Acoustic forcing of a liquid drop

NASA Technical Reports Server (NTRS)

Lyell, M. J.

1992-01-01

The development of systems such as acoustic levitation chambers will allow for the positioning and manipulation of material samples (drops) in a microgravity environment. This provides the capability for fundamental studies in droplet dynamics as well as containerless processing work. Such systems use acoustic radiation pressure forces to position or to further manipulate (e.g., oscillate) the sample. The primary objective was to determine the effect of a viscous acoustic field/tangential radiation pressure forcing on drop oscillations. To this end, the viscous acoustic field is determined. Modified (forced) hydrodynamic field equations which result from a consistent perturbation expansion scheme are solved. This is done in the separate cases of an unmodulated and a modulated acoustic field. The effect of the tangential radiation stress on the hydrodynamic field (drop oscillations) is found to manifest as a correction to the velocity field in a sublayer region near the drop/host interface. Moreover, the forcing due to the radiation pressure vector at the interface is modified by inclusion of tangential stresses.

High-Frequency Intermuscular Coherence between Arm Muscles during Robot-Mediated Motor Adaptation

PubMed Central

Pizzamiglio, Sara; De Lillo, Martina; Naeem, Usman; Abdalla, Hassan; Turner, Duncan L.

2017-01-01

Adaptation of arm reaching in a novel force field involves co-contraction of upper limb muscles, but it is not known how the co-ordination of multiple muscle activation is orchestrated. We have used intermuscular coherence (IMC) to test whether a coherent intermuscular coupling between muscle pairs is responsible for novel patterns of activation during adaptation of reaching in a force field. Subjects (N = 16) performed reaching trials during a null force field, then during a velocity-dependent force field and then again during a null force field. Reaching trajectory error increased during early adaptation to the force-field and subsequently decreased during later adaptation. Co-contraction in the majority of all possible muscle pairs also increased during early adaptation and decreased during later adaptation. In contrast, IMC increased during later adaptation and only in a subset of muscle pairs. IMC consistently occurred in frequencies between ~40–100 Hz and during the period of arm movement, suggesting that a coherent intermuscular coupling between those muscles contributing to adaptation enable a reduction in wasteful co-contraction and energetic cost during reaching. PMID:28119620

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

PubMed

Bandura, A V; Sofo, J O; Kubicki, J D

2006-04-27

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

PubMed

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

2012-02-14

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

Interactions between Nanoparticles and Polymer Brushes: Molecular Dynamics Simulations and Self-consistent Field Theory Calculations

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Wen, Chengyuan; Egorov, Sergei

2015-03-01

Molecular dynamics simulations and self-consistent field theory calculations are employed to study the interactions between a nanoparticle and a polymer brush at various densities of chains grafted to a plane. Simulations with both implicit and explicit solvent are performed. In either case the nanoparticle is loaded to the brush at a constant velocity. Then a series of simulations are performed to compute the force exerted on the nanoparticle that is fixed at various distances from the grafting plane. The potential of mean force is calculated and compared to the prediction based on a self-consistent field theory. Our simulations show that the explicit solvent leads to effects that are not captured in simulations with implicit solvent, indicating the importance of including explicit solvent in molecular simulations of such systems. Our results also demonstrate an interesting correlation between the force on the nanoparticle and the density profile of the brush. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.

Characteristics on electodynamic suspension simulator with HTS levitation magnet

NASA Astrophysics Data System (ADS)

Lee, J.; Bae, D. K.; Sim, K.; Chung, Y. D.; Lee, Y.-S.

2009-10-01

High- Tc superconducting (HTSC) electrodynamic suspension (EDS) system basically consists of the HTSC levitation magnet and the ground conductor. The levitation force of EDS system is forms by the interaction between the moving magnetic field produced by the onboard levitation magnet and the induced magnetic field produced by eddy current in the ground conductor. This paper deals with the characteristics of the EDS simulators with high- Tc superconducting (HTS) levitation magnet. Two EDS simulator systems, rotating type EDS simulator and static type EDS simulator, were studied in this paper. The rotating type EDS simulator consists of a HTS levitation magnet and a 1.5 m diameter rotating ground conductor, a motor, the supporting structure and force measuring devices. In the static type EDS simulator, instead of moving magnetic field, AC current was applied to the fixed HTS levitation magnet to induce the eddy current. The static type EDS simulator consists of a HTS levitation magnet, a ground conductor, force measuring devices and supporting structure. The double-pancake type HTSC levitation magnet was designed, manufactured and tested in the EDS simulator.

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

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

PubMed

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.

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

PubMed

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

2013-02-12

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Jong-Kyu; Logan, Nikolas C.

Toroidal torque is one of the most important consequences of non-axisymmetric fields in tokamaks. The well-known neoclassical toroidal viscosity (NTV) is due to the second-order toroidal force from anisotropic pressure tensor in the presence of these asymmetries. This work shows that the first-order toroidal force originating from the same anisotropic pressure tensor, despite having no flux surface average, can significantly modify the local perturbed force balance and thus must be included in perturbed equilibrium self-consistent with NTV. The force operator with an anisotropic pressure tensor is not self-adjoint when the NTV torque is finite and thus is solved directly formore » each component. This approach yields a modified, non-self-adjoint Euler-Lagrange equation that can be solved using a variety of common drift-kinetic models in generalized tokamak geometry. The resulting energy and torque integral provides a unique way to construct a torque response matrix, which contains all the information of self-consistent NTV torque profiles obtainable by applying non-axisymmetric fields to the plasma. This torque response matrix can then be used to systematically optimize non-axisymmetric field distributions for desired NTV profiles. Published by AIP Publishing.« less

Microwave ac Zeeman force for ultracold atoms

NASA Astrophysics Data System (ADS)

Fancher, C. T.; Pyle, A. J.; Rotunno, A. P.; Aubin, S.

2018-04-01

We measure the ac Zeeman force on an ultracold gas of 87Rb due to a microwave magnetic field targeted to the 6.8 GHz hyperfine splitting of these atoms. An atom chip produces a microwave near field with a strong amplitude gradient, and we observe a force over three times the strength of gravity. Our measurements are consistent with a simple two-level theory for the ac Zeeman effect and demonstrate its resonant, bipolar, and spin-dependent nature. We observe that the dressed-atom eigenstates gradually mix over time and have mapped out this behavior as a function of magnetic field and detuning. We demonstrate the practical spin selectivity of the force by pushing or pulling a specific spin state while leaving other spin states unmoved.

Lorentz Force on Sodium and Chlorine Ions in a Salt Water Solution Flow under a Transverse Magnetic Field

ERIC Educational Resources Information Center

De Luca, R.

2009-01-01

It is shown that, by applying elementary concepts in electromagnetism and electrochemistry to a system consisting of salt water flowing in a thin rectangular pipe at an average velocity v[subscript A] under the influence of a transverse magnetic field B[subscript 0], an electromotive force generator can be conceived. In fact, the Lorentz force…

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

Chameleon field is one of the promising candidates of dark energy scalar fields. As in all viable candidate field theories, a screening mechanism is implemented to be consistent with all existing tests of general relativity. The screening effect in the chameleon theory manifests its influence limited only to the thin outer layer of a bulk object, thus producing extra forces orders of magnitude weaker than that of the gravitational force of the bulk. For pointlike particles such as atoms, the depth of screening is larger than the size of the particle, such that the screening mechanism is ineffective and the chameleon force is fully expressed on the atomic test particles. Extra force measurements using atom interferometry are thus much more sensitive than bulk mass based measurements, and indeed have placed the most stringent constraints on the parameters characterizing chameleon field. In this paper, we present a conceptual measurement approach for chameleon force detection using atom interferometry in microgravity, in which multiloop atom interferometers exploit specially designed periodic modulation of chameleon fields. We show that major systematics of the dark energy force measurements, i.e., effects of gravitational forces and their gradients, can be suppressed below all hypothetical chameleon signals in the parameter space of interest.

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

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

PubMed Central

2015-01-01

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

A contact-force regulated photoplethysmography (PPG) platform

NASA Astrophysics Data System (ADS)

Sim, Jai Kyoung; Ahn, Bongyoung; Doh, Il

2018-04-01

A photoplethysmography (PPG) platform integrated with a miniaturized force-regulator is proposed in this study. Because a thermo-pneumatic type regulator maintains a consistent contact-force between the PPG probe and the measuring site, a consistent and stable PPG signal can be obtained. We designed and fabricated a watch-type PPG platform with an overall size of 35 mm × 19 mm. In the PPG measurement on the radial artery wrist while posture of the wrist is changed to extension, neutral, or flexion, regulation of the contact-force provides consistent PPG measurements for which the variations in the PPG amplitude (PPGA) was 7.2 %. The proposed PPG platform can be applied to biosignal measurements in various fields such as PPG-based ANS monitoring to estimate nociception, sleep apnea syndrome, and psychological stress.

Force, torque, linear momentum, and angular momentum in classical electr odynamics

NASA Astrophysics Data System (ADS)

Mansuripur, Masud

2017-10-01

The classical theory of electrodynamics is built upon Maxwell's equations and the concepts of electromagnetic (EM) field, force, energy, and momentum, which are intimately tied together by Poynting's theorem and by the Lorentz force law. Whereas Maxwell's equations relate the fields to their material sources, Poynting's theorem governs the flow of EM energy and its exchange between fields and material media, while the Lorentz law regulates the back-and-forth transfer of momentum between the media and the fields. An alternative force law, first proposed by Einstein and Laub, exists that is consistent with Maxwell's equations and complies with the conservation laws as well as with the requirements of special relativity. While the Lorentz law requires the introduction of hidden energy and hidden momentum in situations where an electric field acts on a magnetized medium, the Einstein-Laub (E-L) formulation of EM force and torque does not invoke hidden entities under such circumstances. Moreover, total force/torque exerted by EM fields on any given object turns out to be independent of whether the density of force/torque is evaluated using the law of Lorentz or that of Einstein and Laub. Hidden entities aside, the two formulations differ only in their predicted force and torque distributions inside matter. Such differences in distribution are occasionally measurable, and could serve as a guide in deciding which formulation, if either, corresponds to physical reality.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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

PubMed

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

2017-03-28

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

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

DOE PAGES

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; ...

2017-03-28

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex

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

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Ozone Sensitivity to Varying Greenhouse Gases and Ozone-Depleting Substances in CCMI-1 Simulations

NASA Technical Reports Server (NTRS)

Morgenstern, Olaf; Stone, Kane A.; Schofield, Robyn; Akiyoshi, Hideharu; Yamashita, Yousuke; Kinnison, Douglas E.; Garcia, Rolando R.; Sudo, Kengo; Plummer, David A.; Scinocca, John;

Ozone sensitivity to varying greenhouse gases and ozone-depleting substances in CCMI-1 simulations

NASA Astrophysics Data System (ADS)

Morgenstern, Olaf; Stone, Kane A.; Schofield, Robyn; Akiyoshi, Hideharu; Yamashita, Yousuke; Kinnison, Douglas E.; Garcia, Rolando R.; Sudo, Kengo; Plummer, David A.; Scinocca, John; Oman, Luke D.; Manyin, Michael E.; Zeng, Guang; Rozanov, Eugene; Stenke, Andrea; Revell, Laura E.; Pitari, Giovanni; Mancini, Eva; Di Genova, Glauco; Visioni, Daniele; Dhomse, Sandip S.; Chipperfield, Martyn P.

2018-01-01

Ozone fields simulated for the first phase of the Chemistry-Climate Model Initiative (CCMI-1) will be used as forcing data in the 6th Coupled Model Intercomparison Project. Here we assess, using reference and sensitivity simulations produced for CCMI-1, the suitability of CCMI-1 model results for this process, investigating the degree of consistency amongst models regarding their responses to variations in individual forcings. We consider the influences of methane, nitrous oxide, a combination of chlorinated or brominated ozone-depleting substances, and a combination of carbon dioxide and other greenhouse gases. We find varying degrees of consistency in the models' responses in ozone to these individual forcings, including some considerable disagreement. In particular, the response of total-column ozone to these forcings is less consistent across the multi-model ensemble than profile comparisons. We analyse how stratospheric age of air, a commonly used diagnostic of stratospheric transport, responds to the forcings. For this diagnostic we find some salient differences in model behaviour, which may explain some of the findings for ozone. The findings imply that the ozone fields derived from CCMI-1 are subject to considerable uncertainties regarding the impacts of these anthropogenic forcings. We offer some thoughts on how to best approach the problem of generating a consensus ozone database from a multi-model ensemble such as CCMI-1.

Strong-field dynamo action in rapidly rotating convection with no inertia.

PubMed

Hughes, David W; Cattaneo, Fausto

2016-06-01

The earth's magnetic field is generated by dynamo action driven by convection in the outer core. For numerical reasons, inertial and viscous forces play an important role in geodynamo models; however, the primary dynamical balance in the earth's core is believed to be between buoyancy, Coriolis, and magnetic forces. The hope has been that by setting the Ekman number to be as small as computationally feasible, an asymptotic regime would be reached in which the correct force balance is achieved. However, recent analyses of geodynamo models suggest that the desired balance has still not yet been attained. Here we adopt a complementary approach consisting of a model of rapidly rotating convection in which inertial forces are neglected from the outset. Within this framework we are able to construct a branch of solutions in which the dynamo generates a strong magnetic field that satisfies the expected force balance. The resulting strongly magnetized convection is dramatically different from the corresponding solutions in which the field is weak.

An analysis of the extension of a ZnO piezoelectric semiconductor nanofiber under an axial force

NASA Astrophysics Data System (ADS)

Zhang, Chunli; Wang, Xiaoyuan; Chen, Weiqiu; Yang, Jiashi

2017-02-01

This paper presents a theoretical analysis on the axial extension of an n-type ZnO piezoelectric semiconductor nanofiber under an axial force. The phenomenological theory of piezoelectric semiconductors consisting of Newton’s second law of motion, the charge equation of electrostatics and the conservation of charge was used. The equations were linearized for small axial force and hence small electron concentration perturbation, and were reduced to one-dimensional equations for thin fibers. Simple and analytical expressions for the electromechanical fields and electron concentration in the fiber were obtained. The fields are either totally or partially described by hyperbolic functions relatively large near the ends of the fiber and change rapidly there. The behavior of the fields is sensitive to the initial electron concentration and the applied axial force. For higher initial electron concentrations the fields are larger near the ends and change more rapidly there.

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

PubMed

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.

Nonlinear Bubble Interactions in Acoustic Pressure Fields

NASA Technical Reports Server (NTRS)

Barbat, Tiberiu; Ashgriz, Nasser; Liu, Ching-Shi

1996-01-01

The systems consisting of a two-phase mixture, as clouds of bubbles or drops, have shown many common features in their responses to different external force fields. One of particular interest is the effect of an unsteady pressure field applied to these systems, case in which the coupling of the vibrations induced in two neighboring components (two drops or two bubbles) may result in an interaction force between them. This behavior was explained by Bjerknes by postulating that every body that is moving in an accelerating fluid is subjected to a 'kinetic buoyancy' equal with the product of the acceleration of the fluid multiplied by the mass of the fluid displaced by the body. The external sound wave applied to a system of drops/bubbles triggers secondary sound waves from each component of the system. These secondary pressure fields integrated over the surface of the neighboring drop/bubble may result in a force additional to the effect of the primary sound wave on each component of the system. In certain conditions, the magnitude of these secondary forces may result in significant changes in the dynamics of each component, thus in the behavior of the entire system. In a system containing bubbles, the sound wave radiated by one bubble at the location of a neighboring one is dominated by the volume oscillation mode and its effects can be important for a large range of frequencies. The interaction forces in a system consisting of drops are much smaller than those consisting of bubbles. Therefore, as a first step towards the understanding of the drop-drop interaction subject to external pressure fluctuations, it is more convenient to study the bubble interactions. This paper presents experimental results and theoretical predictions concerning the interaction and the motion of two levitated air bubbles in water in the presence of an acoustic field at high frequencies (22-23 KHz).

Force Balance at the Magnetopause Determined with MMS: Application to Flux Transfer Events

NASA Technical Reports Server (NTRS)

Zhao, C.; Russell, C. T.; Strangeway, R. J.; Petrinec, S. M.; Paterson, W. R.; Zhou, M.; Anderson, B. J.; Baumjohann, W.; Bromund, K. R.; Chutter, M.;

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

NASA Astrophysics Data System (ADS)

Saez, David Adrian; Vöhringer-Martinez, Esteban

2015-10-01

S-Adenosylmethionine (AdoMet) is involved in many biological processes as cofactor in enzymes transferring its sulfonium methyl group to various substrates. Additionally, it is used as drug and nutritional supplement to reduce the pain in osteoarthritis and against depression. Due to the biological relevance of AdoMet it has been part of various computational simulation studies and will also be in the future. However, to our knowledge no rigorous force field parameter development for its simulation in biological systems has been reported. Here, we use electronic structure calculations combined with molecular dynamics simulations in explicit solvent to develop force field parameters compatible with the AMBER99 force field. Additionally, we propose new dynamic Hirshfeld-I atomic charges which are derived from the polarized electron density of AdoMet in aqueous solution to describe its electrostatic interactions in biological systems. The validation of the force field parameters and the atomic charges is performed against experimental interproton NOE distances of AdoMet in aqueous solution and crystal structures of AdoMet in the cavity of three representative proteins.

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

Macroscopic kinematics of the Hall electric field under influence of carrier magnetic moments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakai, Masamichi, E-mail: sakai@fms.saitama-u.ac.jp

2016-06-15

The relativistic effect on electromagnetic forces yields two types of forces which depend on the velocity of the relevant particles: (i) the usual Lorentz force exerted on a moving charged particle and (ii) the apparent Lorentz force exerted on a moving magnetic moment. In sharp contrast with type (i), the type (ii) force originates due to the transverse field induced by the Hall effect (HE). This study incorporates both forces into a Drude-type equation with a fully spin-polarized condition to investigate the effects of self-consistency of the source and the resultant fields on the HE. We also examine the self-consistencymore » of the carrier kinematics and electromagnetic dynamics by simultaneously considering the Drude type equation and Maxwell equations at low frequencies. Thus, our approach can predict both the dc and ac characteristics of the HE, demonstrating that the dc current condition solely yields the ordinary HE, while the ac current condition yields generation of both fundamental and second harmonic modes of the HE field. When the magnetostatic field is absent, the simultaneous presence of dc and ac longitudinal currents generates the ac HE that has both fundamental frequency and second harmonic.« less

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Nonlinear scalar forcing based on a reaction analogy

NASA Astrophysics Data System (ADS)

Daniel, Don; Livescu, Daniel

2017-11-01

We present a novel reaction analogy (RA) based forcing method for generating stationary passive scalar fields in incompressible turbulence. The new method can produce more general scalar PDFs (e.g. double-delta) than current methods, while ensuring that scalar fields remain bounded, unlike existent forcing methodologies that can potentially violate naturally existing bounds. Such features are useful for generating initial fields in non-premixed combustion or for studying non-Gaussian scalar turbulence. The RA method mathematically models hypothetical chemical reactions that convert reactants in a mixed state back into its pure unmixed components. Various types of chemical reactions are formulated and the corresponding mathematical expressions derived. For large values of the scalar dissipation rate, the method produces statistically steady double-delta scalar PDFs. Gaussian scalar statistics are recovered for small values of the scalar dissipation rate. In contrast, classical forcing methods consistently produce unimodal Gaussian scalar fields. The ability of the new method to produce fully developed scalar fields is discussed using 2563, 5123, and 10243 periodic box simulations.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Vertical Magnetic Levitation Force Measurement on Single Crystal YBaCuO Bulk at Different Temperatures

NASA Astrophysics Data System (ADS)

Celik, Sukru; Guner, Sait Baris; Ozturk, Kemal; Ozturk, Ozgur

Magnetic levitation force measurements of HTS samples are performed with the use of liquid nitrogen. It is both convenient and cheap. However, the temperature of the sample cannot be changed (77 K) and there is problem of frost. So, it is necessary to build another type of system to measure the levitation force high Tc superconductor at different temperatures. In this study, we fabricated YBaCuO superconducting by top-seeding-melting-growth (TSMG) technique and measured vertical forces of them at FC (Field Cooling) and ZFC (Zero Field Cooling) regimes by using our new designed magnetic levitation force measurement system. It was used to investigate the three-dimensional levitation force and lateral force in the levitation system consisting of a cylindrical magnet and a permanent cylindrical superconductor at different temperatures (37, 47, 57, 67 and 77 K).

PRESSURE TRANSDUCER

DOEpatents

Sander, H.H.

1959-10-01

A pressure or mechanical force transducer particularly adaptable to miniature telemetering systems is described. Basically the device consists of a transistor located within a magnetic field adapted to change in response to mechanical force. The conduction characteristics of the transistor in turn vary proportionally with changes in the magnetic flux across the transistor such that the output (either frequency of amplitude) of the transistor circuit is proportional to mechanical force or pressure.

Three-dimensional cascaded lattice Boltzmann method: Improved implementation and consistent forcing scheme

NASA Astrophysics Data System (ADS)

Fei, Linlin; Luo, Kai H.; Li, Qing

2018-05-01

The cascaded or central-moment-based lattice Boltzmann method (CLBM) proposed in [Phys. Rev. E 73, 066705 (2006), 10.1103/PhysRevE.73.066705] possesses very good numerical stability. However, two constraints exist in three-dimensional (3D) CLBM simulations. First, the conventional implementation for 3D CLBM involves cumbersome operations and requires much higher computational cost compared to the single-relaxation-time (SRT) LBM. Second, it is a challenge to accurately incorporate a general force field into the 3D CLBM. In this paper, we present an improved method to implement CLBM in 3D. The main strategy is to adopt a simplified central moment set and carry out the central-moment-based collision operator based on a general multi-relaxation-time (GMRT) framework. Next, the recently proposed consistent forcing scheme for CLBM [Fei and Luo, Phys. Rev. E 96, 053307 (2017), 10.1103/PhysRevE.96.053307] is extended to incorporate a general force field into 3D CLBM. Compared with the recently developed nonorthogonal CLBM [Rosis, Phys. Rev. E 95, 013310 (2017), 10.1103/PhysRevE.95.013310], our implementation is proved to reduce the computational cost significantly. The inconsistency of adopting the discrete equilibrium distribution functions in the nonorthogonal CLBM is analyzed and validated. The 3D CLBM developed here in conjunction with the consistent forcing scheme is verified through numerical simulations of several canonical force-driven flows, highlighting very good properties in terms of accuracy, convergence, and consistency with the nonslip rule. Finally, the techniques developed here for 3D CLBM can be applied to make the implementation and execution of 3D MRT-LBM more efficient.

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

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

2013-08-07

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonthuis, Douwe Jan, E-mail: douwe.bonthuis@physics.ox.ac.uk; Mamatkulov, Shavkat I.; Netz, Roland R.

We optimize force fields for H{sub 3}O{sup +} and OH{sup −} that reproduce the experimental solvation free energies and the activities of H{sub 3}O{sup +} Cl{sup −} and Na{sup +} OH{sup −} solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H{sub 3}O{sup +} force field is 0.8 ± 0.1|e|—significantly higher than the value typically used for nonpolarizable water models and H{sub 3}O{sup +} force fields. In contrast,more » the optimal partial charge on the hydrogen atom of OH{sup −} turns out to be zero. Standard combination rules can be used for H{sub 3}O{sup +} Cl{sup −} solutions, while for Na{sup +} OH{sup −} solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.« less

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

PubMed Central

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

2015-01-01

Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG–X–GTGT host–guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard–Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid–liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields.

PubMed

Eleftheriou, Maria; Germain, Robert S; Royyuru, Ajay K; Zhou, Ruhong

2006-10-18

Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between the currently accessible simulation time scale and the experimental time scale for many important protein folding processes. In this study, molecular dynamics simulations were carried out for both the wild-type and the mutant hen lysozyme (TRP62GLY) to study the single mutation effect on lysozyme stability and misfolding. Our thermal denaturing simulations at 400-500 K with both the OPLSAA and the CHARMM force fields show that the mutant structure is indeed much less stable than the wild-type, which is consistent with the recent urea denaturing experiment (Dobson et al. Science 2002, 295, 1719-1722; Nature 2003, 424, 783-788). Detailed results also reveal that the single mutation TRP62GLY first induces the loss of native contacts in the beta-domain region of the lysozyme protein at high temperatures, and then the unfolding process spreads into the alpha-domain region through Helix C. Even though the OPLSAA force field in general shows a more stable protein structure than does the CHARMM force field at high temperatures, the two force fields examined here display qualitatively similar results for the misfolding process, indicating that the thermal denaturing of the single mutation is robust and reproducible with various modern force fields.

Effect of self-consistent magnetic field on plasma sheet penetration to the inner magnetosphere under enhanced convection: RCM simulations combined with force-balance magnetic field solver

NASA Astrophysics Data System (ADS)

Gkioulidou, M.; Wang, C.; Lyons, L. R.; Wolf, R. A.

2010-12-01

Transport of plasma sheet particles into the inner magnetosphere is strongly affected by the penetration of the convection electric field, which is the result of the large-scale magnetosphere-ionosphere electromagnetic coupling. This transport, on the other hand, results in plasma heating and magnetic field stretching, which become very significant in the inner plasma sheet (inside 20 RE). We have previously run simulations with the Rice Convection Model (RCM) to investigate how the earthward penetration of convection electric field, and therefore plasma sheet population, depends on plasma sheet boundary conditions. Outer boundary conditions at r ~20 RE are a function of MLT and interplanetary conditions based on 11 years of Geotail data. In the previous simulations, Tsyganenko 96 magnetic field model (T96) was used so force balance between plasma pressure and magnetic fields was not maintained. We have now integrated the RCM with a magnetic field solver (Liu et al., 2006) to obtain the required force balance in the equatorial plane. We have run the self-consistent simulations under enhanced convection with different boundary conditions in which we kept different parameters (flux tube particle content, plasma pressure, plasma beta, or magnetic fields) at the outer boundary to be MLT-dependent but time independent. Different boundary conditions result in qualitatively similar plasma sheet profiles. The results show that magnetic field has a dawn dusk asymmetry with field lines being more stretched in the pre-midnight sector, due to relatively higher plasma pressure there. The asymmetry in the magnetic fields in turn affects the radial distance and MLT of plasma sheet penetration into the inner magnetosphere. In comparison with results using the T96, plasma transport under self-consistent magnetic field results in proton and electron plasma sheet inner edges that are located in higher latitudes, weaker pressure gradients, and more efficient shielding of the near-Earth convection electric field (since auroral conductance is also confined to higher latitudes). We are currently evaluating the simulated plasma sheet properties by comparing them with statistical results obtained from Geotail and THEMIS observations.

Mapping the Drude polarizable force field onto a multipole and induced dipole model

NASA Astrophysics Data System (ADS)

Huang, Jing; Simmonett, Andrew C.; Pickard, Frank C.; MacKerell, Alexander D.; Brooks, Bernard R.

2017-10-01

The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.

The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

NASA Astrophysics Data System (ADS)

Mollica, Luca; Curioni, Alessandro; Andreoni, Wanda; Bianchi, Marco E.; Musco, Giovanna

2008-05-01

We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand-protein complex resulting from QRFF-MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand-protein binding is dominated by non-directional interactions.

A Simple Force-Motion Relation for Migrating Cells Revealed by Multipole Analysis of Traction Stress

PubMed Central

Tanimoto, Hirokazu; Sano, Masaki

2014-01-01

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. PMID:24411233

A stochastically forced time delay solar dynamo model: Self-consistent recovery from a maunder-like grand minimum necessitates a mean-field alpha effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazra, Soumitra; Nandy, Dibyendu; Passos, Dário, E-mail: s.hazra@iiserkol.ac.in, E-mail: dariopassos@ist.utl.pt, E-mail: dnandi@iiserkol.ac.in

Fluctuations in the Sun's magnetic activity, including episodes of grand minima such as the Maunder minimum have important consequences for space and planetary environments. However, the underlying dynamics of such extreme fluctuations remain ill-understood. Here, we use a novel mathematical model based on stochastically forced, non-linear delay differential equations to study solar cycle fluctuations in which time delays capture the physics of magnetic flux transport between spatially segregated dynamo source regions in the solar interior. Using this model, we explicitly demonstrate that the Babcock-Leighton poloidal field source based on dispersal of tilted bipolar sunspot flux, alone, cannot recover the sunspotmore » cycle from a grand minimum. We find that an additional poloidal field source effective on weak fields—e.g., the mean-field α effect driven by helical turbulence—is necessary for self-consistent recovery of the sunspot cycle from grand minima episodes.« less

Kinetic Approaches to Shear-Driven Magnetic Reconnection for Multi-Scale Modeling of CME Initiation

NASA Astrophysics Data System (ADS)

Black, C.; Antiochos, S. K.; DeVore, C.; Germaschewski, K.; Karpen, J. T.

2013-12-01

In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance, consisting of an upward force due to the magnetic pressure of the sheared field balanced by a downward tension due to overlying un-sheared field, is widely believed to be disrupted by magnetic reconnection. Therefore, understanding initiation of solar explosive phenomena requires a true multi-scale model of reconnection onset driven by the buildup of magnetic shear. While the application of magnetic-field shear is a trivial matter in MHD simulations, it is a significant challenge in a PIC code. The driver must be implemented in a self-consistent manner and with boundary conditions that avoid the generation of waves that destroy the applied shear. In this work, we describe drivers for 2.5D, aperiodic, PIC systems and discuss the implementation of driver-consistent boundary conditions that allow a net electric current to flow through the walls. Preliminary tests of these boundaries with a MHD equilibrium are shown. This work was supported, in part, by the NASA Living With a Star TR&T Program.

Quantum theory of multiscale coarse-graining.

PubMed

Han, Yining; Jin, Jaehyeok; Wagner, Jacob W; Voth, Gregory A

2018-03-14

Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

Temperature and field direction dependences of first-order reversal curve (FORC) diagrams of hot-deformed Nd-Fe-B magnets

NASA Astrophysics Data System (ADS)

Yomogita, Takahiro; Okamoto, Satoshi; Kikuchi, Nobuaki; Kitakami, Osamu; Sepehri-Amin, Hossein; Ohkubo, Tadakatsu; Hono, Kazuhiro; Akiya, Takahiro; Hioki, Keiko; Hattori, Atsushi

2018-02-01

First-order reversal curve (FORC) diagram has been previously adopted for the analyses of magnetization reversal process and/or quantitative evaluation of coercivity and interaction field dispersions in various magnetic samples. Although these kinds of information are valuable for permanent magnets, previously reported FORC diagrams of sintered Nd-Fe-B magnets exhibit very complicated patterns. In this paper, we have studied the FORC diagrams of hot-deformed Nd-Fe-B magnets under various conditions. Contrary to the previous reports on sintered Nd-Fe-B magnets, the FORC diagram of the hot-deformed Nd-Fe-B magnet exhibits a very simple pattern consisting of a strong spot and a weak line. From this FORC diagram pattern, it is revealed that the coercivity dispersion of the hot-deformed Nd-Fe-B magnets is surprisingly small. Moreover, this feature of the FORC diagram pattern is very robust and unaffected by changes in various conditions such as grain boundary diffusion process, temperature, and field direction, whereas these conditions significantly change the coercivity and the shape of magnetization curve. This fact indicates that the magnetization reversal process of the hot-deformed Nd-Fe-B magnets is almost unchanged against these conditions.

Optical forces, torques, and force densities calculated at a microscopic level using a self-consistent hydrodynamics method

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-04-01

The calculation of optical force density distribution inside a material is challenging at the nanoscale, where quantum and nonlocal effects emerge and macroscopic parameters such as permittivity become ill-defined. We demonstrate that the microscopic optical force density of nanoplasmonic systems can be defined and calculated using the microscopic fields generated using a self-consistent hydrodynamics model that includes quantum, nonlocal, and retardation effects. We demonstrate this technique by calculating the microscopic optical force density distributions and the optical binding force induced by external light on nanoplasmonic dimers. This approach works even in the limit when the nanoparticles are close enough to each other so that electron tunneling occurs, a regime in which classical electromagnetic approach fails completely. We discover that an uneven distribution of optical force density can lead to a light-induced spinning torque acting on individual particles. The hydrodynamics method offers us an accurate and efficient approach to study optomechanical behavior for plasmonic systems at the nanoscale.

A Real Alternative: The Final Report and Recommendations of the Community National Field Task Force on the Improvement and Reform of American Education.

ERIC Educational Resources Information Center

Office of Education (DHEW), Washington, DC.

This report is one of six to be released by as many task forces on educational improvement and reform. The main body of this report consists of five sections: (a) an introduction, which briefly describes the work of the task force; (b) a description of the alternative of community participation in education; (c) recommendations; (d) access to…

Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Dayle MA; Xiong, Yijia; Straatsma, TP

2012-05-09

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

[Forced Oscillations of DNA Bases].

PubMed

Yakushevich, L V; Krasnobaeva, L A

2016-01-01

This paper presents the results of the studying of forced angular oscillations of the DNA bases with the help of the mathematical model consisting of two coupled nonlinear differential equations that take into account the effects of dissipation and the influence of an external periodic field. The calculation results are illustrated for sequence of gene encoding interferon alpha 17 (IFNA 17).

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

PubMed Central

2016-01-01

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

Large Electric Field-Enhanced-Hardness Effect in a SiO2 Film

NASA Astrophysics Data System (ADS)

Revilla, Reynier I.; Li, Xiao-Jun; Yang, Yan-Lian; Wang, Chen

2014-03-01

Silicon dioxide films are extensively used in nano and micro-electromechanical systems. Here we studied the influence of an external electric field on the mechanical properties of a SiO2 film by using nanoindentation technique of atomic force microscopy (AFM) and friction force microscopy (FFM). A giant augmentation of the relative elastic modulus was observed by increasing the localized electric field. A slight decrease in friction coefficients was also clearly observed by using FFM with the increase of applied tip voltage. The reduction of the friction coefficients is consistent with the great enhancement of sample hardness by considering the indentation-induced deformation during the friction measurements.

Particle physics meets cosmology - The search for decaying neutrinos

NASA Technical Reports Server (NTRS)

Henry, R. C.

1982-01-01

The fundamental physical implications of the possible detection of massive neutrinos are discussed, with an emphasis on the Grand Unified Theories (GUTs) of matter. The Newtonian and general-relativistic pictures of the fundamental forces are compared, and the reduction of electromagnetic and weak forces to one force in the GUTs is explained. The cosmological consequences of the curved-spacetime gravitation concept are considered. Quarks, leptons, and neutrinos are characterized in a general treatment of elementary quantum mechanics. The universe is described in terms of quantized fields, the noninteractive 'particle' fields and the force fields, and cosmology becomes the study of the interaction of gravitation with the other fields, of the 'freezing out' of successive fields with the expansion and cooling of the universe. While the visible universe is the result of the clustering of the quark and electron fields, the distribution of the large number of quanta in neutrino field, like the mass of the neutrino, are unknown. Cosmological models which attribute anomalies in the observed motions of galaxies and stars to clusters or shells of massive neutrinos are shown to be consistent with a small but nonzero neutrino mass and a universe near the open/closed transition point, but direct detection of the presence of massive neutrinos by the UV emission of their decay is required to verify these hypotheses.

Traction force and tension fluctuations in growing axons

NASA Astrophysics Data System (ADS)

Urbach, Jeffrey; Polackwich, Jamie; Koch, Daniel; McAllister, Ryan; Geller, Herbert

Actively generated mechanical forces play a central role in axon growth and guidance during nervous system development. We describe the dynamics of traction stresses from growth cones of actively advancing axons from postnatal rat DRG neurons. By tracking the movement of the growth cone and analyzing the traction stresses in a co-moving reference frame, we show that there is a clear and consistent average stress field underlying the complex spatial stresses present at any one time. The average stress field has strong maxima on the sides of the growth cone, directed inward toward the growth cone neck. This pattern represents a Contractile stress contained within the growth cone, and a net force that is balanced by the axon tension. In addition, using high time-resolution measurements, we show that the stress field is composed of fluctuating local stress peaks, with a population of peaks whose lifetime distribution follows an exponential decay, and a small number of very long-lived peaks. We also find that the tension appears to vary randomly over short time scales, roughly consistent with the lifetime of the stress peaks, suggesting that the tension fluctuations originate from stochastic adhesion dynamics.

Combining configurational energies and forces for molecular force field optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

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

DTIC Science & Technology

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

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

PubMed Central

2015-01-01

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

Magnetohydrodynamics of atmospheric transients. IV - Nonplane two-dimensional analyses of energy conversion and magnetic field evolution. [during corona following solar flare

NASA Technical Reports Server (NTRS)

Wu, S. T.; Nakagawa, Y.; Han, S. M.; Dryer, M.

1982-01-01

The evolution of the magnetic field and the manner of conversion of thermal energy into different forms in the corona following a solar flare are investigated by means of a nonplane magnetohydrodynamic (MHD) analysis. All three components of magnetic field and velocity are treated in a physically self-consistent manner, with all physical variables as functions of time (t) and two spatial coordinates (r, theta). The difference arising from the initial magnetic field, either twisted (force-free) or non-twisted (potential), is demonstrated. Consideration is given to two initial field topologies (open vs. closed). The results demonstrate that the conversion of magnetic energy is faster for the case of the initially twisted (force-free) field than for the initially untwisted (potential) field. In addition, the twisted field is found to produce a complex structure of the density enhancements.

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

PubMed

Miller, Mark S; Lay, Wesley K; Li, Shuxiang; Hacker, William C; An, Jiadi; Ren, Jianlan; Elcock, Adrian H

2017-04-11

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

A simple force-motion relation for migrating cells revealed by multipole analysis of traction stress.

PubMed

Tanimoto, Hirokazu; Sano, Masaki

2014-01-07

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prasad, A.; Bhattacharyya, R.; Kumar, Sanjay

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 atmore » 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.« less

Influence of nonuniform magnetic fields on orientation of plant seedlings in microgravity conditions

NASA Astrophysics Data System (ADS)

Nechitailo, G. S.; Mashinsky, A. L.; Kuznetsov, A. A.; Chikov, V. M.; Kuznetsov, O. A.

2001-01-01

Experiments on the spatial behavior of the flax ( Linum usitatissimum, L.) seedlings in a nonuniform magnetic field were conducted on the orbital space stations «Salutå and «Mirå. This field can displace sensory organelles (statoliths) inside receptor cells and such displacement should cause a physiological reaction of the plant - tropistic curvature. Experiments were conducted in the custom-built «Magnetogravistatå facility, where seeds were germinated and grown for 3-4 days in a magnetic field with the dynamic factor grad(H 2/2)≈ 10 7 Oe 2/cm, then fixed on orbit and returned to Earth for analysis. It was found, that 93% of the seedlings were oriented in the field consistently with curvature in response to displacement of statoliths along the field gradient by ponderomotive magnetic forces, while control seedlings grew in the direction of the initial orientation of the seed. This suggests, that gravity receptors of plants recognized magnetic forces on statoliths as gravity, and that gravity stimulus can be substituted for plants by a force of a different physical nature.

Self-consistent mean-field approach to the statistical level density in spherical nuclei

NASA Astrophysics Data System (ADS)

Kolomietz, V. M.; Sanzhur, A. I.; Shlomo, S.

2018-06-01

A self-consistent mean-field approach within the extended Thomas-Fermi approximation with Skyrme forces is applied to the calculations of the statistical level density in spherical nuclei. Landau's concept of quasiparticles with the nucleon effective mass and the correct description of the continuum states for the finite-depth potentials are taken into consideration. The A dependence and the temperature dependence of the statistical inverse level-density parameter K is obtained in a good agreement with experimental data.

Torsional Oscillations with Lorentz Force

ERIC Educational Resources Information Center

Gluck, Paul

2007-01-01

We have built a device that uses the Lorentz force on a current-carrying wire situated in a magnetic field, F = I L x B, in order to demonstrate a slowly varying alternating current by means of an optical lever. The apparatus consists of a horseshoe magnet, a length of thin enamel-coated wire (ours was 0.3 mm thick), a signal generator, a…

The effects of forcing on a single stream shear layer and its parent boundary layer

NASA Technical Reports Server (NTRS)

Haw, R. C.; Foss, J. F.

1989-01-01

The detailed response of a large single-stream shear layer to a sinusoidal forcing at x = 0 is quantitatively defined. Phase-averaged data are used to characterize the increased disturbance convection velocity and a width measure of the disturbance field. These findings are consistent with and complement those of Fiedler and Mensing (1985).

Representing delayed force feedback as a combination of current and delayed states.

PubMed

Avraham, Guy; Mawase, Firas; Karniel, Amir; Shmuelof, Lior; Donchin, Opher; Mussa-Ivaldi, Ferdinando A; Nisky, Ilana

2017-10-01

To adapt to deterministic force perturbations that depend on the current state of the hand, internal representations are formed to capture the relationships between forces experienced and motion. However, information from multiple modalities travels at different rates, resulting in intermodal delays that require compensation for these internal representations to develop. To understand how these delays are represented by the brain, we presented participants with delayed velocity-dependent force fields, i.e., forces that depend on hand velocity either 70 or 100 ms beforehand. We probed the internal representation of these delayed forces by examining the forces the participants applied to cope with the perturbations. The findings showed that for both delayed forces, the best model of internal representation consisted of a delayed velocity and current position and velocity. We show that participants relied initially on the current state, but with adaptation, the contribution of the delayed representation to adaptation increased. After adaptation, when the participants were asked to make movements with a higher velocity for which they had not previously experienced with the delayed force field, they applied forces that were consistent with current position and velocity as well as delayed velocity representations. This suggests that the sensorimotor system represents delayed force feedback using current and delayed state information and that it uses this representation when generalizing to faster movements. NEW & NOTEWORTHY The brain compensates for forces in the body and the environment to control movements, but it is unclear how it does so given the inherent delays in information transmission and processing. We examined how participants cope with delayed forces that depend on their arm velocity 70 or 100 ms beforehand. After adaptation, participants applied opposing forces that revealed a partially correct representation of the perturbation using the current and the delayed information. Copyright © 2017 the American Physiological Society.

Self-force via m-mode regularization and 2+1D evolution. II. Scalar-field implementation on Kerr spacetime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolan, Sam R.; Barack, Leor; Wardell, Barry

2011-10-15

This is the second in a series of papers aimed at developing a practical time-domain method for self-force calculations in Kerr spacetime. The key elements of the method are (i) removal of a singular part of the perturbation field with a suitable analytic 'puncture' based on the Detweiler-Whiting decomposition, (ii) decomposition of the perturbation equations in azimuthal (m-)modes, taking advantage of the axial symmetry of the Kerr background, (iii) numerical evolution of the individual m-modes in 2+1 dimensions with a finite-difference scheme, and (iv) reconstruction of the physical self-force from the mode sum. Here we report an implementation of themore » method to compute the scalar-field self-force along circular equatorial geodesic orbits around a Kerr black hole. This constitutes a first time-domain computation of the self-force in Kerr geometry. Our time-domain code reproduces the results of a recent frequency-domain calculation by Warburton and Barack, but has the added advantage of being readily adaptable to include the backreaction from the self-force in a self-consistent manner. In a forthcoming paper--the third in the series--we apply our method to the gravitational self-force (in the Lorenz gauge).« less

Energy release and transfer in guide field reconnection

NASA Astrophysics Data System (ADS)

Birn, J.; Hesse, M.

2010-01-01

Properties of energy release and transfer by magnetic reconnection in the presence of a guide field are investigated on the basis of 2.5-dimensional magnetohydrodynamic (MHD) and particle-in-cell (PIC) simulations. Two initial configurations are considered: a plane current sheet with a uniform guide field of 80% of the reconnecting magnetic field component and a force-free current sheet in which the magnetic field strength is constant but the field direction rotates by 180° through the current sheet. The onset of reconnection is stimulated by localized, temporally limited compression. Both MHD and PIC simulations consistently show that the outgoing energy fluxes are dominated by (redirected) Poynting flux and enthalpy flux, whereas bulk kinetic energy flux and heat flux (in the PIC simulation) are small. The Poynting flux is mainly associated with the magnetic energy of the guide field which is carried from inflow to outflow without much alteration. The conversion of annihilated magnetic energy to enthalpy flux (that is, thermal energy) stems mainly from the fact that the outflow occurs into a closed field region governed by approximate force balance between Lorentz and pressure gradient forces. Therefore, the energy converted from magnetic to kinetic energy by Lorentz force acceleration becomes immediately transferred to thermal energy by the work done by the pressure gradient force. Strong similarities between late stages of MHD and PIC simulations result from the fact that conservation of mass and entropy content and footpoint displacement of magnetic flux tubes, imposed in MHD, are also approximately satisfied in the PIC simulations.

Matter in the form of toroidal electromagnetic vortices

NASA Astrophysics Data System (ADS)

Hagen, Wilhelm F.

2015-09-01

The creation of charged elementary particles from neutral photons is explained as a conversion process of electromagnetic (EM) energy from linear to circular motion at the speed of light into two localized, toroidal shaped vortices of trapped EM energy that resist change of motion, perceptible as particles with inertia and hence mass. The photon can be represented as a superposition of left and right circular polarized transverse electric fields of opposite polarity originating from a common zero potential axis, the optical axis of the photon. If these components are separated by interaction with a strong field (nucleon) they would curl up into two electromagnetic vortices (EMV) due to longitudinal magnetic field components forming toroids. These vortices are perceptible as opposite charged elementary particles e+/- . These spinning toroids generate extended oscillating fields that interact with stationary field oscillations. The velocity-dependent frequency differences cause beat signals equivalent to matter waves, leading to interference. The extended fields entangled with every particle explain wave particle duality issues. Spin and magnetic moment are the natural outcome of these gyrating particles. As the energy and hence mass of the electron increases with acceleration so does its size shrink proportional to its reduced wavelength. The artificial weak and strong nuclear forces can be easily explained as different manifestations of the intermediate EM forces. The unstable neutron consists of a proton surrounded by a contracted and captured electron. The associated radial EM forces represent the weak nuclear force. The deuteron consists of two axially separated protons held together by a centrally captured electron. The axial EM forces represent the strong nuclear force, providing stability for "neutrons" only within nucleons. The same principles were applied to determine the geometries of force-balanced nuclei. The alpha-particle emerges as a very compact symmetric cuboid that provides a unique building block to assemble the isotopic chart. Exotic neutron- 4 appears viable which may explain dark matter. The recognition that all heavy particles, including the protons, are related to electrons via muons and pions explains the identity of all charges to within 10-36. Greater deviations would overpower gravitation. Gravitation can be traced to EM vacuum fluctuations generated by standing EM waves between interacting particles. On that basis, gravity can be correlated via microscopic quantities to the age of the universe of 13.5 billion years. All forces and particles and potentially dark matter and dark energy are different manifestations of EM energy.

Understanding Magnetic Reconnection: The Physical Mechanism Driving Space Weather

NASA Astrophysics Data System (ADS)

Black, Carrie; Antiochos, Spiro K.; Karpen, Judith T.; Germaschewski, Kai; Bessho, Naoki

2015-04-01

The explosive energy release in solar eruptive events is believed to be due to magnetic reconnection. In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance consists of an upward force due to the magnetic pressure of the sheared field countered by the downward tension of the overlying unsheared field. Magnetic reconnection disrupts this force balance. Therefore, to understand CME/flare initiation, it is critical to model the onset of reconnection driven by the build-up of magnetic shear. In MHD simulations, the application of a magnetic-field shear is trivial. However, kinetic effects are important in the diffusion region and thus, it is important to examine this process with PIC simulations as well. The implementation of such a driver in PIC methods is nontrivial, however, and indicates the necessity of a true multiscale model for such processes in the solar environment. The field must be sheared self-consistently and indirectly to prevent the generation of waves that destroy the desired system. In the work presented here, we show reconnection in an X-Point geometry due to a velocity shear driver perpendicular to the plane of reconnection.This material is based upon work supported by the National Science Foundation under Award No. AGS-1331356 and NASA's Living With a Star Targeted Research and Technology program.

Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons.

PubMed

Prampolini, Giacomo; Campetella, Marco; De Mitri, Nicola; Livotto, Paolo Roberto; Cacelli, Ivo

2016-11-08

A robust and automated protocol for the derivation of sound force field parameters, suitable for condensed-phase classical simulations, is here tested and validated on several halogenated hydrocarbons, a class of compounds for which standard force fields have often been reported to deliver rather inaccurate performances. The major strength of the proposed protocol is that all of the parameters are derived only from first principles because all of the information required is retrieved from quantum mechanical data, purposely computed for the investigated molecule. This a priori parametrization is carried out separately for the intra- and intermolecular contributions to the force fields, respectively exploiting the Joyce and Picky programs, previously developed in our group. To avoid high computational costs, all quantum mechanical calculations were performed exploiting the density functional theory. Because the choice of the functional is known to be crucial for the description of the intermolecular interactions, a specific procedure is proposed, which allows for a reliable benchmark of different functionals against higher-level data. The intramolecular and intermolecular contribution are eventually joined together, and the resulting quantum mechanically derived force field is thereafter employed in lengthy molecular dynamics simulations to compute several thermodynamic properties that characterize the resulting bulk phase. The accuracy of the proposed parametrization protocol is finally validated by comparing the computed macroscopic observables with the available experimental counterparts. It is found that, on average, the proposed approach is capable of yielding a consistent description of the investigated set, often outperforming the literature standard force fields, or at least delivering results of similar accuracy.

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

PubMed Central

Miller, Mark S.; Lay, Wesley K.; Li, Shuxiang; Hacker, William C.; An, Jiadi; Ren, Jianlan; Elcock, Adrian H.

2017-01-01

There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparameterize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models. In general, for both the amino acids and the small molecules, the tested force fields produce computed osmotic coefficients that are lower than experiment; this is indicative of excessively favorable solute-solute interactions. The sole exception to this general trend is provided by GROMOS54a7 when applied to amino acids: in this case, the computed osmotic coefficients are consistently too high. Importantly, we show that all of the force fields tested can be made to accurately reproduce the experimental osmotic coefficients of the amino acids when minor modifications – some previously reported by others and some that are new to this study – are made to the van der Waals interactions of the charged terminal groups. Special care is required, however, when simulating Proline with a number of the force fields, and a hydroxyl-group specific modification is required in order to correct Serine and Threonine when simulated with AMBER ff99SB-ILDN. Interestingly, an alternative parameterization of the van der Waals interactions in the latter force field, proposed by the Nerenberg and Head-Gordon groups, is shown to immediately produce osmotic coefficients that are in excellent agreement with experiment. Overall, this study reinforces the idea that osmotic coefficient measurements can be used to identify general shortcomings in commonly used force fields’ descriptions of solute-solute interactions, and further demonstrates that modifications to van der Waals parameters provides a simple route to optimizing agreement with experiment. PMID:28296391

Polymer-induced forces at interfaces

NASA Astrophysics Data System (ADS)

Rangarajan, Murali

This dissertation concerns studies of forces generated by confined and physisorbed flexible polymers using lattice mean-field theories, and those generated by confined and clamped semiflexible polymers modeled as slender elastic rods. Lattice mean-field theories have been used in understanding and predicting the behavior of polymeric interfacial systems. In order to efficiently tailor such systems for various applications of interest, one has to understand the forces generated in the interface due to the polymer molecules. The present work examines the abilities and limitations of lattice mean-field theories in predicting the structure of physisorbed polymer layers and the resultant forces. Within the lattice mean-field theory, a definition of normal force of compression as the negative derivative of the partition-function-based excess free energy with surface separation gives misleading results because the theory does not explicitly account for the normal stresses involved in the system. Correct expressions for normal and tangential forces are obtained from a continuum-mechanics-based formulation. Preliminary comparisons with lattice Monte Carlo simulations show that mean-field theories fail to predict significant attractive forces when the surfaces are undersaturated, as one would expect. The corrections to the excluded volume (non-reversal chains) and the mean-field (anisotropic field) approximations improve the predictions of layer structure, but not the forces. Bending of semiflexible polymer chains (elastic rods) is considered for two boundary conditions---where the chain is hinged on both ends and where the chain is clamped on one end and hinged on the other. For the former case, the compressive forces and chain shapes obtained are consistent with the inflexional elastica published by Love. For the latter, multiple and higher-order solutions are observed for the hinged-end position for a given force. Preliminary studies are conducted on actin-based motility of Listeria monocytogenes by treating actin filaments as elastic rods, using the actoclampin model. The results show qualitative agreement with calculations where the filaments are modeled as Hookean springs. The feasibility of the actoclampin model to address long length-scale rotation of Listeria during actin-based motility is addressed.

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

PubMed

Henriques, João; Cragnell, Carolina; Skepö, Marie

2015-07-14

An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment.

The Force-Free Magnetosphere of a Rotating Black Hole

NASA Technical Reports Server (NTRS)

Contopoulos, Ioannis; Kazanas, Demosthenes; Papadopoulos, Demetrios B.

2013-01-01

We revisit the Blandford-Znajek process and solve the fundamental equation that governs the structure of the steady-state force-free magnetosphere around a Kerr black hole. The solution depends on the distributions of the magnetic field angular velocity and the poloidal electric current. These are not arbitrary. They are determined self-consistently by requiring that magnetic field lines cross smoothly the two singular surfaces of the problem: the inner "light surface" located inside the ergosphere and the outer "light surface" which is the generalization of the pulsar light cylinder.We find the solution for the simplest possible magnetic field configuration, the split monopole, through a numerical iterative relaxation method analogous to the one that yields the structure of the steady-state axisymmetric force-free pulsar magnetosphere. We obtain the rate of electromagnetic extraction of energy and confirm the results of Blandford and Znajek and of previous time-dependent simulations. Furthermore, we discuss the physical applicability of magnetic field configurations that do not cross both "light surfaces."

Local conductance: A means to extract polarization and depolarizing fields near domain walls in ferroelectrics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douglas, A. M.; Kumar, A.; Gregg, J. M.

Conducting atomic force microscopy images of bulk semiconducting BaTiO{sub 3} surfaces show clear stripe domain contrast. High local conductance correlates with strong out-of-plane polarization (mapped independently using piezoresponse force microscopy), and current-voltage characteristics are consistent with dipole-induced alterations in Schottky barriers at the metallic tip-ferroelectric interface. Indeed, analyzing current-voltage data in terms of established Schottky barrier models allows relative variations in the surface polarization, and hence the local domain structure, to be determined. Fitting also reveals the signature of surface-related depolarizing fields concentrated near domain walls. Domain information obtained from mapping local conductance appears to be more surface-sensitive than thatmore » from piezoresponse force microscopy. In the right materials systems, local current mapping could therefore represent a useful complementary technique for evaluating polarization and local electric fields with nanoscale resolution.« less

A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

PubMed

Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

2014-03-11

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Unorthodox theoretical methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nedd, Sean

2012-01-01

The use of the ReaxFF force field to correlate with NMR mobilities of amine catalytic substituents on a mesoporous silica nanosphere surface is considered. The interfacing of the ReaxFF force field within the Surface Integrated Molecular Orbital/Molecular Mechanics (SIMOMM) method, in order to replicate earlier SIMOMM published data and to compare with the ReaxFF data, is discussed. The development of a new correlation consistent Composite Approach (ccCA) is presented, which incorporates the completely renormalized coupled cluster method with singles, doubles and non-iterative triples corrections towards the determination of heats of formations and reaction pathways which contain biradical species.

World's simplest electric train

NASA Astrophysics Data System (ADS)

Criado, C.; Alamo, N.

2016-01-01

We analyze the physics of the "world's simplest electric train." The "train" consists of a AA battery with a strong magnet on each end that moves through a helical coil of copper wire. The motion of the train results from the interaction between the magnetic field created by the current in the wire and the magnetic field of the magnets. We calculate the force of this interaction and the terminal velocity of the train due to eddy currents and friction. Our calculations provide a good illustration of Faraday's and Lenz's laws, as well as of the concepts of the Lorentz force and eddy currents.

The effect of low force chiropractic adjustments for 4 weeks on body surface electromagnetic field.

PubMed

Zhang, John; Snyder, Brian J

2005-01-01

To study the effects of 4 weeks of low-force chiropractic adjustments on body surface electromagnetic fields (EMFs). Thirty-five chiropractic students randomly assigned into control (17 subjects) and experimental groups (28 subjects). A triaxial fluxgate magnetometer was used for EMF detection. The subjects' body surface EMF was determined in the prone position before and after the chiropractic adjustment. A Toftness low-force chiropractic adjustment was applied to the cervical, thoracic, lumbar, and sacral areas as determined by the practitioner. Heart rate variability analysis was recorded once a week to determine autonomic nervous system activity in both the control and experimental groups. The EMF on the subjects' body surface decreased after chiropractic adjustment at the cervical, thoracic, lumbar, and sacral regions in all 6 visits during the 4-week treatment period. The EMF showed a downtrend over the 4-week period after the low-force adjustment. The same changes were not observed in the control group. The chiropractic adjustment group had a slight decrease in heart rate over the 4-week treatment period, and no significant change was observed in the control group. Heart rate variability analysis did not show consistent changes before and after the low-force adjustments during the treatment period. Low-force chiropractic adjustment in the cervical and thoracic areas resulted in a consistent reduction of the body surface EMF after 4 weeks of active treatment. No statistically significant differences were found in the heart rate and heart rate variability in the 4-week study.

Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-03-01

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later Shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modeled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

LIPID11: A Modular Framework for Lipid Simulations using Amber

PubMed Central

Skjevik, Åge A.; Madej, Benjamin D.; Walker, Ross C.; eigen, Knut T

2013-01-01

Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach, and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that Lipid11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field. PMID:22916730

Simplified TiO2 force fields for studies of its interaction with biomolecules

NASA Astrophysics Data System (ADS)

Luan, Binquan; Huynh, Tien; Zhou, Ruhong

2015-06-01

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

Parametric study of an acoustic levitation system. [for thermophysical properties determination of nonmetal materials

NASA Technical Reports Server (NTRS)

Oran, W. A.; Berge, L. H.; Parker, H. W.

1980-01-01

The performance of an acoustic levitation system designed for the containerless processing of materials and consisting of a St. Clair generator and a reflector arranged in a six-axis configuration, is examined in order to define critical parameters of high-temperature systems and limitations of earth-based devices. The fields and forces along the axis of the system are measured and the forces are plotted versus body volume. It is found that for a range of shapes and sizes the levitation force is roughly proportional to body volume until the characteristic 'diameter' reaches a value of about lambda/2. A significant (i.e., factor of four) enhancement in the levitation force is obtained by curving the faces of the driver and reflector. In addition, the behavior of liquid materials in the acoustic fields is studied, and the radius at which the deformation of a levitated drop occurs is calculated.

Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength.

PubMed

Zhang, Chao; Raugei, Simone; Eisenberg, Bob; Carloni, Paolo

2010-07-13

The monovalent ions Na(+) and K(+) and Cl(-) are present in any living organism. The fundamental thermodynamic properties of solutions containing such ions is given as the excess (electro-)chemical potential differences of single ions at finite ionic strength. This quantity is key for many biological processes, including ion permeation in membrane ion channels and DNA-protein interaction. It is given by a chemical contribution, related to the ion activity, and an electric contribution, related to the Galvani potential of the water/air interface. Here we investigate molecular dynamics based predictions of these quantities by using a variety of ion/water force fields commonly used in biological simulation, namely the AMBER (the newly developed), CHARMM, OPLS, Dang95 with TIP3P, and SPC/E water. Comparison with experiment is made with the corresponding values for salts, for which data are available. The calculations based on the newly developed AMBER force field with TIP3P water agrees well with experiment for both KCl and NaCl electrolytes in water solutions, as previously reported. The simulations based on the CHARMM-TIP3P and Dang95-SPC/E force fields agree well for the KCl and NaCl solutions, respectively. The other models are not as accurate. Single cations excess (electro-)chemical potential differences turn out to be similar for all the force fields considered here. In the case of KCl, the calculated electric contribution is consistent with higher level calculations. Instead, such agreement is not found with NaCl. Finally, we found that the calculated activities for single Cl(-) ions turn out to depend clearly on the type of counterion used, with all the force fields investigated. The implications of these findings for biomolecular systems are discussed.

An improved DNA force field for ssDNA interactions with gold nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Xiankai; Huai, Ping; Fan, Chunhai

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thusmore » the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.« less

An improved DNA force field for ssDNA interactions with gold nanoparticles

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-01

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

An improved DNA force field for ssDNA interactions with gold nanoparticles.

PubMed

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-21

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics: effects of the long-range van der Waals treatment on the apparent particle mobility.

PubMed

Miličević, Zoran; Marrink, Siewert J; Smith, Ana-Sunčana; Smith, David M

2014-08-01

Despite considerable effort over the last decade, the interactions between solutes and solvents in the presence of electric fields have not yet been fully understood. A very useful manner in which to study these systems is through the application of molecular dynamics (MD) simulations. However, a number of MD studies have shown a tremendous sensitivity of the migration rate of a hydrophobic solute to the treatment of the long range part of the van der Waals interactions. While the origin of this sensitivity was never explained, the mobility is currently regarded as an artifact of an improper simulation setup. We explain the spread in observed mobilites by performing extensive molecular dynamics simulations using the GROMACS software package on a system consisting of a model hydrophobic object (Lennard-Jones particle) immersed in water both in the presence and absence of a static electric field. We retrieve a unidirectional field-induced mobility of the hydrophobic object when the forces are simply truncated. Careful analysis of the data shows that, only in the specific case of truncated forces, a non-zero van der Waals force acts, on average, on the Lennard-Jones particle. Using the Stokes law we demonstrate that this force yields quantitative agreement with the field-induced mobility found within this setup. In contrast, when the treatment of forces is continuous, no net force is observed. In this manner, we provide a simple explanation for the previously controversial reports.

Combining experimental and simulation data of molecular processes via augmented Markov models.

PubMed

Olsson, Simon; Wu, Hao; Paul, Fabian; Clementi, Cecilia; Noé, Frank

2017-08-01

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

Effect of Pore Topology and Accessibility on Gas Adsorption Capacity in Zeolitic-Imidazolate Frameworks: Bringing Molecular Simulation Close to Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babarao, Ravichandar; Dai, Sheng; Jiang, Deen

2011-01-01

When all cages are assumed to be accessible, popular force fields such as universal force field (UFF) and DREIDING dramatically overpredicted gas adsorption capacity in two widely studied zeolitic-imidazolate frameworks (ZIFs), ZIF-68 and -69. Instead of adjusting the force-field parameters to match the experiments, herein we show that when the pore topology and accessibility are correctly taken into account, simulations with the standard force fields agree very well with the experiments. Careful inspection shows that ZIF-68 and -69 have two one-dimensional channels, which are not interaccessible to gases. The small channel consists of alternating small (HPR) and medium (GME) cages,more » while the large channel comprises the large (KNO) cages. Our analysis indicates that the small channel is not accessible to gases such as CO{sub 2}. So when the cages in the small channel are intentionally blocked in our simulation, the predicted adsorption capacities of CO{sub 2}, CH{sub 4} and N{sub 2} at room temperature from standard force-field parameters for the framework show excellent agreement with the experimental results. In the case of H{sub 2}, all cages are accessible, so simulation results without cage-blocking show excellent agreement with experiment. Due to the promising potential of ZIFs in gas storage and separation, our work here shows that pore topology and accessibility should be carefully examined to understand how gases adsorb in ZIFs.« less

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

PubMed

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.

Estimation of motion fields by non-linear registration for local lung motion analysis in 4D CT image data.

PubMed

Werner, René; Ehrhardt, Jan; Schmidt-Richberg, Alexander; Heiss, Anabell; Handels, Heinz

2010-11-01

Motivated by radiotherapy of lung cancer non- linear registration is applied to estimate 3D motion fields for local lung motion analysis in thoracic 4D CT images. Reliability of analysis results depends on the registration accuracy. Therefore, our study consists of two parts: optimization and evaluation of a non-linear registration scheme for motion field estimation, followed by a registration-based analysis of lung motion patterns. The study is based on 4D CT data of 17 patients. Different distance measures and force terms for thoracic CT registration are implemented and compared: sum of squared differences versus a force term related to Thirion's demons registration; masked versus unmasked force computation. The most accurate approach is applied to local lung motion analysis. Masked Thirion forces outperform the other force terms. The mean target registration error is 1.3 ± 0.2 mm, which is in the order of voxel size. Based on resulting motion fields and inter-patient normalization of inner lung coordinates and breathing depths a non-linear dependency between inner lung position and corresponding strength of motion is identified. The dependency is observed for all patients without or with only small tumors. Quantitative evaluation of the estimated motion fields indicates high spatial registration accuracy. It allows for reliable registration-based local lung motion analysis. The large amount of information encoded in the motion fields makes it possible to draw detailed conclusions, e.g., to identify the dependency of inner lung localization and motion. Our examinations illustrate the potential of registration-based motion analysis.

Tidal dissipation in rotating fluid bodies: the presence of a magnetic field

NASA Astrophysics Data System (ADS)

Lin, Yufeng; Ogilvie, Gordon I.

2018-02-01

We investigate effects of the presence of a magnetic field on tidal dissipation in rotating fluid bodies. We consider a simplified model consisting of a rigid core and a fluid envelope, permeated by a background magnetic field (either a dipolar field or a uniform axial field). The wave-like tidal responses in the fluid layer are in the form of magnetic Coriolis waves, which are restored by both the Coriolis force and the Lorentz force. Energy dissipation occurs through viscous damping and Ohmic damping of these waves. Our numerical results show that the tidal dissipation can be dominated by Ohmic damping even with a weak magnetic field. The presence of a magnetic field smooths out the complicated frequency dependence of the dissipation rate, and broadens the frequency spectrum of the dissipation rate, depending on the strength of the background magnetic field. However, the frequency-averaged dissipation is independent of the strength and structure of the magnetic field, and of the dissipative parameters in the approximation that the wave-like response is driven only by the Coriolis force acting on the non-wavelike tidal flow. Indeed, the frequency-averaged dissipation quantity is in good agreement with previous analytical results in the absence of magnetic fields. Our results suggest that the frequency-averaged tidal dissipation of the wave-like perturbations is insensitive to detailed damping mechanisms and dissipative properties.

Mechanism of travelling-wave transport of particles

NASA Astrophysics Data System (ADS)

Kawamoto, Hiroyuki; Seki, Kyogo; Kuromiya, Naoyuki

2006-03-01

Numerical and experimental investigations have been carried out on transport of particles in an electrostatic travelling field. A three-dimensional hard-sphere model of the distinct element method was developed to simulate the dynamics of particles. Forces applied to particles in the model were the Coulomb force, the dielectrophoresis force on polarized dipole particles in a non-uniform field, the image force, gravity and the air drag. Friction and repulsion between particle-particle and particle-conveyer were included in the model to replace initial conditions after mechanical contacts. Two kinds of experiments were performed to confirm the model. One was the measurement of charge of particles that is indispensable to determine the Coulomb force. Charge distribution was measured from the locus of free-fallen particles in a parallel electrostatic field. The averaged charge of the bulk particle was confirmed by measurement with a Faraday cage. The other experiment was measurements of the differential dynamics of particles on a conveyer consisting of parallel electrodes to which a four-phase travelling electrostatic wave was applied. Calculated results agreed with measurements, and the following characteristics were clarified. (1) The Coulomb force is the predominant force to drive particles compared with the other kinds of forces, (2) the direction of particle transport did not always coincide with that of the travelling wave but changed partially. It depended on the frequency of the travelling wave, the particle diameter and the electric field, (3) although some particles overtook the travelling wave at a very low frequency, the motion of particles was almost synchronized with the wave at the low frequency and (4) the transport of some particles was delayed to the wave at medium frequency; the majority of particles were transported backwards at high frequency and particles were not transported but only vibrated at very high frequency.

On the theory of hysteretic magnetostriction of soft ferrogels

NASA Astrophysics Data System (ADS)

Zubarev, Andrey; Chirikov, Dmitry; Stepanov, Gennady; Borin, Dmitry; Lopez-Lopez, M. T.

2018-05-01

The paper deals with theoretical study of hysteretic magnetostriction of soft ferrogels - composite materials, consisting of the micron-sized magnetizable particles embedded into gel matrices. It is supposed that initially, before application of an external magnetic field, the particles are homogeneously and isotropically distributed in an elastic matrix. The theoretical explanation of the hysteresis phenomena is based on the conception that, under the field action, the particles rearrange into the linear chain-like aggregates. The typical length of the chains is determined by the competition between the force of magnetic attraction of the particles and the force of elastic deformation of the matrix.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

Present-day stress field of Southeast Asia

NASA Astrophysics Data System (ADS)

Tingay, Mark; Morley, Chris; King, Rosalind; Hillis, Richard; Coblentz, David; Hall, Robert

2010-02-01

It is now well established that ridge push forces provide a major control on the plate-scale stress field in most of the Earth's tectonic plates. However, the Sunda plate that comprises much of Southeast Asia is one of only two plates not bounded by a major spreading centre and thus provides an opportunity to evaluate other forces that control the intraplate stress field. The Cenozoic tectonic evolution of the Sunda plate is usually considered to be controlled by escape tectonics associated with India-Eurasia collision. However, the Sunda plate is bounded by a poorly understood and complex range of convergent and strike-slip zones and little is known about the effect of these other plate boundaries on the intraplate stress field in the region. We compile the first extensive stress dataset for Southeast Asia, containing 275 A-D quality (177 A-C) horizontal stress orientations, consisting of 72 stress indicators from earthquakes (located mostly on the periphery of the plate), 202 stress indicators from breakouts and drilling-induced fractures and one hydraulic fracture test within 14 provinces in the plate interior. This data reveals that a variable stress pattern exists throughout Southeast Asia that is largely inconsistent with the Sunda plate's approximately ESE absolute motion direction. The present-day maximum horizontal stress in Thailand, Vietnam and the Malay Basin is predominately north-south, consistent with the radiating stress patterns arising from the eastern Himalayan syntaxis. However, the present-day maximum horizontal stress is primarily oriented NW-SE in Borneo, a direction that may reflect plate-boundary forces or topographic stresses exerted by the central Borneo highlands. Furthermore, the South and Central Sumatra Basins exhibit a NE-SW maximum horizontal stress direction that is perpendicular to the Indo-Australian subduction front. Hence, the plate-scale stress field in Southeast Asia appears to be controlled by a combination of Himalayan orogeny-related deformation, forces related to subduction (primarily trench suction and collision) and intraplate sources of stress such as topography and basin geometry.

Dendrimer Interactions with Lipid Bilayer: Comparison of Force Field and Effect of Implicit vs Explicit Solvation.

PubMed

Kanchi, Subbarao; Gosika, Mounika; Ayappa, K G; Maiti, Prabal K

2018-06-13

The understanding of dendrimer interactions with cell membranes has great importance in drug/gene delivery based therapeutics. Although molecular simulations have been used to understand the nature of dendrimer interactions with lipid membranes, its dependency on available force field parameters is poorly understood. In this study, we have carried out fully atomistic molecular dynamics (MD) simulations of a protonated G3 poly(amido amine) (PAMAM) dendrimer-dimyristoylphosphatidylcholine (DMPC) lipid bilayer complex using three different force fields (FFs) namely, CHARMM, GAFF, and GROMOS in the presence of explicit water to understand the structure of the lipid-dendrimer complex and nature of their interaction. CHARMM and GAFF dendrimers initially in contact with the lipid head groups were found to move away from the lipid bilayer during the course of simulation; however, the dendrimer remained strongly bound to the lipid head groups with the GROMOS FF. Potential of the mean force (PMF) computations of the dendrimer along the bilayer normal showed a repulsive barrier (∼20 kcal/mol) between dendrimer and lipid bilayer in the case of CHARMM and GAFF force fields. In contrast, an attractive interaction (∼40 kcal/mol) is obtained with the GROMOS force field, consistent with experimental observations of membrane binding observed with lower generation G3 PAMAM dendrimers. This difference with the GROMOS dendrimer is attributed to the strong dendrimer-lipid interaction and lowered surface hydration of the dendrimer. Assessing the role of solvent, we find that the CHARMM and GAFF dendrimers strongly bind to the lipid bilayer with an implicit solvent (Generalized Born) model, whereas binding is not observed with explicit water (TIP3P). The opposing nature of dendrimer-membrane interactions in the presence of explicit and implicit solvents demonstrates that hydration effects play an important role in modulating the dendrimer-lipid interaction warranting a case for refinement of the existing dendrimer/lipid force fields.

Experimental Investigation of the Effect of the Driving Voltage of an Electroadhesion Actuator.

PubMed

Koh, Keng Huat; Sreekumar, M; Ponnambalam, S G

2014-06-25

This paper investigates the effect of driving voltage on the attachment force of an electroadhesion actuator, as the existing literature on the saturation of the adhesive force at a higher electric field is incomplete. A new type of electroadhesion actuator using normally available materials, such as aluminum foil, PVC tape and a silicone rubber sheet used for keyboard protection, has been developed with a simple layered structure that is capable of developing adhesive force consistently. The developed actuator is subjected to the experiment for the evaluation of various test surfaces; aluminum, brick, ceramic, concrete and glass. The driving high voltage is varied in steps to determine the characteristics of the output holding force. Results show a quadratic relation between F (adhesion force) and V (driving voltage) within the 2 kV range. After this range, the F - V responses consistently show a saturation trend at high electric fields. Next, the concept of the leakage current that can occur in the dielectric material and the corona discharge through air has been introduced. Results show that the voltage level, which corresponds to the beginning of the supply current, matches well with the beginning of the force saturation. With the confirmation of this hypothesis, a working model for electroadhesion actuation is proposed. Based on the experimental results, it is proposed that such a kind of actuator can be driven within a range of optimum high voltage to remain electrically efficient. This practice is recommended for the future design, development and characterization of electroadhesion actuators for robotic applications.

Experimental Investigation of the Effect of the Driving Voltage of an Electroadhesion Actuator

PubMed Central

Koh, Keng Huat; Sreekumar, M.; Ponnambalam, S. G.

2014-01-01

This paper investigates the effect of driving voltage on the attachment force of an electroadhesion actuator, as the existing literature on the saturation of the adhesive force at a higher electric field is incomplete. A new type of electroadhesion actuator using normally available materials, such as aluminum foil, PVC tape and a silicone rubber sheet used for keyboard protection, has been developed with a simple layered structure that is capable of developing adhesive force consistently. The developed actuator is subjected to the experiment for the evaluation of various test surfaces; aluminum, brick, ceramic, concrete and glass. The driving high voltage is varied in steps to determine the characteristics of the output holding force. Results show a quadratic relation between F (adhesion force) and V (driving voltage) within the 2 kV range. After this range, the F-V responses consistently show a saturation trend at high electric fields. Next, the concept of the leakage current that can occur in the dielectric material and the corona discharge through air has been introduced. Results show that the voltage level, which corresponds to the beginning of the supply current, matches well with the beginning of the force saturation. With the confirmation of this hypothesis, a working model for electroadhesion actuation is proposed. Based on the experimental results, it is proposed that such a kind of actuator can be driven within a range of optimum high voltage to remain electrically efficient. This practice is recommended for the future design, development and characterization of electroadhesion actuators for robotic applications. PMID:28788114

Detonation Characteristics of Mixtures of HMX and Emulsion Explosives

DTIC Science & Technology

1989-04-01

and an aqueous emulsion explo- sive have been determined. The emulsion explosive consisted of amonium - nitrate , sodium- nitrate and water in the...1989 D Cb ID A Final Report C14 Approved for public release; distribution unlimited. AIR FORCE WEAPONS LABORATORY Air Force Systems Command Kirtland...TERMS (ContInue on nvwn Nf ocosury and idsŘ by block number) FIELD GROUP SUB-GROUP Explosives; Ammonium Nitrate ;- 19 01Emulsion Explosives; ( 07 04

Free Energy Landscape of GAGA and UUCG RNA Tetraloops.

PubMed

Bottaro, Sandro; Banáš, Pavel; Šponer, Jiří; Bussi, Giovanni

2016-10-20

We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination with well-tempered metadynamics. A key ingredient is the use of a recently developed metric distance, eRMSD, as a biased collective variable. We find that the native fold of both tetraloops is not the global free energy minimum using the Amberχ OL3 force field. The estimated folding free energies are 30.2 ± 0.5 kJ/mol for UUCG and 7.5 ± 0.6 kJ/mol for GAGA, in striking disagreement with experimental data. We evaluate the viability of all possible one-dimensional backbone force field corrections. We find that disfavoring the gauche + region of α and ζ angles consistently improves the existing force field. The level of accuracy achieved with these corrections, however, cannot be considered sufficient by judging on the basis of available thermodynamic data and solution experiments.

Nano-funnels as electro-osmotic ``tweezers and pistons''

NASA Astrophysics Data System (ADS)

Wang, Yanqian; Panyukov, Sergey; Zhou, Jinsheng; Menard, Laurent D.; Ramsey, J. Michael; Rubinstien, Michael

2014-03-01

An electric field is used to force a DNA molecule into a nano-channel by compensating the free energy penalty that results from the reduced conformational entropy of the confined macromolecule. Narrow nano-channels require high critical electric fields to achieve DNA translocation, leading to short dwell times of DNA in these channels. We demonstrate that nano-funnels integrated with nano-channels reduce the free energy barrier and lower the critical electric field required for DNA translocation. A focused electric field within the funnel increases the electric force on the DNA, compresses the molecule, and increases the osmotic pressure at the nano-channel entrance. This ``electro-osmotic piston'' forces the molecule into the nano-channel at lower electric fields than those observed without the funnel. Appropirately designed nano-funnels can also function as tweezers that allow manipulation of the position of the DNA molecule. The predictions of our theory describing double-stranded DNA behavior in nano-funnel - nano-channel devices are consistent with experimental results. Thanks for the financial support from NSF (DMR-1309892, DMR-1121107, DMR-1122483), NIH (1-P50-HL107168, 1-P01-HL108808-01A1, R01HG02647), NHGRI and CF Foundation.

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

NASA Astrophysics Data System (ADS)

Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan; Ponder, Jay; Head-Gordon, Teresa; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-09-01

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.

Theoretical analysis for the design of the French watt balance experiment force comparator

NASA Astrophysics Data System (ADS)

Pinot, Patrick; Genevès, Gerard; Haddad, Darine; David, Jean; Juncar, Patrick; Lecollinet, Michel; Macé, Stéphane; Villar, François

2007-09-01

This paper presents a preliminary analysis for designing a force comparator to be used in the French watt balance experiment. The first stage of this experiment consists in a static equilibrium, by means of a mechanical beam balance, between a gravitational force (a weight of an artefact having a known mass submitted to the acceleration due to the gravity) and a vertical electromagnetic force acting on a coil driven by a current subject to the magnetic induction field provided by a permanent magnet. The principle of the force comparison in the French experiment is explained. The general design configuration of the force balance using flexure strips as pivots is discussed and theoretical calculation results based on realistic assumptions of the static and dynamic behaviors of the balance are presented.

Theoretical analysis for the design of the French watt balance experiment force comparator.

PubMed

Pinot, Patrick; Genevès, Gerard; Haddad, Darine; David, Jean; Juncar, Patrick; Lecollinet, Michel; Macé, Stéphane; Villar, François

2007-09-01

This paper presents a preliminary analysis for designing a force comparator to be used in the French watt balance experiment. The first stage of this experiment consists in a static equilibrium, by means of a mechanical beam balance, between a gravitational force (a weight of an artefact having a known mass submitted to the acceleration due to the gravity) and a vertical electromagnetic force acting on a coil driven by a current subject to the magnetic induction field provided by a permanent magnet. The principle of the force comparison in the French experiment is explained. The general design configuration of the force balance using flexure strips as pivots is discussed and theoretical calculation results based on realistic assumptions of the static and dynamic behaviors of the balance are presented.

Parametric Transformation Analysis

NASA Technical Reports Server (NTRS)

Gary, G. Allan

2003-01-01

Because twisted coronal features are important proxies for predicting solar eruptive events, and, yet not clearly understood, we present new results to resolve the complex, non-potential magnetic field configurations of active regions. This research uses free-form deformation mathematics to generate the associated coronal magnetic field. We use a parametric representation of the magnetic field lines such that the field lines can be manipulated to match the structure of EUV and SXR coronal loops. The objective is to derive sigmoidal magnetic field solutions which allows the beta greater than 1 regions to be included, aligned and non-aligned electric currents to be calculated, and the Lorentz force to be determined. The advantage of our technique is that the solution is independent of the unknown upper and side boundary conditions, allows non-vanishing magnetic forces, and provides a global magnetic field solution, which contains high- and low-beta regimes and is consistent with all the coronal images of the region. We show that the mathematical description is unique and physical.

A mixed pseudospectral/finite difference method for a thermally driven fluid in a nonuniform gravitational field

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study of the steady, axisymmetric flow in a heated, rotating spherical shell is conducted to model the Atmospheric General Circulation Experiment (AGCE) proposed to run aboard a later shuttle mission. The AGCE will consist of concentric rotating spheres confining a dielectric fluid. By imposing a dielectric field across the fluid a radial body force will be created. The numerical solution technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is based on the incompressible Navier-Stokes equations. In the method a pseudospectral technique is used in the latitudinal direction, and a second-order accurate finite difference scheme discretizes time and radial derivatives. This paper discusses the development and performance of this numerical scheme for the AGCE which has been modelled in the past only by pure FD formulations. In addition, previous models have not investigated the effect of using a dielectric force to simulate terrestrial gravity. The effect of this dielectric force on the flow field is investigated as well as a parameter study of varying rotation rates and boundary temperatures. Among the effects noted are the production of larger velocities and enhanced reversals of radial temperature gradients for a body force generated by the electric field.

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

2012-01-01

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

Magnetic Fluctuation-Driven Intrinsic Flow in a Toroidal Plasma

NASA Astrophysics Data System (ADS)

Brower, D. L.; Ding, W. X.; Lin, L.; Almagri, A. F.; den Hartog, D. J.; Sarff, J. S.

2012-10-01

Magnetic fluctuations have been long observed in various magnetic confinement configurations. These perturbations may arise naturally from plasma instabilities such as tearing modes and energetic particle driven modes, but they can also be externally imposed by error fields or external magnetic coils. It is commonly observed that large MHD modes lead to plasma locking (no rotation) due to torque produced by eddy currents on the wall, and it is predicted that stochastic field induces flow damping where the radial electric field is reduced. Flow generation is of great importance to fusion plasma research, especially low-torque devices like ITER, as it can act to improve performance. Here we describe new measurements in the MST reversed field pinch (RFP) showing that the coherent interaction of magnetic and particle density fluctuations can produce a turbulent fluctuation-induced kinetic force, which acts to drive intrinsic plasma rotation. Key observations include; (1) the average kinetic force resulting from density fluctuations, ˜ 0.5 N/m^3, is comparable to the intrinsic flow acceleration, and (2) between sawtooth crashes, the spatial distribution of the kinetic force is directed to create a sheared parallel flow profile that is consistent with the measured flow profile in direction and amplitude, suggesting the kinetic force is responsible for intrinsic plasma rotation.

ASTROPHYSICS. Atom-interferometry constraints on dark energy.

PubMed

Hamilton, P; Jaffe, M; Haslinger, P; Simmons, Q; Müller, H; Khoury, J

2015-08-21

If dark energy, which drives the accelerated expansion of the universe, consists of a light scalar field, it might be detectable as a "fifth force" between normal-matter objects, in potential conflict with precision tests of gravity. Chameleon fields and other theories with screening mechanisms, however, can evade these tests by suppressing the forces in regions of high density, such as the laboratory. Using a cesium matter-wave interferometer near a spherical mass in an ultrahigh-vacuum chamber, we reduced the screening mechanism by probing the field with individual atoms rather than with bulk matter. We thereby constrained a wide class of dark energy theories, including a range of chameleon and other theories that reproduce the observed cosmic acceleration. Copyright © 2015, American Association for the Advancement of Science.

Measurements of the Casimir-Lifshitz force in fluids: The effect of electrostatic forces and Debye screening

NASA Astrophysics Data System (ADS)

Munday, J. N.; Capasso, Federico; Parsegian, V. Adrian; Bezrukov, Sergey M.

2008-09-01

We present detailed measurements of the Casimir-Lifshitz force between two gold surfaces (a sphere and a plate) immersed in ethanol and study the effect of residual electrostatic forces, which are dominated by static fields within the apparatus and can be reduced with proper shielding. Electrostatic forces are further reduced by Debye screening through the addition of salt ions to the liquid. Additionally, the salt leads to a reduction of the Casimir-Lifshitz force by screening the zero-frequency contribution to the force; however, the effect is small between gold surfaces at the measured separations and within experimental error. An improved calibration procedure is described and compared with previous methods. Finally, the experimental results are compared with Lifshitz’s theory and found to be consistent for the materials used in the experiment.

Application of small-angle neutron scattering to the study of forces between magnetically chained monodisperse ferrofluid emulsion droplets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jain, Dr Nirmesh; Liu, Dr C K; Hawkett, Dr B. S.

2014-01-01

The optical magnetic chaining technique (MCT) developed by Leal-Calderon, Bibette and co-workers in the 1990 s allows precise measurements of force profiles between droplets in monodisperse ferrofluid emulsions. However, the method lacks an in-situ determination of droplet size and therefore requires the combination of separately acquired measurements of droplet chain periodicity versus an applied magnetic field from optical Bragg scattering and droplet diameter inferred from dynamic light scattering (DLS) to recover surface force-distance profiles between the colloidal particles. Compound refractive lens (CRL) focussed small-angle scattering (SANS) MCT should result in more consistent measurements of droplet size (form factor measurements inmore » the absence of field) and droplet chaining period (from structure factor peaks when the magnetic field is applied); and, with access to shorter length scales, extend force measurements to closer approaches than possible by optical measurements. We report on CRL-SANS measurements of monodisperse ferrofluid emulsion droplets aligned in straight chains by an applied field perpendicular to the incident beam direction. Analysis of the scattering from the closely spaced droplets required algorithms that carefully treated resolution and its effect on mean scattering vector magnitudes in order to determine droplet size and chain periods to sufficient accuracy. At lower applied fields scattering patterns indicate structural correlations transverse to the magnetic field direction due to the formation of intermediate structures in early chain growth.« less

Vacillations induced by interference of stationary and traveling planetary waves

NASA Technical Reports Server (NTRS)

Salby, Murry L.; Garcia, Rolando R.

1987-01-01

The interference pattern produced when a traveling planetary wave propagates over a stationary forced wave is explored, examining the interference signature in a variety of diagnostics. The wave field is first restricted to a diatomic spectrum consisting of two components: a single stationary wave and a single monochromatic traveling wave. A simple barotropic normal mode propagating over a simple stationary plane wave is considered, and closed form solutions are obtained. The wave fields are then restricted spatially, providing more realistic structures without sacrificing the advantages of an analytical solution. Both stationary and traveling wave fields are calculated numerically with the linearized Primitive Equations in a realistic basic state. The mean flow reaction to the fluctuating eddy forcing which results from interference is derived. Synoptic geopotential behavior corresponding to the combined wave and mean flow fields is presented, and the synoptic signature in potential vorticity on isentropic surfaces is examined.

Psychophysical testing of visual prosthetic devices: a call to establish a multi-national joint task force

NASA Astrophysics Data System (ADS)

Rizzo, Joseph F., III; Ayton, Lauren N.

2014-04-01

Recent advances in the field of visual prostheses, as showcased in this special feature of Journal of Neural Engineering , have led to promising results from clinical trials of a number of devices. However, as noted by these groups there are many challenges involved in assessing vision of people with profound vision loss. As such, it is important that there is consistency in the methodology and reporting standards for clinical trials of visual prostheses and, indeed, the broader vision restoration research field. Two visual prosthesis research groups, the Boston Retinal Implant Project (BRIP) and Bionic Vision Australia (BVA), have agreed to work cooperatively to establish a multi-national Joint Task Force. The aim of this Task Force will be to develop a consensus statement to guide the methods used to conduct and report psychophysical and clinical results of humans who receive visual prosthetic devices. The overarching goal is to ensure maximum benefit to the implant recipients, not only in the outcomes of the visual prosthesis itself, but also in enabling them to obtain accurate information about this research with ease. The aspiration to develop a Joint Task Force was first promulgated at the inaugural 'The Eye and the Chip' meeting in September 2000. This meeting was established to promote the development of the visual prosthetic field by applying the principles of inclusiveness, openness, and collegiality among the growing body of researchers in this field. These same principles underlie the intent of this Joint Task Force to enhance the quality of psychophysical research within our community. Despite prior efforts, a critical mass of interested parties could not congeal. Renewed interest for developing joint guidelines has developed recently because of a growing awareness of the challenges of obtaining reliable measurements of visual function in patients who are severely visually impaired (in whom testing is inherently noisy), and of the importance of comparing outcomes amongst the many research teams that have entered this field, all of which are using different devices implanted at various locations within the visual system and different methods of assessing efficacy. Researchers at the BRIP and BVA believe that use of common methods for testing and for reporting results would benefit all scientists and clinicians in the field, the agencies that regulate human testing, corporations that are invested in the success of this field, and, most importantly, potential patients. The Task Force will be formed with the intent of developing substantive recommendations to provide a measure of consistency and quality control within the field. The guidelines will offer recommendations for the assessment of the: (1) baseline (pre-implant) visual status of potential patients (including specification of the disease diagnosis and impact on visual functioning) and (2) post-operative visual function. The guidelines will be available to the public, research groups and companies. Any groups that choose to adopt the recommendations would be encouraged to include a formal statement of compliance in their presentations and publications. The Task Force will develop these guidelines with the understanding that the ability to perform experiments in the suggested manner might be limited by the particular engineering design and functionality of different prosthesis devices. It is not the intent of the Task Force to write strict test protocols for all parties to follow, but instead to work cooperatively as a research field to develop guidelines about the types of tests that should be implemented, and how they could be reported in a similar format between groups. The opportunity to participate on the Task Force is open to all researchers, clinicians and other specialists who work in the fields of sensory prostheses (both visual and cochlear implants), molecular therapy, stem cells, optogenetics or other fields that share a similar goal of restoring vision to the blind. Decisions about the guidelines will be made democratically, with precautions to prevent any one group or company from having a more dominant voice than any other. One or more smaller working groups may be established to delve more deeply into specific issues, like the ethics of testing or governance structure, and to develop specific wording for recommendations that would be voted on by the entire Task Force group. Ultimately, the various recommendations, once approved democratically, will serve as the consensus document for the Multi-National Joint Task Force. The full list of members of the Task Force and the rules of governance will be published to promote transparency. The Joint Task force will post its guidelines with all signatories on a dedicated page within the website of the Henry Ford Department of Ophthalmology (Detroit). This site was chosen in recognition of the consistent support that Phillip Hessburg MD and the Board of Directors of the Detroit Institute of Ophthalmology, which has recently merged with the Henry Ford Department of Ophthalmology, have so generously and selflessly provided to our field over the past 14 years. This website will also contain a list of all human psychophysical testing that has been performed in the visual prosthetic field, with designations for those studies that were performed in accordance with the guidelines of the Multi-National Task Force, which will assume responsibility for the accuracy of the material. For those who wish to join this Task Force or have further questions, Dr Rizzo and Dr Ayton can be contacted at the email addresses listed above. The founding members of the Task Force anticipate that this digital resource will prove valuable to anyone who has interest in learning more about the achievements in our field, especially our prospective patients, to whom we dedicate our work.

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

Developing a Novel Eye Tracking Paradigm to Assess Mild Traumatic Brain Injury: A Feasibility Study of the Bethesda Eye and Attention Measure (BEAM)

DTIC Science & Technology

2012-10-01

system, which includes the retina, lateral geniculate nucleus, striate cortex, superior colliculus, parietal cortex, frontal eye fields... body penetrating the brain, forces generated from events such as a blast or explosion, or other forces yet to be defined. Consistent with the...and loss of productivity (47-57%; Tanielian & Jaycox, 2008). With advances in modern medicine and neuroimaging, more Service Members and civilians

Multipolar Ewald methods, 1: theory, accuracy, and performance.

PubMed

Giese, Timothy J; Panteva, Maria T; Chen, Haoyuan; York, Darrin M

2015-02-10

The Ewald, Particle Mesh Ewald (PME), and Fast Fourier–Poisson (FFP) methods are developed for systems composed of spherical multipole moment expansions. A unified set of equations is derived that takes advantage of a spherical tensor gradient operator formalism in both real space and reciprocal space to allow extension to arbitrary multipole order. The implementation of these methods into a novel linear-scaling modified “divide-and-conquer” (mDC) quantum mechanical force field is discussed. The evaluation times and relative force errors are compared between the three methods, as a function of multipole expansion order. Timings and errors are also compared within the context of the quantum mechanical force field, which encounters primary errors related to the quality of reproducing electrostatic forces for a given density matrix and secondary errors resulting from the propagation of the approximate electrostatics into the self-consistent field procedure, which yields a converged, variational, but nonetheless approximate density matrix. Condensed-phase simulations of an mDC water model are performed with the multipolar PME method and compared to an electrostatic cutoff method, which is shown to artificially increase the density of water and heat of vaporization relative to full electrostatic treatment.

A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

NASA Astrophysics Data System (ADS)

Patel, Sandeep; Brooks, Charles L.

2005-01-01

We study the bulk and interfacial properties of methanol via molecular dynamics simulations using a CHARMM (Chemistry at HARvard Molecular Mechanics) fluctuating charge force field. We discuss the parametrization of the electrostatic model as part of the ongoing CHARMM development for polarizable protein force fields. The bulk liquid properties are in agreement with available experimental data and competitive with existing fixed-charge and polarizable force fields. The liquid density and vaporization enthalpy are determined to be 0.809 g/cm3 and 8.9 kcal/mol compared to the experimental values of 0.787 g/cm3 and 8.94 kcal/mol, respectively. The liquid structure as indicated by radial distribution functions is in keeping with the most recent neutron diffraction results; the force field shows a slightly more ordered liquid, necessarily arising from the enhanced condensed phase electrostatics (as evidenced by an induced liquid phase dipole moment of 0.7 D), although the average coordination with two neighboring molecules is consistent with the experimental diffraction study as well as with recent density functional molecular dynamics calculations. The predicted surface tension of 19.66±1.03 dyn/cm is slightly lower than the experimental value of 22.6 dyn/cm, but still competitive with classical force fields. The interface demonstrates the preferential molecular orientation of molecules as observed via nonlinear optical spectroscopic methods. Finally, via canonical molecular dynamics simulations, we assess the model's ability to reproduce the vapor-liquid equilibrium from 298 to 423 K, the simulation data then used to obtain estimates of the model's critical temperature and density. The model predicts a critical temperature of 470.1 K and critical density of 0.312 g/cm3 compared to the experimental values of 512.65 K and 0.279 g/cm3, respectively. The model underestimates the critical temperature by 8% and overestimates the critical density by 10%, and in this sense is roughly equivalent to the underlying fixed-charge CHARMM22 force field.

Ponderomotive Forces in Cosmos

NASA Astrophysics Data System (ADS)

Lundin, R.; Guglielmi, A.

2006-12-01

This review is devoted to ponderomotive forces and their importance for the acceleration of charged particles by electromagnetic waves in space plasmas. Ponderomotive forces constitute time-averaged nonlinear forces acting on a media in the presence of oscillating electromagnetic fields. Ponderomotive forces represent a useful analytical tool to describe plasma acceleration. Oscillating electromagnetic fields are also related with dissipative processes, such as heating of particles. Dissipative processes are, however, left outside these discussions. The focus will be entirely on the (conservative) ponderomotive forces acting in space plasmas. The review consists of seven sections. In Section 1, we explain the rational for using the auxiliary ponderomotive forces instead of the fundamental Lorentz force for the study of particle motions in oscillating fields. In Section 2, we present the Abraham, Miller, Lundin-Hultqvist and Barlow ponderomotive forces, and the Bolotovsky-Serov ponderomotive drift. The hydrodynamic, quasi-hydrodynamic, and ‘`test-particle’' approaches are used for the study of ponderomotive wave-particle interaction. The problems of self-consistency and regularization are discussed in Section 3. The model of static balance of forces (Section 4) exemplifies the interplay between thermal, gravitational and ponderomotive forces, but it also introduces a set of useful definitions, dimensionless parameters, etc. We analyze the Alfvén and ion cyclotron waves in static limit with emphasis on the specific distinction between traveling and standing waves. Particular attention has been given to the impact of traveling Alfvén waves on the steady state anabatic wind that blows over the polar regions (Section~5). We demonstrate the existence of a wave-induced cold anabatic wind. We also show that, at a critical point, the ponderomotive acceleration of the wind is a factor of 3 greater than the thermal acceleration. Section 6 demonstrates various manifestations of ponderomotive forces in the Earth's magnetosphere, for instance the ionospheric plasma acceleration and outflow. The polar wind and the auroral density cavities are considered in relation to results from the Freja and Viking satellites. The high-altitude energization and escape of ions is discussed. The ponderomotive anharmonicity of standing Alfvén waves is analyzed from ground based ULF wave measurements. The complexity of the many challenging problems related with plasma processes near the magnetospheric boundaries is discussed in the light of recent Cluster observations. At the end of Section 6, we consider the application of ponderomotive forces to the diversity of phenomena on the Sun, in the interstellar environment, on newborn stars, pulsars and active galaxies. We emphasize the role of forcing of magnetized plasmas in general and ponderomotive forcing in particular, presenting some simple conceivable scenarios for massive outflow and jets from astrophysical objects.

Large Electric Field–Enhanced–Hardness Effect in a SiO2 Film

PubMed Central

Revilla, Reynier I.; Li, Xiao-Jun; Yang, Yan-Lian; Wang, Chen

2014-01-01

Silicon dioxide films are extensively used in nano and micro–electromechanical systems. Here we studied the influence of an external electric field on the mechanical properties of a SiO2 film by using nanoindentation technique of atomic force microscopy (AFM) and friction force microscopy (FFM). A giant augmentation of the relative elastic modulus was observed by increasing the localized electric field. A slight decrease in friction coefficients was also clearly observed by using FFM with the increase of applied tip voltage. The reduction of the friction coefficients is consistent with the great enhancement of sample hardness by considering the indentation–induced deformation during the friction measurements. PMID:24681517

The electrobrachistochrone

NASA Astrophysics Data System (ADS)

Lipscombe, Trevor C.; Mungan, Carl E.

2018-05-01

The brachistochrone problem consists of finding the track of shortest travel time between given initial and final points for a particle sliding frictionlessly along it under the influence of a given external force field. Solvable variations of the standard example of a uniform gravitational field would be suitable for homework and computer projects by undergraduate physics students studying intermediate mechanics and electromagnetism. An electrobrachistochrone problem is here proposed, in which a charged particle moves along a frictionless track under the influence of its electrostatic force of attraction to an image charge in a grounded conducting plane below the track. The path of least time is found to be a foreshortened cycloid and its properties are investigated analytically and graphically.

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

PubMed

Tian, Ye; Schwieters, Charles D; Opella, Stanley J; Marassi, Francesca M

2017-01-01

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

Sequential vortex hopping in an array of artificial pinning centers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keay, J. C.

2010-02-24

We use low-temperature magnetic force microscopy (MFM) to study the hopping motion of vortices in an array of artificial pinning centers (APCs). The array consists of nanoscale holes etched in a niobium thin film by Ar-ion sputtering through an anodic aluminum-oxide template. Variable-temperature magnetometry shows a transition temperature of 7.1 K and an enhancement of the magnetization up to the third matching field at 5 K. Using MFM with attractive and repulsive tip-vortex interaction, we measure the vortex-pinning strength and investigate the motion of individual vortices in the APC array. The depinning force for individual vortices at low field rangedmore » from 0.7 to 1.2 pN. The motion of individual vortices was found to be reproducible and consistent with movement between adjacent holes in the film. The movements are repeatable but the sequence of hops depends on the scan direction. This asymmetry in the motion indicates nonuniform local pinning, a consequence of array disorder and hole-size variation.« less

Plasma rotation by electric and magnetic fields in a discharge cylinder

NASA Technical Reports Server (NTRS)

Wilhelm, H. E.; Hong, S. H.

1977-01-01

A theoretical model for an electric discharge consisting of a spatially diverging plasma sustained electrically between a small ring cathode and a larger ring anode in a cylindrical chamber with an axial magnetic field is developed to study the rotation of the discharge plasma in the crossed electric and magnetic fields. The associated boundary-value problem for the coupled partial differential equations which describe the electric potential and the plasma velocity fields is solved in closed form. The electric field, current density, and velocity distributions are discussed in terms of the Hartmann number and the Hall coefficient. As a result of Lorentz forces, the plasma rotates with speeds as high as 1 million cm/sec around its axis of symmetry at typical conditions. As an application, it is noted that rotating discharges of this type could be used to develop a high-density plasma-ultracentrifuge driven by j x B forces, in which the lighter (heavier) ion and atom components would be enriched in (off) the center of the discharge cylinder.

Visco-Resistive MHD Modeling Benchmark of Forced Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Beidler, M. T.; Hegna, C. C.; Sovinec, C. R.; Callen, J. D.; Ferraro, N. M.

2016-10-01

The presence of externally-applied 3D magnetic fields can affect important phenomena in tokamaks, including mode locking, disruptions, and edge localized modes. External fields penetrate into the plasma and can lead to forced magnetic reconnection (FMR), and hence magnetic islands, on resonant surfaces if the local plasma rotation relative to the external field is slow. Preliminary visco-resistive MHD simulations of FMR in a slab geometry are consistent with theory. Specifically, linear simulations exhibit proper scaling of the penetrated field with resistivity, viscosity, and flow, and nonlinear simulations exhibit a bifurcation from a flow-screened to a field-penetrated, magnetic island state as the external field is increased, due to the 3D electromagnetic force. These results will be compared to simulations of FMR in a circular cross-section, cylindrical geometry by way of a benchmark between the NIMROD and M3D-C1 extended-MHD codes. Because neither this geometry nor the MHD model has the physics of poloidal flow damping, the theory of will be expanded to include poloidal flow effects. The resulting theory will be tested with linear and nonlinear simulations that vary the resistivity, viscosity, flow, and external field. Supported by OFES DoE Grants DE-FG02-92ER54139, DE-FG02-86ER53218, DE-AC02-09CH11466, and the SciDAC Center for Extended MHD Modeling.

Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other

PubMed Central

Andrews, Casey T.

2013-01-01

Although it is now commonly accepted that the highly crowded conditions encountered inside biological cells have the potential to significantly alter the thermodynamic properties of biomolecules, it is not known to what extent the thermodynamics of fundamental types of interactions such as salt bridges and hydrophobic interactions are strengthened or weakened by high biomolecular concentrations. As one way of addressing this question we have performed a series of all-atom explicit solvent molecular dynamics (MD) simulations to investigate the effect of increasing solute concentration on the behavior of four types of zwitterionic amino acids in aqueous solution. We have simulated systems containing glycine, valine, phenylalanine or asparagine at concentrations of 50, 100, 200 and 300 mg/ml. Each molecular system has been simulated for 1 μs in order to obtain statistically converged estimates of thermodynamic parameters, and each has been conducted with 8 different force fields and water models; the combined simulation time is 128 μs. The density, viscosity, and dielectric increments of the four amino acids calculated from the simulations have been compared to corresponding experimental measurements. While all of the force fields perform well at reproducing the density increments, discrepancies for the viscosity and dielectric increments raise questions both about the accuracy of the simulation force fields and, in certain cases, the experimental data. We also observe large differences between the various force fields' descriptions of the interaction thermodynamics of salt bridges and, surprisingly, these differences also lead to qualitatively different predictions of their dependences on solute concentration. For the aliphatic interactions of valine sidechains, fewer differences are observed between the force fields, but significant differences are again observed for aromatic interactions of phenylalanine sidechains. Taken together, the results highlight the potential power of using explicit-solvent simulation methods to understand behavior in concentrated systems but also hint at potential difficulties in using these methods to obtain consistent views of behavior in intracellular environments. PMID:24409104

Lorentz force on sodium and chlorine ions in a salt water solution flow under a transverse magnetic field

NASA Astrophysics Data System (ADS)

DeLuca, R.

2009-05-01

It is shown that, by applying elementary concepts in electromagnetism and electrochemistry to a system consisting of salt water flowing in a thin rectangular pipe at an average velocity vA under the influence of a transverse magnetic field B0, an electromotive force generator can be conceived. In fact, the Lorentz force acting on the sodium and chlorine ions in a water solution gives rise to a so-called Faraday voltage across the two metal electrodes, positioned at the sides of the pipe. The effect is carried along the following chemical reactions at the electrodes: at the cathode, water is reduced (instead of sodium ions) and hydrogen gas is generated; at the anode, chlorine gas is produced. In college physics teaching, this interdisciplinary subject can be adopted to stress analogies and differences between the Hall voltage in conductors and the Faraday voltage in electrolyte solutions.

Short-Range Action, Focusing, and Saturation of Nuclear Forces in a Gravitational-Electrodynamic Model of GRT

NASA Astrophysics Data System (ADS)

Sukhanova, L. A.; Khlestkov, Yu. A.

2015-12-01

An equation for a massive vector field that explains the short-range action of nuclear forces has been obtained via a consistent solution of the Einstein-Maxwell-Lorentz equations in curved spacetime. The nucleus is identified with the throat, whose radius of curvature is adopted as the radius of the nucleus. In this gravitational model the experimentally observed proportionality of the radius of the nucleus to the cubic root of the mass number is obtained.

Air Force Civil Engineer, Volume 16, Number 2, 2008

DTIC Science & Technology

2008-01-01

HORSE and Prime BEEF work together to put up a legal complex for JTF Guantanamo 11 Building Information Modeling in the Air Force Going beyond CADD 14...construction team. Engineers from the 823rd RED HORSE Squadron, Hurlburt Field, Fla., were responsible for most of the design work. The 474th...BEEF construction team and a RED HORSE design team, we quickly became known as the “Red Bulls.” The advance party — consisting of the first sergeant

Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields.

PubMed

Hassan, Sergio A

2012-08-21

A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response.

Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

NASA Astrophysics Data System (ADS)

Hassan, Sergio A.

2012-08-01

A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response.

Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

PubMed Central

Hassan, Sergio A.

2012-01-01

A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response. PMID:22920098

Generalized Landau Equation for a System with a Self-Consistent Mean Field - Derivation from an N-Particle Liouville Equation

NASA Astrophysics Data System (ADS)

Kandrup, H.

1981-02-01

Assume that the evolution of a system is determined by an N-particle Liouville equation. Suppose, moreover, that the particles which compose the system interact via a long range force like gravity so that the system will be spatially inhomogeneous. In this case, the mean force acting upon a test particle does not vanish, so that one wishes to isolate a self-consistent mean field and distinguish its "systematic" effects from the effects of "fluctuations." This is done here. The time-dependent projection operator formalism of Willis and Picard is used to obtain an exact equation for the time evolution of an appropriately defined one-particle probability density. If one implements the assumption that the "fluctuation" time scale is much shorter than both the relaxation and dynamical time scales, this exact equation can be approximated as a closed Markovian equation. In the limiting case of spatial homogeneity, one recovers precisely the standard Landau equation, which is customarily derived by a stochastic binary-encounter argument. This equation is contrasted with the standard heuristic equation for a mean field theory, as formulated for a Newtonian r-1 gravitational potential in stellar dynamics.

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

PubMed

Havrila, Marek; Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Krepl, Miroslav; Otyepka, Michal; Šponer, Jiří

2015-12-10

We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

The Management Implications of Appil.

ERIC Educational Resources Information Center

Bodey, D. W.

1985-01-01

The Advanced Physics Project for Independent Learning (Appil) consists of 10 units based on three themes, namely, materials, forces and fields, and waves. Discusses the content and aims of the project, its emphasis on student-centered learning, managerial advantages, characteristics of the teacher's role, resource implications, and other topics.…

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

PubMed

Islam, Barira; Stadlbauer, Petr; Gil-Ley, Alejandro; Pérez-Hernández, Guillermo; Haider, Shozeb; Neidle, Stephen; Bussi, Giovanni; Banas, Pavel; Otyepka, Michal; Sponer, Jiri

2017-06-13

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory.

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

PubMed Central

2017-01-01

We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

Consistency of Field-Based Measures of Neuromuscular Control Using Force-Plate Diagnostics in Elite Male Youth Soccer Players.

PubMed

Read, Paul J; Oliver, Jon L; Croix, Mark Ba De Ste; Myer, Gregory D; Lloyd, Rhodri S

2016-12-01

Read, P, Oliver, JL, Croix, MD, Myer, GD, and Lloyd, RS. Consistency of field-based measures of neuromuscular control using force-plate diagnostics in elite male youth soccer players. J Strength Cond Res 30(12): 3304-3311, 2016-Deficits in neuromuscular control during movement patterns such as landing are suggested pathomechanics that underlie sport-related injury. A common mode of assessment is measurement of landing forces during jumping tasks; however, these measures have been used less frequently in male youth soccer players, and reliability data are sparse. The aim of this study was to examine the reliability of a field-based neuromuscular control screening battery using force-plate diagnostics in this cohort. Twenty-six pre-peak height velocity (PHV) and 25 post-PHV elite male youth soccer players completed a drop vertical jump (DVJ), single-leg 75% horizontal hop and stick (75%HOP), and single-leg countermovement jump (SLCMJ). Measures of peak landing vertical ground reaction force (pVGRF), time to stabilization, time to pVGRF, and pVGRF asymmetry were recorded. A test-retest design was used, and reliability statistics included change in mean, intraclass correlation coefficient, and coefficient of variation (CV). No significant differences in mean score were reported for any of the assessed variables between test sessions. In both groups, pVGRF and asymmetry during the 75%HOP and SLCMJ demonstrated largely acceptable reliability (CV ≤ 10%). Greater variability was evident in DVJ pVGRF and all other assessed variables, across the 3 protocols (CV range = 13.8-49.7%). Intraclass correlation coefficient values ranged from small to large and were generally higher in the post-PHV players. The results of this study suggest that pVGRF and asymmetry can be reliably assessed using a 75%HOP and SLCMJ in this cohort. These measures could be used to support a screening battery for elite male youth soccer players and for test-retest comparison.

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

PubMed Central

Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; MacKerell, Alexander D.

2011-01-01

Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick (WC) base pair opening which is not consistent with experiment while analysis of MD simulations show the 2′-hydroxyl moiety to almost exclusively sample the O3′ orientation. Quantum mechanical studies of RNA related model compounds indicate the energy minimum associated with the O3′ orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2′-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3′ orientations of the 2′-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and non-canonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′-hydroxyl moiety and support a model whereby the 2′-hydroxyl can enhance the probability of conformational transitions in RNA. PMID:21469161

Effect of tail plasma sheet conditions on the penetration of the convection electric field in the inner magnetosphere: RCM simulations with self-consistent magnetic field

NASA Astrophysics Data System (ADS)

Gkioulidou, M.; Wang, C.; Lyons, L. R.; Wolf, R.

2009-12-01

Transport of plasma sheet particles into the inner magnetosphere is strongly affected by the penetration of the convection electric field, which is the result of the large-scale magnetosphere ionosphere electromagnetic coupling. This transport, on the other hand, results in plasma heating and magnetic field stretching, which become very significant in the inner plasma sheet (inside 20 RE). We have previously run simulations with the Rice Convection Model (RCM), using the Tsyganenko 96 magnetic field model, to investigate how the earthward penetration of electric field depends on plasma sheet conditions. Outer proton and electron sources at r ~20 RE, are based on 11 years of Geotail data, and realistically represent the mixture of cold and hot plasma sheet population as a function of MLT and interplanetary conditions. We found that shielding of the inner magnetosphere electric field is more efficient for a colder and denser plasma sheet, which is found following northward IMF, than for the hotter and more tenuous plasma sheet found following southward IMF. Our simulation results so far indicate further earthward penetration of plasma sheet particles in response to enhanced convection if the preceding IMF is southward, which leads to weaker electric field shielding. Recently we have integrated the RCM with a magnetic field solver to obtain magnetic fields that are in force balance with given plasma pressures in the equatorial plane. We expect the self-consistent magnetic field to have a pronounced dawn dusk asymmetry due to the asymmetric inner magnetospheric pressure. This should affect the radial distance and MLT of plasma sheet penetration into the inner magnetosphere. We are currently using this force-balanced and self-consistent model with our realistic boundary conditions to evaluate the dependence of the shielding timescale on pre-existing plasma sheet number density and temperature and to more quantitatively determine the correlation between the plasma sheet conditions and spatial distribution of the penetrating particles. Our results are potentially crucial to understanding the contribution of plasma sheet penetration to the development of the storm-time ring current.

Gravitational matter-antimatter asymmetry and four-dimensional Yang-Mills gauge symmetry

NASA Technical Reports Server (NTRS)

Hsu, J. P.

1981-01-01

A formulation of gravity based on the maximum four-dimensional Yang-Mills gauge symmetry is studied. The theory predicts that the gravitational force inside matter (fermions) is different from that inside antimatter. This difference could lead to the cosmic separation of matter and antimatter in the evolution of the universe. Moreover, a new gravitational long-range spin-force between two fermions is predicted, in addition to the usual Newtonian force. The geometrical foundation of such a gravitational theory is the Riemann-Cartan geometry, in which there is a torsion. The results of the theory for weak fields are consistent with previous experiments.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

PubMed Central

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-01-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

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

PubMed Central

Mohamed, Noor Asidah; Bradshaw, Richard T.

2016-01-01

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

Potential theory of radiation

NASA Technical Reports Server (NTRS)

Chiu, Huei-Huang

1989-01-01

A theoretical method is being developed by which the structure of a radiation field can be predicted by a radiation potential theory, similar to a classical potential theory. The introduction of a scalar potential is justified on the grounds that the spectral intensity vector is irrotational. The vector is also solenoidal in the limits of a radiation field in complete radiative equilibrium or in a vacuum. This method provides an exact, elliptic type equation that will upgrade the accuracy and the efficiency of the current CFD programs required for the prediction of radiation and flow fields. A number of interesting results emerge from the present study. First, a steady state radiation field exhibits an optically modulated inverse square law distribution character. Secondly, the unsteady radiation field is structured with two conjugate scalar potentials. Each is governed by a Klein-Gordon equation with a frictional force and a restoring force. This steady potential field structure and the propagation of radiation potentials are consistent with the well known results of classical electromagnetic theory. The extension of the radiation potential theory for spray combustion and hypersonic flow is also recommended.

An oppositely charged insect exclusion screen with gap-free multiple electric fields

NASA Astrophysics Data System (ADS)

Matsuda, Yoshinori; Kakutani, Koji; Nonomura, Teruo; Kimbara, Junji; Kusakari, Shin-ichi; Osamura, Kazumi; Toyoda, Hideyoshi

2012-12-01

An electric field screen was constructed to examine insect attraction mechanisms in multiple electric fields generated inside the screen. The screen consisted of two parallel insulated conductor wires (ICWs) charged with equal but opposite voltages and two separate grounded nets connected to each other and placed on each side of the ICW layer. Insects released inside the fields were charged either positively or negatively as a result of electricity flow from or to the insect, respectively. The force generated between the charged insects and opposite ICW charges was sufficient to capture all insects.

Rigorous derivation of electromagnetic self-force

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gralla, Samuel E.; Harte, Abraham I.; Wald, Robert M.

2009-07-15

During the past century, there has been considerable discussion and analysis of the motion of a point charge in an external electromagnetic field in special relativity, taking into account 'self-force' effects due to the particle's own electromagnetic field. We analyze the issue of 'particle motion' in classical electromagnetism in a rigorous and systematic way by considering a one-parameter family of solutions to the coupled Maxwell and matter equations corresponding to having a body whose charge-current density J{sup a}({lambda}) and stress-energy tensor T{sub ab}({lambda}) scale to zero size in an asymptotically self-similar manner about a worldline {gamma} as {lambda}{yields}0. In thismore » limit, the charge, q, and total mass, m, of the body go to zero, and q/m goes to a well-defined limit. The Maxwell field F{sub ab}({lambda}) is assumed to be the retarded solution associated with J{sup a}({lambda}) plus a homogeneous solution (the 'external field') that varies smoothly with {lambda}. We prove that the worldline {gamma} must be a solution to the Lorentz force equations of motion in the external field F{sub ab}({lambda}=0). We then obtain self-force, dipole forces, and spin force as first-order perturbative corrections to the center-of-mass motion of the body. We believe that this is the first rigorous derivation of the complete first-order correction to Lorentz force motion. We also address the issue of obtaining a self-consistent perturbative equation of motion associated with our perturbative result, and argue that the self-force equations of motion that have previously been written down in conjunction with the 'reduction of order' procedure should provide accurate equations of motion for a sufficiently small charged body with negligible dipole moments and spin. (There is no corresponding justification for the non-reduced-order equations.) We restrict consideration in this paper to classical electrodynamics in flat spacetime, but there should be no difficulty in extending our results to the motion of a charged body in an arbitrary globally hyperbolic curved spacetime.« less

Effect of Position- and Velocity-Dependent Forces on Reaching Movements at Different Speeds

PubMed Central

Summa, Susanna; Casadio, Maura; Sanguineti, Vittorio

2016-01-01

The speed of voluntary movements is determined by the conflicting needs of maximizing accuracy and minimizing mechanical effort. Dynamic perturbations, e.g., force fields, may be used to manipulate movements in order to investigate these mechanisms. Here, we focus on how the presence of position- and velocity-dependent force fields affects the relation between speed and accuracy during hand reaching movements. Participants were instructed to perform reaching movements under visual control in two directions, corresponding to either low or high arm inertia. The subjects were required to maintain four different movement durations (very slow, slow, fast, very fast). The experimental protocol included three phases: (i) familiarization—the robot generated no force; (ii) force field—the robot generated a force; and (iii) after-effect—again, no force. Participants were randomly assigned to four groups, depending on the type of force that was applied during the “force field” phase. The robot was programmed to generate position-dependent forces—with positive (K+) or negative stiffness (K−)—or velocity-dependent forces, with either positive (B+) or negative viscosity (B−). We focused on path curvature, smoothness, and endpoint error; in the latter we distinguished between bias and variability components. Movements in the high-inertia direction are smoother and less curved; smoothness also increases with movement speed. Endpoint bias and variability are greater in, respectively, the high and low inertia directions. A robust dependence on movement speed was only observed in the longitudinal components of both bias and variability. The strongest and more consistent effects of perturbation were observed with negative viscosity (B−), which resulted in increased variability during force field adaptation and in a reduction of the endpoint bias, which was retained in the subsequent after-effect phase. These findings confirm that training with negative viscosity produces lasting effects in movement accuracy at all speeds. PMID:27965559

A level-set method for two-phase flows with moving contact line and insoluble surfactant

NASA Astrophysics Data System (ADS)

Xu, Jian-Jun; Ren, Weiqing

2014-04-01

A level-set method for two-phase flows with moving contact line and insoluble surfactant is presented. The mathematical model consists of the Navier-Stokes equation for the flow field, a convection-diffusion equation for the surfactant concentration, together with the Navier boundary condition and a condition for the dynamic contact angle derived by Ren et al. (2010) [37]. The numerical method is based on the level-set continuum surface force method for two-phase flows with surfactant developed by Xu et al. (2012) [54] with some cautious treatment for the boundary conditions. The numerical method consists of three components: a flow solver for the velocity field, a solver for the surfactant concentration, and a solver for the level-set function. In the flow solver, the surface force is dealt with using the continuum surface force model. The unbalanced Young stress at the moving contact line is incorporated into the Navier boundary condition. A convergence study of the numerical method and a parametric study are presented. The influence of surfactant on the dynamics of the moving contact line is illustrated using examples. The capability of the level-set method to handle complex geometries is demonstrated by simulating a pendant drop detaching from a wall under gravity.

Telephone Equipment Installation and Repair Specialist (AFSC 36254).

ERIC Educational Resources Information Center

Air Univ., Gunter AFS, Ala. Extension Course Inst.

This document contains the four volumes of an Air Force correspondence course in telephone equipment installation and repair. Each volume consists of student learning objectives, information, exercises, and answers to exercises; a volume review exercise is included for each volume. The first volume includes information about career field duties…

Topology Counts: Force Distributions in Circular Spring Networks.

PubMed

Heidemann, Knut M; Sageman-Furnas, Andrew O; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F; Wardetzky, Max

2018-02-09

Filamentous polymer networks govern the mechanical properties of many biological materials. Force distributions within these networks are typically highly inhomogeneous, and, although the importance of force distributions for structural properties is well recognized, they are far from being understood quantitatively. Using a combination of probabilistic and graph-theoretical techniques, we derive force distributions in a model system consisting of ensembles of random linear spring networks on a circle. We show that characteristic quantities, such as the mean and variance of the force supported by individual springs, can be derived explicitly in terms of only two parameters: (i) average connectivity and (ii) number of nodes. Our analysis shows that a classical mean-field approach fails to capture these characteristic quantities correctly. In contrast, we demonstrate that network topology is a crucial determinant of force distributions in an elastic spring network. Our results for 1D linear spring networks readily generalize to arbitrary dimensions.

Implementation of robotic force control with position accommodation

NASA Technical Reports Server (NTRS)

Ryan, Michael J.

1992-01-01

As the need for robotic manipulation in fields such as manufacturing and telerobotics increases, so does the need for effective methods of controlling the interaction forces between the manipulators and their environment. Position Accommodation (PA) is a form of robotic force control where the nominal path of the manipulator is modified in response to forces and torques sensed at the tool-tip of the manipulator. The response is tailored such that the manipulator emulates a mechanical impedance to its environment. PA falls under the category of position-based robotic force control, and may be viewed as a form of Impedance Control. The practical implementations are explored of PA into an 18 degree-of-freedom robotic testbed consisting of two PUMA 560 arms mounted on two 3 DOF positioning platforms. Single and dual-arm architectures for PA are presented along with some experimental results. Characteristics of position-based force control are discussed, along with some of the limitations of PA.

VizieR Online Data Catalog: Protonated oxirane characterization (Puzzarini+, 2014)

NASA Astrophysics Data System (ADS)

Puzzarini, C.; Ali, A.; Biczysko, M.; Barone, V.

2017-04-01

The coupled-cluster (CC) singles and doubles approximation augmented by a perturbative treatment of triple excitations (CCSD(T); Raghavachari et al., 1989, ChPhL, 157, 479) was employed in molecular structure and anharmonic force-field calculations. Harmonic force fields were also computed using the less expensive and less accurate second-order Moller-Plesset perturbation theory (MP2; Moller & Plesset, 1934, PhRv, 46, 618). CCSD(T) and MP2 calculations were carried out in conjunction with the correlation-consistent basis sets, (aug)-cc-p(C)VnZ (n = T, Q) (Dunning, 1989, JChPh, 90, 1007; Kendall et al., 1992, JChPh, 96, 6796; Woon & Dunning, 1995, JChPh, 103, 4572), with the quantum-chemical CFour program package employed throughout. (4 data files).

Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

PubMed Central

Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

2009-01-01

15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

PubMed Central

Liwo, Adam; Khalili, Mey; Czaplewski, Cezary; Kalinowski, Sebastian; Ołdziej, Stanisław; Wachucik, Katarzyna; Scheraga, Harold A.

2011-01-01

We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential-energy function. PMID:17201450

Novel Hamiltonian method for collective dynamics analysis of an intense charged particle beam propagating through a periodic focusing quadrupole lattice a)

NASA Astrophysics Data System (ADS)

Startsev, Edward A.; Davidson, Ronald C.

2011-05-01

Identifying regimes for quiescent propagation of intense beams over long distances has been a major challenge in accelerator research. In particular, the development of systematic theoretical approaches that are able to treat self-consistently the applied oscillating force and the nonlinear self-field force of the beam particles simultaneously has been a major challenge of modern beam physics. In this paper, the recently developed Hamiltonian averaging technique [E. A. Startsev, R. C. Davidson, and M. Dorf, Phys. Rev. ST Accel. Beams 13, 064402 (2010)] which incorporates both the applied periodic focusing force and the self-field force of the beam particles, is generalized to the case of time-dependent beam distributions. The new formulation allows not only a determination of quasi-equilibrium solutions of the non-linear Vlasov-Poison system of equations but also a detailed study of their stability properties. The corrections to the well-known "smooth-focusing" approximation are derived, and the results are applied to a matched beam with thermal equilibrium distribution function. It is shown that the corrections remain small even for moderate values of the vacuum phase advance συ. Nonetheless, because the corrections to the average self-field potential are non-axisymmetric, the stability properties of the different beam quasi-equilibria can change significantly.

Dynamically Consistent Parameterization of Mesoscale Eddies This work aims at parameterization of eddy effects for use in non-eddy-resolving ocean models and focuses on the effect of the stochastic part of the eddy forcing that backscatters and induces eastward jet extension of the western boundary currents and its adjacent recirculation zones.

NASA Astrophysics Data System (ADS)

Berloff, P. S.

2016-12-01

This work aims at developing a framework for dynamically consistent parameterization of mesoscale eddy effects for use in non-eddy-resolving ocean circulation models. The proposed eddy parameterization framework is successfully tested on the classical, wind-driven double-gyre model, which is solved both with explicitly resolved vigorous eddy field and in the non-eddy-resolving configuration with the eddy parameterization replacing the eddy effects. The parameterization focuses on the effect of the stochastic part of the eddy forcing that backscatters and induces eastward jet extension of the western boundary currents and its adjacent recirculation zones. The parameterization locally approximates transient eddy flux divergence by spatially localized and temporally periodic forcing, referred to as the plunger, and focuses on the linear-dynamics flow solution induced by it. The nonlinear self-interaction of this solution, referred to as the footprint, characterizes and quantifies the induced eddy forcing exerted on the large-scale flow. We find that spatial pattern and amplitude of each footprint strongly depend on the underlying large-scale flow, and the corresponding relationships provide the basis for the eddy parameterization and its closure on the large-scale flow properties. Dependencies of the footprints on other important parameters of the problem are also systematically analyzed. The parameterization utilizes the local large-scale flow information, constructs and scales the corresponding footprints, and then sums them up over the gyres to produce the resulting eddy forcing field, which is interactively added to the model as an extra forcing. Thus, the assumed ensemble of plunger solutions can be viewed as a simple model for the cumulative effect of the stochastic eddy forcing. The parameterization framework is implemented in the simplest way, but it provides a systematic strategy for improving the implementation algorithm.

Characteristics of a Strongly-Pulsed Non-Premixed Jet Flame in Cross-flow

NASA Astrophysics Data System (ADS)

Gamba, Mirko; Clemens, Noel T.; Ezekoye, Ofodike A.

2006-11-01

The effects of large-amplitude, high-frequency harmonic forcing of turbulent nonpremixed hydrogen/methane jet flames in cross-flow (JFICF) are investigated experimentally. Flame lengths, penetration lengths, and mixing characteristics are studied using flame luminosity imaging, planar laser Mie scattering visualization and particle image velocimetry. Mean jet Reynolds numbers of 1,600 and 3,250 (peak Re ˜2,500--6,500) with corresponding mean momentum flux ratios, r, of 1.9 and 3.7 (peak r ˜2.6--8.3) are considered. Forcing frequencies of 100 Hz and 300 Hz with amplitudes of ˜60%--300% are investigated. Consistent with previous work, a drastic decrease in flame length and soot emission, an increase in flame penetration and an improved jet fuel/cross-flow air mixing are observed for the larger forcing amplitude cases. Partial pre-mixing induced by near-field reverse flow, near-field vortex/vortex interaction and large-scale stirring, rendered stronger by large forcing amplitudes and frequencies, are thought to play a key role on the observed effects.

Alpha1 LASSO data bundles Lamont, OK

DOE Data Explorer

Gustafson, William Jr; Vogelmann, Andrew; Endo, Satoshi; Toto, Tami; Xiao, Heng; Li, Zhijin; Cheng, Xiaoping; Krishna, Bhargavi (ORCID:000000018828528X)

2016-08-03

A data bundle is a unified package consisting of LASSO LES input and output, observations, evaluation diagnostics, and model skill scores. LES input includes model configuration information and forcing data. LES output includes profile statistics and full domain fields of cloud and environmental variables. Model evaluation data consists of LES output and ARM observations co-registered on the same grid and sampling frequency. Model performance is quantified by skill scores and diagnostics in terms of cloud and environmental variables.

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

PubMed Central

Siwy, Christopher M.

2017-01-01

By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the differences in the conformational ensembles of Aβ10-40 and Aβ1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aβ10-40 conformational ensemble. PMID:28085875

Permanent magnet system to guide superparamagnetic particles

NASA Astrophysics Data System (ADS)

Baun, Olga; Blümler, Peter

2017-10-01

A new concept of using permanent magnet systems for guiding superparamagnetic nano-particles on arbitrary trajectories over a large volume is proposed. The basic idea is to use one magnet system which provides a strong, homogeneous, dipolar magnetic field to magnetize and orient the particles, and a second constantly graded, quadrupolar field, superimposed on the first, to generate a force on the oriented particles. In this configuration the motion of the particles is driven predominantly by the component of the gradient field which is parallel to the direction of the homogeneous field. As a result, particles are guided with constant force and in a single direction over the entire volume. The direction is simply adjusted by varying the angle between quadrupole and dipole. Since a single gradient is impossible due to Gauß' law, the other gradient component of the quadrupole determines the angular deviation of the force. However, the latter can be neglected if the homogeneous field is stronger than the local contribution of the quadrupole field. A possible realization of this idea is a coaxial arrangement of two Halbach cylinders. A dipole to evenly magnetize and orient the particles, and a quadrupole to generate the force. The local force was calculated analytically for this particular geometry and the directional limits were analyzed and discussed. A simple prototype was constructed to demonstrate the principle in two dimensions on several nano-particles of different size, which were moved along a rough square by manual adjustment of the force angle. The observed velocities of superparamagnetic particles in this prototype were always several orders of magnitude higher than the theoretically expected value. This discrepancy is attributed to the observed formation of long particle chains as a result of their polarization by the homogeneous field. The magnetic moment of such a chain is then the combination of that of its constituents, while its hydrodynamic radius stays low. A complete system will consist of another quadrupole (third cylinder) to additionally enable scaling of the gradient/force strength by another rotation. In this configuration the device could then also be used as a simple MRI machine to image the particles between movement intervals. Finally, a concept is proposed by which superparamagnetic particles can be guided in three-dimensional space.

Navy Oceanographer Shuttle Observations, STS 41-G Mission Report

DTIC Science & Technology

1986-03-26

Maracaibo-great internal waves in sunglint/none in high color, no photo- too many on flight deck. Rev#55. Internal waves off Costa Rica . Not a strong...PHYSICAL PAX RIVER PSYCHOLOGICAL EAFB CLAUSTROPHOBIA GEOLOGY FIELD TRIP DENTAL OTHER TRAINING DSO’S FDF REVIEWS DSO PROC T/L REVIEWS SASSE (ETC) BENCH...and Edwards Air Force Base, CA, and a geology field trip in New Mexico. Pax River consisted of aviation physiology, a high altitude chamber run and

Temperature-and field dependent characterization of a twisted stacked-tape cable

NASA Astrophysics Data System (ADS)

Barth, C.; Takayasu, M.; Bagrets, N.; Bayer, C. M.; Weiss, K.-P.; Lange, C.

2015-04-01

The twisted stacked-tape cable (TSTC) is one of the major high temperature superconductor cable concepts combining scalability, ease of fabrication and high current density making it a possible candidate as conductor for large scale magnets. To simulate the boundary conditions of such a magnets as well as the temperature dependence of TSTCs a 1.16 m long sample consisting of 40, 4 mm wide SuperPower REBCO tapes is characterized using the ‘FBI’ (force-field-current) superconductor test facility of the Institute for Technical Physics of the Karlsruhe Institute of Technology. In a first step, the magnetic background field is cycled while measuring the current carrying capabilities to determine the impact of Lorentz forces on the TSTC sample performance. In the first field cycle, the critical current of the TSTC sample is tested up to 12 T. A significant Lorentz force of up to 65.6 kN m-1 at the maximal magnetic background field of 12 T result in a 11.8% irreversible degradation of the current carrying capabilities. The degradation saturates (critical cable current of 5.46 kA at 4.2 K and 12 T background field) and does not increase in following field cycles. In a second step, the sample is characterized at different background fields (4-12 T) and surface temperatures (4.2-37.8 K) utilizing the variable temperature insert of the ‘FBI’ test facility. In a third step, the performance along the length of the sample is determined at 77 K, self-field. A 15% degradation is obtained for the central part of the sample which was within the high field region of the magnet during the in-field measurements.

Self-consistent current sheet structures in the quiet-time magnetotail

NASA Technical Reports Server (NTRS)

Holland, Daniel L.; Chen, James

1993-01-01

The structure of the quiet-time magnetotail is studied using a test particle simulation. Vlasov equilibria are obtained in the regime where v(D) = E(y) c/B(z) is much less than the ion thermal velocity and are self-consistent in that the current and magnetic field satisfy Ampere's law. Force balance between the plasma and magnetic field is satisfied everywhere. The global structure of the current sheet is found to be critically dependent on the source distribution function. The pressure tensor is nondiagonal in the current sheet with anisotropic temperature. A kinetic mechanism is proposed whereby changes in the source distribution results in a thinning of the current sheet.

Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N-Methylacetamide

NASA Technical Reports Server (NTRS)

Gregurick, Susan K.; Chaban, Galina M.; Gerber, R. Benny; Kwak, Dochou (Technical Monitor)

2001-01-01

The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans(sub ct) configuration, including all degrees of freedom. The vibrational states and the spectroscopy are directly computed from this potential surface using the Correlation Corrected Vibrational Self-Consistent Field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low temperature experimental matrix data. Analysis of our calculated spectroscopic results show that: (1) The excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality; (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field; (3) The empirical force field in particular overestimates anharmonic couplings for the amide-2 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions; (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution;and (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide-1 and other internal modes. The implication of this is that the intramolecular energy flow between the amide-1 and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.

Effect of particle velocity fluctuations on the inertia coupling in two-phase flow

NASA Technical Reports Server (NTRS)

Drew, Donald A.

1989-01-01

Consistent forms for the interfacial force, the interfacial pressure, the Reynolds stresses and the particle stress have been derived for the inviscid, irrotational incompressible flow of fluid in a dilute suspension of spheres. The particles are assumed to have a velocity distribution, giving rise to an effective pressure and stress in the particle phase. The velocity fluctuations also contribute in the fluid Reynolds stress and in the (elastic) stress field inside the spheres. The relation of these constitutive equations to the force on an individual sphere is discussed.

Calculation of the radial electric field with RF sheath boundary conditions in divertor geometry

NASA Astrophysics Data System (ADS)

Gui, B.; Xia, T. Y.; Xu, X. Q.; Myra, J. R.; Xiao, X. T.

2018-02-01

The equilibrium electric field that results from an imposed DC bias potential, such as that driven by a radio frequency (RF) sheath, is calculated using a new minimal two-field model in the BOUT++ framework. Biasing, using an RF-modified sheath boundary condition, is applied to an axisymmetric limiter, and a thermal sheath boundary is applied to the divertor plates. The penetration of the bias potential into the plasma is studied with a minimal self-consistent model that includes the physics of vorticity (charge balance), ion polarization currents, force balance with E× B , ion diamagnetic flow (ion pressure gradient) and parallel electron charge loss to the thermal and biased sheaths. It is found that a positive radial electric field forms in the scrape-off layer and it smoothly connects across the separatrix to the force-balanced radial electric field in the closed flux surface region. The results are in qualitative agreement with the experiments. Plasma convection related to the E× B net flow in front of the limiter is also obtained from the calculation.

Development of the Large-Scale Forcing Data to Support MC3E Cloud Modeling Studies

NASA Astrophysics Data System (ADS)

Xie, S.; Zhang, Y.

2011-12-01

The large-scale forcing fields (e.g., vertical velocity and advective tendencies) are required to run single-column and cloud-resolving models (SCMs/CRMs), which are the two key modeling frameworks widely used to link field data to climate model developments. In this study, we use an advanced objective analysis approach to derive the required forcing data from the soundings collected by the Midlatitude Continental Convective Cloud Experiment (MC3E) in support of its cloud modeling studies. MC3E is the latest major field campaign conducted during the period 22 April 2011 to 06 June 2011 in south-central Oklahoma through a joint effort between the DOE ARM program and the NASA Global Precipitation Measurement Program. One of its primary goals is to provide a comprehensive dataset that can be used to describe the large-scale environment of convective cloud systems and evaluate model cumulus parameterizations. The objective analysis used in this study is the constrained variational analysis method. A unique feature of this approach is the use of domain-averaged surface and top-of-the atmosphere (TOA) observations (e.g., precipitation and radiative and turbulent fluxes) as constraints to adjust atmospheric state variables from soundings by the smallest possible amount to conserve column-integrated mass, moisture, and static energy so that the final analysis data is dynamically and thermodynamically consistent. To address potential uncertainties in the surface observations, an ensemble forcing dataset will be developed. Multi-scale forcing will be also created for simulating various scale convective systems. At the meeting, we will provide more details about the forcing development and present some preliminary analysis of the characteristics of the large-scale forcing structures for several selected convective systems observed during MC3E.

The relationship between the instantaneous velocity field and the rate of moment release in the lithosphere

USGS Publications Warehouse

Pollitz, F.F.

2003-01-01

Instantaneous velocity gradients within the continental lithosphere are often related to the tectonic driving forces. This relationship is direct if the forces are secular, as for the case of loading of a locked section of a subduction interface by the downgoing plate. If the forces are static, as for the case of lateral variations in gravitational potential energy, then velocity gradients can be produced only if the lithosphere has, on average, zero strength. The static force model may be related to the long-term velocity field but not the instantaneous velocity field (typically measured geodetically over a period of several years) because over short time intervals the upper lithosphere behaves elastically. In order to describe both the short- and long-term behaviour of an (elastic) lithosphere-(viscoelastic) asthenosphere system in a self-consistent manner, I construct a deformation model termed the expected interseismic velocity (EIV) model. Assuming that the lithosphere is populated with faults that rupture continually, each with a definite mean recurrence time, and that the Earth is well approximated as a linear elastic-viscoelastic coupled system, I derive a simple relationship between the instantaneous velocity field and the average rate of moment release in the lithosphere. Examples with synthetic fault networks demonstrate that velocity gradients in actively deforming regions may to a large extent be the product of compounded viscoelastic relaxation from past earthquakes on hundreds of faults distributed over large ( ≥106 km2) areas.

Vibrational modes in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

1997-03-01

Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

From strings to coils: Rotational dynamics of DNA-linked colloidal chains

NASA Astrophysics Data System (ADS)

Kuei, Steve; Garza, Burke; Biswal, Sibani Lisa

2017-10-01

We investigate the dynamical behavior of deformable filaments experimentally using a tunable model system consisting of linked paramagnetic colloidal particles, where the persistence length lp, the contour length lc, and the strength and frequency of the external driving force are controlled. We find that upon forcing by an external magnetic field, a variety of structural and conformational regimes exist. Depending on the competition of forces and torques on the chain, we see classic rigid rotator behavior, as well as dynamically rich wagging, coiling, and folding behavior. Through a combination of experiments, computational models, and theoretical calculations, we are able to observe, classify, and predict these dynamics as a function of the dimensionless Mason and magnetoelastic numbers.

Preliminary characterization of a one-axis acoustic system. [acoustic levitation for space processing

NASA Technical Reports Server (NTRS)

Oran, W. A.; Reiss, D. A.; Berge, L. H.; Parker, H. W.

1979-01-01

The acoustic fields and levitation forces produced along the axis of a single-axis resonance system were measured. The system consisted of a St. Clair generator and a planar reflector. The levitation force was measured for bodies of various sizes and geometries (i.e., spheres, cylinders, and discs). The force was found to be roughly proportional to the volume of the body until the characteristic body radius reaches approximately 2/k (k = wave number). The acoustic pressures along the axis were modeled using Huygens principle and a method of imaging to approximate multiple reflections. The modeled pressures were found to be in reasonable agreement with those measured with a calibrated microphone.

Magnetic forces and localized resonances in electron transfer through quantum rings.

PubMed

Poniedziałek, M R; Szafran, B

2010-11-24

We study the current flow through semiconductor quantum rings. In high magnetic fields the current is usually injected into the arm of the ring preferred by classical magnetic forces. However, for narrow magnetic field intervals that appear periodically on the magnetic field scale the current is injected into the other arm of the ring. We indicate that the appearance of the anomalous-non-classical-current circulation results from Fano interference involving localized resonant states. The identification of the Fano interference is based on the comparison of the solution of the scattering problem with the results of the stabilization method. The latter employs the bound-state type calculations and allows us to extract both the energy of metastable states localized within the ring and the width of resonances by analysis of the energy spectrum of a finite size system as a function of its length. The Fano resonances involving states of anomalous current circulation become extremely narrow on both the magnetic field and energy scales. This is consistent with the orientation of the Lorentz force that tends to keep the electron within the ring and thus increases the lifetime of the electron localization within the ring. Absence of periodic Fano resonances in electron transfer probability through a quantum ring containing an elastic scatterer is also explained.

SOLDESIGN user's manual copyright

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pillsbury, R.D. Jr.

1991-02-01

SOLDESIGN is a general purpose program for calculating and plotting magnetic fields, Lorentz body forces, resistances and inductances for a system of coaxial uniform current density solenoidal elements. The program was originally written in 1980 and has been evolving ever since. SOLDESIGN can be used with either interactive (terminal) or file input. Output can be to the terminal or to a file. All input is free-field with comma or space separators. SOLDESIGN contains an interactive help feature that allows the user to examine documentation while executing the program. Input to the program consists of a sequence of word commands andmore » numeric data. Initially, the geometry of the elements or coils is defined by specifying either the coordinates of one corner of the coil or the coil centroid, a symmetry parameter to allow certain reflections of the coil (e.g., a split pair), the radial and axial builds, and either the overall current density or the total ampere-turns (NI). A more general quadrilateral element is also available. If inductances or resistances are desired, the number of turns must be specified. Field, force, and inductance calculations also require the number of radial current sheets (or integration points). Work is underway to extend the field, force, and, possibly, inductances to non-coaxial solenoidal elements.« less

The dynamics of copper intercalated molybdenum ditelluride

NASA Astrophysics Data System (ADS)

Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

2016-11-01

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties, and interaction with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations connecting first principle methods and devices. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the energetics, atomic charges, and mechanical properties of (i) layered MoTe2, Mo, and Cu in various phases, (ii) the intercalation of Cu atoms and small clusters within the van der Waals gap of MoTe2, and (iii) bond dissociation curves. The training set consists of an extensive set of first principles calculations computed using density functional theory (DFT). We validate the force field via the prediction of the adhesion of a single layer MoTe2 on a Cu(111) surface and find good agreement with DFT results not used in the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric field via finite temperature molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/Å and that mobility increases with Cu ion concentration.

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

Secondary Structure of Rat and Human Amylin across Force Fields

PubMed Central

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

2015-01-01

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils. PMID:26221949

Secondary structure of rat and human amylin across force fields

DOE PAGES

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

2015-07-29

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

Determination of Coronal Magnetic Fields from Vector Magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1997-01-01

During the course of the present contract we developed an 'evolutionary technique' for the determination of force-free coronal magnetic fields from vector magnetograph observations. The method can successfully generate nonlinear force- free fields (with non-constant-a) that match vector magnetograms. We demonstrated that it is possible to determine coronal magnetic fields from photospheric measurements, and we applied it to vector magnetograms of active regions. We have also studied theoretical models of coronal fields that lead to disruptions. Specifically, we have demonstrated that the determination of force-free fields from exact boundary data is a well-posed mathematical problem, by verifying that the computed coronal field agrees with an analytic force-free field when boundary data for the analytic field are used; demonstrated that it is possible to determine active-region coronal magnetic fields from photospheric measurements, by computing the coronal field above active region 5747 on 20 October 1989, AR6919 on 15 November 1991, and AR7260 on 18 August 1992, from data taken with the Stokes Polarimeter at Mees Solar Observatory, University of Hawaii; started to analyze active region 7201 on 19 June 1992 using measurements made with the Advanced Stokes Polarimeter at NSO/Sac Peak; investigated the effects of imperfections in the photospheric data on the computed coronal magnetic field; documented the coronal field structure of AR5747 and compared it to the morphology of footpoint emission in a flare, showing that the 'high- pressure' H-alpha footpoints are connected by coronal field lines; shown that the variation of magnetic field strength along current-carrying field lines is significantly different from the variation in a potential field, and that the resulting near-constant area of elementary flux tubes is consistent with observations; begun to develop realistic models of coronal fields which can be used to study flare trigger mechanisms; demonstrated that magnetic nonequilibrium can disrupt sheared coronal arcades, and that helmet streamers can disrupt, leading to coronal mass ejections. Our model has significantly extended the realism with which the coronal magnetic field can be inferred from actual observations. In a subsequent contract awarded by NASA, we have continued to apply and improve the evolutionary technique, to study the physical properties of active regions, and to develop theoretical models of magnetic fields.

Vibration and shape control of hinged light structures using electromagnetic forces

NASA Astrophysics Data System (ADS)

Matsuzaki, Yuji; Miyachi, Shigenobu; Sasaki, Toshiyuki

2003-08-01

This paper describes a new electromagnetic device for vibration control of a light-weighted deployable/retractable structure which consists of many small units connected with mechanical hinges. A typical example of such a structure is a solar cell paddle of an artificial satellite which is composed of many thin flexible blankets connected in series. Vibration and shape control of the paddle is not easy, because control force and energy do not transmit well between the blankets which are discretely connected by hinges with each other. The new device consists of a permanent magnet glued along an edge of a blanket and an electric current-conducting coil glued along an adjoining edge of another adjacent blanket. Conduction of the electric current in a magnetic field from the magnet generates an electromagnetic force on the coil. By changing the current in the coil, therefore, we may control the vibration and shape of the blankets. To confirm the effectiveness of the new device, constructing a simple paddle model consisting eight hinge- panels, we have carried out a model experiment of vibration and shape control of the paddle. In addition, a numerical simulation of vibration control of the hinge structure is performed to compare with measured data.

Salt dependence of compression normal forces of quenched polyelectrolyte brushes

NASA Astrophysics Data System (ADS)

Hernandez-Zapata, Ernesto; Tamashiro, Mario N.; Pincus, Philip A.

2001-03-01

We obtained mean-field expressions for the compression normal forces between two identical opposing quenched polyelectrolyte brushes in the presence of monovalent salt. The brush elasticity is modeled using the entropy of ideal Gaussian chains, while the entropy of the microions and the electrostatic contribution to the grand potential is obtained by solving the non-linear Poisson-Boltzmann equation for the system in contact with a salt reservoir. For the polyelectrolyte brush we considered both a uniformly charged slab as well as an inhomogeneous charge profile obtained using a self-consistent field theory. Using the Derjaguin approximation, we related the planar-geometry results to the realistic two-crossed cylinders experimental set up. Theoretical predictions are compared to experimental measurements(Marc Balastre's abstract, APS March 2001 Meeting.) of the salt dependence of the compression normal forces between two quenched polyelectrolyte brushes formed by the adsorption of diblock copolymers poly(tert-butyl styrene)-sodium poly(styrene sulfonate) [PtBs/NaPSS] onto an octadecyltriethoxysilane (OTE) hydrophobically modified mica, as well as onto bare mica.

Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

PubMed

Fenn, Timothy D; Schnieders, Michael J; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S; Brunger, Axel T

2011-04-13

Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints, and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here, we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen-bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. Copyright © 2011 Elsevier Ltd. All rights reserved.

Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration

PubMed Central

Fenn, Timothy D.; Schnieders, Michael J.; Mustyakimov, Marat; Wu, Chuanjie; Langan, Paul; Pande, Vijay S.; Brunger, Axel T.

2011-01-01

Summary Most current crystallographic structure refinements augment the diffraction data with a priori information consisting of bond, angle, dihedral, planarity restraints and atomic repulsion based on the Pauli exclusion principle. Yet, electrostatics and van der Waals attraction are physical forces that provide additional a priori information. Here we assess the inclusion of electrostatics for the force field used for all-atom (including hydrogen) joint neutron/X-ray refinement. Two DNA and a protein crystal structure were refined against joint neutron/X-ray diffraction data sets using force fields without electrostatics or with electrostatics. Hydrogen bond orientation/geometry favors the inclusion of electrostatics. Refinement of Z-DNA with electrostatics leads to a hypothesis for the entropic stabilization of Z-DNA that may partly explain the thermodynamics of converting the B form of DNA to its Z form. Thus, inclusion of electrostatics assists joint neutron/X-ray refinements, especially for placing and orienting hydrogen atoms. PMID:21481775

The forced sound transmission of finite single leaf walls using a variational technique.

PubMed

Brunskog, Jonas

2012-09-01

The single wall is the simplest element of concern in building acoustics, but there still remain some open questions regarding the sound insulation of this simple case. The two main reasons for this are the effects on the excitation and sound radiation of the wall when it has a finite size, and the fact that the wave field in the wall is consisting of two types of waves, namely forced waves due to the exciting acoustic field, and free bending waves due to reflections in the boundary. The aim of the present paper is to derive simple analytical formulas for the forced part of the airborne sound insulation of a single homogeneous wall of finite size, using a variational technique based on the integral-differential equation of the fluid loaded wall. The so derived formulas are valid in the entire audible frequency range. The results are compared with full numerical calculations, measurements and alternative theory, with reasonable agreement.

Analysis of Plasma Detachment through Magnetic Nozzle via Canonical Field Theory

NASA Astrophysics Data System (ADS)

Takagaki, Yu

In this paper, I have investigated the mechanism of plasma detachment through magnetic nozzle via canonical field theory, especially by considering canonical vorticity flux Psisigma contour and dissipative force vector Rsigma. As one of the most recent experimental proofs of plasma detachment, Olsen et al., observed and investigated three key indications of plasma detachment. However, after solving for numerical fits with their experimental data, I found that constant ion flux lines did not actually separate from constant magnetic flux lines. Thus, their first key indication becomes incorrect now. Whereas, my analytical results are consistent with the other two key indications. At the beginning, plasma detached from canonical vorticity flux contours due to non-zero dissipative force and attached on magnetic flux lines instead. However, vector Rsigma [is asymptotically equal to] 0 force makes plasma re-attach on canonical vorticity flux contours around the plume edge region. As the most significant and notable result through my analysis, I confirmed the existence of returning plasma flow around the plume edge region.

Quantum Monte Carlo calculations of neutron matter with chiral three-body forces

DOE PAGES

Tews, I.; Gandolfi, Stefano; Gezerlis, A.; ...

2016-02-02

Chiral effective field theory (EFT) enables a systematic description of low-energy hadronic interactions with controlled theoretical uncertainties. For strongly interacting systems, quantum Monte Carlo (QMC) methods provide some of the most accurate solutions, but they require as input local potentials. We have recently constructed local chiral nucleon-nucleon (NN) interactions up to next-to-next-to-leading order (N 2LO). Chiral EFT naturally predicts consistent many-body forces. In this paper, we consider the leading chiral three-nucleon (3N) interactions in local form. These are included in auxiliary field diffusion Monte Carlo (AFDMC) simulations. We present results for the equation of state of neutron matter and formore » the energies and radii of neutron drops. Specifically, we study the regulator dependence at the Hartree-Fock level and in AFDMC and find that present local regulators lead to less repulsion from 3N forces compared to the usual nonlocal regulators.« less

Classification of singularities in the problem of motion of the Kovalevskaya top in a double force field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryabov, Pavel E; Kharlamov, Mikhail P

2012-02-28

The problem of motion of the Kovalevskaya top in a double force field is investigated (the integrable case of A.G. Reyman and M.A. Semenov-Tian-Shansky without a gyrostatic momentum). It is a completely integrable Hamiltonian system with three degrees of freedom not reducible to a family of systems with two degrees of freedom. The critical set of the integral map is studied. The critical subsystems and bifurcation diagrams are described. The classification of all nondegenerate critical points is given. The set of these points consists of equilibria (nondegenerate singularities of rank 0), of singular periodic motions (nondegenerate singularities of rank 1),more » and also of critical two-frequency motions (nondegenerate singularities of rank 2). Bibliography: 32 titles.« less

Exact Solution for Capillary Bridges Properties by Shooting Method

NASA Astrophysics Data System (ADS)

Qiang-Nian, Li; Jia-Qi, Zhang; Feng-Xi, Zhou

2017-04-01

The investigation of liquid bridge force acting between wet particles has great significance in many fields. In this article, the exact solution of capillary force between two unequal-sized spherical particles is investigated. Firstly, The Young-Laplace equation with moving boundary is converted into a set of ordinary differential equations with two fix point boundary using variable substitution technique, in which the gravity effects have been neglected. The geometry of the liquid bridge between two particles is solved by shooting method. After that, the gorge method is applied to calculate the capillary-bridge force that is consists of contributions from the capillary suction and surface tension. Finally, the effect of various parameters including distance between two spheres, radii of spheres, and contact angles on the capillary force are investigated. It is shown that the presented approach is an efficient and accurate algorithm for capillary force between two particles in complex situations.

The interference effects of non-rotated versus counter-rotated trials in visuomotor adaptation.

PubMed

Hinder, Mark R; Walk, Laura; Woolley, Daniel G; Riek, Stephan; Carson, Richard G

2007-07-01

An isometric torque-production task was used to investigate interference and retention in adaptation to multiple visuomotor environments. Subjects produced isometric flexion-extension and pronation-supination elbow torques to move a cursor to acquire targets as quickly as possible. Adaptation to a 30 degrees counter-clockwise (CCW) rotation (task A), was followed by a period of rest (control), trials with no rotation (task B0), or trials with a 60 degrees clockwise (CW) rotation (task B60). For all groups, retention of task A was assessed 5 h later. With initial training, all groups reduced the angular deviation of cursor paths early in the movements, indicating feedforward adaptation. For the control group, performance at commencement of the retest was significantly better than that at the beginning of the initial learning. For the B0 group, performance in the retest of task A was not dissimilar to that at the start of the initial learning, while for the B60 group retest performance in task A was markedly worse than initially observed. Our results indicate that close juxtaposition of two visuomotor environments precludes improved retest performance in the initial environment. Data for the B60 group, specifically larger angular errors upon retest compared with initial exposures, are consistent with the presence of anterograde interference. Furthermore, full interference occurred even when the visuomotor environment encountered in the second task was not rotated (B0). This latter novel result differs from those obtained for force field learning, where interference does not occur when task B does not impose perturbing forces, i.e., when B consists of a null field (Brashers-Krug et al., Nature 382:252-255, 1996). The results are consistent with recent proposals suggesting different interference mechanisms for visuomotor (kinematic) compared to force field (dynamic) adaptations, and have implications for the use of washout trials when studying interference between multiple visuomotor environments.

The Third General Scientific Assembly of the International Association of Geomagnetism and Aeronomy - Special sessions of auroral processes

NASA Technical Reports Server (NTRS)

Russell, C. T.

1978-01-01

Methods of timing magnetic substorms, the rapid fluctuations of aurorae, electromagnetic and electrostatic instabilities observed on the field lines of aurorae, the auroral microstructure, and the relationship of currents, electric field and particle precipitation to auroral form are discussed. Attention is given to such topics as D-perturbations as an indicator of substorm onset, the role of the magnetotail in substorms, spectral information derived from imaging data on aurorae, terrestrial kilometric radiation, and the importance of the mirror force in self-consistent models of particle fluxes, currents and potentials on auroral field lines.

Thermodynamic and mechanical properties of epoxy resin DGEBF crosslinked with DETDA by molecular dynamics.

PubMed

Tack, Jeremy L; Ford, David M

2008-06-01

Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of diglycidyl ether of bisphenol F (DGEBF) crosslinked with curing agent diethyltoluenediamine (DETDA). This polymer is a commercially important epoxy resin and a candidate for applications in nanocomposites. The calculated properties were density and bulk modulus (at near-ambient pressure and temperature) and glass transition temperature (at near-ambient pressure). The molecular topology, degree of curing, and MD force-field were investigated as variables. The models were created by densely packing pre-constructed oligomers of different composition and connectivity into a periodic simulation box. For high degrees of curing (greater than 90%), the density was found to be insensitive to the molecular topology and precise value of degree of curing. Of the two force-fields that were investigated, cff91 and COMPASS, the latter clearly gave more accurate values for the density as compared to experiment. In fact, the density predicted by COMPASS was within 6% of reported experimental values for the highly crosslinked polymer. The predictions of both force-fields for glass transition temperature were within the range of reported experimental values, with the predictions of cff91 being more consistent with a highly cured resin.

The Origins of the Field Concept in Physics

NASA Astrophysics Data System (ADS)

McMullin, Ernan

The term, ``field,'' made its first appearance in physics as a technical term in the mid-nineteenth century. But the notion of what later came to be called a field had been a long time in gestation. Early discussions of magnetism and of the cause of the ocean tides had long ago suggested the idea of a ``zone of influence'' surrounding certain bodies. Johannes Kepler's mathematical rendering of the orbital motion of Mars encouraged him to formulate what he called ``a true theory of gravity'' involving the notion of attraction. Isaac Newton went on to construct an eminently effective dynamics, with attraction as its primary example of force. Was his a field theory? Historians of science disagree. Much depends on whether a theory consistent with the notion of action at a distance ought qualify as a ``field'' theory. Roger Boscovich and Immanuel Kant later took the Newtonian concept of attraction in new directions. It was left to Michael Faraday to propose the ``physical existence'' of lines of force and to James Clerk Maxwell to add as criterion the presence of energy as the ontological basis for a full-blown ``field theory'' of electromagnetic phenomena.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

PubMed

Yong, Chin W

2016-08-22

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

Familiar trajectories facilitate the interpretation of physical forces when intercepting a moving target.

PubMed

Mijatović, Antonija; La Scaleia, Barbara; Mercuri, Nicola; Lacquaniti, Francesco; Zago, Myrka

2014-12-01

Familiarity with the visual environment affects our expectations about the objects in a scene, aiding in recognition and interaction. Here we tested whether the familiarity with the specific trajectory followed by a moving target facilitates the interpretation of the effects of underlying physical forces. Participants intercepted a target sliding down either an inclined plane or a tautochrone. Gravity accelerated the target by the same amount in both cases, but the inclined plane represented a familiar trajectory whereas the tautochrone was unfamiliar to the participants. In separate sessions, the gravity field was consistent with either natural gravity or artificial reversed gravity. Target motion was occluded from view over the last segment. We found that the responses in the session with unnatural forces were systematically delayed relative to those with natural forces, but only for the inclined plane. The time shift is consistent with a bias for natural gravity, in so far as it reflects an a priori expectation that a target not affected by natural forces will arrive later than one accelerated downwards by gravity. Instead, we did not find any significant time shift with unnatural forces in the case of the tautochrone. We argue that interception of a moving target relies on the integration of the high-level cue of trajectory familiarity with low-level cues related to target kinematics.

A thermostatted kinetic theory model for event-driven pedestrian dynamics

NASA Astrophysics Data System (ADS)

Bianca, Carlo; Mogno, Caterina

2018-06-01

This paper is devoted to the modeling of the pedestrian dynamics by means of the thermostatted kinetic theory. Specifically the microscopic interactions among pedestrians and an external force field are modeled for simulating the evacuation of pedestrians from a metro station. The fundamentals of the stochastic game theory and the thermostatted kinetic theory are coupled for the derivation of a specific mathematical model which depicts the time evolution of the distribution of pedestrians at different exits of a metro station. The perturbation theory is employed in order to establish the stability analysis of the nonequilibrium stationary states in the case of a metro station consisting of two exits. A general sensitivity analysis on the initial conditions, the magnitude of the external force field and the number of exits is presented by means of numerical simulations which, in particular, show how the asymptotic distribution and the convergence time are affected by the presence of an external force field. The results show how, in evacuation conditions, the interaction dynamics among pedestrians can be negligible with respect to the external force. The important role of the thermostat term in allowing the reaching of the nonequilibrium stationary state is stressed out. Research perspectives are underlined at the end of paper, in particular for what concerns the derivation of frameworks that take into account the definition of local external actions and the introduction of the space and velocity dynamics.

Folding and insertion thermodynamics of the transmembrane WALP peptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Bennett, W. F. Drew; Pfaendtner, Jim

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of meanmore » force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.« less

Numerical investigations of two-degree-of-freedom vortex-induced vibration in shear flow

NASA Astrophysics Data System (ADS)

Zhang, Hui; Liu, Mengke; Han, Yang; Li, Jian; Gui, Mingyue; Chen, Zhihua

2017-06-01

Exponential-polar coordinates attached to a moving cylinder are used to deduce the stream function-vorticity equations for two-degree-of-freedom vortex-induced vibration, the initial and boundary conditions, and the distribution of the hydrodynamic force, which consists of the vortex-induced force, inertial force, and viscous damping force. The fluid-structure interactions occurring from the motionless cylinder to the steady vibration are investigated numerically, and the variations of the flow field, pressure, lift/drag, and cylinder displacement are discussed. Both the dominant vortex and the cylinder shift, whose effects are opposite, affect the shear layer along the transverse direction and the secondary vortex along the streamwise direction. However, the effect of the cylinder shift is larger than that of the dominant vortices. Therefore, the former dominates the total effects of the flow field. Moreover, the symmetry of the flow field is broken with the increasing shear rate. With the effect of the background vortex, the upper vortices are strengthened, and the lower vortices are weakened; thus, the shear layer and the secondary vortices induced by the upper shedding vortices are strengthened, while the shear layer and the secondary vortices induced by the lower shedding vortices are weakened. Therefore, the amplitudes of the displacement and drag/lift dominated by the upper vortex are larger than those of the displacement and drag/lift dominated by the lower vortex.

Folding and insertion thermodynamics of the transmembrane WALP peptide

NASA Astrophysics Data System (ADS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-12-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

Low-energy vibrations of the group 10 metal monocarbonyl MCO (M = Ni, Pd, and Pt): rotational spectroscopy and force field analysis.

PubMed

Okabayashi, Toshiaki; Yamamoto, Takuya; Okabayashi, Emi Y; Tanimoto, Mitsutoshi

2011-03-17

The rotational spectra of NiCO and PdCO in the ground and ν(2) excited vibrational states were observed by employing a source-modulated microwave spectrometer. The NiCO and PdCO molecules were generated in a free space cell by the sputtering reaction of nickel and palladium sheets, respectively, lining the inner surface of a stainless steel cathode with a dc glow plasma of CO and Ar. The molecular constants of NiCO and PdCO were determined by least-squares analysis. By force field analysis for the molecular constants of not only NiCO and PdCO but also of PtCO as previously reported, the harmonic force constants were determined for these three group 10 metal monocarbonyls. The vibrational wavenumbers derived for the lower M-C stretching vibrations were in good agreement with those obtained from the IR spectra in noble gas matrices and those predicted by several quantum chemical calculations published in the past. The bending vibrational wavenumbers derived by the force field analysis were also consistent with most quantum chemical calculations previously reported, but showed systematic discrepancies from the matrix IR values by about 40 cm(-1), even after reassignment (ν(2) band → 2ν(2) band) of the matrix IR spectra of PdCO and PtCO.

Effect of particle-particle interactions on the acoustic radiation force in an ultrasonic standing wave

NASA Astrophysics Data System (ADS)

Lipkens, Bart; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.

2015-10-01

Ultrasonic standing waves are widely used for separation applications. In MEMS applications, a half wavelength standing wave field is generated perpendicular to a laminar flow. The acoustic radiation force exerted on the particle drives the particle to the center of the MEMS channel, where concentrated particles are harvested. In macro-scale applications, the ultrasonic standing wave spans multiple wavelengths. Examples of such applications are oil/water emulsion splitting [1], and blood/lipid separation [2]. In macro-scale applications, particles are typically trapped in the standing wave, resulting in clumping or coalescence of particles/droplets. Subsequent gravitational settling results in separation of the secondary phase. An often used expression for the radiation force on a particle is that derived by Gorkov [3]. The assumptions are that the particle size is small relative to the wavelength, and therefore, only monopole and dipole scattering contributions are used to calculate the radiation force. This framework seems satisfactory for MEMS scale applications where each particle is treated separately by the standing wave, and concentrations are typically low. In macro-scale applications, particle concentration is high, and particle clumping or droplet coalescence results in particle sizes not necessarily small relative to the wavelength. Ilinskii et al. developed a framework for calculation of the acoustic radiation force valid for any size particle [4]. However, this model does not take into account particle to particle effects, which can become important as particle concentration increases. It is known that an acoustic radiation force on a particle or a droplet is determined by the local field. An acoustic radiation force expression is developed that includes the effect of particle to particle interaction. The case of two neighboring particles is considered. The approach is based on sound scattering by the particles. The acoustic field at the location of one particle then consists of two components, the incident sound wave and the scattered field generated by the neighboring particle. The radiation force calculation then includes the contributions of these two fields and incorporates the mutual particle influence. In this investigation the droplet/particle influence on each other has been analyzed theoretically by using the method developed by Gorkov and modified by Ilinskii et al.

Effect of particle-particle interactions on the acoustic radiation force in an ultrasonic standing wave

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipkens, Bart, E-mail: blipkens@wne.edu; Ilinskii, Yurii A., E-mail: ilinskii@gmail.com; Zabolotskaya, Evgenia A., E-mail: zheniazabolotskaya@gmail.com

Ultrasonic standing waves are widely used for separation applications. In MEMS applications, a half wavelength standing wave field is generated perpendicular to a laminar flow. The acoustic radiation force exerted on the particle drives the particle to the center of the MEMS channel, where concentrated particles are harvested. In macro-scale applications, the ultrasonic standing wave spans multiple wavelengths. Examples of such applications are oil/water emulsion splitting [1], and blood/lipid separation [2]. In macro-scale applications, particles are typically trapped in the standing wave, resulting in clumping or coalescence of particles/droplets. Subsequent gravitational settling results in separation of the secondary phase. Anmore » often used expression for the radiation force on a particle is that derived by Gorkov [3]. The assumptions are that the particle size is small relative to the wavelength, and therefore, only monopole and dipole scattering contributions are used to calculate the radiation force. This framework seems satisfactory for MEMS scale applications where each particle is treated separately by the standing wave, and concentrations are typically low. In macro-scale applications, particle concentration is high, and particle clumping or droplet coalescence results in particle sizes not necessarily small relative to the wavelength. Ilinskii et al. developed a framework for calculation of the acoustic radiation force valid for any size particle [4]. However, this model does not take into account particle to particle effects, which can become important as particle concentration increases. It is known that an acoustic radiation force on a particle or a droplet is determined by the local field. An acoustic radiation force expression is developed that includes the effect of particle to particle interaction. The case of two neighboring particles is considered. The approach is based on sound scattering by the particles. The acoustic field at the location of one particle then consists of two components, the incident sound wave and the scattered field generated by the neighboring particle. The radiation force calculation then includes the contributions of these two fields and incorporates the mutual particle influence. In this investigation the droplet/particle influence on each other has been analyzed theoretically by using the method developed by Gorkov and modified by Ilinskii et al.« less

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

The Expected but Well-Hidden EMF in the Jumping Wire Experiment and Its Unexpected Role

ERIC Educational Resources Information Center

Donoso, G.; Ladera, C. L.

2015-01-01

As presented in physics textbooks, as well as in a few papers, the typical example of an induced motional electromotive force e[subscript mot] = "Blv" consists of a conductive rod of length "l" frictionlessly sliding with speed v along parallel wires within an orthogonal and constant uniform magnetic field of magnitude…

Electromagnetic Momentum in Magnetic Media and the Abraham-Minkowski Controversy

ERIC Educational Resources Information Center

Jimenez, J. L.; Campos, I.; Lopez-Marino, M. A.

2011-01-01

We explore the consequences of a force density, [image omitted], studied by some authors, for the device designed by Lai (1980 "Am. J. Phys. 48" 658) to analyse which definition of electromagnetic momentum density, either Minkowski's or Abraham's, is consistent with mechanical torques that arise from the change in time of a magnetic field, which…

Alternative to particle dark matter

NASA Astrophysics Data System (ADS)

Khoury, Justin

2015-01-01

We propose an alternative to particle dark matter that borrows ingredients of modified Newtonian dynamics (MOND) while adding new key components. The first new feature is a dark matter fluid, in the form of a scalar field with small equation of state and sound speed. This component is critical in reproducing the success of cold dark matter for the expansion history and the growth of linear perturbations, but does not cluster significantly on nonlinear scales. Instead, the missing mass problem on nonlinear scales is addressed by a modification of the gravitational force law. The force law approximates MOND at large and intermediate accelerations, and therefore reproduces the empirical success of MOND at fitting galactic rotation curves. At ultralow accelerations, the force law reverts to an inverse-square law, albeit with a larger Newton's constant. This latter regime is important in galaxy clusters and is consistent with their observed isothermal profiles, provided the characteristic acceleration scale of MOND is mildly varying with scale or mass, such that it is 12 times higher in clusters than in galaxies. We present an explicit relativistic theory in terms of two scalar fields. The first scalar field is governed by a Dirac-Born-Infeld action and behaves as a dark matter fluid on large scales. The second scalar field also has single-derivative interactions and mediates a fifth force that modifies gravity on nonlinear scales. Both scalars are coupled to matter via an effective metric that depends locally on the fields. The form of this effective metric implies the equality of the two scalar gravitational potentials, which ensures that lensing and dynamical mass estimates agree. Further work is needed in order to make both the acceleration scale of MOND and the fraction at which gravity reverts to an inverse-square law explicitly dynamical quantities, varying with scale or mass.

TPX: Contractor preliminary design review. Volume 3, Design and analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-06-30

Several models have been formed for investigating the maximum electromagnetic loading and magnetic field levels associated with the Tokamak Physics eXperiment (TPX) superconducting Poloidal Field (PF) coils. The analyses have been performed to support the design of the individual fourteen hoop coils forming the PF system. The coils have been sub-divided into three coil systems consisting of the central solenoid (CS), PF5 coils, and the larger radius PF6 and PF7 coils. Various electromagnetic analyses have been performed to determine the electromagnetic loadings that the coils will experience during normal operating conditions, plasma disruptions, and fault conditions. The loadings are presentedmore » as net body forces acting individual coils, spatial variations throughout the coil cross section, and force variations along the path of the conductor due to interactions with the TF coils. Three refined electromagnetic models of the PF coil system that include a turn-by-turn description of the fields and forces during a worst case event are presented in this report. A global model including both the TF and PF system was formed to obtain the force variations along the path of the PF conductors resulting from interactions with the TF currents. In addition to spatial variations, the loadings are further subdivided into time-varying and steady components so that structural fatigue issues can be addressed by designers and analysts. Other electromagnetic design issues such as the impact of the detailed coil designs on field errors are addressed in this report. Coil features that are analyzed include radial transitions via short jogs vs. spiral type windings and the effects of layer-to-layer rotations (i.e clocking) on the field errors.« less

Force adaptation transfers to untrained workspace regions in children: evidence for developing inverse dynamic motor models.

PubMed

Jansen-Osmann, Petra; Richter, Stefanie; Konczak, Jürgen; Kalveram, Karl-Theodor

2002-03-01

When humans perform goal-directed arm movements under the influence of an external damping force, they learn to adapt to these external dynamics. After removal of the external force field, they reveal kinematic aftereffects that are indicative of a neural controller that still compensates the no longer existing force. Such behavior suggests that the adult human nervous system uses a neural representation of inverse arm dynamics to control upper-extremity motion. Central to the notion of an inverse dynamic model (IDM) is that learning generalizes. Consequently, aftereffects should be observable even in untrained workspace regions. Adults have shown such behavior, but the ontogenetic development of this process remains unclear. This study examines the adaptive behavior of children and investigates whether learning a force field in one hemifield of the right arm workspace has an effect on force adaptation in the other hemifield. Thirty children (aged 6-10 years) and ten adults performed 30 degrees elbow flexion movements under two conditions of external damping (negative and null). We found that learning to compensate an external damping force transferred to the opposite hemifield, which indicates that a model of the limb dynamics rather than an association of visited space and experienced force was acquired. Aftereffects were more pronounced in the younger children and readaptation to a null-force condition was prolonged. This finding is consistent with the view that IDMs in children are imprecise neural representations of the actual arm dynamics. It indicates that the acquisition of IDMs is a developmental achievement and that the human motor system is inherently flexible enough to adapt to any novel force within the limits of the organism's biomechanics.

Analysis of mixed-mode crack propagation using the boundary integral method

NASA Technical Reports Server (NTRS)

Mendelson, A.; Ghosn, L. J.

1986-01-01

Crack propagation in a rotating inner raceway of a high speed roller bearing is analyzed using the boundary integral equation method. The method consists of an edge crack in a plate under tension, upon which varying Hertzian stress fields are superimposed. A computer program for the boundary integral equation method was written using quadratic elements to determine the stress and displacement fields for discrete roller positions. Mode I and Mode II stress intensity factors and crack extension forces G sub 00 (energy release rate due to tensile opening mode) and G sub r0 (energy release rate due to shear displacement mode) were computed. These calculations permit determination of that crack growth angle for which the change in the crack extension forces is maximum. The crack driving force was found to be the alternating mixed-mode loading that occurs with each passage of the most heavily loaded roller. The crack is predicted to propagate in a step-like fashion alternating between radial and inclined segments, and this pattern was observed experimentally. The maximum changes DeltaG sub 00 and DeltaG sub r0 of the crack extension forces are found to be good measures of the crack propagation rate and direction.

First-principles simulations of electrostatic interactions between dust grains

NASA Astrophysics Data System (ADS)

Itou, H.; Amano, T.; Hoshino, M.

2014-12-01

We investigated the electrostatic interaction between two identical dust grains of an infinite mass immersed in homogeneous plasma by employing first-principles N-body simulations combined with the Ewald method. We specifically tested the possibility of an attractive force due to overlapping Debye spheres (ODSs), as was suggested by Resendes et al. [Phys. Lett. A 239, 181-186 (1998)]. Our simulation results demonstrate that the electrostatic interaction is repulsive and even stronger than the standard Yukawa potential. We showed that the measured electric field acting on the grain is highly consistent with a model electrostatic potential around a single isolated grain that takes into account a correction due to the orbital motion limited theory. Our result is qualitatively consistent with the counterargument suggested by Markes and Williams [Phys. Lett. A 278, 152-158 (2000)], indicating the absence of the ODS attractive force.

Collisionless distribution function for the relativistic force-free Harris sheet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stark, C. R.; Neukirch, T.

A self-consistent collisionless distribution function for the relativistic analogue of the force-free Harris sheet is presented. This distribution function is the relativistic generalization of the distribution function for the non-relativistic collisionless force-free Harris sheet recently found by Harrison and Neukirch [Phys. Rev. Lett. 102, 135003 (2009)], as it has the same dependence on the particle energy and canonical momenta. We present a detailed calculation which shows that the proposed distribution function generates the required current density profile (and thus magnetic field profile) in a frame of reference in which the electric potential vanishes identically. The connection between the parameters ofmore » the distribution function and the macroscopic parameters such as the current sheet thickness is discussed.« less

Regional model simulation of summer rainfall over the Philippines: Effect of choice of driving fields and ocean flux schemes

NASA Astrophysics Data System (ADS)

Francisco, R. V.; Argete, J.; Giorgi, F.; Pal, J.; Bi, X.; Gutowski, W. J.

2006-09-01

The latest version of the Abdus Salam International Centre for Theoretical Physics (ICTP) regional model RegCM is used to investigate summer monsoon precipitation over the Philippine archipelago and surrounding ocean waters, a region where regional climate models have not been applied before. The sensitivity of simulated precipitation to driving lateral boundary conditions (NCEP and ERA40 reanalyses) and ocean surface flux scheme (BATS and Zeng) is assessed for 5 monsoon seasons. The ability of the RegCM to simulate the spatial patterns and magnitude of monsoon precipitation is demonstrated, both in response to the prominent large scale circulations over the region and to the local forcing by the physiographical features of the Philippine islands. This provides encouraging indications concerning the development of a regional climate modeling system for the Philippine region. On the other hand, the model shows a substantial sensitivity to the analysis fields used for lateral boundary conditions as well as the ocean surface flux schemes. The use of ERA40 lateral boundary fields consistently yields greater precipitation amounts compared to the use of NCEP fields. Similarly, the BATS scheme consistently produces more precipitation compared to the Zeng scheme. As a result, different combinations of lateral boundary fields and surface ocean flux schemes provide a good simulation of precipitation amounts and spatial structure over the region. The response of simulated precipitation to using different forcing analysis fields is of the same order of magnitude as the response to using different surface flux parameterizations in the model. As a result it is difficult to unambiguously establish which of the model configurations is best performing.

Helical structures in a Rosette elephant trunk

NASA Astrophysics Data System (ADS)

Carlqvist, Per; Kristen, Helmuth; Gahm, Gosta F.

1998-04-01

We discuss small-scale, helical, interstellar filaments on the basis of optical observations of an elephant trunk in the Rosette nebula. The trunk studied is composed of a number of sinusoidal or serpentine-like dark filaments, preferentially in the outer part of the trunk, where their wavelength is 7-9 times the trunk radius. The diameters are down to the limit of resolution of 1.0 arcsec, corresponding to 1600 au, and ranging up to about 6400 au. At some positions filament crossings give rise to enhanced extinction. We suggest that the sinusoidal filaments are helices lined up by magnetic fields. We derive average extinctions of 0.5-1.0 mag in the filaments, implying molecular densities of n_H2 ~ 10(4) cm(-3) . From existing data on the Rosette HiI region, we conclude that the surrounding kinetic and dynamic pressure and the background radiation field suffice to balance even the denser filaments and to exert drag forces on the trunk as a whole, consistent with evidence of stretching of the trunk. The helical magnetic structures imply the presence of electric currents along the trunk axis. These currents should form a nearly force-free geometry and are consistent with a model consisting of 4-7 helical cables on the surface of a cylinder and which produce the observed wavelength of the helices. We suggest that the Rosette elephant trunks form an interconnected system of rope-like structures which are relics from filamentary skeletons of magnetic fields in the primordial cloud. Based on observations collected at the Nordic Optical Telescope, La Palma, Spain

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lynch, Vickie E.; Borreguero, Jose M.; Bhowmik, Debsindhu

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) parametersmore » 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.« less

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

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2014-01-01

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

Long-term evolution of the force-free twisted magnetosphere of a magnetar

NASA Astrophysics Data System (ADS)

Akgün, T.; Cerdá-Durán, P.; Miralles, J. A.; Pons, J. A.

2017-12-01

We study the long-term quasi-steady evolution of the force-free magnetosphere of a magnetar coupled to its internal magnetic field. We find that magnetospheric currents can be maintained on long time-scales of the order of thousands of years. Meanwhile, the energy, helicity and twist stored in the magnetosphere all gradually increase over the course of this evolution, until a critical point is reached, beyond which a force-free magnetosphere cannot be constructed. At this point, some large-scale magnetospheric rearrangement, possibly resulting in an outburst or a flare, must occur, releasing a large fraction of the stored energy, helicity and twist. After that, the quasi-steady evolution should continue in a similar manner from the new initial conditions. The time-scale for reaching this critical point depends on the overall magnetic field strength and on the relative fraction of the toroidal field. The energy stored in the force-free magnetosphere is found to be up to ∼30 per cent larger than the corresponding vacuum energy. This implies that for a 1014 G field at the pole, the energy budget available for fast magnetospheric events is of the order of a few 1044 erg. The spin-down rate is estimated to increase by up to ∼60 per cent, since the dipole content in the magnetosphere is enhanced by the currents present there. A rough estimate of the braking index n reveals that it is systematically n < 3 for the most part of the evolution, consistent with actual measurements for pulsars and early estimates for several magnetars.

Fundamental study on the magnetic field control method using multiple HTS coils for Magnetic Drug Delivery System

NASA Astrophysics Data System (ADS)

Hirano, R.; Kim, S. B.; Nakagawa, T.; Tomisaka, Y.; Ueda, H.

2017-07-01

The magnetic drug delivery system (MDDS) is a key technology to reduce the side effects in the medical applications, and the magnetic force control is very important issue in MDDS. In this application, the strength of magnetic field and gradient required to MDDS devices are 54 mT and 5.5 T/m, respectively. We proposed the new magnetic force control system that consists of the multiple racetrack HTS magnets. We can control the magnetic field gradient along the longitudinal direction by the arrangement of the multiple racetrack HTS magnets and operating current of each magnet. When the racetrack HTS magnets were used, the critical current was reduced by the self-magnetic field. Therefore, the shape design of HTS magnet to reduce the magnet field into the surface of HTS tapes was required. Therefore, the electromagnetic analysis based on finite element method (FEM) was carried out to design and optimize the shape of multiple racetrack HTS magnet. We were able to suppress the reduction of critical current by placing the magnetic substance at upper and lower side of the HTS magnets. It was confirmed that obtained maximum values of magnetic field strength and field gradient were 33 mT and 0.18 T/m, respectively.

Evaluation of candidate geomagnetic field models for IGRF-11

NASA Astrophysics Data System (ADS)

Finlay, C. C.; Maus, S.; Beggan, C. D.; Hamoudi, M.; Lowes, F. J.; Olsen, N.; Thébault, E.

2010-10-01

The eleventh generation of the International Geomagnetic Reference Field (IGRF) was agreed in December 2009 by a task force appointed by the International Association of Geomagnetism and Aeronomy (IAGA) Division V Working Group V-MOD. New spherical harmonic main field models for epochs 2005.0 (DGRF-2005) and 2010.0 (IGRF-2010), and predictive linear secular variation for the interval 2010.0-2015.0 (SV-2010-2015) were derived from weighted averages of candidate models submitted by teams led by DTU Space, Denmark (team A); NOAA/NGDC, U.S.A. (team B); BGS, U.K. (team C); IZMIRAN, Russia (team D); EOST, France (team E); IPGP, France (team F); GFZ, Germany (team G) and NASA-GSFC, U.S.A. (team H). Here, we report the evaluations of candidate models carried out by the IGRF-11 task force during October/November 2009 and describe the weightings used to derive the new IGRF-11 model. The evaluations include calculations of root mean square vector field differences between the candidates, comparisons of the power spectra, and degree correlations between the candidates and a mean model. Coefficient by coefficient analysis including determination of weighting factors used in a robust estimation of mean coefficients is also reported. Maps of differences in the vertical field intensity at Earth's surface between the candidates and weighted mean models are presented. Candidates with anomalous aspects are identified and efforts made to pinpoint both troublesome coefficients and geographical regions where large variations between candidates originate. A retrospective analysis of IGRF-10 main field candidates for epoch 2005.0 and predictive secular variation candidates for 2005.0-2010.0 using the new IGRF-11 models as a reference is also reported. The high quality and consistency of main field models derived using vector satellite data is demonstrated; based on internal consistency DGRF-2005 has a formal root mean square vector field error over Earth's surface of 1.0 nT. Difficulties nevertheless remain in accurately forecasting field evolution only five years into the future.

MagnetoSperm: A microrobot that navigates using weak magnetic fields

NASA Astrophysics Data System (ADS)

Khalil, Islam S. M.; Dijkslag, Herman C.; Abelmann, Leon; Misra, Sarthak

2014-06-01

In this work, a propulsion system similar in motion to a sperm-cell is investigated. This system consists of a structure resembling a sperm-cell with a magnetic head and a flexible tail of 42 μm and 280 μm in length, respectively. The thickness, length, and width of this structure are 5.2 μm, 322 μm, and 42 μm, respectively. The magnetic head includes a 200 nm-thick cobalt-nickel layer. The cobalt-nickel layer provides a dipole moment and allows the flexible structure to align along oscillating weak (less than 5 mT) magnetic field lines, and hence generates a propulsion thrust force that overcomes the drag force. The frequency response of this system shows that the propulsion mechanism allows for swimming at an average speed of 158 ± 32 μm/s at alternating weak magnetic field of 45 Hz. In addition, we experimentally demonstrate controlled steering of the flexible structure towards reference positions.

Magnetic field experiment on the SUNSAT satellite

NASA Astrophysics Data System (ADS)

Kotzé, P. B.; Langenhoven, B.; Risbo, T.

2002-03-01

On Tuesday 23 February 1999, at 10:29 UTC, SUNSAT was launched into an 857×655 km, 96.47° polar orbit on a Boeing-Delta II rocket from Vandenberg Air Force Base in California, USA. Both SUNSAT and Ørsted were NASA-sponsored secondary payloads accompanying the USA Air Force Argos satellite. In the process it became South Africa's (and Africa's) first satellite in space. Although sponsored by several private industrial organisations, it is essentially a student project with more than 96 graduate students in the Department of Electronic and Electrical Engineering at the University of Stellenbosch providing the majority of SUNSAT's engineering development and operation since 1992. This paper reports on the magnetic field experiment on board the Sunsat satellite, consisting of two fluxgate magnetometers, called Orimag and Scimag, both built and calibrated by the Hermanus Magnetic Observatory. Orimag is mainly used for orientation control purposes on SUNSAT, while Scimag, mounted on a boom of 2.2 m is designed to perform geomagnetic field observations, employing standard navigation fluxgate technology.

Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A

PubMed Central

Davis, Joseph E.; Patel, Sandeep

2009-01-01

Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modelled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, headgroup orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation, since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties. PMID:19526999

A Simulation Model for Drift Resistive Ballooning Turbulence Examining the Influence of Self-consistent Zonal Flows

NASA Astrophysics Data System (ADS)

Cohen, Bruce; Umansky, Maxim; Joseph, Ilon

2015-11-01

Progress is reported on including self-consistent zonal flows in simulations of drift-resistive ballooning turbulence using the BOUT + + framework. Previous published work addressed the simulation of L-mode edge turbulence in realistic single-null tokamak geometry using the BOUT three-dimensional fluid code that solves Braginskii-based fluid equations. The effects of imposed sheared ExB poloidal rotation were included, with a static radial electric field fitted to experimental data. In new work our goal is to include the self-consistent effects on the radial electric field driven by the microturbulence, which contributes to the sheared ExB poloidal rotation (zonal flow generation). We describe a model for including self-consistent zonal flows and an algorithm for maintaining underlying plasma profiles to enable the simulation of steady-state turbulence. We examine the role of Braginskii viscous forces in providing necessary dissipation when including axisymmetric perturbations. We also report on some of the numerical difficulties associated with including the axisymmetric component of the fluctuating fields. This work was performed under the auspices of the U.S. Department of Energy under contract DE-AC52-07NA27344 at the Lawrence Livermore National Laboratory (LLNL-ABS-674950).

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

PubMed Central

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

2012-01-01

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

Alongshore wind forcing of coastal sea level as a function of frequency

USGS Publications Warehouse

Ryan, H.F.; Noble, M.A.

2006-01-01

The amplitude of the frequency response function between coastal alongshore wind stress and adjusted sea level anomalies along the west coast of the United States increases linearly as a function of the logarithm (log10) of the period for time scales up to at least 60, and possibly 100, days. The amplitude of the frequency response function increases even more rapidly at longer periods out to at least 5 yr. At the shortest periods, the amplitude of the frequency response function is small because sea level is forced only by the local component of the wind field. The regional wind field, which controls the wind-forced response in sea level for periods between 20 and 100 days, not only has much broader spatial scales than the local wind, but also propagates along the coast in the same direction as continental shelf waves. Hence, it has a stronger coupling to and an increased frequency response for sea level. At periods of a year or more, observed coastal sea level fluctuations are not only forced by the regional winds, but also by joint correlations among the larger-scale climatic patterns associated with El Nin??o. Therefore, the amplitude of the frequency response function is large, despite the fact that the energy in the coastal wind field is relatively small. These data show that the coastal sea level response to wind stress forcing along the west coast of the United States changes in a consistent and predictable pattern over a very broad range of frequencies with time scales from a few days to several years.

Fabrication and characterization of artificial hair cell sensor based on MWCNT-PDMS composite

NASA Astrophysics Data System (ADS)

Kim, Chi Yeon; Lee, Hyun Sup; Cho, Yo Han; Joh, Cheeyoung; Choi, Pyung; Park, Seong Jin

2011-06-01

The aim of this work is to design and fabricate a flow sensor using an artificial hair cell (AHC) inspired by biological hair cells of fish. The sensor consists of a single cilium structure with high aspect ratio and a mechanoreceptor using force sensitive resistor (FSR). The cilium structure is designed for capturing a drag force with direction due to flow field around the sensor and the mechanoreceptor is designed for sensing the drag force with direction from the cilium structure and converting it into an electric signal. The mechanoreceptor has a symmetric four electrodes to sense the drag force and its direction. To fabricate the single cilium structure with high aspect ratio, we have proposed a new design concept using a separated micro mold system (SMS) fabricated by the LIGA process. For a successful replication of the cilium structure, we used the hot embossing process with the help of a double-sided mold system. We used a composite of multiwall carbon nanotube and polydimethylsiloxane (MWCNT-PDMS). The performance of the mechanoreceptors was measured by a computer-controlled nanoindenter. We carried out several experiments with the sensor in the different flow rate and direction using the experimental test apparatus. To calibrate the sensor and calculate the velocity with direction based the signal from the sensor, we analyzed the coupled phenomena between flow field and the cilium structure to calculate the deflection of the cilium structure and the drag force applying to the cilium structure due to the flow field around sensor.

Generalization of Dynamics Learning Across Changes in Movement Amplitude

PubMed Central

Mattar, Andrew A. G.

2010-01-01

Studies on generalization show the nature of how learning is encoded in the brain. Previous studies have shown rather limited generalization of dynamics learning across changes in movement direction, a finding that is consistent with the idea that learning is primarily local. In contrast, studies show a broader pattern of generalization across changes in movement amplitude, suggesting a more general form of learning. To understand this difference, we performed an experiment in which subjects held a robotic manipulandum and made movements to targets along the body midline. Subjects were trained in a velocity-dependent force field while moving to a 15 cm target. After training, subjects were tested for generalization using movements to a 30 cm target. We used force channels in conjunction with movements to the 30 cm target to assess the extent of generalization. Force channels restricted lateral movements and allowed us to measure force production during generalization. We compared actual lateral forces to the forces expected if dynamics learning generalized fully. We found that, during the test for generalization, subjects produced reliably less force than expected. Force production was appropriate for the portion of the transfer movement in which velocities corresponded to those experienced with the 15 cm target. Subjects failed to produce the expected forces when velocities exceeded those experienced in the training task. This suggests that dynamics learning generalizes little beyond the range of one's experience. Consistent with this result, subjects who trained on the 30 cm target showed full generalization to the 15 cm target. We performed two additional experiments that show that interleaved trials to the 30 cm target during training on the 15 cm target can resolve the difference between the current results and those reported previously. PMID:20463200

Fibrous mini-collagens in hydra nematocysts.

PubMed

Holstein, T W; Benoit, M; Herder, G V; David, C N; Wanner, G; Gaub, H E

1994-07-15

Nematocysts (cnidocysts) are exocytotic organelles found in all cnidarians. Here, atomic force microscopy and field emission scanning electron microscopy reveal the structure of the nematocyst capsule wall. The outer wall consists of globular proteins of unknown function. The inner wall consists of bundles of collagen-like fibrils having a spacing of 50 to 100 nanometers and cross-striations at intervals of 32 nanometers. The fibrils consist of polymers of "mini-collagens," which are abundant in the nematocysts of Hydra. The distinct pattern of mini-collagen fibers in the inner wall can provide the tensile strength necessary to withstand the high osmotic pressure (15 megapascals) in the capsules.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

PubMed Central

Vanommeslaeghe, K.

2014-01-01

Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274

Assessing Strain Mapping by Electron Backscatter Diffraction and Confocal Raman Microscopy Using Wedge-indented Si

PubMed Central

Friedman, Lawrence H.; Vaudin, Mark D.; Stranick, Stephan J.; Stan, Gheorghe; Gerbig, Yvonne B.; Osborn, William; Cook, Robert F.

2016-01-01

The accuracy of electron backscatter diffraction (EBSD) and confocal Raman microscopy (CRM) for small-scale strain mapping are assessed using the multi-axial strain field surrounding a wedge indentation in Si as a test vehicle. The strain field is modeled using finite element analysis (FEA) that is adapted to the near-indentation surface profile measured by atomic force microscopy (AFM). The assessment consists of (1) direct experimental comparisons of strain and deformation and (2) comparisons in which the modeled strain field is used as an intermediate step. Direct experimental methods (1) consist of comparisons of surface elevation and gradient measured by AFM and EBSD and of Raman shifts measured and predicted by CRM and EBSD, respectively. Comparisons that utilize the combined FEA-AFM model (2) consist of predictions of distortion, strain, and rotation for comparison with EBSD measurements and predictions of Raman shift for comparison with CRM measurements. For both EBSD and CRM, convolution of measurements in depth-varying strain fields is considered. The interconnected comparisons suggest that EBSD was able to provide an accurate assessment of the wedge indentation deformation field to within the precision of the measurements, approximately 2 × 10−4 in strain. CRM was similarly precise, but was limited in accuracy to several times this value. PMID:26939030

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

PubMed

Vanommeslaeghe, K; MacKerell, A D

2015-05-01

Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1μs on proteins, DNA, lipids and carbohydrates. Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled "Recent developments of molecular dynamics". Copyright © 2014 Elsevier B.V. All rights reserved.

Non-invasive measurement of instantaneous forces during aquatic locomotion: a case study of the bluegill sunfish pectoral fin.

PubMed

Peng, Jifeng; Dabiri, John O; Madden, Peter G; Lauder, George V

2007-02-01

Swimming and flying animals generate unsteady locomotive forces by delivering net momentum into the fluid wake. Hence, swimming and flying forces can be quantified by measuring the momentum of animal wakes. A recently developed model provides an approach to empirically deduce swimming and flying forces based on the measurement of velocity and vortex added-mass in the animal wake. The model is contingent on the identification of the vortex boundary in the wake. This paper demonstrates the application of that method to a case study quantifying the instantaneous locomotive forces generated by the pectoral fins of the bluegill sunfish (Lepomis macrochirus Rafinesque), measured using digital particle image velocimetry (DPIV). The finite-time Lyapunov exponent (FTLE) field calculated from the DPIV data was used to determine the wake vortex boundary, according to recently developed fluid dynamics theory. Momentum of the vortex wake and its added-mass were determined and the corresponding instantaneous locomotive forces were quantified at discrete time points during the fin stroke. The instantaneous forces estimated in this study agree in magnitude with the time-averaged forces quantified for the pectoral fin of the same species swimming in similar conditions and are consistent with the observed global motion of the animals. A key result of this study is its suggestion that the dynamical effect of the vortex wake on locomotion is to replace the real animal fin with an ;effective appendage', whose geometry is dictated by the FTLE field and whose interaction with the surrounding fluid is wholly dictated by inviscid concepts from potential flow theory. Benefits and limitations of this new framework for non-invasive instantaneous force measurement are discussed, and its application to comparative biomechanics and engineering studies is suggested.

Control of the electromagnetic drag using fluctuating light fields

NASA Astrophysics Data System (ADS)

Pastor, Víctor J. López; Marqués, Manuel I.

2018-05-01

An expression for the electromagnetic drag force experienced by an electric dipole in a light field consisting of a monochromatic plane wave with polarization and phase randomly fluctuating is obtained. The expression explicitly considers the transformations of the field and frequency due to the Doppler shift and the change of the polarizability response of the electric dipole. The conditions to be fulfilled by the polarizability of the dipole in order to obtain a positive, a null, and a negative drag coefficient are analytically determined and checked against numerical simulations for the dynamics of a silver nanoparticle. The theoretically predicted diffusive, superdiffusive, and exponentially accelerated dynamical regimes are numerically confirmed.

Design and analysis of a field modulated magnetic screw for artificial heart

NASA Astrophysics Data System (ADS)

Ling, Zhijian; Ji, Jinghua; Wang, Fangqun; Bian, Fangfang

2017-05-01

This paper proposes a new electromechanical energy conversion system, called Field Modulated Magnetic Screw (FMMS) as a high force density linear actuator for artificial heart. This device is based on the concept of magnetic screw and linear magnetic gear. The proposed FMMS consists of three parts with the outer and inner carrying the radially magnetized helically permanent-magnet (PM), and the intermediate having a set of helically ferromagnetic pole pieces, which modulate the magnetic fields produced by the PMs. The configuration of the newly designed FMMS is presented and its electromagnetic performances are analyzed by using the finite-element analysis, verifying the advantages of the proposed structure.

Effect of head pitch and roll orientations on magnetically induced vertigo.

PubMed

Mian, Omar S; Li, Yan; Antunes, Andre; Glover, Paul M; Day, Brian L

2016-02-15

Lying supine in a strong magnetic field, such as in magnetic resonance imaging scanners, can induce a perception of whole-body rotation. The leading hypothesis to explain this invokes a Lorentz force mechanism acting on vestibular endolymph that acts to stimulate semicircular canals. The hypothesis predicts that the perception of whole-body rotation will depend on head orientation in the field. Results showed that the direction and magnitude of apparent whole-body rotation while stationary in a 7 T magnetic field is influenced by head orientation. The data are compatible with the Lorentz force hypothesis of magnetic vestibular stimulation and furthermore demonstrate the operation of a spatial transformation process from head-referenced vestibular signals to Earth-referenced body motion. High strength static magnetic fields are known to induce vertigo, believed to be via stimulation of the vestibular system. The leading hypothesis (Lorentz forces) predicts that the induced vertigo should depend on the orientation of the magnetic field relative to the head. In this study we examined the effect of static head pitch (-80 to +40 deg; 12 participants) and roll (-40 to +40 deg; 11 participants) on qualitative and quantitative aspects of vertigo experienced in the dark by healthy humans when exposed to the static uniform magnetic field inside a 7 T MRI scanner. Three participants were additionally examined at 180 deg pitch and roll orientations. The effect of roll orientation on horizontal and vertical nystagmus was also measured and was found to affect only the vertical component. Vertigo was most discomforting when head pitch was around 60 deg extension and was mildest when it was around 20 deg flexion. Quantitative analysis of vertigo focused on the induced perception of horizontal-plane rotation reported online with the aid of hand-held switches. Head orientation had effects on both the magnitude and the direction of this perceived rotation. The data suggest sinusoidal relationships between head orientation and perception with spatial periods of 180 deg for pitch and 360 deg for roll, which we explain is consistent with the Lorentz force hypothesis. The effects of head pitch on vertigo and previously reported nystagmus are consistent with both effects being driven by a common vestibular signal. To explain all the observed effects, this common signal requires contributions from multiple semicircular canals. © 2015 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.

Dust trap formation in a non-self-sustained discharge with external gas ionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippov, A. V., E-mail: fav@triniti.ru; Babichev, V. N.; Pal’, A. F.

2015-11-15

Results from numerical studies of a non-self-sustained gas discharge containing micrometer dust grains are presented. The non-self-sustained discharge (NSSD) was controlled by a stationary fast electron beam. The numerical model of an NSSD is based on the diffusion drift approximation for electrons and ions and self-consistently takes into account the influence of the dust component on the electron and ion densities. The dust component is described by the balance equation for the number of dust grains and the equation of motion for dust grains with allowance for the Stokes force, gravity force, and electric force in the cathode sheath. Themore » interaction between dust grains is described in the self-consistent field approximation. The height of dust grain levitation over the cathode is determined and compared with experimental results. It is established that, at a given gas ionization rate and given applied voltage, there is a critical dust grain size above which the levitation condition in the cathode sheath cannot be satisfied. Simulations performed for the dust component consisting of dust grains of two different sizes shows that such grains levitate at different heights, i.e., size separation of dust drains levitating in the cathode sheath of an NSSD takes place.« less

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

Sanford, Dustin; Brooks, Beau; Ellis, Naoki; Matthews, Lorin; Hyde, Truell

2017-10-01

In a complex plasma, positively charged ions often have a directed flow with respect to the negatively charged dust grains. The resulting interaction between the dust and the flowing plasma creates an ion wakefield downstream from the dust particles, with the resulting positive space region modifying the interaction between the grains and contributing to the observed dynamics and equilibrium structure of the system. Here we present a proof of concept method that uses a molecular dynamics simulation to model the ion wakefield allowing the dynamics of the dust particles to be determined self-consistently. The trajectory of each ion is calculated including the forces from all other ions, which are treated as ``Yukawa particles'' and shielded from thermal electrons and the forces of the charged dust particles. Both the dust grain charge and the wakefield structure are also self-consistently determined for various particle configurations. The resultant wakefield potentials are then used to provide dynamic simulations of dust particle pairs. These results will be employed to analyze the formation and dynamics of field-aligned chains in CASPER's PK4 experiment onboard the International Space Station, allowing examination of extended dust chains without the masking force of gravity. This work was supported by the National Science Foundation under Grants PHY-1414523 and PHY-1740203.

Consistent simulation of droplet evaporation based on the phase-field multiphase lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Safari, Hesameddin; Rahimian, Mohammad Hassan; Krafczyk, Manfred

2014-09-01

In the present article, we extend and generalize our previous article [H. Safari, M. H. Rahimian, and M. Krafczyk, Phys. Rev. E 88, 013304 (2013), 10.1103/PhysRevE.88.013304] to include the gradient of the vapor concentration at the liquid-vapor interface as the driving force for vaporization allowing the evaporation from the phase interface to work for arbitrary temperatures. The lattice Boltzmann phase-field multiphase modeling approach with a suitable source term, accounting for the effect of the phase change on the velocity field, is used to solve the two-phase flow field. The modified convective Cahn-Hilliard equation is employed to reconstruct the dynamics of the interface topology. The coupling between the vapor concentration and temperature field at the interface is modeled by the well-known Clausius-Clapeyron correlation. Numerous validation tests including one-dimensional and two-dimensional cases are carried out to demonstrate the consistency of the presented model. Results show that the model is able to predict the flow features around and inside an evaporating droplet quantitatively in quiescent as well as convective environments.

Consistent simulation of droplet evaporation based on the phase-field multiphase lattice Boltzmann method.

PubMed

Safari, Hesameddin; Rahimian, Mohammad Hassan; Krafczyk, Manfred

2014-09-01

In the present article, we extend and generalize our previous article [H. Safari, M. H. Rahimian, and M. Krafczyk, Phys. Rev. E 88, 013304 (2013)] to include the gradient of the vapor concentration at the liquid-vapor interface as the driving force for vaporization allowing the evaporation from the phase interface to work for arbitrary temperatures. The lattice Boltzmann phase-field multiphase modeling approach with a suitable source term, accounting for the effect of the phase change on the velocity field, is used to solve the two-phase flow field. The modified convective Cahn-Hilliard equation is employed to reconstruct the dynamics of the interface topology. The coupling between the vapor concentration and temperature field at the interface is modeled by the well-known Clausius-Clapeyron correlation. Numerous validation tests including one-dimensional and two-dimensional cases are carried out to demonstrate the consistency of the presented model. Results show that the model is able to predict the flow features around and inside an evaporating droplet quantitatively in quiescent as well as convective environments.

Mean-field studies of time reversal breaking states in super-heavy nuclei with the Gogny force

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robledo, L. M., E-mail: luis.robledo@uam.es

2015-10-15

Recent progress on the description of time reversal breaking (odd mass and multi-quasiparticle excitation) states in super-heavy nuclei within a mean field framework and using several flavors of the Gogny interaction is reported. The study includes ground and excited states in selected odd mass isotopes of nobelium and mendelevium as well as high K isomeric states in {sup 254}No. These are two and four-quasiparticle excitations that are treated in the same self-consistent HFB plus blocking framework as the odd mass states.

A space-frequency multiplicative regularization for force reconstruction problems

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

Dynamic forces reconstruction from vibration data is an ill-posed inverse problem. A standard approach to stabilize the reconstruction consists in using some prior information on the quantities to identify. This is generally done by including in the formulation of the inverse problem a regularization term as an additive or a multiplicative constraint. In the present article, a space-frequency multiplicative regularization is developed to identify mechanical forces acting on a structure. The proposed regularization strategy takes advantage of one's prior knowledge of the nature and the location of excitation sources, as well as that of their spectral contents. Furthermore, it has the merit to be free from the preliminary definition of any regularization parameter. The validity of the proposed regularization procedure is assessed numerically and experimentally. It is more particularly pointed out that properly exploiting the space-frequency characteristics of the excitation field to identify can improve the quality of the force reconstruction.

Recent Developments and Applications of the CHARMM force fields

PubMed Central

Zhu, Xiao; Lopes, Pedro E.M.; MacKerell, Alexander D.

2011-01-01

Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields. PMID:23066428

Magnetic levitation-based Martian and Lunar gravity simulator

NASA Technical Reports Server (NTRS)

Valles, J. M. Jr; Maris, H. J.; Seidel, G. M.; Tang, J.; Yao, W.

2005-01-01

Missions to Mars will subject living specimens to a range of low gravity environments. Deleterious biological effects of prolonged exposure to Martian gravity (0.38 g), Lunar gravity (0.17 g), and microgravity are expected, but the mechanisms involved and potential for remedies are unknown. We are proposing the development of a facility that provides a simulated Martian and Lunar gravity environment for experiments on biological systems in a well controlled laboratory setting. The magnetic adjustable gravity simulator will employ intense, inhomogeneous magnetic fields to exert magnetic body forces on a specimen that oppose the body force of gravity. By adjusting the magnetic field, it is possible to continuously adjust the total body force acting on a specimen. The simulator system considered consists of a superconducting solenoid with a room temperature bore sufficiently large to accommodate small whole organisms, cell cultures, and gravity sensitive bio-molecular solutions. It will have good optical access so that the organisms can be viewed in situ. This facility will be valuable for experimental observations and public demonstrations of systems in simulated reduced gravity. c2005 Published by Elsevier Ltd on behalf of COSPAR.

Plasma Component of Self-gravitating Disks and Relevant Magnetic Configurations

NASA Astrophysics Data System (ADS)

Bertin, G.; Coppi, B.

2006-04-01

Astrophysical disks in which the disk self-gravity is more important than the gravity force associated with the central object can have significant plasma components where appreciable toroidal current densities are produced. When the vertical confinement of the plasma rotating structures that can form is kept by the Lorentz force rather than by the vertical component of the gravity force, the disk self-gravity remains important only in the radial equilibrium condition, modifying the rotation curve from the commonly considered Keplerian rotation. The equilibrium equations that are solved involve the vertical and the horizontal components of the total momentum conservation equations, coupled with the lowest order form of the gravitational Poisson's equation. The resulting poloidal field configuration can be visualized as a sequence [1] of Field Reverse Configurations, in the radial direction, consisting of pairs of oppositely directed current channels. The plasma density thus acquires a significant radial modulation that may grow to the point where plasma rings can form [2]. [1] B. Coppi, Phys. Plasmas, 12, 057302 (2005) [2] B. Coppi and F. Rousseau, to be published in Astrophys. J. (April 2006)

Magnetic levitation-based Martian and Lunar gravity simulator.

PubMed

Valles, J M; Maris, H J; Seidel, G M; Tang, J; Yao, W

2005-01-01

Missions to Mars will subject living specimens to a range of low gravity environments. Deleterious biological effects of prolonged exposure to Martian gravity (0.38 g), Lunar gravity (0.17 g), and microgravity are expected, but the mechanisms involved and potential for remedies are unknown. We are proposing the development of a facility that provides a simulated Martian and Lunar gravity environment for experiments on biological systems in a well controlled laboratory setting. The magnetic adjustable gravity simulator will employ intense, inhomogeneous magnetic fields to exert magnetic body forces on a specimen that oppose the body force of gravity. By adjusting the magnetic field, it is possible to continuously adjust the total body force acting on a specimen. The simulator system considered consists of a superconducting solenoid with a room temperature bore sufficiently large to accommodate small whole organisms, cell cultures, and gravity sensitive bio-molecular solutions. It will have good optical access so that the organisms can be viewed in situ. This facility will be valuable for experimental observations and public demonstrations of systems in simulated reduced gravity. c2005 Published by Elsevier Ltd on behalf of COSPAR.

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

PubMed Central

Karniel, Amir; Nisky, Ilana

2015-01-01

During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain. PMID:25717155

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

PubMed

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

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

Gene delivery in conjunction with gold nanoparticle and tumor treating electric field

NASA Astrophysics Data System (ADS)

Tiwari, Pawan K.; Soo Lee, Yeon

2013-08-01

The advances in electrotherapy to treat the diseased biological cell instigate its extension in gene therapy through the delivery of gene into the nucleus. The objective of this study is to investigate the application of moderate intensity alternating electric field, also known as tumor treating electric field on a carrier system consisting of a charged gene complex conjugated to the surface of a gold nanoparticle. The gene delivery mechanism relies on the magnitude and direction of the induced electric field inside the cytoplasm in presence of carrier system. The induced electric field strength is significant in breaking the gene complex-gold nanoparticle bonding, and exerting an electric force pushing the charged gene into the nucleus. The electric force orientation is dependent on the aspect ratio (AR) of the gold nanoparticle and a relationship between them is studied via Maxwell two-dimensional (2D) finite element simulation analyzer. The development of charge density on the surface of carrier system and the required electric field strength to break the bonding are investigated utilizing the Gouy-Chapman-Grahame-Stern (GCGS) theoretical model. A carrier system having the aspect ratio of the gold nanoparticle in the range 1 < AR ≤ 5 and AR = 1 are substantial delivering cationic and anionic genes into the nucleus, respectively.

Calculations of the Electric Fields in Liquid Solutions

PubMed Central

Fried, Stephen D.; Wang, Lee-Ping; Boxer, Steven G.; Ren, Pengyu; Pande, Vijay S.

2014-01-01

The electric field created by a condensed phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe non-polar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins. PMID:24304155

Effect of hurricane paths on storm surge response at Tianjin, China

NASA Astrophysics Data System (ADS)

Feng, Xingru; Yin, Baoshu; Yang, Dezhou

2012-06-01

A hurricane induced storm surge simulation system was developed for Tianjin coast, which consists of a hurricane model and a storm surge model. The peak storm surge result of the simulation agreed well with that of the observation. Three observed paths (Rita, Mimie and WINNIE) and a hypothetical path (Rita2) were chosen as the selective hurricane paths according to their positions relative to Tianjin. The sensitivity of Tianjin storm surge to the four paths was investigated using the validated storm surge simulation system. Three groups of experiments were done. In group one, the models were forced by the wind field and air pressure; in group two and three the models were forced by the wind only and the air pressure only respectively. In the experiments, the hurricane moved with a fixed speed and an intensity of 50 year return period. The simulation results show that path of the type Rita2 is the easiest to cause storm surge disaster in Tianjin, and the effect of air pressure forcing is most evident for path of the type Rita in Tianjin storm surge process. The above conclusions were analyzed through the evolution of the wind fields and the air pressure distributions. Comparing the experiment results of Group one, two and three, it can be seen that the storm surge is mainly induced by the wind forcing and the nonlinear interaction between the effect of wind forcing and air pressure forcing on the storm surge tends to weaken the storm surge.

Confined Rayleigh-Bénard, Rotating Rayleigh-Bénard, and Double Diffusive Convection: A Unifying View on Turbulent Transport Enhancement through Coherent Structure Manipulation

NASA Astrophysics Data System (ADS)

Chong, Kai Leong; Yang, Yantao; Huang, Shi-Di; Zhong, Jin-Qiang; Stevens, Richard J. A. M.; Verzicco, Roberto; Lohse, Detlef; Xia, Ke-Qing

2017-08-01

Many natural and engineering systems are simultaneously subjected to a driving force and a stabilizing force. The interplay between the two forces, especially for highly nonlinear systems such as fluid flow, often results in surprising features. Here we reveal such features in three different types of Rayleigh-Bénard (RB) convection, i.e., buoyancy-driven flow with the fluid density being affected by a scalar field. In the three cases different stabilizing forces are considered, namely (i) horizontal confinement, (ii) rotation around a vertical axis, and (iii) a second stabilizing scalar field. Despite the very different nature of the stabilizing forces and the corresponding equations of motion, at moderate strength we counterintuitively but consistently observe an enhancement in the flux, even though the flow motion is weaker than the original RB flow. The flux enhancement occurs in an intermediate regime in which the stabilizing force is strong enough to alter the flow structures in the bulk to a more organized morphology, yet not too strong to severely suppress the flow motions. Near the optimal transport enhancements all three systems exhibit a transition from a state in which the thermal boundary layer (BL) is nested inside the momentum BL to the one with the thermal BL being thicker than the momentum BL. The observed optimal transport enhancement is explained through an optimal coupling between the suction of hot or fresh fluid and the corresponding scalar fluctuations.

Overview--Development of a geodatabase and conceptual model of the hydrogeologic units beneath Air Force Plant 4 and Naval Air Station-Joint Reserve Base Carswell Field, Fort Worth, Texas

USGS Publications Warehouse

Shah, Sachin D.

2004-01-01

Air Force Plant 4 (AFP4) and adjacent Naval Air Station-Joint Reserve Base Carswell Field (NAS–JRB) at Fort Worth, Tex., constitute a contractor-owned, government-operated facility that has been in operation since 1942. Contaminants from the 3,600-acre facility, primarily volatile organic compounds (VOCs) and metals, have entered the ground-water-flow system through leakage from waste-disposal sites and from manufacturing processes. Environmental data collected at AFP4 and NAS–JRB during 1993–2002 created the need for consolidation of the data into a comprehensive temporal and spatial geodatabase. The U.S. Geological Survey (USGS), in cooperation with the U.S. Air Force Aeronautical Systems Center Environmental Management Directorate, developed a comprehensive geodatabase of temporal and spatial environmental data associated with the hydrogeologic units beneath the facility. A three-dimensional conceptual model of the hydrogeologic units integrally linked to the geodatabase was designed concurrently. Three hydrogeologic units—from land surface downward, the alluvial aquifer, the GoodlandWalnut confining unit, and the Paluxy aquifer—compose the subsurface of interest at AFP4 and NAS–JRB. The alluvial aquifer consists primarily of clay and silt with sand and gravel channel deposits that might be interconnected or interfingered. The Goodland-Walnut confining unit directly underlies the alluvial aquifer and consists of limestone, marl, shale, and clay. The Paluxy aquifer is composed of dense mudstone and fine- to coarse-grained sandstone

Coarse-grained Simulations of Sugar Transport and Conformational Changes of Lactose Permease

NASA Astrophysics Data System (ADS)

Liu, Jin; Jewel, S. M. Yead; Dutta, Prashanta

2016-11-01

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves sugar translocation, H+ transfer, as well as large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the transport of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule across a wild-type LacY during lactose/H+ symport process. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Protonation of Glu325 stabilizes the TDG and inward-facing conformation of LacY. Protonation of Glu269 induces a dramatic protein structural reorganization and causes the expulsion of TDG from LacY to both sides of the membrane. The structural changes occur primarily in the N-terminal domain of LacY. This work is supported by NSF Grants: CBET-1250107 and CBET -1604211.

Exploration of Structural Changes in Lactose Permease on Sugar Binding and Proton Transport through Atomistic Simulations

NASA Astrophysics Data System (ADS)

Liu, Jin; Jewel, Yead; Dutta, Prashanta

2017-11-01

Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H+ symport process. Lactose/H+ symport is a highly complex process that involves large-scale protein conformational changes. The complete picture of lactose/H+ symport is largely unclear. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-D-galactopyranosyl-1-thio- β-D-galactopyranoside (TDG) molecule to a wild-type LacY. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from microsecond simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with experiments. Our analysis suggest that the conformational changes of LacY are a cumulative consequence of inter-domain H-bonds breaking at the periplasmic side, inter-domain salt-bridge formation at the cytoplasmic side, as well as the TDG orientational changes during the transition. This work is supported by US National Science Foundation under Grant No. CBET-1604211.

[The medical assistance of Swedish Red Cross Field Hospital in Busan during and after the Korean war].

PubMed

Park, Jiwook

2010-06-30

After the outbreak of the Korean war, the Kingdom of Sweden, a permanent neutral nation, dispatched the Swedish Red Cross Field Hospital(SRCFH) instead of armed forces for humanitarian support to the allied forces in South Korea. The Hospital consisted of about 170 Swedes, all volunteers. From the early part of the Korean War, SRCFH took part in the medical assistance in Busan. When the frontline advanced to northern Korea, the number of inflowing casualties to this field hospital decreased. At that time, earnest medical aid for civilians commenced, and many Koreans were treated in available beds in SRCFH. After the armistice in July 1953, SRCFH became the Swedish Hospital in Busan, serving not only the military but also civilians, and continued its humanitarian mission until April 1957 for the Korean who were suffering from a collapsed medical system in the midst of war. When the Hospital returned to Sweden, it had treated over two million patients from twenty countries, including wounded UN allied force, Korean (south and north), Chinese prisoner of war and Korean civilian. Moreover, it left a transformative legacy, the National Medical Center in Seoul which was established in collaboration with other Scandinavian countries who dispatched medical assistance during the Korean War.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

Numerical study of acoustophoretic motion of particles in a PDMS microchannel driven by surface acoustic waves.

PubMed

Nama, Nitesh; Barnkob, Rune; Mao, Zhangming; Kähler, Christian J; Costanzo, Francesco; Huang, Tony Jun

2015-06-21

We present a numerical study of the acoustophoretic motion of particles suspended in a liquid-filled PDMS microchannel on a lithium niobate substrate acoustically driven by surface acoustic waves. We employ a perturbation approach where the flow variables are divided into first- and second-order fields. We use impedance boundary conditions to model the PDMS microchannel walls and we model the acoustic actuation by a displacement function from the literature based on a numerical study of piezoelectric actuation. Consistent with the type of actuation, the obtained first-order field is a horizontal standing wave that travels vertically from the actuated wall towards the upper PDMS wall. This is in contrast to what is observed in bulk acoustic wave devices. The first-order fields drive the acoustic streaming, as well as the time-averaged acoustic radiation force acting on suspended particles. We analyze the motion of suspended particles driven by the acoustic streaming drag and the radiation force. We examine a range of particle diameters to demonstrate the transition from streaming-drag-dominated acoustophoresis to radiation-force-dominated acoustophoresis. Finally, as an application of our numerical model, we demonstrate the capability to tune the position of the vertical pressure node along the channel width by tuning the phase difference between two incoming surface acoustic waves.

A Lorentz force actuated magnetic field sensor with capacitive read-out

NASA Astrophysics Data System (ADS)

Stifter, M.; Steiner, H.; Kainz, A.; Keplinger, F.; Hortschitz, W.; Sauter, T.

2013-05-01

We present a novel design of a resonant magnetic field sensor with capacitive read-out permitting wafer level production. The device consists of a single-crystal silicon cantilever manufactured from the device layer of an SOI wafer. Cantilevers represent a very simple structure with respect to manufacturing and function. On the top of the structure, a gold lead carries AC currents that generate alternating Lorentz forces in an external magnetic field. The free end oscillation of the actuated cantilever depends on the eigenfrequencies of the structure. Particularly, the specific design of a U-shaped structure provides a larger force-to-stiffness-ratio than standard cantilevers. The electrodes for detecting cantilever deflections are separately fabricated on a Pyrex glass-wafer. They form the counterpart to the lead on the freely vibrating planar structure. Both wafers are mounted on top of each other. A custom SU-8 bonding process on wafer level creates a gap which defines the equilibrium distance between sensing electrodes and the vibrating structure. Additionally to the capacitive read-out, the cantilever oscillation was simultaneously measured with laser Doppler vibrometry through proper windows in the SOI handle wafer. Advantages and disadvantages of the asynchronous capacitive measurement configuration are discussed quantitatively and presented by a comprehensive experimental characterization of the device under test.

New Results on a Stochastic Duel Game with Each Force Consisting of Heterogeneous Units

DTIC Science & Technology

2013-02-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA NEW RESULTS ON A STOCHASTIC DUEL GAME WITH EACH FORCE CONSISTING OF...on a Stochastic Duel Game With Each Force Consisting of Heterogeneous Units 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...distribution is unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Two forces engage in a duel , with each force initially consisting of several

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

PubMed

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.

Conformal invariance and the metrication of the fundamental forces

NASA Astrophysics Data System (ADS)

Mannheim, Philip D.

2016-07-01

We revisit Weyl’s metrication (geometrization) of electromagnetism. We show that by making Weyl’s proposed geometric connection be pure imaginary, not only are we able to metricate electromagnetism, an underlying local conformal invariance makes the geometry be strictly Riemannian and prevents observational gravity from being complex. Via torsion, we achieve an analogous metrication for axial-vector fields. We generalize our procedure to Yang-Mills theories, and achieve a metrication of all the fundamental forces. Only in the gravity sector does our approach differ from the standard picture of fundamental forces, with our approach requiring that standard Einstein gravity be replaced by conformal gravity. We show that quantum conformal gravity is a consistent and unitary quantum gravitational theory, one that, unlike string theory, only requires four spacetime dimensions.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-01

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ɛ(r) is close to one everywhere inside the protein. The Gaussian widths σi of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σi. A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

PubMed

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-14

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Steps towards Improving GNSS Systematic Errors and Biases

NASA Astrophysics Data System (ADS)

Herring, T.; Moore, M.

2017-12-01

Four general areas of analysis method improvements, three related to data analysis models and the fourth to calibration methods, have been recommended at the recent unified analysis workshop (UAW) and we discuss aspects of these areas for improvement. The gravity fields used in the GNSS orbit integrations should be updated to match modern fields to make them consistent with the fields being used by the other IAG services. The update would include the static part of the field and a time variable component. The force models associated with radiation forces are the most uncertain and modeling of these forces can be made more consistent with the exchange of attitude information. The international GNSS service (IGS) will develop an attitude format and make attitude information available so that analysis centers can validate their models. The IGS has noted the appearance of the GPS draconitic period and harmonics of this period in time series of various geodetic products (e.g., positions and Earth orientation parameters). An updated short-period (diurnal and semidiurnal) model is needed and a method to determine the best model developed. The final area, not directly related to analysis models, is the recommendation that site dependent calibration of GNSS antennas are needed since these have a direct effect on the ITRF realization and position offsets when antennas are changed. Evaluation of the effects of the use of antenna specific phase center models will be investigated for those sites where these values are available without disturbing an existing antenna installation. Potential development of an in-situ antenna calibration system is strongly encouraged. In-situ calibration would be deployed at core sites where GNSS sites are tied to other geodetic systems. With recent expansion of the number of GPS satellites transmitting unencrypted codes on the GPS L2 frequency and the availability of software GNSS receivers in-situ calibration between an existing installation and a movable directional antenna is now more likely to generate accurate results than earlier analog switching systems. With all of these improvements, there is the expectation that there will be better agreement between the space geodetic methods thus allowing more definitive assessment and modeling of the Earth's time variable shape and gravity field.

A chip for catching, separating, and transporting bio-particles with dielectrophoresis.

PubMed

Huang, Jung-Tang; Wang, Guo-Chen; Tseng, Kuang-Ming; Fang, Shiuh-Bin

2008-11-01

This study aims at developing a 3D device for catching, separating, and transporting bio-particles based on dielectrophoresis (DEP). Target particles can be simultaneously caught and transported using the negative DEP method. In non-uniform electric fields, the levitation height or complex permittivity of certain particle may be different from that of another and this property can facilitate separation of particles. We have designed and constructed a 3D device consisting of two layers of electrodes separated by a channel formed by 50 microm thick photoresist. The electrodes can operate effectively with 10-15 V and 5-7 MHz to catch all particles in the channel, and can move particles after switching the electric field to 5-15 V and 500-1,000 KHz. Hence, particles experienced coupling force of two different directional twDEP forces, and tallied with our estimation to move along the coupling direction.

Controlling electron transfer processes on insulating surfaces with the non-contact atomic force microscope.

PubMed

Trevethan, Thomas; Shluger, Alexander

2009-07-01

We present the results of theoretical modelling that predicts how a process of transfer of single electrons between two defects on an insulating surface can be induced using a scanning force microscope tip. A model but realistic system is employed which consists of a neutral oxygen vacancy and a noble metal (Pt or Pd) adatom on the MgO(001) surface. We show that the ionization potential of the vacancy and the electron affinity of the metal adatom can be significantly modified by the electric field produced by an ionic tip apex at close approach to the surface. The relative energies of the two states are also a function of the separation of the two defects. Therefore the transfer of an electron from the vacancy to the metal adatom can be induced either by the field effect of the tip or by manipulating the position of the metal adatom on the surface.

Does High Plasma-β Dynamics ``Load'' Active Regions?

NASA Astrophysics Data System (ADS)

McIntosh, Scott W.

2007-03-01

Using long-duration observations in the He II 304 Å passband of SOHO EIT, we investigate the spatial and temporal appearance of impulsive intensity fluctuations in the pixel light curves. These passband intensity fluctuations come from plasma emitting in the chromosphere, in the transition region, and in the lowest portions of the corona. We see that they are spatially tied to the supergranular scale and that their rate of occurrence is tied to the unsigned imbalance of the magnetic field in which they are observed. The signature of the fluctuations (in space and time) is consistent with their creation by magnetoconvection-forced reconnection, which is driven by the flow field in the high-β plasma. The signature of the intensity fluctuations around an active region suggests that the bulk of the mass and energy going into the active region complex observed in the hotter coronal plasma is supplied by this process, dynamically forcing the looped structure from beneath.

Coarse-Grained Simulation of Solvated Cellulose Ib Microfibril

NASA Astrophysics Data System (ADS)

Fan, Bingxin; Maranas, Janna; Zhong, Linghao; Zhen Zhao Collaboration

2013-03-01

We construct a coarse-grained (CG) model of cellulose microfibrils in water. The force field is derived from atomistic simulation of a 40 glucose-unit-long microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Intermolecular interactions such as hydrogen bonding are added sequentially until the force field holds the microfibril crystal structure. This stepwise process enables us to evaluate the importance of each potential and provides insight to ordered and disordered regions. We simulate cellulose microfibrils with 100 to 400 residues, comparable to the smallest observed microfibrils. Microfibrils longer than 100nm would form a bending region along their longitudinal direction. Multiple bends are observed in the microfibril containing 400 residues. Although the cause is not clear, the bending regions may provide us insights about the periodicity and the behavior of the disordered regions in the microfibril.

Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

Experimental and numerical study on optimization of the single point incremental forming of AINSI 304L stainless steel sheet

NASA Astrophysics Data System (ADS)

Saidi, B.; Giraud-Moreau, L.; Cherouat, A.; Nasri, R.

2017-09-01

AINSI 304L stainless steel sheets are commonly formed into a variety of shapes for applications in the industrial, architectural, transportation and automobile fields, it’s also used for manufacturing of denture base. In the field of dentistry, there is a need for personalized devises that are custom made for the patient. The single point incremental forming process is highly promising in this area for manufacturing of denture base. The single point incremental forming process (ISF) is an emerging process based on the use of a spherical tool, which is moved along CNC controlled tool path. One of the major advantages of this process is the ability to program several punch trajectories on the same machine in order to obtain different shapes. Several applications of this process exist in the medical field for the manufacturing of personalized titanium prosthesis (cranial plate, knee prosthesis...) due to the need of product customization to each patient. The objective of this paper is to study the incremental forming of AISI 304L stainless steel sheets for future applications in the dentistry field. During the incremental forming process, considerable forces can occur. The control of the forming force is particularly important to ensure the safe use of the CNC milling machine and preserve the tooling and machinery. In this paper, the effect of four different process parameters on the maximum force is studied. The proposed approach consists in using an experimental design based on experimental results. An analysis of variance was conducted with ANOVA to find the input parameters allowing to minimize the maximum forming force. A numerical simulation of the incremental forming process is performed with the optimal input process parameters. Numerical results are compared with the experimental ones.

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

Self-consistent simulations of a von Kármán type dynamo in a spherical domain with metallic walls.

PubMed

Guervilly, Céline; Brummell, Nicholas H

2012-10-01

We have performed numerical simulations of boundary-driven dynamos using a three-dimensional nonlinear magnetohydrodynamical model in a spherical shell geometry. A conducting fluid of magnetic Prandtl number Pm=0.01 is driven into motion by the counter-rotation of the two hemispheric walls. The resulting flow is of von Kármán type, consisting of a layer of zonal velocity close to the outer wall and a secondary meridional circulation. Above a certain forcing threshold, the mean flow is unstable to non-axisymmetric motions within an equatorial belt. For fixed forcing above this threshold, we have studied the dynamo properties of this flow. The presence of a conducting outer wall is essential to the existence of a dynamo at these parameters. We have therefore studied the effect of changing the material parameters of the wall (magnetic permeability, electrical conductivity, and thickness) on the dynamo. In common with previous studies, we find that dynamos are obtained only when either the conductivity or the permeability is sufficiently large. However, we find that the effect of these two parameters on the dynamo process are different and can even compete to the detriment of the dynamo. Our self-consistent approach allow us to analyze in detail the dynamo feedback loop. The dynamos we obtain are typically dominated by an axisymmetric toroidal magnetic field and an axial dipole component. We show that the ability of the outer shear layer to produce a strong toroidal field depends critically on the presence of a conducting outer wall, which shields the fluid from the vacuum outside. The generation of the axisymmetric poloidal field, on the other hand, occurs in the equatorial belt and does not depend on the wall properties.

Validating empirical force fields for molecular-level simulation of cellulose dissolution

USDA-ARS?s Scientific Manuscript database

The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

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

PubMed

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

2016-03-15

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

A force field for dynamic Cu-BTC metal-organic framework.

PubMed

Zhao, Lei; Yang, Qingyuan; Ma, Qintian; Zhong, Chongli; Mi, Jianguo; Liu, Dahuan

2011-02-01

A new force field that can describe the flexibility of Cu-BTC metal-organic framework (MOF) was developed in this work. Part of the parameters were obtained using density functional theory calculations, and the others were taken from other force fields. The new force field could reproduce well the experimental crystal structure, negative thermal expansion, vibrational properties as well as adsorption behavior in Cu-BTC. In addition, the bulk modulus of Cu-BTC was predicted using the new force field. We believe the new force field is useful in understanding the structure-property relationships for MOFs, and the approach can be extended to other MOFs.

Report on the Work of the Bureau of Education for the Natives of Alaska, 1913-14. Bulletin, 1915, No. 48

ERIC Educational Resources Information Center

Bureau of Education, Department of the Interior, 1915

1915-01-01

During the fiscal year ended June 30, 1914, the field force of the Bureau of Education in Alaska consisted of 5 superintendents, 1 assistant superintendent, 106 teachers, 11 physicians, 11 nurses, and 3 hospital attendants. Seventy-one schools were maintained, with an enrollment of 3,666 and an average attendance of 1,991. The following…

Ion Channel Conductance Measurements on a Silicon-Based Platform

DTIC Science & Technology

2006-01-01

calculated using the molecular dynamics code, GROMACS . Reasonable agreement is obtained in the simulated versus measured conductance over the range of...measurements of the lipid giga-seal characteristics have been performed, including AC conductance measurements and statistical analysis in order to...Dynamics kernel self-consistently coupled to Poisson equations using a P3M force field scheme and the GROMACS description of protein structure and

Work of the Bureau of Education for the Natives of Alaska, 1917-18. Bulletin, 1919, No. 40

ERIC Educational Resources Information Center

Bureau of Education, Department of the Interior, 1919

1919-01-01

During the year the field force of the Bureau of Education in Alaska consisted of 5 superintendents, 1 assistant superintendent, 116 teachers, 9 physicians, and 11 nurses. Sixty-nine schools were maintained with an enrollment of 3,635. School buildings were erected at White Mountain, whither the Eskimos had migrated from Council; at Elim, within a…

Combined influences of gravitoinertial force level and visual field pitch on visually perceived eye level

NASA Technical Reports Server (NTRS)

DiZio, P.; Li, W.; Lackner, J. R.; Matin, L.

1997-01-01

Psychophysical measurements of the level at which observers set a small visual target so as to appear at eye level (VPEL) were made on 13 subjects in 1.0 g and 1.5 g environments in the Graybiel Laboratory rotating room while they viewed a pitched visual field or while in total darkness. The gravitoinertial force was parallel to the z-axis of the head and body during the measurements. The visual field consisted of two 58 degrees high, luminous, pitched-from-vertical, bilaterally symmetric, parallel lines, viewed in otherwise total darkness. The lines were horizontally separated by 53 degrees and presented at each of 7 angles of pitch ranging from 30 degrees with the top of the visual field turned away from the subject (top backward) to 30 degrees with the top turned toward the subject (top forward). At 1.5 g, VPEL changed linearly with the pitch of the 2-line stimulus and was depressed with top backward pitch and elevated with top forward pitch as had been reported previously at 1.0 g (1,2); however, the slopes of the VPEL-vs-pitch functions at 1.0 g and 1.5 g were indistinguishable. As reported previously also (3,4), the VPEL in darkness was considerably lower at 1.5 g than at 1.0 g; however, although the y-intercept of the VPEL-vs-pitch function in the presence of the 2-line visual field (visual field erect) was also lower at 1.5 g than at 1.0 g as it was in darkness, the G-related difference was significantly attenuated by the presence of the visual field. The quantitative characteristics of the results are consistent with a model in which VPEL is treated as a consequence of an algebraic weighted average or a vector sum of visual and nonvisual influences although the two combining rules lead to fits that are equally good.

The Role of Self-Organized Criticality in the Substorm Phenomenon and its Relation to Localized Reconnection in the Magnetospheric Plasma Sheet

NASA Technical Reports Server (NTRS)

Klimas, Alex J.; Valdivia, J. A.; Vassiliadis, D.; Baker, D. N.; Hesse, M.; Takalo, J.

1999-01-01

Evidence is presented that suggests there is a significant self-organized criticality (SOC) component in the dynamics of substorms in the magnetosphere. Observations of BBFs, fast flows, localized dipolarizations, plasma turbulence, etc. are taken to show that multiple localized reconnection sites provide the basic avalanche phenomenon in the establishment of SOC in the plasma sheet. First results are presented from a continuing plasma physical study of this avalanche process. A one-dimensional resistive MHD model of a magnetic field reversal is discussed. Resistivity, in this model, is self-consistently generated in response to the excitation of an idealized current-driven instability. When forced by convection of magnetic flux into the field reversal region, the model yields rapid magnetic field annihilation through a dynamic behavior that is shown to exhibit many of the characteristics of SOC. Over a large range of forcing strengths, the annihilation rate is shown to self-adjust to balance the rate at which flux is convected into the reversal region. Several analogies to magnetotail dynamics are discussed: (1) It is shown that the presence of a localized criticality in the model produces a remarkable stability in the global configuration of the field reversal while simultaneously exciting extraordinarily dynamic internal evolution. (2) Under steady forcing, it is shown that a loading-unloading cycle may arise that, as a consequence of the global stability, is quasi-periodic and, therefore, predictable despite the presence of internal turbulence in the field distribution. Indeed, it is shown that the global loading-unloading cycle is a consequence of the internal turbulence. (3) It is shown that, under steady, strong forcing the loading-unloading cycle vanishes. Instead, a recovery from a single unloading persists indefinitely. The field reversal is globally very steady while internally it is very dynamic as field annihilation goes on at the rate necessary to match the strong forcing. From this result we speculate that steady magnetospheric convection events result when the plasma sheet has been driven close to criticality over an extended spatial domain. During these events, we would expect to find localized reconnection sites distributed over the spatial domain of near criticality and we would expect to find plasma sheet transport in that domain to be closely related to that of BBF and fast flow events.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

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

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

PubMed

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.

MMS Examination of FTEs at the Earth's Subsolar Magnetopause

NASA Astrophysics Data System (ADS)

Akhavan-Tafti, M.; Slavin, J. A.; Le, G.; Eastwood, J. P.; Strangeway, R. J.; Russell, C. T.; Nakamura, R.; Baumjohann, W.; Torbert, R. B.; Giles, B. L.; Gershman, D. J.; Burch, J. L.

2018-02-01

Determining the magnetic field structure, electric currents, and plasma distributions within flux transfer event (FTE)-type flux ropes is critical to the understanding of their origin, evolution, and dynamics. Here the Magnetospheric Multiscale mission's high-resolution magnetic field and plasma measurements are used to identify FTEs in the vicinity of the subsolar magnetopause. The constant-α flux rope model is used to identify quasi-force free flux ropes and to infer the size, the core magnetic field strength, the magnetic flux content, and the spacecraft trajectories through these structures. Our statistical analysis determines a mean diameter of 1,700 ± 400 km ( 30 ± 9 di) and an average magnetic flux content of 100 ± 30 kWb for the quasi-force free FTEs at the Earth's subsolar magnetopause which are smaller than values reported by Cluster at high latitudes. These observed nonlinear size and magnetic flux content distributions of FTEs appear consistent with the plasmoid instability theory, which relies on the merging of neighboring, small-scale FTEs to generate larger structures. The ratio of the perpendicular to parallel components of current density, RJ, indicates that our FTEs are magnetically force-free, defined as RJ < 1, in their core regions (<0.6 Rflux rope). Plasma density is shown to be larger in smaller, newly formed FTEs and dropping with increasing FTE size. It is also shown that parallel ion velocity dominates inside FTEs with largest plasma density. Field-aligned flow facilitates the evacuation of plasma inside newly formed FTEs, while their core magnetic field strengthens with increasing FTE size.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-07-27

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

A Maximum-Likelihood Approach to Force-Field Calibration.

PubMed

Zaborowski, Bartłomiej; Jagieła, Dawid; Czaplewski, Cezary; Hałabis, Anna; Lewandowska, Agnieszka; Żmudzińska, Wioletta; Ołdziej, Stanisław; Karczyńska, Agnieszka; Omieczynski, Christian; Wirecki, Tomasz; Liwo, Adam

2015-09-28

A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental conformations, calculated with the current energy function. Because the theoretical distribution is given in the form of the simulated conformations only, the contributions from all of the simulated conformations, with Gaussian weights in the distances from a given experimental conformation, are added to give the contribution to the target function from this conformation. In contrast to earlier methods for force-field calibration, the approach does not suffer from the arbitrariness of dividing the decoy set into native-like and non-native structures; however, if such a division is made instead of using Gaussian weights, application of the maximum-likelihood method results in the well-known energy-gap maximization. The computational procedure consists of cycles of decoy generation and maximum-likelihood-function optimization, which are iterated until convergence is reached. The method was tested with Gaussian distributions and then applied to the physics-based coarse-grained UNRES force field for proteins. The NMR structures of the tryptophan cage, a small α-helical protein, determined at three temperatures (T = 280, 305, and 313 K) by Hałabis et al. ( J. Phys. Chem. B 2012 , 116 , 6898 - 6907 ), were used. Multiplexed replica-exchange molecular dynamics was used to generate the decoys. The iterative procedure exhibited steady convergence. Three variants of optimization were tried: optimization of the energy-term weights alone and use of the experimental ensemble of the folded protein only at T = 280 K (run 1); optimization of the energy-term weights and use of experimental ensembles at all three temperatures (run 2); and optimization of the energy-term weights and the coefficients of the torsional and multibody energy terms and use of experimental ensembles at all three temperatures (run 3). The force fields were subsequently tested with a set of 14 α-helical and two α + β proteins. Optimization run 1 resulted in better agreement with the experimental ensemble at T = 280 K compared with optimization run 2 and in comparable performance on the test set but poorer agreement of the calculated folding temperature with the experimental folding temperature. Optimization run 3 resulted in the best fit of the calculated ensembles to the experimental ones for the tryptophan cage but in much poorer performance on the training set, suggesting that use of a small α-helical protein for extensive force-field calibration resulted in overfitting of the data for this protein at the expense of transferability. The optimized force field resulting from run 2 was found to fold 13 of the 14 tested α-helical proteins and one small α + β protein with the correct topologies; the average structures of 10 of them were predicted with accuracies of about 5 Å C(α) root-mean-square deviation or better. Test simulations with an additional set of 12 α-helical proteins demonstrated that this force field performed better on α-helical proteins than the previous parametrizations of UNRES. The proposed approach is applicable to any problem of maximum-likelihood parameter estimation when the contributions to the maximum-likelihood function cannot be evaluated at the experimental points and the dimension of the configurational space is too high to construct histograms of the experimental distributions.

Analysis of the mechanical behavior of single wall carbon nanotubes by a modified molecular structural mechanics model incorporating an advanced chemical force field

NASA Astrophysics Data System (ADS)

Eberhardt, Oliver; Wallmersperger, Thomas

2018-03-01

The outstanding properties of carbon nanotubes (CNTs) keep attracting the attention of researchers from different fields. CNTs are promising candidates for applications e.g. in lightweight construction but also in electronics, medicine and many more. The basis for the realization of the manifold applications is a detailed knowledge of the material properties of the carbon nanotubes. In particular for applications in lightweight constructions or in composites, the knowledge of the mechanical behavior of the CNTs is of vital interest. Hence, a lot of effort is put into the experimental and theoretical determination of the mechanical material properties of CNTs. Due to their small size, special techniques have to be applied. In this research, a modified molecular structural mechanics model for the numerical determination of the mechanical behavior of carbon nanotubes is presented. It uses an advanced approach for the geometrical representation of the CNT structure while the covalent bonds in the CNTs are represented by beam elements. Furthermore, the model is specifically designed to overcome major drawbacks in existing molecular structural mechanics models. This includes energetic consistency with the underlying chemical force field. The model is developed further to enable the application of a more advanced chemical force field representation. The developed model is able to predict, inter alia, the lateral and radial stiffness properties of the CNTs. The results for the lateral stiffness are given and discussed in order to emphasize the progress made with the presented approach.

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

PubMed Central

Lange, Oliver F.; van der Spoel, David; de Groot, Bert L.

2010-01-01

Abstract Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data. PMID:20643085

Development of a linear induction motor based artificial muscle system.

PubMed

Gruber, A; Arguello, E; Silva, R

2013-01-01

We present the design of a linear induction motor based on electromagnetic interactions. The engine is capable of producing a linear movement from electricity. The design consists of stators arranged in parallel, which produce a magnetic field sufficient to displace a plunger along its axial axis. Furthermore, the winding has a shell and cap of ferromagnetic material that amplifies the magnetic field. This produces a force along the length of the motor that is similar to that of skeletal muscle. In principle, the objective is to use the engine in the development of an artificial muscle system for prosthetic applications, but it could have multiple applications, not only in the medical field, but in other industries.

A novel integrated multifunction micro-sensor for three-dimensional micro-force measurements.

PubMed

Wang, Weizhong; Zhao, Yulong; Qin, Yafei

2012-01-01

An integrated multifunction micro-sensor for three-dimensional micro-force precision measurement under different pressure and temperature conditions is introduced in this paper. The integrated sensor consists of three kinds of sensors: a three-dimensional micro-force sensor, an absolute pressure sensor and a temperature sensor. The integrated multifunction micro-sensor is fabricated on silicon wafers by micromachining technology. Different doping doses of boron ion, placement and structure of resistors are tested for the force sensor, pressure sensor and temperature sensor to minimize the cross interference and optimize the properties. A glass optical fiber, with a ladder structure and sharp tip etched by buffer oxide etch solution, is glued on the micro-force sensor chip as the tactile probe. Experimental results show that the minimum force that can be detected by the force sensor is 300 nN; the lateral sensitivity of the force sensor is 0.4582 mV/μN; the probe length is linearly proportional to sensitivity of the micro-force sensor in lateral; the sensitivity of the pressure sensor is 0.11 mv/KPa; the sensitivity of the temperature sensor is 5.836 × 10(-3) KΩ/°C. Thus it is a cost-effective method to fabricate integrated multifunction micro-sensors with different measurement ranges that could be used in many fields.

Physically consistent data assimilation method based on feedback control for patient-specific blood flow analysis.

PubMed

Ii, Satoshi; Adib, Mohd Azrul Hisham Mohd; Watanabe, Yoshiyuki; Wada, Shigeo

2018-01-01

This paper presents a novel data assimilation method for patient-specific blood flow analysis based on feedback control theory called the physically consistent feedback control-based data assimilation (PFC-DA) method. In the PFC-DA method, the signal, which is the residual error term of the velocity when comparing the numerical and reference measurement data, is cast as a source term in a Poisson equation for the scalar potential field that induces flow in a closed system. The pressure values at the inlet and outlet boundaries are recursively calculated by this scalar potential field. Hence, the flow field is physically consistent because it is driven by the calculated inlet and outlet pressures, without any artificial body forces. As compared with existing variational approaches, although this PFC-DA method does not guarantee the optimal solution, only one additional Poisson equation for the scalar potential field is required, providing a remarkable improvement for such a small additional computational cost at every iteration. Through numerical examples for 2D and 3D exact flow fields, with both noise-free and noisy reference data as well as a blood flow analysis on a cerebral aneurysm using actual patient data, the robustness and accuracy of this approach is shown. Moreover, the feasibility of a patient-specific practical blood flow analysis is demonstrated. Copyright © 2017 John Wiley & Sons, Ltd.

Topology determines force distributions in one-dimensional random spring networks.

PubMed

Heidemann, Knut M; Sageman-Furnas, Andrew O; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F; Wardetzky, Max

2018-02-01

Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber-reinforced materials are also common in technology. An important characteristic of such materials is their resistance to failure under load. Rupture occurs when fibers break under excessive force and when that failure propagates. Therefore, it is crucial to understand force distributions. Force distributions within such networks are typically highly inhomogeneous and are not well understood. Here we construct a simple one-dimensional model system with periodic boundary conditions by randomly placing linear springs on a circle. We consider ensembles of such networks that consist of N nodes and have an average degree of connectivity z but vary in topology. Using a graph-theoretical approach that accounts for the full topology of each network in the ensemble, we show that, surprisingly, the force distributions can be fully characterized in terms of the parameters (N,z). Despite the universal properties of such (N,z) ensembles, our analysis further reveals that a classical mean-field approach fails to capture force distributions correctly. We demonstrate that network topology is a crucial determinant of force distributions in elastic spring networks.

Topology determines force distributions in one-dimensional random spring networks

NASA Astrophysics Data System (ADS)

Heidemann, Knut M.; Sageman-Furnas, Andrew O.; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F.; Wardetzky, Max

2018-02-01

Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber-reinforced materials are also common in technology. An important characteristic of such materials is their resistance to failure under load. Rupture occurs when fibers break under excessive force and when that failure propagates. Therefore, it is crucial to understand force distributions. Force distributions within such networks are typically highly inhomogeneous and are not well understood. Here we construct a simple one-dimensional model system with periodic boundary conditions by randomly placing linear springs on a circle. We consider ensembles of such networks that consist of N nodes and have an average degree of connectivity z but vary in topology. Using a graph-theoretical approach that accounts for the full topology of each network in the ensemble, we show that, surprisingly, the force distributions can be fully characterized in terms of the parameters (N ,z ) . Despite the universal properties of such (N ,z ) ensembles, our analysis further reveals that a classical mean-field approach fails to capture force distributions correctly. We demonstrate that network topology is a crucial determinant of force distributions in elastic spring networks.

Prediction of Mechanical Properties of Polymers With Various Force Fields

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

Measurement method of magnetic field for the wire suspended micro-pendulum accelerometer.

PubMed

Lu, Yongle; Li, Leilei; Hu, Ning; Pan, Yingjun; Ren, Chunhua

2015-04-13

Force producer is one of the core components of a Wire Suspended Micro-Pendulum Accelerometer; and the stability of permanent magnet in the force producer determines the consistency of the acceleration sensor's scale factor. For an assembled accelerometer; direct measurement of magnetic field strength is not a feasible option; as the magnetometer probe cannot be laid inside the micro-space of the sensor. This paper proposed an indirect measurement method of the remnant magnetization of Micro-Pendulum Accelerometer. The measurement is based on the working principle of the accelerometer; using the current output at several different scenarios to resolve the remnant magnetization of the permanent magnet. Iterative Least Squares algorithm was used for the adjustment of the data due to nonlinearity of this problem. The calculated remnant magnetization was 1.035 T. Compared to the true value; the error was less than 0.001 T. The proposed method provides an effective theoretical guidance for measuring the magnetic field of the Wire Suspended Micro-Pendulum Accelerometer; correcting the scale factor and temperature influence coefficients; etc.

Fields and Plasma Structures Around ``Shining'' Black Holes: Solitary Rings and Tri-dimensional Topologies

NASA Astrophysics Data System (ADS)

Coppi, B.

2012-03-01

Field and plasma configurations that can be the distinguishing feature of and surround ``shining'' black holes have been identified. Considering the observation of the Quasi Periodic Oscillations that can be associated with inhomogeneous rotating plasmas, tri-dimensional rotating configurations have been looked for and found under special conditions. One is that these configurations are radially localized, such as narrow plasma ring pairs. Another is that the rotation frequency is nearly constant over the rings. Only axisymmetric local configurations consisting of solitary plasma rings or periodic sequences of rings are found when the gradient of the rotation frequency is (locally) significant. Assuming that the plasma pressure is scalar the problem is reduced to the solution of two coupled non-linear differential equations. One, the ``Master Equation'' [1], relates the magnetic surface function to the plasma rotation frequency that is connected to the gravity field. The other, the Vertical Equilibrium Equation, relates the plasma pressure gradient to both the Lorentz force and to the plasma density profile through the gravitational force.[4pt] [1] B. Coppi, Phys. Plasmas 18, 032901 (2011).

Ab initio calculation of harmonic force fields and vibrational spectra for the arsine oxides and sulfides R sub 3 AsY (R = H, F; Y = O, S) and related compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schneider, W.; Thiel, W.; Komornicki, A.

1990-04-05

Ab initio self-consistent-field calculations using effective core potentials and polarized double-zeta basis sets are reported for the arsenic compounds H{sub 3}As, H{sub 3}AsO, H{sub 3}AsS, F{sub 3}As, F{sub 3}AsO, F{sub 3}AsS, cis- and trans-H{sub 2}AsOH, and HAsO. The calculated geometries, rotational constants, vibrational frequencies, Coriolis coupling constants, centrifugal distortion constants, infrared band intensities, and force fields are compared with the available experimental data. Good agreement is found in the case of the known molecules, especially H{sub 3}As and F{sub 3}As, so that the predictions for the unknown molecules are expected to be realistic. The theoretical results confirm a recent spectroscopicmore » identification of H{sub 3}AsO, H{sub 2}AsOH, and HAsO and suggest reassignment of several observed frequencies.« less

A novel look at the pulsar force-free magnetosphere

NASA Astrophysics Data System (ADS)

Petrova, S. A.; Flanchik, A. B.

2018-03-01

The stationary axisymmetric force-free magnetosphere of a pulsar is considered. We present an exact dipolar solution of the pulsar equation, construct the magnetospheric model on its basis and examine its observational support. The new model has toroidal rather than common cylindrical geometry, in line with that of the plasma outflow observed directly as the pulsar wind nebula at much larger spatial scale. In its new configuration, the axisymmetric magnetosphere consumes the neutron star rotational energy much more efficiently, implying re-estimation of the stellar magnetic field, B_{new}0=3.3×10^{-4}B/P, where P is the pulsar period. Then the 7-order scatter of the magnetic field derived from the rotational characteristics of the pulsars observed appears consistent with the \\cotχ-law, where χ is a random quantity uniformly distributed in the interval [0,π/2]. Our result is suggestive of a unique actual magnetic field strength of the neutron stars along with a random angle between the magnetic and rotational axes and gives insight into the neutron star unification on the geometrical basis.

High-displacement spiral piezoelectric actuators

NASA Astrophysics Data System (ADS)

Mohammadi, F.; Kholkin, A. L.; Jadidian, B.; Safari, A.

1999-10-01

A high-displacement piezoelectric actuator, employing spiral geometry of a curved piezoelectric strip is described. The monolithic actuators are fabricated using a layered manufacturing technique, fused deposition of ceramics, which is capable of prototyping electroceramic components with complex shapes. The spiral actuators (2-3 cm in diameter) consisted of 4-5 turns of a lead zirconate titanate ceramic strip with an effective length up to 28 cm. The width was varied from 0.9 to 1.75 mm with a height of 3 mm. When driven by the electric field applied across the width of the spiral wall, the tip of the actuator was found to displace in both radial and tangential directions. The tangential displacement of the tip was about 210 μm under the field of 5 kV/cm. Both the displacement and resonant frequency of the spirals could be tailored by changing the effective length and wall width. The blocking force of the actuator in tangential direction was about 1 N under the field of 5 kV/cm. These properties are advantageous for high-displacement low-force applications where bimorph or monomorph actuators are currently employed.

Compressible liquid flow in nano- or micro-sized circular tubes considering wall-liquid Lifshitz-van der Waals interaction

NASA Astrophysics Data System (ADS)

Zhang, Xueling; Zhu, Weiyao; Cai, Qiang; Shi, Yutao; Wu, Xuehong; Jin, Tingxiang; Yang, Lianzhi; Song, Hongqing

2018-06-01

Although nano- and micro-scale phenomena for fluid flows are ubiquitous in tight oil reservoirs or in nano- or micro-sized channels, the mechanisms behind them remain unclear. In this study, we consider the wall-liquid interaction to investigate the flow mechanisms behind a compressible liquid flow in nano- or micro-sized circular tubes. We assume that the liquid is attracted by the wall surface primarily by the Lifshitz-van der Waals (LW) force, whereas electrostatic forces are negligible. The long-range LW force is thus introduced into the Navier-Stokes equations. The nonlinear equations of motion are decoupled by using the hydrodynamic vorticity-stream functions, from which an approximate analytical perturbation solution is obtained. The proposed model considers the LW force and liquid compressibility to obtain the velocity and pressure fields, which are consistent with experimentally observed micro-size effects. A smaller tube radius implies smaller dimensionless velocity, and when the tube radius decreases to a certain radius Rm, a fluid no longer flows, where Rm is the lower limit of the movable-fluid radius. The radius Rm is calculated, and the results are consistent with previous experimental results. These results reveal that micro-size effects are caused by liquid compressibility and wall-liquid interactions, such as the LW force, for a liquid flowing in nano- or micro-sized channels or pores. The attractive LW force enhances the flow's radial resistance, and the liquid compressibility transmits the radial resistance to the streaming direction via volume deformation, thereby decreasing the streaming velocity.

Force Field for Water Based on Neural Network.

PubMed

Wang, Hao; Yang, Weitao

2018-05-18

We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: non-polarizable and polarizable force fields. Simulation results show that the non-polarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build the next generation force fields at high accuracy and low computational costs, especially for large systems.

The edge of supersymmetry: Stability walls in heterotic theory

DOE PAGES

Anderson, Lara B.; Gray, James; Lukas, Andre; ...

2009-05-15

We explicitly describe, in the language of four-dimensional N = 1 supersymmetric field theory, what happens when the moduli of a heterotic Calabi-Yau compactification change so as to make the internal non-Abelian gauge fields non-supersymmetric. At the edge of the region in Kähler moduli space where supersymmetry can be preserved, an additional anomalous U(1) gauge symmetry appears in the four-dimensional theory. The D-term contribution to the scalar potential associated to this U(1) attempts to force the system back into a supersymmetric configuration and provides a consistent low-energy description of gauge bundle stability.

Material transport in a wind and buoyancy forced mixed layer

NASA Astrophysics Data System (ADS)

Mensa, J. A.; Özgökmen, T.; Poje, A. C.; Imberger, J.

2016-02-01

Flows in the upper ocean mixed layer are responsible for the transport and dispersion of biogeochemical tracers, phytoplankton and buoyant pollutants, such as hydrocarbons from an oil spill. Material dispersion in mixed layer flows subject to diurnal buoyancy forcing and weak winds (|u10|=5ms-1) are investigated using a non-hydrostatic model. Both purely buoyancy-forced and combined wind- and buoyancy-forced flows are sampled using passive tracers, as well as 2D and 3D particles to explore characteristics of horizontal and vertical dispersion. It is found that the surface tracer patterns are determined by the convergence zones created by convection cells within a time scale of just a few hours. For pure convection, the results displayed the classic signature of Rayleigh-Benard cells. When combined with a wind stress, the convective cells become anisotropic in that the along-wind length scale gets much larger than the cross-wind scale. Horizontal relative dispersion computed by sampling the flow fields using both 2D and 3D passive particles is found to be consistent with the Richardson regime. Relative dispersion is an order of magnitude higher and 2D surface releases transition to Richardson regime faster in the wind-forced case. We also show that the buoyancy-forced case results in significantly lower amplitudes of scale-dependent horizontal relative diffusivity, kD(l), than those reported by Okubo (1970), while the wind- and buoyancy forced case shows a good agreement with Okubo's diffusivity amplitude, and scaling consistent with Richardson's 4/3rd law, kD(l) l4/3. The modelling results provide a framework for measuring material dispersion by mixed layer flow in future observational programs.

Material transport in a convective surface mixed layer under weak wind forcing

NASA Astrophysics Data System (ADS)

Mensa, Jean A.; Özgökmen, Tamay M.; Poje, Andrew C.; Imberger, Jörg

2015-12-01

Flows in the upper ocean mixed layer are responsible for the transport and dispersion of biogeochemical tracers, phytoplankton and buoyant pollutants, such as hydrocarbons from an oil spill. Material dispersion in mixed layer flows subject to diurnal buoyancy forcing and weak winds (| u10 | = 5m s-1) are investigated using a non-hydrostatic model. Both purely buoyancy-forced and combined wind- and buoyancy-forced flows are sampled using passive tracers, as well as 2D and 3D particles to explore characteristics of horizontal and vertical dispersion. It is found that the surface tracer patterns are determined by the convergence zones created by convection cells within a time scale of just a few hours. For pure convection, the results displayed the classic signature of Rayleigh-Benard cells. When combined with a wind stress, the convective cells become anisotropic in that the along-wind length scale gets much larger than the cross-wind scale. Horizontal relative dispersion computed by sampling the flow fields using both 2D and 3D passive particles is found to be consistent with the Richardson regime. Relative dispersion is an order of magnitude higher and 2D surface releases transition to Richardson regime faster in the wind-forced case. We also show that the buoyancy-forced case results in significantly lower amplitudes of scale-dependent horizontal relative diffusivity, kD(ℓ), than those reported by Okubo (1970), while the wind- and buoyancy-forced case shows a good agreement with Okubo's diffusivity amplitude, and the scaling is consistent with Richardson's 4/3rd law, kD ∼ ℓ4/3. These modeling results provide a framework for measuring material dispersion by mixed layer flows in future observational programs.

Anharmonic vibrational spectra and mode-mode couplings analysis of 2-aminopyridine

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Alam, Mohammad Jane; Afroz, Ziya; Bhat, Sheeraz Ahmad; Ahmad, Shabbir

2018-01-01

Vibrational spectra of 2-aminopyridine (2AP) have been analyzed using the vibrational self-consistence field theory (VSCF), correlated corrected vibrational self-consistence field theory (CC-VSCF) and vibrational perturbation theory (VPT2) at B3LYP/6-311G(d,p) framework. The mode-mode couplings affect the vibrational frequencies and intensities. The coupling integrals between pairs of normal modes have been obtained on the basis of quartic force field (2MR-QFF) approximation. The overtone and combination bands are also assigned in the FTIR spectrum with the help of anharmonic calculation at VPT2 method. A statistical analysis of deviations shows that estimated anharmonic frequencies are closer to the experiment over harmonic approximation. Furthermore, the anharmonic correction has also been carried out for the dimeric structure of 2AP. The fundamental vibration bands have been assigned on the basis of potential energy distribution (PED) and visual look over the animated modes. Other important molecular properties such as frontier molecular orbitals and molecular electrostatics potential mapping have also been analyzed.

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

PubMed

Plocková, J; Chmelík, J

2001-05-25

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

The Impact of Model and Rainfall Forcing Errors on Characterizing Soil Moisture Uncertainty in Land Surface Modeling

NASA Technical Reports Server (NTRS)

Maggioni, V.; Anagnostou, E. N.; Reichle, R. H.

2013-01-01

The contribution of rainfall forcing errors relative to model (structural and parameter) uncertainty in the prediction of soil moisture is investigated by integrating the NASA Catchment Land Surface Model (CLSM), forced with hydro-meteorological data, in the Oklahoma region. Rainfall-forcing uncertainty is introduced using a stochastic error model that generates ensemble rainfall fields from satellite rainfall products. The ensemble satellite rain fields are propagated through CLSM to produce soil moisture ensembles. Errors in CLSM are modeled with two different approaches: either by perturbing model parameters (representing model parameter uncertainty) or by adding randomly generated noise (representing model structure and parameter uncertainty) to the model prognostic variables. Our findings highlight that the method currently used in the NASA GEOS-5 Land Data Assimilation System to perturb CLSM variables poorly describes the uncertainty in the predicted soil moisture, even when combined with rainfall model perturbations. On the other hand, by adding model parameter perturbations to rainfall forcing perturbations, a better characterization of uncertainty in soil moisture simulations is observed. Specifically, an analysis of the rank histograms shows that the most consistent ensemble of soil moisture is obtained by combining rainfall and model parameter perturbations. When rainfall forcing and model prognostic perturbations are added, the rank histogram shows a U-shape at the domain average scale, which corresponds to a lack of variability in the forecast ensemble. The more accurate estimation of the soil moisture prediction uncertainty obtained by combining rainfall and parameter perturbations is encouraging for the application of this approach in ensemble data assimilation systems.

Generation of 24 T at 4.2 K using a layer-wound GdBCO insert coil with Nb3Sn and Nb-Ti external magnetic field coils

NASA Astrophysics Data System (ADS)

Matsumoto, S.; Kiyoshi, T.; Otsuka, A.; Hamada, M.; Maeda, H.; Yanagisawa, Y.; Nakagome, H.; Suematsu, H.

2012-02-01

High-temperature superconducting (HTS) magnets are believed to be a practical option in the development of high field nuclear magnetic resonance (NMR) systems. The development of a 600 MHz NMR system that uses an HTS magnet and a probe with an HTS radio frequency coil is underway. The HTS NMR magnet is expected to reduce the volume occupied by the magnet and to encourage users to install higher field NMR systems. The tolerance to high tensile stress is expected for HTS conductors in order to reduce the magnet in volume. A layer-wound Gd-Ba-Cu-O (GdBCO) insert coil was fabricated in order to investigate its properties under a high electromagnetic force in a high magnetic field. The GdBCO insert coil was successfully operated at a current of up to 321 A and an electromagnetic force BJR of 408 MPa in an external magnetic field generated by Nb3Sn and Nb-Ti low-temperature superconducting coils. The GdBCO insert coil also managed to generate a magnetic field of 6.8 T at the center of the coil in an external magnetic field of 17.2 T. The superconducting magnet consisting of GdBCO, Nb3Sn and Nb-Ti coils successfully generated a magnetic field of 24.0 T at 4.2 K, which represents a new record for a superconducting magnet.

The average magnetic field draping and consistent plasma properties of the Venus magnetotail

NASA Technical Reports Server (NTRS)

Mccomas, D. J.; Spence, H. E.; Russell, C. T.; Saunders, M. A.

1986-01-01

The detailed average draping pattern of the magnetic field in the deep Venus magnetotail is examined. The variability of the data ordered by spatial location is studied, and the groundwork is laid for developing a coordinate system which measured locations with respect to the tail structures. The reconstruction of the tail in the presence of flapping using a new technique is shown, and the average variations in the field components are examined, including the average field vectors, cross-tail current density distribution, and J x B forces as functions of location across the tail. The average downtail velocity is derived as a function of distance, and a simple model based on the field variations is defined from which the average plasma acceleration is obtained as a function of distance, density, and temperature.

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

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

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

Force Concept Inventory-Based Multiple-Choice Test for Investigating Students' Representational Consistency

ERIC Educational Resources Information Center

Nieminen, Pasi; Savinainen, Antti; Viiri, Jouni

2010-01-01

This study investigates students' ability to interpret multiple representations consistently (i.e., representational consistency) in the context of the force concept. For this purpose we developed the Representational Variant of the Force Concept Inventory (R-FCI), which makes use of nine items from the 1995 version of the Force Concept Inventory…

Installation Restoration Program Records Search for Kingsley Field, Oregon.

DTIC Science & Technology

1982-06-01

Hazardous Assesment Rating Methodology (HARM), is now used for all Air Force IRP studies. To maintain consistency, AFESC had their on-call contractors review...Installation History D. Industrial Facilities E. POL Storage Tanks F. Abandoned Tanks G. Oil/Water Separators :" H. Site Hazard Rating Methodology I. Site...and implementing regulations. The pur- pose of DOD policy is to control the migration of hazardous material contaminants from DOD installations. 3

Battle Staff Training and Synchronization in Light Infantry Battalions and Task Forces

DTIC Science & Technology

1991-12-01

Institute for the Behavioral and Social Sciences Fort Benning Field Unit (ARI-Benning) joined the Training Research Laboratory’s Determinants of Effective ...and unforgiving. The effective management and manipulation of stressors in a continuous operations environment, along with an efficient and consistent...an organizational effectiveness model grounded in the General Systems Theory model. An extensive body of work was reviewed, but two authors stand out

Introduction of Women into Work Groups in Traditionally Male Career Fields: Annotated Bibliography.

DTIC Science & Technology

1980-06-01

based on Bass’ theory of interpersonal behavior in organizations, consists of 27 forced-choice interest and opinion items. There are three scales in...Constantinople reviews the theory and measurement of mas- culinity-femininity as a unidimensional bipolar concept. She concludes that evidence...tends toward traditional stereotypes (male-task oriented, female- socioemotional ), but in mixed-sex groups they are less likely to indulge in stereo

Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide

PubMed Central

MacKerell, Alexander D.; Shim, Ji Hyun; Anisimov, Victor M.

2010-01-01

The accuracy of empirical force fields is inherently related to the quality of the target data used for optimization of the model. With the heat of vaporization (ΔHvap) of N-methylacetamide (NMA), a range of values have been reported as target data for optimization of the nonbond parameters associated with the peptide bond in proteins. In the present work, the original experimental data and Antoine constants used for the determination of the ΔHvap of NMA are reanalyzed. Based on this analysis, the wide range of ΔHvap values reported in the literature are shown to be due to incorrect reporting of the temperatures at which the original values were extracted and limitations in the quality of experimental vapor pressure-temperature data over a wide range of temperatures. Taking these problems into account, a consistent ΔHvap value is extracted from three studies for which experimental data are available. This analysis suggests that the most reliable value for ΔHvap is 13.0±0.1 at 410 K for use in force field optimization studies. The present results also indicate that similar analyses, including analysis of Antoine constants alone, may be of utility when reported ΔHvap values are not consistent for a given neat liquid. PMID:20445813

The Layered Structure of The Universe

NASA Astrophysics Data System (ADS)

Kursunoglu, Behram N.

2003-06-01

It has now become a habit for the cosmologists to introduce attraction or repulsion generating substances to describe the observed cosmological behavior of matter. Examples are dark energy to provide repulsive force to cause increasing acceleration accompanying the expansion of the universe, quintessence providing repulsive force. In this paper we believe that what is needed in the final analysis is attraction and repulsion. We show here that universe can be conceived to consist of attractive and repulsive layers of matter expanding with increasing acceleration. The generalized theory of gravitation as developed originally by Einstein and Schrödinger as a non-symmetric theory was modified by this author using Bianchi-Einstein Identities yielding coupling between the field and electric charge as well as between the field and magnetic charge, and there appears a fundamental length parameter ro where quintessence constitute magnetic repulsive layers while dark energy and all other kinds of names invented by cosmologists refer to attractive electric layers. This layered structure of the universe resembles the layered structure of the elementary particle predicted by this theory decades ago (1, 3, and 6). This implies a layer Doughnut structure of the universe. We have therefore, obtained a unification of the structure of the universe and the structure of elementary particles. Overall the forces consist of long range attractive, long range repulsive, short-range attractive, and short-range repulsive variety. We further discovered the existence of space oscillations whose roles in the expansion of the universe with increasing acceleration and further the impact in the propagation of the gravitational waves can be expected to play a role in their observation.

Experimental investigation of SDBD plasma actuator driven by AC high voltage with a superimposed positive pulse bias voltage

NASA Astrophysics Data System (ADS)

Qi, Xiao-Hua; Yan, Hui-Jie; Yang, Liang; Hua, Yue; Ren, Chun-Sheng

2017-08-01

In this work, a driven voltage consisting of AC high voltage with a superimposed positive pulse bias voltage ("AC+ Positive pulse bias" voltage) is adopted to study the performance of a surface dielectric barrier discharge plasma actuator under atmospheric conditions. To compare the performance of the actuator driven by single-AC voltage and "AC+ Positive pulse bias" voltage, the actuator-induced thrust force and power consumption are measured as a function of the applied AC voltage, and the measured results indicate that the thrust force can be promoted significantly after superimposing the positive pulse bias voltage. The physical mechanism behind the thrust force changes is analyzed by measuring the optical properties, electrical characteristics, and surface potential distribution. Experimental results indicate that the glow-like discharge in the AC voltage half-cycle, next to the cycle where a bias voltage pulse has been applied, is enhanced after applying the positive pulse bias voltage, and this perhaps is the main reason for the thrust force increase. Moreover, surface potential measurement results reveal that the spatial electric field formed by the surface charge accumulation after positive pulse discharge can significantly affect the applied external electric field, and this perhaps can be responsible for the experimental phenomenon that the decrease of thrust force is delayed by pulse bias voltage action after the filament discharge occurs in the glow-like discharge region. The schlieren images further verify that the actuator-induced airflow velocity increases with the positive pulse voltage.

Dynamic Kerr effect in a strong uniform AC electric field for interacting polar and polarizable molecules in the mean field approximation

NASA Astrophysics Data System (ADS)

Deshmukh, Snehal D.; Déjardin, Pierre-Michel; Kalmykov, Yuri P.

2017-09-01

Analytical formulas for the electric birefringence response of interacting polar and anisotropically polarizable molecules due to a uniform alternating electric field are derived using Berne's forced rotational diffusion model [B. J. Berne, J. Chem. Phys. 62, 1154 (1975)] in the nonlinear version described by Warchol and Vaughan [J. Chem. Phys. 71, 502 (1979)]. It is found for noninteracting molecules that the signal consists of a frequency-dependent DC component superimposed on an oscillatory part with a frequency twice that of the AC driving field. However, unlike noninteracting molecules, the AC part strongly deviates from its dilute counterpart. This suggests a possible way of motivating new experimental studies of intermolecular interactions involving electro-optical methods and complementary nonlinear dielectric relaxation experiments.

Lagrangian equations of motion of particles and photons in a Schwarzschild field

NASA Astrophysics Data System (ADS)

Ritus, V. I.

2015-11-01

The equations of motion of a particle in the gravitational field of a black hole are considered in a formulation that uses generalized coordinates, velocities, and accelerations and is convenient for finding the integrals of motion. The equations are rewritten in terms of the physical velocities and accelerations measured in the Schwarzschild frame by a stationary observer using proper local length and time standards. The attractive force due to the field and the centripetal acceleration of a particle is proportional to the particle kinetic energy m/\\sqrt{1 - v^2}, consistently with the fact that the particle kinetic energy and the photon energy \\hbarω in the field increase by the same factor compared with their values without a field. The attraction exerted on particles and photons by a gravitational field source is proportional to their kinetic energies. The particle trajectory in the ultrarelativistic limit v \\to 1 coincides with the photon trajectory.

Alchemical prediction of hydration free energies for SAMPL

PubMed Central

Mobley, David L.; Liu, Shaui; Cerutti, David S.; Swope, William C.; Rice, Julia E.

2013-01-01

Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge. Our calculations are largely based on the Generalized Amber Force Field (GAFF) with several different charge models, and we achieved RMS errors in the 1.4-2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies1-5. The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings5. Switching to OPLS Lennard-Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. PMID:22198475

Force Limited Random Vibration Test of TESS Camera Mass Model

NASA Technical Reports Server (NTRS)

Karlicek, Alexandra; Hwang, James Ho-Jin; Rey, Justin J.

2015-01-01

The Transiting Exoplanet Survey Satellite (TESS) is a spaceborne instrument consisting of four wide field-of-view-CCD cameras dedicated to the discovery of exoplanets around the brightest stars. As part of the environmental testing campaign, force limiting was used to simulate a realistic random vibration launch environment. While the force limit vibration test method is a standard approach used at multiple institutions including Jet Propulsion Laboratory (JPL), NASA Goddard Space Flight Center (GSFC), European Space Research and Technology Center (ESTEC), and Japan Aerospace Exploration Agency (JAXA), it is still difficult to find an actual implementation process in the literature. This paper describes the step-by-step process on how the force limit method was developed and applied on the TESS camera mass model. The process description includes the design of special fixtures to mount the test article for properly installing force transducers, development of the force spectral density using the semi-empirical method, estimation of the fuzzy factor (C2) based on the mass ratio between the supporting structure and the test article, subsequent validating of the C2 factor during the vibration test, and calculation of the C.G. accelerations using the Root Mean Square (RMS) reaction force in the spectral domain and the peak reaction force in the time domain.

Numerical analysis of multicomponent responses of surface-hole transient electromagnetic method

NASA Astrophysics Data System (ADS)

Meng, Qing-Xin; Hu, Xiang-Yun; Pan, He-Ping; Zhou, Feng

2017-03-01

We calculate the multicomponent responses of surface-hole transient electromagnetic method. The methods and models are unsuitable as geoelectric models of conductive surrounding rocks because they are based on regular local targets. We also propose a calculation and analysis scheme based on numerical simulations of the subsurface transient electromagnetic fields. In the modeling of the electromagnetic fields, the forward modeling simulations are performed by using the finite-difference time-domain method and the discrete image method, which combines the Gaver-Stehfest inverse Laplace transform with the Prony method to solve the initial electromagnetic fields. The precision in the iterative computations is ensured by using the transmission boundary conditions. For the response analysis, we customize geoelectric models consisting of near-borehole targets and conductive wall rocks and implement forward modeling simulations. The observed electric fields are converted into induced electromotive force responses using multicomponent observation devices. By comparing the transient electric fields and multicomponent responses under different conditions, we suggest that the multicomponent-induced electromotive force responses are related to the horizontal and vertical gradient variations of the transient electric field at different times. The characteristics of the response are determined by the varying the subsurface transient electromagnetic fields, i.e., diffusion, attenuation and distortion, under different conditions as well as the electromagnetic fields at the observation positions. The calculation and analysis scheme of the response consider the surrounding rocks and the anomalous field of the local targets. It therefore can account for the geological data better than conventional transient field response analysis of local targets.

Three Dimensional Distribution of Sensitive Field and Stress Field Inversion of Force Sensitive Materials under Constant Current Excitation.

PubMed

Zhao, Shuanfeng; Liu, Min; Guo, Wei; Zhang, Chuanwei

2018-02-28

Force sensitive conductive composite materials are functional materials which can be used as the sensitive material of force sensors. However, the existing sensors only use one-dimensional electrical properties of force sensitive conductive materials. Even in tactile sensors, the measurement of contact pressure is achieved by large-scale arrays and the units of a large-scale array are also based on the one-dimensional electrical properties of force sensitive materials. The main contribution of this work is to study the three-dimensional electrical properties and the inversion method of three-dimensional stress field of a force sensitive material (conductive rubber), which pushes the application of force sensitive material from one dimensional to three-dimensional. First, the mathematical model of the conductive rubber current field distribution under a constant force is established by the effective medium theory, and the current field distribution model of conductive rubber with different geometry, conductive rubber content and conductive rubber relaxation parameters is deduced. Secondly, the inversion method of the three-dimensional stress field of conductive rubber is established, which provides a theoretical basis for the design of a new tactile sensor, three-dimensional stress field and space force based on force sensitive materials.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelley, Anne Myers

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 formore » 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.« less

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

PubMed

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.

Two-fluid model of the pulsar magnetosphere represented as an axisymmetric force-free dipole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrova, S.A., E-mail: petrova@rian.kharkov.ua

Based on the exact dipolar solution of the pulsar equation the self-consistent two-fluid model of the pulsar magnetosphere is developed. We concentrate on the low-mass limit of the model, taking into account the radiation damping. As a result, we obtain the particle distributions sustaining the dipolar force-free configuration of the pulsar magnetosphere in case of a slight velocity shear of the electron and positron components. Over most part of the force-free region, the particles follow the poloidal magnetic field lines, with the azimuthal velocities being small. Close to the Y-point, however, the particle motion is chiefly azimuthal and the Lorentz-factormore » grows unrestrictedly. This may result in the very-high-energy emission from the vicinity of the Y-point and may also imply the magnetocentrifugal formation of a jet. As for the first-order quantities, the longitudinal accelerating electric field is found to change the sign, hinting at coexistence of the polar and outer gaps. Besides that, the components of the plasma conductivity tensor are derived and the low-mass analogue of the pulsar equation is formulated as well.« less

Magnetically adjustable intraocular lens.

PubMed

Matthews, Michael Wayne; Eggleston, Harry Conrad; Pekarek, Steven D; Hilmas, Greg Eugene

2003-11-01

To provide a noninvasive, magnetic adjustment mechanism to the repeatedly and reversibly adjustable, variable-focus intraocular lens (IOL). University of Missouri-Rolla, Rolla, and Eggleston Adjustable Lens, St. Louis, Missouri, USA. Mechanically adjustable IOLs have been fabricated and tested. Samarium and cobalt rare-earth magnets have been incorporated into the poly(methyl methacrylate) (PMMA) optic of these adjustable lenses. The stability of samarium and cobalt in the PMMA matrix was examined with leaching studies. Operational force testing of the magnetic optics with emphasis on the rotational forces of adjustment was done. Prototype optics incorporating rare-earth magnetic inserts were consistently produced. After 32 days in solution, samarium and cobalt concentration reached a maximum of 5 ppm. Operational force measurements indicate that successful adjustments of this lens can be made using external magnetic fields with rotational torques in excess of 0.6 ounce inch produced. Actual lenses were remotely adjusted using magnetic fields. The magnetically adjustable version of this IOL is a viable and promising means of handling the common issues of postoperative refractive errors without the requirement of additional surgery. The repeatedly adjustable mechanism of this lens also holds promise for the developing eyes of pediatric patients and the changing needs of all patients.

Insole optical fiber Bragg grating sensors network for dynamic vertical force monitoring

NASA Astrophysics Data System (ADS)

Domingues, Maria Fátima; Tavares, Cátia; Leitão, Cátia; Frizera-Neto, Anselmo; Alberto, Nélia; Marques, Carlos; Radwan, Ayman; Rodriguez, Jonathan; Postolache, Octavian; Rocon, Eduardo; André, Paulo; Antunes, Paulo

2017-09-01

In an era of unprecedented progress in technology and increase in population age, continuous and close monitoring of elder citizens and patients is becoming more of a necessity than a luxury. Contributing toward this field and enhancing the life quality of elder citizens and patients with disabilities, this work presents the design and implementation of a noninvasive platform and insole fiber Bragg grating sensors network to monitor the vertical ground reaction forces distribution induced in the foot plantar surface during gait and body center of mass displacements. The acquired measurements are a reliable indication of the accuracy and consistency of the proposed solution in monitoring and mapping the vertical forces active on the foot plantar sole, with a sensitivity up to 11.06 pm/N. The acquired measurements can be used to infer the foot structure and health condition, in addition to anomalies related to spine function and other pathologies (e.g., related to diabetes); also its application in rehabilitation robotics field can dramatically reduce the computational burden of exoskeletons' control strategy. The proposed technology has the advantages of optical fiber sensing (robustness, noninvasiveness, accuracy, and electromagnetic insensitivity) to surpass all drawbacks verified in traditionally used sensing systems (fragility, instability, and inconsistent feedback).

Optimization of robotic welding procedures for maintenance repair of hydraulic turbines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamarche, L.; Galopin, M.; Simoneau, R.

1996-12-31

A six axes super-compact robot is used for field repair of cavitation damages found on the discharge ring of hydraulic turbines. Optimization of overlay welding procedures to minimize surface distortion and reduce tearing forces on anchors in concrete, were studied through experimentation and FEM modelling. Planned experimentation has been used to develop optimum pulsed GMAW schedules of stainless steel overlays in 2G position. Best welding sequence was resolved through over lay welding of free plates. Each overlay consisted in one or two layers which were welded in the longitudinal and/or transverse direction of the rectangular plate. A bidirectional welding mode,more » a longitudinal layer followed by a transverse layer position and no cooling between the two layers, were found to be most effective in reducing distortion. The optimized 2G welding procedure was applied to a simulated field repair. Plate was anchored on a massive iron bracket with a set of instrumented bolts, to understand how normal tearing forces in anchors evolve. Preliminary results on FEM modelling of lateral force on anchors indicate good correlation with experiments, for an elementary design.« less

Insole optical fiber Bragg grating sensors network for dynamic vertical force monitoring.

PubMed

Domingues, Maria Fátima; Tavares, Cátia; Leitão, Cátia; Frizera-Neto, Anselmo; Alberto, Nélia; Marques, Carlos; Radwan, Ayman; Rodriguez, Jonathan; Postolache, Octavian; Rocon, Eduardo; André, Paulo; Antunes, Paulo

2017-09-01

In an era of unprecedented progress in technology and increase in population age, continuous and close monitoring of elder citizens and patients is becoming more of a necessity than a luxury. Contributing toward this field and enhancing the life quality of elder citizens and patients with disabilities, this work presents the design and implementation of a noninvasive platform and insole fiber Bragg grating sensors network to monitor the vertical ground reaction forces distribution induced in the foot plantar surface during gait and body center of mass displacements. The acquired measurements are a reliable indication of the accuracy and consistency of the proposed solution in monitoring and mapping the vertical forces active on the foot plantar sole, with a sensitivity up to 11.06 ?? pm / N . The acquired measurements can be used to infer the foot structure and health condition, in addition to anomalies related to spine function and other pathologies (e.g., related to diabetes); also its application in rehabilitation robotics field can dramatically reduce the computational burden of exoskeletons’ control strategy. The proposed technology has the advantages of optical fiber sensing (robustness, noninvasiveness, accuracy, and electromagnetic insensitivity) to surpass all drawbacks verified in traditionally used sensing systems (fragility, instability, and inconsistent feedback).

Mechanical testing and development of the helical field coil joint for the Advanced Toroidal Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, B.E.; Bryan, W.E.; Goranson, P.L.

1985-01-01

The helical field (HF) coil set for the Advanced Toroidal Facility (ATF) is an M = 12, l = 2, constant-ratio torsatron winding consisting of 2 coils, each with 14 turns of heavy copper conductor. The coils are divided into 24 identical segments to facilitate fabrication and minimize the assembly schedule. The segments are connected across through-bolted lap joints that must carry up to 124,000 A per turn for 5 s or 62,500 A steady-state. In addition, the joints must carry the high magnetic and thermal loads induced in the conductor and still fit within the basic 140- by 30-mmmore » copper envelope. Extensive testing and development were undertaken to verify and refine the basic joint design. Tests included assembly force and clamping force for various types of misalignment; joint resistance as a function of clamping force; clamp bolt relaxation due to thermal cycling; fatigue testing of full-size, multiturn joint prototypes; and low-cycle fatigue and tensile tests of annealed CDA102 copper. The required performance parameters and actual test results, as well as the final joint configuration, are presented. 2 refs., 9 figs., 4 tabs.« less

Nonlinear oscillations and waves in multi-species cold plasmas

NASA Astrophysics Data System (ADS)

Verma, Prabal Singh

2016-12-01

The spatio-temporal evolution of nonlinear oscillations in multi-species plasma is revisited to provide more insight into the physics of phase mixing by constructing two sets of nonlinear solutions up to the second order. The first solution exhibits perfect oscillations in the linear regime and phase mixing appears only nonlinearly in the second order as a response to the ponderomotive forces. This response can be both direct and indirect. The indirect contribution of the ponderomotive forces appears through self-consistently generated low frequency fields. Furthermore, the direct and indirect contributions of the ponderomotive forces on the phase mixing process is explored and it is found that the indirect contribution is negligible in an electron-ion plasma and it disappears in the case of electron-positron plasma, yet represents an equal contribution in the electron-positron-ion plasma. However, the second solution does not exhibit any phase mixing due to the absence of ponderomotive forces but results in an undistorted nonlinear traveling wave. These investigations have relevance for laboratory/astrophysical multi-species plasma.

Dynamically balanced absolute sea level of the global ocean derived from near-surface velocity observations

NASA Astrophysics Data System (ADS)

Niiler, Pearn P.; Maximenko, Nikolai A.; McWilliams, James C.

2003-11-01

The 1992-2002 time-mean absolute sea level distribution of the global ocean is computed for the first time from observations of near-surface velocity. For this computation, we use the near-surface horizontal momentum balance. The velocity observed by drifters is used to compute the Coriolis force and the force due to acceleration of water parcels. The anomaly of horizontal pressure gradient is derived from satellite altimetry and corrects the temporal bias in drifter data distribution. NCEP reanalysis winds are used to compute the force due to Ekman currents. The mean sea level gradient force, which closes the momentum balance, is integrated for mean sea level. We find that our computation agrees, within uncertainties, with the sea level computed from the geostrophic, hydrostatic momentum balance using historical mean density, except in the Antarctic Circumpolar Current. A consistent horizontally and vertically dynamically balanced, near-surface, global pressure field has now been derived from observations.

Dust ion-acoustic shock waves in magnetized pair-ion plasma with kappa distributed electrons

NASA Astrophysics Data System (ADS)

Kaur, B.; Singh, M.; Saini, N. S.

2018-01-01

We have performed a theoretical and numerical analysis of the three dimensional dynamics of nonlinear dust ion-acoustic shock waves (DIASWs) in a magnetized plasma, consisting of positive and negative ion fluids, kappa distributed electrons, immobile dust particulates along with positive and negative ion kinematic viscosity. By employing the reductive perturbation technique, we have derived the nonlinear Zakharov-Kuznetsov-Burgers (ZKB) equation, in which the nonlinear forces are balanced by dissipative forces (associated with kinematic viscosity). It is observed that the characteristics of DIASWs are significantly affected by superthermality of electrons, magnetic field strength, direction cosines, dust concentration, positive to negative ions mass ratio and viscosity of positive and negative ions.

Detection of pure inverse spin-Hall effect induced by spin pumping at various excitation

NASA Astrophysics Data System (ADS)

Inoue, H. Y.; Harii, K.; Ando, K.; Sasage, K.; Saitoh, E.

2007-10-01

Electric-field generation due to the inverse spin-Hall effect (ISHE) driven by spin pumping was detected and separated experimentally from the extrinsic magnetogalvanic effects in a Ni81Fe19/Pt film. By applying a sample-cavity configuration in which the extrinsic effects are suppressed, the spin pumping using ferromagnetic resonance gives rise to a symmetric spectral shape in the electromotive force spectrum, indicating that the motive force is due entirely to ISHE. This method allows the quantitative analysis of the ISHE and the spin-pumping effect. The microwave-power dependence of the ISHE amplitude is consistent with the prediction of a direct current-spin-pumping scenario.

Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

NASA Astrophysics Data System (ADS)

Hofmann, D. W. M.; Kuleshova, L. N.

2018-05-01

Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

Ecological risk assessment for Mather Air Force Base, California: Phase 1, screening assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyers-Schoene, L.; Fischer, N.T.; Rabe, J.J.

Mather Air Force Base (AFB) is among the numerous facilities scheduled for closure under the US Air Force (USAF) Installation Restoration Program (IRP). A component of the Mather AFB IRP is to prepare risk assessments for each of the chemically contaminated sites. Because no previous ecological risk related studies have been conducted on Mather AFB, the authors proposed a phased approach to assessing ecological risks at the base. Phase 1 consisted of baseline ecological surveys that collected data over a 12-month period. In addition, benchmark screening criteria were used in conjunction with modeling results that utilized measured concentrations of chemicalmore » analytes in abiotic samples. Phase 2 may consist of the collection of more site-specific data and toxicity testing, if warranted by the Phase 1 screening analysis. This approach was in agreement with the USAF`s ecological risk assessment guidance and met the approval of the Air Force and USEPA Region 9. The authors found the use of established and derived screening values to effectively aid in the focusing of the ecological risk assessment on those chemicals most likely to be hazardous to ecological receptors at the base. Disadvantages in the use of screening values include the uncertainties associated with the conservative assumptions inherent in the derivation of benchmark values and the difficulty in extrapolating from laboratory determined benchmark values to impacts in the field.« less

Field measurement of basal forces generated by erosive debris flows

USGS Publications Warehouse

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

2013-01-01

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

Magnetic fields in giant planet formation and protoplanetary discs

NASA Astrophysics Data System (ADS)

Keith, Sarah Louise

2015-12-01

Protoplanetary discs channel accretion onto their host star. How this is achieved is critical to the growth of giant planets which capture their massive gaseous atmosphere from the surrounding flow. Theoretical studies find that an embedded magnetic field could power accretion by hydromagnetic turbulence or torques from a large-scale field. This thesis presents a study of the inuence of magnetic fields in three key aspects of this process: circumplanetary disc accretion, gas flow across gaps in protoplanetary discs, and magnetic-braking in accretion discs. The first study examines the conditions needed for self-consistent accretion driven by magnetic fields or gravitational instability. Models of these discs typically rely on hydromagnetic turbulence as the source of effective viscosity. However, magnetically coupled,accreting regions may be so limited that the disc may not support sufficient inflow. An improved Shakura-Sunyaev ? disc is used to calculate the ionisation fraction and strength of non-ideal effects. Steady magnetically-driven accretion is limited to the thermally ionised, inner disc so that accretion in the remainder of the disc is time-dependent. The second study addresses magnetic flux transport in an accretion gap evacuated by a giant planet. Assuming the field is passively drawn along with the gas, the hydrodynamical simulation of Tanigawa, Ohtsuki & Machida (2012) is used for an a posteriori analysis of the gap field structure. This is used to post-calculate magnetohydrodynamical quantities. This assumption is self-consistent as magnetic forces are found to be weak, and good magnetic coupling ensures the field is frozen into the gas. Hall drift dominates across much of the gap, with the potential to facilitate turbulence and modify the toroidal field according to the global field orientation. The third study considers the structure and stability of magnetically-braked accretion discs. Strong evidence for MRI dead-zones has renewed interest in accretion powered by large-scale fields. An equilibrium model is presented for the radial structure of an axisymmetric, magnetically-braked accretion disc connected to a force-free external field. The accretion rate is multivalued at protoplanetary disc column densities, featuring an `S-curve' associated with models of accretion outbursting. A local, linear analysis of the stability of radial modes finds that the rapidly accreting, middle and upper solution branches are unstable, further highlighting the potential for eruptive accretion events.

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

PubMed

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.

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

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

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

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

Measurement of the adhesion force between particles for high gradient magnetic separation of pneumatic conveyed powder products

NASA Astrophysics Data System (ADS)

Senkawa, K.; Nakai, Y.; Mishima, F.; Akiyama, Y.; Nishijima, S.

2011-11-01

In the industrial plants such as foods, medicines or industrial materials, there are big amount of issues on contamination by metallic wear debris originated from pipes of manufacturing lines. In this study, we developed a high gradient magnetic separation system (HGMS) under the dry process by using superconducting magnet to remove the ferromagnetic particles. One of the major problems of dry HGMS systems is, however, the blockage of magnetic filter caused by particle coagulation or deposition. In order to actualize the magnetic separation without blockage, we introduced pneumatic conveyance system as a new method to feed the powder. It is important to increase the drag force acting on the sufficiently dispersed particles, which require strong magnetic fields. To generate the strong magnetic fields, HGMS technique was examined which consists of a magnetic filter and a superconducting solenoid magnet. As a result of the magnetic separation experiment, it was shown that the separation efficiency changes due to the difference of the cohesive property of the particles. On the basis of the result, the adhesion force which acts between the ferromagnetic particles and the medium particles used for the magnetic separation was measured by Atomic Force Microscope (AFM), and cohesion of particles was studied from the aspect of interparticle interaction. We assessed a suitable flow velocity for magnetic separation according to the cohesive property of each particle based on the result.

QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

PubMed

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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

PubMed

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

2016-11-09

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

The electromagnetic force field, fluid flow field and temperature profiles in levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation was developed for the electromagnetic force field, the flow field, the temperature field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was employed for the calculation of the electromagnetic force field, while the turbulent Navier - Stokes equations and the turbulent convective transport equations were used to represent the fluid flow field, the temperature field and the concentration field. The governing differential equations, written in spherical coordinates, were solved numerically. The computed results were in good agreement with measurements, regarding the lifting force, and the average temperature of the specimen and carburization rates, which were transport controlled.

Extracting the potential-well of a near-field optical trap using the Helmholtz-Hodge decomposition

NASA Astrophysics Data System (ADS)

Zaman, Mohammad Asif; Padhy, Punnag; Hansen, Paul C.; Hesselink, Lambertus

2018-02-01

The non-conservative nature of the force field generated by a near-field optical trap is analyzed. A plasmonic C-shaped engraving on a gold film is considered as the trap. The force field is calculated using the Maxwell stress tensor method. The Helmholtz-Hodge decomposition is used to extract the conservative and the non-conservative component of the force. Due to the non-negligible non-conservative component, it is found that the conventional approach of extracting the potential by direct integration of the force is not accurate. Despite the non-conservative nature of the force field, it is found that the statistical properties of a trapped nanoparticle can be estimated from the conservative component of the force field alone. Experimental and numerical results are presented to support the claims.

Muscle co-contraction patterns in robot-mediated force field learning to guide specific muscle group training.

PubMed

Pizzamiglio, Sara; Desowska, Adela; Shojaii, Pegah; Taga, Myriam; Turner, Duncan L

2017-01-01

Muscle co-contraction is a strategy of increasing movement accuracy and stability employed in dealing with force perturbation of movement. It is often seen in neuropathological populations. The direction of movement influences the pattern of co-contraction, but not all movements are easily achievable for populations with motor deficits. Manipulating the direction of the force instead, may be a promising rehabilitation protocol to train movement with use of a co-contraction reduction strategy. Force field learning paradigms provide a well described procedure to evoke and test muscle co-contraction. The aim of this study was to test the muscle co-contraction pattern in a wide range of arm muscles in different force-field directions utilising a robot-mediated force field learning paradigm of motor adaptation. Forty-two participants volunteered to participate in a study utilising robot-mediated force field motor adaptation paradigm with a clockwise or counter-clockwise force field. Kinematics and surface electromyography (EMG) of eight arm muscles were measured. Both muscle activation and co-contraction was earlier and stronger in flexors in the clockwise condition and in extensors in the counter-clockwise condition. Manipulating the force field direction leads to changes in the pattern of muscle co-contraction.

Report on the Work of the Bureau of Education for the Natives of Alaska, 1912-13. Bulletin, 1914, No. 31. Whole Number 605

ERIC Educational Resources Information Center

United States Bureau of Education, Department of the Interior, 1914

1914-01-01

During the fiscal year that ended June 30, 1913, the field force of the Alaska school service consisted of 5 superintendents, 109 teachers, 11 physicians (1 of whom also filled another position), 9 nurses, and 3 hospital attendants. Seventy-seven schools were maintained, with an enrollment of 3,563, and an average attendance of 1.797. This…

SERS substrate based on silver nanoparticles and graphene: Dependence on the layer number of graphene

NASA Astrophysics Data System (ADS)

Garg, Preeti; Soni, R. K.; Raman, R.

2018-05-01

In this report, we describe a low-cost fabrication process for highly sensitive SERS substrate by using thermal evaporation technique. The SERS substrate structure consists of silver nanoparticles deposited on monolayer, bilayer and few layer graphene. The fabricated SERS substrates are investigated by field emission scanning electron microscope (FE-SEM), atomic force microscope (AFM), and confocal Raman spectroscope. From the surface morphology we have verified that the fabricated SERS substrate consist of high-density of silver nanoparticles with their size distribution varies from 10 to 150 nm. The surface-enhanced Raman scattering activities of these nanostructures is highest for monolayer graphene.

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Current systems of coronal loops in 3D MHD simulations

NASA Astrophysics Data System (ADS)

Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.

2017-11-01

Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system and the complex interaction of the plasma and the magnetic field in the coronal loop, despite the fact that the loop is under low-β conditions.

Thermal and Lorentz Force Analysis of Beryllium Windows for the Rectilinear Muon Cooling Channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Tianhuan; Li, D.; Virostek, S.

Reduction of the 6-dimensional phase-space of a muon beam by several orders of magnitude is a key requirement for a Muon Collider. Recently, a 12-stage rectilinear ionization cooling channel has been proposed to achieve that goal. The channel consists of a series of low frequency (325 MHz-650 MHz) normal conducting pillbox cavities, which are enclosed with thin beryllium windows (foils) to increase shunt impedance and give a higher field on-axis for a given amount of power. These windows are subject to ohmic heating from RF currents and Lorentz force from the EM field in the cavity, both of which willmore » produce out of the plane displacements that can detune the cavity frequency. In this study, using the TEM3P code, we report on a detailed thermal and mechanical analysis for the actual Be windows used on a 325 MHz cavity in a vacuum ionization cooling rectilinear channel for a Muon Collider.« less

Thermal and Lorentz force analysis of beryllium windows for a rectilinear muon cooling channel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, T.; Stratakis, D.; Li, D.

Reduction of the 6-dimensional phase-space of a muon beam by several orders of magnitude is a key requirement for a Muon Collider. Recently, a 12-stage rectilinear ionization cooling channel has been proposed to achieve that goal. The channel consists of a series of low frequency (325 MHz-650 MHz) normal conducting pillbox cavities, which are enclosed with thin beryllium windows (foils) to increase shunt impedance and give a higher field on-axis for a given amount of power. These windows are subject to ohmic heating from RF currents and Lorentz force from the EM field in the cavity, both of which willmore » produce out of the plane displacements that can detune the cavity frequency. In this study, using the TEM3P code, we report on a detailed thermal and mechanical analysis for the actual Be windows used on a 325 MHz cavity in a vacuum ionization cooling rectilinear channel for a Muon Collider.« less

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Study of VTOL in ground-effect flow field including temperature effect

NASA Technical Reports Server (NTRS)

Hill, W. G.; Jenkins, R. C.; Kalemaris, S. G.; Siclari, M. J.

1982-01-01

Detailed pressure, temperature, and velocity data were obtained for twin-fan configurations in-ground-effect and flow models to aid in predicting pressures and upwash forces on aircraft surfaces were developed. For the basic experiments, 49.5 mm-diameter jets were used, oriented normal to a simulated round plane, with pressurized, heated air providing a jet. The experimental data consisted of: (1) the effect of jet height and temperature on the ground, model, and upwash pressures, and temperatures, (2) the effect of simulated aircraft surfaces on the isolated flow field, (3) the jet-induced forces on a three-dimensional body with various strakes, (4) the effects of non-uniform coannular jets. For the uniform circular jets, temperature was varied from room temperature (24 C) to 232 C. Jet total pressure was varied between 9,300 Pascals and 31,500 Pascals. For the coannular jets, intended to represent turbofan engines, fan temperature was maintained at room temperature while core temperature was varied from room temperature to 437 C. Results are presented.

Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association

PubMed Central

2018-01-01

Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data. PMID:29424543

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

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

DTIC Science & Technology

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

Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

PubMed Central

2017-01-01

We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol). PAC-MAC shows a RMSE of 0.151 kBT with a calculation speed being potentially 1.0 × 104 times greater than TI. OPLS-AA force field parameters are optimized using PAC-MAC based on vapor–liquid equilibrium data, instead of enthalpies of vaporization or densities. The RMSE of PAC-MAC is reduced to 0.099 kBT by optimizing 50 force field parameters. The resulting OPLS-PM force field has a comparable accuracy as the OPLS-AA force field in the calculation of mixing free energies using TI. PMID:28418655

Magnetic moment of solar plasma and the Kelvin force: -The driving force of plasma up-flow -

NASA Astrophysics Data System (ADS)

Shibasaki, Kiyoto

2017-04-01

Thermal plasma in the solar atmosphere is magnetized (diamagnetic). The magnetic moment does not disappear by collisions because complete gyration is not a necessary condition to have magnetic moment. Magnetized fluid is subjected to Kelvin force in non-uniform magnetic field. Generally, magnetic field strength decreases upwards in the solar atmosphere, hence the Kelvin force is directed upwards along the field. This force is not included in the fluid treatment of MHD. By adding the Kelvin force to the MHD equation of motion, we can expect temperature dependent plasma flows along the field which are reported by many observations. The temperature dependence of the flow speed is explained by temperature dependence of magnetic moment. From the observed parameters, we can infer physical parameters in the solar atmosphere such as scale length of the magnetic field strength and the friction force acting on the flowing plasma. In case of closed magnetic field lines, loop-top concentration of hot plasma is expected which is frequently observed.

The Influence of Shape on the Output Potential of ZnO Nanostructures: Sensitivity to Parallel versus Perpendicular Forces.

PubMed

Cardoso, José; Oliveira, Filipe F; Proenca, Mariana P; Ventura, João

2018-05-22

With the consistent shrinking of devices, micro-systems are, nowadays, widely used in areas such as biomedics, electronics, automobiles, and measurement devices. As devices shrunk, so too did their energy consumptions, opening the way for the use of nanogenerators (NGs) as power sources. In particular, to harvest energy from an object's motion (mechanical vibrations, torsional forces, or pressure), present NGs are mainly composed of piezoelectric materials in which, upon an applied compressive or strain force, an electrical field is produced that can be used to power a device. The focus of this work is to simulate the piezoelectric effect in different ZnO nanostructures to optimize the output potential generated by a nanodevice. In these simulations, cylindrical nanowires, nanomushrooms, and nanotrees were created, and the influence of the nanostructures' shape on the output potential was studied as a function of applied parallel and perpendicular forces. The obtained results demonstrated that the output potential is linearly proportional to the applied force and that perpendicular forces are more efficient in all structures. However, nanotrees were found to have an increased sensitivity to parallel applied forces, which resulted in a large enhancement of the output efficiency. These results could then open a new path to increase the efficiency of piezoelectric nanogenerators.

Discrimination of Thermal versus Mechanical Effects of Shock on Rock Magnetic Properties of Spherically Shocked up to 10-160 GPa Basalt and Diabase

NASA Astrophysics Data System (ADS)

Bezaeva, N. S.; Swanson-Hysell, N.; Tikoo, S.; Badyukov, D. D.; Kars, M. A. C.; Egli, R.; Chareev, D. A.; Fairchild, L. M.

2016-12-01

Understanding how shock waves generated during hypervelocity impacts affect rock magnetic properties is key for interpreting the paleomagnetic records of lunar rocks, meteorites, and cratered planetary surfaces. Laboratory simulations of impacts show that ultra-high shocks may induce substantial post-shock heating of the target material. At high pressures (>10 GPa), shock heating occurs in tandem with mechanical effects, such as grain fracturing and creation of crystallographic defects and dislocations within magnetic grains. This makes it difficult to conclude whether shock-induced changes in the rock magnetic properties of target materials are primarily associated with mechanical or thermal effects. Here we present novel experimental methods to discriminate between mechanical and thermal effects of shock on magnetic properties and illustrate it with two examples of spherically shocked terrestrial basalt and diabase [1], which were shocked to pressures of 10 to >160 GPa, and investigate possible explanations for the observed shock-induced magnetic hardening (i.e., increase in remanent coercivity Bcr). The methods consist of i) conducting extra heating experiments at temperatures resembling those experienced during high-pressure shock events on untreated equivalents of shocked rocks (with further comparison of Bcr of shocked and heated samples) and ii) quantitative comparison of high-resolution first-order reversal curve (FORC) diagrams (field step: 0.5-0.7 mT) for shocked, heated and untreated specimens. Using this approach, we demonstrated that the shock-induced coercivity hardening in our samples is predominantly due to solid-state, mechanical effects of shock rather than alteration associated with shock heating. Indeed, heating-induced changes in Bcr in the post-shock temperature range were minor. Visual inspection of FORC contours (in addition to detailed analyses) reveals a stretching of the FORC distribution of shocked sample towards higher coercivities, consistent with shock-induced hardening. However, shock does not alter the intrinsic shape of coercivity and the shape of FORC contours (apart from field scaling) while heating does, which is seen as a significant alteration of FORC contours. Reference: [1] Swanson-Hysell N. L. et al. 2014. G3 15:2039-2047.

Enhancing microscopic cascading contributions to higher-order nonlinear-optical responses through forced geometric constraints

NASA Astrophysics Data System (ADS)

Dawson, Nathan J.; Andrews, James H.; Crescimanno, Michael

2012-10-01

We review a model that was developed to take into account all possible microscopic cascading schemes in a single species system out to the fifth order using a self-consistent field approach. This model was designed to study the effects of boundaries in mesoscopic systems with constrained boundaries. These geometric constraints on the macroscopic structure show how the higher-ordered susceptibilities are manipulated by increasing the surface to volume ratio, while the microscopic structure influences the local field from all other molecules in the system. In addition to the review, we discuss methods of modeling real systems of molecules, where efforts are currently underway.

Astronomically Forced Hydrology of the Late Cretaceous Sub-tropical Potosí Basin, Bolivia

NASA Astrophysics Data System (ADS)

Tasistro-Hart, A.; Maloof, A. C.; Schoene, B.; Eddy, M. P.

2017-12-01

Orbital forcings paced the ice ages of the Pleistocene, demonstrating that periodic variations in the latitudinal distribution of insolation amplified by ice-albedo feedbacks can guide global climate. How these forcings operate in the hot-houses that span most of the planet's history, however, is unknown. The lacustrine El Molino formation of the late Cretaceous-early Paleogene Potosí Basin in present-day Bolivia contains carbonate-mud parasequences that record fluctuating hydrological conditions from 73 to 63 Ma. This study presents the first cyclostratigraphic analysis using high-resolution drone-derived imagery and 3D elevation models, combined with conventional stratigraphic measurements and magnetic susceptibility data. The drone-derived data are integrated over the entire outcrop at two field areas using a novel application of stratigraphic potential field modeling that increases signal-to-noise ratios prior to spectral analysis. We demonstrate that these parasequences exhibit significant periodicities consistent with eccentricity (400 and 100 kyr), obliquity (50 kyr, 40 kyr, and 29 kyr), precession (17-23 kyr), and semi-precession (9-11 kyr). New U-Pb ID-TIMS zircon ages from intercalacted ash beds corroborate the interpreted sedimentation rates at two sites, indicating that the Potosí Basin contains evidence for hot-house astronomical forcing of sub-tropical lacustrine hydrology. Global climate simulations of late Cretaceous orbital end-member configurations demonstrate precessional-eccentricity and obliquity driven modulation of basin hydrology. In model simulations, the forcings drive long-term shifts in the location of the intertropical convergence zone, changing precipitation along the northern extent of the Potosí Basin's catchment area. This study is the first to demonstrate orbital forcing of a lacustrine system during the Maastrichtian and could ultimately contribute to a precise age for the Cretaceous-Paleogene boundary.

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunár, Stanislav; Mackay, Duncan H.

2015-04-20

We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique tomore » consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.« less

Multi-wavelength Observations and Modeling of Solar Flares: Magnetic Structures

NASA Astrophysics Data System (ADS)

Su, Y.

2017-12-01

We present a review of our recent investigations on multi-wavelength observations and magnetic field modeling of solar flares. High-resolution observations taken by NVST and BBSO/NST reveal unprecedented fine structures of the flaring regions. Observations by SDO, IRIS, and GOES provide the complementary information. The magnetic field models are constructed using either non-linear force free field extrapolations or flux rope insertion method. Our studies have shown that the flaring regions often consist of double or multiple flux ropes, which often exist at different heights. The fine flare ribbon structures may be due to the magnetic reconnection in the complex quasi separatrix layers. The magnetic field modeling of several large flares suggests that the so called hot-channel structure is corresponding to the erupting flux rope above the X-point in a magnetic configuration with Hyperbolic Flux Tube.

A finite element study on the mechanical response of the head-neck interface of hip implants under realistic forces and moments of daily activities: Part 1, level walking.

PubMed

Farhoudi, Hamidreza; Fallahnezhad, Khosro; Oskouei, Reza H; Taylor, Mark

2017-11-01

This paper investigates the mechanical response of a modular head-neck interface of hip joint implants under realistic loads of level walking. The realistic loads of the walking activity consist of three dimensional gait forces and the associated frictional moments. These forces and moments were extracted for a 32mm metal-on-metal bearing couple. A previously reported geometry of a modular CoCr/CoCr head-neck interface with a proximal contact was used for this investigation. An explicit finite element analysis was performed to investigate the interface mechanical responses. To study the level of contribution and also the effect of superposition of the load components, three different scenarios of loading were studied: gait forces only, frictional moments only, and combined gait forces and frictional moments. Stress field, micro-motions, shear stresses and fretting work at the contacting nodes of the interface were analysed. Gait forces only were found to significantly influence the mechanical environment of the head-neck interface by temporarily extending the contacting area (8.43% of initially non-contacting surface nodes temporarily came into contact), and therefore changing the stress field and resultant micro-motions during the gait cycle. The frictional moments only did not cause considerable changes in the mechanical response of the interface (only 0.27% of the non-contacting surface nodes temporarily came into contact). However, when superposed with the gait forces, the mechanical response of the interface, particularly micro-motions and fretting work, changed compared to the forces only case. The normal contact stresses and micro-motions obtained from this realistic load-controlled study were typically in the range of 0-275MPa and 0-38µm, respectively. These ranges were found comparable to previous experimental displacement-controlled pin/cylinder-on-disk fretting corrosion studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

Broken Symmetry

ScienceCinema

Englert, Francois

2018-05-24

- Physics, as we know it, attempts to interpret the diverse natural phenomena as particular manifestations of general laws. This vision of a world ruled by general testable laws is relatively recent in the history of mankind. Basically it was initiated by the Galilean inertial principle. The subsequent rapid development of large-scale physics is certainly tributary to the fact that gravitational and electromagnetic forces are long-range and hence can be perceived directly without the mediation of highly sophisticated technical devices. - The discovery of subatomic structures and of the concomitant weak and strong short-range forces raised the question of how to cope with short-range forces in relativistic quantum field theory. The Fermi theory of weak interactions, formulated in terms of point-like current-current interaction, was well-defined in lowest order perturbation theory and accounted for existing experimental data.However, it was inconsistent in higher orders because of uncontrollable divergent quantum fluctuations. In technical terms, in contradistinction to quantum electrodynamics, the Fermi theorywas not “renormalizable”. This difficulty could not be solved by smoothing the point-like interaction by a massive, and therefore short-range, charged “vector” particle exchange: theories with massive charged vector bosons were not renormalizable either. In the early nineteen sixties, there seemed to be insuperable obstacles to formulating a consistent theory with short-range forces mediated by massive vectors. - The breakthrough came from the notion of spontaneous symmetry breaking which arose in the study of phase transitions and was introduced in field theory by Nambu in 1960. - Ferromagnets illustrate the notion in phase transitions. Although no direction is dynamically preferred, the magnetization selects a global orientation. This is a spontaneous broken symmetry(SBS)of rotational invariance. Such continuous SBS imply the existence of “massless” modes (here spin-waves), which are the ancestors of the NG bosons discussed below. Fluctuations of the order parameter (the magnetization) are described by a “massive” SBS mode. - In field theory, Nambu showed that broken chiral symmetry from a spontaneous generation of hadron masses induces massless pseudoscalar modes (identified with a massless limit of pion fields). This illustrates a general phenomenon made explicit by Goldstone: massless Nambu-Goldstone (NG) bosons are a necessary concomitant of spontaneously broken continuous symmetries. Massive SBS scalars bosons describe, as in phase transitions, the fluctuations of the SBS order parameters. - In 1964, with Robert Brout, we discovered a mechanism based on SBS by which short range interactions are generated from long range ones. A similar proposal was then made independently by Higgs in a different approach. Qualitatively, our mechanism works as follows. The long range fundamental electromagnetic and gravitational interactions are governed by extended symmetries,called gauge symmetries, which were supposed to guarantee that the elementary field constituents which transmit the forces, photons or gravitons, be massless. We considered a generalization of the electromagnetic “vector” field, known as Yang-Mills fields, and coupled them to fields which acquire from SBS constant values in the vacuum. These fields pervade space, as did magnetization, but they have no spatial orientation: they are “scalar’’ fields. The vector Yang-Mills fields which interact with the scalar fields become massive and hence the forces they mediate become short ranged. We also showed that the mechanism can survive in absence of elementary scalar fields. - Because of the extended symmetries, the nature of SBS is profoundly altered: the NG fields are absorbed into the massive vector Yang-Mills fields and restore the gauge symmetry. This has a dramatic consequence. To confront precision experiments, the mechanism should be consistent at the quantum mechanical level, or in technical terms, should yield a “renormalizable” theory. From our analysis of the preserved gauge symmetry, we suggested in 1966 that this is indeed the case, in contradistinction to the aforementioned earlier theories of charged massive vector fields. The full proof of “renormalizability” is subtle and was achieved in the impressive work of ‘t Hooft and Veltman. One gains some insight into the subtleties by making explicit the equivalence of Higgs’ approach with ours. - To a large extend, the LHC was build to detect the massive SBS scalar boson, i.e. the fluctuations of the scalar field. More elaborate realizations of the mechanism without elementary scalars are possible, but their experimental confirmation may (or may not) be outside the scope of present available technology. - The mechanism of Brout, Englert and Higgs unified in the same theoretical framework short- and long-range forces. It became the cornerstone of the electroweak theory and opened the way to a modern view on unified laws of nature.

The Canadian Forces ILDS: a militarily fielded multisensor vehicle-mounted teleoperated landmine detection system

NASA Astrophysics Data System (ADS)

McFee, John E.; Russell, Kevin L.; Chesney, Robert H.; Faust, Anthony A.; Das, Yogadhish

2006-05-01

The Improved Landmine Detection System (ILDS) is intended to meet Canadian military mine clearance requirements in rear area combat situations and peacekeeping on roads and tracks. The system consists of two teleoperated vehicles and a command vehicle. The teleoperated protection vehicle precedes, clearing antipersonnel mines and magnetic and tilt rod-fuzed antitank mines. It consists of an armoured personnel carrier with a forward looking infrared imager, a finger plow or roller and a magnetic signature duplicator. The teleoperated detection vehicle follows to detect antitank mines. The purpose-built vehicle carries forward looking infrared and visible imagers, a 3 m wide, down-looking sensitive electromagnetic induction detector array and a 3 m wide down-looking ground probing radar, which scan the ground in front of the vehicle. Sensor information is combined using navigation sensors and custom navigation, registration, spatial correspondence and data fusion algorithms. Suspicious targets are then confirmed by a thermal neutron activation detector. The prototype, designed and built by Defence R&D Canada, was completed in October 1997. General Dynamics Canada delivered four production units, based on the prototype concept and technologies, to the Canadian Forces (CF) in 2002. ILDS was deployed in Afghanistan in 2003, making the system the first militarily fielded, teleoperated, multi-sensor vehicle-mounted mine detector and the first with a fielded confirmation sensor. Performance of the prototype in Canadian and independent US trials is summarized and recent results from the production version of the confirmation sensor are discussed. CF operations with ILDS in Afghanistan are described.

Three-dimensional Kinetic Pulsar Magnetosphere Models: Connecting to Gamma-Ray Observations

NASA Astrophysics Data System (ADS)

Kalapotharakos, Constantinos; Brambilla, Gabriele; Timokhin, Andrey; Harding, Alice K.; Kazanas, Demosthenes

2018-04-01

We present three-dimensional (3D) global kinetic pulsar magnetosphere models, where the charged particle trajectories and the corresponding electromagnetic fields are treated self-consistently. For our study, we have developed a Cartesian 3D relativistic particle-in-cell code that incorporates radiation reaction forces. We describe our code and discuss the related technical issues, treatments, and assumptions. Injecting particles up to large distances in the magnetosphere, we apply arbitrarily low to high particle injection rates, and obtain an entire spectrum of solutions from close to the vacuum-retarded dipole to close to the force-free (FF) solution, respectively. For high particle injection rates (close to FF solutions), significant accelerating electric field components are confined only near the equatorial current sheet outside the light cylinder. A judicious interpretation of our models allows the particle emission to be calculated, and consequently, the corresponding realistic high-energy sky maps and spectra to be derived. Using model parameters that cover the entire range of spin-down powers of Fermi young and millisecond pulsars, we compare the corresponding model γ-ray light curves, cutoff energies, and total γ-ray luminosities with those observed by Fermi to discover a dependence of the particle injection rate, { \\mathcal F }, on the spin-down power, \\dot{{ \\mathcal E }}, indicating an increase of { \\mathcal F } with \\dot{{ \\mathcal E }}. Our models, guided by Fermi observations, provide field structures and particle distributions that are not only consistent with each other but also able to reproduce a broad range of the observed γ-ray phenomenologies of both young and millisecond pulsars.

Characterization of the liquid Li-solid Mo (1 1 0) interface from classical molecular dynamics for plasma-facing applications

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Fürstenberg, Sven; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-11-01

An understanding of the wetting properties and a characterization of the interface between liquid lithium (Li) and solid molybdenum (Mo) are relevant to assessing the efficacy of Li as a plasma-facing component in fusion reactors. In this work, a new second-nearest neighbor modified embedded-atom method (2NN MEAM) force field is parameterized to describe the interactions between Li and Mo. The new force field reproduces several benchmark properties obtained from first-principles quantum mechanics simulations, including binding curves for Li at three different adsorption sites and the corresponding forces on Li atoms adsorbed on the Mo (1 1 0) surface. This force field is then used to study the wetting of liquid Li on the (1 1 0) surface of Mo and to examine the Li-Mo interface using molecular dynamics simulations. From droplet simulations, we find that liquid Li tends to completely wet the perfect Mo (1 1 0) surface, in contradiction with previous experimental measurements that found non-zero contact angles for liquid Li on a Mo substrate. However, these experiments were not carried out under ultra-high vacuum conditions or with a perfect (1 1 0) Mo surface, suggesting that the presence of impurities, such as oxygen, and surface structure play a crucial role in this wetting process. From thin-film simulations, it is observed that the first layer of Li on the Mo (1 1 0) surface has many solid-like properties such as a low mobility and a larger degree of ordering when compared to layers further away from the surface, even at temperatures well above the bulk melting temperature of Li. These findings are consistent with temperature-programmed desorption experiments.

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

PubMed Central

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

2011-01-01

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

Self-consistent analysis of radiation and relativistic electron beam dynamics in a helical wiggler using Lienard-Wiechert fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tecimer, M.; Elias, L.R.

1995-12-31

Lienard-Wiechert (LW) fields, which are exact solutions of the Wave Equation for a point charge in free space, are employed to formulate a self-consistent treatment of the electron beam dynamics and the evolution of the generated radiation in long undulators. In a relativistic electron beam the internal forces leading to the interaction of the electrons with each other can be computed by means of retarded LW fields. The resulting electron beam dynamics enables us to obtain three dimensional radiation fields starting from an initial incoherent spontaneous emission, without introducing a seed wave at start-up. Based on the formalism employed here,more » both the evolution of the multi-bucket electron phase space dynamics in the beam body as well as edges and the relative slippage of the radiation with respect to the electrons in the considered short bunch are naturally embedded into the simulation model. In this paper, we present electromagnetic radiation studies, including multi-bucket electron phase dynamics and angular distribution of radiation in the time and frequency domain produced by a relativistic short electron beam bunch interacting with a circularly polarized magnetic undulator.« less

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

PubMed Central

Petrov, Drazen; Zagrovic, Bojan

2014-01-01

The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD) simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded) and oxidatively damaged (unfolded) forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP) as well as indirectly shown for additional two (AMBER94, OPLS-AAL), and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields may distort the picture of protein behavior in biologically relevant crowded environments. PMID:24854339

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers.

PubMed

Bennett, W F Drew; Hong, Chun Kit; Wang, Yi; Tieleman, D Peter

2016-09-13

Due to antimicrobial resistance, the development of new drugs to combat bacterial and fungal infections is an important area of research. Nature uses short, charged, and amphipathic peptides for antimicrobial defense, many of which disrupt the lipid membrane in addition to other possible targets inside the cell. Computer simulations have revealed atomistic details for the interactions of antimicrobial peptides and cell-penetrating peptides with lipid bilayers. Strong interactions between the polar interface and the charged peptides can induce bilayer deformations - including membrane rupture and peptide stabilization of a hydrophilic pore. Here, we performed microsecond-long simulations of the antimicrobial peptide CM15 in a POPC bilayer expecting to observe pore formation (based on previous molecular dynamics simulations). We show that caution is needed when interpreting results of equilibrium peptide-membrane simulations, given the length of time single trajectories can dwell in local energy minima for 100's of ns to microseconds. While we did record significant membrane perturbations from the CM15 peptide, pores were not observed. We explain this discrepancy by computing the free energy for pore formation with different force fields. Our results show a large difference in the free energy barrier (ca. 40 kJ/mol) against pore formation predicted by the different force fields that would result in orders of magnitude differences in the simulation time required to observe spontaneous pore formation. This explains why previous simulations using the Berger lipid parameters reported pores induced by charged peptides, while with CHARMM based models pores were not observed in our long time-scale simulations. We reconcile some of the differences in the distance dependent free energies by shifting the free energy profiles to account for thickness differences between force fields. The shifted curves show that all the models describe small defects in lipid bilayers in a consistent manner, suggesting a common physical basis.

Novel strategies in feedforward adaptation to a position-dependent perturbation.

PubMed

Hinder, Mark R; Milner, Theodore E

2005-08-01

To investigate the control mechanisms used in adapting to position-dependent forces, subjects performed 150 horizontal reaching movements over 25 cm in the presence of a position-dependent parabolic force field (PF). The PF acted only over the first 10 cm of the movement. On every fifth trial, a virtual mechanical guide (double wall) constrained subjects to move along a straight-line path between the start and target positions. Its purpose was to register lateral force to track formation of an internal model of the force field, and to look for evidence of possible alternative adaptive strategies. The force field produced a force to the right, which initially caused subjects to deviate in that direction. They reacted by producing deviations to the left, "into" the force field, as early as the second trial. Further adaptation resulted in rapid exponential reduction of kinematic error in the latter portion of the movement, where the greatest perturbation to the handpath was initially observed, whereas there was little modification of the handpath in the region where the PF was active. Significant force directed to counteract the PF was measured on the first guided trial, and was modified during the first half of the learning set. The total force impulse in the region of the PF increased throughout the learning trials, but it always remained less than that produced by the PF. The force profile did not resemble a mirror image of the PF in that it tended to be more trapezoidal than parabolic in shape. As in previous studies of force-field adaptation, we found that changes in muscle activation involved a general increase in the activity of all muscles, which increased arm stiffness, and selectively-greater increases in the activation of muscles which counteracted the PF. With training, activation was exponentially reduced, albeit more slowly than kinematic error. Progressive changes in kinematics and EMG occurred predominantly in the region of the workspace beyond the force field. We suggest that constraints on muscle mechanics limit the ability of the central nervous system to employ an inverse dynamics model to nullify impulse-like forces by generating mirror-image forces. Consequently, subjects adopted a strategy of slightly overcompensating for the first half of the force field, then allowing the force field to push them in the opposite direction. Muscle activity patterns in the region beyond the boundary of the force field were subsequently adjusted because of the relatively-slow response of the second-order mechanics of muscle impedance to the force impulse.

Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

NASA Astrophysics Data System (ADS)

Meyer, Sam; Everaers, Ralf

2015-02-01

The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

Effect of force fields on pool boiling flow patterns in normal and reduced gravity

NASA Astrophysics Data System (ADS)

di Marco, P.; Grassi, W.

2009-05-01

This paper reports the observations of boiling flow patterns in FC-72, performed during a microgravity experiment, recently flown aboard of Foton-M2 satellite, in some instances with the additional aid of an electrostatic field to replace the buoyancy force. The heater consisted of a flat plate, 20 × 20 mm2, directly heated by direct current. Several levels of liquid subcooling (from 20 to 6 K) and heat fluxes up to 200 kW/m2 were tested. A complete counterpart test, carried out on ground before the mission, allowed direct comparison with terrestrial data. The void fraction in microgravity revealed much larger than in normal gravity condition: this may be attributed to increased bubble coalescence that hinders vapor condensation in the bulk of the subcooled fluid. In several cases, an oscillatory boiling behavior was detected, leading to periodical variation of average wall overheating of some degrees. The electric field confirmed to be very effective, even at low values of applied voltage, in reducing bubble size, thus improving their condensation rate in the bulk fluid, and in enhancing heat transfer performance, suppressing the boiling oscillations and preventing surface dryout.

Field Studies of Broadband Aerosol Optical Extinction in the Ultraviolet Spectral Region

NASA Astrophysics Data System (ADS)

Washenfelder, R. A.; Attwood, A.; Brock, C. A.; Brown, S. S.

2013-12-01

Aerosols influence the Earth's radiative budget by scattering and absorbing incoming solar radiation. The optical properties of aerosols vary as a function of wavelength, but few measurements have reported the wavelength dependence of aerosol extinction cross sections and complex refractive indices. In the case of brown carbon, its wavelength-dependent absorption in the ultraviolet spectral region has been suggested as an important component of aerosol radiative forcing. We describe a new field instrument to measure aerosol optical extinction as a function of wavelength, using cavity enhanced spectroscopy with a broadband light source. The instrument consists of two broadband channels which span the 360-390 and 385-420 nm spectral regions using two light emitting diodes (LED) and a grating spectrometer with charge-coupled device (CCD) detector. We deployed this instrument during the Fire Lab at Missoula Experiment during Fall 2012 to measure biomass burning aerosol, and again during the Southern Oxidant and Aerosol Study in summer 2013 to measure organic aerosol in the Southeastern U.S. In both field experiments, we determined aerosol optical extinction as a function of wavelength and can interpret this together with size distribution and composition measurements to characterize the aerosol optical properties and radiative forcing.

Modeling polymer-induced interactions between two grafted surfaces: comparison between interfacial statistical associating fluid theory and self-consistent field theory.

PubMed

Jain, Shekhar; Ginzburg, Valeriy V; Jog, Prasanna; Weinhold, Jeffrey; Srivastava, Rakesh; Chapman, Walter G

2009-07-28

The interaction between two polymer grafted surfaces is important in many applications, such as nanocomposites, colloid stabilization, and polymer alloys. In our previous work [Jain et al., J. Chem. Phys. 128, 154910 (2008)], we showed that interfacial statistical associating fluid density theory (iSAFT) successfully calculates the structure of grafted polymer chains in the absence/presence of a free polymer. In the current work, we have applied this density functional theory to calculate the force of interaction between two such grafted monolayers in implicit good solvent conditions. In particular, we have considered the case where the segment sizes of the free (sigma(f)) and grafted (sigma(g)) polymers are different. The interactions between the two monolayers in the absence of the free polymer are always repulsive. However, in the presence of the free polymer, the force either can be purely repulsive or can have an attractive minimum depending upon the relative chain lengths of the free (N(f)) and grafted polymers (N(g)). The attractive minimum is observed only when the ratio alpha = N(f)/N(g) is greater than a critical value. We find that these critical values of alpha satisfy the following scaling relation: rho(g) square root(N(g)) beta(3) proportional to alpha(-lambda), where beta = sigma(f)/sigma(g) and lambda is the scaling exponent. For beta = 1 or the same segment sizes of the free and grafted polymers, this scaling relation is in agreement with those from previous theoretical studies using self-consistent field theory (SCFT). Detailed comparisons between iSAFT and SCFT are made for the structures of the monolayers and their forces of interaction. These comparisons lead to interesting implications for the modeling of nanocomposite thermodynamics.

An Application of Multi-band Forced Photometry to One Square Degree of SERVS: Accurate Photometric Redshifts and Implications for Future Science

NASA Astrophysics Data System (ADS)

Nyland, Kristina; Lacy, Mark; Sajina, Anna; Pforr, Janine; Farrah, Duncan; Wilson, Gillian; Surace, Jason; Häußler, Boris; Vaccari, Mattia; Jarvis, Matt

2017-05-01

We apply The Tractor image modeling code to improve upon existing multi-band photometry for the Spitzer Extragalactic Representative Volume Survey (SERVS). SERVS consists of post-cryogenic Spitzer observations at 3.6 and 4.5 μm over five well-studied deep fields spanning 18 deg2. In concert with data from ground-based near-infrared (NIR) and optical surveys, SERVS aims to provide a census of the properties of massive galaxies out to z ≈ 5. To accomplish this, we are using The Tractor to perform “forced photometry.” This technique employs prior measurements of source positions and surface brightness profiles from a high-resolution fiducial band from the VISTA Deep Extragalactic Observations survey to model and fit the fluxes at lower-resolution bands. We discuss our implementation of The Tractor over a square-degree test region within the XMM Large Scale Structure field with deep imaging in 12 NIR/optical bands. Our new multi-band source catalogs offer a number of advantages over traditional position-matched catalogs, including (1) consistent source cross-identification between bands, (2) de-blending of sources that are clearly resolved in the fiducial band but blended in the lower resolution SERVS data, (3) a higher source detection fraction in each band, (4) a larger number of candidate galaxies in the redshift range 5 < z < 6, and (5) a statistically significant improvement in the photometric redshift accuracy as evidenced by the significant decrease in the fraction of outliers compared to spectroscopic redshifts. Thus, forced photometry using The Tractor offers a means of improving the accuracy of multi-band extragalactic surveys designed for galaxy evolution studies. We will extend our application of this technique to the full SERVS footprint in the future.

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

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

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

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

Liu, Hao; Song, Dong; Lu, Hui; Luo, Ray; Chen, Hai-Feng

2018-05-28

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X-ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here we report our development for the CHARMM community. Our residue-specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections of for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J-couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

How accurately do force fields represent protein side chain ensembles?

PubMed

Petrović, Dušan; Wang, Xue; Strodel, Birgit

2018-05-23

Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Three-dimensional constrained variational analysis: Approach and application to analysis of atmospheric diabatic heating and derivative fields during an ARM SGP intensive observational period

NASA Astrophysics Data System (ADS)

Tang, Shuaiqi; Zhang, Minghua

2015-08-01

Atmospheric vertical velocities and advective tendencies are essential large-scale forcing data to drive single-column models (SCMs), cloud-resolving models (CRMs), and large-eddy simulations (LESs). However, they cannot be directly measured from field measurements or easily calculated with great accuracy. In the Atmospheric Radiation Measurement Program (ARM), a constrained variational algorithm (1-D constrained variational analysis (1DCVA)) has been used to derive large-scale forcing data over a sounding network domain with the aid of flux measurements at the surface and top of the atmosphere (TOA). The 1DCVA algorithm is now extended into three dimensions (3DCVA) along with other improvements to calculate gridded large-scale forcing data, diabatic heating sources (Q1), and moisture sinks (Q2). Results are presented for a midlatitude cyclone case study on 3 March 2000 at the ARM Southern Great Plains site. These results are used to evaluate the diabatic heating fields in the available products such as Rapid Update Cycle, ERA-Interim, National Centers for Environmental Prediction Climate Forecast System Reanalysis, Modern-Era Retrospective Analysis for Research and Applications, Japanese 55-year Reanalysis, and North American Regional Reanalysis. We show that although the analysis/reanalysis generally captures the atmospheric state of the cyclone, their biases in the derivative terms (Q1 and Q2) at regional scale of a few hundred kilometers are large and all analyses/reanalyses tend to underestimate the subgrid-scale upward transport of moist static energy in the lower troposphere. The 3DCVA-gridded large-scale forcing data are physically consistent with the spatial distribution of surface and TOA measurements of radiation, precipitation, latent and sensible heat fluxes, and clouds that are better suited to force SCMs, CRMs, and LESs. Possible applications of the 3DCVA are discussed.

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

Testing the Cubic Galileon Gravity Model by the Milky Way Rotation Curve and SPARC Data

NASA Astrophysics Data System (ADS)

Chan, Man Ho; Hui, Hon Ka

2018-04-01

Recently, the cubic Galileon gravity (CGG) model has been suggested as an alternative gravity theory to general relativity. The model consists of an extra field potential term that can serve as the “fifth force.” In this article, we examine the possibility of whether or not this extra force term can explain the missing mass problem in galaxies without the help of dark matter. By using the Milky Way rotation curve and the Spitzer Photomery and Accurate Rotation Curves data, we show that this CGG model can satisfactorily explain the shapes of these rotation curves without dark matter. The CGG model can be regarded as a new alternative theory to challenge the existing dark matter paradigm.

Small satellite multi mission C2 for maximum effect

USGS Publications Warehouse

Miller, E.; Medina, O.; Lane, C.R.; Kirkham, A.; Ivancic, W.; Jones, B.; Risty, R.

2006-01-01

This paper discusses US Air Force, US Army, US Navy, and NASA demonstrations based around the Virtual Mission Operations Center (VMOC) and its application in fielding a Multi Mission Satellite Operations Center (MMSOC) designed to integrate small satellites into the inherently tiered system environment of operations. The intent is to begin standardizing the spacecraft to ground interfaces needed to reduce costs, maximize space effects to the user, and allow the generation of Tactics, Techniques and Procedures (TTPs) that lead to Responsive Space employment. Combining the US Air Force/Army focus of theater command and control of payloads with the US Navy's user collaboration and FORCEnet consistent approach lays the groundwork for the fundamental change needed to maximize responsive space effects.

Vertical plasmonic nanowires for 3D nanoparticle trapping

NASA Astrophysics Data System (ADS)

Wu, Jingzhi; Gan, Xiaosong

2011-12-01

Nanoparticle trapping is considered to be more challenging than trapping micron-sized objects because of the diffraction limit of light and the severe Brownian motion of the nanoparticles. We introduce a nanoparticle trapping approach based on plasmonic nanostructures, which consist of nanopillars with high aspect ratio. The plasmonic nanopillars behave as plasmonic resonators that rely on paired nano-pillars supporting gap plasmon modes. The localized surface plasmon resonance effect provides strong electromagnetic field enhancement and enables confinement of nanoparticles in three dimensional space. Numerical simulations indicate that the plasmonic structure provides stronger optical forces for trapping nanoparticles. The study of thermal effect of the plasmonic structure shows that the impact of the thermal force is significant, which may determine the outcome of the nanoparticle trapping.

Research on a new fiber-optic axial pressure sensor of transformer winding based on fiber Bragg grating

NASA Astrophysics Data System (ADS)

Liu, Yuan; Li, Lianqing; Zhao, Lin; Wang, Jiqiang; Liu, Tongyu

2017-12-01

Based on the principle of the fiber Bragg grating, a new type of fiber-optic pressure sensor for axial force measurement of transformer winding is designed, which is designed with the structure of bending plate beam, the optimization of the packaging process, and material of the sensor. Through the calibration experiment to calibrate the sensor, the field test results of the Taikai transformer factory show that the sensitivity of the sensor is 0.133 pm/kPa and the repeatability error is 2.7% FS. The data of the fiber-optic pressure sensor in different positions maintain consistent and repeatable, which can meet the requirement of the real-time monitoring of the axial force of transformer winding.

3D-QSAR based on quantum-chemical molecular fields: toward an improved description of halogen interactions.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Müller, Marco; Schmidt, Friedemann; Clark, Timothy

2012-09-24

Current 3D-QSAR methods such as CoMFA or CoMSIA make use of classical force-field approaches for calculating molecular fields. Thus, they can not adequately account for noncovalent interactions involving halogen atoms like halogen bonds or halogen-π interactions. These deficiencies in the underlying force fields result from the lack of treatment of the anisotropy of the electron density distribution of those atoms, known as the "σ-hole", although recent developments have begun to take specific interactions such as halogen bonding into account. We have now replaced classical force field derived molecular fields by local properties such as the local ionization energy, local electron affinity, or local polarizability, calculated using quantum-mechanical (QM) techniques that do not suffer from the above limitation for 3D-QSAR. We first investigate the characteristics of QM-based local property fields to show that they are suitable for statistical analyses after suitable pretreatment. We then analyze these property fields with partial least-squares (PLS) regression to predict biological affinities of two data sets comprising factor Xa and GABA-A/benzodiazepine receptor ligands. While the resulting models perform equally well or even slightly better in terms of consistency and predictivity than the classical CoMFA fields, the most important aspect of these augmented field-types is that the chemical interpretation of resulting QM-based property field models reveals unique SAR trends driven by electrostatic and polarizability effects, which cannot be extracted directly from CoMFA electrostatic maps. Within the factor Xa set, the interaction of chlorine and bromine atoms with a tyrosine side chain in the protease S1 pocket are correctly predicted. Within the GABA-A/benzodiazepine ligand data set, PLS models of high predictivity resulted for our QM-based property fields, providing novel insights into key features of the SAR for two receptor subtypes and cross-receptor selectivity of the ligands. The detailed interpretation of regression models derived using improved QM-derived property fields thus provides a significant advantage by revealing chemically meaningful correlations with biological activity and helps in understanding novel structure-activity relationship features. This will allow such knowledge to be used to design novel molecules on the basis of interactions additional to steric and hydrogen-bonding features.

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field.

PubMed

Yang, Y M; Bednarz, B

2013-02-21

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

Consistency evaluation between EGSnrc and Geant4 charged particle transport in an equilibrium magnetic field

NASA Astrophysics Data System (ADS)

Yang, Y. M.; Bednarz, B.

2013-02-01

Following the proposal by several groups to integrate magnetic resonance imaging (MRI) with radiation therapy, much attention has been afforded to examining the impact of strong (on the order of a Tesla) transverse magnetic fields on photon dose distributions. The effect of the magnetic field on dose distributions must be considered in order to take full advantage of the benefits of real-time intra-fraction imaging. In this investigation, we compared the handling of particle transport in magnetic fields between two Monte Carlo codes, EGSnrc and Geant4, to analyze various aspects of their electromagnetic transport algorithms; both codes are well-benchmarked for medical physics applications in the absence of magnetic fields. A water-air-water slab phantom and a water-lung-water slab phantom were used to highlight dose perturbations near high- and low-density interfaces. We have implemented a method of calculating the Lorentz force in EGSnrc based on theoretical models in literature, and show very good consistency between the two Monte Carlo codes. This investigation further demonstrates the importance of accurate dosimetry for MRI-guided radiation therapy (MRIgRT), and facilitates the integration of a ViewRay MRIgRT system in the University of Wisconsin-Madison's Radiation Oncology Department.

Computational and Experimental Characterization of Ribosomal DNA and RNA G-Quadruplexes

NASA Astrophysics Data System (ADS)

Cho, Samuel

DNA G-quadruplexes in human telomeres and gene promoters are being extensively studied for their role in controlling the growth of cancer cells. Recent studies strongly suggest that guanine (G)-rich genes encoding pre-ribosomal RNA (pre-rRNA) are a potential anticancer target through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis. However, the structures of ribosomal G-quadruplexes at atomic resolution are unknown, and very little biophysical characterization has been performed on them to date. Here, we have modeled two putative rDNA G-quadruplex structures, NUC 19P and NUC 23P, which we observe via circular dichroism (CD) spectroscopy to adopt a predominantly parallel topology, and their counterpart rRNA. To validate and refine the putative ribosomal G-quadruplex structures, we performed all-atom molecular dynamics (MD) simulations using the CHARMM36 force field in the presence and absence of stabilizing K + or Na + ions. We optimized the CHARMM36 force field K + parameters to be more consistent with quantum mechanical calculations (and the polarizable Drude model force field) so that the K + ion is predominantly in the G-quadruplex channel. Our MD simulations show that the rDNA G-quadruplex have more well-defined, predominantly parallel-topology structures than rRNA and NUC 19P is more structured than NUC 23P, which features extended loops. Our study demonstrates that they are both potential targets for the design of novel chemotherapeutics.

Vibration control of a ship engine system using high-load magnetorheological mounts associated with a new indirect fuzzy sliding mode controller

NASA Astrophysics Data System (ADS)

Phu, Do Xuan; Choi, Seung-Bok

2015-02-01

In this work, a new high-load magnetorheological (MR) fluid mount system is devised and applied to control vibration in a ship engine. In the investigation of vibration-control performance, a new modified indirect fuzzy sliding mode controller is formulated and realized. The design of the proposed MR mount is based on the flow mode of MR fluid, and it includes two separated coils for generating a magnetic field. An optimization process is carried out to achieve maximal damping force under certain design constraints, such as the allowable height of the mount. As an actuating smart fluid, a new plate-like iron-particle-based MR fluid is used, instead of the conventional spherical iron-particle-based MR fluid. After evaluating the field-dependent yield stress of the MR fluid, the field-dependent damping force required to control unwanted vibration in the ship engine is determined. Subsequently, an appropriate-sized MR mount is manufactured and its damping characteristics are evaluated. After confirming the sufficient damping force level of the manufactured MR mount, a medium-sized ship engine mount system consisting of eight MR mounts is established, and its dynamic governing equations are derived. A new modified indirect fuzzy sliding mode controller is then formulated and applied to the engine mount system. The displacement and velocity responses show that the unwanted vibrations of the ship engine system can be effectively controlled in both the axial and radial directions by applying the proposed control methodology.

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

2013-06-01

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

A mechanism for magnetospheric substorms

NASA Technical Reports Server (NTRS)

Erickson, G. M.; Heinemann, M.

1994-01-01

Energy-principle analysis performed on two-dimensional, self-consistent solutions for magnetospheric convection indicates that the magnetosphere is unstable to isobaric (yet still frozen-in) fluctuations of plasma-sheet flux tubes. Normally, pdV work associated with compression maintains stability of the inward/outward oscillating normal mode. However, if Earth's ionosphere can provide sufficient mass flux, isobaric expansion of flux tubes can occur. The growth of a field-aligned potential drop in the near-Earth, midnight portion of the plasma sheet, associated with upward field-aligned currents responsible for the Harang discontinuity, redistributes plasma along field lines in a manner that destabilizes the normal mode. The growth of this unstable mode results in an out-of-equilibrium situation near the inner edge. When this occurs over a downtail extent comparable to the half-thickness of the plasma sheet, collapse ensues and forces thinning of the plasma sheet whereby conditions favorable to reconnection occur. This scenario for substorm onset is consistent with observed upward fluxes of ions, parallel potential drops, and observations of substorm onset. These observations include near Earth onset, pseudobreakups, the substorm current wedge, and local variations of plasma-sheet thickness.

STEADY GENERAL RELATIVISTIC MAGNETOHYDRODYNAMIC INFLOW/OUTFLOW SOLUTION ALONG LARGE-SCALE MAGNETIC FIELDS THAT THREAD A ROTATING BLACK HOLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pu, Hung-Yi; Nakamura, Masanori; Hirotani, Kouichi

2015-03-01

General relativistic magnetohydrodynamic (GRMHD) flows along magnetic fields threading a black hole can be divided into inflow and outflow parts, according to the result of the competition between the black hole gravity and magneto-centrifugal forces along the field line. Here we present the first self-consistent, semi-analytical solution for a cold, Poynting flux–dominated (PFD) GRMHD flow, which passes all four critical (inner and outer, Alfvén, and fast magnetosonic) points along a parabolic streamline. By assuming that the dominating (electromagnetic) component of the energy flux per flux tube is conserved at the surface where the inflow and outflow are separated, the outflowmore » part of the solution can be constrained by the inflow part. The semi-analytical method can provide fiducial and complementary solutions for GRMHD simulations around the rotating black hole, given that the black hole spin, global streamline, and magnetizaion (i.e., a mass loading at the inflow/outflow separation) are prescribed. For reference, we demonstrate a self-consistent result with the work by McKinney in a quantitative level.« less

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

Force Field Development from Periodic Density Functional Theory Calculations for Gas Separation Applications Using Metal–Organic Frameworks

DOE PAGES

Mercado, Rocio; Vlaisavljevich, Bess; Lin, Li -Chiang; ...

2016-05-25

We present accurate force fields developed from density functional theory (DFT) calculations with periodic boundary conditions for use in molecular simulations involving M 2(dobdc) (M-MOF-74; dobdc 4– = 2,5-dioxidobenzenedicarboxylate; M = Mg, Mn, Fe, Co, Ni, Zn) and frameworks of similar topology. In these systems, conventional force fields fail to accurately model gas adsorption due to the strongly binding open-metal sites. The DFT-derived force fields predict the adsorption of CO 2, H 2O, and CH 4 inside these frameworks much more accurately than other common force fields. We show that these force fields can also be used for M 2(dobpdc)more » (dobpdc 4– = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate), an extended version of MOF-74, and thus are a promising alternative to common force fields for studying materials similar to MOF-74 for carbon capture applications. Furthermore, it is anticipated that the approach can be applied to other metal–organic framework topologies to obtain force fields for different systems. We have used this force field to study the effect of contaminants such as H 2O and N 2 upon these materials’ performance for the separation of CO 2 from the emissions of natural gas reservoirs and coal-fired power plants. Specifically, mixture adsorption isotherms calculated with these DFT-derived force fields showed a significant reduction in the uptake of many gas components in the presence of even trace amounts of H 2O vapor. The extent to which the various gases are affected by the concentration of H 2O in the reservoir is quantitatively different for the different frameworks and is related to their heats of adsorption. Additionally, significant increases in CO 2 selectivities over CH 4 and N 2 are observed as the temperature of the systems is lowered.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gavignet, A.A.; Bradbury, L.J.; Quetier, F.P.

In current practice, the optimization of drilling hydraulics consists of the selection of nozzle sizes that maximize either jet impact or hydraulic power at the nozzle. But what is required for a real optimization is the knowledge of the hydraulic forces available for cleaning at the rock face, not at the nozzle. This paper shows the results of hot-wire anemometry experiments that provide insight into the flow distribution in a jet bit. Direct measurements of the flow field, including turbulence levels, are reported and discussed.

Charge patterns as templates for the assembly of layered biomolecular structures.

PubMed

Naujoks, Nicola; Stemmer, Andreas

2006-08-01

Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

Hydrodynamic theory of diffusion in two-temperature multicomponent plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramshaw, J.D.; Chang, C.H.

Detailed numerical simulations of multicomponent plasmas require tractable expressions for species diffusion fluxes, which must be consistent with the given plasma current density J{sub q} to preserve local charge neutrality. The common situation in which J{sub q} = 0 is referred to as ambipolar diffusion. The use of formal kinetic theory in this context leads to results of formidable complexity. We derive simple tractable approximations for the diffusion fluxes in two-temperature multicomponent plasmas by means of a generalization of the hydrodynamical approach used by Maxwell, Stefan, Furry, and Williams. The resulting diffusion fluxes obey generalized Stefan-Maxwell equations that contain drivingmore » forces corresponding to ordinary, forced, pressure, and thermal diffusion. The ordinary diffusion fluxes are driven by gradients in pressure fractions rather than mole fractions. Simplifications due to the small electron mass are systematically exploited and lead to a general expression for the ambipolar electric field in the limit of infinite electrical conductivity. We present a self-consistent effective binary diffusion approximation for the diffusion fluxes. This approximation is well suited to numerical implementation and is currently in use in our LAVA computer code for simulating multicomponent thermal plasmas. Applications to date include a successful simulation of demixing effects in an argon-helium plasma jet, for which selected computational results are presented. Generalizations of the diffusion theory to finite electrical conductivity and nonzero magnetic field are currently in progress.« less

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

PubMed Central

Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

2010-01-01

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

Electron diamagnetic effect in a magnetic nozzle on a helicon plasma thruster performance

NASA Astrophysics Data System (ADS)

Takahashi, Kazunori; Lafleur, Trevor; Charles, Christine; Alexander, Peter; Boswell, Rod

2012-10-01

The axial force, which is called thrust sometimes, imparted from a magnetically expanding helicon plasma thruster is directly measured and the results are compared with a two-dimensional fluid theory. The force component solely transmitted to the expanding field is directly measured and identified as an axial force produced by the azimuthal current due to an electron diamagnetic drift and the radial component of the applied magnetic field. In this type of configuration, plasma diffusion in magnetic field affects a spatial profile of the plasma density and the resultant axial force onto the magnetic field. It is observed that the force component onto the magnetic field increases with an increase in the magnetic field strength, simultaneously with an increase in the plasma density downstream of the source exit, which could be due to suppression of the cross field diffusion in the magnetic nozzle.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle.

PubMed

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle

NASA Astrophysics Data System (ADS)

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Force fields for describing the solution-phase synthesis of shape-selective metal nanoparticles

NASA Astrophysics Data System (ADS)

Zhou, Ya; Al-Saidi, Wissam; Fichthorn, Kristen

2013-03-01

Polyvinylpyrrolidone (PVP) and polyethylene oxide (PEO) are structure-directing agents that exhibit different performance in the polyol synthesis of Ag nanostructures. The success of these structure-directing agents in selective nanostructure synthesis is often attributed to their selective binding to Ag(100) facets. We use first-principles, density-functional theory (DFT) calculations in a vacuum environment to show that PVP has a stronger preference to bind to Ag(100) than to Ag(111), whereas PEO exhibits much weaker selectivity. To understand the role of solvent in the surface-sensitive binding, we develop classical force fields to describe the interactions of the structure-directing (PVP and PEO) and solvent (ethylene glycol) molecules with various Ag substrates. We parameterize the force fields through force-and-energy matching to DFT results using simulated annealing. We validate the force fields by comparisons to DFT and experimental binding energies. Our force fields reproduce the surface-sensitive binding predicted by DFT calculations. Molecular dynamics simulations based on these force fields can be used to reveal the role of solvent, polymer chain length, and polymer concentration in the selective synthesis of Ag nanostructures.

Magnetodynamic stability of a fluid cylinder under the Lundquist force-free magnetic field

NASA Astrophysics Data System (ADS)

Radwan, Ahmed E.; Halawa, Mohamed A.

1990-04-01

The magnetodynamic (in)stability of a conducting fluid cylinder subject to the capillarity and electromagnetic forces has been developed. The cylinder is pervaded by a uniform magnetic field but embedded in the Lundquist force-free varying field that allows for flowing a current surrounding the fluid. A general eigenvalue relation is derived based on a study of the equilibrium and perturbed states. The stability criterion is discussed analytically in general terms. The surface tension is destabilizing for small axisymmetric mode and stable for all others. The principle of the exchange of stability is allowed for the present problem due to the non-uniform behavior of the force-free field. Each of the axial and transverse force-free fields separately exerts a stabilizing influence in the most dangerous mode but the combined contribution of them is strongly destabilizing. Whether the model is acted upon the electromagnetic force (with the Lundquist field) the stability restrictions or/and the capillarity force are identified. Several reported works can be recovered as limiting cases with appropriate simplifications.

Validation and Application of the ReaxFF Reactive Force Field to Hydrocarbon Oxidation Kinetics

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0278 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics Adrianus Van Duin...application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1-0355 5c.  PROGRAM...Chenoweth Dec14 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics DISTRIBUTION A: Distribution approved for

Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Swarnava; Suryanarayana, Phanish, E-mail: phanish.suryanarayana@ce.gatech.edu

2016-02-15

We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we develop a generalized framework for performing OF-DFT simulations with different variants of the electronic kinetic energy. In particular, we propose a self-consistent field (SCF) type fixed-point method for calculations involving linear-response kinetic energy functionals. In this framework, evaluation of both the electronic ground-state and forces on the nuclei are amenable to computations that scale linearly with the number of atoms. We develop a parallel implementation of this formulation using the finite-difference discretization.more » We demonstrate that higher-order finite-differences can achieve relatively large convergence rates with respect to mesh-size in both the energies and forces. Additionally, we establish that the fixed-point iteration converges rapidly, and that it can be further accelerated using extrapolation techniques like Anderson's mixing. We validate the accuracy of the results by comparing the energies and forces with plane-wave methods for selected examples, including the vacancy formation energy in Aluminum. Overall, the suitability of the proposed formulation for scalable high performance computing makes it an attractive choice for large-scale OF-DFT calculations consisting of thousands of atoms.« less

Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

2014-11-01

The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

Covariant kaon dynamics and kaon flow in heavy ion collisions

NASA Astrophysics Data System (ADS)

Zheng, Yu-Ming; Fuchs, C.; Faessler, Amand; Shekhter, K.; Yan, Yu-Peng; Kobdaj, Chinorat

2004-03-01

The influence of the chiral mean field on the K+ transverse flow in heavy ion collisions at SIS energy is investigated within covariant kaon dynamics. For the kaon mesons inside the nuclear medium a quasiparticle picture including scalar and vector fields is adopted and compared to the standard treatment with a static potential. It is confirmed that a Lorentz force from spatial component of the vector field provides an important contribution to the in-medium kaon dynamics and strongly counterbalances the influence of the vector potential on the K+ in-plane flow. The FOPI data can be reasonably described using in-medium kaon potentials based on effective chiral models. The information on the in-medium K+ potential extracted from kaon flow is consistent with the knowledge from other sources.

Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes.

PubMed

Kondratyuk, Nikolay D; Norman, Genri E; Stegailov, Vladimir V

2016-11-28

Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.

The effect of power-law body forces on a thermally driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1986-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

The effect of power law body forces on a thermally-driven flow between concentric rotating spheres

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

A numerical study is conducted to determine the effect of power-law body forces on a thermally-driven axisymmetric flow field confined between concentric co-rotating spheres. This study is motivated by Spacelab geophysical fluid-flow experiments, which use an electrostatic force on a dielectric fluid to simulate gravity; this force exhibits a (1/r)sup 5 distribution. Meridional velocity is found to increase when the electrostatic body force is imposed, relative to when the body force is uniform. Correlation among flow fields with uniform, inverse-square, and inverse-quintic force fields is obtained using a modified Grashof number.

The Electromotive Force in Different Reference Frames

NASA Astrophysics Data System (ADS)

Adler, Charles L.

2018-05-01

The electromotive force (EMF) is the work per unit charge around a wire loop caused by a time-varying magnetic flux threading the loop. It is due to a force moving the charges around the loop. This is true whether the change in flux is due to the wire loop being stationary and the field changing in time, or the loop moving through a spatially varying field. In the first case, we say that the time-varying magnetic field induces an electric field that provides the force; in the second, we say that the force is due to the magnetic field acting on the charges in the moving loop. The theory of relativity states that both viewpoints must be equivalent, but it is sometimes difficult to harmonize them.

In pursuit of photo-induced magnetic and chiral microscopy

NASA Astrophysics Data System (ADS)

Zeng, Jinwei; Kamandi, Mohammad; Darvishzadeh-Varcheie, Mahsa; Albooyeh, Mohammad; Veysi, Mehdi; Guclu, Caner; Hanifeh, Mina; Rajaei, Mohsen; Potma, Eric O.; Wickramasinghe, H. Kumar; Capolino, Filippo

2018-06-01

Light-matter interactions enable the perception of specimen properties such as its shape and dimensions by measuring the subtle differences carried by an illuminating beam after interacting with the sample. However, major obstacles arise when the relevant properties of the specimen are weakly coupled to the incident beam, for example when measuring optical magnetism and chirality. To address this challenge we propose the idea of detecting such weakly-coupled properties of matter through the photo-induced force, aiming at developing photo-induced magnetic or chiral force microscopy. Here we review our pursuit consisting of the following steps: (1) Development of a theoretical blueprint of a magnetic nanoprobe to detect a magnetic dipole oscillating at an optical frequency when illuminated by an azimuthally polarized beam via the photo-induced magnetic force; (2) Conducting an experimental study using an azimuthally polarized beam to probe the near fields and axial magnetism of a Si disk magnetic nanoprobe, based on photo-induced force microscopy; (3) Extending the concept of force microscopy to probe chirality at the nanoscale, enabling enantiomeric detection of chiral molecules. Finally, we discuss difficulties and how they could be overcome, as well as our plans for future work. Invited Paper

The importance of accurate muscle modelling for biomechanical analyses: a case study with a lizard skull

PubMed Central

Gröning, Flora; Jones, Marc E. H.; Curtis, Neil; Herrel, Anthony; O'Higgins, Paul; Evans, Susan E.; Fagan, Michael J.

2013-01-01

Computer-based simulation techniques such as multi-body dynamics analysis are becoming increasingly popular in the field of skull mechanics. Multi-body models can be used for studying the relationships between skull architecture, muscle morphology and feeding performance. However, to be confident in the modelling results, models need to be validated against experimental data, and the effects of uncertainties or inaccuracies in the chosen model attributes need to be assessed with sensitivity analyses. Here, we compare the bite forces predicted by a multi-body model of a lizard (Tupinambis merianae) with in vivo measurements, using anatomical data collected from the same specimen. This subject-specific model predicts bite forces that are very close to the in vivo measurements and also shows a consistent increase in bite force as the bite position is moved posteriorly on the jaw. However, the model is very sensitive to changes in muscle attributes such as fibre length, intrinsic muscle strength and force orientation, with bite force predictions varying considerably when these three variables are altered. We conclude that accurate muscle measurements are crucial to building realistic multi-body models and that subject-specific data should be used whenever possible. PMID:23614944

Friction laws at the nanoscale.

PubMed

Mo, Yifei; Turner, Kevin T; Szlufarska, Izabela

2009-02-26

Macroscopic laws of friction do not generally apply to nanoscale contacts. Although continuum mechanics models have been predicted to break down at the nanoscale, they continue to be applied for lack of a better theory. An understanding of how friction force depends on applied load and contact area at these scales is essential for the design of miniaturized devices with optimal mechanical performance. Here we use large-scale molecular dynamics simulations with realistic force fields to establish friction laws in dry nanoscale contacts. We show that friction force depends linearly on the number of atoms that chemically interact across the contact. By defining the contact area as being proportional to this number of interacting atoms, we show that the macroscopically observed linear relationship between friction force and contact area can be extended to the nanoscale. Our model predicts that as the adhesion between the contacting surfaces is reduced, a transition takes place from nonlinear to linear dependence of friction force on load. This transition is consistent with the results of several nanoscale friction experiments. We demonstrate that the breakdown of continuum mechanics can be understood as a result of the rough (multi-asperity) nature of the contact, and show that roughness theories of friction can be applied at the nanoscale.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

Bespoke optical springs and passive force clamps from shaped dielectric particles

NASA Astrophysics Data System (ADS)

Simpson, S. H.; Phillips, D. B.; Carberry, D. M.; Hanna, S.

2013-09-01

By moulding optical fields, holographic optical tweezers are able to generate structured force fields with magnitudes and length scales of great utility for experiments in soft matter and biological physics. It has recently been noted that optically induced force fields are determined not only by the incident optical field, but by the shape and composition of the particles involved [Gluckstad J. Optical manipulation: sculpting the object. Nat Photonics 2011;5:7-8]. Indeed, there are desirable but simple attributes of a force field, such as orientational control, that cannot be introduced by sculpting optical fields alone. With this insight in mind, we show, theoretically, how relationships between force and displacement can be controlled by optimizing particle shapes. We exhibit a constant force optical spring, made from a tapered microrod and discuss methods by which it could be fabricated. In addition, we investigate the optical analogue of streamlining, and show how objects can be shaped so as to reduce the effects of radiation pressure, and hence switch from non-trapping to trapping regimes.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-02-01

A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

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

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

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

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE PAGES

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; ...

2017-02-01

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

Evaluation of the structural, electronic, topological and vibrational properties of N-(3,4-dimethoxybenzyl)-hexadecanamide isolated from Maca (Lepidium meyenii) using different spectroscopic techniques

NASA Astrophysics Data System (ADS)

Chain, Fernando; Iramain, Maximiliano Alberto; Grau, Alfredo; Catalán, César A. N.; Brandán, Silvia Antonia

2017-01-01

N-(3,4-dimethoxybenzyl)-hexadecanamide (DMH) was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet- Visible (UV-Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance (1H and 13C NMR) spectroscopies. The structural, electronic, topological and vibrational properties were evaluated in gas phase and in n-hexane employing ONIOM and self-consistent force field (SCRF) calculations. The atomic charges, molecular electrostatic potentials, stabilization energies and topological properties of DMH were analyzed and compared with those calculated for N-(3,4-dimethoxybenzyl)-acetamide (DMA) in order to evaluate the effect of the side chain on the properties of DMH. The reactivity and behavior of this alkamide were predicted by using the gap energies and some descriptors. Force fields and the corresponding force constants were reported for DMA only in gas phase and n-hexane due to the high number of vibration normal modes showed by DMH, while the complete vibrational assignments are presented for DMA and both forms of DMH. The comparisons between the experimental FTIR, FT-Raman, UV-Visible and 1H and 13C NMR spectra with the corresponding theoretical ones showed a reasonable concordance.

Closed Loop Control of a Tethered Magnetic Capsule Endoscope

PubMed Central

Taddese, Addisu Z.; Slawinski, Piotr R.; Obstein, Keith L.; Valdastri, Pietro

2017-01-01

Magnetic field gradients have repeatedly been shown to be the most feasible mechanism for gastrointestinal capsule endoscope actuation. An inverse quartic magnetic force variation with distance results in large force gradients induced by small movements of a driving magnet; this necessitates robotic actuation of magnets to implement stable control of the device. A typical system consists of a serial robot with a permanent magnet at its end effector that actuates a capsule with an embedded permanent magnet. We present a tethered capsule system where a capsule with an embedded magnet is closed loop controlled in 2 degree-of-freedom in position and 2 degree-of-freedom in orientation. Capitalizing on the magnetic field of the external driving permanent magnet, the capsule is localized in 6-D allowing for both position and orientation feedback to be used in a control scheme. We developed a relationship between the serial robot's joint parameters and the magnetic force and torque that is exerted onto the capsule. Our methodology was validated both in a dynamic simulation environment where a custom plug-in for magnetic interaction was written, as well as on an experimental platform. The tethered capsule was demonstrated to follow desired trajectories in both position and orientation with accuracy that is acceptable for colonoscopy. PMID:28286886

Damping of Quasi-stationary Waves Between Two Miscible Liquids

NASA Technical Reports Server (NTRS)

Duval, Walter M. B.

2002-01-01

Two viscous miscible liquids with an initially sharp interface oriented vertically inside a cavity become unstable against oscillatory external forcing due to Kelvin-Helmholtz instability. The instability causes growth of quasi-stationary (q-s) waves at the interface between the two liquids. We examine computationally the dynamics of a four-mode q-s wave, for a fixed energy input, when one of the components of the external forcing is suddenly ceased. The external forcing consists of a steady and oscillatory component as realizable in a microgravity environment. Results show that when there is a jump discontinuity in the oscillatory excitation that produced the four-mode q-s wave, the interface does not return to its equilibrium position, the structure of the q-s wave remains imbedded between the two fluids over a long time scale. The damping characteristics of the q-s wave from the time history of the velocity field show overdamped and critically damped response; there is no underdamped oscillation as the flow field approaches steady state. Viscous effects serve as a dissipative mechanism to effectively damp the system. The stability of the four-mode q-s wave is dependent on both a geometric length scale as well as the level of background steady acceleration.

Modeling tensional homeostasis in multicellular clusters.

PubMed

Tam, Sze Nok; Smith, Michael L; Stamenović, Dimitrije

2017-03-01

Homeostasis of mechanical stress in cells, or tensional homeostasis, is essential for normal physiological function of tissues and organs and is protective against disease progression, including atherosclerosis and cancer. Recent experimental studies have shown that isolated cells are not capable of maintaining tensional homeostasis, whereas multicellular clusters are, with stability increasing with the size of the clusters. Here, we proposed simple mathematical models to interpret experimental results and to obtain insight into factors that determine homeostasis. Multicellular clusters were modeled as one-dimensional arrays of linearly elastic blocks that were either jointed or disjointed. Fluctuating forces that mimicked experimentally measured cell-substrate tractions were obtained from Monte Carlo simulations. These forces were applied to the cluster models, and the corresponding stress field in the cluster was calculated by solving the equilibrium equation. It was found that temporal fluctuations of the cluster stress field became attenuated with increasing cluster size, indicating that the cluster approached tensional homeostasis. These results were consistent with previously reported experimental data. Furthermore, the models revealed that key determinants of tensional homeostasis in multicellular clusters included the cluster size, the distribution of traction forces, and mechanical coupling between adjacent cells. Based on these findings, we concluded that tensional homeostasis was a multicellular phenomenon. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Closed Loop Control of a Tethered Magnetic Capsule Endoscope.

PubMed

Taddese, Addisu Z; Slawinski, Piotr R; Obstein, Keith L; Valdastri, Pietro

2016-06-01

Magnetic field gradients have repeatedly been shown to be the most feasible mechanism for gastrointestinal capsule endoscope actuation. An inverse quartic magnetic force variation with distance results in large force gradients induced by small movements of a driving magnet; this necessitates robotic actuation of magnets to implement stable control of the device. A typical system consists of a serial robot with a permanent magnet at its end effector that actuates a capsule with an embedded permanent magnet. We present a tethered capsule system where a capsule with an embedded magnet is closed loop controlled in 2 degree-of-freedom in position and 2 degree-of-freedom in orientation. Capitalizing on the magnetic field of the external driving permanent magnet, the capsule is localized in 6-D allowing for both position and orientation feedback to be used in a control scheme. We developed a relationship between the serial robot's joint parameters and the magnetic force and torque that is exerted onto the capsule. Our methodology was validated both in a dynamic simulation environment where a custom plug-in for magnetic interaction was written, as well as on an experimental platform. The tethered capsule was demonstrated to follow desired trajectories in both position and orientation with accuracy that is acceptable for colonoscopy.

Lorentz Body Force Induced by Traveling Magnetic Fields

NASA Technical Reports Server (NTRS)

Volz, M. P.; Mazuruk, K.

2003-01-01

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

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

PubMed

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

2012-01-01

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

Mechanisms of force production during linear accelerations in bluegill sunfish Lepomis macrochirus

NASA Astrophysics Data System (ADS)

Tytell, Eric D.; Wise, Tyler N.; Boden, Alexandra L.; Sanders, Erin K.; Schwalbe, Margot A. B.

2016-11-01

In nature, fish rarely swim steadily. Although unsteady behaviors are common, we know little about how fish change their swimming kinematics for routine accelerations, and how these changes affect the fluid dynamic forces and the wake produced. To study force production during acceleration, particle image velocimetry was used to quantify the wake of bluegill sunfish Lepomis macrochirus and to estimate the pressure field during linear accelerations and steady swimming. We separated "steady" and "unsteady" trials and quantified the forward acceleration using inertial measurement units. Compared to steady sequences, unsteady sequences had larger accelerations and higher body amplitudes. The wake consisted of single vortices shed during each tail movement (a '2S' wake). The structure did not change during acceleration, but the circulation of the vortices increased, resulting in larger forces. A fish swimming unsteadily produced significantly more force than the same fish swimming steadily, even when the accelerations were the same. This increase is likely due to increased added mass during unsteady swimming, as a result of the larger body amplitude. Pressure estimates suggest that the increase in force is correlated with more low pressure regions on the anterior body. This work was supported by ARO W911NF-14-1-0494 and NSF RCN-PLS 1062052.

Quantum Gravitational Force Between Polarizable Objects.

PubMed

Ford, L H; Hertzberg, Mark P; Karouby, J

2016-04-15

Since general relativity is a consistent low energy effective field theory, it is possible to compute quantum corrections to classical forces. Here we compute a quantum correction to the gravitational potential between a pair of polarizable objects. We study two distant bodies and compute a quantum force from their induced quadrupole moments due to two-graviton exchange. The effect is in close analogy to the Casimir-Polder and London-van der Waals forces between a pair of atoms from their induced dipole moments due to two photon exchange. The new effect is computed from the shift in vacuum energy of metric fluctuations due to the polarizability of the objects. We compute the potential energy at arbitrary distances compared to the wavelengths in the system, including the far and near regimes. In the far distance, or retarded, regime, the potential energy takes on a particularly simple form: V(r)=-3987ℏcG^{2}α_{1S}α_{2S}/(4πr^{11}), where α_{1S}, α_{2S} are the static gravitational quadrupole polarizabilities of each object. We provide estimates of this effect.

Propulsive Forces of a Biomimetic Undulating Fin

NASA Astrophysics Data System (ADS)

Kalumuck, Kenneth; Brandt, Alan; Armand, Mehran

2007-11-01

Understanding gained from much recent work on force production mechanisms of aquatic organisms holds great promise for improved undersea vehicle propulsion and maneuvering. One class of fish locomotion is that of the median fin utilized by animals such as squid, cuttlefish, knifefish, and seahorse. It is characterized by undulatory motion that creates traveling waves along the fin. Results of experiments conducted on a submerged mechanical underwater undulating fin test bed are presented. The 0.5 m long fin is mounted to a cylindrical body and consists of a flexible skin attached to ribs driven by an adjustable cam mechanism and variable speed motor that enables changing the characteristics of the undulating wave(s). Forces produced were measured in a captive mode under quiescent conditions as well in the presence of an ambient current. Propulsive forces are characterized as a function of the fin width, oscillation frequency, amplitude, and wavelength. Free swimming experiments were also conducted to determine the point of self propulsion. Flow field structure visualization using dye tracers is presented for selected cases. Estimates of performance and applications for use with larger scale vehicles are discussed.

Stronger Intermolecular Forces or Closer Molecular Spacing? Key Impact Factor Research of Gelator Self-Assembly Mechanism.

PubMed

Chen, Si; An, Zhihang; Tong, Xiaoqian; Chen, Yining; Ma, Meng; Shi, Yanqin; Wang, Xu

2017-12-19

The benzene ring of low-molecular-weight gelators provides strong intermolecular forces but increases molecular spacing during self-assembly. To explore both of the above influences on the gel properties, we synthesize two gelators (Glu-CBZ and Glu-DPA) consisting of the same terminal long side chain but different aliphatic functional groups. The aliphatic functional groups are carbobenzoxy group and diphenyl phosphate group. The self-assembly driving forces, self-organization patterns, network morphologies, rheological properties, and the influences of solvents are researched through 1 H NMR spectra, Fourier transform infrared spectra, field-emission scanning electron microscopy images, rheological characterizations curves, tube-inversion experiment, and calculation of van't Hoff plots. The results show that the carbobenzoxy group of Glu-CBZ makes molecules pack more tightly such that it improves the gel properties during static equilibrium. Whereas the diphenyl phosphate group of Glu-DPA provides stronger intermolecular forces, performing outstandingly during dynamic equilibrium. It is advantageous to further investigate the competitive relationship in gel system between the increased number of functional groups and the consequent steric effect.

Numerical simulation of present day tectonic stress across the Indian subcontinent

NASA Astrophysics Data System (ADS)

Yadav, R.; Tiwari, V. M.

2018-04-01

In situ measurements of maximum horizontal stress (S Hmax) in the Indian subcontinent are limited and do not present regional trends of intraplate stress orientation. The observed orientations of S Hmax vary considerably and often differ from the plate velocity direction. We have simulated orientation and magnitude of S Hmax through finite element modeling incorporating heterogeneities in elastic property of the Indian continent and plain stress approximation to understand the variability of S Hmax. Four different scenarios are tested in simulation: (1) homogeneous plate with fixed plate boundary (2) homogeneous plate with boundary forces (3) heterogeneous plate with fixed boundary (4) heterogeneous plate with boundary forces. The estimated orientation and magnitude of S Hmax with a heterogeneous plate with boundary forces in the Himalayan region and an eastern plate boundary comprising the Indo-Burmese arc and Andaman subduction zone are consistent with measured maximum horizontal stress. This study suggests that plate boundary force varies along the northern Indian plate margin and also provides a constraint on the intraplate stress field in the Indian subcontinent.

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

NASA Astrophysics Data System (ADS)

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.

Transition from steady to periodic liquid-metal magnetohydrodynamic flow in a sliding electrical contact

NASA Astrophysics Data System (ADS)

Talmage, Gita; Walker, John S.; Brown, Samuel H.; Sondergaard, Neal A.

1993-09-01

In homopolar motors and generators, large dc electric currents pass through the sliding electrical contacts between rotating copper disks (rotors) and static copper surfaces shrouding the rotor tips (stators). A liquid metal in the small radial gap between the rotor tip and concentric stator surface can provide a low-resistance, low-drag electrical contact. Since there is a strong magnetic field in the region of the electrical contacts, there are large electromagnetic body forces on the liquid metal. The primary, azimuthal motion consists of simple Couette flow, plus an electromagnetically driven flow with large extremes of the azimuthal velocity near the rotor corners. The secondary flow involves the radial and axial velocity components, is driven by the centrifugal force associated with the primary flow, and is opposed by the electromagnetic body force, so that the circulation varies inversely as the square of the magnetic-field strength. Three flow regimes are identified as the angular velocity Ω of the rotor is increased. For small Ω, the primary flow is decoupled from the secondary flow. As Ω increases, the secondary flow begins to convect the azimuthal-velocity peaks radially outward, which in turn changes the centrifugal force driving the secondary flow. At some critical value of Ω, the flow becomes periodic through the coupling of the primary and secondary flows. The azimuthal-velocity peaks begin to move radially in and out with an accompanying oscillation in the secondary-flow strength.

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

DOE PAGES

Gao, Zhiwen; Gao, Yanfei

2016-05-14

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zhiwen; Gao, Yanfei

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

A Single-Ion Reservoir as a High-Sensitive Sensor of Electric Signals.

PubMed

Domínguez, Francisco; Arrazola, Iñigo; Doménech, Jaime; Pedernales, Julen S; Lamata, Lucas; Solano, Enrique; Rodríguez, Daniel

2017-08-21

A single-ion reservoir has been tested, and characterized in order to be used as a highly sensitive optical detector of electric signals arriving at the trapping electrodes. Our system consists of a single laser-cooled 40 Ca + ion stored in a Paul trap with rotational symmetry. The performance is observed through the axial motion of the ion, which is equivalent to an underdamped and forced oscillator. Thus, the results can be projected also to Penning traps. We have found that, for an ion oscillator temperature T axial  ≲ 10 mK in the forced-frequency range ω z  = 2π × (80,200 kHz), the reservoir is sensitive to a time-varying electric field equivalent to an electric force of 5.3(2) neV/μm, for a measured quality factor Q = 3875(45), and a decay time constant γ z  = 88(2) s -1 . This method can be applied to measure optically the strength of an oscillating field or induced (driven) charge in this frequency range within times of tens of milliseconds. Furthermore the ion reservoir has been proven to be sensitive to electrostatic forces by measuring the ion displacement. Since the heating rate is below 0.3 μeV/s, this reservoir might be used as optical detector for any ion or bunch of charged particles stored in an adjacent trap.

Full Field Deformation Measurements in Tensile Kolsky Bar Experiments: Studies and Detailed Analysis of the Early Time History

NASA Astrophysics Data System (ADS)

Sutton, M. A.; Gilat, A.; Seidt, J.; Rajan, S.; Kidane, A.

2018-01-01

The very early stages of high rate tensile loading are important when attempting to characterize the response of materials during the transient loading time. To improve understanding of the conditions imposed on the specimen during the transient stage, a series of high rate loading experiments are performed using a Kolsky tensile bar system. Specimen forces and velocities during the high rate loading experiment are obtained by performing a thorough method of characteristics analysis of the system employed in the experiments. The in-situ full-field specimen displacements, velocities and accelerations during the loading process are quantified using modern ultra-high-speed imaging systems to provide detailed measurements of specimen response, with emphasis on the earliest stages of loading. Detailed analysis of the image-based measurements confirms that conditions are nominally consistent with those necessary for use of the one-dimensional wave equation within the relatively thin, dog-bone shaped tensile specimen. Specifically, measurements and use of the one-dimensional wave equation show clearly that the specimen has low inertial stresses in comparison to the applied transmitted force. Though the accelerations of the specimen continue for up to 50 μs, measurements show that the specimen is essentially in force equilibrium beginning a few microseconds after initial loading. These local measurements contrast with predictions based on comparison of the wave-based incident force measurements, which suggest that equilibrium occurs much later, on the order of 40-50 μs .

U.S. Field Artillery after World War I: Modernizing the Force While Downsizing

DTIC Science & Technology

2014-06-13

weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and......weapons, and tactics. It convened several boards to assess the requirements for an effective field artillery force, studying the materiel and

The Energetics of Motivated Cognition: A Force-Field Analysis

ERIC Educational Resources Information Center

Kruglanski, Arie W.; Belanger, Jocelyn J.; Chen, Xiaoyan; Kopetz, Catalina; Pierro, Antonio; Mannetti, Lucia

2012-01-01

A force-field theory of motivated cognition is presented and applied to a broad variety of phenomena in social judgment and self-regulation. Purposeful cognitive activity is assumed to be propelled by a "driving force" and opposed by a "restraining force". "Potential" driving force represents the maximal amount of energy an individual is prepared…

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

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

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

Accuracy of the Generalized Self-Consistent Method in Modelling the Elastic Behaviour of Periodic Composites

NASA Technical Reports Server (NTRS)

Walker, Kevin P.; Freed, Alan D.; Jordan, Eric H.

1993-01-01

Local stress and strain fields in the unit cell of an infinite, two-dimensional, periodic fibrous lattice have been determined by an integral equation approach. The effect of the fibres is assimilated to an infinite two-dimensional array of fictitious body forces in the matrix constituent phase of the unit cell. By subtracting a volume averaged strain polarization term from the integral equation we effectively embed a finite number of unit cells in a homogenized medium in which the overall stress and strain correspond to the volume averaged stress and strain of the constrained unit cell. This paper demonstrates that the zeroth term in the governing integral equation expansion, which embeds one unit cell in the homogenized medium, corresponds to the generalized self-consistent approximation. By comparing the zeroth term approximation with higher order approximations to the integral equation summation, both the accuracy of the generalized self-consistent composite model and the rate of convergence of the integral summation can be assessed. Two example composites are studied. For a tungsten/copper elastic fibrous composite the generalized self-consistent model is shown to provide accurate, effective, elastic moduli and local field representations. The local elastic transverse stress field within the representative volume element of the generalized self-consistent method is shown to be in error by much larger amounts for a composite with periodically distributed voids, but homogenization leads to a cancelling of errors, and the effective transverse Young's modulus of the voided composite is shown to be in error by only 23% at a void volume fraction of 75%.

High-resolution Observations of Flares in an Arch Filament System

NASA Astrophysics Data System (ADS)

Su, Yingna; Liu, Rui; Li, Shangwei; Cao, Wenda; Ahn, Kwangsu; Ji, Haisheng

2018-03-01

We study five sequential solar flares (SOL2015-08-07) occurring in Active Region 12396 observed with the Goode Solar Telescope (GST) at the Big Bear Solar Observatory, complemented by Interface Region Imaging Spectrograph and SDO observations. The main flaring region is an arch filament system (AFS) consisting of multiple bundles of dark filament threads enclosed by semicircular flare ribbons. We study the magnetic configuration and evolution of the active region by constructing coronal magnetic field models based on SDO/HMI magnetograms using two independent methods, i.e., the nonlinear force-free field (NLFFF) extrapolation and the flux rope insertion method. The models consist of multiple flux ropes with mixed signs of helicity, i.e., positive (negative) in the northern (southern) region, which is consistent with the GST observations of multiple filament bundles. The footprints of quasi-separatrix layers (QSLs) derived from the extrapolated NLFFF compare favorably with the observed flare ribbons. An interesting double-ribbon fine structure located at the east border of the AFS is consistent with the fine structure of the QSL’s footprint. Moreover, magnetic field lines traced along the semicircular footprint of a dome-like QSL surrounding the AFS are connected to the regions of significant helicity and Poynting flux injection. The maps of magnetic twist show that positive twist became dominant as time progressed, which is consistent with the injection of positive helicity before the flares. We hence conclude that these circular shaped flares are caused by 3D magnetic reconnection at the QSLs associated with the AFS possessing mixed signs of helicity.

Alpha 2 LASSO Data Bundles

DOE Data Explorer

Gustafson, William Jr; Vogelmann, Andrew; Endo, Satoshi; Toto, Tami; Xiao, Heng; Li, Zhijin; Cheng, Xiaoping; Kim, Jinwon; Krishna, Bhargavi

2015-08-31

The Alpha 2 release is the second release from the LASSO Pilot Phase that builds upon the Alpha 1 release. Alpha 2 contains additional diagnostics in the data bundles and focuses on cases from spring-summer 2016. A data bundle is a unified package consisting of LASSO LES input and output, observations, evaluation diagnostics, and model skill scores. LES input include model configuration information and forcing data. LES output includes profile statistics and full domain fields of cloud and environmental variables. Model evaluation data consists of LES output and ARM observations co-registered on the same grid and sampling frequency. Model performance is quantified by skill scores and diagnostics in terms of cloud and environmental variables.

Bubble Dynamics, Two-Phase Flow, and Boiling Heat Transfer in Microgravity

NASA Technical Reports Server (NTRS)

Chung, Jacob N.

1996-01-01

The objective of the research is to study the feasibility of employing an external force to replace the buoyancy force in order to maintain nucleate boiling in microgravity. We have found that a bulk velocity field, an electric field and an acoustic field could each play the role of the gravity field in microgravity. Nucleate boiling could be maintained by any one of the three external force fields in space.

Performance improvement of magnetized coaxial plasma gun by magnetic circuit on a bias coil

NASA Astrophysics Data System (ADS)

Edo, Takahiro; Matsumoto, Tadafumi; Asai, Tomohiko; Kamino, Yasuhiro; Inomoto, Michiaki; Gota, Hiroshi

2016-10-01

A magnetized coaxial plasmoid accelerator has been utilized for compact torus (CT) injection to refuel into fusion reactor core plasma. Recently, CT injection experiments have been conducted on the C-2/C-2U facility at Tri Alpha Energy. In the series of experiments successful refueling, i.e. increased particle inventory of field-reversed configuration (FRC) plasma, has been observed. In order to improve the performance of CT injector and to refuel in the upgraded FRC device, called C-2W, with higher confinement magnetic field, magnetic circuit consisting of magnetic material onto a bias magnetic coil is currently being tested at Nihon University. Numerical work suggests that the optimized bias magnetic field distribution realizes the increased injection velocity because of higher conversion efficiency of Lorenz self force to kinetic energy. Details of the magnetic circuit design as well as results of the test experiment and field calculations will be presented and discussed.

Directional solidification of Bi-Mn alloys using an applied magnetic field

NASA Technical Reports Server (NTRS)

Decarlo, J. L.; Pirich, R. G.

1987-01-01

Off-eutectic compositions of Bi-Mn were directionally solidified in applied transverse magnetic fields up to 3 kG, to determine the effects on thermal and solutal convection. Plane front directional solidification of eutectic and near-eutectic Bi-Mn results in a two-phase rodlike morphology consisting of ferromagnetic MnBi rods in a Bi solid solution matrix. Compositions of either side of the eutectic were studied in growth orientations vertically up and down. Temperature gradient was monitored during growth by means of an in-situ thermocouple. For Bi-rich compositions, the magnetic field appeared to increase mixing as determined from thermal, morphological, chemical, and magnetic analyses. For Mn-rich compositions, morphological and chemical analyses suggest some reduction in mixing due to application of the magnetic force. The capability for carrying out directional solidification of Bi-Mn in high longitudinal magnetic fields was established.

Electric-field-stimulated protein mechanics

PubMed Central

Hekstra, Doeke R.; White, K. Ian; Socolich, Michael A.; Henning, Robert W.; Šrajer, Vukica; Ranganathan, Rama

2017-01-01

The internal mechanics of proteins—the coordinated motions of amino acids and the pattern of forces constraining these motions—connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2PDZ2) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function. PMID:27926732

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

PubMed Central

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 during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases. PMID:19493356

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

PubMed

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 locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases.

Radiation Forces and Torques without Stress (Tensors)

ERIC Educational Resources Information Center

Bohren, Craig F.

2011-01-01

To understand radiation forces and torques or to calculate them does not require invoking photon or electromagnetic field momentum transfer or stress tensors. According to continuum electromagnetic theory, forces and torques exerted by radiation are a consequence of electric and magnetic fields acting on charges and currents that the fields induce…

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

PubMed Central

2016-01-01

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

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Commensurability effects in the critical forces of a superconducting film with Kagomé pinning array at submatching fields

NASA Astrophysics Data System (ADS)

Vizarim, Nicolas P.; Carlone, Maicon; Verga, Lucas G.; Venegas, Pablo A.

2017-09-01

Using molecular dynamics simulations, we find the commensurability force peaks in a two-dimensional superconducting thin-film with a Kagomé pinning array. A transport force is applied in two mutually perpendicular directions, and the magnetic field is increased up to the first matching field. Usually the condition to have pronounced force peaks in systems with periodic pinning is associated to the rate between the applied magnetic field and the first matching field, it must be an integer or a rational fraction. Here, we show that another condition must be satisfied, the vortex ground state must be ordered. Our calculations show that the pinning size and strength may dramatically change the vortex ground state. Small pinning radius and high values of pinning strength may lead to disordered vortex configurations, which fade the critical force peaks. The critical forces show anisotropic behavior, but the same dependence on pinning strength and radius is observed for both driven force directions. Different to cases where the applied magnetic field is higher than the first matching field, here the depinning process begins with vortices weakly trapped on top of a pinning site and not with interstitial vortices. Our results are in good agreement with recent experimental results.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

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 (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Force illusions and drifts observed during muscle vibration.

PubMed

Reschechtko, Sasha; Cuadra, Cristian; Latash, Mark L

2018-01-01

We explored predictions of a scheme that views position and force perception as a result of measuring proprioceptive signals within a reference frame set by ongoing efferent process. In particular, this hypothesis predicts force illusions caused by muscle vibration and mediated via changes in both afferent and efferent components of kinesthesia. Healthy subjects performed accurate steady force production tasks by pressing with the four fingers of one hand (the task hand) on individual force sensors with and without visual feedback. At various times during the trials, subjects matched the perceived force using the other hand. High-frequency vibration was applied to one or both of the forearms (over the hand and finger extensors). Without visual feedback, subjects showed a drop in the task hand force, which was significantly smaller under the vibration of that forearm. Force production by the matching hand was consistently higher than that of the task hand. Vibrating one of the forearms affected the matching hand in a manner consistent with the perception of higher magnitude of force produced by the vibrated hand. The findings were consistent between the dominant and nondominant hands. The effects of vibration on both force drift and force mismatching suggest that vibration led to shifts in both signals from proprioceptors and the efferent component of perception, the referent coordinate and/or coactivation command. The observations fit the hypothesis on combined perception of kinematic-kinetic variables with little specificity of different groups of peripheral receptors that all contribute to perception of forces and coordinates. NEW & NOTEWORTHY We show that vibration of hand/finger extensors produces consistent errors in finger force perception. Without visual feedback, finger force drifted to lower values without a drift in the matching force produced by the other hand; hand extensor vibration led to smaller finger force drift. The findings fit the scheme with combined perception of kinematic-kinetic variables and suggest that vibration leads to consistent shifts of the referent coordinate and, possibly, of coactivation command to the effector.

The influence of centrifugal forces on the B field structure of an axially symmetric equilibrium magnetosphere

NASA Technical Reports Server (NTRS)

Ye, Gang; Voigt, Gerd-Hannes

1989-01-01

A model is presented of an axially symmetric pole-on magnetosphere in MHD force balance, in which both plasma thermal pressure gradients and centrifugal force are taken into account. Assuming that planetary rotation leads to differentially rotating magnetotail field lines, the deformation of magnetotail field lines under the influence of both thermal plasma pressure and centrifugal forces was calculated. Analytic solutions to the Grad-Shafranov equation are presented, which include the centrifugal force term. It is shown that the nonrotational magnetosphere with hot thermal plasma leads to a field configuration without a toroidal B(phi) component and without field-aligned Birkeland currents. The other extreme, a rapidly rotating magnetosphere with cold plasma, leads to a configuration in which plasma must be confined within a thin disk in a plane where the radial magnetic field component B(r) vanishes locally.

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

PubMed

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

2017-01-01

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

Preface: Special Topic: From Quantum Mechanics to Force Fields.

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

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