Forces in electromagnetic field and gravitational field

OpenAIRE

Weng, Zihua

2008-01-01

The force can be defined from the linear momentum in the gravitational field and electromagnetic field. But this definition can not cover the gradient of energy. In the paper, the force will be defined from the energy and torque in a new way, which involves the gravitational force, electromagnetic force, inertial force, gradient of energy, and some other new force terms etc. One of these new force terms can be used to explain why the solar wind varies velocity along the magnetic force line in...

Mechanisms explaining Coulomb's electric force & Lorentz's magnetic force from a classical perspective

Science.gov (United States)

Correnti, Dan S.

2018-06-01

The underlying mechanisms of the fundamental electric and magnetic forces are not clear in current models; they are mainly mathematical constructs. This study examines the underlying physics from a classical viewpoint to explain Coulomb's electric force and Lorentz's magnetic force. This is accomplished by building upon already established physics. Although no new physics is introduced, extension of existing models is made by close examination. We all know that an electron carries a bound cylindrical B-field (CBF) as it translates. Here, we show how the electron CBF plays an intrinsic role in the generation of the electric and magnetic forces.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

Science.gov (United States)

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Quantum mechanical force fields for condensed phase molecular simulations

Science.gov (United States)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Study on electromagnetism force of CARR control rod drive mechanism experimental machine

International Nuclear Information System (INIS)

Zhu Xuewei; Zhen Jianxiao; Wang Yulin; Jia Yueguang; Yang Kun; Yin Haozhe

2015-01-01

With the aim of acquiring electromagnetic force and electromagnetic field distributions of control rod drive mechanism (CRDM) in China Advanced Research Reactor (CARR), the force analysis on the CRDM was taken. Manufacturing the experimental machine, the electromagnetic force experiment was taken on it. The electromagnetic field and electromagnetic force simulation analyses of experimental machine were taken, working out distribution data of electromagnetic force and magnetic induction intensity distribution curve, and the effects of permanent magnetic field on electromagnetic field and structure parameters on electromagnetic force. The simulation value is accord with experiment value, the research results provide a reference to electromagnetic force study on CRDM in CARR, and also provide a reference to design of the same type CRDM. (authors)

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.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Science.gov (United States)

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

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

A study on fixing force generation mechanism of ER gel

International Nuclear Information System (INIS)

Tanaka, H; Kakinuma, Y; Aoyama, T; Anzai, H

2009-01-01

Electro-rheological Gel (ERG) is a new functional elastomer which changes its surface frictional and adhesive property according to the intensity of applied electrical field. This unique property is called ERG effect. The upper sliding electrode placed on the surface of ERG is fixed by the adhesive effect of ERG under electrical field. Variable fixing forces due to adhesion are generated by this effect. However, relationship between physical factors and generated fixing force has not yet been clarified. In this study, physical mechanism of fixing phenomenon is elucidated experimentally from the view point of frictional force and adhesive force. From the results, empirical equation of generated fixing force is originally derived to establish the theory of ERG effect.

A study on fixing force generation mechanism of ER gel

Energy Technology Data Exchange (ETDEWEB)

Tanaka, H; Kakinuma, Y; Aoyama, T [School of Integrated Design Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522 (Japan); Anzai, H [Fujikura kasei Co., Ltd., 2-6-15 Shibakouen, Minato-ku, Tokyo (Japan)], E-mail: h-tanaka@ina.sd.keio.ac.jp

2009-02-01

Electro-rheological Gel (ERG) is a new functional elastomer which changes its surface frictional and adhesive property according to the intensity of applied electrical field. This unique property is called ERG effect. The upper sliding electrode placed on the surface of ERG is fixed by the adhesive effect of ERG under electrical field. Variable fixing forces due to adhesion are generated by this effect. However, relationship between physical factors and generated fixing force has not yet been clarified. In this study, physical mechanism of fixing phenomenon is elucidated experimentally from the view point of frictional force and adhesive force. From the results, empirical equation of generated fixing force is originally derived to establish the theory of ERG effect.

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.

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

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...

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

The Martini Coarse-Grained Force Field

NARCIS (Netherlands)

Periole, X.; Marrink, S.J.; Monticelli, Luca; Salonen, Emppu

2013-01-01

The Martini force field is a coarse-grained force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parameterized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical

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.

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...

The Cytoskeleton and Force Response Mechanisms

Science.gov (United States)

Allen, Philip Goodwin

2003-01-01

The long term aim of this project was to define the mechanisms by which cells sense and respond to the physical forces experienced at 1g and missing in microgravity. Identification and characterization of the elements of the cells force response mechanism could provide pathways and molecules to serve as targets for pharmacological intervention to mitigate the pathologic effects of microgravity. Mechanical forces experienced by the organism can be transmitted to cells through molecules that allow cells to bind to the extracellular matrix and through other types of molecules which bind cells to each other. These molecules are coupled in large complexes of proteins to structural elements such as the actin cytoskeleton that give the cell the ability to sense, resist and respond to force. Application of small forces to tissue culture cells causes local elevation of intracellular calcium through stretch activated ion channels, increased tyrosine phosphorylation and a restructuring of the actin cytoskeleton. Using collagen coated iron oxide beads and strong magnets, we can apply different levels of force to cells in culture. We have found that force application causes the cells to polymerize actin at the site of mechanical deformation and unexpectedly, to depolymerize actin across the rest of the cell. Observations of GFP- actin expressing cells demonstrate that actin accumulates at the site of deformation within the first five minutes of force application and is maintained for many tens of minutes after force is removed. Consistent with the reinforcement of the cytoskeletal structures underlying the integrin-bead interaction, force also alters the motion of bound magnetic beads. This effect is seen following the removal of the magnetic field, and is only partially ablated by actin disruption with cytochalsin B. While actin is polymerizing locally at the site of force application, force also stimulates a global reduction in actin filament content within the cells. We have

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.

A molecular dynamic simulation study of mechanical properties of graphene–polythiophene composite with Reax force field

International Nuclear Information System (INIS)

Nayebi, Payman; Zaminpayma, Esmaeil

2016-01-01

In this paper, we performed molecular dynamic simulations by Reax force field to study the mechanical properties of graphene–polythiophene nanocomposite. By computing elastic constant, breaking stress, breaking strain and Young's modulus from the stress–strain curve for the nanocomposites, we investigated effects of tension orientation, graphene loading to the polymer, temperature of nanocomposite and defect of graphene on these mechanical characters. It is found that mechanical characters of tension along the zigzag orientation are higher than other directions. Also, by increasing the weight concentration of graphene in composite, the Young's modulus and breaking strain increase. Our results showed that the Young's modulus decreased with increasing temperature. Finally by applying defect on graphene structure, we found that one atom missing defect has lower Young's modulus. Also, by increasing the defects concentration, elastic modulus decreases gradually. - Highlights: • We studied mechanical properties of graphene–polythiophene nanocomposite. • Mechanical characters of tension along the zigzag are higher than other directions. • By increasing the weight concentration of graphene in composite, the Young's modulus increases. • Young's modulus decreased with increasing temperature. • By increasing the defects concentration, elastic modulus decreases gradually.

Embryo mechanics: balancing force production with elastic resistance during morphogenesis.

Science.gov (United States)

Davidson, Lance A

2011-01-01

Morphogenesis requires the spatial and temporal control of embryo mechanics, including force production and mechanical resistance to those forces, to coordinate tissue deformation and large-scale movements. Thus, biomechanical processes play a key role in directly shaping the embryo. Additional roles for embryo mechanics during development may include the patterning of positional information and to provide feedback to ensure the success of morphogenetic movements in shaping the larval body and organs. To understand the multiple roles of mechanics during development requires familiarity with engineering principles of the mechanics of structures, the viscoelastic properties of biomaterials, and the integration of force and stress within embryonic structures as morphogenesis progresses. In this chapter, we review the basic engineering principles of biomechanics as they relate to morphogenesis, introduce methods for quantifying embryo mechanics and the limitations of these methods, and outline a formalism for investigating the role of embryo mechanics in birth defects. We encourage the nascent field of embryo mechanics to adopt standard engineering terms and test methods so that studies of diverse organisms can be compared and universal biomechanical principles can be revealed. Copyright © 2011 Elsevier Inc. All rights reserved.

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

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.

Near field plasmon and force microscopy

NARCIS (Netherlands)

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

1995-01-01

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

Ehrenfest force in inhomogeneous magnetic field

International Nuclear Information System (INIS)

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

2000-01-01

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

Microtubules as mechanical force sensors.

Science.gov (United States)

Karafyllidis, Ioannis G; Lagoudas, Dimitris C

2007-03-01

Microtubules are polymers of tubulin subunits (dimers) arranged on a hexagonal lattice. Each tubulin dimer comprises two monomers, the alpha-tubulin and beta-tubulin, and can be found in two states. In the first state a mobile negative charge is located into the alpha-tubulin monomer and in the second into the beta-tubulin monomer. Each tubulin dimer is modeled as an electrical dipole coupled to its neighbors by electrostatic forces. The location of the mobile charge in each dimer depends on the location of the charges in the dimer's neighborhood. Mechanical forces that act on the microtubule affect the distances between the dimers and alter the electrostatic potential. Changes in this potential affect the mobile negative charge location in each dimer and the charge distribution in the microtubule. The net effect is that mechanical forces affect the charge distribution in microtubules. We propose to exploit this effect and use microtubules as mechanical force sensors. We model each dimer as a two-state quantum system and, following the quantum computation paradigm, we use discrete quantum random walk on the hexagonal microtubule lattice to determine the charge distribution. Different forces applied on the microtubule are modeled as different coin biases leading to different probability distributions of the quantum walker location, which are directly connected to different charge distributions. Simulation results show that there is a strong indication that microtubules can be used as mechanical force sensors and that they can also detect the force directions and magnitudes.

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

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.

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.

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.

Analysis of mechanical characteristics of superconducting field coil for 17 MW class high temperature superconducting synchronous motor

International Nuclear Information System (INIS)

Kim, J. H.; Park, S. I.; Im, S. H.; Kim, H. M.

2013-01-01

Superconducting field coils using a high-temperature superconducting (HTS) wires with high current density generate high magnetic field of 2 to 5 [T] and electromagnetic force (Lorentz force) acting on the superconducting field coils also become a very strong from the point of view of a mechanical characteristics. Because mechanical stress caused by these powerful electromagnetic force is one of the factors which worsens the critical current performance and structural characteristics of HTS wire, the mechanical stress analysis should be performed when designing the superconducting field coils. In this paper, as part of structural design of superconducting field coils for 17 MW class superconducting ship propulsion motor, mechanical stress acting on the superconducting field coils was analyzed and structural safety was also determined by the coupling analysis system that is consists of commercial electromagnetic field analysis program and structural analysis program.

Study on a mechanical snubber with an adjustment mechanism for resisting force

International Nuclear Information System (INIS)

Ohmata, Kenichiro; Miyanaga, Hiroyuki.

1991-01-01

The mechanical snubber is an earthquakeproof device for a piping system under particular circumstances such as high temperature and radioactivity. It restrains the piping system by a strong resisting force during an earthquake. This strong force can cause elastic failure of grooves on a brake disk, where steel balls are placed. In this report, an improved mechanical snubber having an adjustment mechanism for resisting force is proposed in order to obtain a mechanical snubber which has almost the same restraint effect and less resisting force in comparison with a conventional mechanical snubber. The resisting force characteristics and the restraint effect of the improved mechanical snubber applied to a simple beam are discussed both numerically and experimentally. The digital simulations are carried out using the Continuous System Simulation Language (CSSL). (author)

Brown algal morphogenesis: Atomic Force Microscopy as a tool to study the role of mechanical forces

Directory of Open Access Journals (Sweden)

Benoit eTesson

2014-09-01

Full Text Available Over the last few years, a growing interest has been directed toward the use of macroalgae as a source of energy, food and molecules for the cosmetic and pharmaceutical industries. Besides this, macroalgal development remains poorly understood compared to other multicellular organisms. Brown algae (Phaeophyceae form a monophyletic lineage of usually large multicellular algae which evolved independently from land plants. In their environment, they are subjected to strong mechanical forces (current, waves and tide, in response to which they modify rapidly and reversibly their morphology. Because of their specific cellular features (cell wall composition, cytoskeleton organization, deciphering how they cope with these forces might help discover new control mechanisms of cell wall softening and cellulose synthesis. Despite the current scarcity in knowledge on brown algal cell wall dynamics and protein composition, we will illustrate, in the light of methods adapted to Ectocarpus siliculosus, to what extent atomic force microscopy can contribute to advance this field of investigation.

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.

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

Quantum mechanics. Mechanically detecting and avoiding the quantum fluctuations of a microwave field.

Science.gov (United States)

Suh, J; Weinstein, A J; Lei, C U; Wollman, E E; Steinke, S K; Meystre, P; Clerk, A A; Schwab, K C

2014-06-13

Quantum fluctuations of the light field used for continuous position detection produce stochastic back-action forces and ultimately limit the sensitivity. To overcome this limit, the back-action forces can be avoided by giving up complete knowledge of the motion, and these types of measurements are called "back-action evading" or "quantum nondemolition" detection. We present continuous two-tone back-action evading measurements with a superconducting electromechanical device, realizing three long-standing goals: detection of back-action forces due to the quantum noise of a microwave field, reduction of this quantum back-action noise by 8.5 ± 0.4 decibels (dB), and measurement imprecision of a single quadrature of motion 2.4 ± 0.7 dB below the mechanical zero-point fluctuations. Measurements of this type will find utility in ultrasensitive measurements of weak forces and nonclassical states of motion. Copyright © 2014, American Association for the Advancement of Science.

Near field plasmon and force microscopy

OpenAIRE

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

1995-01-01

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

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

Science.gov (United States)

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

2016-07-28

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

Mechanical forces as information: an integrated approach to plant and animal development

Directory of Open Access Journals (Sweden)

Valeria eHernández-Hernández

2014-06-01

Full Text Available Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes.

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

Science.gov (United States)

Yang, Honghua

near-field response of a linear rod antenna is studied with Babinet's principle. Babinet's principle connects the magnetic field of a structure to the electric field of its complement structure. Using combined far- and near-field spectroscopy, imaging, and theory, I identify magnetic dipole and higher order bright and dark magnetic resonances at mid-infrared frequencies. From resonant length scaling and spatial field distributions, I confirm that the theoretical requirement of Babinet's principle for a structure to be infinitely thin and perfectly conducting is still fulfilled to a good approximation in the mid-infrared. Thus Babinet's principle provides access to spatial and spectral magnetic field properties, leading to targeted design and control of magnetic optical antennas. Lastly, a novel form of nanoscale optical spectroscopy based on mechanical detection of optical gradient force is explored. It is to measure the optical gradient force between induced dipole moments of a sample and an atomic force microscope (AFM) tip. My study provides the theoretical basis in terms of spectral behavior, resonant enhancement, and distance dependence of the optical gradient force from numerical simulations for a coupled nanoparticle model geometry. I show that the optical gradient force is dispersive for local electronic and vibrational resonances, yet can be absorptive for collective polaronic excitations. This spectral behavior together with the distance dependence scaling provides the key characteristics for its measurement and distinction from competing processes such as thermal expansion. Furthermore, I provide a perspective for resonant enhancement and control of optical forces in general.

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.

Mechanical design and force calibration of dual-axis micromechanical probe for friction force microscopy

International Nuclear Information System (INIS)

Fukuzawa, Kenji; Terada, Satoshi; Shikida, Mitsuhiro; Amakawa, Hiroaki; Zhang, Hedong; Mitsuya, Yasunaga

2007-01-01

A dual-axis micromechanical probe that combines a double cantilever and torsion beams is presented. This probe can reduce the mechanical cross-talk between the lateral and vertical force detections. In addition, dual-axis forces can be detected by measuring the dual-axis displacement of the probe end using the optical lever-based method used in conventional friction force microscopes (FFMs). In this paper, the mechanical design of the probe, the details of the fabrication method, FFM performance, and calibration of the friction force are discussed. The mechanical design and the microfabrication method for probes that can provide a force resolution of the order of 1 nN without mechanical cross-talk are presented. Calibration of the lateral force signal is possible by using the relationship between the lateral force and the piezodisplacement at the onset of the probe scanning. The micromechanical probe enables simultaneous and independent detection of atomic and friction forces. This leads to accurate investigation of nanotribological phenomena and visualization of the distribution of the friction properties, which helps the identification of the material properties

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

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

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.)

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

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

Quantifying mechanical force in axonal growth and guidance

Directory of Open Access Journals (Sweden)

Ahmad Ibrahim Mahmoud Athamneh

2015-09-01

Full Text Available Mechanical force plays a fundamental role in neuronal development, physiology, and regeneration. In particular, research has shown that force is involved in growth cone-mediated axonal growth and guidance as well as stretch-induced elongation when an organism increases in size after forming initial synaptic connections. However, much of the details about the exact role of force in these fundamental processes remain unknown. In this review, we highlight (1 standing questions concerning the role of mechanical force in axonal growth and guidance and (2 different experimental techniques used to quantify forces in axons and growth cones. We believe that satisfying answers to these questions will require quantitative information about the relationship between elongation, forces, cytoskeletal dynamics, axonal transport, signaling, substrate adhesion, and stiffness contributing to directional growth advance. Furthermore, we address why a wide range of force values have been reported in the literature, and what these values mean in the context of neuronal mechanics. We hope that this review will provide a guide for those interested in studying the role of force in development and regeneration of neuronal networks.

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.

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.

Electromagnetic field and mechanical stress analysis code

International Nuclear Information System (INIS)

1978-01-01

Analysis TEXMAGST is a two stage linear finite element code for the analysis of static magnetic fields in three dimensional structures and associated mechanical stresses produced by the anti J x anti B forces within these structures. The electromagnetic problem is solved in terms of magnetic vector potential A for a given current density anti J as curl 1/μ curl anti A = anti J considering the magnetic permeability as constant. The Coulombian gauge (div anti A = o) was chosen and was implemented through the use of Lagrange multipliers. The second stage of the problem - the calculation of mechanical stresses in the same three dimensional structure is solved by using the same code with few modifications - through a restart card. Body forces anti J x anti B within each element are calculated from the solution of the first stage run and represent the input to the second stage run which will give the solution for the stress problem

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.

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

Science.gov (United States)

1996-03-01

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

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)

Force fields for silicas and aluminophosphates based on ab initio calculations

NARCIS (Netherlands)

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

1990-01-01

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

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.

Mechanical stress calculations for toroidal field coils by the finite element method

International Nuclear Information System (INIS)

Soell, M.; Jandl, O.; Gorenflo, H.

1976-09-01

After discussing fundamental relationships of the finite element method, this report describes the calculation steps worked out for mechanical stress calculations in the case of magnetic forces and forces produced by thermal expansion or compression of toroidal field coils using the SOLID SAP IV computer program. The displacement and stress analysis are based on the 20-node isoparametric solid element. The calculation of the nodal forces produced by magnetic body forces are discussed in detail. The computer programs, which can be used generally for mesh generation and determination of the nodal forces, are published elsewhere. (orig.) [de

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.

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/ .

Approximate photochemical dynamics of azobenzene with reactive force fields

Science.gov (United States)

Li, Yan; Hartke, Bernd

2013-12-01

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

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.

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

Science.gov (United States)

2014-01-01

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

The 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.

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.

DNA under Force: Mechanics, Electrostatics, and Hydration

Directory of Open Access Journals (Sweden)

Jingqiang Li

2015-02-01

Full Text Available Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

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.

Software Process Improvement Using Force Field Analysis ...

African Journals Online (AJOL)

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

Force-free magnetic fields - The magneto-frictional method

Science.gov (United States)

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

1986-01-01

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

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

Science.gov (United States)

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

2014-09-16

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

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.

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

National Research Council Canada - National Science Library

Bunte, Steven

2000-01-01

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

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

Mechanism of force mode dip-pen nanolithography

Energy Technology Data Exchange (ETDEWEB)

Yang, Haijun, E-mail: yanghaijun@sinap.ac.cn, E-mail: swguo@sjtu.edu.cn, E-mail: wanghuabin@cigit.ac.cn [Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Research Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, Shanghai 200240 (China); Interfacial Water Division and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, CAS, Shanghai 201800 (China); Xie, Hui; Rong, Weibin; Sun, Lining [State Key Laboratory of Robotics and Systems, Harbin Institute of Technology, Harbin 150080 (China); Wu, Haixia; Guo, Shouwu, E-mail: yanghaijun@sinap.ac.cn, E-mail: swguo@sjtu.edu.cn, E-mail: wanghuabin@cigit.ac.cn [Key Laboratory for Thin Film and Microfabrication of the Ministry of Education, Research Institute of Micro/Nano Science and Technology, Shanghai Jiao Tong University, Shanghai 200240 (China); Wang, Huabin, E-mail: yanghaijun@sinap.ac.cn, E-mail: swguo@sjtu.edu.cn, E-mail: wanghuabin@cigit.ac.cn [Centre for Tetrahertz Research, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714 (China)

2014-05-07

In this work, the underlying mechanism of the force mode dip-pen nanolithography (FMDPN) is investigated in depth by analyzing force curves, tapping mode deflection signals, and “Z-scan” voltage variations during the FMDPN. The operation parameters including the relative “trigger threshold” and “surface delay” parameters are vital to control the loading force and dwell time for ink deposition during FMDPN. A model is also developed to simulate the interactions between the atomic force microscope tip and soft substrate during FMDPN, and verified by its good performance in fitting our experimental data.

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.

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.

Friction Force: From Mechanics to Thermodynamics

Science.gov (United States)

Ferrari, Christian; Gruber, Christian

2010-01-01

We study some mechanical problems in which a friction force is acting on a system. Using the fundamental concepts of state, time evolution and energy conservation, we explain how to extend Newtonian mechanics to thermodynamics. We arrive at the two laws of thermodynamics and then apply them to investigate the time evolution and heat transfer of…

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)

Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review.

Science.gov (United States)

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-09-01

Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades has yielded remarkable novel insights in understanding the development and progression of certain diseases, such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine. In this paper, we reviewed the utilization of AFM to characterize cell mechanics. First, the principle and method of AFM single-cell mechanical analysis was presented, along with the mechanical responses of cells to representative external stimuli measured by AFM. Next, the unique changes of cell mechanics in two types of physiological processes (stem cell differentiation, cancer metastasis) revealed by AFM were summarized. After that, the molecular mechanisms guiding cell mechanics were analyzed. Finally the challenges and future directions were discussed.

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

Force decay of elastomeric chains - a mechanical design and product comparison study.

Science.gov (United States)

Balhoff, David A; Shuldberg, Matthew; Hagan, Joseph L; Ballard, Richard W; Armbruster, Paul C

2011-03-01

To evaluate the percentage force decay of elastomeric chain products utilizing three different design mechanisms simulating canine retraction; and to evaluate the percentage force decay of elastomeric chain products from four different companies. In vitro, laboratory study. LSUHSC Dental School, New Orleans, LA, USA. Closed (non-spaced), grey elastomeric chains from four companies were selected for the study. Three acrylic resin jigs were constructed to provide a framework for three simulated space closure mechanisms. The 6-5-3, the chain loop, and the 6-3 were the configuration mechanisms used in the study. An electronic force gauge was used to measure the percentage force decay associated with each elastomeric chain over 28 days at preselected times. There was a significant difference in the mean percentage force decay for the three different mechanisms (P < 0·001). For all four companies, the 6-3 mechanical design had the smallest mean percentage force decay. There was a significant difference in the mean percentage force decay for the different companies (P < 0·001). For all three mechanisms, Ormco had the smallest percentage force decay while Unitek had the highest percentage force decay. The significant difference in the mean percentage force decay for the different mechanisms suggests that the 6-3 design is a more efficient means of closing extraction spaces utilizing elastomeric chains.

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

International Nuclear Information System (INIS)

Stroscio, M.A.

1985-01-01

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

Improved Parameters for the Martini Coarse-Grained Protein Force Field

NARCIS (Netherlands)

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

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

Mechanics of nonplanar membranes with force-dipole activity

DEFF Research Database (Denmark)

Lomholt, Michael Andersen

2006-01-01

A study is made of how active membrane proteins can modify the long wavelength mechanics of fluid membranes. The activity of the proteins is modelled as disturbing the protein surroundings through nonlocal force distributions of which a force-dipole distribution is the simplest example. An analytic...... contributions to mechanical properties such as tension and bending moments become apparent. It is also explained how the activity can induce a hydrodynamic attraction between the active proteins in the membrane....

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.

Scrambled eggs: mechanical forces as ecological factors in early development.

Science.gov (United States)

Moore, Steven W

2003-01-01

Many ecological interactions involve, at some level, mechanical forces and the movements or structural deformations they produce. Although the most familiar examples involve the functional morphology of adult structures, all life history stages (not just the adults) are subject to the laws of physics. Moreover, the success of every lineage depends on the success of every life history stage (again, not just the adults). Therefore, insights gained by using mechanical engineering principles and techniques to study ecological interactions between gametes, embryos, larvae, and their environment are essential to a well-rounded understanding of development, ecology, and evolution. Here I draw on examples from the literature and my own research to illustrate ways in which mechanical forces in the environment shape development. These include mechanical forces acting as selective factors (e.g., when coral gamete size and shape interact with turbulent water flow to determine fertilization success) and as developmental cues (e.g., when plant growth responds to gravity or bone growth responds to mechanical loading). I also examine the opposite cause-and-effect relationship by considering examples in which the development of organisms impacts ecologically relevant mechanical forces. Finally, I discuss the potential for ecological pattern formation as a result of feedback loops created by such bidirectional interactions between developmental processes and mechanical forces in the environment.

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

Knudsen torque: A rotational mechanism driven by thermal force

Science.gov (United States)

Li, Qi; Liang, Tengfei; Ye, Wenjing

2014-09-01

Thermally induced mechanical loading has been shown to have significant effects on micro- and nano-objects immersed in a gas with a nonuniform temperature field. While the majority of existing studies and related applications focus on forces, we investigate the torque, and thus the rotational motion, produced by such a mechanism. Our study has found that a torque can be induced if the configuration of the system is asymmetric. In addition, both the magnitude and the direction of the torque depend highly on the system configuration, indicating the possibility of manipulating the rotational motion via geometrical design. Based on this feature, two types of rotational micromotor that are of practical importance, namely pendulum motor and unidirectional motor, are designed. The magnitude of the torque at Kn =0.5 can reach to around 2nN×μm for a rectangular microbeam with a length of 100μm.

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.

Vibrations of a molecule in an external force field.

Science.gov (United States)

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

2018-05-01

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

Investigation of mechanical field weakening of axial flux permanent magnet motor

Science.gov (United States)

Syaifuddin Mohd, M.; Aziz, A. Rashid A.; Syafiq Mohd, M.

2015-12-01

An investigation of axial flux permanent magnet motor (AFPM) characteristics was conducted with a proposed mechanical field weakening control mechanisms (by means of stator-rotor force manipulation) on the motor through modeling and experimentation. By varying the air gap between at least two bistable positions, the peak torque and top speed of the motor can be extended. The motor high efficiency region can also be extended to cover greater part of the motor operating points. An analytical model of the motor had been developed to study the correlation between the total attraction force (between the rotor and the stator) and the operating parameters of the motor. The test results shows that the motor output complies with the prediction of the research hypothesis and it is likely that a spring locking mechanism can be built to dynamically adjust the air gap of the motor to increase the operating range and could be applied in electric drivetrain applications to improve overall efficiency of electric and hybrid electric vehicles.

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.

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.

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

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.

Reaction Force/Torque Sensing in a Master-Slave Robot System without Mechanical Sensors

Directory of Open Access Journals (Sweden)

Kyoko Shibata

2010-07-01

Full Text Available In human-robot cooperative control systems, force feedback is often necessary in order to achieve high precision and high stability. Usually, traditional robot assistant systems implement force feedback using force/torque sensors. However, it is difficult to directly mount a mechanical force sensor on some working terminals, such as in applications of minimally invasive robotic surgery, micromanipulation, or in working environments exposed to radiation or high temperature. We propose a novel force sensing mechanism for implementing force feedback in a master-slave robot system with no mechanical sensors. The system consists of two identical electro-motors with the master motor powering the slave motor to interact with the environment. A bimanual coordinated training platform using the new force sensing mechanism was developed and the system was verified in experiments. Results confirm that the proposed mechanism is capable of achieving bilateral force sensing and mirror-image movements of two terminals in two reverse control directions.

Contact force and mechanical loss of multistage cable under tension and bending

Science.gov (United States)

Ru, Yanyun; Yong, Huadong; Zhou, Youhe

2016-10-01

A theoretical model for calculating the stress and strain states of cabling structures with different loadings has been developed in this paper. We solve the problem for the first- and second-stage cable with tensile or bending strain. The contact and friction forces between the strands are presented by two-dimensional contact model. Several theoretical models have been proposed to verify the results when the triplet subjected to the tensile strain, including contact force, contact stresses, and mechanical loss. It is found that loadings will affect the friction force and the mechanical loss of the triplet. The results show that the contact force and mechanical loss are dependent on the twist pitch. A shorter twist pitch can lead to higher contact force, while the trend of mechanical loss with twist pitch is complicated. The mechanical loss may be reduced by adjusting the twist pitch reasonably. The present model provides a simple analysis method to investigate the mechanical behaviors in multistage-structures under different loads.

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.

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

Science.gov (United States)

Geng, Yanan; Wu, Weida

2014-05-01

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

Multi-Stage Flotation for the Removal of Ash from Fine Graphite Using Mechanical and Centrifugal Forces

OpenAIRE

Xiangning Bu; Tuantuan Zhang; Yaoli Peng; Guangyuan Xie; Erdong Wu

2018-01-01

Graphite ore collected from Hunan province, south China was characterized by chemical analysis, X-ray diffraction, and optical microscopy. Rougher and multi-stage flotation tests using a mechanical flotation cell and a flotation column containing an additional centrifugal force field were carried out to promote its grade and economic value. In rougher flotation, both the mechanical flotation cell and flotation column reduced the ash content of the graphite ore from 15.43% to 10.8%, while the ...

Nuclear Forces from Effective Field Theory

International Nuclear Information System (INIS)

Krebs, H.

2011-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-07

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

On the quantum mechanical theory of stress and force

International Nuclear Information System (INIS)

Nielsen, O.H.; Martin, R.M.

1985-01-01

The stress theorem presented previously by the present authors is derived in detail and is related to the virial and force theorems. Stress fields are considered in two alternative forms, which both give the same macroscopic stress and forces on nuclei when integrated over appropriate surfaces. A crucial concept is interactions that ''cross'' surfaces. Explicit forms of the stress field within the local-density approximation are given, together with a generalization of the approximate Liberman form for pressure. Reciprocal-space expressions and ab-initio calculations are considered in detail in an accompanying paper. (orig.)

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)

Comparison of mechanical concepts for $Nb_3Sn$ high field accelerator magnets

CERN Document Server

AUTHOR|(CDS)2084469; Peter, Schmolz

Several magnets using Nb$_{3}$Sn as conductor are currently developed at CERN; these magnets are either slated for future updates of the LHC or for research purposes relating to future accelerators. The mechanical structure is one of the challenging aspects of superconducting high-field magnets. The main purpose of the mechanical structure is to keep the coils in compression till the emergence of the highest electromagnetic forces that are developed in the ultimate field of the magnet. Any loss of pre-compression during the magnet’s excitation would cause too large deformation of the coil and possibly a quench in the conductor owing to relative movements of strands in contact associated with excessive local heat release. However, too high pre-compression would overstrain the conductor and thereby limit the performance of the magnet. This thesis focuses on the mechanical behaviour of three of these magnets. All of them are based on different mechanical designs, “bladder and key” and “collar-based”, ...

Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

Science.gov (United States)

Wu, Xiangyang

1999-07-01

The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

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...

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.

Topological and statistical properties of nonlinear force-free fields

Science.gov (United States)

Mangalam, A.; Prasad, A.

2018-01-01

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

Charm production and the confining force field

International Nuclear Information System (INIS)

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

1983-03-01

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

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

Science.gov (United States)

Riniker, Sereina

2018-03-26

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-08-14

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

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

International Nuclear Information System (INIS)

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

2016-01-01

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

Flow Field Characteristics and Lift Changing Mechanism for Half-Rotating Wing in Hovering Flight

Science.gov (United States)

Li, Q.; Wang, X. Y.; Qiu, H.; Li, C. M.; Qiu, Z. Z.

2017-12-01

Half-rotating wing (HRW) is a new similar-flapping wing system based on half-rotating mechanism which could perform rotating-type flapping instead of oscillating-type flapping. The characteristics of flow field and lift changing mechanism for HRW in hovering flight are important theoretical basis to improve the flight capability of HRW aircraft. The driving mechanism and work process of HRW were firstly introduced in this paper. Aerodynamic simulation model of HRW in hovering flight was established and solved using XFlow software, by which lift changing rule of HRW was drawn from the simulation solution. On the other hand, the development and shedding of the distal vortex throughout one stroke would lead to the changes of the lift force. Based on analyzing distribution characteristics of vorticity, velocity and pressure around wing blade, the main features of the flow field for HRW were further given. The distal attached vortex led to the increase of the lift force, which would gradually shed into the wake with a decline of lift in the later downstroke. The wake ring directed by the distal end of the blade would generate the downward accelerating airflow which produced the upward anti-impulse to HRW. The research results mentioned above illustrated that the behavior characteristics of vortex formed in flow field were main cause of lift changing for HRW.

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

Mechanical Kerr nonlinearities due to bipolar optical forces between deformable silicon waveguides.

Science.gov (United States)

Ma, Jing; Povinelli, Michelle L

2011-05-23

We use an analytical method based on the perturbation of effective index at fixed frequency to calculate optical forces between silicon waveguides. We use the method to investigate the mechanical Kerr effect in a coupled-waveguide system with bipolar forces. We find that a positive mechanical Kerr coefficient results from either an attractive or repulsive force. An enhanced mechanical Kerr coefficient several orders of magnitude larger than the intrinsic Kerr coefficient is obtained in waveguides for which the optical mode approaches the air light line, given appropriate design of the waveguide dimensions.

Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides.

Science.gov (United States)

Kato, Rodrigo B; Silva, Frederico T; Pappa, Gisele L; Belchior, Jadson C

2015-01-28

We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.e., GA coupled with QM calculations. Overall, RMSE comparison with recent published results for ribonucleosides energies shows an improvement, on average, of 50%. Finally, the new reparametrized potential energy function is used to determine the spatial structure of RNA (PDB code ) that was not taken into account in the parametrization process. This structure was improved about 82% comparable with previously published results.

Generation of macroscopic magnetic-field-aligned electric fields by the convection surge ion acceleratiom mechanism

International Nuclear Information System (INIS)

Mauk, B.H.

1989-01-01

The ''convection surge'' computer model presented previously (concerning the dramatic, nonadiabatic, magnetic-field-aligned energization of ions near the Earth's geosynchronous orbit in the presence of strong, transient, magnetic-field-perpendicular inductive electric fields) has been extended to include the self-consistent generation of magnetic-field-aligned electric fields. The field-aligned electric potential is obtained by imposing the quasi-neutrality condition using approximated electron distribution forms. The ions are forced to respond self-consistently to this potential. It is found that field-aligned potential drops up to 1 to 10 kV can be generated depending on electron temperatures and on the mass species of the ions. During transient periods of the process, these large potential drops can be confined to a few degrees of magnetic latitude at positions close to the magnetic equator. Anomalous, sometimes dramatic, additional magnetic-field-aligned ion acceleration also occurs in part as a result of a quasi-resonance between the parallel velocities of some ions and the propagating electric potential fronts. It is speculated that the convection surge mechanism could be a key player in the transient, field-aligned electromagnetic processes observed to operate within the middle (e.g., geosynchronous) magnetosphere. copyright American Geophysical Union 1989

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.

Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

Energy Technology Data Exchange (ETDEWEB)

Williams, Robert W. [Department of Biomedical Informatics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20815 (United States)], E-mail: bob@bob.usuhs.mil; Schluecker, Sebastian [Institute of Physical Chemistry, University of Wuerzburg, Wuerzburg (Germany); Hudson, Bruce S. [Department of Chemistry, Syracuse University, Syracuse, NY (United States)

2008-01-22

A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes.

Inelastic neutron scattering, Raman, vibrational analysis with anharmonic corrections, and scaled quantum mechanical force field for polycrystalline L-alanine

International Nuclear Information System (INIS)

Williams, Robert W.; Schluecker, Sebastian; Hudson, Bruce S.

2008-01-01

A scaled quantum mechanical harmonic force field (SQMFF) corrected for anharmonicity is obtained for the 23 K L-alanine crystal structure using van der Waals corrected periodic boundary condition density functional theory (DFT) calculations with the PBE functional. Scale factors are obtained with comparisons to inelastic neutron scattering (INS), Raman, and FT-IR spectra of polycrystalline L-alanine at 15-23 K. Calculated frequencies for all 153 normal modes differ from observed frequencies with a standard deviation of 6 wavenumbers. Non-bonded external k = 0 lattice modes are included, but assignments to these modes are presently ambiguous. The extension of SQMFF methodology to lattice modes is new, as are the procedures used here for providing corrections for anharmonicity and van der Waals interactions in DFT calculations on crystals. First principles Born-Oppenheimer molecular dynamics (BOMD) calculations are performed on the L-alanine crystal structure at a series of classical temperatures ranging from 23 K to 600 K. Corrections for zero-point energy (ZPE) are estimated by finding the classical temperature that reproduces the mean square displacements (MSDs) measured from the diffraction data at 23 K. External k = 0 lattice motions are weakly coupled to bonded internal modes

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)

Dynamical mechanism of symmetry breaking and particle mass generation in gauge field theories

International Nuclear Information System (INIS)

Miranskij, V.A.; Fomin, P.I.

1985-01-01

The dynamics of the spotaneous symmetry breaking and the particle mass generation in gauge theories with no fundamental scalar fields is considered. The emphasis is on the consideration of the symmetry breaking mechanism connected with the dynamics of the supercritical Coulomb-like forces caused by the gauge boson exchange between fermions. This mechanism is applied to different gauge theories, in particular, to the description of the spontaneous chira symmetry breaking in quantum chromodynamics. The mass relations for pseudoscalar meson nonet are obtained and it is shown that this mechanism resuls in the dynamical realisation of the hypothesis of the partial conservation of the axial-vector currents. The qualitative description of scalar mesons is given. The nature of the ultraviolet divergencies in quantum electrodynamics (QED) is investigated from the viewpoint of the dynamics of the fermion mass generation. The mechanism of the appearance of the additional (in comparison with perturbation theory) ultraviolet divergencies in QED with large bare coupling constant is indicated. The physical phenomenon underlying this mechanism is identified as the field theory analogue of the quantum mechanical ''fall into the centre'' (collapse) phenomenon. The similr phenomenon is shown to take place in some two-dimensional quantum field models. The dynamics of the bifermion condensates formation in tumblin gauge theories is briefly discussed

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

Active mechanics in living oocytes reveal molecular-scale force kinetics

Science.gov (United States)

Ahmed, Wylie; Fodor, Etienne; Almonacid, Maria; Bussonnier, Matthias; Verlhac, Marie-Helene; Gov, Nir; Visco, Paolo; van Wijland, Frederic; Betz, Timo

Unlike traditional materials, living cells actively generate forces at the molecular scale that change their structure and mechanical properties. This nonequilibrium activity is essential for cellular function, and drives processes such as cell division. Single molecule studies have uncovered the detailed force kinetics of isolated motor proteins in-vitro, however their behavior in-vivo has been elusive due to the complex environment inside the cell. Here, we quantify active forces and intracellular mechanics in living oocytes using in-vivo optical trapping and laser interferometry of endogenous vesicles. We integrate an experimental and theoretical framework to connect mesoscopic measurements of nonequilibrium properties to the underlying molecular- scale force kinetics. Our results show that force generation by myosin-V drives the cytoplasmic-skeleton out-of-equilibrium (at frequencies below 300 Hz) and actively softens the environment. In vivo myosin-V activity generates a force of F ~ 0 . 4 pN, with a power-stroke of length Δx ~ 20 nm and duration τ ~ 300 μs, that drives vesicle motion at vv ~ 320 nm/s. This framework is widely applicable to characterize living cells and other soft active materials.

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.

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-10-01

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

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

Stress fields in the Antarctic plate inferred from focal mechanisms of intraplate earthquakes

Directory of Open Access Journals (Sweden)

Atsuki Kubo

1999-03-01

Full Text Available Typical directional features of intraplate stresses are extracted from focal mechanism solutions of earthquakes in the Antarctic plate. Typical directions of stresses are obtained in the following regions, 1 Bellingshausen Sea, 2 south of Juan-Fernandez microplate, 3 Balleny Island region and 4 Kerguelen region. P axes in regions 1 and 2 have been interpreted by ridge push force. However these interpretations are based on one focal mechanism for each event and on crude physical concept of ridge push. It is difficult to explain intraplate stress fields in these regions only by the local ridge push force. The stress direction in region 3 can be interpreted by both deformation near triple junction and deformation due to deglaciation. Earthquakes near region 4 appear to be normal fault event. Because normal fault events appear only in the younger ocean floor, the stress field may be affected by thermal features such as hot spots Quantitative modeling and superposition of various stress factors are required to discriminate among stress origins. It is difficult to discuss stress directions in and around Antarctic continent, because number of the earthquakes is not enough.

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%

On the calculation of internal forces in mechanically stressed polyatomic molecules

International Nuclear Information System (INIS)

Avdoshenko, Stanislav M.; Konda, Sai Sriharsha M.; Makarov, Dmitrii E.

2014-01-01

We discuss how to define and to compute internal forces in a molecule subjected to mechanical stress. Because of the inherently many-body character of intramolecular interactions, internal forces cannot be uniquely defined without specifying a set of internal coordinates used to describe the molecular structure. When such a set is comprised of 3N − 6 interactomic distances (N being the number of atoms) and includes the bond lengths of interest, we show that the associated forces, while satisfying the equation F = ∂V/∂R (where R is the bond length, F is the internal force in this bond, and V is the potential energy of the molecule), can be determined from the molecular geometry alone. We illustrate these ideas using several toy models ranging from small molecules to a graphene sheet and show that the magnitude of the internal force in a bond is not necessarily a good predictor of its strength in response to mechanical loading. At the same time, analysis of internal forces reveals interesting phenomena such as the force multiplication effect, where weak external forces may, e.g., be used to break strong bonds, and offers insight into the catch-bond phenomenon where chemical reactivity is suppressed through application of a force

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.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase.

Science.gov (United States)

Wang, Xianwei; Zhang, John Z H; He, Xiao

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein's internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

Energy Technology Data Exchange (ETDEWEB)

Wang, Xianwei [Center for Optics and Optoelectronics Research, College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023 (China); State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); Zhang, John Z. H.; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062 (China); NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062 (China)

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. In this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.

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...

Distributed force feedback in the spinal cord and the regulation of limb mechanics.

Science.gov (United States)

Nichols, T Richard

2018-03-01

This review is an update on the role of force feedback from Golgi tendon organs in the regulation of limb mechanics during voluntary movement. Current ideas about the role of force feedback are based on modular circuits linking idealized systems of agonists, synergists, and antagonistic muscles. In contrast, force feedback is widely distributed across the muscles of a limb and cannot be understood based on these circuit motifs. Similarly, muscle architecture cannot be understood in terms of idealized systems, since muscles cross multiple joints and axes of rotation and further influence remote joints through inertial coupling. It is hypothesized that distributed force feedback better represents the complex mechanical interactions of muscles, including the stresses in the musculoskeletal network born by muscle articulations, myofascial force transmission, and inertial coupling. Together with the strains of muscle fascicles measured by length feedback from muscle spindle receptors, this integrated proprioceptive feedback represents the mechanical state of the musculoskeletal system. Within the spinal cord, force feedback has excitatory and inhibitory components that coexist in various combinations based on motor task and integrated with length feedback at the premotoneuronal and motoneuronal levels. It is concluded that, in agreement with other investigators, autogenic, excitatory force feedback contributes to propulsion and weight support. It is further concluded that coexistent inhibitory force feedback, together with length feedback, functions to manage interjoint coordination and the mechanical properties of the limb in the face of destabilizing inertial forces and positive force feedback, as required by the accelerations and changing directions of both predator and prey.

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

Science.gov (United States)

Hu, Xiaotang; Li, Hongbin

2014-10-01

Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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.

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...

Dressed dibaryon production as a new mechanism for basic nuclear force and meson-exchange currents

International Nuclear Information System (INIS)

Kukulin, V.I.

2003-01-01

A novel concept for the nuclear force is introduced. The approach assumes that a specific dressed six-quark state (dressed dibaryon) is generated in NN collision at intermediate and short ranges. The new dressing mechanism providing π-, σ-, ρ- and ω-meson clouds around the six quark core is discussed. These novel components produce both strong intermediate-range attraction and short-range repulsion in the NN sector due to the s-channel exchange mechanism which is supplemented with conventional π- and 2π- Yukawa exchanges at intermediate and long ranges. The model developed is demonstrated to lead to numerous new effects and contributions in many fields of nuclear physics. (author)

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

International Nuclear Information System (INIS)

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

2012-01-01

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

Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

Directory of Open Access Journals (Sweden)

Raiker Witter

2015-01-01

Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

Martini Coarse-Grained Force Field : Extension to DNA

NARCIS (Netherlands)

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

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

Martini Coarse-Grained Force Field : Extension to Carbohydrates

NARCIS (Netherlands)

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

2009-01-01

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

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

NARCIS (Netherlands)

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

2012-01-01

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

Synthetic oligorotaxanes exert high forces when folding under mechanical load

Science.gov (United States)

Sluysmans, Damien; Hubert, Sandrine; Bruns, Carson J.; Zhu, Zhixue; Stoddart, J. Fraser; Duwez, Anne-Sophie

2018-01-01

Folding is a ubiquitous process that nature uses to control the conformations of its molecular machines, allowing them to perform chemical and mechanical tasks. Over the years, chemists have synthesized foldamers that adopt well-defined and stable folded architectures, mimicking the control expressed by natural systems1,2. Mechanically interlocked molecules, such as rotaxanes and catenanes, are prototypical molecular machines that enable the controlled movement and positioning of their component parts3-5. Recently, combining the exquisite complexity of these two classes of molecules, donor-acceptor oligorotaxane foldamers have been synthesized, in which interactions between the mechanically interlocked component parts dictate the single-molecule assembly into a folded secondary structure6-8. Here we report on the mechanochemical properties of these molecules. We use atomic force microscopy-based single-molecule force spectroscopy to mechanically unfold oligorotaxanes, made of oligomeric dumbbells incorporating 1,5-dioxynaphthalene units encircled by cyclobis(paraquat-p-phenylene) rings. Real-time capture of fluctuations between unfolded and folded states reveals that the molecules exert forces of up to 50 pN against a mechanical load of up to 150 pN, and displays transition times of less than 10 μs. While the folding is at least as fast as that observed in proteins, it is remarkably more robust, thanks to the mechanically interlocked structure. Our results show that synthetic oligorotaxanes have the potential to exceed the performance of natural folding proteins.

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

Science.gov (United States)

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

2018-03-01

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

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...

Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (phi-psi) space

NARCIS (Netherlands)

Liu, Z.; Ensing, B.; Moore, P.B.

2011-01-01

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (phi-psi) conformational space. The FES is obtained from metadynamics simulations with five commonly used

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

Multiscale modeling of interaction of alane clusters on Al(111) surfaces : a reactive force field and infrared absorbtion spectroscopy approach

NARCIS (Netherlands)

Ojwang, J.G.O.; Chaudhuri, S.; Duin, van A.C.T.; Chabal, Y.J.; Veyan, J.-F.; Santen, van R.A.; Kramer, G.J.; Goddard III, W.A.

2010-01-01

We have used reactive force field (ReaxFF) to investigate the mechanism of interaction of alanes on Al(111) surface. Our simulations show that, on the Al(111) surface, alanes oligomerize into larger alanes. In addition, from our simulations, adsorption of atomic hydrogen on Al(111) surface leads to

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

Atomic force microscope image contrast mechanisms on supported lipid bilayers.

Science.gov (United States)

Schneider, J; Dufrêne, Y F; Barger, W R; Lee, G U

2000-08-01

This work presents a methodology to measure and quantitatively interpret force curves on supported lipid bilayers in water. We then use this method to correlate topographic imaging contrast in atomic force microscopy (AFM) images of phase-separated Langmuir-Blodgett bilayers with imaging load. Force curves collected on pure monolayers of both distearoylphosphatidylethanolamine (DSPE) and monogalactosylethanolamine (MGDG) and dioleoylethanolamine (DOPE) deposited at similar surface pressures onto a monolayer of DSPE show an abrupt breakthrough event at a repeatable, material-dependent force. The breakthrough force for DSPE and MGDG is sizable, whereas the breakthrough force for DOPE is too small to measure accurately. Contact-mode AFM images on 1:1 mixed monolayers of DSPE/DOPE and MGDG/DOPE have a high topographic contrast at loads between the breakthrough force of each phase, and a low topographic contrast at loads above the breakthrough force of both phases. Frictional contrast is inverted and magnified at loads above the breakthrough force of both phases. These results emphasize the important role that surface forces and mechanics can play in imaging multicomponent biomembranes with AFM.

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.

Damping forces-a friend or a foe in explaining mechanical motion?

International Nuclear Information System (INIS)

Bartos, JirI; Musilova, Jana

2006-01-01

This paper presents simple, cheap, easily accessible and, for students, impressive demonstration experiments for three typical examples of physical systems for which damping forces ought to be involved in the equations of motion: a body falling in air, a damped mechanical oscillator, and Foucault currents. The various models of such forces are studied using an elementary physical and mathematical approach. It appears, maybe as a slightly surprising result, that a commonly used model of damping forces in mechanics-air drag force linearly depending on velocity-is not realistic in many typical situations. Equations of motion are solved numerically with standard software packages, even in cases where an analytical solution exists. Thus, the explanation of solved problems is on a level corresponding to an undergraduate university course in general physics. The results of these demonstration experiments are compared with the graphical outputs of numerical solutions

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

Mechanism Research of Arch Dam Abutment Forces during Overload

Directory of Open Access Journals (Sweden)

Yu Xia

2015-01-01

Full Text Available This paper presents research on the abutment forces of a double-curvature arch dam during overload based on numerical calculation results obtained through finite element method by Ansys. Results show that, with an increase in elevation, the abutment forces and bending moment of the arch dam increase first and then decrease from the bottom to the top of the dam. Abutment forces and bending moment reach their maximum at the middle or middle-down portion of the dam. The distributions of abutment forces and moment do not change during overload. The magnitude of each arch layer’s forces and moment increases linearly during overload. This result indicates that each arch layer transmits bearing loads to the rocks of the left and right banks steadily. This research explains the operating mechanism of an arch dam under normal and overload conditions. It provides a simple method to calculate the distribution of forces Fx and Fy and a new method to calculate the overload factor of an arch dam through the estimation of arch layers based on the redistribution characteristic of arch abutment forces.

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.

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.

Development of Physics and Control of Multiple Forcing Mechanisms for the Alaska Tsunami Forecast Model

Science.gov (United States)

Bahng, B.; Whitmore, P.; Macpherson, K. A.; Knight, W. R.

2016-12-01

The Alaska Tsunami Forecast Model (ATFM) is a numerical model used to forecast propagation and inundation of tsunamis generated by earthquakes or other mechanisms in either the Pacific Ocean, Atlantic Ocean or Gulf of Mexico. At the U.S. National Tsunami Warning Center (NTWC), the use of the model has been mainly for tsunami pre-computation due to earthquakes. That is, results for hundreds of hypothetical events are computed before alerts, and are accessed and calibrated with observations during tsunamis to immediately produce forecasts. The model has also been used for tsunami hindcasting due to submarine landslides and due to atmospheric pressure jumps, but in a very case-specific and somewhat limited manner. ATFM uses the non-linear, depth-averaged, shallow-water equations of motion with multiply nested grids in two-way communications between domains of each parent-child pair as waves approach coastal waters. The shallow-water wave physics is readily applicable to all of the above tsunamis as well as to tides. Recently, the model has been expanded to include multiple forcing mechanisms in a systematic fashion, and to enhance the model physics for non-earthquake events.ATFM is now able to handle multiple source mechanisms, either individually or jointly, which include earthquake, submarine landslide, meteo-tsunami and tidal forcing. As for earthquakes, the source can be a single unit source or multiple, interacting source blocks. Horizontal slip contribution can be added to the sea-floor displacement. The model now includes submarine landslide physics, modeling the source either as a rigid slump, or as a viscous fluid. Additional shallow-water physics have been implemented for the viscous submarine landslides. With rigid slumping, any trajectory can be followed. As for meteo-tsunami, the forcing mechanism is capable of following any trajectory shape. Wind stress physics has also been implemented for the meteo-tsunami case, if required. As an example of multiple

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.

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

Force spectroscopy of collagen fibers to investigate their mechanical properties and structural organization.

Science.gov (United States)

Gutsmann, Thomas; Fantner, Georg E; Kindt, Johannes H; Venturoni, Manuela; Danielsen, Signe; Hansma, Paul K

2004-05-01

Tendons are composed of collagen and other molecules in a highly organized hierarchical assembly, leading to extraordinary mechanical properties. To probe the cross-links on the lower level of organization, we used a cantilever to pull substructures out of the assembly. Advanced force probe technology, using small cantilevers (length exponential increase in force and two different periodic rupture events, one with strong bonds (jumps in force of several hundred pN) with a periodicity of 78 nm and one with weak bonds (jumps in force of <7 pN) with a periodicity of 22 nm. We demonstrate a good correlation between the measured mechanical behavior of collagen fibers and their appearance in the micrographs taken with the atomic force microscope.

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

Science.gov (United States)

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

2014-12-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-12-28

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

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

Science.gov (United States)

Dokur, Derya; Keskin, Seda

2018-02-14

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

Design of a Novel Telerehabilitation System with a Force-Sensing Mechanism

Directory of Open Access Journals (Sweden)

Songyuan Zhang

2015-05-01

Full Text Available Many stroke patients are expected to rehabilitate at home, which limits their access to proper rehabilitation equipment, treatment, or assessment by therapists. We have developed a novel telerehabilitation system that incorporates a human-upper-limb-like device and an exoskeleton device. The system is designed to provide the feeling of real therapist–patient contact via telerehabilitation. We applied the principle of a series elastic actuator to both the master and slave devices. On the master side, the therapist can operate the device in a rehabilitation center. When performing passive training, the master device can detect the therapist’s motion while controlling the deflection of elastic elements to near-zero, and the patient can receive the motion via the exoskeleton device. When performing active training, the design of the force-sensing mechanism in the master device can detect the assisting force added by the therapist. The force-sensing mechanism also allows force detection with an angle sensor. Patients’ safety is guaranteed by monitoring the motor’s current from the exoskeleton device. To compensate for any possible time delay or data loss, a torque-limiter mechanism was also designed in the exoskeleton device for patients’ safety. Finally, we successfully performed a system performance test for passive training with transmission control protocol/internet protocol communication.

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-10-15

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

Force scanning: a rapid, high-resolution approach for spatial mechanical property mapping

International Nuclear Information System (INIS)

Darling, E M

2011-01-01

Atomic force microscopy (AFM) can be used to co-localize mechanical properties and topographical features through property mapping techniques. The most common approach for testing biological materials at the microscale and nanoscale is force mapping, which involves taking individual force curves at discrete sites across a region of interest. The limitations of force mapping include long testing times and low resolution. While newer AFM methodologies, like modulated scanning and torsional oscillation, circumvent this problem, their adoption for biological materials has been limited. This could be due to their need for specialized software algorithms and/or hardware. The objective of this study is to develop a novel force scanning technique using AFM to rapidly capture high-resolution topographical images of soft biological materials while simultaneously quantifying their mechanical properties. Force scanning is a straightforward methodology applicable to a wide range of materials and testing environments, requiring no special modification to standard AFMs. Essentially, if a contact-mode image can be acquired, then force scanning can be used to produce a spatial modulus map. The current study first validates this technique using agarose gels, comparing results to ones achieved by the standard force mapping approach. Biologically relevant demonstrations are then presented for high-resolution modulus mapping of individual cells, cell-cell interfaces, and articular cartilage tissue.

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

Directory of Open Access Journals (Sweden)

R. Hedayati

2018-03-01

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

Repulsive gravitational forces: A possible mechanism for clustering

International Nuclear Information System (INIS)

Eisenstaedt, J.

1977-01-01

It is well known that, in a homogeneous cosmological universe, a positive cosmological constant induces repulsive forces. We show here that in a locally inhomogeneous cosmological model these repulsive forces are related to the sign of q, the deceleration parameter of the associated cosmological space, and to the sign of m, the apparent mass of the central perturbation (which can be negative with a positive energy density everywhere). When q is almost zero--crossing the value zero--small random perturbations of the matter density are the sources of a gravitational instability which can generate a mechanism of fragmentation in an a priori homogeneous universe

Screening fifth forces in k-essence and DBI models

Energy Technology Data Exchange (ETDEWEB)

Brax, Philippe [Institut de Physique Théorique, CEA, IPhT, CNRS, URA2306, F-91191 Gif-sur-Yvette cédex (France); Burrage, Clare [School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD (United Kingdom); Davis, Anne-Christine, E-mail: Philippe.Brax@cea.fr, E-mail: Clare.Burrage@nottingham.ac.uk, E-mail: A.C.Davis@damtp.cam.ac.uk [Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Cambridge CB3 0WA (United Kingdom)

2013-01-01

New fifth forces have not yet been detected in the laboratory or in the solar system, hence it is typically difficult to introduce new light scalar fields that would mediate such forces. In recent years it has been shown that a number of non-linear scalar field theories allow for a dynamical mechanism, such as the Vainshtein and chameleon ones, that suppresses the strength of the scalar fifth force in experimental environments. This is known as screening, however it is unclear how common screening is within non-linear scalar field theories. k-essence models are commonly studied examples of non-linear models, with DBI as the best motivated example, and so we ask whether these non-linearities are able to screen a scalar fifth force. We find that a Vainshtein-like screening mechanism exists for such models although with limited applicability. For instance, we cannot find a screening mechanism for DBI models. On the other hand, we construct a large class of k-essence models which lead to the acceleration of the Universe in the recent past for which the fifth force mediated by the scalar can be screened.

The vacuum structure, special relativity theory and quantum mechanics revisited: a field theory-no-geometry approach

International Nuclear Information System (INIS)

Bogolubov, N.N. Jr.; Prykarpatsky, A.K.; Ufuk Taneri

2008-07-01

The main fundamental principles characterizing the vacuum field structure are formulated and the modeling of the related vacuum medium and charged point particle dynamics by means of de- vised field theoretic tools are analyzed. The Maxwell electrodynamic theory is revisited and newly derived from the suggested vacuum field structure principles and the classical special relativity theory relationship between the energy and the corresponding point particle mass is revisited and newly obtained. The Lorentz force expression with respect to arbitrary non-inertial reference frames is revisited and discussed in detail, and some new interpretations of relations between the special relativity theory and quantum mechanics are presented. The famous quantum-mechanical Schroedinger type equations for a relativistic point particle in the external potential and magnetic fields within the quasiclassical approximation as the Planck constant (h/2π) → 0 and the light velocity c → ∞ are obtained. (author)

Multiphase-field model of small strain elasto-plasticity according to the mechanical jump conditions

Science.gov (United States)

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

2018-04-01

We introduce a small strain elasto-plastic multiphase-field model according to the mechanical jump conditions. A rate-independent J_2 -plasticity model with linear isotropic hardening and without kinematic hardening is applied exemplary. Generally, any physically nonlinear mechanical model is compatible with the subsequently presented procedure. In contrast to models with interpolated material parameters, the proposed model is able to apply different nonlinear mechanical constitutive equations for each phase separately. The Hadamard compatibility condition and the static force balance are employed as homogenization approaches to calculate the phase-inherent stresses and strains. Several verification cases are discussed. The applicability of the proposed model is demonstrated by simulations of the martensitic transformation and quantitative parameters.

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

New mechanism of cluster-field evaporation in rf breakdown

Directory of Open Access Journals (Sweden)

Z. Insepov

2004-12-01

Full Text Available Using a simple field evaporation model and molecular dynamics simulations of nanoscale copper tip evolution in a high electric field gradient typical for linacs, we have studied a new mechanism for rf-field evaporation. The mechanism consists of simultaneous (collective field evaporation of a large group of tip atoms in high-gradient fields. Thus, evaporation of large clusters is energetically more favorable when compared with the conventional, “one-by-one” mechanism. The studied mechanism could also be considered a new mechanism for the triggering of rf-vacuum breakdown. This paper discusses the mechanism and the experimental data available for electric field evaporation of field-emission microscopy tips.

In-depth Study on Cylinder Wake Controlled by Lorentz Force

International Nuclear Information System (INIS)

Zhang Hui; Fan Bao-Chun; Chen Zhi-Hua

2011-01-01

The underlying mechanisms of the electromagnetic control of cylinder wake are investigated and discussed. The effects of Lorentz force are found to be composed of two parts, one is its direct action on the cylinder (the wall Lorentz force) and the other is applied to the fluid (called the field Lorentz force) near the cylinder surface. Our results show that the wall Lorentz force can generate thrust and reduce the drag; the field Lorentz force increases the drag. However, the cylinder drag is dominated by the wall Lorentz force. In addition, the field Lorentz force above the upper surface decreases the lift, while the upper wall Lorentz force increases it. The total lift is dominated by the upper wall Lorentz force. (fundamental areas of phenomenology(including applications))

Introduction to nonequilibrium statistical mechanics with quantum field theory

International Nuclear Information System (INIS)

Kita, Takafumi

2010-01-01

quantum field theory, including fluctuations. We also discuss a derivation of the quantum transport equations for electrons in electromagnetic fields based on the gauge-invariant Wigner transformation so that the Lorentz force is reproduced naturally. As for (3), the Gibbs entropy of equilibrium statistical mechanics suffers from the flaw that it does not evolve in time. We show here that a microscopic expression of nonequilibrium dynamical entropy can be derived from the quantum transport equations so as to be compatible with the law of increase in entropy as well as equilibrium statistical mechanics. (author)

Effects of mechanical properties of thermoplastic materials on the initial force of thermoplastic appliances.

Science.gov (United States)

Kohda, Naohisa; Iijima, Masahiro; Muguruma, Takeshi; Brantley, William A; Ahluwalia, Karamdeep S; Mizoguchi, Itaru

2013-05-01

To measure the forces delivered by thermoplastic appliances made from three materials and investigate effects of mechanical properties, material thickness, and amount of activation on orthodontic forces. Three thermoplastic materials, Duran (Scheu Dental), Erkodur (Erkodent Erich Kopp GmbH), and Hardcast (Scheu Dental), with two different thicknesses were selected. Values of elastic modulus and hardness were obtained from nanoindentation measurements at 28°C. A custom-fabricated system with a force sensor was employed to obtain measurements of in vitro force delivered by the thermoplastic appliances for 0.5-mm and 1.0-mm activation for bodily tooth movement. Experimental results were subjected to several statistical analyses. Hardcast had significantly lower elastic modulus and hardness than Duran and Erkodur, whose properties were not significantly different. Appliances fabricated from thicker material (0.75 mm or 0.8 mm) always produced significantly greater force than those fabricated from thinner material (0.4 mm or 0.5 mm). Appliances with 1.0-mm activation produced significantly lower force than those with 0.5-mm activation, except for 0.4-mm thick Hardcast appliances. A strong correlation was found between mechanical properties of the thermoplastic materials and force produced by the appliances. Orthodontic forces delivered by thermoplastic appliances depend on the material, thickness, and amount of activation. Mechanical properties of the polymers obtained by nanoindentation testing are predictive of force delivery by these appliances.

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

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

Science.gov (United States)

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

1995-01-01

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

ATK-ForceField: a new generation molecular dynamics software package

Science.gov (United States)

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

2017-12-01

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

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

Science.gov (United States)

Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

2013-02-19

Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

A simple mechanism for measuring and adjusting distraction forces during maxillary advancement.

Science.gov (United States)

Suzuki, Eduardo Yugo; Suzuki, Boonsiva

2009-10-01

Direct measurement of distraction forces on the craniofacial skeleton has never been reported. The present report describes the development of a method of assessing and adjusting traction forces applied through maxillary distraction osteogenesis. A simple mechanism to measure and adjust tension force during maxillary distraction osteogenesis was developed and connected bilaterally to the traction screws of a rigid external distraction device. Measurements were carried out before and after activation using a Shimpo (Nidec-Shimpo America Corporation, Itasca, IL) force gauge in 4 patients (2 with unilateral cleft lip and/or palate, 1 with bilateral cleft lip and palate, and 1 with noncleft) during the distraction process. Activation was performed twice a day at a rate of 1 mm/day. The average maximum force applied throughout the distraction period was 42.5 N (range 16.4 to 65.3 N), with increments, after activation, averaging 10.5 N (range 7.9 to 15.7 N). In patients with unilateral cleft lip and/or palate, distraction forces on the larger segment were 65.1% higher than on the lesser segment. A differential pattern of forces was also observed in the patients with asymmetric noncleft. However, the differential forces between lateral segments were not observed in the patient with bilateral cleft lip and palate. During the activation period, distraction forces progressively increased, whereas the amount of maxillary movement decreased. Pain and discomfort were reported with high forces. Through this mechanism, direct measurement and adjustment of distraction forces during maxillary advancement was possible. The unbalanced pattern of forces observed in patients with cleft suggests the necessity of individual adjustments for controlling pain and clinical symptoms. Accordingly, assessment of distraction forces during maxillary distraction osteogenesis is extremely helpful in understanding the biomechanics of the distraction process.

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

International Nuclear Information System (INIS)

Maeda, N.

1988-01-01

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

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

Science.gov (United States)

Marston, Philip L; Zhang, Likun

2017-05-01

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

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.

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.

Magnetization reversal mechanisms under oblique magnetic fields

Energy Technology Data Exchange (ETDEWEB)

Ntallis, N.; Efthimiadis, K.G., E-mail: kge@auth.gr

2017-03-01

In this work finite element micromagnetic simulations were performed in order to study the reversal mechanisms of spherical ferromagnetic particles with uniaxial magnetocrystalline anisotropy, when they are magnetized along an oblique direction with respect to the anisotropy axis. Magnetization loops are taken in different directions of external magnetic field, at different anisotropy constants and particle sizes. In the simulation results, the three reversal mechanisms (coherent, curling and domains) are observed and new phenomena arise due to the action of oblique magnetic fields. Moreover, the dependence of the critical fields with respect to the angle of the external field is presented. - Highlights: • Finite element micromagnetic simulation of the three different reversal mechanisms. • For the curling mechanism, the new phenomenon is the rotation of the vortex. • In the domain reversal mechanism, the formed domain wall is smaller than 180°. • In soft ferromagnetic particles a rearrangement of the magnetic domains is observed.

Defect forces, defect couples and path integrals in fracture mechanics

International Nuclear Information System (INIS)

Roche, R.L.

1979-07-01

In this work, it is shown that the path integrals can be introduced without any reference to the material behavior. The method is based on the definition in a continuous medium of a set of vectors and couples having the dimension of a force or a moment. More precisely, definitions are given of volume defect forces, surface defect forces, volume defect couples, and surface defect couples. This is done with the help of the stress working variation of a particule moving through the solid. The most important result is: the resultant of all the defect forces included in a volume V is the J integral on the surface surrounding V and the moment resultant is the L integral. So these integrals are defined without any assumption on the material constitutive equation. Another result is the material form of the virtual work principle - defect forces are acting like conventional forces in the conventional principles of virtual work. This lead to the introduction of the energy momentum tensor and of the associated couple stress. Application of this method is made to fracture mechanics in studying the defect forces distribution around a crack [fr

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

On the axioms of the forces in the mechanics of rigid bodies

Directory of Open Access Journals (Sweden)

Lámer Géza

2017-01-01

Full Text Available Newton summarised knowledge related to forces in three axioms. The first and second ones define the mechanical state and motion of the examined body when there is no force or when force is exerted on the body. The third defines the law of action and reaction. Newton did not define it as separate axiom but assumed that forces are completely independent from each other. The statics applies four axioms. The first applies to the balance of two forces while the second one applies of three forces. The third axiom defines the relationships inside an equilibrium force system. The fourth one is the axiom of action and reaction. The two axiom systems are independent from each other. Further the independent axioms are applied in case of constraint forces: frictionless reaction force orthogonal on the forced surface, friction force acts in the direction of the motion, the deformation can be elastic, plastic and viscous.

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

Some connections between relativistic classical mechanics, statistical mechanics, and quantum field theory

International Nuclear Information System (INIS)

Remler, E.A.

1977-01-01

A gauge-invariant version of the Wigner representation is used to relate relativistic mechanics, statistical mechanics, and quantum field theory in the context of the electrodynamics of scalar particles. A unified formulation of quantum field theory and statistical mechanics is developed which clarifies the physics interpretation of the single-particle Wigner function. A covariant form of Ehrenfest's theorem is derived. Classical electrodynamics is derived from quantum field theory after making a random-phase approximation. The validity of this approximation is discussed

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

Quantum mechanical methods for calculation of force constants

International Nuclear Information System (INIS)

Mullally, D.J.

1985-01-01

The focus of this thesis is upon the calculation of force constants; i.e., the second derivatives of the potential energy with respect to nuclear displacements. This information is useful for the calculation of molecular vibrational modes and frequencies. In addition, it may be used for the location and characterization of equilibrium and transition state geometries. The methods presented may also be applied to the calculation of electric polarizabilities and infrared and Raman vibrational intensities. Two approaches to this problem are studied and evaluated: finite difference methods and analytical techniques. The most suitable method depends on the type and level of theory used to calculate the electronic wave function. Double point displacement finite differencing is often required for accurate calculation of the force constant matrix. These calculations require energy and gradient calculations on both sides of the geometry of interest. In order to speed up these calculations, a novel method is presented that uses geometry dependent information about the wavefunction. A detailed derivation for the analytical evaluation of force constants with a complete active space multiconfiguration self consistent field wave function is presented

The Role of Mechanical Force in Molecular and Cellular during Orthodontic Tooth Movement

Directory of Open Access Journals (Sweden)

Ida Bagus Narmada

2012-10-01

Full Text Available Application of mechanical force on abnormally positioned tooth, cause changes in tooth location and transmitted to the bone ia the periodontal ligament (PDL produce orthodontic tooth movement. This force application is further way that remodeling in the area occurs. In order to develop biological strategies for enhancing this movement of teeth in bone, the underlying mechanisms of bone resorption and apposition should be understood in detail. Analysis of gingival crevicular fluid (GCF may be a good means of examining the on going molecular and cellular process associated with gingival and bone turnover during orthodontic tooth movement. If it could be possible to biologically monitor and predict the outcome of orthodontic force, then the appliance management could be based on dividual tissue response and the effectiveness of the treatment could be improved and understanding their biology is critical to finding ways to modify bone biology to move teeth faster. The present article reviewed a short introduction to some mayors advanced mechanical force in molecular and cellular biology during orthodontic tooth movement.DOI: 10.14693/jdi.v15i3.30

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.

Mechanism for boundary crises in quasiperiodically forced period-doubling systems

International Nuclear Information System (INIS)

Kim, Sang-Yoon; Lim, Woochang

2005-01-01

We investigate the mechanism for boundary crises in the quasiperiodically forced logistic map which is a representative model for quasiperiodically forced period-doubling systems. For small quasiperiodic forcing ε, a chaotic attractor disappears suddenly via a 'standard' boundary crisis when it collides with the smooth unstable torus. However, when passing a threshold value of ε, a basin boundary metamorphosis occurs, and then the smooth unstable torus is no longer accessible from the interior of the basin of the attractor. For this case, using the rational approximations to the quasiperiodic forcing, it is shown that a nonchaotic attractor (smooth torus or strange nonchaotic attractor) as well as a chaotic attractor is destroyed abruptly through a new type of boundary crisis when it collides with an invariant 'ring-shaped' unstable set which has no counterpart in the unforced case

Mechanism for boundary crises in quasiperiodically forced period-doubling systems

Energy Technology Data Exchange (ETDEWEB)

Kim, Sang-Yoon [Department of Physics, Kangwon National University, Chunchon, Kangwon-Do 200-701 (Korea, Republic of)]. E-mail: sykim@kangwon.ac.kr; Lim, Woochang [Department of Physics, Kangwon National University, Chunchon, Kangwon-Do 200-701 (Korea, Republic of)]. E-mail: wclim@kwnu.kangwon.ac.kr

2005-01-10

We investigate the mechanism for boundary crises in the quasiperiodically forced logistic map which is a representative model for quasiperiodically forced period-doubling systems. For small quasiperiodic forcing {epsilon}, a chaotic attractor disappears suddenly via a 'standard' boundary crisis when it collides with the smooth unstable torus. However, when passing a threshold value of {epsilon}, a basin boundary metamorphosis occurs, and then the smooth unstable torus is no longer accessible from the interior of the basin of the attractor. For this case, using the rational approximations to the quasiperiodic forcing, it is shown that a nonchaotic attractor (smooth torus or strange nonchaotic attractor) as well as a chaotic attractor is destroyed abruptly through a new type of boundary crisis when it collides with an invariant 'ring-shaped' unstable set which has no counterpart in the unforced case.

Gauge field copies and Higgs mechanism

International Nuclear Information System (INIS)

Gleiser, M.

1982-07-01

From the algebric classification of the possible solutions of the necessary and sufficient condition for the existence of gauge field copies in two possible classes the Higgs mechanism for the potential obtained from the difference between two copied potentials is applied. It is shown that for class I 'electric type' it is possible to construct a vector field that satisfies an electromagnetic wave equation. For class I 'magnetic type', a vector field that satisfies a non-linear equation as a consequence of the non-abelianity of the theory, is obtained. It is shown that for class II it's not possible to apply the Higgs mechanism. A possible physical interpretation for the 'gauge field copies' phenomenon, is obtained. (author) [pt

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.

Generation mechanisms for magnetic-field-aligned electric fields in the magnetosphere

International Nuclear Information System (INIS)

Faelthammar, C.-G.

1977-09-01

Magnetic-field-aligned electric fields in the magnetosphere can be generated in several different ways, and in this review some possible mechanisms are presented. Observational data now available indicates that more than one of the mechanisms mentioned are operative in the magnetosphere but it is not yet possible to evaluate their relative importance. (author)

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.

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.

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.)

On a mechanism of excitation of a reccurent stream and electric field on the front side of the magnetosphere

International Nuclear Information System (INIS)

Samokhin, M.V.

1983-01-01

The purpose of the paper is generalization of the mechanism of electric field excitation on the front side of the magnetosphere due to solar wind pressure gradient along the magnetopause for the case of curved magnetic force lines. Motion of geomagnetic force tubes near the magnetopause from the front point in the direction of the magnetotail is considered. Models with n approximately L -4 (Gold relation), n approximately L -3 (straight force lines), n approximately L -6 (Chapmen-Ferraro model) are analyzed. Decrease in the tangential component of the magnetic field with removal from the front point in the head part of the magnetopause due to a reduction in the solar wind pressure caused by a change in the magnetopause inclination in relation to unperturbed solar wind velocity results in appearance of recurrent stream inside the magnetosphere with increase in the stream rate with removal from the front point and to the corresponding generation of the electric field component normal to the magnetopause. The rate of recurrent stream and electric field are determined by two parameters in the point of plasma stagnation: the Alfven speed and gas/magnetic pressure ratio

Study on force mechanism for therapeutic effect of pushing manipulation with one-finger meditation base on similarity analysis of force and waveform.

Science.gov (United States)

Fang, Lei; Fang, Min; Guo, Min-Min

2016-12-27

To reveal the force mechanism for therapeutic effect of pushing manipulation with one-finger meditation. A total of 15 participants were recruited in this study and assigned to an expert group, a skilled group and a novice group, with 5 participants in each group. Mechanical signals were collected from a biomechanical testing platform, and these data were further observed via similarity analysis and cluster analysis. Comparing the force waveforms of manipulation revealed that the manipulation forces were similar between the expert group and the skilled group (P>0.05). The mean value of vertical force was 9.8 N, and 95% CI rang from 6.37 to 14.70 N, but there were significant differences compared with the novice group (PPushing manipulation with one-finger meditation is a kind of light stimulation manipulation on the acupoint, and force characteristics of double waveforms continuously alternated during manual operation.

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

NARCIS (Netherlands)

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

2007-01-01

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

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

NARCIS (Netherlands)

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

2009-01-01

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

Mechanism for the generation of 109 G magnetic fields in the interaction of ultraintense short laser pulse with an overdense plasma target

International Nuclear Information System (INIS)

Sudan, R.N.

1993-01-01

The physical mechanism for the generation of very high ''dc'' magnetic fields in the interaction of ultraintense short laser pulse with an overdense plasma target originates in the spatial gradients and nonstationary character of the ponderomotive force. A set of model equations to determine the evolution of the ''dc'' fields is derived and it is shown that the ''dc'' magnetic field is of the same order of magnitude as the high frequency laser magnetic field

Particles, fields, quanta. From quantum mechanics to the Standard Model of particle physics; Teilchen, Felder, Quanten. Von der Quantenmechanik zum Standardmodell der Teilchenphysik

Energy Technology Data Exchange (ETDEWEB)

Ecker, Gerhard [Wien Univ. (Austria). Fakultaet fuer Physik

2017-07-01

The following topics are dealt with: Physics around 1900, the way to quantum mechanics, quantum field theory with quantum electrodynamics as prototype, the crisis of quantum field theory, from the beta decay to the electroweak gauge theory, quantum chromodynamics as quantum field theory of the strong nuclear force, the standard model of the fundamental interactions, physics beyond the standard model. (HSI)

Efficient nonparametric n -body force fields from machine learning

Science.gov (United States)

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

2018-05-01

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

Force field inside the void in complex plasmas under microgravity conditions

International Nuclear Information System (INIS)

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

2005-01-01

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

Nonlinear gravitational self-force: Field outside a small body

Science.gov (United States)

Pound, Adam

2012-10-01

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

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.

A model considering mechanical anisotropy of magnetic-field-induced superelastic strain in magnetic shape memory alloys

International Nuclear Information System (INIS)

Zhu, Yuping; Yu, Kai

2013-01-01

Highlights: ► The model analyzes mechanical anisotropy of magnetic shape memory alloy. ► The numerical evaluation of Eshelby tensor of shape memory alloy is obtained. ► Interaction energy of magnetic shape memory alloy is analyzed. - Abstract: Under applied mechanical load and magnetic field, a micromechanics-based thermodynamic model taking account of mechanical anisotropy of magnetic shape memory alloys (MSMAs) is developed in this work. Considering the crystallographic and magnetic microstructure, the internal state variables are chosen and the model can capture the magnetic shape memory effect caused by the martensitic variant reorientation process. It is assumed that the Gibbs free energy is consisted of the mechanical potential energy of anisotropic matrix, the Zeeman energy and the magnetocrystalline anisotropy energy in the model. In terms of the balance between the thermodynamic driving force derived from the reduction of Gibbs free energy and the resistive force for the variant reorientation, the kinetic equation is established and the Eshelby tensor of anisotropic MSMAs is then obtained by using numerical evaluation. At last, the effects of the anisotropy on interaction energy and macroscopic strain are discussed. The assumption of isotropy tends to underestimate interaction energy and macroscopic strain. The results considering mechanical anisotropy are in good agreement with the experimental data.

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.

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.

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.

Chameleons with Field Dependent Couplings

CERN Document Server

Brax, Philippe; Mota, David F; Nunes, Nelson J; Winther, Hans A

2010-01-01

Certain scalar-tensor theories exhibit the so-called chameleon mechanism, whereby observational signatures of scalar fields are hidden by a combination of self-interactions and interactions with ambient matter. Not all scalar-tensor theories exhibit such a chameleon mechanism, which has been originally found in models with inverse power run-away potentials and field independent couplings to matter. In this paper we investigate field-theories with field-dependent couplings and a power-law potential for the scalar field. We show that the theory indeed is a chameleon field theory. We find the thin-shell solution for a spherical body and investigate the consequences for E\\"ot-Wash experiments, fifth-force searches and Casimir force experiments. Requiring that the scalar-field evades gravitational tests, we find that the coupling is sensitive to a mass-scale which is of order of the Hubble scale today.

Chameleons with field-dependent couplings

International Nuclear Information System (INIS)

Brax, Philippe; Bruck, Carsten van de; Mota, David F.; Winther, Hans A.; Nunes, Nelson J.

2010-01-01

Certain scalar-tensor theories exhibit the so-called chameleon mechanism, whereby observational signatures of scalar fields are hidden by a combination of self-interactions and interactions with ambient matter. Not all scalar-tensor theories exhibit such a chameleon mechanism, which has been originally found in models with inverse power runaway potentials and field-independent couplings to matter. In this paper we investigate field theories with field-dependent couplings and a power-law potential for the scalar field. We show that the theory indeed is a chameleon field theory. We find the thin-shell solution for a spherical body and investigate the consequences for Eoet-Wash experiments, fifth-force searches and Casimir-force experiments. Requiring that the scalar field evades gravitational tests, we find that the coupling is sensitive to a mass scale which is of order of the Hubble scale today.

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

The Virtual Fields Method Extracting Constitutive Mechanical Parameters from Full-field Deformation Measurements

CERN Document Server

Pierron, Fabrice

2012-01-01

The Virtual Fields Method: Extracting Constitutive Mechanical Parameters from Full-field Deformation Measurements is the first book on the Virtual Fields Method (VFM), a technique to identify materials mechanical properties from full-field measurements. Firmly rooted with extensive theoretical description of the method, the book presents numerous examples of application to a wide range of materials (composites, metals, welds, biomaterials) and situations (static, vibration, high strain rate). The authors give a detailed training section with examples of progressive difficulty to lead the reader to program the VFM and include a set of commented Matlab programs as well as GUI Matlab-based software for more general situations. The Virtual Fields Method: Extracting Constitutive Mechanical Parameters from Full-field Deformation Measurements is an ideal book for researchers, engineers, and students interested in applying the VFM to new situations motivated by their research.  

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

Science.gov (United States)

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

2016-03-05

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

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

Science.gov (United States)

Yao, Shuang; Zhang, Yang; Guan, Baiou

2015-08-01

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

On justification of efficient Energy-Force parameters of Hydraulic-excavator main mechanisms

Science.gov (United States)

Komissarov, Anatoliy; Lagunova, Yuliya; Shestakov, Viktor; Lukashuk, Olga

2018-03-01

The article formulates requirements for energy-efficient designs of the operational equipment of a hydraulic excavator (its boom, stick and bucket) and defines, for a mechanism of that equipment, a new term “performance characteristic”. The drives of main rotation mechanisms of the equipment are realized by hydraulic actuators (hydraulic cylinders) and transmission (leverage) mechanisms, with the actuators (the cylinders themselves, their pistons and piston rods) also acting as links of the leverage. Those drives are characterized by the complexity of translating mechanical-energy parameters of the actuators into energy parameters of the driven links (a boom, a stick and a bucket). Relations between those parameters depend as much on the types of mechanical characteristics of the hydraulic actuators as on the types of structural schematics of the transmission mechanisms. To assess how energy-force parameters of the driven links change when a typical operation is performed, it was proposed to calculate performance characteristics of the main mechanisms as represented by a set of values of transfer functions, i.e. by functional dependences between driven links and driving links (actuators). Another term “ideal performance characteristic” of a mechanism was introduced. Based on operation-emulating models for the main mechanisms of hydraulic excavators, analytical expressions were derived to calculate kinematic and force transfer functions of the main mechanisms.

Constraining Carbonaceous Aerosol Climate Forcing by Bridging Laboratory, Field and Modeling Studies

Science.gov (United States)

Dubey, M. K.; Aiken, A. C.; Liu, S.; Saleh, R.; Cappa, C. D.; Williams, L. R.; Donahue, N. M.; Gorkowski, K.; Ng, N. L.; Mazzoleni, C.; China, S.; Sharma, N.; Yokelson, R. J.; Allan, J. D.; Liu, D.

2014-12-01

Biomass and fossil fuel combustion emits black (BC) and brown carbon (BrC) aerosols that absorb sunlight to warm climate and organic carbon (OC) aerosols that scatter sunlight to cool climate. The net forcing depends strongly on the composition, mixing state and transformations of these carbonaceous aerosols. Complexities from large variability of fuel types, combustion conditions and aging processes have confounded their treatment in models. We analyse recent laboratory and field measurements to uncover fundamental mechanism that control the chemical, optical and microphysical properties of carbonaceous aerosols that are elaborated below: Wavelength dependence of absorption and the single scattering albedo (ω) of fresh biomass burning aerosols produced from many fuels during FLAME-4 was analysed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCEFI)—higher MCEFI results in lower ω values and greater spectral dependence of ω (Liu et al GRL 2014). A parameterization of ω as a function of MCEFI for fresh BB aerosols is derived from the laboratory data and is evaluated by field data, including BBOP. Our laboratory studies also demonstrate that BrC production correlates with BC indicating that that they are produced by a common mechanism that is driven by MCEFI (Saleh et al NGeo 2014). We show that BrC absorption is concentrated in the extremely low volatility component that favours long-range transport. We observe substantial absorption enhancement for internally mixed BC from diesel and wood combustion near London during ClearFlo. While the absorption enhancement is due to BC particles coated by co-emitted OC in urban regions, it increases with photochemical age in rural areas and is simulated by core-shell models. We measure BrC absorption that is concentrated in the extremely low volatility components and attribute it to wood burning. Our results support

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

Directory of Open Access Journals (Sweden)

Jiang Hualiang

2010-11-01

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

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

Science.gov (United States)

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

2002-03-01

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

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

International Nuclear Information System (INIS)

Jiang Chaowei; Feng Xueshang; Xiang Changqing

2012-01-01

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

On the possible detection of quantum-mechanical interferences between gravitational forces and nucleus-nucleus Coulomb forces

International Nuclear Information System (INIS)

Silveira, R. da

1996-07-01

Possible effects of quantum-mechanical interferences between gravitational forces and the nucleus-nucleus Coulomb interaction are discussed. It is shown that, although very small, these effects could be measured using low energy scattering between identical heavy nuclei, e.g. for the system 208 Pb + 208 Pb (E L = 5 MeV). (author)

Quantitative Study of Nanoscale Contact and Pre-Contact Mechanics Using Force Modulation

National Research Council Canada - National Science Library

Syed Asif, S. A; Wahl, K. J; Colton, R. J

1999-01-01

.... However cantilever instability, conventional force detection and displacement sensing make contact area measurement difficult, hence the measured mechanical properties are usually only qualitative...

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.

Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field

DEFF Research Database (Denmark)

Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena

2013-01-01

The phase behavior of the coarse-grained MARTINI model for three-component lipid bilayers composed of dipalmytoyl-phosphatidylcholine (DPPC), cholesterol (Chol), and an unsaturated phosphatidylcholine (PC) was systematically investigated by molecular dynamics simulations. The aim of this study...... is to understand which types of unsaturated PC induce the formation of thermodynamically stable coexisting phases when added to mixtures of DPPC and Chol and to unravel the mechanisms that drive phase separation in such three-component mixtures. Our simulations indicate that the currently used MARTINI force field...... PCs, such as dilinoleyl-phosphatidylcholine (DUPC) and diarachidonoyl-phosphatidylcholine (DAPC). Through systematic tweaking of the interactions between the hydrophobic groups of the PC molecules, we show that the appearance of phase separation in three-component lipid bilayers, as modeled through...

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

Energy Technology Data Exchange (ETDEWEB)

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

1993-04-01

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

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

OpenAIRE

吉田, 欣二郎; 松田, 茂雄; 松本, 洋和

2000-01-01

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

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

Science.gov (United States)

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

1994-01-01

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

Nano Scale Mechanical Analysis of Biomaterials Using Atomic Force Microscopy

Science.gov (United States)

Dutta, Diganta

The atomic force microscope (AFM) is a probe-based microscope that uses nanoscale and structural imaging where high resolution is desired. AFM has also been used in mechanical, electrical, and thermal engineering applications. This unique technique provides vital local material properties like the modulus of elasticity, hardness, surface potential, Hamaker constant, and the surface charge density from force versus displacement curve. Therefore, AFM was used to measure both the diameter and mechanical properties of the collagen nanostraws in human costal cartilage. Human costal cartilage forms a bridge between the sternum and bony ribs. The chest wall of some humans is deformed due to defective costal cartilage. However, costal cartilage is less studied compared to load bearing cartilage. Results show that there is a difference between chemical fixation and non-chemical fixation treatments. Our findings imply that the patients' chest wall is mechanically weak and protein deposition is abnormal. This may impact the nanostraws' ability to facilitate fluid flow between the ribs and the sternum. At present, AFM is the only tool for imaging cells' ultra-structure at the nanometer scale because cells are not homogeneous. The first layer of the cell is called the cell membrane, and the layer under it is made of the cytoskeleton. Cancerous cells are different from normal cells in term of cell growth, mechanical properties, and ultra-structure. Here, force is measured with very high sensitivity and this is accomplished with highly sensitive probes such as a nano-probe. We performed experiments to determine ultra-structural differences that emerge when such cancerous cells are subject to treatments such as with drugs and electric pulses. Jurkat cells are cancerous cells. These cells were pulsed at different conditions. Pulsed and non-pulsed Jurkat cell ultra-structures were investigated at the nano meter scale using AFM. Jurkat cell mechanical properties were measured under

Relativistic quantum mechanics of leptons and fields

International Nuclear Information System (INIS)

Grandy, W.T. Jr.

1991-01-01

This book serves as an advanced text on the Dirac theory, and provides a monograph summarizing the description of relativistic quantum mechanics and quantum electrodynamics as classical field theories. It presents a broad, detailed, and up-to-date exposition of relativistic quantum mechanics, including the two-body problem. It also demonstrates the extent to which the behavior of stable particles and their interactions can be understood without introducing operator (second-quantized) fields. The subsequent difficulties are studied in detail and possible resolutions are presented through quantum field theory

Three-axis optical force plate for studies in small animal locomotor mechanics

International Nuclear Information System (INIS)

Hsieh, S. Tonia

2006-01-01

The use of force plates to measure whole-body locomotor mechanics is a well-established technique. However, commercially available force plates are not sensitive enough for use on small-bodied vertebrates or invertebrates. The standard design for single- and multiple-axis, high-sensitivity force plates built by individual research groups uses semiconductor foil strain gauges to measure deflections; yet foil strain gauges are highly temperature and position sensitive, resulting in a drifting base line and nonlinear responses. I present here a design for a three-axis optical force plate that was successfully calibrated to measure forces as small as 1.5 mN and is capable of determining the position of center of pressure with a mean error of 0.07 cm along the X axis and 0.13 cm along the Y axis. Using optical sensors instead of foil strain gauges to measure deflection, this force plate is not subject to temperature-related drift and is more robust against slight positioning inaccuracies. This force plate was used to measure forces produced by amphibious fishes weighing less than 2 g as they jumped off the force platform

Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics1[W][OA

Science.gov (United States)

Routier-Kierzkowska, Anne-Lise; Weber, Alain; Kochova, Petra; Felekis, Dimitris; Nelson, Bradley J.; Kuhlemeier, Cris; Smith, Richard S.

2012-01-01

Although growth and morphogenesis are controlled by genetics, physical shape change in plant tissue results from a balance between cell wall loosening and intracellular pressure. Despite recent work demonstrating a role for mechanical signals in morphogenesis, precise measurement of mechanical properties at the individual cell level remains a technical challenge. To address this challenge, we have developed cellular force microscopy (CFM), which combines the versatility of classical microindentation techniques with the high automation and resolution approaching that of atomic force microscopy. CFM’s large range of forces provides the possibility to map the apparent stiffness of both plasmolyzed and turgid tissue as well as to perform micropuncture of cells using very high stresses. CFM experiments reveal that, within a tissue, local stiffness measurements can vary with the level of turgor pressure in an unexpected way. Altogether, our results highlight the importance of detailed physically based simulations for the interpretation of microindentation results. CFM’s ability to be used both to assess and manipulate tissue mechanics makes it a method of choice to unravel the feedbacks between mechanics, genetics, and morphogenesis. PMID:22353572

The three-dimension model for the rock-breaking mechanism of disc cutter and analysis of rock-breaking forces

Science.gov (United States)

Zhang, Zhao-Huang; Sun, Fei

2012-06-01

To study the rock deformation with three-dimensional model under rolling forces of disc cutter, by carrying out the circular-grooving test with disc cutter rolling around on the rock, the rock mechanical behavior under rolling disc cutter is studied, the mechanical model of disc cutter rolling around the groove is established, and the theory of single-point and double-angle variables is proposed. Based on this theory, the physics equations and geometric equations of rock mechanical behavior under disc cutters of tunnel boring machine (TBM) are studied, and then the balance equations of interactive forces between disc cutter and rock are established. Accordingly, formulas about normal force, rolling force and side force of a disc cutter are derived, and their validity is studied by tests. Therefore, a new method and theory is proposed to study rock-breaking mechanism of disc cutters.

Casimir Force Between Quantum Plasmas

International Nuclear Information System (INIS)

Buenzli, P.

2005-01-01

Field fluctuations are responsible for an attractive force - the Casimir force - between two parallel (globally neutral) metallic plates separated by a distance d. At high temperature, or equivalently large d, this force is known to exhibit a classical and universal character (independent of the material constitution of the plates). In a recent work, we have displayed the microscopic mechanisms responsible for this universality within a classical model. The plates consist of slabs containing classical charged particles in fluid phase and thermal equilibrium (plasmas). The universality of the force proves to originate from screening sum rules satisfied by the charge correlations. Here we show how this result is altered when the quantum-mechanical nature of the particles is taken into account. It turns out that in addition to the classical result, the asymptotic force for large d comprises a non-universal quantum correction, which is, however, small at high temperature. The method relies on an exact representation of the charge correlations by quantum Mayer graphs, based on the Feynman-Kac path integral formalism. (author)

Lateral bending of tapered piezo-semiconductive nanostructures for ultra-sensitive mechanical force to voltage conversion.

Science.gov (United States)

Araneo, Rodolfo; Falconi, Christian

2013-07-05

Quasi-1D piezoelectric nanostructures may offer unprecedented sensitivity for transducing minuscule input mechanical forces into high output voltages due to both scaling laws and increased piezoelectric coefficients. However, until now both theoretical and experimental studies have suggested that, for a given mechanical force, lateral bending of piezoelectric nanowires results in lower output electric potentials than vertical compression. Here we demonstrate that this result only applies to nanostructures with a constant cross-section. Moreover, though it is commonly believed that the output electric potential of a strained piezo-semiconductive device can only be reduced by the presence of free charges, we show that the output piezopotential of laterally bent tapered nanostructures, with typical doping levels and very small input forces, can be even increased up to two times by free charges.Our analyses confirm that, though not optimal for piezoelectric energy harvesting, lateral bending of tapered nanostructures with typical doping levels can be ideal for transducing tiny input mechanical forces into high and accessible piezopotentials. Our results provide guidelines for designing high-performance piezo-nano-devices for energy harvesting, mechanical sensing, piezotronics, piezo-phototronics, and piezo-controlled chemical reactions, among others.

Lateral bending of tapered piezo-semiconductive nanostructures for ultra-sensitive mechanical force to voltage conversion

International Nuclear Information System (INIS)

Araneo, Rodolfo; Falconi, Christian

2013-01-01

Quasi-1D piezoelectric nanostructures may offer unprecedented sensitivity for transducing minuscule input mechanical forces into high output voltages due to both scaling laws and increased piezoelectric coefficients. However, until now both theoretical and experimental studies have suggested that, for a given mechanical force, lateral bending of piezoelectric nanowires results in lower output electric potentials than vertical compression. Here we demonstrate that this result only applies to nanostructures with a constant cross-section. Moreover, though it is commonly believed that the output electric potential of a strained piezo-semiconductive device can only be reduced by the presence of free charges, we show that the output piezopotential of laterally bent tapered nanostructures, with typical doping levels and very small input forces, can be even increased up to two times by free charges. Our analyses confirm that, though not optimal for piezoelectric energy harvesting, lateral bending of tapered nanostructures with typical doping levels can be ideal for transducing tiny input mechanical forces into high and accessible piezopotentials. Our results provide guidelines for designing high-performance piezo-nano-devices for energy harvesting, mechanical sensing, piezotronics, piezo-phototronics, and piezo-controlled chemical reactions, among others. (paper)

Silicon Nano fabrication by Atomic Force Microscopy-Based Mechanical Processing

International Nuclear Information System (INIS)

Miyake, Sh.; Wang, M.; Kim, J.

2014-01-01

This paper reviews silicon nano fabrication processes using atomic force microscopy (AFM). In particular, it summarizes recent results obtained in our research group regarding AFM-based silicon nano fabrication through mechanochemical local oxidation by diamond tip sliding, as well as mechanical, electrical, and electromechanical processing using an electrically conductive diamond tip. Microscopic three-dimensional manufacturing mainly relies on etching, deposition, and lithography. Therefore, a special emphasis was placed on nano mechanical processes, mechanochemical reaction by potassium hydroxide solution etching, and mechanical and electrical approaches. Several important surface characterization techniques consisting of scanning tunneling microscopy and related techniques, such as scanning probe microscopy and AFM, were also discussed.

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

Science.gov (United States)

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

2016-04-12

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

Probing the Importance of Charge Flux in Force Field Modeling.

Science.gov (United States)

Sedghamiz, Elaheh; Nagy, Balazs; Jensen, Frank

2017-08-08

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

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

Directory of Open Access Journals (Sweden)

Mustapha Carab Ahmed

2018-06-01

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

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

Science.gov (United States)

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

2017-10-01

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

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.

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

Science.gov (United States)

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

2015-02-11

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

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

DEFF Research Database (Denmark)

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

2014-01-01

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

Near-field NanoThermoMechanical memory

International Nuclear Information System (INIS)

Elzouka, Mahmoud; Ndao, Sidy

2014-01-01

In this letter, we introduce the concept of NanoThermoMechanical Memory. Unlike electronic memory, a NanoThermoMechanical memory device uses heat instead of electricity to record, store, and recover data. Memory function is achieved through the coupling of near-field thermal radiation and thermal expansion resulting in negative differential thermal resistance and thermal latching. Here, we demonstrate theoretically via numerical modeling the concept of near-field thermal radiation enabled negative differential thermal resistance that achieves bistable states. Design and implementation of a practical silicon based NanoThermoMechanical memory device are proposed along with a study of its dynamic response under write/read cycles. With more than 50% of the world's energy losses being in the form of heat along with the ever increasing need to develop computer technologies which can operate in harsh environments (e.g., very high temperatures), NanoThermoMechanical memory and logic devices may hold the answer

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.

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

International Nuclear Information System (INIS)

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

2006-01-01

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

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

DEFF Research Database (Denmark)

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

2017-01-01

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

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.

Mechanical separation of chiral dipoles by chiral light

International Nuclear Information System (INIS)

Canaguier-Durand, Antoine; Hutchison, James A; Genet, Cyriaque; Ebbesen, Thomas W

2013-01-01

We calculate optical forces and torques exerted on a chiral dipole by chiral light fields and reveal genuine chiral forces in combining the chiral contents of both light field and dipolar matter. Here, the optical chirality is characterized in a general way through the definition of optical chirality density and chirality flow. We show, in particular, that both terms have mechanical effects associated, respectively, with reactive and dissipative components of the chiral forces. Remarkably, these chiral force components are directly related to standard observables: optical rotation for the reactive component and circular dichroism for the dissipative one. As a consequence, the resulting forces and torques are dependent on the enantiomeric form of the chiral dipole. This suggests promising strategies for using chiral light forces to mechanically separate chiral objects according to their enantiomeric form. (paper)

Physical Limits on the Precision of Mitotic Spindle Positioning by Microtubule Pushing forces: Mechanics of mitotic spindle positioning.

Science.gov (United States)

Howard, Jonathon; Garzon-Coral, Carlos

2017-11-01

Tissues are shaped and patterned by mechanical and chemical processes. A key mechanical process is the positioning of the mitotic spindle, which determines the size and location of the daughter cells within the tissue. Recent force and position-fluctuation measurements indicate that pushing forces, mediated by the polymerization of astral microtubules against- the cell cortex, maintain the mitotic spindle at the cell center in Caenorhabditis elegans embryos. The magnitude of the centering forces suggests that the physical limit on the accuracy and precision of this centering mechanism is determined by the number of pushing microtubules rather than by thermally driven fluctuations. In cells that divide asymmetrically, anti-centering, pulling forces generated by cortically located dyneins, in conjunction with microtubule depolymerization, oppose the pushing forces to drive spindle displacements away from the center. Thus, a balance of centering pushing forces and anti-centering pulling forces localize the mitotic spindles within dividing C. elegans cells. © 2017 The Authors. BioEssays published by Wiley Periodicals, Inc.

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

International Nuclear Information System (INIS)

Prajapati, R.P.

2013-01-01

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

Field measurement of basal forces generated by erosive debris flows

Science.gov (United States)

McCoy, S.W.; Tucker, G.E.; Kean, J.W.; Coe, J.A.

2013-01-01

It has been proposed that debris flows cut bedrock valleys in steeplands worldwide, but field measurements needed to constrain mechanistic models of this process remain sparse due to the difficulty of instrumenting natural flows. Here we present and analyze measurements made using an automated sensor network, erosion bolts, and a 15.24 cm by 15.24 cm force plate installed in the bedrock channel floor of a steep catchment. These measurements allow us to quantify the distribution of basal forces from natural debris‒flow events that incised bedrock. Over the 4 year monitoring period, 11 debris‒flow events scoured the bedrock channel floor. No clear water flows were observed. Measurements of erosion bolts at the beginning and end of the study indicated that the bedrock channel floor was lowered by 36 to 64 mm. The basal force during these erosive debris‒flow events had a large‒magnitude (up to 21 kN, which was approximately 50 times larger than the concurrent time‒averaged mean force), high‒frequency (greater than 1 Hz) fluctuating component. We interpret these fluctuations as flow particles impacting the bed. The resulting variability in force magnitude increased linearly with the time‒averaged mean basal force. Probability density functions of basal normal forces were consistent with a generalized Pareto distribution, rather than the exponential distribution that is commonly found in experimental and simulated monodispersed granular flows and which has a lower probability of large forces. When the bed sediment thickness covering the force plate was greater than ~ 20 times the median bed sediment grain size, no significant fluctuations about the time‒averaged mean force were measured, indicating that a thin layer of sediment (~ 5 cm in the monitored cases) can effectively shield the subjacent bed from erosive impacts. Coarse‒grained granular surges and water‒rich, intersurge flow had very similar basal force distributions despite

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

Directory of Open Access Journals (Sweden)

S. Mahdiuon-Rad

2013-08-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2015-10-31

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

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

Directory of Open Access Journals (Sweden)

Cui Rong

2016-10-01

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

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

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

International Nuclear Information System (INIS)

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

2012-01-01

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

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

NARCIS (Netherlands)

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

2014-01-01

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

A vacuum--generated inertia reaction force

International Nuclear Information System (INIS)

Rueda, Alfonso; Haisch, Bernard

2001-01-01

A clear and succinct covariant approach shows that, in principle, there must be a contribution to the inertia reaction force on an accelerated object by the surrounding vacuum electromagnetic field in which the object is embedded. No details of the vacuum to object electromagnetic interaction need to be specified other than the fact that the object is made of electromagnetically interacting particles. Some interesting consequences of this feature are discussed. This analysis strongly supports the concept that inertia is indeed an opposition of the vacuum fields to any attempt to change the uniform state of motion of material bodies. This also definitely shows that inertia should be viewed as extrinsic to mass and that causing agents and/or mechanisms responsible for the inertia reaction force are neither intrinsic to the notion of mass nor to the entities responsible for the existence of mass in elementary particles (as, e.g., the Higgs field). In other words the mechanism that produces the inertia-reaction-force requires an explicit explanation. This explicit explanation is that inertia is an opposition of the vacuum fields to the accelerated motion of any material entities, i.e., of entities that possess mass. It is briefly commented why the existence of a Higgs field responsible for the generation of mass in elementary particles does not contradict the view presented here. It is also briefly discussed why a strict version of Mach's Principle does really contradict this view, though a broad sense version of Mach's Principle may be in agreement

Experimental Searches for Exotic Short-Range Forces Using Mechanical Oscillators

Science.gov (United States)

Weisman, Evan

Experimental searches for forces beyond gravity and electromagnetism at short range have attracted a great deal of attention over the last decade. In this thesis I describe the test mass development for two new experiments searching for forces below 1 mm. Both modify a previous experiment that used 1 kHz mechanical oscillators as test masses with a stiff conducting shield between them to suppress backgrounds, a promising technique for probing exceptionally small distances at the limit of instrumental thermal noise. To further reduce thermal noise, one experiment will use plated silicon test masses at cryogenic temperatures. The other experiment, which searches for spin-dependent interactions, will apply the spin-polarizable material Dy3Fe5O 12 to the test mass surfaces. This material exhibits orbital compensation of the magnetism associated with its intrinsic electron spin, minimizing magnetic backgrounds. Several plated silicon test mass prototypes were fabricated using photolithography (useful in both experiments), and spin-dependent materials were synthesized with a simple chemical recipe. Both silicon and spin-dependent test masses demonstrate the mechanical and magnetic properties necessary for sensitive experiments. I also describe sensitivity calculations of another proposed spin-dependent experiment, based on a modified search for the electron electric dipole moment, which show unprecedented sensitivity to exotic monopole-dipole forces. Inspired by a finite element model, a study attempting to maximize detector quality factor versus geometry is also presented, with experimental results so far not explained by the model.

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.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

Science.gov (United States)

Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

2014-12-23

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

Mechanical design in embryos: mechanical signalling, robustness and developmental defects.

Science.gov (United States)

Davidson, Lance A

2017-05-19

Embryos are shaped by the precise application of force against the resistant structures of multicellular tissues. Forces may be generated, guided and resisted by cells, extracellular matrix, interstitial fluids, and how they are organized and bound within the tissue's architecture. In this review, we summarize our current thoughts on the multiple roles of mechanics in direct shaping, mechanical signalling and robustness of development. Genetic programmes of development interact with environmental cues to direct the composition of the early embryo and endow cells with active force production. Biophysical advances now provide experimental tools to measure mechanical resistance and collective forces during morphogenesis and are allowing integration of this field with studies of signalling and patterning during development. We focus this review on concepts that highlight this integration, and how the unique contributions of mechanical cues and gradients might be tested side by side with conventional signalling systems. We conclude with speculation on the integration of large-scale programmes of development, and how mechanical responses may ensure robust development and serve as constraints on programmes of tissue self-assembly.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'. © 2017 The Author(s).

Control of forced vibrations of mechanical structures by an electromagnetic controller with a permanent magnet

DEFF Research Database (Denmark)

Stein, George Juraj; Darula, Radoslav; Sorokin, Sergey

2012-01-01

A theoretical analysis of an electromagnetic vibration controller is presented. The analyzed device consists of a pot-type iron core with a coil and a permanent magnet as a source of constant magnetic flux. The magnetic circuit is closed by a yoke, excited by an external harmonic mechanical force....... The so generated magnetic flux variation induces alternating voltage in the electric circuit, which is dissipated in a shunt resistor. The induced current driven through the coil generates magnetic force, which damps the excitation force and changes the damped natural frequency of the oscillatory system....... Due to the hysteretic effects in the magnetic material the internal losses influence the overall system’s performance. A mathematical model of the force balance in the oscillatory system is derived in a simplified, linearised form. The electric as well as mechanical system is modelled using lumped...

Nonlocal quantum field theory and stochastic quantum mechanics

International Nuclear Information System (INIS)

Namsrai, K.

1986-01-01

This volume presents a systematic development of the implications to both quantum mechanics and quantum field theory of the hypothesis of a stochastic structure of space-time. Some applications to elementary particle physics are also considered. Part 1 is concerned with nonlocal quantum field theory and, among other topics, deals with quantized fields, electromagnetic and weak processes, the Schroedinger equation, and functional methods and their applications. Part 2 presents an introduction to stochastic mechanics and many specific problems of interest are discussed. (Auth.)

Robust Clamping Force Control of an Electro-Mechanical Brake System for Application to Commercial City Buses

Directory of Open Access Journals (Sweden)

Sangjune Eum

2017-02-01

Full Text Available This paper proposes a sensor-less robust force control method for improving the control performance of an electro-mechanical brake (EMB which is applicable to commercial city buses. The EMB generates the accurate clamping force commanded by a driver through an independent motor control at each wheel instead of using existing mechanical components. In general, an EMB undergoes parameter variation and a backdrivability problem. For this reason, the cascade control strategy (e.g., force-position cascade control structure is proposed and the disturbance observer is employed to enhance control robustness against model variations. Additionally, this paper proposed the clamping force estimation method for a sensor-less control, i.e., the clamping force observer (CFO. Finally, in order to confirm the performance and effectiveness of a proposed robust control method, several experiments are performed and analyzed.

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

Statistical mechanics and field theory

International Nuclear Information System (INIS)

Samuel, S.A.

1979-05-01

Field theory methods are applied to statistical mechanics. Statistical systems are related to fermionic-like field theories through a path integral representation. Considered are the Ising model, the free-fermion model, and close-packed dimer problems on various lattices. Graphical calculational techniques are developed. They are powerful and yield a simple procedure to compute the vacuum expectation value of an arbitrary product of Ising spin variables. From a field theorist's point of view, this is the simplest most logical derivation of the Ising model partition function and correlation functions. This work promises to open a new area of physics research when the methods are used to approximate unsolved problems. By the above methods a new model named the 128 pseudo-free vertex model is solved. Statistical mechanics intuition is applied to field theories. It is shown that certain relativistic field theories are equivalent to classical interacting gases. Using this analogy many results are obtained, particularly for the Sine-Gordon field theory. Quark confinement is considered. Although not a proof of confinement, a logical, esthetic, and simple picture is presented of how confinement works. A key ingredient is the insight gained by using an analog statistical system consisting of a gas of macromolecules. This analogy allows the computation of Wilson loops in the presence of topological vortices and when symmetry breakdown occurs in the topological quantum number. Topological symmetry breakdown calculations are placed on approximately the same level of rigor as instanton calculations. The picture of confinement that emerges is similar to the dual Meissner type advocated by Mandelstam. Before topological symmetry breakdown, QCD has monopoles bound linearly together by three topological strings. Topological symmetry breakdown corresponds to a new phase where these monopoles are liberated. It is these liberated monopoles that confine quarks. 64 references

Mechanical forces regulate the interactions of fibronectin and collagen I in extracellular matrix.

Science.gov (United States)

Kubow, Kristopher E; Vukmirovic, Radmila; Zhe, Lin; Klotzsch, Enrico; Smith, Michael L; Gourdon, Delphine; Luna, Sheila; Vogel, Viola

2015-08-14

Despite the crucial role of extracellular matrix (ECM) in directing cell fate in healthy and diseased tissues--particularly in development, wound healing, tissue regeneration and cancer--the mechanisms that direct the assembly and regulate hierarchical architectures of ECM are poorly understood. Collagen I matrix assembly in vivo requires active fibronectin (Fn) fibrillogenesis by cells. Here we exploit Fn-FRET probes as mechanical strain sensors and demonstrate that collagen I fibres preferentially co-localize with more-relaxed Fn fibrils in the ECM of fibroblasts in cell culture. Fibre stretch-assay studies reveal that collagen I's Fn-binding domain is responsible for the mechano-regulated interaction. Furthermore, we show that Fn-collagen interactions are reciprocal: relaxed Fn fibrils act as multivalent templates for collagen assembly, but once assembled, collagen fibres shield Fn fibres from being stretched by cellular traction forces. Thus, in addition to the well-recognized, force-regulated, cell-matrix interactions, forces also tune the interactions between different structural ECM components.

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

A new loss mechanism in graphene nanoresonators due to the synthetic electric fields caused by inherent out-of-plane membrane corrugations

International Nuclear Information System (INIS)

Firsova, N E; Firsov, Yu A

2012-01-01

For the first time the influence of out-of-plane deformations, which always exist in graphene, on the non-stationary processes is considered for the case of a monolayer graphene nanoresonator. A new loss mechanism for this device caused by dissipative intra-valley currents stipulated by synthetic electric fields is studied. These fields are generated by time-dependent gauge fields arising in a graphene membrane due to its intrinsic out-of-plane distortions and the influence of the external periodic electromotive force. The corresponding formula for the quality factor has a quantum mechanical origin and includes quantum mechanical parameters. This loss mechanism accounts for an essential part (about 40%) of losses in a graphene nanoresonator and it is specific just for graphene. The ways of minimization of this kind of dissipation (an increase in the quality factor of the electromechanical system) are discussed. It is explained why one can enhance the quality factor by correctly choosing a combination of strains (by strain engineering). In addition, it is shown that the quality factor can be increased by switching on a magnetic field perpendicular to the graphene membrane.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-06

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

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.

Condensation Mechanism of Hydrocarbon Field Formation.

Science.gov (United States)

Batalin, Oleg; Vafina, Nailya

2017-08-31

Petroleum geology explains how hydrocarbon fluids are generated, but there is a lack of understanding regarding how oil is expelled from source rocks and migrates to a reservoir. To clarify the process, the multi-layer Urengoy field in Western Siberia was investigated. Based on this example, we have identified an alternative mechanism of hydrocarbon field formation, in which oil and gas accumulations result from the phase separation of an upward hydrocarbon flow. There is evidence that the flow is generated by the gases released by secondary kerogen destruction. This study demonstrates that oil components are carried by the gas flow and that when the flow reaches a low-pressure zone, it condenses into a liquid with real oil properties. The transportation of oil components in the gas flow provides a natural explanation for the unresolved issues of petroleum geology concerning the migration process. The condensation mechanism can be considered as the main process of oil field formation.

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)

Lift vs. drag based mechanisms for vertical force production in the smallest flying insects.

Science.gov (United States)

Jones, S K; Laurenza, R; Hedrick, T L; Griffith, B E; Miller, L A

2015-11-07

We used computational fluid dynamics to determine whether lift- or drag-based mechanisms generate the most vertical force in the flight of the smallest insects. These insects fly at Re on the order of 4-60 where viscous effects are significant. Detailed quantitative data on the wing kinematics of the smallest insects is not available, and as a result both drag- and lift-based strategies have been suggested as the mechanisms by which these insects stay aloft. We used the immersed boundary method to solve the fully-coupled fluid-structure interaction problem of a flexible wing immersed in a two-dimensional viscous fluid to compare three idealized hovering kinematics: a drag-based stroke in the vertical plane, a lift-based stroke in the horizontal plane, and a hybrid stroke on a tilted plane. Our results suggest that at higher Re, a lift-based strategy produces more vertical force than a drag-based strategy. At the Re pertinent to small insect hovering, however, there is little difference in performance between the two strategies. A drag-based mechanism of flight could produce more vertical force than a lift-based mechanism for insects at Re<5; however, we are unaware of active fliers at this scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantization in classical mechanics and its relation to the Bohmian Ψ-field

International Nuclear Information System (INIS)

Rusov, V.D.; Vlasenko, D.S.; Mavrodiev, S.Cht.

2011-01-01

Research highlights: →The Schroedinger equation is derived from the classical Hamiltonian mechanics. →This derivation is based on the Chetaev theorem on stable dynamical trajectories. →The conditions for correctness of trajectory quantum mechanics are discussed. - Abstract: Based on the Chetaev theorem on stable dynamical trajectories in the presence of dissipative forces, we obtain the generalized condition for stability of Hamilton systems in the form of the Schroedinger equation. It is shown that the energy of dissipative forces, which generate the Chetaev generalized condition of stability, coincides exactly with the Bohm 'quantum' potential. Within the frame-work of Bohmian quantum mechanics supplemented by the generalized Chetaev theorem and on the basis of the principle of least action for dissipative forces, we show that the squared amplitude of a wave function in the Schroedinger equation is equivalent semantically and syntactically to the probability density function for the number of particle trajectories, relative to which the velocity and the position of the particle are not hidden parameters. The conditions for the correctness of trajectory interpretation of quantum mechanics are discussed.

Understanding the Mechanical forces of Self-Expandable Metal Stents in the Biliary Ducts.

Science.gov (United States)

Isayama, Hiroyuki; Nakai, Yousuke; Hamada, Tsuyoshi; Matsubara, Saburo; Kogure, Hirofumi; Koike, Kazuhiko

2016-12-01

Self-expandable metallic stent (SEMS) was an effective biliary endoprosthesis. Mechanical properties of SEMS, radial and axial force (RF, AF), may play important roles in the bile duct after placement. RF was well known dilation force and influenced on the occurrence of migration. AF, newly proposed by this author, was defined as the recovery force when the SEMS vended. AF was related with the cause of bile duct kinking, pancreatitis, and cholecystitis due to the compression of the bile duct, orifice of the cystic duct, and pancreatic orifice. Ideal SEMS may show high RF and low AF.

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

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

Indentation analysis of nano-particle using nano-contact mechanics models during nano-manipulation based on atomic force microscopy

International Nuclear Information System (INIS)

Daeinabi, Khadijeh; Korayem, Moharam Habibnejad

2011-01-01

Atomic force microscopy is applied to measure intermolecular forces and mechanical properties of materials, nano-particle manipulation, surface scanning and imaging with atomic accuracy in the nano-world. During nano-manipulation process, contact forces cause indentation in contact area between nano-particle and tip/substrate which is considerable at nano-scale and affects the nano-manipulation process. Several nano-contact mechanics models such as Hertz, Derjaguin–Muller–Toporov (DMT), Johnson–Kendall–Roberts–Sperling (JKRS), Burnham–Colton–Pollock (BCP), Maugis–Dugdale (MD), Carpick–Ogletree–Salmeron (COS), Pietrement–Troyon (PT), and Sun et al. have been applied as the continuum mechanics approaches at nano-scale. In this article, indentation depth and contact radius between tip and substrate with nano-particle for both spherical and conical tip shape during nano-manipulation process are analyzed and compared by applying theoretical, semiempirical, and empirical nano-contact mechanics models. The effects of adhesion force, as the main contrast point in different nano-contact mechanics models, on nano-manipulation analysis is investigated for different contact radius, and the critical point is discussed for mentioned models.

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.

Relation of twist of magnetic force tube and flare magnetic field

International Nuclear Information System (INIS)

Tanaka, H.

1978-01-01

The configuration of magnetic field and its development in the regions of big flare were investigated to study the features of magnetic force tubes. The photographs of delta type solar spots taken at Mt. Wilson Observatory were selected. 94 percent of the delta type spots belong to the class B activity or more active class. The features of delta type spots are the reverse configuration and the shear motion. The reverse configuration is divided into the p/f configuration and the f/p configuration. The shear motion is divided into the normal motion, the reverse motion, and the indefinite motion. Vortex structures appeared around the solar spots of reverse configuration showing normal motion. The relation among the direction of twist, reverse configuration and the direction of shear motion was deduced. In the region of normal motion, the p/f configuration corresponds to the reverse S type vortices and the f/p configuration to S type. In the region of reverse motion, the p/f configuration corresponds to the S type vortices and the f/p corresponds to the reverse S type vortices. The mechanism of development of delta type solar spots is discussed. (Kato, T.)

Energy loss mechanism for suspended micro- and nanoresonators due to the Casimir force

OpenAIRE

Gusso, André

2011-01-01

A so far not considered energy loss mechanism in suspended micro- and nanoresonators due to noncontact acoustical energy loss is investigated theoretically. The mechanism consists on the conversion of the mechanical energy from the vibratory motion of the resonator into acoustic waves on large nearby structures, such as the substrate, due to the coupling between the resonator and those structures resulting from the Casimir force acting over the separation gaps. Analytical expressions for the ...

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.

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.

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.

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

Directory of Open Access Journals (Sweden)

Jörg Grunenberg

2016-03-01

Full Text Available We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a the isolated and b the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants. The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

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.

Cross-bridge mechanism of residual force enhancement after stretching in a skeletal muscle.

Science.gov (United States)

Tamura, Youjiro

2018-01-01

A muscle model that uses a modified Langevin equation with actomyosin potentials was used to describe the residual force enhancement after active stretching. Considering that the new model uses cross-bridge theory to describe the residual force enhancement, it is different from other models that use passive stretching elements. Residual force enhancement was simulated using a half sarcomere comprising 100 myosin molecules. In this paper, impulse is defined as the integral of an excess force from the steady isometric force over the time interval for which a stretch is applied. The impulse was calculated from the force response due to fast and slow muscle stretches to demonstrate the viscoelastic property of the cross-bridges. A cross-bridge mechanism was proposed as a way to describe the residual force enhancement on the basis of the impulse results with reference to the compliance of the actin filament. It was assumed that the period of the actin potential increased by 0.5% and the amplitude of the potential decreased by 0.5% when the half sarcomere was stretched by 10%. The residual force enhancement after 21.0% sarcomere stretching was 6.9% of the maximum isometric force of the muscle; this value was due to the increase in the number of cross-bridges.

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

Science.gov (United States)

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

2015-07-27

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

Nano-mechanics of Tunable Adhesion using Non Covalent Forces

Energy Technology Data Exchange (ETDEWEB)

Kenneth Liechti

2012-09-08

The objective of this program was to examine, via experiment and atomistic and continuum analysis, coordinated noncovalent bonding over a range of length scales with a view to obtaining modulated, patterned and reversible bonding at the molecular level. The first step in this project was to develop processes for depositing self-assembled monolayers (SAMs) bearing carboxylic acid and amine moieties on Si (111) surfaces and probe tips of an interfacial force microscope (IFM). This allowed the adhesive portion of the interactions between functionalized surfaces to be fully captured in the force-displacement response (force profiles) that are measured by the IFM. The interactionswere extracted in the form of traction-separation laws using combined molecular and continuum stress analyses. In this approach, the results of molecular dynamics analyses of SAMs subjected to simple stress states are used to inform continuum models of their stress-strain behavior. Continuum analyses of the IFM experiment were then conducted, which incorporate the stress-strain behavior of the SAMs and traction-separation relations that represent the interactions between the tip and functionalized Si surface. Agreement between predicted and measured force profiles was taken to imply that the traction-separation relations have been properly extracted. Scale up to larger contact areas was considered by forming Si/SAM/Si sandwiches and then separating them via fracture experiments. The mode 1 traction-separation relations have been extracted using fracture mechanics concepts under mode 1 and mixed-mode conditions. Interesting differences were noted between the three sets of traction-separation relations.

[Mechanism of ablation with nanosecond pulsed electric field].

Science.gov (United States)

Cen, Chao; Chen, Xin-hua; Zheng, Shu-sen

2015-11-01

Nanosecond pulsed electric field ablation has been widely applied in clinical cancer treatment, while its molecular mechanism is still unclear. Researchers have revealed that nanosecond pulsed electric field generates nanopores in plasma membrane, leading to a rapid influx of Ca²⁺; it has specific effect on intracellular organelle membranes, resulting in endoplasmic reticulum injuries and mitochondrial membrane potential changes. In addition, it may also change cellular morphology through damage of cytoskeleton. This article reviews the recent research advances on the molecular mechanism of cell membrane and organelle changes induced by nanosecond pulsed electric field ablation.

Quantum mechanics of Proca fields

International Nuclear Information System (INIS)

Zamani, Farhad; Mostafazadeh, Ali

2009-01-01

We construct the most general physically admissible positive-definite inner product on the space of Proca fields. Up to a trivial scaling this defines a five-parameter family of Lorentz invariant inner products that we use to construct a genuine Hilbert space for the quantum mechanics of Proca fields. If we identify the generator of time translations with the Hamiltonian, we obtain a unitary quantum system that describes first-quantized Proca fields and does not involve the conventional restriction to the positive-frequency fields. We provide a rather comprehensive analysis of this system. In particular, we examine the conserved current density responsible for the conservation of the probabilities, explore the global gauge symmetry underlying the conservation of the probabilities, obtain a probability current density, construct position, momentum, helicity, spin, and angular momentum operators, and determine the localized Proca fields. We also compute the generalized parity (P), generalized time-reversal (T), and generalized charge or chirality (C) operators for this system and offer a physical interpretation for its PT-, C-, and CPT-symmetries.

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.

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.

Warp Field Mechanics 101

Science.gov (United States)

White, Harold

2011-01-01

This paper will begin with a short review of the Alcubierre warp drive metric and describes how the phenomenon might work based on the original paper. The canonical form of the metric was developed and published in [6] which provided key insight into the field potential and boost for the field which remedied a critical paradox in the original Alcubierre concept of operations. A modified concept of operations based on the canonical form of the metric that remedies the paradox is presented and discussed. The idea of a warp drive in higher dimensional space-time (manifold) will then be briefly considered by comparing the null-like geodesics of the Alcubierre metric to the Chung-Freese metric to illustrate the mathematical role of hyperspace coordinates. The net effect of using a warp drive technology coupled with conventional propulsion systems on an exploration mission will be discussed using the nomenclature of early mission planning. Finally, an overview of the warp field interferometer test bed being implemented in the Advanced Propulsion Physics Laboratory: Eagleworks (APPL:E) at the Johnson Space Center will be detailed. While warp field mechanics has not had a Chicago Pile moment, the tools necessary to detect a modest instance of the phenomenon are near at hand.

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.

Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

Energy Technology Data Exchange (ETDEWEB)

Treweek, Benjamin C., E-mail: btreweek@utexas.edu; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F. [Applied Research Laboratories, The University of Texas at Austin, P.O. Box 8029, Austin, TX 78713-8029 (United States)

2015-10-28

Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.

Hybrid magnetic mechanism for active locomotion based on inchworm motion

International Nuclear Information System (INIS)

Kim, Sung Hoon; Hashi, Shuichiro; Ishiyama, Kazushi

2013-01-01

Magnetic robots have been studied in the past. Insect-type micro-robots are used in various biomedical applications; researchers have developed inchworm micro-robots for endoscopic use. A biological inchworm has a looping locomotion gait. However, most inchworm micro-robots depend on a general bending, or bellows, motion. In this paper, we introduce a new robotic mechanism using magnetic force and torque control in a rotating magnetic field for a looping gait. The proposed robot is controlled by the magnetic torque, attractive force, and body mechanisms (two stoppers, flexible body, and different frictional legs). The magnetic torque generates a general bending motion. In addition, the attractive force and body mechanisms produce the robot’s looping motion within a rotating magnetic field and without the use of an algorithm for field control. We verified the device’s performance and analyzed the motion through simulations and various experiments. The robot mechanism can be applied to active locomotion for various medical robots, such as wireless endoscopes. (technical note)

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

Suspended sediment diffusion mechanisms in the Yangtze Estuary influenced by wind fields

Science.gov (United States)

Wang, Lihua; Zhou, Yunxuan; Shen, Fang

2018-01-01

The complexity of suspended sediment concentration (SSC) distribution and diffusion has been widely recognized because it is influenced by sediment supply and various hydrodynamic forcing conditions that vary over space and over time. Sediment suspended by waves and transported by currents are the dominant sediment transport mechanisms in estuarine and coastal areas. However, it is unclear to what extent the SSC distribution is impacted by each hydrodynamic factor. Research on the quantitative influence of wind fields on the SSC diffusion range will contribute to a better understanding of the characteristics of sediment transport change and sedimentary geomorphic evolution. This study determined SSC from three Envisat Medium-Resolution Imaging Spectrometer acquisitions, covering the Yangtze Estuary and adjacent water area under the same season and tidal conditions but with varying wind conditions. SSC was examined based on the Semi-Empirical Radiative Transfer model, which has been well validated with the observation data. Integrating the corresponding wind field information from European Centre for Medium-Range Weather Forecasts further facilitated the discussion of wind fields affecting SSC, and in turn the influence of water and suspended sediment transportation and diffusion in the Yangtze estuarine and coastal area. The results demonstrated that the SSC present much more distinctive fluvial features in the inner estuary and wind fields are one of the major factors controlling the range of turbid water diffusion.

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.

Handbook of Molecular Force Spectroscopy

CERN Document Server

Noy, Aleksandr

2008-01-01

"...Noy's Handbook of Molecular Force Spectroscopy is both a timely and useful summary of fundamental aspects of molecular force spectroscopy, and I believe it would make a worthwhile addition to any good scientific library. New research groups that are entering this field would be well advisedto study this handbook in detail before venturing into the exciting and challenging world of molecular force spectroscopy." Matthew F. Paige, University of Saskatchewan, Journal of the American Chemical Society Modern materials science and biophysics are increasingly focused on studying and controlling intermolecular interactions on the single-molecule level. Molecular force spectroscopy was developed in the past decade as the result of several unprecedented advances in the capabilities of modern scientific instrumentation, and defines a number of techniques that use mechanical force measurements to study interactions between single molecules and molecular assemblies in chemical and biological systems. Examples of these...

Multi-Stage Flotation for the Removal of Ash from Fine Graphite Using Mechanical and Centrifugal Forces

Directory of Open Access Journals (Sweden)

Xiangning Bu

2018-01-01

Full Text Available Graphite ore collected from Hunan province, south China was characterized by chemical analysis, X-ray diffraction, and optical microscopy. Rougher and multi-stage flotation tests using a mechanical flotation cell and a flotation column containing an additional centrifugal force field were carried out to promote its grade and economic value. In rougher flotation, both the mechanical flotation cell and flotation column reduced the ash content of the graphite ore from 15.43% to 10.8%, while the yield of the flotation column (91.41% was much higher than that of the mechanical flotation cell (50%. In the presence of hydrophobic graphite, the seriously entrained gangue restricted further improvement in the quality and economic value of the graphite ore. Therefore, multi-stage flotation circuits were employed to diminish this entrainment. Multi-stage flotation circuits using the two flotation devices further decreased the ash content of the graphite ore to ~8%, while the yield when using the flotation column was much higher than that obtained from the mechanical flotation cell employed. On the other hand, the ash removal efficiency of the flotation column was 3.82-fold higher than that observed for the mechanical flotation cell. The Cleaner 3 flotation circuit using the flotation column decreased the ash content in graphite from 15.43% to 7.97% with a yield of 77.53%.

Field failure mechanisms for photovoltaic modules

Science.gov (United States)

Dumas, L. N.; Shumka, A.

1981-01-01

Beginning in 1976, Department of Energy field centers have installed and monitored a number of field tests and application experiments using current state-of-the-art photovoltaic modules. On-site observations of module physical and electrical degradation, together with in-depth laboratory analysis of failed modules, permits an overall assessment of the nature and causes of early field failures. Data on failure rates are presented, and key failure mechanisms are analyzed with respect to origin, effect, and prospects for correction. It is concluded that all failure modes identified to date are avoidable or controllable through sound design and production practices.

Multi-MHz micro-electro-mechanical sensors for atomic force microscopy

Energy Technology Data Exchange (ETDEWEB)

Legrand, Bernard, E-mail: bernard.legrand@laas.fr [LAAS-CNRS, Université de Toulouse, CNRS, 7 avenue du colonel Roche, F-31400 Toulouse (France); Salvetat, Jean-Paul [CRPP, 115 avenue Schweitzer, F-33600 Pessac (France); Walter, Benjamin; Faucher, Marc; Théron, Didier [IEMN, avenue Henri Poincaré, F-59652 Villeneuve d’Ascq (France); Aimé, Jean-Pierre [CBMN, allée Geoffroy Saint Hilaire, Bât. B14, F-33600 Pessac (France)

2017-04-15

Silicon ring-shaped micro-electro-mechanical resonators have been fabricated and used as probes for dynamic atomic force microscopy (AFM) experiments. They offer resotnance frequency above 10 MHz, which is notably greater than that of usual cantilevers and quartz-based AFM probes. On-chip electrical actuation and readout of the tip oscillation are obtained by means of built-in capacitive transducers. Displacement and force resolutions have been determined from noise analysis at 1.5 fm/√Hz and 0.4 pN/√Hz, respectively. Despite the high effective stiffness of the probes, the tip-surface interaction force is kept below 1 nN by using vibration amplitude significantly below 100 pm and setpoint close to the free vibration conditions. Imaging capabilities in amplitude- and frequency-modulation AFM modes have been demonstrated on block copolymer surfaces. Z-spectroscopy experiments revealed that the tip is vibrating in permanent contact with the viscoelastic material, with a pinned contact line. Results are compared to those obtained with commercial AFM cantilevers driven at large amplitudes (>10 nm). - Highlights: • Silicon MEMS resonators are used as AFM probes above 10 MHz. • Integrated capacitive transducers drive and sense sub-nanometer tip oscillation. • Force resolution is below 1 pN/√Hz. • Block copolymer surface is imaged using AM and FM AFM modes. • Probes are operated at small vibration amplitude in permanent viscoelastic contact.

Multi-MHz micro-electro-mechanical sensors for atomic force microscopy

International Nuclear Information System (INIS)

Legrand, Bernard; Salvetat, Jean-Paul; Walter, Benjamin; Faucher, Marc; Théron, Didier; Aimé, Jean-Pierre

2017-01-01

Silicon ring-shaped micro-electro-mechanical resonators have been fabricated and used as probes for dynamic atomic force microscopy (AFM) experiments. They offer resotnance frequency above 10 MHz, which is notably greater than that of usual cantilevers and quartz-based AFM probes. On-chip electrical actuation and readout of the tip oscillation are obtained by means of built-in capacitive transducers. Displacement and force resolutions have been determined from noise analysis at 1.5 fm/√Hz and 0.4 pN/√Hz, respectively. Despite the high effective stiffness of the probes, the tip-surface interaction force is kept below 1 nN by using vibration amplitude significantly below 100 pm and setpoint close to the free vibration conditions. Imaging capabilities in amplitude- and frequency-modulation AFM modes have been demonstrated on block copolymer surfaces. Z-spectroscopy experiments revealed that the tip is vibrating in permanent contact with the viscoelastic material, with a pinned contact line. Results are compared to those obtained with commercial AFM cantilevers driven at large amplitudes (>10 nm). - Highlights: • Silicon MEMS resonators are used as AFM probes above 10 MHz. • Integrated capacitive transducers drive and sense sub-nanometer tip oscillation. • Force resolution is below 1 pN/√Hz. • Block copolymer surface is imaged using AM and FM AFM modes. • Probes are operated at small vibration amplitude in permanent viscoelastic contact.

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

Effect of force-induced mechanical stress at the coronary artery bifurcation stenting: Relation to in-stent restenosis

Energy Technology Data Exchange (ETDEWEB)

Lee, Cheng-Hung [Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Tao-Yuan, Taiwan (China); Department of Mechanical Engineering, Chang Gung University, Tao-Yuan, Taiwan (China); Jhong, Guan-Heng [Graduate Institute of Medical Mechatronics, Chang Gung University, Tao-Yuan, Taiwan (China); Hsu, Ming-Yi; Wang, Chao-Jan [Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Linkou, Tao-Yuan, Taiwan (China); Liu, Shih-Jung, E-mail: shihjung@mail.cgu.edu.tw [Department of Mechanical Engineering, Chang Gung University, Tao-Yuan, Taiwan (China); Hung, Kuo-Chun [Division of Cardiology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou, Chang Gung University College of Medicine, Tao-Yuan, Taiwan (China)

2014-05-28

The deployment of metallic stents during percutaneous coronary intervention has become common in the treatment of coronary bifurcation lesions. However, restenosis occurs mostly at the bifurcation area even in present era of drug-eluting stents. To achieve adequate deployment, physicians may unintentionally apply force to the strut of the stents through balloon, guiding catheters, or other devices. This force may deform the struts and impose excessive mechanical stresses on the arterial vessels, resulting in detrimental outcomes. This study investigated the relationship between the distribution of stress in a stent and bifurcation angle using finite element analysis. The unintentionally applied force following stent implantation was measured using a force sensor that was made in the laboratory. Geometrical information on the coronary arteries of 11 subjects was extracted from contrast-enhanced computed tomography scan data. The numerical results reveal that the application of force by physicians generated significantly higher mechanical stresses in the arterial bifurcation than in the proximal and distal parts of the stent (post hoc P < 0.01). The maximal stress on the vessels was significantly higher at bifurcation angle <70° than at angle ≧70° (P < 0.05). The maximal stress on the vessels was negatively correlated with bifurcation angle (P < 0.01). Stresses at the bifurcation ostium may cause arterial wall injury and restenosis, especially at small bifurcation angles. These finding highlight the effect of force-induced mechanical stress at coronary artery bifurcation stenting, and potential mechanisms of in-stent restenosis, along with their relationship with bifurcation angle.

Effect of force-induced mechanical stress at the coronary artery bifurcation stenting: Relation to in-stent restenosis

International Nuclear Information System (INIS)

Lee, Cheng-Hung; Jhong, Guan-Heng; Hsu, Ming-Yi; Wang, Chao-Jan; Liu, Shih-Jung; Hung, Kuo-Chun

2014-01-01

The deployment of metallic stents during percutaneous coronary intervention has become common in the treatment of coronary bifurcation lesions. However, restenosis occurs mostly at the bifurcation area even in present era of drug-eluting stents. To achieve adequate deployment, physicians may unintentionally apply force to the strut of the stents through balloon, guiding catheters, or other devices. This force may deform the struts and impose excessive mechanical stresses on the arterial vessels, resulting in detrimental outcomes. This study investigated the relationship between the distribution of stress in a stent and bifurcation angle using finite element analysis. The unintentionally applied force following stent implantation was measured using a force sensor that was made in the laboratory. Geometrical information on the coronary arteries of 11 subjects was extracted from contrast-enhanced computed tomography scan data. The numerical results reveal that the application of force by physicians generated significantly higher mechanical stresses in the arterial bifurcation than in the proximal and distal parts of the stent (post hoc P < 0.01). The maximal stress on the vessels was significantly higher at bifurcation angle <70° than at angle ≧70° (P < 0.05). The maximal stress on the vessels was negatively correlated with bifurcation angle (P < 0.01). Stresses at the bifurcation ostium may cause arterial wall injury and restenosis, especially at small bifurcation angles. These finding highlight the effect of force-induced mechanical stress at coronary artery bifurcation stenting, and potential mechanisms of in-stent restenosis, along with their relationship with bifurcation angle.

Quantum control mechanism analysis through field based Hamiltonian encoding

International Nuclear Information System (INIS)

Mitra, Abhra; Rabitz, Herschel

2006-01-01

Optimal control of quantum dynamics in the laboratory is proving to be increasingly successful. The control fields can be complex, and the mechanisms by which they operate have often remained obscure. Hamiltonian encoding (HE) has been proposed as a method for understanding mechanisms in quantum dynamics. In this context mechanism is defined in terms of the dominant quantum pathways leading to the final state of the controlled system. HE operates by encoding a special modulation into the Hamiltonian and decoding its signature in the dynamics to determine the dominant pathway amplitudes. Earlier work encoded the modulation directly into the Hamiltonian operators. This present work introduces the alternative scheme of field based HE, where the modulation is encoded into the control field and not directly into the Hamiltonian operators. This distinct form of modulation yields a new perspective on mechanism and is computationally faster than the earlier approach. Field based encoding is also an important step towards a laboratory based algorithm for HE as it is the only form of encoding that may be experimentally executed. HE is also extended to cover systems with noise and uncertainty and finally, a hierarchical algorithm is introduced to reveal mechanism in a stepwise fashion of ever increasing detail as desired. This new hierarchical algorithm is an improvement over earlier approaches to HE where the entire mechanism was determined in one stroke. The improvement comes from the use of less complex modulation schemes, which leads to fewer evaluations of Schroedinger's equation. A number of simulations are presented on simple systems to illustrate the new field based encoding technique for mechanism assessment

Mechanism of the quasi-zero axial acoustic radiation force experienced by elastic and viscoelastic spheres in the field of a quasi-Gaussian beam and particle tweezing.

Science.gov (United States)

Mitri, F G; Fellah, Z E A

2014-01-01

The present analysis investigates the (axial) acoustic radiation force induced by a quasi-Gaussian beam centered on an elastic and a viscoelastic (polymer-type) sphere in a nonviscous fluid. The quasi-Gaussian beam is an exact solution of the source free Helmholtz wave equation and is characterized by an arbitrary waist w₀ and a diffraction convergence length known as the Rayleigh range z(R). Examples are found where the radiation force unexpectedly approaches closely to zero at some of the elastic sphere's resonance frequencies for kw₀≤1 (where this range is of particular interest in describing strongly focused or divergent beams), which may produce particle immobilization along the axial direction. Moreover, the (quasi)vanishing behavior of the radiation force is found to be correlated with conditions giving extinction of the backscattering by the quasi-Gaussian beam. Furthermore, the mechanism for the quasi-zero force is studied theoretically by analyzing the contributions of the kinetic, potential and momentum flux energy densities and their density functions. It is found that all the components vanish simultaneously at the selected ka values for the nulls. However, for a viscoelastic sphere, acoustic absorption degrades the quasi-zero radiation force. Copyright © 2013 Elsevier B.V. All rights reserved.

Eletromagnetic radiation and the mechanical reactions arising from it

CERN Document Server

Schott, G A

1912-01-01

Fundamental equations of the electron theory ; transformation of the potentials ; other types of solution ; physical interpretation of the solutions obtained ; illustrative examples ; remarks on the solutions obtained and on the methods of calculating the potentials in general ; periodic motions ; on the distant field due to a moving charge ; pseudo-periodic and aperiodic motions ; on the field near the orbit of a moving charge or group ; the mechanical forces acting on electric charges in motion ; the motion of groups of electric charges ; on the Doppler effect ; on the disturbed motion of a ring of electrons ; on the field close to a point charge in motion ; the mechanical force exterted by an electron on itself ; the mechanical explanation of the electron ; the mechanics of the Lorentz electron ; problems illustrative of the motion of the Lorentz electron.

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.

Force Balance and Substorm Effects in the Magnetotail

Science.gov (United States)

Kaufmann, Richard L.; Larson, Douglas J.; Kontodinas, Ioannis D.; Ball, Bryan M.

1997-01-01

A model of the quiet time middle magnetotail is developed using a consistent orbit tracing technique. The momentum equation is used to calculate geocentric solar magnetospheric components of the particle and electromagnetic forces throughout the current sheet. Ions generate the dominant x and z force components. Electron and ion forces almost cancel in the y direction because the two species drift earthward at comparable speeds. The force viewpoint is applied to a study of some substorm processes. Generation of the rapid flows seen during substorm injection and bursty bulk flow events implies substantial force imbalances. The formation of a substorm diversion loop is one cause of changes in the magnetic field and therefore in the electromagnetic force. It is found that larger forces are produced when the cross-tail current is diverted to the ionosphere than would be produced if the entire tail current system simply decreased. Plasma is accelerated while the forces are unbalanced resulting in field lines within a diversion loop becoming more dipolar. Field lines become more stretched and the plasma sheet becomes thinner outside a diversion loop. Mechanisms that require thin current sheets to produce current disruption then can create additional diversion loops in the newly thinned regions. This process may be important during multiple expansion substorms and in differentiating pseudoexpansions from full substorms. It is found that the tail field model used here can be generated by a variety of particle distribution functions. However, for a given energy distribution the mixture of particle mirror or reflection points is constrained by the consistency requirement. The study of uniqueness also leads to the development of a technique to select guiding center electrons that will produce charge neutrality all along a flux tube containing nonguiding center ions without the imposition of a parallel electric field.

Respiratory mechanics

CERN Document Server

Wilson, Theodore A

2016-01-01

This book thoroughly covers each subfield of respiratory mechanics: pulmonary mechanics, the respiratory pump, and flow. It presents the current understanding of the field and serves as a guide to the scientific literature from the golden age of respiratory mechanics, 1960 - 2010. Specific topics covered include the contributions of surface tension and tissue forces to lung recoil, the gravitational deformation of the lung, and the interdependence forces that act on pulmonary airways and blood vessels. The geometry and kinematics of the ribs is also covered in detail, as well as the respiratory action of the external and internal intercostal muscles, the mechanics of the diaphragm, and the quantitative compartmental models of the chest wall is also described. Additionally, flow in the airways is covered thoroughly, including the wave-speed and viscous expiratory flow-limiting mechanisms; convection, diffusion and the stationary front; and the distribution of ventilation. This is an ideal book for respiratory ...

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

Science.gov (United States)

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

2018-03-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2014-04-07

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

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

Science.gov (United States)

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

2015-10-01

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

Using stamping punch force variation for the identification of changes in lubrication and wear mechanism

Science.gov (United States)

Voss, B. M.; Pereira, M. P.; Rolfe, B. F.; Doolan, M. C.

2017-09-01

The growth in use of Advanced High Strength Steels in the automotive industry for light-weighting and safety has increased the rates of tool wear in sheet metal stamping. This is an issue that adds significant costs to production in terms of manual inspection and part refinishing. To reduce these costs, a tool condition monitoring system is required and a firm understanding of process signal variation must form the foundation for any such monitoring system. Punch force is a stamping process signal that is widely collected by industrial presses and has been linked closely to part quality and tool condition, making it an ideal candidate as a tool condition monitoring signal. In this preliminary investigation, the variation of punch force due to different lubrication conditions and progressive wear are examined. Linking specific punch force signature changes to developing lubrication and wear events is valuable for die wear and stamping condition monitoring. A series of semi-industrial channel forming trials were conducted under different lubrication regimes and progressive die wear. Punch force signatures were captured for each part and Principal Component Analysis (PCA) was applied to determine the key Principal Components of the signature data sets. These Principal Components were linked to the evolution of friction conditions over the course of the stroke for the different lubrication regimes and mechanism of galling wear. As a result, variation in punch force signatures were correlated to the current mechanism of wear dominant on the formed part; either abrasion or adhesion, and to changes in lubrication mechanism. The outcomes of this study provide important insights into punch force signature variation, that will provide a foundation for future work into the development of die wear and lubrication monitoring systems for sheet metal stamping.