposed system to estimate the force applied in the axial direction. The performance of the system based on the IPMC material has proved to be comparable with that of sensors based on other sensing mechanisms. This suggests the possibility of using this class of polymeric devices to realize PMEMS (plastic micro electrical mechanical systems) sensors

A resonant force sensor based on ionic polymer metal composites

Science.gov (United States)

Bonomo, Claudia; Fortuna, Luigi; Giannone, Pietro; Graziani, Salvatore; Strazzeri, Salvatore

2008-02-01

In this paper a novel force sensor, based on ionic polymer metal composites (IPMCs), is presented. The system has DC sensing capabilities and is able to work in the range of a few millinewtons. IPMCs are emerging materials used to realize motion actuators and sensors. An IPMC strip is activated in a beam fixed/simply-supported configuration. The beam is tightened at the simply-supported end by a force. This influences the natural resonant frequency of the beam; the value of the resonant frequency is used in the proposed system to estimate the force applied in the axial direction. The performance of the system based on the IPMC material has proved to be comparable with that of sensors based on other sensing mechanisms. This suggests the possibility of using this class of polymeric devices to realize PMEMS (plastic micro electrical mechanical systems) sensors.

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...

Investigations on the Effects of Vortex-Induced Vibration with Different Distributions of Lorentz Forces

Directory of Open Access Journals (Sweden)

Hui Zhang

2017-01-01

Full Text Available The control of vortex-induced vibration (VIV in shear flow with different distributions of Lorentz force is numerically investigated based on the stream function–vorticity equations in the exponential-polar coordinates exerted on moving cylinder for Re = 150. The cylinder motion equation coupled with the fluid, including the mathematical expressions of the lift force coefficient C l , is derived. The initial and boundary conditions as well as the hydrodynamic forces on the surface of cylinder are also formulated. The Lorentz force applied to suppress the VIV has no relationship with the flow field, and involves two categories, i.e., the field Lorentz force and the wall Lorentz force. With the application of symmetrical Lorentz forces, the symmetric field Lorentz force can amplify the drag, suppress the flow separation, decrease the lift fluctuation, and then suppress the VIV while the wall Lorentz force decreases the drag only. With the application of asymmetrical Lorentz forces, besides the above-mentioned effects, the field Lorentz force can increase additional lift induced by shear flow, whereas the wall Lorentz force can counteract the additional lift, which is dominated on the total effect.

A Knowledge base representing Porter's Five Forces Model

OpenAIRE

Swaan Arons, H.; Waalewijn, Ph.

1999-01-01

textabstractStrategic Analysis and Planning is a field in which expertise and experience are key factors. In order to decide on strategic matters such as the competitive position of a company experts heavily lean on their ability to reason with uncertain or incomplete knowledge, or in other words on their experience and expertise. An important aspect is to assess a company's profit potential in the industry for which Porter's Competitive Forces Model is by far the most widely used framework. ...

Nanoscale electrowetting effects observed by using friction force microscopy.

Science.gov (United States)

Revilla, Reynier; Guan, Li; Zhu, Xiao-Yang; Yang, Yan-Lian; Wang, Chen

2011-06-21

We report the study of electrowetting (EW) effects under strong electric field on poly(methyl methacrylate) (PMMA) surface by using friction force microscopy (FFM). The friction force dependence on the electric field at nanometer scale can be closely related to electrowetting process based on the fact that at this scale frictional behavior is highly affected by capillary phenomena. By measuring the frictional signal between a conductive atomic force microscopy (AFM) tip and the PMMA surface, the ideal EW region (Young-Lippmann equation) and the EW saturation were identified. The change in the interfacial contact between the tip and the PMMA surface with the electric field strength is closely associated with the transition from the ideal EW region to the EW saturation. In addition, a reduction of the friction coefficient was observed when increasing the applied electric field in the ideal EW region. © 2011 American Chemical Society

Sensitivity-based virtual fields for the non-linear virtual fields method