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.

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.

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

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

Treesearch

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

2015-01-01

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

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

The calculation of transport phenomena in electromagnetically levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation has been developed for the electromagnetic force field, fluid flow field, and solute concentration field of levitation-melted metal specimens. The governing equations consist of the conventional transport equations combined with the appropriate expressions for the electromagnetic force field. The predictions obtained by solving the governing equations numerically on a digital computer are in good agreement with lifting force and average temperature measurements reported in the literature.

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.

Improving Development Teams to Support Deliberate Development of Air Force Officers

DTIC Science & Technology

2015-01-01

the USAF Cyber Force (Scott et al., 2010) • Understrength Air Force Officer Career Fields: A Force Management Approach ( Galway et al., 2005...D., “The New Way of Officer Assignments,” Air Force Magazine, June 1998, pp. 64–67. Galway , Lionel A., Richard J. Buddin, Michael R. Thirtle, Peter

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

DTIC Science & Technology

2016-06-09

C O R P O R A T I O N Research Report Air Force Officer Accession Planning Addressing Key Gaps in Meeting Career Field Academic Degree Requirements...various Air Force missions in particular career fields. Key to this goal for nonrated officers is establishing and enforcing academic degree...35 Developing Accession Targets by Academic Degree Type

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Molecular Mechanics

PubMed Central

Vanommeslaeghe, Kenno; Guvench, Olgun; MacKerell, Alexander D.

2014-01-01

Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The section ends with a brief overview of common force fields in CSBDD. PMID:23947650

Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents.

PubMed

Borodin, Oleg; Smith, Grant D

2006-03-30

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.

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

Comparing Molecular Dynamics Force Fields in the Essential Subspace

PubMed Central

Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

2015-01-01

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

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

Skill Needs and Human Resources Development in the Emerging Field of Nanotechnology

ERIC Educational Resources Information Center

Yawson, Robert Mayfield

2010-01-01

Strong societal requirements and consumer acceptance are the driving force of nanotechnology development. The necessity for qualified experts and strong demand on education in the multi-, trans- and interdisciplinary field of nanotechnology is a logical consequence of this driving force. There is the need for a comprehensive national…

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.

[Present situation and development trends of asymmetrical flow field-flow fractionation].

PubMed

Liang, Qihui; Wu, Di; Qiu, Bailing; Han, Nanyin

2017-09-08

Field-flow fractionation (FFF) is a kind of mature separation technologies in the field of bioanalysis, feasible of separating analytes with the differences of certain physical and chemical properties by the combination effects of two orthogonal force fields (flow field and external force field). Asymmetrical flow field-flow fractionation (AF4) is a vital subvariant of FFF, which applying a vertical flow field as the second dimension force field. The separation in AF4 opening channel is carried out by any composition carrier fluid, universally and effectively used in separation of bioparticles and biopolymers due to the non-invasivity feature. Herein, bio-analytes are held in bio-friendly environment and easily sterilized without using degrading carrier fluid which is conducive to maintain natural conformation. In this review, FFF and AF4 principles are briefly described, and some classical and emerging applications and developments in the bioanalytical fields are concisely introduced and tabled. Also, special focus is given to the hyphenation of AF4 with highly specific, sensitive detection technologies.

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

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.

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

Lipid14: The Amber Lipid Force Field

PubMed Central

2015-01-01

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

The near-field acoustic levitation of high-mass rotors

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

Hong, Z. Y.; Lü, P.; Geng, D. L.

2014-10-15

Here we demonstrate that spherical rotors with 40 mm diameter and 0-1 kg mass can be suspended more than tens of micrometers away from an ultrasonically vibrating concave surface by near-field acoustic radiation force. Their rotating speeds exceed 3000 rpm. An acoustic model has been developed to evaluate the near-field acoustic radiation force and the resonant frequencies of levitation system. This technique has potential application in developing acoustic gyroscope.

The near-field acoustic levitation of high-mass rotors.

PubMed

Hong, Z Y; Lü, P; Geng, D L; Zhai, W; Yan, N; Wei, B

2014-10-01

Here we demonstrate that spherical rotors with 40 mm diameter and 0-1 kg mass can be suspended more than tens of micrometers away from an ultrasonically vibrating concave surface by near-field acoustic radiation force. Their rotating speeds exceed 3000 rpm. An acoustic model has been developed to evaluate the near-field acoustic radiation force and the resonant frequencies of levitation system. This technique has potential application in developing acoustic gyroscope.

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.

Force-field prediction of materials properties in metal-organic frameworks

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

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew

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 bemore » observed when looking at properties sensitive to framework vibrational modes. As a result, this observation is more pronounced upon the introduction of framework charges.« less

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Force-field prediction of materials properties in metal-organic frameworks

DOE PAGES

Boyd, Peter G.; Moosavi, Seyed Mohamad; Witman, Matthew; ...

2016-12-23

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 bemore » observed when looking at properties sensitive to framework vibrational modes. As a result, this observation is more pronounced upon the introduction of framework charges.« 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.

Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

PubMed

Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

2014-01-14

The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development.

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

PubMed

García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

2014-08-14

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

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.

Rapid parameterization of small molecules using the Force Field Toolkit.

PubMed

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

2013-12-15

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

Controlling Casimir force via coherent driving field

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

In Situ Biological Treatment Test at Kelly Air Force Base. Volume 2. Field Test Results and Cost Model

DTIC Science & Technology

1987-07-01

Groundwater." Developments in Industrial Microbiology, Volume 24, pp. 225-234. Society of Industrial Microbiology, Arlington, Virginia. 18. Product ...ESL-TR-85-52 cv) VOLUME II CN IN SITU BIOLOGICAL TREATMENT TEST AT KELLY AIR FORCE BASE, VOLUME !1: FIELD TEST RESULTS AND COST MODEL R.S. WETZEL...Kelly Air Force Base, Volume II: Field Test Results and Cost Model (UNCLASSIFIED) 12 PERSONAL AUTHOR(S) Roger S. Wetzel, Connie M. Durst, Donald H

The Tai Chi in Star Formation

NASA Astrophysics Data System (ADS)

Li, Hua-bai

2017-10-01

Tai Chi, a Chinese martial art developed based on the laws of nature, emphasises how 'to conquer the unyielding with the yielding'. The recent observation of star formation shows that stars result from the interaction between gravity, turbulence and magnetic fields. This interaction again follows the nature rules that inspired Tai Chi. For example, if self-gravity is the force that dominates, the molecular cloud will collapse isotropically, which compresses magnetic field lines. The density of the yielding field lines increases until magnetic pressure reaches the critical value to support the cloud against the gravitational force in directions perpendicular to the field lines (Lorentz force). Then gravity gives way to Lorentz force, accumulating gas only along the field lines till the gas density achieves the critical value to again compress the field lines. The Tai Chi goes on in a self-similar way.

Current state of the art in small mass and force metrology within the International System of Units

NASA Astrophysics Data System (ADS)

Shaw, Gordon A.

2018-07-01

This review article summarizes new scientific trends in research for metrology of small mass (1 mg and lower) and small force (10 micronewtons and lower). After a brief introduction to the field, this paper provides an overview of recent developments in methods that demonstrate traceability to the International System of Units (SI) with emphasis on the implications of redefining the kilogram in terms of Planck’s constant. Specific research applications include new metrology facilities, calibration of small mass and force references such as milligram to submilligram masses or atomic force microscope (AFM) cantilevers, and laser power measurement using radiation pressure forces. Also discussed are recent scientific developments that may impact the field moving forward in the study of ultrasmall forces present in trapped and cooled quantum mechanical systems, resonant micro- and nanomechanical mass sensors, and other areas that are potentially well suited for SI metrology. The work reviewed is not intended as a comprehensive review of all research in which small forces are measured, but rather as an overview of a field in which the accurate measurement of small mass and force with quantified uncertainty is the primary goal.

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.

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

PubMed

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

2010-07-28

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

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.

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.

New measuring system for the distribution of a magnetic force by using an optical fiber

NASA Astrophysics Data System (ADS)

Ishigaki, H.; Oya, T.; Itoh, M.; Hida, A.; Iwata, K.

1993-01-01

A new measuring system using an optical fiber and a position sensing photodetector was developed to measure a three-dimensional distribution of a magnetic force. A steel ball attached to a cantilever made of an optical fiber generated force in a magnetic field. The displacement of the ball due to the force was detected by a position-sensing photodetector with the capability of detecting two-directional coordinates of the position. By scanning the sensing system in a magnetic field, we obtained distributions of two-directional component of the magnetic force vector. The component represents the gradient of a squared magnetic field. The usefulness of the system for measuring the magnetic field distribution in a narrow clearance and for evaluating superconducting machine components such as magnetic bearings was verified experimentally.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Force Balance and Substorm Effects in the Magnetotail

NASA Technical Reports Server (NTRS)

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

1997-01-01

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

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

NASA Technical Reports Server (NTRS)

Lyell, Margaret J.

1992-01-01

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

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.

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

PubMed

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

2014-09-16

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

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.

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.

Students' Development of Representational Competence through the Sense of Touch

ERIC Educational Resources Information Center

Magana, Alejandra J.; Balachandran, Sadhana

2017-01-01

Electromagnetism is an umbrella encapsulating several different concepts like electric current, electric fields and forces, and magnetic fields and forces, among other topics. However, a number of studies in the past have highlighted the poor conceptual understanding of electromagnetism concepts by students even after instruction. This study aims…

Alternating Magnetic Field Forces for Satellite Formation Flying

NASA Technical Reports Server (NTRS)

Youngquist, Robert C.; Nurge, Mark A.; Starr, Stnaley O.

2012-01-01

Selected future space missions, such as large aperture telescopes and multi-component interferometers, will require the precise positioning of a number of isolated satellites, yet many of the suggested approaches for providing satellites positioning forces have serious limitations. In this paper we propose a new approach, capable of providing both position and orientation forces, that resolves or alleviates many of these problems. We show that by using alternating fields and currents that finely-controlled forces can be induced on the satellites, which can be individually selected through frequency allocation. We also show, through analysis and experiment, that near field operation is feasible and can provide sufficient force and the necessary degrees of freedom to accurately position and orient small satellites relative to one another. In particular, the case of a telescope with a large number of free mirrors is developed to provide an example of the concept. We. also discuss the far field extension of this concept.

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

Statically determined slip-line field solution for the axial forming force estimation in the radial-axial ring rolling process

NASA Astrophysics Data System (ADS)

Quagliato, Luca; Berti, Guido A.

2017-10-01

In this paper, a statically determined slip-line solution algorithm is proposed for the calculation of the axial forming force in the radial-axial ring rolling process of flat rings. The developed solution is implemented in an Excel spreadsheet for the construction of the slip-line field and the calculation of the pressure factor to be used in the force model. The comparison between analytical solution and authors' FE simulation allows stating that the developed model supersedes the previous literature ones and proves the reliability of the proposed approach.

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

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

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

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

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes

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

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

PubMed

Radosinski, Lukasz; Labus, Karolina

2017-10-05

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

PubMed

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

2015-10-08

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

A 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.

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.

Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface.

PubMed

Sandoval-Perez, Angelica; Pluhackova, Kristyna; Böckmann, Rainer A

2017-05-09

Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.

Observation of the Field, Current and Force Distributions in an Optimized Superconducting Levitation with Translational Symmetry

NASA Astrophysics Data System (ADS)

Ye, Chang-Qing; Ma, Guang-Tong; Liu, Kun; Wang, Jia-Su

2017-01-01

The superconducting levitation realized by immersing the high-temperature superconductors (HTSs) into nonuniform magnetic field is deemed promising in a wide range of industrial applications such as maglev transportation and kinetic energy storage. Using a well-established electromagnetic model to mathematically describe the HTS, we have developed an efficient scheme that is capable of intelligently and globally optimizing the permanent magnet guideway (PMG) with single or multiple HTSs levitated above for the maglev transportation applications. With maximizing the levitation force as the principal objective, we optimized the dimensions of a Halbach-derived PMG to observe how the field, current and force distribute inside the HTSs when the optimized situation is achieved. Using a pristine PMG as a reference, we have analyzed the critical issues for enhancing the levitation force through comparing the field, current and force distributions between the optimized and pristine PMGs. It was also found that the optimized dimensions of the PMG are highly dependent upon the levitated HTS. Moreover, the guidance force is not always contradictory to the levitation force and may also be enhanced when the levitation force is prescribed to be the principle objective, depending on the configuration of levitation system and lateral displacement.

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.

Aquatic toxicology: fact or fiction?

PubMed Central

Macek, K J

1980-01-01

A brief history of the development of the field of aquatic toxicology is provided. In order to provide a perspective on the state-of-the-art in aquatic toxicology relative to classical toxicology, the two fields are compared from the standpoint of the type of scientist practicing each field, the respective objectives of each, the forces which drive the activity in each field, and the major advantages and disadvantages accruing to the practitioner of aquatic toxicology as a result of the differences in objectives and driving forces. PMID:6993200

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

PubMed

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

2017-11-01

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

How Well Can the Observed Flux Ropes in the Solar Wind be Fitted by a Uniform-twist Flux Rope Model?

NASA Astrophysics Data System (ADS)

Wang, Y.

2015-12-01

In the solar wind, flux ropes, e.g., magnetic clouds (MCs), are a frequently observational phenomenon. Their magnetic field configuration or the way that the field lines wind around the flux rope axis is one of the most important information to understand the formation and evolution of the observed flux ropes. Most MCs are believed to be in the force-free state, and widely modeled by the Lundquist force-free solution, in which the twist of the field line increases from zero at the axis to infinity at the boundary. However, Lundquist solution is not the only form of a force-free magnetic field. Some studies based on suprathermal electron observations and models have shown that MCs may carry magnetic field lines more likely to be uniformly twisted. The nonlinear force-free field extrapolation of solar magnetic field also suggests that the field lines of a flux rope twist limitedly. In this study, we have developed a velocity-modified uniform-twist force-free flux rope model, and fit observed MCs with this model. By using this approach, we test how well the observed MCs can be fitted into a uniform-twist flux rope. Some interesting results will be given in this presentation.

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

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.

Direct folding simulation of helical proteins using an effective polarizable bond force field.

PubMed

Duan, Lili; Zhu, Tong; Ji, Changge; Zhang, Qinggang; Zhang, John Z H

2017-06-14

We report a direct folding study of seven helical proteins (, Trpcage, , C34, N36, , ) ranging from 17 to 53 amino acids through standard molecular dynamics simulations using a recently developed polarizable force field-Effective Polarizable Bond (EPB) method. The backbone RMSDs, radius of gyrations, native contacts and native helix content are in good agreement with the experimental results. Cluster analysis has also verified that these folded structures with the highest population are in good agreement with their corresponding native structures for these proteins. In addition, the free energy landscape of seven proteins in the two dimensional space comprised of RMSD and radius of gyration proved that these folded structures are indeed of the lowest energy conformations. However, when the corresponding simulations were performed using the standard (nonpolarizable) AMBER force fields, no stable folded structures were observed for these proteins. Comparison of the simulation results based on a polarizable EPB force field and a nonpolarizable AMBER force field clearly demonstrates the importance of polarization in the folding of stable helical structures.

Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM

PubMed Central

Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger

2015-01-01

Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455

Machine learning of accurate energy-conserving molecular force fields.

PubMed

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

2017-05-01

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

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

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

2017-01-01

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

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

NASA Astrophysics Data System (ADS)

Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

2017-10-01

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

Complexion of forces in an anisotropic self-gravitating system

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

Kandrup, H.E.

Chandrasekhar and von Neumann developed a completely stochastic formalism to analyze the complexion of forces acting upon a test star situated in an infinite, homogeneous distribution of field stars. This formalism is generalized here to allow for more realistic inhomogeneous and anisotropic systems. It is demonstrated that the forces acting upon a test star decompose ''naturally'' into the incoherent sum of a mean force associated with the average spatial inhomogeneity and a fluctuating force associated with stochastic deviations from these mean conditions. Moreover, as in the special case considered by Chandrasekhar and von Neumann, one can apparently associate the fluctuatingmore » forces with the effects of particularly proximate field stars, thereby motivating the ''nearest neighbor'' interpretation first introduced by Chandrasekhar.« less

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.

Mathematical and experimental modelling of the dynamic bubble processes occurring in a two-phase cyclonic separation device

NASA Astrophysics Data System (ADS)

Schrage, Dean Stewart

1998-11-01

This dissertation presents a combined mathematical and experimental analysis of the fluid dynamics of a gas- liquid, dispersed-phase cyclonic separation device. The global objective of this research is to develop a simulation model of separation process in order to predict the void fraction field within a cyclonic separation device. The separation process is approximated by analyzing the dynamic motion of many single-bubbles, moving under the influence of the far-field, interacting with physical boundaries and other bubbles. The dynamic motion of the bubble is described by treating the bubble as a point-mass and writing an inertial force balance, equating the force applied to the bubble-point-location to the inertial acceleration of the bubble mass (also applied to the point-location). The forces which are applied to the bubble are determined by an integration of the surface pressure over the bubble. The surface pressure is coupled to the intrinsic motion of the bubble, and is very difficult to obtain exactly. However, under moderate Reynolds number, the wake trailing a bubble is small and the near-field flow field can be approximated as an inviscid flow field. Unconventional potential flow techniques are employed to solve for the surface pressure; the hydrodyamic forces are described as a hydrodynamic mass tensor operating on the bubble acceleration vector. The inviscid flow model is augmented with adjunct forces which describe: drag forces, dynamic lift, far-field pressure forces. The dynamic equations of motion are solved both analytically and numerically for the bubble trajectory in specific flow field examples. A validation of these equations is performed by comparing to an experimentally-derived trajectory of a single- bubble, which is released into a cylindrical Couette flow field (inner cylinder rotating) at varying positions. Finally, a simulation of a cyclonic separation device is performed by extending the single-bubble dynamic model to a multi-bubble ensemble. A simplified model is developed to predict the effects of bubble-interaction. The simulation qualitatively depicts the separation physics encountered in an actual cyclonic separation device, supporting the original tenet that the separation process can be approximated by the collective motions of single- bubbles.

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

NASA Astrophysics Data System (ADS)

Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.; Volkov, Sergey N.; Solov'yov, Andrey V.

2016-01-01

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Gustavo Garcia and Eugene Surdutovich.

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

NASA Astrophysics Data System (ADS)

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

2015-12-01

Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field.

Drag and Lift Forces Between a Rotating Conductive Sphere and a Cylindrical Magnet

NASA Technical Reports Server (NTRS)

Nurge, Mark A.; Youngquist, Robert C.

2017-01-01

Modeling the interaction between a non-uniform magnetic field and a rotating conductive object allows study of the drag force which is used in applications such as eddy current braking and linear induction motors as well as the transition to a repulsive force that is the basis for magnetic levitation systems. Here, we study the interaction between a non-uniform field generated by a cylindrical magnet and a rotating conductive sphere. Each eddy current in the sphere generates a magnetic field which in turn generates another eddy current, eventually feeding back on itself. A two step mathematics process is developed to find a closed form solution in terms of only two eddy currents. However, the complete solution requires decomposition of the magnetic field into a summation of spherical harmonics, making it more suitable for a graduate level electromagnetism lecture or lab. Finally, the forces associated with these currents are calculated and then verified experimentally.

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

PubMed

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

2018-04-05

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

Drag and lift forces between a rotating conductive sphere and a cylindrical magnet

NASA Astrophysics Data System (ADS)

Nurge, Mark A.; Youngquist, Robert C.; Starr, Stanley O.

2018-06-01

Modeling the interaction between a non-uniform magnetic field and a rotating conductive object provides insight into the drag force, which is used in applications such as eddy current braking and linear induction motors, as well as the transition to a repulsive force, which is the basis for magnetic levitation systems. Here, we study the interaction between a non-uniform field generated by a cylindrical magnet and a rotating conductive sphere. Each eddy current in the sphere generates a magnetic field which in turn generates another eddy current, eventually feeding back on itself. A two-step mathematical process is developed to find a closed-form solution in terms of only three eddy currents. However, the complete solution requires decomposition of the magnetic field into a summation of spherical harmonics, making it more suitable for a graduate-level electromagnetism lecture or lab. Finally, the forces associated with these currents are calculated and then verified experimentally.

Combining single-molecule manipulation and single-molecule detection.

PubMed

Cordova, Juan Carlos; Das, Dibyendu Kumar; Manning, Harris W; Lang, Matthew J

2014-10-01

Single molecule force manipulation combined with fluorescence techniques offers much promise in revealing mechanistic details of biomolecular machinery. Here, we review force-fluorescence microscopy, which combines the best features of manipulation and detection techniques. Three of the mainstay manipulation methods (optical traps, magnetic traps and atomic force microscopy) are discussed with respect to milestones in combination developments, in addition to highlight recent contributions to the field. An overview of additional strategies is discussed, including fluorescence based force sensors for force measurement in vivo. Armed with recent exciting demonstrations of this technology, the field of combined single-molecule manipulation and single-molecule detection is poised to provide unprecedented views of molecular machinery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Current and Emerging Forces Impacting Special Education.

ERIC Educational Resources Information Center

Yates, James R.

Using the methodology of force field analysis, the paper develops possible futures for special education based on current trends. Demographic forces impacting special education include age changes, ethnicity changes, the needs of emerging language minorities, specific change in the youth population, environmental factors and the incidence of…

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.

Force fields and scoring functions for carbohydrate simulation.

PubMed

Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

2015-01-12

Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Anomalous resistivity and the evolution of magnetic field topology

NASA Technical Reports Server (NTRS)

Parker, E. N.

1993-01-01

This paper explores the topological restructuring of a force-free magnetic field caused by the hypothetical sudden onset of a localized region of strong anomalous resistivity. It is shown that the topological complexity increases, with the primitive planar force-free field with straight field lines developing field lines that wrap half a turn around each other, evidently providing a surface of tangential discontinuity in the wraparound region. It is suggested that the topological restructuring contributes to the complexity of the geomagnetic substorm, the aurora, and perhaps some of the flare activity on the sun, or other star, and the Galactic halo.

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

A micropatterning and image processing approach to simplify measurement of cellular traction forces

PubMed Central

Polio, Samuel R.; Rothenberg, Katheryn E.; Stamenović, Dimitrije; Smith, Michael L.

2012-01-01

Quantification of the traction forces that cells apply to their surroundings has been critical to the advancement of our understanding of cancer, development and basic cell biology. This field was made possible through the development of engineered cell culture systems that permit optical measurement of cell-mediated displacements and computational algorithms that allow conversion of these displacements into stresses and forces. Here, we present a novel advancement of traction force microscopy on polyacrylamide (PAA) gels that addresses limitations of existing technologies. Through an indirect patterning technique, we generated PAA gels with fluorescent 1 μm dot markers in a regularized array. This improves existing traction measurements since (i) multiple fields of view can be measured in one experiment without the need for cell removal; (ii) traction vectors are modeled as discrete point forces, and not as a continuous field, using an extremely simple computational algorithm that we have made available online; and (iii) the pattern transfer technique is amenable to any of the published techniques for producing patterns on glass. In the future, this technique will be used for measuring traction forces on complex patterns with multiple, spatially distinct ligands in systems for applying strain to the substrate, and in sandwich cultures that generate quasi-three-dimensional environments for cells. PMID:21884832

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

PubMed Central

2015-01-01

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

Magnetic Field, Force, and Inductance Computations for an Axially Symmetric Solenoid

NASA Technical Reports Server (NTRS)

Lane, John E.; Youngquist, Robert C.; Immer, Christopher D.; Simpson, James C.

2001-01-01

The pumping of liquid oxygen (LOX) by magnetic fields (B field), using an array of electromagnets, is a current topic of research and development at Kennedy Space Center, FL. Oxygen is paramagnetic so that LOX, like a ferrofluid, can be forced in the direction of a B field gradient. It is well known that liquid oxygen has a sufficient magnetic susceptibility that a strong magnetic gradient can lift it in the earth's gravitational field. It has been proposed that this phenomenon can be utilized in transporting (i.e., pumping) LOX not only on earth, but on Mars and in the weightlessness of space. In order to design and evaluate such a magnetic pumping system, it is essential to compute the magnetic and force fields, as well as inductance, of various types of electromagnets (solenoids). In this application, it is assumed that the solenoids are air wrapped, and that the current is essentially time independent.

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.

Machine Learning Force Field Parameters from Ab Initio Data

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

Li, Ying; Li, Hui; Pickard, Frank C.

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor duringmore » the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.« less

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

PubMed

Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

2017-06-05

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

PubMed Central

Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng

2017-01-01

Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738

Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride).

PubMed

Lachet, V; Teuler, J-M; Rousseau, B

2015-01-08

A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.

Toward structure prediction of cyclic peptides.

PubMed

Yu, Hongtao; Lin, Yu-Shan

2015-02-14

Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

PubMed

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

2018-06-14

The activity and function of many macromolecules in cellular environments are coupled with the binding of divalent ions such as calcium or magnesium. In principle, computer simulations can be used to understand the molecular level aspects of how many important macromolecules interact with ions. However, most of the force fields currently available often fail to accurately reproduce the properties of divalent ions in aqueous environments. Here we develop classical non-polarizable force fields for the aqueous alkaline earth metal halides (MX 2 ), where M = Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ and X = Cl - , Br - , I - , which can be used in bimolecular simulations and which are compatible with the Simple Point Charge/Extended (SPC/E) water model. The force field parameters are specifically developed to reproduce the experimental Kirkwood-Buff integrals for aqueous solutions and thereby the experimental activity derivatives, partial molar volumes, and excess coordination numbers. This ensures that a reasonable balance between ion-ion, ion-water, and water-water distributions is obtained. However, this requires a scaling of the cation to water oxygen interaction strength in order to accurately reproduce the integrals. The scaling factors developed for chloride salts are successfully transferable to the bromide and iodide salts. Use of these new models leads to reasonable diffusion constants and dielectric decrements. However, the performance of the models decreases with increasing salt concentration (>4m), and simulations of the pure crystals exhibited unstable behavior.

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.

Development of Finite Elements for Two-Dimensional Structural Analysis Using the Integrated Force Method

NASA Technical Reports Server (NTRS)

Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

1996-01-01

The Integrated Force Method has been developed in recent years for the analysis of structural mechanics problems. This method treats all independent internal forces as unknown variables that can be calculated by simultaneously imposing equations of equilibrium and compatibility conditions. In this paper a finite element library for analyzing two-dimensional problems by the Integrated Force Method is presented. Triangular- and quadrilateral-shaped elements capable of modeling arbitrary domain configurations are presented. The element equilibrium and flexibility matrices are derived by discretizing the expressions for potential and complementary energies, respectively. The displacement and stress fields within the finite elements are independently approximated. The displacement field is interpolated as it is in the standard displacement method, and the stress field is approximated by using complete polynomials of the correct order. A procedure that uses the definitions of stress components in terms of an Airy stress function is developed to derive the stress interpolation polynomials. Such derived stress fields identically satisfy the equations of equilibrium. Moreover, the resulting element matrices are insensitive to the orientation of local coordinate systems. A method is devised to calculate the number of rigid body modes, and the present elements are shown to be free of spurious zero-energy modes. A number of example problems are solved by using the present library, and the results are compared with corresponding analytical solutions and with results from the standard displacement finite element method. The Integrated Force Method not only gives results that agree well with analytical and displacement method results but also outperforms the displacement method in stress calculations.

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

EUV emission, filament activation and magnetic fields in a slow-rise flare

NASA Technical Reports Server (NTRS)

Rust, D. M.; Nakagawa, Y.; Neupert, W. M.

1975-01-01

Results are reported for observations and analysis of synoptic data on a 1B flare that occurred on January 19, 1972. The observations include large-scale H-alpha movies of the flare and pre-flare developments, OSO-7 satellite data on soft X-ray and EUV developments, magnetograms, and hard X-ray observations. Theoretical force-free magnetic field configurations are compared with structures seen in the soft X-ray, EUV, and H-alpha images, and the evolution of the flare is described. The energy available for the flare is estimated from the change of magnetic field inferred from the H-alpha filtergrams and from force-free field calculations. It is suggested that the flare originated in a twisted filament where it was compressed by emerging fields, and it is shown that the flare started below the corona and appeared to derive its energy from the magnetic fields in or near the filament.

Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

DOE PAGES

Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; ...

2015-11-20

Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength goldmore » disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.« less

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

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

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

Using Magnetic Forces to Probe the Gravi-response of Swimming Paramecium

NASA Astrophysics Data System (ADS)

Guevorkian, Karine; Valles, James M., Jr.

2004-03-01

Paramecium Caudatum, a single celled ciliate, alters its swimming behavior when subjected to different gravity environments (e.g. centrifugation and micro-gravity). To dissect the mechanisms behind this gravi-response and that of other biological systems, we are developing the use of magnetic body forces as a means of creating a rapidly tunable, simulated variable gravity environment. Since biological materials are weakly diamagnetic, we must subject them to intense inhomogeneous magnetic fields with characteristic field-field gradient products on the order of 16 T^2/cm. We will describe experiments on Paramecium Caudatum in which we adjust their net buoyancy with magnetic forces and measure the resulting changes in their swimming behavior.

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

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

MCPB.py: A Python Based Metal Center Parameter Builder.

PubMed

Li, Pengfei; Merz, Kenneth M

2016-04-25

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

Microscopic analysis of shape transition in neutron-deficient Yb isotopes

NASA Astrophysics Data System (ADS)

Fu, Y.; Tong, H.; Wang, X. F.; Wang, H.; Wang, D. Q.; Wang, X. Y.; Yao, J. M.

2018-01-01

The development of nuclear collectivity in even-even Yb-170152 is studied with three types of mean-field calculations: the nonrelativistic Hartree-Fock plus BCS calculation using the Skyrme SLy4 force plus a density-dependent δ pairing force and the relativistic mean-field calculation using a point-coupling energy functional supplemented with either a density-independent δ pairing force or a separable pairing force. The low-lying states are obtained by solving a five-dimensional collective Hamiltonian with parameters determined from the three mean-field solutions. The energy surfaces, excitation energies, electric multiple transition strengths, and differential isotope shifts are presented in comparison with available data. Our results show that different treatments of pairing correlations have a significant influence on the speed of developing collectivity as the increase of neutron number. All the calculations demonstrate the important role of dynamic shape-mixing effects in resolving the puzzle in the dramatic increase of charge radius from 152Yb to 154Yb and the role of triaxiality in Yb 160 ,162 ,164 .

Developing and Fielding Information Dominance

DTIC Science & Technology

2002-01-01

Developing and Fielding Information Dominance Space and Naval Warfare Systems Command’s IT-21 Blocks 1 and 2 2002 Command and Control Research and...00-00-2002 4. TITLE AND SUBTITLE Developing and Fielding Information Dominance 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...force levels were uncertain, the necessary role of information dominance to maintaining strategic superiority was not. Platform Centric Warfare, with its

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

PubMed

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

2016-08-24

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

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

PubMed Central

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

2016-01-01

Tactile sensors are essential if robots are to safely interact with the external world and to dexterously manipulate objects. Current tactile sensors have limitations restricting their use, notably being too fragile or having limited performance. Magnetic field-based soft tactile sensors offer a potential improvement, being durable, low cost, accurate and high bandwidth, but they are relatively undeveloped because of the complexities involved in design and calibration. This paper presents a general design methodology for magnetic field-based three-axis soft tactile sensors, enabling researchers to easily develop specific tactile sensors for a variety of applications. All aspects (design, fabrication, calibration and evaluation) of the development of tri-axis soft tactile sensors are presented and discussed. A moving least square approach is used to decouple and convert the magnetic field signal to force output to eliminate non-linearity and cross-talk effects. A case study of a tactile sensor prototype, MagOne, was developed. This achieved a resolution of 1.42 mN in normal force measurement (0.71 mN in shear force), good output repeatability and has a maximum hysteresis error of 3.4%. These results outperform comparable sensors reported previously, highlighting the efficacy of our methodology for sensor design. PMID:27563908

Self-organization of granular media in airborne ultrasonic fields

NASA Astrophysics Data System (ADS)

Bobrovskaya, A. I.; Stepanenko, D. A.; Minchenya, V. T.

2012-05-01

The article presents results of experimental and theoretical studies of behaviour of granular media (powder materials) in airborne ultrasonic field created by flexurally-vibrating ring-shaped waveguide with resonant frequency in the range 20-40 kHz. Experiments show that action of acoustic radiation forces results in formation of ordered structures in the form of ultrathin walls (monolayers) with number corresponding to the number of ring nodal points. Action of secondary radiation forces (König forces) results in formation of collateral (secondary) walls situated nearby primary walls. Experimental observations are compared with results of modelling of acoustic radiation force field inside the ring by means of COMSOL Multiphysics and MathCad software. Results of the studies can be used in development of devices for ultrasonic separation and concentration of particles as well as for formation of ordered monolayers from spherical particles.

Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study.

PubMed

Zhu, Shun; Travis, Sue M; Elcock, Adrian H

2013-07-09

A major current challenge for drug design efforts focused on protein kinases is the development of drug resistance caused by spontaneous mutations in the kinase catalytic domain. The ubiquity of this problem means that it would be advantageous to develop fast, effective computational methods that could be used to determine the effects of potential resistance-causing mutations before they arise in a clinical setting. With this long-term goal in mind, we have conducted a combined experimental and computational study of the thermodynamic effects of active-site mutations on a well-characterized and high-affinity interaction between a protein kinase and a small-molecule inhibitor. Specifically, we developed a fluorescence-based assay to measure the binding free energy of the small-molecule inhibitor, SB203580, to the p38α MAP kinase and used it measure the inhibitor's affinity for five different kinase mutants involving two residues (Val38 and Ala51) that contact the inhibitor in the crystal structure of the inhibitor-kinase complex. We then conducted long, explicit-solvent thermodynamic integration (TI) simulations in an attempt to reproduce the experimental relative binding affinities of the inhibitor for the five mutants; in total, a combined simulation time of 18.5 μs was obtained. Two widely used force fields - OPLS-AA/L and Amber ff99SB-ILDN - were tested in the TI simulations. Both force fields produced excellent agreement with experiment for three of the five mutants; simulations performed with the OPLS-AA/L force field, however, produced qualitatively incorrect results for the constructs that contained an A51V mutation. Interestingly, the discrepancies with the OPLS-AA/L force field could be rectified by the imposition of position restraints on the atoms of the protein backbone and the inhibitor without destroying the agreement for other mutations; the ability to reproduce experiment depended, however, upon the strength of the restraints' force constant. Imposition of position restraints in corresponding simulations that used the Amber ff99SB-ILDN force field had little effect on their ability to match experiment. Overall, the study shows that both force fields can work well for predicting the effects of active-site mutations on small molecule binding affinities and demonstrates how a direct combination of experiment and computation can be a powerful strategy for developing an understanding of protein-inhibitor interactions.

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

A reactive force field study of Li/C systems for electrical energy storage

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

Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.

Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less

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

PubMed

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

2017-12-01

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

A reactive force field study of Li/C systems for electrical energy storage

DOE PAGES

Raju, Muralikrishna; Ganesh, P.; Kent, Paul R. C.; ...

2015-04-02

Graphitic carbon is still the most ubiquitously used anode material in Li-ion batteries. In spite of its ubiquity, there are few theoretical studies that fully capture the energetics and kinetics of Li in graphite and related nanostructures at experimentally relevant length, time-scales, and Li-ion concentrations. In this paper, we describe the development and application of a ReaxFF reactive force field to describe Li interactions in perfect and defective carbon-based materials using atomistic simulations. We develop force field parameters for Li–C systems using van der Waals-corrected density functional theory (DFT). Grand canonical Monte Carlo simulations of Li intercalation in perfect graphitemore » with this new force field not only give a voltage profile in good agreement with known experimental and DFT results but also capture the in-plane Li ordering and interlayer separations for stage I and II compounds. In defective graphite, the ratio of Li/C (i.e., the capacitance increases and voltage shifts) both in proportion to the concentration of vacancy defects and metallic lithium is observed to explain the lithium plating seen in recent experiments. We also demonstrate the robustness of the force field by simulating model carbon nanostructures (i.e., both 0D and 1D structures) that can be potentially used as battery electrode materials. Whereas a 0D defective onion-like carbon facilitates fast charging/discharging rates by surface Li adsorption, a 1D defect-free carbon nanorod requires a critical density of Li for intercalation to occur at the edges. Our force field approach opens the opportunity for studying energetics and kinetics of perfect and defective Li/C structures containing thousands of atoms as a function of intercalation. As a result, this is a key step toward modeling of realistic carbon materials for energy applications.« less

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

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

PubMed

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

2016-12-12

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

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Molecular dynamics simulations of AP/HMX composite with a modified force field.

PubMed

Zhu, Wei; Wang, Xijun; Xiao, Jijun; Zhu, Weihua; Sun, Huai; Xiao, Heming

2009-08-15

An all-atom force field for ammonium perchlorate (AP) is developed with the framework of pcff force field. The structural parameters of AP obtained with the modified force field are in good agreement with experimental values. Molecular dynamics (MD) simulations have been performed to investigate AP/HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane) composite at different temperatures. The binding energies, thermal expansion coefficient, and the trigger bond lengths of HMX in the AP/HMX composite have been obtained. The binding energies of the system increase slightly with temperature increasing, peak at 245K, and then gradually decrease. The volume thermal expansion coefficient of the AP/HMX composite has been derived from the volume variation with temperature. As the temperature rises, the maximal lengths of the trigger bond N-NO(2) of HMX increase gradually. The simulated results indicate that the maximal length of trigger bond can be used as a criterion for judging the sensitivity of energetic composite.

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

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

Algorithms to automate gap-dependent integral tuning for the 2.8-meter long horizontal field undulator with a dynamic force compensation mechanism

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

Xu, Joseph Z., E-mail: x@anl.gov; Vasserman, Isaac; Strelnikov, Nikita

2016-07-27

A 2.8-meter long horizontal field prototype undulator with a dynamic force compensation mechanism has been developed and tested at the Advanced Photon Source (APS) at Argonne National Laboratory (Argonne). The magnetic tuning of the undulator integrals has been automated and accomplished by applying magnetic shims. A detailed description of the algorithms and performance is reported.

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

PubMed

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

2015-06-25

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

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Effect of self-consistent magnetic field on plasma sheet penetration to the inner magnetosphere: Rice convection model simulations combined with modified Dungey force-balanced magnetic field solver

NASA Astrophysics Data System (ADS)

Gkioulidou, Matina; Wang, Chih-Ping; Lyons, Larry R.

2011-12-01

Transport of plasma sheet particles into the inner magnetosphere is crucial to the development of the region 2 (R2) field-aligned current system (FAC), which results in the shielding of the penetration electric field and the formation of subauroral polarization streams (SAPS) and the Harang reversal, phenomena closely associated with storms and substorms. In addition to the electric field, this transport is also strongly affected by the magnetic field, which changes with plasma pressure and is distinctly different from the dipole field in the inner plasma sheet. To determine the feedback of force-balanced magnetic field to the transport, we have integrated the Rice convection model (RCM) with a modified Dungey magnetic field solver to obtain the required force balance in the equatorial plane. Comparing our results with those from a RCM run using a T96 magnetic field, we find that transport under a force-balanced magnetic field results in weaker pressure gradients and thus weaker R2 FAC in the near-Earth region and weaker shielding of the penetration electric field. As a result, plasma sheet protons and electrons penetrate farther earthward, and their inner edges become closer together and more azimuthally symmetric than in the T96 case. The Harang reversal extends farther dawnward, and the SAPS become more confined in radial and latitudinal extents. The magnitudes of azimuthal pressure gradient, the inner edges of thermal protons and electrons, the latitudinal range of the Harang reversal, and the radial and latitudinal widths of the SAPS from the force-balanced run are found to be more consistent with observations.

A simulation of dielectrophoresis force actuated liquid lens

NASA Astrophysics Data System (ADS)

Yao, Xiaoyin; Xia, Jun

2009-11-01

Dielectrophoresis (DEP) and electrowetting on dielectric (EWOD) are based on the electrokinetic mechanisms which have great potential in microfluidic manipulation. DEP dominate the movement of particles induced by polarization effects in nonuniform electric field ,while EWOD has become one of the most widely used tools for manipulating tiny amounts of liquids on solid surfaces. Liquid lens driven by EWOD have been well studied and developed. But liquid lens driven by DEP has not been studied adequately. This paper focuses on modeling liquid lens driven by DEP force. A simulation of DEP driven droplet dynamics was performed by coupling of the electrostatic field and the two-phase flow field. Two incompressible and dielectric liquids with different permittivity were chosen in the two-phase flow field. The DEP force density, in direct proportion to gradient of the square of the electric field intensity, was used as a body force density in Navier-Stokes equation. When voltage applied, the liquid with high permittivity flowed to the place where the gradient of the square of the electric field intensity was higher, and thus change the curvature of interface between two immiscible liquid. The differences between DEP and EWOD liquid lens were also presented.

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

PubMed

Giulianotti, Richard; Robertson, Roland

2012-06-01

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

Pumping Liquid Oxygen by Use of Pulsed Magnetic Fields

NASA Technical Reports Server (NTRS)

Youngquist, Robert; Lane, John; Immer, Christopher; Simpson, James

2004-01-01

An effort is underway to develop a method of pumping small amounts of liquid oxygen by use of pulsed magnetic fields. This development is motivated by a desire to reduce corrosion and hazards of explosion and combustion by eliminating all moving pump parts in contact with the pumped oxygen. The method exploits the known paramagnetism of liquid oxygen. Since they both behave similarly, the existing theory of ferrofluids (liquids with colloidally suspended magnetic particles) is directly applicable to paramagnetic liquid oxygen. In general, the force density of the paramagnetic interaction is proportional to the magnetic susceptibility multiplied by the gradient of the square of the magnitude of the magnetic field. The local force is in the direction of intensifying magnetic field. In the case of liquid oxygen, the magnetic susceptibility is large enough that a strong magnetic-field gradient can lift the liquid in normal Earth gravitation.

Predator Force Structure Changes at Indian Springs Air Force Auxiliary Field, Nevada Environmental Assessment

DTIC Science & Technology

2003-07-01

Office Agency for Nuclear Projects Energy Agriculture Business & Industry Minerals Economic Development Tourism Fire Marshal Human Resources...Agriculture Business & Industry Minerals Economic Development Tourism Fire Marshal Human Resources A in Services Indian Commission Colorado...Data EIAP Environmental Impact Analysis Process EMCS Central Energy Management System ERP Environmental Restoration Program ESA Endangered

Pilot Field Demonstration of Alternative Fuels in Force Projection Petroleum and Water Distribution Equipment

DTIC Science & Technology

2014-09-04

They included two Force Projection Technology (FPT) diesel driven pumping assemblies of 350 and 600 gallons per minute (GPM), and the Advanced...Army Tank Automotive Research Development and Engineering Center (TARDEC). They included two Force Projection Technology (FPT) diesel driven...research programs. The first two systems identified were Force Projection Technology (FPT) diesel -driven pumping assemblies of 350 and 600 gallons per

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

Ocean Wave Simulation Based on Wind Field

PubMed Central

2016-01-01

Ocean wave simulation has a wide range of applications in movies, video games and training systems. Wind force is the main energy resource for generating ocean waves, which are the result of the interaction between wind and the ocean surface. While numerous methods to handle simulating oceans and other fluid phenomena have undergone rapid development during the past years in the field of computer graphic, few of them consider to construct ocean surface height field from the perspective of wind force driving ocean waves. We introduce wind force to the construction of the ocean surface height field through applying wind field data and wind-driven wave particles. Continual and realistic ocean waves result from the overlap of wind-driven wave particles, and a strategy was proposed to control these discrete wave particles and simulate an endless ocean surface. The results showed that the new method is capable of obtaining a realistic ocean scene under the influence of wind fields at real time rates. PMID:26808718

Ocean Wave Simulation Based on Wind Field.

PubMed

Li, Zhongyi; Wang, Hao

2016-01-01

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

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

PubMed

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

2012-01-10

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

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

PubMed Central

2011-01-01

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968

Thermodynamic properties of hydrogen dissociation reaction from the small system method and reactive force field ReaxFF

NASA Astrophysics Data System (ADS)

Trinh, Thuat T.; Meling, Nora; Bedeaux, Dick; Kjelstrup, Signe

2017-03-01

We present thermodynamic properties of the H2 dissociation reaction by means of the Small System Method (SSM) using Reactive Force Field (ReaxFF) simulations. Thermodynamic correction factors, partial molar enthalpies and heat capacities of the reactant and product were obtained in the high temperature range; up to 30,000 K. The results obtained from the ReaxFF potential agree well with previous results obtained with a three body potential (TBP). This indicates that the popular reactive force field method can be combined well with the newly developed SSM in realistic simulations of chemical reactions. The approach may be useful in the study of heat and mass transport in combination with chemical reactions.

Decoding gripping force based on local field potentials recorded from subthalamic nucleus in humans

PubMed Central

Tan, Huiling; Pogosyan, Alek; Ashkan, Keyoumars; Green, Alexander L; Aziz, Tipu; Foltynie, Thomas; Limousin, Patricia; Zrinzo, Ludvic; Hariz, Marwan; Brown, Peter

2016-01-01

The basal ganglia are known to be involved in the planning, execution and control of gripping force and movement vigour. Here we aim to define the nature of the basal ganglia control signal for force and to decode gripping force based on local field potential (LFP) activities recorded from the subthalamic nucleus (STN) in patients with deep brain stimulation (DBS) electrodes. We found that STN LFP activities in the gamma (55–90 Hz) and beta (13–30m Hz) bands were most informative about gripping force, and that a first order dynamic linear model with these STN LFP features as inputs can be used to decode the temporal profile of gripping force. Our results enhance the understanding of how the basal ganglia control gripping force, and also suggest that deep brain LFPs could potentially be used to decode movement parameters related to force and movement vigour for the development of advanced human-machine interfaces. DOI: http://dx.doi.org/10.7554/eLife.19089.001 PMID:27855780

Inducing Lift on Spherical Particles by Traveling Magnetic Fields

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Grugel, Richard N.; Rose, M. Franklin (Technical Monitor)

2001-01-01

Gravity induced sedimentation of suspensions is a serious drawback to many materials and biotechnology processes, a factor that can, in principle, be overcome by utilizing an opposing Lorentz body force. In this work we demonstrate the utility of employing a traveling magnetic field (TMF) to induce a lifting force on particles dispersed in the fluid. Theoretically, a model has been developed to ascertain the net force, induced by TMF, acting on a spherical body as a function of the fluid medium's electrical conductivity and other parameters. Experimentally, the model is compared to optical observations of particle motion in the presence of TMF.

Inducing Lift on Spherical Particles by Traveling Magnetic Fields

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Grugel, Richard N.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Gravity induced sedimentation of suspensions is a serious drawback to many materials and biotechnology processes, a factor that can, in principle, be overcome by utilizing an opposing Lorentz body force. In this work we demonstrate the utility of employing a traveling magnetic field (TMF) to induce a lifting force on particles dispersed in the fluid. Theoretically, a model has been developed to ascertain the net force, induced by TMF, acting on a spherical body as a function of the fluid medium's electrical conductivity and other parameters. Experimentally, the model is compared to optical observations of particle motion in the presence of TMF.

Prediction of destabilizing blade tip forces for shrouded and unshrouded turbines

NASA Technical Reports Server (NTRS)

Qiu, Y. J.; Martinezsanchez, M.

1985-01-01

The effect of a nonuniform flow field on the Alford force calculation is investigated. The ideas used here are based on those developed by Horlock and Greitzer. It is shown that the nonuniformity of the flow field does contribute to the Alford force calculation. An attempt is also made to include the effect of whirl speed. The values predicted by the model are compared with those obtained experimentally by Urlicks and Wohlrab. The possibility of using existing turbine tip loss correlations to predict beta is also exploited. The nonuniform flow field induced by the tip clearnance variation tends to increase the resultant destabilizing force over and above what would be predicted on the basis of the local variation of efficiency. On the one hand, the pressure force due to the nonuniform inlet and exit pressure also plays a part even for unshrouded blades, and this counteracts the flow field effects, so that the simple Alford prediction remains a reasonable approximation. Once the efficiency variation with clearance is known, the presented model gives a slightly overpredicted, but reasonably accurate destabilizing force. In the absence of efficiency vs. clearance data, an empirical tip loss coefficient can be used to give a reasonable prediction of destabilizing force. To a first approximation, the whirl does have a damping effect, but only of small magnitude, and thus it can be ignored for some purposes.

Gradiometry and gravitomagnetic field detection

NASA Technical Reports Server (NTRS)

Mashhoon, Bahram

1989-01-01

Gravitomagnetism was apparently first introduced into physics about 120 years ago when major developments in electrodynamics and the strong similarity between Coulomb's law of electricity and Newton's law of gravity led to the hypothesis that mass current generates a fundamental force of gravitational origin analogous to the magnetic force caused by charge current. According to general relativity, the rotation of a body leads to the dragging of the local inertial frames. In the weak-field approximation, the dragging frequency can be interpreted, up to a constant proportionality factor, as a gravitational magnetic field. There is, as yet, no direct evidence regarding the existence of such a field. The possibility is examined of detecting the gravitomagnetic field of the Earth by gravity gradiometry.

Computation of the Hydrodynamic Forces and Moments on a Body of Revolution with and without Appendages

DTIC Science & Technology

1991-08-01

SUPPLEMENTARY NOTATION 1 COSA. CODES 18 SUBJECT TERMS (,ontnuo 0 ner of necessary Atdi, block n" mbr ) FIELD GROUP SUB.GROUP Submarine ’hyoroaynamic ’~ aDS...hydrodynamic forces and moments developed on the hull and appendages of a submerged vehicle is required for determining its stability, control, and...an approximate method has been developed to compute the hydrodynamic forces and moments for a submerged vehicle. As discussed in Reference 1, the

Development and Comparison of Mechanical Structures for FNAL 15 T Nb$$_3$$Sn Dipole Demonstrator

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

Novitski, I.; Zlobin, A. V.

2016-11-08

Main design challenges for 15 T accelerator magnets are large Lorentz forces at this field level. The large Lorentz forces generate high stresses in the coil and mechanical structure and, thus, need stress control to maintain them at the acceptable level for brittle Nb3Sn coils and other elements of magnet mechanical structure. To provide these conditions and achieve the design field in the FNAL 15 T dipole demonstrator, several mechanical structures have been developed and analysed. The possibilities and limitations of these designs are discussed in this paper

Magnetic Nanotweezers for Interrogating Biological Processes in Space and Time.

PubMed

Kim, Ji-Wook; Jeong, Hee-Kyung; Southard, Kaden M; Jun, Young-Wook; Cheon, Jinwoo

2018-04-17

The ability to sense and manipulate the state of biological systems has been extensively advanced during the past decade with the help of recent developments in physical tools. Unlike standard genetic and pharmacological perturbation techniques-knockdown, overexpression, small molecule inhibition-that provide a basic on/off switching capability, these physical tools provide the capacity to control the spatial, temporal, and mechanical properties of the biological targets. Among the various physical cues, magnetism offers distinct advantages over light or electricity. Magnetic fields freely penetrate biological tissues and are already used for clinical applications. As one of the unique features, magnetic fields can be transformed into mechanical stimuli which can serve as a cue in regulating biological processes. However, their biological applications have been limited due to a lack of high-performance magnetism-to-mechanical force transducers with advanced spatiotemporal capabilities. In this Account, we present recent developments in magnetic nanotweezers (MNTs) as a useful tool for interrogating the spatiotemporal control of cells in living tissue. MNTs are composed of force-generating magnetic nanoparticles and field generators. Through proper design and the integration of individual components, MNTs deliver controlled mechanical stimulation to targeted biomolecules at any desired space and time. We first discuss about MNT configuration with different force-stimulation modes. By modulating geometry of the magnetic field generator, MNTs exert pulling, dipole-dipole attraction, and rotational forces to the target specifically and quantitatively. We discuss the key physical parameters determining force magnitude, which include magnetic field strength, magnetic field gradient, magnetic moment of the magnetic particle, as well as distance between the field generator and the particle. MNTs also can be used over a wide range of biological time scales. By simply adjusting the amplitude and phase of the applied current, MNTs based on electromagnets allow for dynamic control of the magnetic field from microseconds to hours. Chemical design and the nanoscale effects of magnetic particles are also essential for optimizing MNT performance. We discuss key strategies to develop magnetic nanoparticles with improved force-generation capabilities with a particular focus on the effects of size, shape, and composition of the nanoparticles. We then introduce various strategies and design considerations for target-specific biomechanical stimulations with MNTs. One-to-one particle-receptor engagement for delivering a defined force to the targeted receptor and the small size of the nanoparticles are important. Finally, we demonstrate the utility of MNTs for manipulating biological functions and activities with various spatial (single molecule/cell to organisms) and temporal resolution (microseconds to days). MNTs have the potential to be utilized in many exciting applications across diverse biological systems spanning from fundamental biology investigations of spatial and mechanical signaling dynamics at the single-cell and systems levels to in vivo therapeutic applications.

The evolution and future of minimalism in neurological surgery.

PubMed

Liu, Charles Y; Wang, Michael Y; Apuzzo, Michael L J

2004-11-01

The evolution of the field of neurological surgery has been marked by a progressive minimalism. This has been evident in the development of an entire arsenal of modern neurosurgical enterprises, including microneurosurgery, neuroendoscopy, stereotactic neurosurgery, endovascular techniques, radiosurgical systems, intraoperative and navigational devices, and in the last decade, cellular and molecular adjuvants. In addition to reviewing the major developments and paradigm shifts in the cyclic reinvention of the field as it currently stands, this paper attempts to identify forces and developments that are likely to fuel the irresistible escalation of minimalism into the future. These forces include discoveries in computational science, imaging, molecular science, biomedical engineering, and information processing as they relate to the theme of minimalism. These areas are explained in the light of future possibilities offered by the emerging field of nanotechnology with molecular engineering.

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.

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

PubMed

Trnka, Tomáš; Tvaroška, Igor; Koča, Jaroslav

2018-01-09

Computational studies of the reaction mechanisms of various enzymes are nowadays based almost exclusively on hybrid QM/MM models. Unfortunately, the success of this approach strongly depends on the selection of the QM region, and computational cost is a crucial limiting factor. An interesting alternative is offered by empirical reactive molecular force fields, especially the ReaxFF potential developed by van Duin and co-workers. However, even though an initial parametrization of ReaxFF for biomolecules already exists, it does not provide the desired level of accuracy. We have conducted a thorough refitting of the ReaxFF force field to improve the description of reaction energetics. To minimize the human effort required, we propose a fully automated approach to generate an extensive training set comprised of thousands of different geometries and molecular fragments starting from a few model molecules. Electrostatic parameters were optimized with QM electrostatic potentials as the main target quantity, avoiding excessive dependence on the choice of reference atomic charges and improving robustness and transferability. The remaining force field parameters were optimized using the VD-CMA-ES variant of the CMA-ES optimization algorithm. This method is able to optimize hundreds of parameters simultaneously with unprecedented speed and reliability. The resulting force field was validated on a real enzymatic system, ppGalNAcT2 glycosyltransferase. The new force field offers excellent qualitative agreement with the reference QM/MM reaction energy profile, matches the relative energies of intermediate and product minima almost exactly, and reduces the overestimation of transition state energies by 27-48% compared with the previous parametrization.

The thermal near-field: Coherence, spectroscopy, heat-transfer, and optical forces

NASA Astrophysics Data System (ADS)

Jones, Andrew C.; O'Callahan, Brian T.; Yang, Honghua U.; Raschke, Markus B.

2013-12-01

One of the most universal physical processes shared by all matter at finite temperature is the emission of thermal radiation. The experimental characterization and theoretical description of far-field black-body radiation was a cornerstone in the development of modern physics with the groundbreaking contributions from Gustav Kirchhoff and Max Planck. With its origin in thermally driven fluctuations of the charge carriers, thermal radiation reflects the resonant and non-resonant dielectric properties of media, which is the basis for far-field thermal emission spectroscopy. However, associated with the underlying fluctuating optical source polarization are fundamentally distinct spectral, spatial, resonant, and coherence properties of the evanescent thermal near-field. These properties have been recently predicted theoretically and characterized experimentally for systems with thermally excited molecular, surface plasmon polariton (SPP), and surface phonon polariton (SPhP) resonances. We review, starting with the early historical developments, the emergence of theoretical models, and the description of the thermal near-field based on the fluctuation-dissipation theory and in terms of the electromagnetic local density of states (EM-LDOS). We discuss the optical and spectroscopic characterization of distance dependence, magnitude, spectral distribution, and coherence of evanescent thermal fields. Scattering scanning near-field microscopy proved instrumental as an enabling technique for the investigations of several of these fundamental thermal near-field properties. We then discuss the role of thermal fields in nano-scale heat transfer and optical forces, and the correlation to the van der Waals, Casimir, and Casimir-Polder forces. We conclude with an outlook on the possibility of intrinsic and extrinsic resonant manipulation of optical forces, control of nano-scale radiative heat transfer with optical antennas and metamaterials, and the use of thermal infrared near-field spectroscopy (TINS) for broadband chemical nano-spectroscopic imaging, where the thermally driven vibrational optical dipoles provide their own intrinsic light source.

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

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

Comparison of force fields on the basis of various model approaches--how to design the best model for the [CnMIM][NTf2] family of ionic liquids.

PubMed

Köddermann, Thorsten; Reith, Dirk; Ludwig, Ralf

2013-10-07

In this contribution, we present two new united-atom force fields (UA-FFs) for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [C(n)MIM][NTf(2)] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient-based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all-atom force field (AA-FF) for [C(n)MIM][NTf(2)] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem- 2007, 8, 2464), the new force fields were derived to fit experimental densities, self-diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C(2)MIM][NTf(2)]. In the manual force field, the alkyl chains of the cation and the CF3 groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA-FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA-FFs are slightly superior for speed-up reasons. The UA-FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction

DTIC Science & Technology

2008-07-29

studied are set to zero and a constrained MM minimization is performed. It is critical that all other force field parameters (for bonds, angles, charges...identifying the symmetry of the problem and tailoring the parameterization accordingly may be critical . For Phase I, the above described procedure was...tasks and the evaluation of their properties. The tremendous number of possible ionic liquids that are within reach makes it critical that a reliable

A Lifting-Surface Program for Contrarotating Propellers

DTIC Science & Technology

1989-04-01

computer program for a set the force and induced flow field could be determined . of CR propellers has been developed based on a modi- The variations of...and their methods. To determine the forces and induced Nelson’s lifting life programs use the same approach, flow field, they applied lifting-line...Velocimetry (LDV). The propeller set, designed wake should be exactly the same as the hub geometry, to operate in uniform flow , was tested in the DTRC The

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

PubMed

Müller, Erich A; Jackson, George

2014-01-01

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

Air Force Pilot Retention: An Economic Analysis

DTIC Science & Technology

1993-01-01

Force impacts retention. Within the field of labor economics , an alternative labor market theory has developed which contrasts with typical competitive...this section. 60 NOTES ON CHAPTER III 1 Sherwin Rosen. "The Theory of Equalizing Differences," _Handboof•f Labor Economics , Volume 1, (New York

Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data

PubMed Central

Wickstrom, Lauren; Okur, Asim; Simmerling, Carlos

2009-01-01

Abstract Force-field validation is essential for the identification of weaknesses in current models and the development of more accurate models of biomolecules. NMR coupling and relaxation methods have been used to effectively diagnose the strengths and weaknesses of many existing force fields. Studies using the ff99SB force field have shown excellent agreement between experimental and calculated order parameters and residual dipolar calculations. However, recent studies have suggested that ff99SB demonstrates poor agreement with J-coupling constants for short polyalanines. We performed extensive replica-exchange molecular-dynamics simulations on Ala3 and Ala5 in TIP3P and TIP4P-Ew solvent models. Our results suggest that the performance of ff99SB is among the best of currently available models. In addition, scalar coupling constants derived from simulations in the TIP4P-Ew model show a slight improvement over those obtained using the TIP3P model. Despite the overall excellent agreement, the data suggest areas for possible improvement. PMID:19651043

Radiation force of an arbitrary acoustic beam on an elastic sphere in a fluid

PubMed Central

Sapozhnikov, Oleg A.; Bailey, Michael R.

2013-01-01

A theoretical approach is developed to calculate the radiation force of an arbitrary acoustic beam on an elastic sphere in a liquid or gas medium. First, the incident beam is described as a sum of plane waves by employing conventional angular spectrum decomposition. Then, the classical solution for the scattering of a plane wave from an elastic sphere is applied for each plane-wave component of the incident field. The net scattered field is expressed as a superposition of the scattered fields from all angular spectrum components of the incident beam. With this formulation, the incident and scattered waves are superposed in the far field to derive expressions for components of the radiation stress tensor. These expressions are then integrated over a spherical surface to analytically describe the radiation force on an elastic sphere. Limiting cases for particular types of incident beams are presented and are shown to agree with known results. Finally, the analytical expressions are used to calculate radiation forces associated with two specific focusing transducers. PMID:23363086

On the Evolution of Pulsatile Flow Subject to a Transverse Impulse Body Force

NASA Astrophysics Data System (ADS)

di Labbio, Giuseppe; Keshavarz-Motamed, Zahra; Kadem, Lyes

2014-11-01

In the event of an unexpected abrupt traffic stop or car accident, automotive passengers will experience an abrupt body deceleration. This may lead to tearing or dissection of the aortic wall known as Blunt Traumatic Aortic Rupture (BTAR). BTAR is the second leading cause of death in automotive accidents and, although quite frequent, the mechanisms leading to BTAR are still not clearly identified, particularly the contribution of the flow field. As such, this work is intended to provide a fundamental framework for the investigation of the flow contribution to BTAR. In this fundamental study, pulsatile flow in a three-dimensional, straight pipe of circular cross-section is subjected to a unidirectional, transverse, impulse body force applied on a strictly bounded volume of fluid. These models were simulated using the Computational Fluid Dynamics (CFD) software FLUENT. The evolution of fluid field characteristics was investigated during and after the application of the force. The application of the force significantly modified the flow field. The force induces a transverse pressure gradient causing the development of secondary flow structures that dissipate the energy added by the acceleration. Once the force ceases to act, these structures are carried downstream and gradually dissipate their excess energy.

A Bidirectional Brain-Machine Interface Algorithm That Approximates Arbitrary Force-Fields

PubMed Central

Semprini, Marianna; Mussa-Ivaldi, Ferdinando A.; Panzeri, Stefano

2014-01-01

We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field) applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop. PMID:24626393

Functional tooth restoration utilising split germs through re-regionalisation of the tooth-forming field

PubMed Central

Yamamoto, Naomi; Oshima, Masamitsu; Tanaka, Chie; Ogawa, Miho; Nakajima, Kei; Ishida, Kentaro; Moriyama, Keiji; Tsuji, Takashi

2015-01-01

The tooth is an ectodermal organ that arises from a tooth germ under the regulation of reciprocal epithelial-mesenchymal interactions. Tooth morphogenesis occurs in the tooth-forming field as a result of reaction-diffusion waves of specific gene expression patterns. Here, we developed a novel mechanical ligation method for splitting tooth germs to artificially regulate the molecules that control tooth morphology. The split tooth germs successfully developed into multiple correct teeth through the re-regionalisation of the tooth-forming field, which is regulated by reaction-diffusion waves in response to mechanical force. Furthermore, split teeth erupted into the oral cavity and restored physiological tooth function, including mastication, periodontal ligament function and responsiveness to noxious stimuli. Thus, this study presents a novel tooth regenerative technology based on split tooth germs and the re-regionalisation of the tooth-forming field by artificial mechanical force. PMID:26673152

Mean-field dynamos: The old concept and some recent developments. Karl Schwarzschild Award Lecture 2013

NASA Astrophysics Data System (ADS)

Rädler, K.-H.

This article elucidates the basic ideas of electrodynamics and magnetohydrodynamics of mean fields in turbulently moving conducting fluids. It is stressed that the connection of the mean electromotive force with the mean magnetic field and its first spatial derivatives is in general neither local nor instantaneous and that quite a few claims concerning pretended failures of the mean-field concept result from ignoring this aspect. In addition to the mean-field dynamo mechanisms of α2 and α Ω type several others are considered. Much progress in mean-field electrodynamics and magnetohydrodynamics results from the test-field method for calculating the coefficients that determine the connection of the mean electromotive force with the mean magnetic field. As an important example the memory effect in homogeneous isotropic turbulence is explained. In magnetohydrodynamic turbulence there is the possibility of a mean electromotive force that is primarily independent of the mean magnetic field and labeled as Yoshizawa effect. Despite of many efforts there is so far no convincing comprehensive theory of α quenching, that is, the reduction of the α effect with growing mean magnetic field, and of the saturation of mean-field dynamos. Steps toward such a theory are explained. Finally, some remarks on laboratory experiments with dynamos are made.

Analytic Solution of the Problem of Additive Formation of an Inhomogeneous Elastic Spherical Body in an Arbitrary Nonstationary Central Force Field

NASA Astrophysics Data System (ADS)

Parshin, D. A.

2017-09-01

We study the processes of additive formation of spherically shaped rigid bodies due to the uniform accretion of additional matter to their surface in an arbitrary centrally symmetric force field. A special case of such a field can be the gravitational or electrostatic force field. We consider the elastic deformation of the formed body. The body is assumed to be isotropic with elasticmoduli arbitrarily varying along the radial coordinate.We assume that arbitrary initial circular stresses can arise in the additional material added to the body in the process of its formation. In the framework of linear mechanics of growing bodies, the mathematical model of the processes under study is constructed in the quasistatic approximation. The boundary value problems describing the development of stress-strain state of the object under study before the beginning of the process and during the entire process of its formation are posed. The closed analytic solutions of the posed problems are constructed by quadratures for some general types of material inhomogeneity. Important typical characteristics of the mechanical behavior of spherical bodies additively formed in the central force field are revealed. These characteristics substantially distinguish such bodies from the already completely composed bodies similar in dimensions and properties which are placed in the force field and are described by problems of mechanics of deformable solids in the classical statement disregarding the mechanical aspects of additive processes.

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

Perspectives on the simulation of protein–surface interactions using empirical force field methods

PubMed Central

Latour, Robert A.

2014-01-01

Protein–surface interactions are of fundamental importance for a broad range of applications in the fields of biomaterials and biotechnology. Present experimental methods are limited in their ability to provide a comprehensive depiction of these interactions at the atomistic level. In contrast, empirical force field based simulation methods inherently provide the ability to predict and visualize protein–surface interactions with full atomistic detail. These methods, however, must be carefully developed, validated, and properly applied before confidence can be placed in results from the simulations. In this perspectives paper, I provide an overview of the critical aspects that I consider being of greatest importance for the development of these methods, with a focus on the research that my combined experimental and molecular simulation groups have conducted over the past decade to address these issues. These critical issues include the tuning of interfacial force field parameters to accurately represent the thermodynamics of interfacial behavior, adequate sampling of these types of complex molecular systems to generate results that can be comparable with experimental data, and the generation of experimental data that can be used for simulation results evaluation and validation. PMID:25028242

Bridging the Technology Valley of Death in Joint Medical Development

DTIC Science & Technology

2015-11-01

Force lieutenant colonel, is the Air Force Medical Support Agency Advanced Development Liaison Field Engineer in Falls Church, Virginia. Prusaczyk is...Awareness, communication and coordination may be mini - mal among Service S&T and AD programs. Joint Transition Planning Process A Joint Transition...Human Proof of Phase III NDA/BLA ling Approval, Launch Concept*** Launch Review Program Initiation Materiel Technology Engineering & Production

Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions.

PubMed

Callahan, Karen M; Casillas-Ituarte, Nadia N; Roeselová, Martina; Allen, Heather C; Tobias, Douglas J

2010-04-22

Magnesium dication plays many significant roles in biochemistry. While it is available to the environment from both ocean waters and mineral salts on land, its roles in environmental and atmospheric chemistry are still relatively unknown. Several pieces of experimental evidence suggest that contact ion pairing may not exist at ambient conditions in solutions of magnesium chloride up to saturation concentrations. This is not typical of most ions. There has been disagreement in the molecular dynamics literature concerning the existence of ion pairing in magnesium chloride solutions. Using a force field developed during this study, we show that contact ion pairing is not energetically favorable. Additionally, we present a concentration-dependent Raman spectroscopic study of the Mg-O(water) hexaaquo stretch that clearly supports the absence of ion pairing in MgCl(2) solutions, although a transition occurring in the spectrum between 0.06x and 0.09x suggests a change in solution structure. Finally, we compare experimental and calculated observables to validate our force field as well as two other commonly used magnesium force fields, and in the process show that ion pairing of magnesium clearly is not observed at higher concentrations in aqueous solutions of magnesium chloride, independent of the choice of magnesium force field, although some force fields give better agreement to experimental results than others.

Solubility of NaCl in water by molecular simulation revisited.

PubMed

Aragones, J L; Sanz, E; Vega, C

2012-06-28

In this paper, the solubility of NaCl in water is evaluated by using computer simulations for three different force fields. The condition of chemical equilibrium (i.e., equal chemical potential of the salt in the solid and in the solution) is obtained at room temperature and pressure to determine the solubility of the salt. We used the same methodology that was described in our previous work [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] although several modifications were introduced to improve the accuracy of the calculations. It is found that the predictions of the solubility are quite sensitive to the details of the force field used. Certain force fields underestimate the experimental solubility of NaCl in water by a factor of four, whereas the predictions of other force fields are within 20% of the experimental value. Direct coexistence molecular dynamic simulations were also performed to determine the solubility of the salt. Reasonable agreement was found between the solubility obtained from free energy calculations and that obtained from direct coexistence simulations. This work shows that the evaluation of the solubility of salts in water can now be performed in computer simulations. The solubility depends on the ion-ion, ion-water, and water-water interactions. For this reason, the prediction of the solubility can be quite useful in future work to develop force fields for ions in water.

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

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

PubMed Central

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

2016-01-01

The recently developed smart strand can be used to measure the prestress force in the prestressed concrete (PSC) structure from the construction stage to the in-service stage. The higher cost of the smart strand compared to the conventional strand renders it unaffordable to replace all the strands by smart strands, and results in the application of only a limited number of smart strands in the PSC structure. However, the prestress forces developed in the strands of the multi-strand system frequently adopted in PSC structures differ from each other, which means that the prestress force in the multi-strand system cannot be obtained by simple proportional scaling using the measurement of the smart strand. Therefore, this study examines the prestress force distribution in the multi-strand system to find the correlation between the prestress force measured by the smart strand and the prestress force distribution in the multi-strand system. To that goal, the prestress force distribution was measured using electromagnetic sensors for various factors of the multi-strand system adopted on site in the fabrication of actual PSC girders. The results verified the possibility to assume normal distribution for the prestress force distribution per anchor head, and a method computing the mean and standard deviation defining the normal distribution is proposed. This paper presents a meaningful finding by proposing an estimation method of the prestress force based upon field-measured data of the prestress force distribution in the multi-strand system of actual PSC structures. PMID:27548172

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

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

PubMed

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-08-24

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

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

PubMed Central

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-01-01

Microelectromechanical systems (MEMS) resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases). PMID:27563912

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.

Near-field Development of a Turbulent Mixing Layer Periodically Forced by a Bimorph PVDF Film Actuator

NASA Astrophysics Data System (ADS)

Naka, Yoshitsugu; Tsuboi, Ken-Ichiro; Kametani, Yukinori; Fukagata, Koji; Obi, Shinnosuke

We have performed experiments in a turbulent mixing layer with periodic forcing introduced by a Piezo Film Actuator (PFA). Three different lengths of PFAs have been used, and the effects of various combinations of forcing amplitudes and frequencies are investigated. The forcing at the first and second sub-harmonic frequencies against the natural frequency enhances the development of the thickness of the mixing layer: the mixing layer spreads due to the forcing. On the other hand, the forcing near the natural frequency suppresses the development: the mean velocity gradient becomes steeper than the no control case. The vector pattern of the periodic velocity components indicated the formation of the vortical structure. By forcing at the natural and its first sub-harmonic frequencies, two counter-rotating vortices are clearly observed in one period of forcing. By forcing at second sub-harmonic frequency, the vortical structure is found only in the downstream region. The distribution of the periodic Reynolds shear stress significantly varies with the forcing frequency and it takes a positive value when forcing occurs near the natural frequency. However, the total value of the Reynolds shear stress remains negative due to the contribution of the turbulent components.

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

Acoustic radiation force acting on elastic and viscoelastic spherical shells placed in a plane standing wave field.

PubMed

Mitri, F G

2005-08-01

The theory of the acoustic radiation force acting on elastic spherical shells suspended in a plane standing wave field is developed in relation to their thickness and the content of their hollow regions. The theory is modified to include the effect of a hysteresis type of absorption of compressional and shear waves in the material. The fluid-loading effect on the acoustic radiation force function Y(st) is analyzed as well. Results of numerical calculations are presented for a number of elastic and viscoelastic materials, with the hollow region filled with water or air. These results show how the damping due to absorption, the change of the interior fluid inside the shells' hollow regions, and the exterior fluid surrounding their structures, affect the acoustic radiation force.

A Job-Oriented Reading Program for the Air Force: Development and Field Evaluation.

DTIC Science & Technology

1977-05-01

spent in a conventional classroom setting, working on word power and phonics. At the end of the week, a diagnostic test is administered and the...and " soft " systems procedures in the Air Force. 3. The candidate career fields should have a large number of job incumbents, and be well represented...written information on page 47, where does the integral brake system obtain braking power ?". For an example of a complete Narrative worksheet, see Figure

In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field.

PubMed

Herges, T; Wenzel, W

2005-01-14

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3 A backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

NASA Astrophysics Data System (ADS)

Herges, T.; Wenzel, W.

2005-01-01

We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

Transition from a beads-on-string to a spike structure in an electrified viscoelastic jet

NASA Astrophysics Data System (ADS)

Li, Fang; Yin, Xie-Yuan; Yin, Xie-Zhen

2017-02-01

A one-dimensional numerical simulation is performed to study the nonlinear behaviors of a perfectly conducting, slightly viscoelastic liquid jet under a large radial electric field. A singular spike structure different from a beads-on-string structure is detected. The electric field is found to be the key factor for the formation of spikes. The transition from a beads-on-string to a spike structure occurs at sufficiently large electric fields. Moreover, the transition occurs more easily for smaller wave numbers. Viscosity is found to suppress spikes while elasticity promotes them. The mechanism responsible for spike formation is further explored by examining the maximum radius of the jet in the beads-on-string case. The capillary and electrostatic forces prove to be dominant in droplets, and the transition takes place when the electrostatic force exceeds the capillary force. The self-similarity in spikes is discussed. Different from the transition moment, the inertial, electrostatic, and solvent viscous forces are important in a developed spike.

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

PubMed

Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

2003-12-01

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

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.

Fraternization in the United States Air Force: Development of a Policy Booklet

DTIC Science & Technology

1988-09-01

perspective. Military custom, the UCMJ, military court decisions, and administrative actions have all played impor- tant roles in defining and enforcing a...your contribution. Good luck on publishing your work. Good job! We need it in the field !" Maj David Barton Chief. Military Affairs. Hq ATC JAG Office...GSM/LSR/88S-5 DEPARTMENT OF THE AIR FORCE AIR UNIVERSITY AIR FORCE INSTITUTE OF TECHNOLOGY Wright-Patterson Air Force Base, Ohio DISTPJBU1• )N

Factors Affecting the Military Environment of North Norway: Its History, International Relations, Physical Characteristics, and Balance of Military Forces.

DTIC Science & Technology

1988-01-01

by the United States Air Force under Contract F49620-86-C-0008. Further information may be obtained from the Long Range Planning and Doctrine Division...published simultaneously with this Note. The work was performed under the Project AIR FORCE project entitled "Concept Development and Project Formulation...warfare aircraft, and 130 ground attack fighters. Norway can field a total armed force of about 366,500 men under a system of universal conscription and

Transpersonal Psychology: Exploring the Frontiers in Human Resource Development.

ERIC Educational Resources Information Center

Brown, Michael H.

Important insights about how to develop human potential are being discovered these days in a field called transpersonal psychology. This new field is called the fourth force in psychology because like psychoanalysis, behaviorism, and humanistic psychology before it, it is on the cutting edge of what it means to be fully human. It seeks to develop…

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.

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

Examination of the U.S. Air Force's Science, Technology, Engineering, and Mathematics (STEM) Workforce Needs in the Future and Its Strategy to Meet Those Needs

ERIC Educational Resources Information Center

National Academies Press, 2010

2010-01-01

The Air Force requires technical skills and expertise across the entire range of activities and processes associated with the development, fielding, and employment of air, space, and cyber operational capabilities. The growing complexity of both traditional and emerging missions is placing new demands on education, training, career development,…

Professional Military Education for Life (PME4L)

DTIC Science & Technology

2014-12-08

The Air Force embracing a continuous educational model which integrates CPE concepts in order to persistently develop professional Airmen, engages...exposure to new ideas and career fields. Due to PME’s importance in an Airman’s career development, PME should be a continuous process with the...current PME courses as anchors. PME4L complements traditional Air Force PME and invests in Airmen at all levels. This paper presents a Continuous

Flow field of flexible flapping wings

NASA Astrophysics Data System (ADS)

Sallstrom, Erik

The agility and maneuverability of natural fliers would be desirable to incorporate into engineered micro air vehicles (MAVs). However, there is still much for engineers to learn about flapping flight in order to understand how such vehicles can be built for efficient flying. The goal of this study is to develop a methodology for capturing high quality flow field data around flexible flapping wings in a hover environment and to interpret it to gain a better understanding of how aerodynamic forces are generated. The flow field data was captured using particle image velocimetry (PIV) and required that measurements be taken around a repeatable flapping motion to obtain phase-averaged data that could be studied throughout the flapping cycle. Therefore, the study includes the development of flapping devices with a simple repeatable single degree of freedom flapping motion. The acquired flow field data has been examined qualitatively and quantitatively to investigate the mechanisms behind force production in hovering flight and to relate it to observations in previous research. Specifically, the flow fields have been investigated around a rigid wing and several carbon fiber reinforced flexible membrane wings. Throughout the whole study the wings were actuated with either a sinusoidal or a semi-linear flapping motion. The semi-linear flapping motion holds the commanded angular velocity nearly constant through half of each half-stroke while the sinusoidal motion is always either accelerating or decelerating. The flow fields were investigated by examining vorticity and vortex structures, using the Q criterion as the definition for the latter, in two and three dimensions. The measurements were combined with wing deflection measurements to demonstrate some of the key links in how the fluid-structure interactions generated aerodynamic forces. The flow fields were also used to calculate the forces generated by the flapping wings using momentum balance methods which yielded details of where along the wing the forces were generated. As expected, these results indicated that the spanwise location of where the forces were generated depended upon the wings membrane material and reinforcement pattern, but in general it was in the outer third of the wing. (Full text of this dissertation may be available via the University of Florida Libraries web site. Please check http://www.uflib.ufl.edu/etd.html)

Rigorous force field optimization principles based on statistical distance minimization

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2015-10-12

We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. Here we exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of themore » approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.« less

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development

PubMed Central

Lu, Zhenyu; Zhou, Nengjie; Wu, Qin; Zhang, Yingkai

2011-01-01

One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding. PMID:22267958

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...

Clinical Evidence for the Relationship between Nail Configuration and Mechanical Forces

PubMed Central

Ogawa, Rei

2014-01-01

Summary: Mechanobiology is an emerging field of science that focuses on the way physical forces and changes in cell or tissue mechanics contribute to development, physiology, and disease. As nails are always exposed to physical stimulation, mechanical forces may have a particularly pronounced effect on nail configuration and could be involved in the development of nail deformities. However, the role of mechanobiology in nail configuration and deformities has rarely been assessed. This review describes what is currently understood regarding the effect of mechanical force on nail configuration and deformities. On the basis of these observations, we hypothesize that nails have an automatic curvature function that allows them to adapt to the daily upward mechanical forces. Under normal conditions, the upward daily mechanical force and the automatic curvature force are well balanced. However, an imbalance between these 2 forces may cause nail deformation. For example, pincer nails may be caused by the absence of upward mechanical forces or a genetic propensity increase in the automatic curvature force, whereas koilonychias may occur when the upward mechanical force exceeds the automatic curvature force, thereby causing the nail to curve outward. This hypothesis is a new concept that could aid the development of innovative methods to prevent and treat nail deformities. PMID:25289309

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

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

PubMed

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

2016-11-01

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

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

PubMed Central

Cunnington, Ross; Mattingley, Jason B.; Riek, Stephan; Carroll, Timothy J.

2016-01-01

There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153–167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. PMID:27582293

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.

Equilibrium electrodeformation of a spheroidal vesicle in an ac electric field

NASA Astrophysics Data System (ADS)

Nganguia, H.; Young, Y.-N.

2013-11-01

In this work, we develop a theoretical model to explain the equilibrium spheroidal deformation of a giant unilamellar vesicle (GUV) under an alternating (ac) electric field. Suspended in a leaky dielectric fluid, the vesicle membrane is modeled as a thin capacitive spheroidal shell. The equilibrium vesicle shape results from the balance between mechanical forces from the viscous fluid, the restoring elastic membrane forces, and the externally imposed electric forces. Our spheroidal model predicts a deformation-dependent transmembrane potential, and is able to capture large deformation of a vesicle under an electric field. A detailed comparison against both experiments and small-deformation (quasispherical) theory showed that the spheroidal model gives better agreement with experiments in terms of the dependence on fluid conductivity ratio, permittivity ratio, vesicle size, electric field strength, and frequency. The spheroidal model also allows for an asymptotic analysis on the crossover frequency where the equilibrium vesicle shape crosses over between prolate and oblate shapes. Comparisons show that the spheroidal model gives better agreement with experimental observations.

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.

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

PubMed

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

2018-06-12

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

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

PubMed

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

2017-10-28

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

It's Rather like Learning a Language: Development of talk and conceptual understanding in mechanics lessons

NASA Astrophysics Data System (ADS)

Rincke, Karsten

2011-01-01

Although a broad literature exists concerning the development of conceptual understanding of force and other topics within mechanics, little is known about the role and development of students' talk about the subject. The paper presents an in-depth investigation of students' talk whilst being introduced to the concept of force. The main research goal was to investigate and understand how students develop an understanding of the concept of force and how they use and understand the term 'force'. Therefore, we make relation to the research field of students' preconceptions and the field of second language learning. Two classes of students (N = 47) were videotaped during a time period of nine lessons, each transcribed and analysed using a category system. Additional data were obtained via written tasks, logs kept by the students, and tests. The detailed analysis of the talk and the results of the tests indicate that students face difficulties in using the term 'force' scientifically similar to those in a foreign language instruction. Vygotsky already recognised a relationship between learning in science and learning a language. In this paper, important aspects of this relationship are discussed based upon empirical data. We conclude that in some respects it might be useful to make reference to the research related to language learning when thinking about improving science education. In particular, according to Selinker's concept of interlanguage describing language-learning processes within language instruction, the language used by the students during physics lessons can be viewed as a 'scientific interlanguage'.

Circular Conditional Autoregressive Modeling of Vector Fields.

PubMed

Modlin, Danny; Fuentes, Montse; Reich, Brian

2012-02-01

As hurricanes approach landfall, there are several hazards for which coastal populations must be prepared. Damaging winds, torrential rains, and tornadoes play havoc with both the coast and inland areas; but, the biggest seaside menace to life and property is the storm surge. Wind fields are used as the primary forcing for the numerical forecasts of the coastal ocean response to hurricane force winds, such as the height of the storm surge and the degree of coastal flooding. Unfortunately, developments in deterministic modeling of these forcings have been hindered by computational expenses. In this paper, we present a multivariate spatial model for vector fields, that we apply to hurricane winds. We parameterize the wind vector at each site in polar coordinates and specify a circular conditional autoregressive (CCAR) model for the vector direction, and a spatial CAR model for speed. We apply our framework for vector fields to hurricane surface wind fields for Hurricane Floyd of 1999 and compare our CCAR model to prior methods that decompose wind speed and direction into its N-S and W-E cardinal components.

Circular Conditional Autoregressive Modeling of Vector Fields*

PubMed Central

Modlin, Danny; Fuentes, Montse; Reich, Brian

2013-01-01

As hurricanes approach landfall, there are several hazards for which coastal populations must be prepared. Damaging winds, torrential rains, and tornadoes play havoc with both the coast and inland areas; but, the biggest seaside menace to life and property is the storm surge. Wind fields are used as the primary forcing for the numerical forecasts of the coastal ocean response to hurricane force winds, such as the height of the storm surge and the degree of coastal flooding. Unfortunately, developments in deterministic modeling of these forcings have been hindered by computational expenses. In this paper, we present a multivariate spatial model for vector fields, that we apply to hurricane winds. We parameterize the wind vector at each site in polar coordinates and specify a circular conditional autoregressive (CCAR) model for the vector direction, and a spatial CAR model for speed. We apply our framework for vector fields to hurricane surface wind fields for Hurricane Floyd of 1999 and compare our CCAR model to prior methods that decompose wind speed and direction into its N-S and W-E cardinal components. PMID:24353452

Correcting Biases in a lower resolution global circulation model with data assimilation

NASA Astrophysics Data System (ADS)

Canter, Martin; Barth, Alexander

2016-04-01

With this work, we aim at developping a new method of bias correction using data assimilation. This method is based on the stochastic forcing of a model to correct bias. First, through a preliminary run, we estimate the bias of the model and its possible sources. Then, we establish a forcing term which is directly added inside the model's equations. We create an ensemble of runs and consider the forcing term as a control variable during the assimilation of observations. We then use this analysed forcing term to correct the bias of the model. Since the forcing is added inside the model, it acts as a source term, unlike external forcings such as wind. This procedure has been developed and successfully tested with a twin experiment on a Lorenz 95 model. It is currently being applied and tested on the sea ice ocean NEMO LIM model, which is used in the PredAntar project. NEMO LIM is a global and low resolution (2 degrees) coupled model (hydrodynamic model and sea ice model) with long time steps allowing simulations over several decades. Due to its low resolution, the model is subject to bias in area where strong currents are present. We aim at correcting this bias by using perturbed current fields from higher resolution models and randomly generated perturbations. The random perturbations need to be constrained in order to respect the physical properties of the ocean, and not create unwanted phenomena. To construct those random perturbations, we first create a random field with the Diva tool (Data-Interpolating Variational Analysis). Using a cost function, this tool penalizes abrupt variations in the field, while using a custom correlation length. It also decouples disconnected areas based on topography. Then, we filter the field to smoothen it and remove small scale variations. We use this field as a random stream function, and take its derivatives to get zonal and meridional velocity fields. We also constrain the stream function along the coasts in order not to have currents perpendicular to the coast. The randomly generated stochastic forcing are then directly injected into the NEMO LIM model's equations in order to force the model at each timestep, and not only during the assimilation step. Results from a twin experiment will be presented. This method is being applied to a real case, with observations on the sea surface height available from the mean dynamic topography of CNES (Centre national d'études spatiales). The model, the bias correction, and more extensive forcings, in particular with a three dimensional structure and a time-varying component, will also be presented.

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.

Vibration analysis and experiment of giant magnetostrictive force sensor

NASA Astrophysics Data System (ADS)

Zhu, Zhiwen; Liu, Fang; Zhu, Xingqiao; Wang, Haibo; Xu, Jia

2017-12-01

In this paper, a kind of giant magnetostrictive force sensor is proposed, ans its magneto-mechanical coupled model is developed. The relationship between output voltage of giant magnetostrictive force sensor and input excitation force is obtained. The phenomena of accuracy aggravation in high frequency and delay of giant magnetostrictive sensor are explained. The experimental results show that the model can describe the actual response of giant magnetostrictive force sensor. The new model of giant magnetostrictive sensor has simple form and is easy to be analyzed in theory, which is helpful to be applied in measuring and control fields.

The Gulf War: U.A.E. Participation in that War

DTIC Science & Technology

1993-04-02

and preserved out of the hollow force that had been allowed to develop in the 1970s. The U.S. Congress was also important in providing the democratic ... leadership support of the force in the field. The Middle East will continue to command attention for the future. The coalition partners in the Gulf

Discrete-vortex model for the symmetric-vortex flow on cones

NASA Technical Reports Server (NTRS)

Gainer, Thomas G.

1990-01-01

A relatively simple but accurate potential flow model was developed for studying the symmetric vortex flow on cones. The model is a modified version of the model first developed by Bryson, in which discrete vortices and straight-line feeding sheets were used to represent the flow field. It differs, however, in the zero-force condition used to position the vortices and determine their circulation strengths. The Bryson model imposed the condition that the net force on the feeding sheets and discrete vortices must be zero. The proposed model satisfies this zero-force condition by having the vortices move as free vortices, at a velocity equal to at the local crossflow velocity at their centers. When the free-vortex assumption is made, a solution is obtained in the form of two nonlinear algebraic equations that relate the vortex center coordinates and vortex strengths to the cone angle and angle of attack. The vortex center locations calculated using the model are in good agreement with experimental values. The cone normal forces as well as center locations are in good agreement with the vortex cloud method of calculating symmetric flow fields.

Radial force on the vacuum chamber wall during thermal quench in tokamaks

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

Pustovitov, V. D., E-mail: pustovitov-vd@nrcki.ru

The radial force balance during a thermal quench in tokamaks is analyzed. As a rule, the duration τ{sub tp} of such events is much shorter than the resistive time τ{sub w} of the vacuum chamber wall. Therefore, the perturbations of the magnetic field B produced by the evolving plasma cannot penetrate the wall, which makes different the magnetic pressures on its inner and outer sides. The goal of this work is the analytical estimation of the resulting integral radial force on the wall. The plasma is considered axially symmetric; for the description of radial forces on the wall, the resultsmore » of V.D. Shafranov’s classical work [J. Nucl. Energy C 5, 251 (1963)] are used. Developed for tokamaks, the standard equilibrium theory considers three interacting systems: plasma, poloidal field coils, and toroidal field coils. Here, the wall is additionally incorporated with currents driven by ∂B/∂t≠0 accompanying the fast loss of the plasma thermal energy. It is shown that they essentially affect the force redistribution, thereby leading to large loads on the wall. The estimates prove that these loads have to be accounted for in the disruptive scenarios in large tokamaks.« less

Characteristic Boundary Conditions for ARO-1

DTIC Science & Technology

1983-05-01

I As shown in Fig. 3, the point designated II is the interior point that was used to define the barred coordinate system , evaluated at time t=. All...L. Jacocks Calspan Field Services, Inc. May 1983 Final Report for Period October 1981 - September 1982 r Approved for public release; destribut ...on unlimited I ARNOLD ENGINEERING DEVELOPMENT CENTER ARNOLD AIR FORCE STATION, TENNESSEE AIR FORCE SYSTEMS COMMAND UNITED STATES AIR FORCE N O T I

Microgravity and Hypogravity Compatible Methods for the Destruction of Solid Wastes by Magnetically Assisted Gasification

NASA Technical Reports Server (NTRS)

Atwater, James E.; Akse, James R.; Wheeler, Richard R., Jr.; Jovanovic, Goran N.; Pinto-Espinoza, Joaquin; Reed, Brian; Sornchamni, Thana

2003-01-01

This report summarizes a three-year collaborative effort between researchers at UMPQUA Research Company (URC) and the Chemical Engineering Department at Oregon State University (OSU). The Magnetically Assisted Gasification (MAG) concept was originally conceived as a microgravity and hypogravity compatible means for the decomposition of solid waste materials generated aboard spacecraft, lunar and planetary habitations, and for the recovery of potentially valuable resources. While a number of methods such as supercritical water oxidation (SCW0), fluidized bed incineration, pyrolysis , composting and related biological processes have been demonstrated for the decomposition of solid wastes, none of these methods are particularly well- suited for employment under microgravity or hypogravity conditions. For example, fluidized bed incineration relies upon a balance between drag forces which the flowing gas stream exerts upon the fluidization particles and the opposing force of gravity. In the absence of gravity, conventional fluidization cannot take place. Hypogravity operation can also be problematic for conventional fluidized bed reactors, because the various factors which govern fluidization phenomena do not all scale linearly with gravity. For this reason it may be difficult to design and test fluidized bed reactors in lg, which are intended to operate under different gravitational conditions. However, fluidization can be achieved in microgravity (and hypogravity) if a suitable replacement force to counteract the forces between fluid and particles can be found. Possible alternatives include: centripetal force, electric fields, or magnetic fields. Of these, magnetic forces created by the action of magnetic fields and magnetic field gradients upon ferromagnetic media offer the most practical approach. The goal of this URC-OSU collaborative effort was to develop magnetic hardware and methods to control the degree of fluidization (or conversely consolidation) of granular ferromagnetic media and to employ these innovations in sequential filtration and fluidized bed processes for the segregation and decomposition of solid waste materials, and for the concentration and collection of inorganic residue (ash). This required the development of numerous enabling technologies and tools.

The Joint Capabilities Integration and Development System: Its Impact on Air Force Acquisition Thirteen Years Later

DTIC Science & Technology

2016-08-01

area denial environments . Near peer adversaries continue to develop low observable aircraft , proliferate counter-precision guided munition systems ...when the Air Force had significantly more control over its requirements validation and acquisition processes. The only tactical aircraft currently in... systems such as the F-35A. Interestingly, upgrades to these previously fielded aircraft also take longer after JCIDS was implemented than it did to

Bubble Detachment in Variable Gravity Under the Influence of a Non-Uniform Electric Field

NASA Technical Reports Server (NTRS)

Chang, Shinan; Herman, Cila; Iacona, Estelle

2002-01-01

The objective of the study reported in this paper is to investigate the effects of variable, reduced gravity on the formation and detachment behavior of individual air bubbles under the influence of a non-uniform electric field. For this purpose, variable gravity experiments were carried out in parabolic nights. The non-uniform electric field was generated by a spherical electrode and a plate electrode. The effect of the magnitude of the non-uniform electric field and gravity level on bubble formation, development and detachment at an orifice was investigated. An image processing code was developed that allows the measurement of bubble volume, dimensions and contact angle at detachment. The results of this research can be used to explore the possibility of enhancing boiling heat transfer in the variable and low gravity environments by substituting the buoyancy force with a force induced by the electric field. The results of experiments and measurements indicate that the level of gravity significantly affects bubble shape, size and frequency. The electric field magnitude also influences bubble detachment, however, its impact is not as profound as that of variable gravity for the range of electric field magnitudes investigated in the present study.

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

PubMed Central

2014-01-01

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

Kestrel: force protection and Intelligence, Surveillance, and Reconnaissance (ISR) persistent surveillance on aerostats

NASA Astrophysics Data System (ADS)

Luber, David R.; Marion, John E.; Fields, David

2012-05-01

Logos Technologies has developed and fielded the Kestrel system, an aerostat-based, wide area persistent surveillance system dedicated to force protection and ISR mission execution operating over forward operating bases. Its development included novel imaging and stabilization capability for day/night operations on military aerostat systems. The Kestrel system's contribution is a substantial enhancement to aerostat-based, force protection systems which to date have relied on narrow field of view ball gimbal sensors to identify targets of interest. This inefficient mechanism to conduct wide area field of view surveillance is greatly enhanced by Kestrel's ability to maintain a constant motion imagery stare of the entire forward operating base (FOB) area. The Kestrel airborne sensor enables 360° coverage out to extended ranges which covers a city sized area at moderate resolution, while cueing a narrow field of view sensor to provide high resolution imagery of targets of interest. The ground station exploitation system enables operators to autonomously monitor multiple regions of interest in real time, and allows for backtracking through the recorded imagery, while continuing to monitor ongoing activity. Backtracking capability allows operators to detect threat networks, their CONOPS, and locations of interest. Kestrel's unique advancement has already been utilized successfully in OEF operations.

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

The Field Shower Wastewater Recycling System: Development of a Program of Instruction and Preliminary Analysis of Its Potential Health Implications.

DTIC Science & Technology

1987-02-01

The FSWRS will be used by forces deployed to Theaters of Operations located in water-short areas of the world, and will greatly reduce water supply... operators take ’ A appropriate precautions in handling sulfuric acid and un- . treat.d waters. Although no health hazards are anticipated to result from...field. The FSWRS will be used by forces deployed to Theaters of Operations located in water short areas of the world, and will greatly reduce water

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.

An Objective Measure of Noseband Tightness and Its Measurement Using a Novel Digital Tightness Gauge.

PubMed

Doherty, Orla; Conway, Thomas; Conway, Richard; Murray, Gerard; Casey, Vincent

2017-01-01

Noseband tightness is difficult to assess in horses participating in equestrian sports such as dressage, show jumping and three-day-eventing. There is growing concern that nosebands are commonly tightened to such an extent as to restrict normal equine behaviour and possibly cause injury. In the absence of a clear agreed definition of noseband tightness, a simple model of the equine nose-noseband interface environment was developed in order to guide further studies in this area. The normal force component of the noseband tensile force was identified as the key contributor to sub-noseband tissue compression. The model was used to inform the design of a digital tightness gauge which could reliably measure the normal force component of the noseband tensile force. A digital tightness gauge was developed to measure this parameter under nosebands fitted to bridled horses. Results are presented for field tests using two prototype designs. Prototype version three was used in field trial 1 (n = 15, frontal nasal plane sub-noseband site). Results of this trial were used to develop an ergonomically designed prototype, version 4, which was tested in a second field trial (n = 12, frontal nasal plane and lateral sub-noseband site). Nosebands were set to three tightness settings in each trial as judged by a single rater using an International Society for Equitation Science (ISES) taper gauge. Normal forces in the range 7-95 N were recorded at the frontal nasal plane while a lower range 1-28 N was found at the lateral site for the taper gauge range used in the trials. The digital tightness gauge was found to be simple to use, reliable, and safe and its use did not agitate the animals in any discernable way. A simple six point tightness scale is suggested to aid regulation implementation and the control of noseband tightness using normal force measurement as the objective tightness discriminant.

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.

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

de Hatten, Xavier; Cournia, Zoe; Huc, Ivan

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

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

De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

Customer loads of two-wheeled vehicles

NASA Astrophysics Data System (ADS)

Gorges, C.; Öztürk, K.; Liebich, R.

2017-12-01

Customer usage profiles are the most unknown influences in vehicle design targets and they play an important role in durability analysis. This publication presents a customer load acquisition system for two-wheeled vehicles that utilises the vehicle's onboard signals. A road slope estimator was developed to reveal the unknown slope resistance force with the help of a linear Kalman filter. Furthermore, an automated mass estimator was developed to consider the correct vehicle loading. The mass estimation is performed by an extended Kalman filter. Finally, a model-based wheel force calculation was derived, which is based on the superposition of forces calculated from measured onboard signals. The calculated wheel forces were validated by measurements with wheel-load transducers through the comparison of rainflow matrices. The calculated wheel forces correspond with the measured wheel forces in terms of both quality and quantity. The proposed methods can be used to gather field data for improved vehicle design loads.

Marine Tactical Command and Control System (MTACCS) Field Development System-1 (FDS-1) assessment: Final report

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

Avery, L.W.; Hunt, S.T.; Savage, S.F.

1992-04-01

The United State Marine Corps (USMC) is continuing the development and fielding of the Marine Corps Tactical Command and Control System (MTACCS), a system which exists in varying states of development, fielding, or modernization. MTACCS is currently composed of the following components: Tactical Combat Operations System (TCO) for ground command and control (C2), Intelligence Analysis System (IAS) with a Genser terminal connected to a TCO workstation for intelligence C2, Marine Integrated Personnel System (MIPS) and a TCO workstation using the Marine Combat Personnel System (MCPERS) software for personnel C2, Marine Integrated Logistics System (MILOGS) which is composed of the Landingmore » Force Asset Distribution System (LFADS), the Marine Air-Ground Task Force (MAGTF) II, and a TCO terminal using the Marine Combat Logistics System (MCLOG) for logistics C2, Marine Corps Fire Support System (MCFSS) for fire support C2, and Advanced Tactical Air Command Central (ATACC) and the Improved Direct Air Support Central for aviation C2.« 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.

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.

Air Force construction automation/robotics

NASA Technical Reports Server (NTRS)

Nease, AL; Dusseault, Christopher

1994-01-01

The Air Force has several unique requirements that are being met through the development of construction robotic technology. The missions associated with these requirements place construction/repair equipment operators in potentially harmful situations. Additionally, force reductions require that human resources be leveraged to the maximum extent possible and that more stringent construction repair requirements push for increased automation. To solve these problems, the U.S. Air Force is undertaking a research and development effort at Tyndall AFB, FL to develop robotic teleoperation, telerobotics, robotic vehicle communications, automated damage assessment, vehicle navigation, mission/vehicle task control architecture, and associated computing environment. The ultimate goal is the fielding of robotic repair capability operating at the level of supervised autonomy. The authors of this paper will discuss current and planned efforts in construction/repair, explosive ordnance disposal, hazardous waste cleanup, fire fighting, and space construction.

The 'Arm Force Field' method to predict manual arm strength based on only hand location and force direction.

PubMed

La Delfa, Nicholas J; Potvin, Jim R

2017-03-01

This paper describes the development of a novel method (termed the 'Arm Force Field' or 'AFF') to predict manual arm strength (MAS) for a wide range of body orientations, hand locations and any force direction. This method used an artificial neural network (ANN) to predict the effects of hand location and force direction on MAS, and included a method to estimate the contribution of the arm's weight to the predicted strength. The AFF method predicted the MAS values very well (r 2  = 0.97, RMSD = 5.2 N, n = 456) and maintained good generalizability with external test data (r 2  = 0.842, RMSD = 13.1 N, n = 80). The AFF can be readily integrated within any DHM ergonomics software, and appears to be a more robust, reliable and valid method of estimating the strength capabilities of the arm, when compared to current approaches. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

S. Chouhan, J. DeKamp, A. Zeller, P. Brindza, S. Lassiter, M. Fowler, E. Sun

A collaboration between NSCL and Jlab has developed the reference design and coil winding for Jlab's Super High Momentum Spectrometer (SHMS) horizontal bend magnet. A warm iron ??C?? type superferric dipole magnet will bend the 12 GeV/c particles horizontally by 3?? to allow the SHMS to reach angles as low as 5.5??. This requires an integral field strength of up to 2.1 T.m. The major challenges are the tight geometry, high and unbalanced forces and a required low fringe field in primary beam path. A coil design based on flattened SSC Rutherford cable that provides a large current margin andmore » commercially available fiberglass prepreg epoxy tape has been developed. A complete test coil has been wound and will be cold tested. This paper present the modified magnet design includes coil forces, coil restraint system and fringe field. In addition, coil properties, quench calculations and the full mechanical details are also presented.« less

A potential method for lift evaluation from velocity field data

NASA Astrophysics Data System (ADS)

de Guyon-Crozier, Guillaume; Mulleners, Karen

2017-11-01

Computing forces from velocity field measurements is one of the challenges in experimental aerodynamics. This work focuses on low Reynolds flows, where the dynamics of the leading and trailing edge vortices play a major role in lift production. Recent developments in 2D potential flow theory, using discrete vortex models, have shown good results for unsteady wing motions. A method is presented to calculate lift from experimental velocity field data using a discrete vortex potential flow model. The model continuously adds new point vortices at leading and trailing edges whose circulations are set directly from vorticity measurements. Forces are computed using the unsteady Blasius equation and compared with measured loads.

Developing model asphalt systems using molecular simulation : final model.

DOT National Transportation Integrated Search

2009-09-01

Computer based molecular simulations have been used towards developing simple mixture compositions whose : physical properties resemble those of real asphalts. First, Monte Carlo simulations with the OPLS all-atom force : field were used to predict t...

Expectations and Realities in Academic Biology.

ERIC Educational Resources Information Center

Nanney, David L.

1988-01-01

Provides a historical look at the development of academic biology. Attempts to project some presently recognized forces and organizational structures influencing the development of the field. Differentiates how the discipline is now as compared with the past. (TW)

Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon–dielectric interactions

PubMed Central

Huang, Qian; Lee, Joon; Arce, Fernando Teran; Yoon, Ilsun; Angsantikul, Pavimol; Liu, Justin; Shi, Yuesong; Villanueva, Josh; Thamphiwatana, Soracha; Ma, Xuanyi; Zhang, Liangfang; Chen, Shaochen; Lal, Ratnesh; Sirbuly, Donald J.

2018-01-01

Ultrasensitive nanomechanical instruments, including the atomic force microscope (AFM)1–4 and optical and magnetic tweezers5–8, have helped shed new light on the complex mechanical environments of biological processes. However, it is difficult to scale down the size of these instruments due to their feedback mechanisms9, which, if overcome, would enable high-density nanomechanical probing inside materials. A variety of molecular force probes including mechanophores10, quantum dots11, fluorescent pairs12,13 and molecular rotors14–16 have been designed to measure intracellular stresses; however, fluorescence-based techniques can have short operating times due to photo-instability and it is still challenging to quantify the forces with high spatial and mechanical resolution. Here, we develop a compact nanofibre optic force transducer (NOFT) that utilizes strong near-field plasmon–dielectric interactions to measure local forces with a sensitivity of <200 fN. The NOFT system is tested by monitoring bacterial motion and heart-cell beating as well as detecting infrasound power in solution. PMID:29576804

Contractile properties of early human embryonic stem cell-derived cardiomyocytes: beta-adrenergic stimulation induces positive chronotropy and lusitropy but not inotropy.

PubMed

Pillekamp, Frank; Haustein, Moritz; Khalil, Markus; Emmelheinz, Markus; Nazzal, Rewa; Adelmann, Roland; Nguemo, Filomain; Rubenchyk, Olga; Pfannkuche, Kurt; Matzkies, Matthias; Reppel, Michael; Bloch, Wilhelm; Brockmeier, Konrad; Hescheler, Juergen

2012-08-10

Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) provide the unique opportunity to study the very early development of the human heart. The aim of this study was to investigate the effect of calcium and beta-adrenergic stimulation on the contractile properties of early hESC-CMs. Beating clusters containing hESC-CMs were co-cultured in vitro with noncontractile slices of neonatal murine ventricles. After 5-7 days, when beating clusters had integrated morphologically into the damaged tissue, isometric force measurements were performed during spontaneous beating as well as during electrical field stimulation. Spontaneous beating stopped when extracellular calcium ([Ca²⁺](ec)) was removed or after administration of the Ca²⁺ channel blocker nifedipine. During field stimulation at a constant rate, the developed force increased with incremental concentrations of [Ca²⁺](ec). During spontaneous beating, rising [Ca²⁺](ec) increased beating rate and developed force up to a [Ca²⁺](ec) of 2.5 mM. When [Ca²⁺](ec) was increased further, spontaneous beating rate decreased, whereas the developed force continued to increase. The beta-adrenergic agonist isoproterenol induced a dose-dependent increase of the frequency of spontaneous beating; however, it did not significantly change the developed force during spontaneous contractions or during electrical stimulation at a constant rate. Force developed by early hESC-CMs depends on [Ca²⁺](ec) and on the L-type Ca²⁺ channel. The lack of an inotropic reaction despite a pronounced chronotropic response after beta-adrenergic stimulation most likely indicates immaturity of the sarcoplasmic reticulum. For cell-replacement strategies, further maturation of cardiac cells has to be achieved either in vitro before or in vivo after transplantation.

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

Advanced Magnetic Materials Methods and Numerical Models for Fluidization in Microgravity and Hypogravity

NASA Technical Reports Server (NTRS)

Atwater, James; Wheeler, Richard, Jr.; Akse, James; Jovanovic, Goran; Reed, Brian

2013-01-01

To support long-duration manned missions in space such as a permanent lunar base, Mars transit, or Mars Surface Mission, improved methods for the treatment of solid wastes, particularly methods that recover valuable resources, are needed. The ability to operate under microgravity and hypogravity conditions is essential to meet this objective. The utilization of magnetic forces to manipulate granular magnetic media has provided the means to treat solid wastes under variable gravity conditions by filtration using a consolidated magnetic media bed followed by thermal processing of the solid wastes in a fluidized bed reactor. Non-uniform magnetic fields will produce a magnetic field gradient in a bed of magnetically susceptible media toward the distributor plate of a fluidized bed reactor. A correctly oriented magnetic field gradient will generate a downward direct force on magnetic media that can substitute for gravitational force in microgravity, or which may augment low levels of gravity, such as on the Moon or Mars. This approach is termed Gradient Magnetically Assisted Fluidization (G-MAFB), in which the magnitude of the force on the fluidized media depends upon the intensity of the magnetic field (H), the intensity of the field gradient (dH/dz), and the magnetic susceptibility of the media. Fluidized beds based on the G-MAFB process can operate in any gravitational environment by tuning the magnetic field appropriately. Magnetic materials and methods have been developed that enable G-MAFB operation under variable gravity conditions.

Quantum friction in two-dimensional topological materials

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

Farias, M. Belén; Kort-Kamp, Wilton J. M.; Dalvit, Diego A. R.

In this paper, we develop the theory of quantum friction in two-dimensional topological materials. The quantum drag force on a metallic nanoparticle moving above such systems is sensitive to the nontrivial topology of their electronic phases, shows a novel distance scaling law, and can be manipulated through doping or via the application of external fields. We use the developed framework to investigate quantum friction due to the quantum Hall effect in magnetic field biased graphene, and to topological phase transitions in the graphene family materials. Finally, it is shown that topologically nontrivial states in two-dimensional materials enable an increase ofmore » two orders of magnitude in the quantum drag force with respect to conventional neutral graphene systems.« less

Quantum friction in two-dimensional topological materials

DOE PAGES

Farias, M. Belén; Kort-Kamp, Wilton J. M.; Dalvit, Diego A. R.

2018-04-24

In this paper, we develop the theory of quantum friction in two-dimensional topological materials. The quantum drag force on a metallic nanoparticle moving above such systems is sensitive to the nontrivial topology of their electronic phases, shows a novel distance scaling law, and can be manipulated through doping or via the application of external fields. We use the developed framework to investigate quantum friction due to the quantum Hall effect in magnetic field biased graphene, and to topological phase transitions in the graphene family materials. Finally, it is shown that topologically nontrivial states in two-dimensional materials enable an increase ofmore » two orders of magnitude in the quantum drag force with respect to conventional neutral graphene systems.« less

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.

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.

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.

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.

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

PubMed Central

2015-01-01

Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact both the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P–O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different. PMID:26574325

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

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

NASA Astrophysics Data System (ADS)

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

2012-07-01

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

Accurate force field for molybdenum by machine learning large materials data

NASA Astrophysics Data System (ADS)

Chen, Chi; Deng, Zhi; Tran, Richard; Tang, Hanmei; Chu, Iek-Heng; Ong, Shyue Ping

2017-09-01

In this work, we present a highly accurate spectral neighbor analysis potential (SNAP) model for molybdenum (Mo) developed through the rigorous application of machine learning techniques on large materials data sets. Despite Mo's importance as a structural metal, existing force fields for Mo based on the embedded atom and modified embedded atom methods do not provide satisfactory accuracy on many properties. We will show that by fitting to the energies, forces, and stress tensors of a large density functional theory (DFT)-computed dataset on a diverse set of Mo structures, a Mo SNAP model can be developed that achieves close to DFT accuracy in the prediction of a broad range of properties, including elastic constants, melting point, phonon spectra, surface energies, grain boundary energies, etc. We will outline a systematic model development process, which includes a rigorous approach to structural selection based on principal component analysis, as well as a differential evolution algorithm for optimizing the hyperparameters in the model fitting so that both the model error and the property prediction error can be simultaneously lowered. We expect that this newly developed Mo SNAP model will find broad applications in large and long-time scale simulations.

Chaos as an intermittently forced linear system.

PubMed

Brunton, Steven L; Brunton, Bingni W; Proctor, Joshua L; Kaiser, Eurika; Kutz, J Nathan

2017-05-30

Understanding the interplay of order and disorder in chaos is a central challenge in modern quantitative science. Approximate linear representations of nonlinear dynamics have long been sought, driving considerable interest in Koopman theory. We present a universal, data-driven decomposition of chaos as an intermittently forced linear system. This work combines delay embedding and Koopman theory to decompose chaotic dynamics into a linear model in the leading delay coordinates with forcing by low-energy delay coordinates; this is called the Hankel alternative view of Koopman (HAVOK) analysis. This analysis is applied to the Lorenz system and real-world examples including Earth's magnetic field reversal and measles outbreaks. In each case, forcing statistics are non-Gaussian, with long tails corresponding to rare intermittent forcing that precedes switching and bursting phenomena. The forcing activity demarcates coherent phase space regions where the dynamics are approximately linear from those that are strongly nonlinear.The huge amount of data generated in fields like neuroscience or finance calls for effective strategies that mine data to reveal underlying dynamics. Here Brunton et al.develop a data-driven technique to analyze chaotic systems and predict their dynamics in terms of a forced linear model.

A Novel Method Of Gradient Forming and Fluid Manipulation in Reduced Gravity Environments

NASA Technical Reports Server (NTRS)

Ramachandran N.; Leslie, F.

1999-01-01

The use of magnetic fields to control the motion and position of non-conducting liquids has received growing interest in recent times. The possibility of using the forces exerted by a nonuniform magnetic field on a ferrofluid to not only achieve fluid manipulation but also to actively control fluid motion makes it an attractive candidate for applications such as heat transfer in space systems. Terrestrial heat transfer equipment often relies on the normal gravitational force to hold liquid in a desired position or to provide a buoyant force to enhance the heat transfer rate. The residual gravitational force present in a space environment may no longer serve these useful functions and other forces, such as surface tension, can play a significant role in determining heat transfer rates. Although typically overwhelmed by gravitational forces in terrestrial applications, the body force induced in a ferrofluid by a nonuniform magnetic field can help to achieve these objectives in a microgravity environment. This paper will address the fluid manipulation aspect and will comprise of results from model fluid experiments and numerical modeling of the problem. Results from a novel method of forming concentration gradients that are applicable to low gravity applications will be presented. The ground based experiments are specifically tailored to demonstrate the magnetic manipulation capability of a ferrofluid and show that gravitational effects can be countered in carefully designed systems. The development of governing equations for the system will be presented along with a sampling of numerical results.

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.

Army Logistician. Volume 38, Issue 3, May-June 2006

DTIC Science & Technology

2006-06-01

that are deployed or preparing to deploy and those in the process of transforming to a modular design find it difficult to keep abreast of emerging...The Air Force and the Marine Corps have well-defined and -established career fields in con- tracting for their NCOs. Now the Army is developing ...How will field -grade officers in a BCT be developed as logistics officers? How will CSS company commanders be developed ? Will there be a female

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.

First Observation of a Hall Effect in a Dusty Plasma: A Charged Granular Flow with Relevance to Planetary Rings

NASA Astrophysics Data System (ADS)

Eiskowitz, Skylar; Ballew, Nolan; Rojas, Rubén; Lathrop, Daniel

2017-11-01

The particles in Saturn's rings exhibit complex dynamic behavior. They experience solar radiation pressure, electromagnetic forces, and granular collisions. To investigate the possibility of the Hall Effect in the dusty plasma that comprise Saturn's rings, we have built an experiment that demonstrates the Hall Effect in granular matter. We focus on the Hall Effect because the rings' grains become collisionally charged and experience Saturn's dipolar magnetic field and Lorentz forces as they orbit. The experimental setup includes a closed ring-like track where granular matter is forced to circulate driven by compressed air. The structure sits between two electromagnets so that a portion of the track experiences up to a 0.2 T magnetic field. We vary the strength of the field and the speed of the particles. We report the voltage differences between two conducting plates on opposite sides of the track. If Saturn's rings do experience the Hall Effect, the inside and outside of the rings will develop a charge separation that can lead to a radial electric field and various phenomena including orbital effects due to the additional electric forces. Observational evidence from Cassini suggests that Saturn's rings exhibit lighting, supporting the notion that they are electrically charged. TREND REU program sponsored by the National Science Foundation.

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.

Spin-orbit induced electronic spin separation in semiconductor nanostructures.

PubMed

Kohda, Makoto; Nakamura, Shuji; Nishihara, Yoshitaka; Kobayashi, Kensuke; Ono, Teruo; Ohe, Jun-ichiro; Tokura, Yasuhiro; Mineno, Taiki; Nitta, Junsaku

2012-01-01

The demonstration of quantized spin splitting by Stern and Gerlach is one of the most important experiments in modern physics. Their discovery was the precursor of recent developments in spin-based technologies. Although electrical spin separation of charged particles is fundamental in spintronics, in non-uniform magnetic fields it has been difficult to separate the spin states of charged particles due to the Lorentz force, as well as to the insufficient and uncontrollable field gradients. Here we demonstrate electronic spin separation in a semiconductor nanostructure. To avoid the Lorentz force, which is inevitably induced when an external magnetic field is applied, we utilized the effective non-uniform magnetic field which originates from the Rashba spin-orbit interaction in an InGaAs-based heterostructure. Using a Stern-Gerlach-inspired mechanism, together with a quantum point contact, we obtained field gradients of 10(8) T m(-1) resulting in a highly polarized spin current.

Spin–orbit induced electronic spin separation in semiconductor nanostructures

PubMed Central

Kohda, Makoto; Nakamura, Shuji; Nishihara, Yoshitaka; Kobayashi, Kensuke; Ono, Teruo; Ohe, Jun-ichiro; Tokura, Yasuhiro; Mineno, Taiki; Nitta, Junsaku

2012-01-01

The demonstration of quantized spin splitting by Stern and Gerlach is one of the most important experiments in modern physics. Their discovery was the precursor of recent developments in spin-based technologies. Although electrical spin separation of charged particles is fundamental in spintronics, in non-uniform magnetic fields it has been difficult to separate the spin states of charged particles due to the Lorentz force, as well as to the insufficient and uncontrollable field gradients. Here we demonstrate electronic spin separation in a semiconductor nanostructure. To avoid the Lorentz force, which is inevitably induced when an external magnetic field is applied, we utilized the effective non-uniform magnetic field which originates from the Rashba spin–orbit interaction in an InGaAs-based heterostructure. Using a Stern–Gerlach-inspired mechanism, together with a quantum point contact, we obtained field gradients of 108 T m−1 resulting in a highly polarized spin current. PMID:23011136

Alternative Futures and Army Force Planning. Implications for the Future Force Era

DTIC Science & Technology

2005-01-01

narcotraffickers had to establish coca fields in other Latin American countries like Bolivia and Peru , build processing labs in remote areas of the Amazon basin...emergence of Al Qaeda as a potent worldwide force, both the scope and the duration of the war on terrorism remain un- certain, as does the level of...future. Our hypothesis was that a drastic downturn in any one of the development variables would drag the remaining four at least into the medium category

National Task Force on a Uniform Measurement Unit for the Recognition of Continuing Education: Working Papers; and The Continuing Education Unit: A Uniform Unit of Measure for Non-Credit Continuing Education Programs (An Interim Statement of the National Task Force).

ERIC Educational Resources Information Center

National Univ. Extension Association, Washington, DC.

In 1968, a national planning conference, under the joint sponsorship of 34 organizations responsing to continuing education needs, created the National Task Force to determine the feasibility of a uniform unit of measurement and develop a proposal for field testing the concept. Stressing that continuing education units should supplement, not…

Sliding mode control of electromagnetic tethered satellite formation

NASA Astrophysics Data System (ADS)

Hallaj, Mohammad Amin Alandi; Assadian, Nima

2016-08-01

This paper investigates the control of tethered satellite formation actuated by electromagnetic dipoles and reaction wheels using the robust sliding mode control technique. Generating electromagnetic forces and moments by electric current coils provides an attractive control actuation alternative for tethered satellite system due to the advantages of no propellant consumption and no obligatory rotational motion. Based on a dumbbell model of tethered satellite in which the flexibility and mass of the tether is neglected, the equations of motion in Cartesian coordinate are derived. In this model, the J2 perturbation is taken into account. The far-field and mid-field models of electromagnetic forces and moments of two satellites on each other and the effect of the Earth's magnetic field are presented. A robust sliding mode controller is designed for precise trajectory tracking purposes and to deal with the electromagnetic force and moment uncertainties and external disturbances due to the Earth's gravitational and magnetic fields inaccuracy. Numerical simulation results are presented to validate the effectiveness of the developed controller and its superiority over the linear controller.

Japanese Magsat Team. A: Crustal structure near Japan and its Antarctic Station. B: Electric currents and hydromagnetic waves in the ionosphere and the magnetosphere

NASA Technical Reports Server (NTRS)

Fukushima, N.; Maeda, H.; Yukutake, T.; Tanaka, M.; Oshima, S.; Ogawa, K.; Kawamura, M.; Miyzaki, Y.; Uyeda, S.; Kobayashi, K. (Principal Investigator)

1981-01-01

Efforts continue in compiling tapes which contain vector and scalar data decimated at an interval of 0.5 sec, together with time and position data. A map of the total force field anomaly around Japan was developed which shows a negative magnetic anomaly in the Okhotsk Sea. Examination of vector residuals from the MGST model shows that the total force perturbation is almost ascribable to the perturbation parallel to the main geomagnetic field and that the contribution from the perturbation transverse to the main field to the total force perturbation is negligibly small. The influences of ionospheric current with equatorial electroject and of the magnetospheric field aligned current on the dawn-dusk asymmetry of daily geomagnetic variations are being considered. The total amount of electric current flowing through the plane of the Magsat orbit loop was calculated by direct application of Maxwell's equation. Results show that the total electric current is 1 to 5 ampheres, and the current direction is either sunward or antisunward.

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

PubMed

Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

2018-04-05

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

Modifiying shallow-water equations as a model for wave-vortex turbulence

NASA Astrophysics Data System (ADS)

Mohanan, A. V.; Augier, P.; Lindborg, E.

2017-12-01

The one-layer shallow-water equations is a simple two-dimensional model to study the complex dynamics of the oceans and the atmosphere. We carry out forced-dissipative numerical simulations, either by forcing medium-scale wave modes, or by injecting available potential energy (APE). With pure wave forcing in non-rotating cases, a statistically stationary regime is obtained for a range of forcing Froude numbers Ff = ɛ /(kf c), where ɛ is the energy dissipation rate, kf the forcing wavenumber and c the wave speed. Interestingly, the spectra scale as k-2 and third and higher order structure functions scale as r. Such statistics is a manifestation of shock turbulence or Burgulence, which dominate the flow. Rotating cases exhibit some inverse energy cascade, along with a stronger forward energy cascade, dominated by wave-wave interactions. We also propose two modifications to the classical shallow-water equations to construct a toy model. The properties of the model are explored by forcing in APE at a small and a medium wavenumber. The toy model simulations are then compared with results from shallow-water equations and a full General Circulation Model (GCM) simulation. The most distinctive feature of this model is that, unlike shallow-water equations, it avoids shocks and conserves quadratic energy. In Fig. 1, for the shallow-water equations, shocks appear as thin dark lines in the divergence (∇ .{u}) field, and as discontinuities in potential temperature (θ ) field; whereas only waves appear in the corresponding fields from toy model simulation. Forward energy cascade results in a wave field with k-5/3 spectrum, along with equipartition of KE and APE at small scales. The vortical field develops into a k-3 spectrum. With medium forcing wavenumber, at large scales, energy converted from APE to KE undergoes inverse cascade as a result of nonlinear fluxes composed of vortical modes alone. Gradually, coherent vortices emerge with a strong preference for anticyclonic motion. The model can serve as a closer representation of real geophysical turbulence than the classical shallow-water equations. Fig 1. Divergence and potential temperature fields of shallow-water (top row) and toy model (bottom row) simulations.

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.

Challenges and Opportunities in Nde, Ishm and Material State Awareness for Aircraft Structures: us Air Force Perspective

NASA Astrophysics Data System (ADS)

Buynak, C. F.; Blackshire, J.; Lindgren, E. A.; Jata, K. V.

2008-02-01

As one of the primary data and information sources in the maintenance of USAF Aging Military Fleet, NDE plays a major role in the definition and operation of maintenance processes on these aircraft. To focus new NDE developmental efforts, the AFRL NDE R&D group has the charter to research, develop and transition new capabilities to the field and depot users. This multi-faceted task is achieved through a balanced NDE and on-board sensor development program with the ultimate goal to transition technology to the Air Force user Commands. Technology requirements for NDE and Material State Awareness emerge from Air Force Initiatives to realize Condition Based Maintenance and to develop the "Depot of the Future". This evening session will present an overview of Air Force Initiatives, emerging R&D issues for Structural Health Monitoring and NDE methodologies as well as basic research initiatives within the Air Force Research Laboratory. It is intended that the session provide an open forum to pursue paths for new technology development and application.

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

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.

Turbofan forced mixer-nozzle internal flowfield. Volume 1: A benchmark experimental study

NASA Technical Reports Server (NTRS)

Paterson, R. W.

1982-01-01

An experimental investigation of the flow field within a model turbofan forced mixer nozzle is described. Velocity and thermodynamic state variable data for use in assessing the accuracy and assisting the further development of computational procedures for predicting the flow field within mixer nozzles are provided. Velocity and temperature data suggested that the nozzle mixing process was dominated by circulations (secondary flows) of a length scale on the order the lobe dimensions which were associated with strong radial velocities observed near the lobe exit plane. The 'benchmark' model mixer experiment conducted for code assessment purposes is discussed.

Expected orbit determination performance for the TOPEX/Poseidon mission

NASA Technical Reports Server (NTRS)

Nerem, R. S.; Putney, Barbara H.; Marshall, J. A.; Lerch, Francis J.; Pavlis, Erricos C.; Klosko, Steven M.; Luthcke, Scott B.; Patel, Girish B.; Williamson, Ronald G.; Zelensky, Nikita P.

1993-01-01

Each of the components required for the computation of precise orbits for the TOPEX/Poseidon (T/P) spacecraft - gravity field modeling, nonconservative force modeling, and satellite tracking technologies - is examined. The research conducted in the Space Geodesy Branch at Goddard Space Flight Center in preparation for meeting the 13-cm radial orbit accuracy requirement for the T/P mission is outlined. New developments in modeling the earth's gravitational field and modeling the complex nonconservative forces acting on T/P are highlighted. The T/P error budget is reviewed, and a prelaunch assessment of the predicted orbit determination accuracies is summarized.

Stage I: Development of VOICE.

ERIC Educational Resources Information Center

Echternacht, Gary J.; And Others

The initial stages of test development of the Vocational and Occupational Interest Choice Examination (VOICE), developed for Air Force recruiters, are described. Reviewed are a number of relevant occupational interest inventories from which a pool of 400 items was drawn corresponding to eight career fields: general accounting, administration,…

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.

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

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

Lerche, I.; Low, B. C.

2014-10-15

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

Life-space foam: A medium for motivational and cognitive dynamics

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir; Aidman, Eugene

2007-08-01

General stochastic dynamics, developed in a framework of Feynman path integrals, have been applied to Lewinian field-theoretic psychodynamics [K. Lewin, Field Theory in Social Science, University of Chicago Press, Chicago, 1951; K. Lewin, Resolving Social Conflicts, and, Field Theory in Social Science, American Psychological Association, Washington, 1997; M. Gold, A Kurt Lewin Reader, the Complete Social Scientist, American Psychological Association, Washington, 1999], resulting in the development of a new concept of life-space foam (LSF) as a natural medium for motivational and cognitive psychodynamics. According to LSF formalisms, the classic Lewinian life space can be macroscopically represented as a smooth manifold with steady force fields and behavioral paths, while at the microscopic level it is more realistically represented as a collection of wildly fluctuating force fields, (loco)motion paths and local geometries (and topologies with holes). A set of least-action principles is used to model the smoothness of global, macro-level LSF paths, fields and geometry. To model the corresponding local, micro-level LSF structures, an adaptive path integral is used, defining a multi-phase and multi-path (multi-field and multi-geometry) transition process from intention to goal-driven action. Application examples of this new approach include (but are not limited to) information processing, motivational fatigue, learning, memory and decision making.

A Multilevel Analysis of a Guided Inquiry Curriculum Unit on Motion and Force for a Diverse Student Population in "Ability-Grouped" Classrooms

ERIC Educational Resources Information Center

Rethinam, Vasuki; Lynch, Sharon J.

2011-01-01

This study is an evaluation of "Exploring Motion and Forces: Speed, Acceleration, and Friction" ("M&F") developed by ARIES of the Harvard-Smithsonian Center for Astrophysics (2001). Although "M&F" has been used in many schools and field-tested, it has never been evaluated in rigorous experimental or…

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

PubMed

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

2012-12-01

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

Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass

PubMed Central

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

2012-01-01

Adsorption free energies for eight host–guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5–9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface. PMID:22941539

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.

Strings: A possible alternative explanation for the Unification of Gravitation Field and Electromagnetic Field

NASA Astrophysics Data System (ADS)

Rivera, Susana

Throughout the last century, since the last decades of the XIX century, until present day, there had been many attempts to achieve the unification of the Forces of Nature. First unification was done by James Clerk Maxwell, with his Electromagnetic Theory. Then Max Plank developed his Quantum Theory. In 1905, Albert Einstein gave birth to the Special Relativity Theory, and in 1916 he came out with his General Relativity Theory. He noticed that there was an evident parallelism between the Gravitational Force, and the Electromagnetic Force. So, he tried to unify these forces of Nature. But Quantum Theory interposed on his way. On the 1940’s it had been developed the Quantum Electrodynamics (QED), and with it, the unified field theory had an arise interest. On the 60’s and 70’s there was developed the Quantum Chromodynamics (QCD). Along with these theories came the discovery of the strong interaction force and weak interaction force. And though there had been many attempts to unify all these forces of the nature, it could only be achieved the Unification of strong interaction, weak interaction and Electromagnetic Force. On the late 80”s and throughout the last two decades, theories such as “super-string theory”, “or the “M-theory”, among others, groups of Scientists, had been doing grand efforts and finally they came out with the unification of the forces of nature, being the only limitation the use of more than 11 dimensions. Using an ingenious mathematical tool known as the super symmetries, based on the Kaluza - Klein work, they achieve this goal. The strings of these theories are in the rank of 10-33 m. Which make them undetectable. There are many other string theories. The GEUFT theory is based on the existence of concentrated energy lines, which vibrates, expands and contracts, submitting and absorbing energy, matter and antimatter, and which yields a determined geometry, that gives as a result the formation of stars, galaxies, nebulae, clusters on the Macrocosmic level, and that allows the formation of fundamental particles on the Microcosmic level. The strings are described by a function named Symbiosis (σ), which depends on four energetic contributions: (1) Radiation Energy (2) Plasma Energy (3) Conducted Flux Energy and (4) Mass Energy. There is an intimate relation between them, and depending on the value they have at a certain moment and at a certain time, the string dynamics and its geometry are settled. That means that symbiosis describes the strings state in any point of the geometer - energy field. σ = F [Er(σ), Ep(σ), Ef(σ), Em(σ)] (1) This work is an attempt to achieve the unification of the forces of nature, based on the existence of a four dimension Universe.

Hydraulic pressures generated in magnetic ionic liquids by paramagnetic fluid/air interfaces inside of uniform tangential magnetic fields.

PubMed

Scovazzo, Paul; Portugal, Carla A M; Rosatella, Andreia A; Afonso, Carlos A M; Crespo, João G

2014-08-15

Magnetic Ionic Liquid (MILs), novel magnetic molecules that form "pure magnetic liquids," will follow the Ferrohydrodynamic Bernoulli Relationship. Based on recent literature, the modeling of this fluid system is an open issue and potentially controversial. We imposed uniform magnetic fields parallel to MIL/air interfaces where the capillary forces were negligible, the Quincke Problem. The size and location of the bulk fluid as well as the size and location of the fluid/air interface inside of the magnetic field were varied. MIL properties varied included the density, magnetic susceptibility, chemical structure, and magnetic element. Uniform tangential magnetic fields pulled the MILs up counter to gravity. The forces per area were not a function of the volume, the surface area inside of the magnetic field, or the volume displacement. However, the presence of fluid/air interfaces was necessary for the phenomena. The Ferrohydrodynamic Bernoulli Relationship predicted the phenomena with the forces being directly related to the fluid's volumetric magnetic susceptibility and the square of the magnetic field strength. [emim][FeCl4] generated the greatest hydraulic head (64-mm or 910 Pa at 1.627 Tesla). This work could aid in experimental design, when free surfaces are involved, and in the development of MIL applications. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering.

PubMed

Slepoy, A; Peters, M D; Thompson, A P

2007-11-30

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. Copyright (c) 2007 Wiley Periodicals, Inc.

Magnetic Field Design for a Strongly Improved PHALL Thruster

NASA Astrophysics Data System (ADS)

Martins, Alexandre A.; Rodrigo, Miranda; Ferreira, José Leonardo

2017-10-01

In this article, we are going to go through some steps that we took in the refining of engineering work related to the development of a permanent magnet Hall thruster. The use of permanent magnets in these thrusters is mainly related to the decrease of used power for propulsion, especially important for low power thrusters as for micro-satellites. The advantage of our chosen configuration is that the magnetic field can be used either perpendicular or parallel to the thruster channel walls, whereas in the last case the generated erosion forces are strongly reduced by at least three orders of magnitude. We are going to show how each magnetic field configuration affects the generated plasma and consequently the generated propulsion force and efficiency.

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

Air Force construction automation/robotics

NASA Technical Reports Server (NTRS)

Nease, A. D.; Alexander, E. F.

1993-01-01

The Air Force has several missions which generate unique requirements that are being met through the development of construction robotic technology. One especially important mission will be the conduct of Department of Defense (DOD) space activities. Space operations and other missions place construction/repair equipment operators in dangerous environments and potentially harmful situations. Additionally, force reductions require that human resources be leveraged to the maximum extent possible, and more stringent construction repair requirements push for increased automation. To solve these problems, the U.S. Air Force is undertaking a research and development effort at Tyndall AFB, FL, to develop robotic construction/repair equipment. This development effort involves the following technologies: teleoperation, telerobotics, construction operations (excavation, grading, leveling, tool change), robotic vehicle communications, vehicle navigation, mission/vehicle task control architecture, and associated computing environment. The ultimate goal is the fielding of a robotic repair capability operating at the level of supervised autonomy. This paper will discuss current and planned efforts in space construction/repair, explosive ordnance disposal, hazardous waste cleanup, and fire fighting.

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.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

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.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

PubMed

Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

2016-05-10

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

[Professional psychological selection system in the Air Force - 50 years].

PubMed

Pokrovskiĭ, B L

2014-08-01

Given the data about the establishment of the professional psychological selection system in the Air Force in 1958-1964 in the NIIIAM Air Force by the team psychological department under the leadership of K.K.Platonova. Given the names of the developers of this system and given the results of their research. The result of all made work the order of Air Force Commander about the introduction of the psychological selection in Higher Military Aviation School of Pilots, starting from a set of 1964 became. Recommendations for professional psychological selection of a wide range of aviation professionals in various fields, and in the future - and other professionals of the Armed Forces, became the results of future work.

Development of a Polarizable Force Field for Molecular Dynamics Simulations of Poly (Ethylene Oxide) in Aqueous Solution.

PubMed

Starovoytov, Oleg N; Borodin, Oleg; Bedrov, Dmitry; Smith, Grant D

2011-06-14

We have developed a quantum chemistry-based polarizable potential for poly(ethylene oxide) (PEO) in aqueous solution based on the APPLE&P polarizable ether and the SWM4-DP polarizable water models. Ether-water interactions were parametrized to reproduce the binding energy of water with 1,2-dimethoxyethane (DME) determined from high-level quantum chemistry calculations. Simulations of DME-water and PEO-water solutions at room temperature using the new polarizable potentials yielded thermodynamic properties in good agreement with experimental results. The predicted miscibility of PEO and water as a function of the temperature was found to be strongly correlated with the predicted free energy of solvation of DME. The developed nonbonded force field parameters were found to be transferrable to poly(propylene oxide) (PPO), as confirmed by capturing, at least qualitatively, the miscibility of PPO in water as a function of the molecular weight.

Influence of Applying Additional Forcing Fans for the Air Distribution in Ventilation Network

NASA Astrophysics Data System (ADS)

Szlązak, Nikodem; Obracaj, Dariusz; Korzec, Marek

2016-09-01

Mining progress in underground mines cause the ongoing movement of working areas. Consequently, it becomes necessary to adapt the ventilation network of a mine to direct airflow into newly-opened districts. For economic reasons, opening new fields is often achieved via underground workings. Length of primary intake and return routes increases and also increases the total resistance of a complex ventilation network. The development of a subsurface structure can make it necessary to change the air distribution in a ventilation network. Increasing airflow into newly-opened districts is necessary. In mines where extraction does not entail gas-related hazards, there is possibility of implementing a push-pull ventilation system in order to supplement airflows to newly developed mining fields. This is achieved by installing subsurface fan stations with forcing fans at the bottom of downcast shaft. In push-pull systems with multiple main fans, it is vital to select forcing fans with characteristic curves matching those of the existing exhaust fans to prevent undesirable mutual interaction. In complex ventilation networks it is necessary to calculate distribution of airflow (especially in networks with a large number of installed fans). In the article the influence of applying additional forcing fans for the air distribution in ventilation network for underground mine were considered. There are also analysed the extent of overpressure caused by the additional forcing fan in branches of the ventilation network (the operating range of additional forcing fan). Possibilities of increasing airflow rate in working areas were conducted.

Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.

PubMed

Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

2014-02-27

We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.

Vertically polarizing undulator with dynamic compensation of magnetic forces

DOE PAGES

Strelnikov, N.; Vasserman, I.; Xu, J.; ...

2017-01-20

As part of the R&D program of the LCLS-II project, a novel 3.4-meter-long undulator prototype with horizontal magnetic field and dynamic force compensation has recently been developed at the Advanced Photon Source (APS). Some previous steps in this development were the shorter 0.8-meter-long and 2.8-meter-long prototypes. Extensive mechanical and magnetic testing was carried out for each prototype, and each prototype was magnetically tuned using magnetic shims. Furthermore, the resulting performance of the 3.4-meter-long undulator prototype meets all requirements for the LCLS-II insertion device, including limits on the field integrals, phase errors, higher-order magnetic moments, and electron-beam trajectory for all operationalmore » gaps, as well as the reproducibility and accuracy of the gap settings.« less

Tunneling magnetic force microscopy

NASA Technical Reports Server (NTRS)

Burke, Edward R.; Gomez, Romel D.; Adly, Amr A.; Mayergoyz, Isaak D.

1993-01-01

We have developed a powerful new tool for studying the magnetic patterns on magnetic recording media. This was accomplished by modifying a conventional scanning tunneling microscope. The fine-wire probe that is used to image surface topography was replaced with a flexible magnetic probe. Images obtained with these probes reveal both the surface topography and the magnetic structure. We have made a thorough theoretical analysis of the interaction between the probe and the magnetic fields emanating from a typical recorded surface. Quantitative data about the constituent magnetic fields can then be obtained. We have employed these techniques in studies of two of the most important issues of magnetic record: data overwrite and maximizing data-density. These studies have shown: (1) overwritten data can be retrieved under certain conditions; and (2) improvements in data-density will require new magnetic materials. In the course of these studies we have developed new techniques to analyze magnetic fields of recorded media. These studies are both theoretical and experimental and combined with the use of our magnetic force scanning tunneling microscope should lead to further breakthroughs in the field of magnetic recording.

Path planning for robotic truss assembly

NASA Technical Reports Server (NTRS)

Sanderson, Arthur C.

1993-01-01

A new Potential Fields approach to the robotic path planning problem is proposed and implemented. Our approach, which is based on one originally proposed by Munger, computes an incremental joint vector based upon attraction to a goal and repulsion from obstacles. By repetitively adding and computing these 'steps', it is hoped (but not guaranteed) that the robot will reach its goal. An attractive force exerted by the goal is found by solving for the the minimum norm solution to the linear Jacobian equation. A repulsive force between obstacles and the robot's links is used to avoid collisions. Its magnitude is inversely proportional to the distance. Together, these forces make the goal the global minimum potential point, but local minima can stop the robot from ever reaching that point. Our approach improves on a basic, potential field paradigm developed by Munger by using an active, adaptive field - what we will call a 'flexible' potential field. Active fields are stronger when objects move towards one another and weaker when they move apart. An adaptive field's strength is individually tailored to be just strong enough to avoid any collision. In addition to the local planner, a global planning algorithm helps the planner to avoid local field minima by providing subgoals. These subgoals are based on the obstacles which caused the local planner to fail. A best-first search algorithm A* is used for graph search.

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.

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.

Large gradient high magnetic field affects the association of MACF1 with actin and microtubule cytoskeleton.

PubMed

Qian, Ai-Rong; Hu, Li-Fang; Gao, Xiang; Zhang, Wei; Di, Sheng-Meng; Tian, Zong-Cheng; Yang, Peng-Fei; Yin, Da-Chuan; Weng, Yuan-Yuan; Shang, Peng

2009-10-01

The intense inhomogeneous magnetic fields acting on the diamagnetic materials naturally present in cells can generate strong magnetic forces. We have developed a superconducting magnet platform with large gradient high magnetic field (LG-HMF), which can produce three magnetic force fields of -1360, 0, and 1312 T(2)/m, and three corresponding apparent gravity levels, namely 0, 1, and 2-g for diamagnetic materials. In this study, the effects of different magnetic force fields on osteoblast-like cells (MG-63 and MC3T3-E1) viability, microtubule actin crosslinking factor 1 (MACF1) expression and its association with cytoskeleton were investigated. Results showed that cell viability increased to different degrees after exposure to 0 or 1-g conditions for 24 h, but it decreased by about 30% under 2-g conditions compared with control conditions. An increase in MACF1 expression at the RNA or protein level was observed in osteoblast-like cells under the magnetic force field of -1360 T(2)/m (0-g) relative to 1312 T(2)/m (2-g). Under control conditions, anti-MACF1 staining was scattered in the cytoplasm and partially colocalized with actin filaments (AFs) or microtubules (MTs) in the majority of osteoblast-like cells. Under 0-g conditions, MACF1 labeling was concentrated at perinuclear region and colocalization was not apparent. The patterns of anti-MACF1 labeling on MTs varied with MTs' changing under LG-HMF environment. In conclusion, LG-HMF affects osteoblast-like cell viability, MACF1 distribution, expression, and its association with cytoskeleton to some extent.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces.

PubMed

Rogers, T Ryan; Wang, Feng

2017-10-28

An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about -0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

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.

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

PubMed

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

2013-10-31

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

A force field for 3,3,3-fluoro-1-propenes, including HFO-1234yf.

PubMed

Raabe, Gabriele; Maginn, Edward J

2010-08-12

The European Union (EU) legislation 2006/40/EC bans from January 2011 the cooperative marketing of new car types that use refrigerants in their heating, ventilation, and air conditioning (HVAC) systems with global warming potentials (GWP) higher than 150. Thus, the phase-out of the presently used tetrafluoroethane refrigerant R134a necessitates the adoption of alternative refrigerants. Fluoropropenes such as 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf) are currently regarded as promising low GWP refrigerants, but the lack of experimental data on their thermophysical properties hampers independent studies on their performance in HVAC systems or in other technical applications. In principle, molecular modeling can be used to predict the relevant properties of refrigerants, but adequate intermolecular potential functions ("force fields") are lacking for fluoropropenes. Thus, we developed a transferable force field for fluoropropenes composed of CF(3)-, -CF=, -CH=, CF(2)=, and CH(2)= groups and applied the force field to study 3,3,3 trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). We performed Gibbs ensemble simulations on these three fluoropropenes to compute the vapor pressure, saturated densities, and heats of vaporization. In addition, molecular dynamics simulations were conducted to provide predictions for the density, thermal expansivity, isobaric heat capacity, and transport properties of liquid HFO-1234yf in the temperature range from 263.15 to 310 K and pressures up to 2 MPa. Agreement between simulation results and experimental data and/or correlations (when available) was good, thereby validating the predictive ability of the force field.

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

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

PubMed

Xu, Dong; Zhang, Yang

2012-07-01

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

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

Calculating forces on thin flat plates with incomplete vorticity-field data

NASA Astrophysics Data System (ADS)

Limacher, Eric; Morton, Chris; Wood, David

2016-11-01

Optical experimental techniques such as particle image velocimetry (PIV) permit detailed quantification of velocities in the wakes of bluff bodies. Patterns in the wake development are significant to force generation, but it is not trivial to quantitatively relate changes in the wake to changes in measured forces. Key difficulties in this regard include: (i) accurate quantification of velocities close to the body, and (ii) the effect of missing velocity or vorticity data in regions where optical access is obscured. In the present work, we consider force formulations based on the vorticity field, wherein mathematical manipulation eliminates the need for accurate near-body velocity information. Attention is restricted to nominally two dimensional problems, namely (i) a linearly accelerating flat plate, investigated using PIV in a water tunnel, and (ii) a pitching plate in a freestream flow, as investigated numerically by Wang & Eldredge (2013). The effect of missing vorticity data on the pressure side of the plate has a significant impact on the calculation of force for the pitching plate test case. Fortunately, if the vorticity on the pressure side remains confined to a thin boundary layer, simple corrections can be applied to recover a force estimate.

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

NASA Technical Reports Server (NTRS)

Haw, Richard C.; Foss, John F.

1990-01-01

Forcing and its effect on fluid flows has become an accepted tool in the study and control of flow systems. It has been used both as a diagnostic tool, to explore the development and interaction of coherent structures, and as a method of controlling the behavior of the flow. A number of forcing methods have been used in order to provide a perturbation to the flow; among these are the use of an oscillating trailing edge, acoustically driven slots, external acoustic forcing, and mechanical piston methods. The effect of a planar mechanical piston forcing on a single stream shear layer is presented; it can be noted that this is one of the lesser studied free shear layers. The single stream shear layer can be characterized by its primary flow velocity scale and the thickness of the separating boundary layer. The velocity scale is constant over the length of the flow field; theta (x) can be used as a width scale to characterize the unforced shear layer. In the case of the forced shear layer the velocity field is a function of phase time and definition of a width measure becomes somewhat problematic.

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.

Simulant Gas Test Technique Feasibility

DTIC Science & Technology

1990-05-01

DY’NAMICS LABORATORY WRIGHT RESEARCH AND DEVELOPMENT CENTER AIR FORCE SYSTEMS COMMAND WRIGHT-PATTERSON AIR FORCE BASE, OHIO 45433-6553 NOTIr’ When...TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Hypersonic-test Air -chemistry Non-equilibrium-flow 0g...ABSTRACT (Continue on reverse if necessary and identify by block number) ’[lie Ulcertaillty engendered by non-equilibrium air effects on hypersonic

Dynamics of elastic interactions in soft and biological matter.

PubMed

Yuval, Janni; Safran, Samuel A

2013-04-01

Cells probe their mechanical environment and can change the organization of their cytoskeletons when the elastic and viscous properties of their environment are modified. We use a model in which the forces exerted by small, contractile acto-myosin filaments (e.g., nascent stress fibers in stem cells) on the extracellular matrix are modeled as local force dipoles. In some cases, the strain field caused by these force dipoles propagates quickly enough so that only static elastic interactions need be considered. On the other hand, in the case of significant energy dissipation, strain propagation is slower and may be eliminated completely by the relaxation of the cellular cytoskeleton (e.g., by cross-link dissociation). Here, we consider several dissipative mechanisms that affect the propagation of the strain field in adhered cells and consider these effects on the interaction between force dipoles and their resulting mutual orientations. This is a first step in understanding the development of orientational (nematic) or layering (smectic) order in the cytoskeleton. We use the theory to estimate the propagation time of the strain fields over a cellular distance for different mechanisms and find that in some cases it can be of the order of seconds, thus competing with the cytoskeletal relaxation time. Furthermore, for a simple system of two force dipoles, we predict that in some cases the orientation of force dipoles might change significantly with time, e.g., for short times the dipoles exhibit parallel alignment while for later times they align perpendicularly.

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.

A comparative analysis of physiological responses at submaximal workloads during different laboratory simulations of field cycling.

PubMed

Kenny, G P; Reardon, F D; Marion, A; Thoden, J S

1995-01-01

The purpose of this study was to evaluate the relationships between heart rate (fc), oxygen consumption (VO2), peak force and average force developed at the crank in response to submaximal exercise employing a racing bicycle which was attached to an ergometer (RE), ridden on a treadmill (TC) and ridden on a 400-m track (FC). Eight male trained competitive cyclists rode at three pre-determined work intensities set at a proportion of their maximal oxygen consumption (VO2max): (1) below lactate threshold [work load that produces a VO2 which is 10% less than the lactate threshold VO2 (sub-LT)], (2) lactate threshold VO2 (LT), and (3) above lactate threshold [workload that produces a VO2 which is 10% greater than lactate threshold VO2 (supra-LT)], and equated across exercise modes on the basis of fc. Voltage signals from the crank arm were recorded as FM signals for subsequent representation of peak and average force. Open circuit VO2 measurements were done in the field by Douglas bag gas collection and in the laboratory by automated gas collection and analysis. fc was recorded with a telemeter (Polar Electro Sport Tester, PE3000). Significant differences (P < 0.05) were observed: (1) in VO2 between FC and both laboratory conditions at sub-LT intensity and LT intensities, (2) in peak force between FC and TC at sub-LT intensity, (3) in average force between FC and RE at sub-LT. No significant differences were demonstrated at supra-LT intensity for VO2. Similarly no significant differences were observed in peak and average force for either LT or supra-LT intensities. These data indicate that equating work intensities on the basis of fc measured in laboratory conditions would overestimate the VO2 which would be generated in the field and conversely, that using fc measured in the laboratory to establish field work intensity would underestimate mechanical workload experienced in the field.

Covariant theory of gravitation in the framework of special relativity

NASA Astrophysics Data System (ADS)

Vieira, R. S.; Brentan, H. B.

2018-04-01

In this work, we study the magnetic effects of gravity in the framework of special relativity. Imposing covariance of the gravitational force with respect to the Lorentz transformations, we show from a thought experiment that a magnetic-like force must be present whenever two or more bodies are in motion. The exact expression for this gravitomagnetic force is then derived purely from special relativity and the consequences of such a covariant theory are developed. For instance, we show that the gravitomagnetic fields satisfy a system of differential equations similar to the Maxwell equations of electrodynamics. This implies that the gravitational waves spread out with the speed of light in a flat spacetime, which is in agreement with the recent results concerning the gravitational waves detection. We also propose that the vector potential can be associated with the interaction momentum in the same way as the scalar potential is usually associated with the interaction energy. Other topics are also discussed, for example, the transformation laws for the fields, the energy and momentum stored in the gravitomagnetic fields, the invariance of the gravitational mass and so on. We remark that is not our intention here to propose an alternative theory of gravitation but, rather, only a first approximation for the gravitational phenomena, so that it can be applied whenever the gravitational force can be regarded as an ordinary effective force field and special relativity can be used with safety. To make this point clear we present briefly a comparison between our approach and that based on the (linearized) Einstein's theory. Finally, we remark that although we have assumed nothing from the electromagnetic theory, we found that gravity and electricity share many properties in common -these similarities, in fact, are just a requirement of special relativity that must apply to any physically acceptable force field.

Movement augmentation to evaluate human control of locomotor stability.

PubMed

Brown, Geoffrey; Wu, Mengnan Mary; Huang, Felix C; Gordon, Keith E

2017-07-01

Controlling center of mass (COM) position and velocity within a dynamic base of support is essential for gait stability. This skill is often compromised following neurologic injury, creating a need to develop effective interventions to enhance gait stability. A movement augmentation paradigm applied to walking could potentially be used to improve control of COM dynamics. We have developed a cable robot system, the Agility Trainer, to apply continuous frontal-plane forces to the pelvis during treadmill walking. This cable robot system uses a set of series elastic actuators powered by linear motors to create bilateral forces. Here we use the Agility Trainer to create a negative viscosity force field proportional to the subject's lateral velocity. Two healthy young subjects performed two 10-minute walking trials, Baseline and Negative Viscosity. During the first minute of walking in the Negative Viscosity field, participants' lateral COM motion became less controlled when compared to the rhythmic sinusoidal motion observed during Baseline walking. By the 10th minute of walking in the Negative Viscosity field the participants had adapted their gait patterns, decreasing their variation in peak lateral COM speed each stride. These results demonstrate that it is feasible to use the Agility Trainer to apply a movement augmentation paradigm to human walking.

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.

New Force Field Model for Propylene Glycol: Insight to Local Structure and Dynamics.

PubMed

Ferreira, Elisabete S C; Voroshylova, Iuliia V; Koverga, Volodymyr A; Pereira, Carlos M; Cordeiro, M Natália D S

2017-12-07

In this work we developed a new force field model (FFM) for propylene glycol (PG) based on the OPLS all-atom potential. The OPLS potential was refined using quantum chemical calculations, taking into account the densities and self-diffusion coefficients. The validation of this new FFM was carried out based on a wide range of physicochemical properties, such as density, enthalpy of vaporization, self-diffusion coefficients, isothermal compressibility, surface tension, and shear viscosity. The molecular dynamics (MD) simulations were performed over a large range of temperatures (293.15-373.15 K). The comparison with other force field models, such as OPLS, CHARMM27, and GAFF, revealed a large improvement of the results, allowing a better agreement with experimental data. Specific structural properties (radial distribution functions, hydrogen bonding and spatial distribution functions) were then analyzed in order to support the adequacy of the proposed FFM. Pure propylene glycol forms a continuous phase, displaying no microstructures. It is shown that the developed FFM gives rise to suitable results not only for pure propylene glycol but also for mixtures by testing its behavior for a 50 mol % aqueous propylene glycol solution. Furthermore, it is demonstrated that the addition of water to the PG phase produces a homogeneous solution and that the hydration interactions prevail over the propylene glycol self-association interactions.

Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice

PubMed Central

Schoenrock, Sarah Adams; Oreper, Daniel; Young, Nancy; Ervin, Robin Betsch; Bogue, Molly A.; Valdar, William; Tarantino, Lisa M.

2017-01-01

Women are at an increased risk for developing affective disorders during times of hormonal flux, including menopause when the ovaries cease production of estrogen. However, while all women undergo menopause, not all develop an affective disorder. Increased vulnerability can result from genetic predisposition, environmental factors and gene by environment interactions. In order to investigate interactions between genetic background and estrogen depletion, we performed bilateral ovariectomy, a surgical procedure that results in estrogen depletion and is thought to model the post-menopausal state, in a genetically defined panel of 37 inbred mouse strains. Seventeen days post-ovariectomy, we assessed behavior in two standard rodent assays of anxiety- and depressive-like behavior, the open field and forced swim tests. We detected a significant interaction between ovariectomy and genetic background on anxiety-like behavior in the open field. No strain specific effects of ovariectomy were observed in the forced swim assay. However, we did observe significant strain effects for all behaviors in both the open field and forced swim tests. This study is the largest to date to look at the effects of ovariectomy on behavior and provides evidence that ovariectomy interacts with genetic background to alter anxiety-like behavior in an animal model of menopause. PMID:27693591

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

MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu

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

Magnetic design and method of a superconducting magnet for muon g - 2/EDM precise measurements in a cylindrical volume with homogeneous magnetic field

NASA Astrophysics Data System (ADS)

Abe, M.; Murata, Y.; Iinuma, H.; Ogitsu, T.; Saito, N.; Sasaki, K.; Mibe, T.; Nakayama, H.

2018-05-01

A magnetic field design method of magneto-motive force (coil block (CB) and iron yoke) placements for g - 2/EDM measurements has been developed and a candidate placements were designed under superconducting limitations of current density 125 A/mm2 and maximum magnetic field on CBs less than 5.5 T. Placements of CBs and an iron yoke with poles were determined by tuning SVD (singular value decomposition) eigenmode strengths. The SVD was applied on a response matrix from magneto-motive forces to the magnetic fields in the muon storage region and two-dimensional (2D) placements of magneto-motive forces were designed by tuning the magnetic field eigenmode strengths obtained by the magnetic field. The tuning was performed iteratively. Magnetic field ripples in the azimuthal direction were minimized for the design. The candidate magnetic design had five CBs and an iron yoke with center iron poles. The magnet satisfied specifications of homogeneity (0.2 ppm peak-to-peak in 2D placements (the cylindrical coordinate of the radial position R and axial position Z) and less than 1.0 ppm ripples in the ring muon storage volume (0.318 m < R < 0 . 348 m and -0.05 < Z < 0.05 m) with 3.0 T strength and a slightly negative BR (magnetic field radial component) at Z > 0.0 m) for the spiral muon injection from the iron yoke at top.

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

PubMed Central

Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew

2008-01-01

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946

High-pressure microhydraulic actuator

DOEpatents

Mosier, Bruce P [San Francisco, CA; Crocker, Robert W [Fremont, CA; Patel, Kamlesh D [Dublin, CA

2008-06-10

Electrokinetic ("EK") pumps convert electric to mechanical work when an electric field exerts a body force on ions in the Debye layer of a fluid in a packed bed, which then viscously drags the fluid. Porous silica and polymer monoliths (2.5-mm O.D., and 6-mm to 10-mm length) having a narrow pore size distribution have been developed that are capable of large pressure gradients (250-500 psi/mm) when large electric fields (1000-1500 V/cm) are applied. Flowrates up to 200 .mu.L/min and delivery pressures up to 1200 psi have been demonstrated. Forces up to 5 lb-force at 0.5 mm/s (12 mW) have been demonstrated with a battery-powered DC-DC converter. Hydraulic power of 17 mW (900 psi@ 180 uL/min) has been demonstrated with wall-powered high voltage supplies. The force and stroke delivered by an actuator utilizing an EK pump are shown to exceed the output of solenoids, stepper motors, and DC motors of similar size, despite the low thermodynamic efficiency.

Deformable membranes actuated by high mechanical power density composite electroactive polymers using tailored electric field

NASA Technical Reports Server (NTRS)

Bar-Cohen, Y.; Bhattacharya, K.

2003-01-01

The objective of the project was to develop a versatile electroactuator based on a specific class of EAP, conductive polymer, that is capable of developing high forces and displacements in both bending and linear contraction/expansion movements.

Learning in Youth Organizing

ERIC Educational Resources Information Center

Kirshner, Ben

2014-01-01

This response identifies several strengths of the article, "Pushing the Boundaries: What Youth Organizers at Boston's Hyde Square Task Force Have to Teach Us about Civic Engagement" and draws connections to recent developments in sibling fields, including social and emotional learning and internet activism. These developments offer ideas…

Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74

PubMed Central

2017-01-01

The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach. PMID:28286598

The ReaxFF reactive force-field: Development, applications, and future directions

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Acoustic radiation force control: Pulsating spherical carriers.

PubMed

Rajabi, Majid; Mojahed, Alireza

2018-02-01

The interaction between harmonic plane progressive acoustic beams and a pulsating spherical radiator is studied. The acoustic radiation force function exerted on the spherical body is derived as a function of the incident wave pressure and the monopole vibration characteristics (i.e., amplitude and phase) of the body. Two distinct strategies are presented in order to alter the radiation force effects (i.e., pushing and pulling states) by changing its magnitude and direction. In the first strategy, an incident wave field with known amplitude and phase is considered. It is analytically shown that the zero- radiation force state (i.e., radiation force function cancellation) is achievable for specific pulsation characteristics belong to a frequency-dependent straight line equation in the plane of real-imaginary components (i.e., Nyquist Plane) of prescribed surface displacement. It is illustrated that these characteristic lines divide the mentioned displacement plane into two regions of positive (i.e., pushing) and negative (i.e., pulling) radiation forces. In the second strategy, the zero, negative and positive states of radiation force are obtained through adjusting the incident wave field characteristics (i.e., amplitude and phase) which insonifies the radiator with prescribed pulsation characteristics. It is proved that zero radiation force state occurs for incident wave pressure characteristics belong to specific frequency-dependent circles in Nyquist plane of incident wave pressure. These characteristic circles divide the Nyquist plane into two distinct regions corresponding to positive (out of circles) and negative (in the circles) values of radiation force function. It is analytically shown that the maximum amplitude of negative radiation force is exactly equal to the amplitude of the (positive) radiation force exerted upon the sphere in the passive state, by the same incident field. The developed concepts are much more deepened by considering the required power supply for distinct cases of zero, negative and positive radiation force states along with the frequency dependent asymmetry index. In addition, considering the effect of phase difference between the incident wave field and the pulsating object, and its possible variation with respect to spatial position of object, some practical points about the spatial average of generated radiation force, the optimal state of operation, the stability of zero radiation force states and the possibly of precise motion control are discussed. This work would extend the novel concept of smart carriers to and may be helpful for robust single-beam acoustic handling techniques. Furthermore, the shown capability of precise motion control may be considered as a new way toward smart acoustic driven micro-mechanisms and micro-machines. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Evaluation of Interfacial Forces and Bubble-Induced Turbulence Using Direct Numerical Simulation

NASA Astrophysics Data System (ADS)

Feng, Jinyong

High fidelity prediction of multiphase flows is important in a wide range of engineering applications. While some multiphase flow scenarios can be successfully modeled, many questions remain unanswered regarding the interaction between the bubbles and the turbulence, and present significant challenges in the development of closure laws for the multiphase computational fluid dynamics (M-CFD) models. To address these challenges, we propose to evaluate the interfacial forces and bubble-induced turbulence in both laminar and turbulent flow field with direct numerical simulation (DNS) approach. Advanced finite-element based flow solver (PHASTA) with level-set interface tracking method is utilized for these studies. The proportional-integral-derivative (PID) controller is adopted to ensure the statistically steady state bubble position and perform the detailed study of the turbulent field around the bubble. Selected numerical capabilities and post-processing codes are developed to achieve the research goals. The interface tracking approach is verified and validated by comparing the interfacial forces with the experiment-based data and correlations. The sign change of transverse lift force is observed as the bubble becomes more deformable. A new correlation is proposed to predict the behavior of the drag coefficient over the wide range of conditions. The wall effect on the interfacial forces are also investigated. In homogeneous turbulent flow, the effect of bubble deformability, turbulent intensity and relative velocity on the bubble-induced turbulence are analyzed. The presented method and novel results will complement the experimental database, provide insight to the bubbleinduced turbulence mechanism and help the development of M-CFD closure models.

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.

Aeroacoustics. [analysis of properties of sound generated by aerodynamic forces

NASA Technical Reports Server (NTRS)

Goldstein, M., E.

1974-01-01

An analysis was conducted to determine the properties of sound generated by aerodynamic forces or motions originating in a flow, such as the unsteady aerodynamic forces on propellers or by turbulent flows around an aircraft. The acoustics of moving media are reviewed and mathematical models are developed. Lighthill's acoustic analogy and the application to turbulent flows are analyzed. The effects of solid boundaries are calculated. Theories based on the solution of linearized vorticity and acoustic field equations are explained. The effects of nonuniform mean flow on the generation of sound are reported.

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.

Combined free and forced convection heat transfer in magneto fluid mechanic pipe flow

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

Gardner, R.A.; Lo, Y.T.

1977-01-01

A study is made of fully developed, laminar, free-and-forced convection heat transfer in an electrically conducting fluid flowing in an electrically insulated, horizontal, circular pipe in a vertical transverse magnetic field. The normalized magnetofluidmechanic and energy equations are reduced to three coupled partial differential equations by the introduction of a stream function of the secondary flow. A perturbation solution is generated in inverse powers of the Lykoudis number, Ly = M/sup 2//..sqrt..Gr, which yields the influence of the magnetic field on the stream function of the secondary flow, axial velocity profiles, temperature profiles, and Nusselt number. 6 figures, 1 table.

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

The Inertia Reaction Force and Its Vacuum Origin

NASA Astrophysics Data System (ADS)

Rueda, Alfonso; Haisch, Bernard

By means of a covariant approach we show that there must be a contribution to the inertial mass and to the inertial reaction force on an accelerated massive object by the zero-point electromagnetic field. This development does not require any detailed model of the accelerated object other than the knowledge that it interacts electromagnetically. It is shown that inertia can indeed be construed as an opposition of the vacuum fields to any change to the uniform state of motion of an object. Interesting insights originating from this result are discussed. It is argued why the proposed existence of a Higgs field in no way contradicts or is at odds with the above statements. The Higgs field is responsible for assigning mass to elementary particles. It is argued that still the underlying reason for the opposition to acceleration that massive objects present requires an explanation. The explanation proposed here fulfills that requirement.

Some limitations on processing materials in acoustic levitation devices

NASA Technical Reports Server (NTRS)

Oran, W. A.; Witherow, W. K.; Ross, B. B.; Rush, J. E.

1979-01-01

The spot heating of samples, suspended in an acoustic field, was investigated to determine if the technique could be used to process materials. A single axis resonance device operating in air at 25 C with an rms pressure maximum of 160 to 170 db was used in the experiments. The heat flow from a hot object suspended in a levitation node is dominated by the effects of the field, with the heat loss approximately 20 times larger than that due to natural convection. The acoustic forces which suspend the body at a node also serve to eject the heated air. The coupling between the locally heated region around the body and the acoustic field results in instabilities in both the pressure wave and force field. The investigations indicated the extreme difficulties in developing a materials processing device based on acoustic/spot heating for use in a terrestrial environment.

Stochastic Forcing for High-Resolution Regional and Global Ocean and Atmosphere-Ocean Coupled Ensemble Forecast System

NASA Astrophysics Data System (ADS)

Rowley, C. D.; Hogan, P. J.; Martin, P.; Thoppil, P.; Wei, M.

2017-12-01

An extended range ensemble forecast system is being developed in the US Navy Earth System Prediction Capability (ESPC), and a global ocean ensemble generation capability to represent uncertainty in the ocean initial conditions has been developed. At extended forecast times, the uncertainty due to the model error overtakes the initial condition as the primary source of forecast uncertainty. Recently, stochastic parameterization or stochastic forcing techniques have been applied to represent the model error in research and operational atmospheric, ocean, and coupled ensemble forecasts. A simple stochastic forcing technique has been developed for application to US Navy high resolution regional and global ocean models, for use in ocean-only and coupled atmosphere-ocean-ice-wave ensemble forecast systems. Perturbation forcing is added to the tendency equations for state variables, with the forcing defined by random 3- or 4-dimensional fields with horizontal, vertical, and temporal correlations specified to characterize different possible kinds of error. Here, we demonstrate the stochastic forcing in regional and global ensemble forecasts with varying perturbation amplitudes and length and time scales, and assess the change in ensemble skill measured by a range of deterministic and probabilistic metrics.

Correlations Between Magnetic Flux and Levitation Force of HTS Bulk Above a Permanent Magnet Guideway

NASA Astrophysics Data System (ADS)

Huang, Huan; Zheng, Jun; Zheng, Botian; Qian, Nan; Li, Haitao; Li, Jipeng; Deng, Zigang

2017-10-01

In order to clarify the correlations between magnetic flux and levitation force of the high-temperature superconducting (HTS) bulk, we measured the magnetic flux density on bottom and top surfaces of a bulk superconductor while vertically moving above a permanent magnet guideway (PMG). The levitation force of the bulk superconductor was measured simultaneously. In this study, the HTS bulk was moved down and up for three times between field-cooling position and working position above the PMG, followed by a relaxation measurement of 300 s at the minimum height position. During the whole processes, the magnetic flux density and levitation force of the bulk superconductor were recorded and collected by a multipoint magnetic field measurement platform and a self-developed maglev measurement system, respectively. The magnetic flux density on the bottom surface reflected the induced field in the superconductor bulk, while on the top, it reveals the penetrated magnetic flux. The results show that the magnetic flux density and levitation force of the bulk superconductor are in direct correlation from the viewpoint of inner supercurrent. In general, this work is instructive for understanding the connection of the magnetic flux density, the inner current density and the levitation behavior of HTS bulk employed in a maglev system. Meanwhile, this magnetic flux density measurement method has enriched present experimental evaluation methods of maglev system.

Surface structure and stability of partially hydroxylated silica surfaces

DOE PAGES

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

2017-04-04

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

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

Rimsza, J. M.; Jones, R. E.; Criscenti, L. J.

Surface energies of silicates influence crack propagation during brittle fracture and decrease with surface relaxation caused by annealing and hydroxylation. Molecular-level simulations are particularly suited for the investigation of surface processes. In this work, classical MD simulations of silica surfaces are performed with two force fields (ClayFF and ReaxFF) to investigate the effect of force field reactivity on surface structure and energy as a function of surface hydroxylation. An unhydroxylated fracture surface energy of 5.1 J/m 2 is calculated with the ClayFF force field, and 2.0 J/m 2 is calculated for the ReaxFF force field. The ClayFF surface energies aremore » consistent with the experimental results from double cantilever beam fracture tests (4.5 J/m 2), whereas ReaxFF underestimated these surface energies. Surface relaxation via annealing and hydroxylation was performed by creating a low-energy equilibrium surface. Annealing condensed neighboring siloxane bonds increased the surface connectivity, and decreased the surface energies by 0.2 J/m 2 for ClayFF and 0.8 J/m 2 for ReaxFF. Posthydroxylation surface energies decreased further to 4.6 J/m 2 with the ClayFF force field and to 0.2 J/m 2 with the ReaxFF force field. Experimental equilibrium surface energies are ~0.35 J/m 2, consistent with the ReaxFF force field. Although neither force field was capable of replicating both the fracture and equilibrium surface energies reported from experiment, each was consistent with one of these conditions. Furthermore, future computational investigations that rely on accurate surface energy values should consider the surface state of the system and select the appropriate force field.« less

Development of a persistent chemical agent simulation system

NASA Technical Reports Server (NTRS)

1983-01-01

A Persistent Chemical Agent Simulation System was developed (PCASS) to simulate, for force-on-force training exercises, the field environment produced by the presence of persistent chemical agents. Such a simulant system must satisfy several requirements to be of value as a training aid. Specifically, it must provide for realistic training which will generate competency in at least the following areas: (1) detection of the persistent agent presence; (2) proper use of protective equipment and procedures; (3) determination of the extent of contamination; and (4) decontamination of equipment and personnel.

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.

Modeling Field-Scale Phosphorus Transfer: Model Strengths and Weaknesses, Gaps in Knowledge, and the Role for Scientists

USDA-ARS?s Scientific Manuscript database

The ultimate goal of applied research of phosphorus (P) transfer from agricultural fields to surface waters should arguably be to develop and apply mathematical models. There are two primary reasons for this assertion: 1) models formalize our understanding of P transfer and force us to test that und...

Hypothesis on the nature of atmospheric UFOs

NASA Astrophysics Data System (ADS)

Mukharev, L. A.

1991-08-01

A hypothesis is developed according to which the atmospheric UFO phenomenon has an electromagnetic nature. It is suggested that an atmospheric UFO is an agglomeration of charged atmospheric dust within which there exists a slowly damped electromagnetic field. This field is considered to be the source of the observed optical effects and the motive force of the UFO.

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

NASA Astrophysics Data System (ADS)

Yang, Honghua

Driven by the progress in nanotechnology, imaging and spectroscopy tools with nanometer spatial resolution are needed for in situ material characterizations. Near-field optics provides a unique way to selectively excite and detect elementary electronic and vibrational interactions at the nanometer scale, through interactions of light with matter in the near-field region. This dissertation discusses the development and applications of near-field optical imaging techniques, including plasmonic material characterization, optical spectral nano-imaging and magnetic field detection using scattering-type scanning near-field optical microscopy (s-SNOM), and exploring new modalities of optical spectroscopy based on optical gradient force detection. Firstly, the optical dielectric functions of one of the most common plasmonic materials---silver is measured with ellipsometry, and analyzed with the Drude model over a broad spectral range from visible to mid-infrared. This work was motivated by the conflicting results of previous measurements, and the need for accurate values for a wide range of applications of silver in plasmonics, optical antennas, and metamaterials. This measurement provides a reference for dielectric functions of silver used in metamaterials, plasmonics, and nanophotonics. Secondly, I implemented an infrared s-SNOM instrument for spectroscopic nano-imaging at both room temperature and low temperature. As one of the first cryogenic s-SNOM instruments, the novel design concept and key specifications are discussed. Initial low-temperature and high-temperature performances of the instrument are examined by imaging of optical conductivity of vanadium oxides (VO2 and V2O 3) across their phase transitions. The spectroscopic imaging capability is demonstrated on chemical vibrational resonances of Poly(methyl methacrylate) (PMMA) and other samples. The third part of this dissertation explores imaging of optical magnetic fields. As a proof-of-principle, the magnetic near-field response of a linear rod antenna is studied with Babinet's principle. Babinet's principle connects the magnetic field of a structure to the electric field of its complement structure. Using combined far- and near-field spectroscopy, imaging, and theory, I identify magnetic dipole and higher order bright and dark magnetic resonances at mid-infrared frequencies. From resonant length scaling and spatial field distributions, I confirm that the theoretical requirement of Babinet's principle for a structure to be infinitely thin and perfectly conducting is still fulfilled to a good approximation in the mid-infrared. Thus Babinet's principle provides access to spatial and spectral magnetic field properties, leading to targeted design and control of magnetic optical antennas. Lastly, a novel form of nanoscale optical spectroscopy based on mechanical detection of optical gradient force is explored. It is to measure the optical gradient force between induced dipole moments of a sample and an atomic force microscope (AFM) tip. My study provides the theoretical basis in terms of spectral behavior, resonant enhancement, and distance dependence of the optical gradient force from numerical simulations for a coupled nanoparticle model geometry. I show that the optical gradient force is dispersive for local electronic and vibrational resonances, yet can be absorptive for collective polaronic excitations. This spectral behavior together with the distance dependence scaling provides the key characteristics for its measurement and distinction from competing processes such as thermal expansion. Furthermore, I provide a perspective for resonant enhancement and control of optical forces in general.

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

On the effect of moving blade grid on the flow field characteristics

NASA Astrophysics Data System (ADS)

Procházka, Pavel; Uruba, Václav; Pešek, Luděk; Bula, VÍtězslav

2018-06-01

The motivation of this paper is the continual development of the blades for the last stage of the steam turbine. The biggest problem is the slenderness of such blades and the extreme sensitivity to aeroelastic vibrations (flutter) caused by the instabilities present in the flow. This experimental research is dealing with the aeroelastic binding of the moving blades located in the blade grid with the flow field and vice versa. A parallelogram is used to ensure one order of freedom of the blade. The grid has five blades in total, three of them are driven by force control using three shakers. The deviation as well as force response is measured by strain gauges and dynamometers. The flow field statistical as well as dynamical characteristics are measured by optical method Particle Image Velocimetry. The grid is connected to the blow-down wind tunnel with velocity range up to 40 m/s. The aeroelastic binding is investigated in dependency on used actuation frequency and maximal amplitude (the intensity of force actuation) and on different Reynolds numbers. The flow field and the wake behind each individual blade are studied and the maximal interaction is examined for individual inter-blade phase angle of the grid.

Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

PubMed

Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) 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 H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) 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.

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.

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.

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

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

PubMed

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

2012-07-21

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

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.

Understanding the effect of side groups in ionic liquids on carbon-capture properties: a combined experimental and theoretical effort

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

Yan, Fangyong; Lartey, Michael; Damodaran, Krishnan

2013-01-01

Ionic liquids are an emerging class of materials with applications in a variety of fields. Steady progress has been made in the creation of ionic liquids tailored to specific applications. However, the understanding of the underlying structure–property relationships has been slower to develop. As a step in the effort to alleviate this deficiency, the influence of side groups on ionic liquid properties has been studied through an integrated approach utilizing synthesis, experimental determination of properties, and simulation techniques. To achieve this goal, a classical force field in the framework of OPLS/Amber force fields has been developed to predict ionic liquidmore » properties accurately. Cu(I)-catalyzed click chemistry was employed to synthesize triazolium-based ionic liquids with diverse side groups. Values of densities were predicted within 3% of experimental values, whereas self-diffusion coefficients were underestimated by about an order of magnitude though the trends were in excellent agreement, the activation energy calculated in simulation correlates well with experimental values. The predicted Henry coefficient for CO{sub 2} solubility reproduced the experimentally observed trends. This study highlights the importance of integrating experimental and computational approaches in property prediction and materials development, which is not only useful in the development of ionic liquids for CO{sub 2} capture but has application in many technological fields.« less

Understanding the effect of side groups in ionic liquids on carbon-capture properties: a combined experimental and theoretical effort

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

Yan, Fangyong; Lartey, Michael; Damodaran, Krishnan

Ionic liquids are an emerging class of materials with applications in a variety of fields. Steady progress has been made in the creation of ionic liquids tailored to specific applications. However, the understanding of the underlying structure–property relationships has been slower to develop. As a step in the effort to alleviate this deficiency, the influence of side groups on ionic liquid properties has been studied through an integrated approach utilizing synthesis, experimental determination of properties, and simulation techniques. To achieve this goal, a classical force field in the framework of OPLS/Amber force fields has been developed to predict ionic liquidmore » properties accurately. Cu(I)-catalyzed click chemistry was employed to synthesize triazolium-based ionic liquids with diverse side groups. Values of densities were predicted within 3% of experimental values, whereas self-diffusion coefficients were underestimated by about an order of magnitude though the trends were in excellent agreement, the activation energy calculated in simulation correlates well with experimental values. The predicted Henry coefficient for CO{sub 2} solubility reproduced the experimentally observed trends. This study highlights the importance of integrating experimental and computational approaches in property prediction and materials development, which is not only useful in the development of ionic liquids for CO{sub 2} capture but has application in many technological fields.« less

Inflection Points in Magnetic Resonance Imaging Technology-35 Years of Collaborative Research and Development.

PubMed

Wood, Michael L; Griswold, Mark A; Henkelman, Mark; Hennig, Jürgen

2015-09-01

The technology for clinical magnetic resonance imaging (MRI) has advanced with remarkable speed and in such a manner reflecting the influence of 3 forces-collaboration between disciplines, collaboration between academia and industry, and the enabling of software applications by hardware. The forces are evident in the key developments from the past and emerging trends for the future highlighted in this review article. These developments are associated with MRI system attributes, such as wider, shorter, and stronger magnets; specialty magnets and hybrid devices; k space; and the notion that magnetic field gradients perform a Fourier transform on the spatial distribution of magnetization, phased-array coils and parallel imaging, the user interface, the wide range of contrast possible, and applications that exploit motion-induced phase shifts. An attempt is made to show connections between these developments and how the 3 forces mentioned previously will continue to shape the technology used so productively in clinical MRI.

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.

Multimodal Career Education for Nursing Students.

ERIC Educational Resources Information Center

Southern, Stephen; Smith, Robert L.

A multimodal career education model entitled BEST IDEA was field tested as an approach to the problem of retaining skilled nurses in the work force. Using multimodal assessment and intervention strategies derived from the multimodal behavior therapy of Arnold Lazarus, researchers developed an individualized career development assessment and…

Travis Kemper | NREL

Science.gov Websites

| 303-275-4066 Dr. Travis Kemper is a post doctorate researcher in the Computational Science Center. He the University of Florida where he developed reactive force fields. During his post doctorate work at

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.

Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates

NASA Astrophysics Data System (ADS)

Opherden, Lars; Sieger, Max; Pahlke, Patrick; Hühne, Ruben; Schultz, Ludwig; Meledin, Alexander; van Tendeloo, Gustaaf; Nast, Rainer; Holzapfel, Bernhard; Bianchetti, Marco; MacManus-Driscoll, Judith L.; Hänisch, Jens

2016-02-01

The addition of mixed double perovskite Ba2Y(Nb/Ta)O6 (BYNTO) to YBa2Cu3O7-δ (YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3 at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fields c-axis component. The exponent N of the current-voltage characteristics (inversely proportional to the creep rate S) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it.

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.

EXTRAPOLATION OF THE SOLAR CORONAL MAGNETIC FIELD FROM SDO/HMI MAGNETOGRAM BY A CESE-MHD-NLFFF CODE

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

Jiang Chaowei; Feng Xueshang, E-mail: cwjiang@spaceweather.ac.cn, E-mail: fengx@spaceweather.ac.cn

Due to the absence of direct measurement, the magnetic field in the solar corona is usually extrapolated from the photosphere in a numerical way. At the moment, the nonlinear force-free field (NLFFF) model dominates the physical models for field extrapolation in the low corona. Recently, we have developed a new NLFFF model with MHD relaxation to reconstruct the coronal magnetic field. This method is based on CESE-MHD model with the conservation-element/solution-element (CESE) spacetime scheme. In this paper, we report the application of the CESE-MHD-NLFFF code to Solar Dynamics Observatory/Helioseismic and Magnetic Imager (SDO/HMI) data with magnetograms sampled for two activemore » regions (ARs), NOAA AR 11158 and 11283, both of which were very non-potential, producing X-class flares and eruptions. The raw magnetograms are preprocessed to remove the force and then inputted into the extrapolation code. Qualitative comparison of the results with the SDO/AIA images shows that our code can reconstruct magnetic field lines resembling the EUV-observed coronal loops. Most important structures of the ARs are reproduced excellently, like the highly sheared field lines that suspend filaments in AR 11158 and twisted flux rope which corresponds to a sigmoid in AR 11283. Quantitative assessment of the results shows that the force-free constraint is fulfilled very well in the strong-field regions but apparently not that well in the weak-field regions because of data noise and numerical errors in the small currents.« less

Combustion Diagnostic Development and Application. Volume 2

DTIC Science & Technology

1990-11-01

diffusion flames in co- flowing air are experimentally determined . The fuel gases are methane and propane. The inert gases are helium argon and nitrogen. The...at one instant of time. The flame is not intentionally forced either experimentally or computationally. The computational flow field is illuminated via...by buoyant forces . At low and transitional fuel flow rates, the rotation of these outside vortices create a dynamic bulging motion in the flame surface

Developing Realistic Behaviors in Adversarial Agents for Air Combat Simulation

DTIC Science & Technology

1993-12-01

34Building Symbolic Primitives with Continuous Control Rou- tines." Proceedings of the 1st International Conference on Aritificial Intelligence Planning...shortcoming is the minimal Air Force participation in this field. 1-1 Some of the artificial intelligence (AI) personnel at the Air Force Institute of... intelligent system that operates in a moderately complex or unpredictable environment must be reactive. In being reactive the intelligent system must

Developing large-scale forcing data for single-column and cloud-resolving models from the Mixed-Phase Arctic Cloud Experiment

DOE PAGES

Xie, Shaocheng; Klein, Stephen A.; Zhang, Minghua; ...

2006-10-05

[1] This study represents an effort to develop Single-Column Model (SCM) and Cloud-Resolving Model large-scale forcing data from a sounding array in the high latitudes. An objective variational analysis approach is used to process data collected from the Atmospheric Radiation Measurement Program (ARM) Mixed-Phase Arctic Cloud Experiment (M-PACE), which was conducted over the North Slope of Alaska in October 2004. In this method the observed surface and top of atmosphere measurements are used as constraints to adjust the sounding data from M-PACE in order to conserve column-integrated mass, heat, moisture, and momentum. Several important technical and scientific issues related tomore » the data analysis are discussed. It is shown that the analyzed data reasonably describe the dynamic and thermodynamic features of the Arctic cloud systems observed during M-PACE. Uncertainties in the analyzed forcing fields are roughly estimated by examining the sensitivity of those fields to uncertainties in the upper-air data and surface constraints that are used in the analysis. Impacts of the uncertainties in the analyzed forcing data on SCM simulations are discussed. Results from the SCM tests indicate that the bulk features of the observed Arctic cloud systems can be captured qualitatively well using the forcing data derived in this study, and major model errors can be detected despite the uncertainties that exist in the forcing data as illustrated by the sensitivity tests. Lastly, the possibility of using the European Center for Medium-Range Weather Forecasts analysis data to derive the large-scale forcing over the Arctic region is explored.« less

Cavity method for force transmission in jammed disordered packings of hard particles.

PubMed

Bo, Lin; Mari, Romain; Song, Chaoming; Makse, Hernán A

2014-10-07

The force distribution of jammed disordered packings has always been considered a central object in the physics of granular materials. However, many of its features are poorly understood. In particular, analytic relations to other key macroscopic properties of jammed matter, such as the contact network and its coordination number, are still lacking. Here we develop a mean-field theory for this problem, based on the consideration of the contact network as a random graph where the force transmission becomes a constraint satisfaction problem. We can thus use the cavity method developed in the past few decades within the statistical physics of spin glasses and hard computer science problems. This method allows us to compute the force distribution P(f) for random packings of hard particles of any shape, with or without friction. We find a new signature of jamming in the small force behavior P(f) ∼ f(θ), whose exponent has attracted recent active interest: we find a finite value for P(f = 0), along with θ = 0. Furthermore, we relate the force distribution to a lower bound of the average coordination number z[combining macron](μ) of jammed packings of frictional spheres with coefficient μ. This bridges the gap between the two known isostatic limits z[combining macron]c (μ = 0) = 2D (in dimension D) and z[combining macron]c(μ → ∞) = D + 1 by extending the naive Maxwell's counting argument to frictional spheres. The theoretical framework describes different types of systems, such as non-spherical objects in arbitrary dimensions, providing a common mean-field scenario to investigate force transmission, contact networks and coordination numbers of jammed disordered packings.

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.

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.

Effects of Traveling Magnetic Field on Dynamics of Solidification

NASA Technical Reports Server (NTRS)

2003-01-01

The Lorentz body force induced in electrically conducting fluids can be utilized for a number of materials processing technologies. An application of strong static magnetic fields can be beneficial for damping convection present during solidification. On the other hand, alternating magnetic fields can be used to reduce as well as to enhance convection. However, only special types of time dependent magnetic fields can induce a non-zero time averaged Lorentz force needed for convection control. One example is the rotating magnetic field. This field configuration induces a swirling flow in circular containers. Another example of a magnetic field configuration is the traveling magnetic field (TMF). It utilizes axisymmetric magnetostatic waves. This type of field induces an axial recirculating flow that can be advantageous for controlling axial mass transport, such as during solidification in long cylindrical tubes. Incidentally, this is the common geometry for crystal growth research. The Lorentz force induced by TMF can potentially counter-balance the buoyancy force, diminishing natural convection, or even setting up the flow in reverse direction. Crystal growth process in presence of TMF can be then significantly modified. Such properties as the growth rate, interface shape and macro segregation can be affected and optimized. Melt homogenization is the other potential application of TMF. It is a necessary step prior to solidification. TMF can be attractive for this purpose, as it induces a basic flow along the axis of the ampoule. TMF can be a practical alloy mixing method especially suited for solidification research in space. In the theoretical part of this work, calculations of the induced Lorentz force in the whole frequency range have been completed. The basic flow characteristics for the finite cylinder geometry are completed and first results on stability analysis for higher Reynolds numbers are obtained. A theoretical model for TMF mixing is also developed. In the experimental part, measurements of flow induced by TMF in a column of mercury (Hg) are presented. Also, an alloy mixing of Bi-Sn of the eutectic composition is demonstrated. A traveling magnetic field of 4mT at 3kHz applied for 120 minutes is found to be sufficient to homogenize an alloy enclosed in a 1cm diameter and 12 cm long tube.

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.

Force-Free Magnetic Fields Calculated from Automated Tracing of Coronal Loops with AIA/SDO

NASA Astrophysics Data System (ADS)

Aschwanden, M. J.

2013-12-01

One of the most realistic magnetic field models of the solar corona is a nonlinear force-free field (NLFFF) solution. There exist about a dozen numeric codes that compute NLFFF solutions based on extrapolations of photospheric vector magnetograph data. However, since the photosphere and lower chromosphere is not force-free, a suitable correction has to be applied to the lower boundary condition. Despite of such "pre-processing" corrections, the resulting theoretical magnetic field lines deviate substantially from observed coronal loop geometries. - Here we developed an alternative method that fits an analytical NLFFF approximation to the observed geometry of coronal loops. The 2D coordinates of the geometry of coronal loop structures observed with AIA/SDO are traced with the "Oriented Coronal CUrved Loop Tracing" (OCCULT-2) code, an automated pattern recognition algorithm that has demonstrated the fidelity in loop tracing matching visual perception. A potential magnetic field solution is then derived from a line-of-sight magnetogram observed with HMI/SDO, and an analytical NLFFF approximation is then forward-fitted to the twisted geometry of coronal loops. We demonstrate the performance of this magnetic field modeling method for a number of solar active regions, before and after major flares observed with SDO. The difference of the NLFFF and the potential field energies allows us then to compute the free magnetic energy, which is an upper limit of the energy that is released during a solar flare.

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…

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.

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

PubMed

Davidson, Lance A

2017-05-19

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

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.

Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

PubMed Central

Xu, Dong; Zhang, Yang

2012-01-01

Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

The development of pressure across membranes in Donnan systems

PubMed Central

Ilani, Asher

2015-01-01

The pressure that develops between the two sides of a Donnan system is equal to the difference between the osmotic values of the two solutions, even though permeant ions may constitute a significant part of that difference. This is amply documented for the case of membranes that allow water movement through them by single molecules diffusing in isolation or in series through specific proteins (such as aquaporins). In this article, the development of pressure was analysed for a system in which membranes contain a few bulk aqueous pores that prevent charged polymers from entering them due to their size. It is shown analytically that the pressure that develops by the action of the electric field on the net charges in the pores is equal to the difference in the osmotic values of the solutions contributed by the permeant ions. Thus, the sum of the pressures that develop in the system due to the action of the electric field in the pores (a pushing force) and the concentration of the impermeant polymers at the interface (a sucking force), accounts for the total colloid osmotic pressure in these systems. PMID:26456154

Ponderomotive Force in the Presence of Electric Fields

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Krivorutsky, E. N.

2013-01-01

This paper presents averaged equations of particle motion in an electromagnetic wave of arbitrary frequency with its wave vector directed along the ambient magnetic field. The particle is also subjected to an E cross B drift and a background electric field slowly changing in space and acting along the magnetic field line. The fields, wave amplitude, and the wave vector depend on the coordinate along the magnetic field line. The derivations of the ponderomotive forces are done by assuming that the drift velocity in the ambient magnetic field is comparable to the particle velocity. Such a scenario leads to new ponderomotive forces, dependent on the wave magnetic field intensity, and, as a result, to the additional energy exchange between the wave and the plasma particles. It is found that the parallel electric field can lead to the change of the particle-wave energy exchange rate comparable to that produced by the previously discussed ponderomotive forces.

Professional Development: Sorting through the Jumble to Achieve Success

ERIC Educational Resources Information Center

Education Week, 2010

2010-01-01

Few in the education field discount the eminently logical idea that teachers should be supported in the continuous improvement of their craft. But as a term for describing ongoing training investments in the teaching force, "professional development" has become both ubiquitous and all but meaningless. Though frequently invoked by…

Some Basic Concepts of Wave-Particle Interactions in Collisionless Plasmas

NASA Technical Reports Server (NTRS)

Lakhina, Gurbax S.; Tsurutani, Bruce T.

1997-01-01

The physical concepts of wave-particle interactions in a collisionless plasma are developed from first principles. Using the Lorentz force, starting with the concepts of gyromotion, particle mirroring and the loss-cone, normal and anomalous cyclotron resonant interactions, pitch-angle scattering, and cross-field diffusion are developed.

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

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

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

Manipulation of particles by weak forces

NASA Technical Reports Server (NTRS)

Adler, M. S.; Savkar, S. D.; Summerhayes, H. R.

1972-01-01

Quantitative relations between various force fields and their effects on the motion of particles of various sizes and physical characteristics were studied. The forces considered were those derived from light, heat, microwaves, electric interactions, magnetic interactions, particulate interactions, and sound. A physical understanding is given of the forces considered as well as formulae which express how the size of the force depends on the physical and electrical properties of the particle. The drift velocity in a viscous fluid is evaluated as a function of initial acceleration and the effects of thermal random motion are considered. A means of selectively sorting or moving particles by choosing a force system and/or environment such that the particle of interest reacts uniquely was developed. The forces considered and a demonstration of how the initial acceleration, drift velocity, and ultimate particle density distribution is affected by particle, input, and environmental parameters are tabulated.

GeoFORCE Texas: An Outreach Program that is Increasing the Number and Diversity of Students Completing STEM Degrees and Entering the Workforce

NASA Astrophysics Data System (ADS)

Snow, E.; Moore, S. L.

2014-12-01

GeoFORCE Texas is an outreach program of the Jackson School of Geosciences, University of Texas at Austin. Established in 2005 with the goal of increasing the number and diversity of students studying geosciences and engineering and entering the high-tech workforce, GeoFORCE has been highly successful. Key elements to that success will be presented here. GeoFORCE targets bright students in rural and inner-city schools where they are generally not academically challenged. Every summer throughout high school we take them on geologic field trips all over the country. In 2014, GeoFORCE led 15 field academies for about 600 students. The program is rigorous and academic. We emphasize college-level thinking skills. Because it is a 4-year program, they have a pretty good grounding in physical geology by the time they graduate. More importantly, they develop confidence in their ability to handle college, and a strong motivation to earn a college degree. GeoFORCE students are mostly minority (85%) and more than half will be the first in their family to graduate from college. GeoFORCE students exceed national averages in rates of going to college (97%), majoring in STEM fields (66%), majoring in geosciences (15%) and engineering (13%), and graduating from college (~85%). GeoFORCE is a public/private partnership and a workforce-focused program. The Jackson School funds staff and operating expenses (37%). Money for student programs comes from private industry (44%), state and federal grants (14%), and foundations and individual donors (5%). Our corporate partners are in the energy sector. In addition to funding, corporate sponsors attend the summer field programs, mentor GeoFORCE students, and provide opportunities for the students to visit the companies. As our students move toward college graduation, our industry and government partners have begun to hire them as interns. GeoFORCE graduates are now entering the workforce. Our first two cohorts are 4 and 5 years past high school graduation. That group of 155 students boasts 70 college graduates and another 60 still pursuing degrees. There are 19 geoscience majors and 9 engineers. They are also contributing to the body of science with a growing list of publications, including at least one at this meeting.

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.

Improved classical united-atom force field for imidazolium-based ionic liquids: tetrafluoroborate, hexafluorophosphate, methylsulfate, trifluoromethylsulfonate, acetate, trifluoroacetate, and bis(trifluoromethylsulfonyl)amide.

PubMed

Zhong, Xiujuan; Liu, Zhiping; Cao, Dapeng

2011-08-25

A cost-effective, classical united-atom (UA) force field for ionic liquids (ILs) was proposed, which can be used in simulations of ILs composed by 1-alkyl-3-methyl-imidazolium cations ([C(n)mim](+)) and seven kinds of anions, including tetrafluoroborate ([BF(4)](-)), hexafluorophosphate ([PF(6)](-)), methylsulfate ([CH(3)SO(4)](-)), trifluoromethylsulfonate ([CF(3)SO(3)](-)), acetate ([CH(3)CO(2)](-)), trifluoroacetate ([CF(3)CO(2)](-)), and bis(trifluoromethylsulfonyl)amide ([NTf(2)](-)). The same strategy in our previous work (J. Phys. Chem. B 2010, 114, 4572) was used to parametrize the force field, in which the effective atom partial charges are fitted by the electrostatic potential surface (ESP) of ion pair dimers to account for the overall effects of polarization in ILs. The total charges (absolute values) on the cation/anion are in the range of 0.64-0.75, which are rescaled to 0.8 for all kinds of ions by a compromise between transferability and accuracy. Extensive molecular dynamics (MD) simulations were performed over a wide range of temperatures to validate the force field, especially on the enthalpies of vaporization (ΔH(vap)) and transport properties, including the self-diffusion coefficient and shear viscosity. The liquid densities were predicted very well for all of the ILs studied in this work with typical deviations of less than 1%. The simulated ΔH(vap) at 298 and 500 K are also in good agreement with the measured values by different experimental methods, with a slight overestimation of about 5 kJ/mol. The influence of ΔC(p) (the difference between the molar heat capacity at constant pressure of the gas and that of liquid) on the calculation of ΔH(vap) is also discussed. The transport coefficients were estimated by the equilibrium MD method using 20-60 ns trajectories to improve the sampling. The proposed force field gives a good description of the self-diffusion coefficients and shear viscosities, which is comparable to the recently developed polarizable force field. Although slightly lower dynamics is found in simulations by our force field, the order of magnitude of the self-diffusion coefficient and viscosity are reproduced for all the ILs very well over a wide temperature range. The largest underestimation of the self-diffusion coefficient is about one-third of the experimental values, while the largest overestimation of the viscosity is about two times the experimental values. © 2011 American Chemical Society

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

NASA Astrophysics Data System (ADS)

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

2011-01-01

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

Students' Development of Representational Competence Through the Sense of Touch

NASA Astrophysics Data System (ADS)

Magana, Alejandra J.; Balachandran, Sadhana

2017-06-01

Electromagnetism is an umbrella encapsulating several different concepts like electric current, electric fields and forces, and magnetic fields and forces, among other topics. However, a number of studies in the past have highlighted the poor conceptual understanding of electromagnetism concepts by students even after instruction. This study aims to identify novel forms of "hands-on" instruction that can result in representational competence and conceptual gain. Specifically, this study aimed to identify if the use of visuohaptic simulations can have an effect on student representations of electromagnetic-related concepts. The guiding questions is How do visuohaptic simulations influence undergraduate students' representations of electric forces? Participants included nine undergraduate students from science, technology, or engineering backgrounds who participated in a think-aloud procedure while interacting with a visuohaptic simulation. The think-aloud procedure was divided in three stages, a prediction stage, a minimally visual haptic stage, and a visually enhanced haptic stage. The results of this study suggest that students' accurately characterized and represented the forces felt around a particle, line, and ring charges either in the prediction stage, a minimally visual haptic stage or the visually enhanced haptic stage. Also, some students accurately depicted the three-dimensional nature of the field for each configuration in the two stages that included a tactile mode, where the point charge was the most challenging one.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Electrodeless plasma thrusters for spacecraft: A review

NASA Astrophysics Data System (ADS)

Bathgate, S. N.; Bilek, M. M. M.; McKenzie, D. R.

2017-08-01

The physics of electrodeless electric thrusters that use directed plasma to propel spacecraft without employing electrodes subject to plasma erosion is reviewed. Electrodeless plasma thrusters are potentially more durable than presently deployed thrusters that use electrodes such as gridded ion, Hall thrusters, arcjets and resistojets. Like other plasma thrusters, electrodeless thrusters have the advantage of reduced fuel mass compared to chemical thrusters that produce the same thrust. The status of electrodeless plasma thrusters that could be used in communications satellites and in spacecraft for interplanetary missions is examined. Electrodeless thrusters under development or planned for deployment include devices that use a rotating magnetic field; devices that use a rotating electric field; pulsed inductive devices that exploit the Lorentz force on an induced current loop in a plasma; devices that use radiofrequency fields to heat plasmas and have magnetic nozzles to accelerate the hot plasma and other devices that exploit the Lorentz force. Using metrics of specific impulse and thrust efficiency, we find that the most promising designs are those that use Lorentz forces directly to expel plasma and those that use magnetic nozzles to accelerate plasma.

A magnetohydrodynamic theory of coronal loop transients

NASA Technical Reports Server (NTRS)

Yeh, T.

1982-01-01

The physical and geometrical characteristics of solar coronal loop transients are described in an MHD model based on Archimedes' MHD buoyancy force. The theory was developed from interpretation of coronagraphic data, particularly from Skylab. The brightness of a loop is taken to indicate the electron density, and successive pictures reveal the electron enhancement in different columns. The forces which lift the loop off the sun surface are analyzed as an MHD buoyancy force affecting every mass element by imparting an inertial force necessary for heliocentrifugal motion. Thermal forces are responsible for transferring the ambient stress to the interior of the loop to begin the process. The kinematic and hydrostatic buoyancy overcome the gravitational force, and a flux rope can then curve upward, spiralling like a corkscrew with varying cross section around the unwinding solar magnetic field lines.

Error analysis regarding the calculation of nonlinear force-free field

NASA Astrophysics Data System (ADS)

Liu, S.; Zhang, H. Q.; Su, J. T.

2012-02-01

Magnetic field extrapolation is an alternative method to study chromospheric and coronal magnetic fields. In this paper, two semi-analytical solutions of force-free fields (Low and Lou in Astrophys. J. 352:343, 1990) have been used to study the errors of nonlinear force-free (NLFF) fields based on force-free factor α. Three NLFF fields are extrapolated by approximate vertical integration (AVI) Song et al. (Astrophys. J. 649:1084, 2006), boundary integral equation (BIE) Yan and Sakurai (Sol. Phys. 195:89, 2000) and optimization (Opt.) Wiegelmann (Sol. Phys. 219:87, 2004) methods. Compared with the first semi-analytical field, it is found that the mean values of absolute relative standard deviations (RSD) of α along field lines are about 0.96-1.19, 0.63-1.07 and 0.43-0.72 for AVI, BIE and Opt. fields, respectively. While for the second semi-analytical field, they are about 0.80-1.02, 0.67-1.34 and 0.33-0.55 for AVI, BIE and Opt. fields, respectively. As for the analytical field, the calculation error of <| RSD|> is about 0.1˜0.2. It is also found that RSD does not apparently depend on the length of field line. These provide the basic estimation on the deviation of extrapolated field obtained by proposed methods from the real force-free field.

High shear rate flow in a linear stroke magnetorheological energy absorber

NASA Astrophysics Data System (ADS)

Hu, W.; Wereley, N. M.; Hiemenz, G. J.; Ngatu, G. T.

2014-05-01

To provide adaptive stroking load in the crew seats of ground vehicles to protect crew from blast or impact loads, a magnetorheological energy absorber (MREA) or shock absorber was developed. The MREA provides appropriate levels of controllable stroking load for different occupant weights and peak acceleration because the viscous stroking load generated by the MREA force increases with velocity squared, thereby reducing its controllable range at high piston velocity. Therefore, MREA behavior at high piston velocity is analyzed and validated experimentally in order to investigate the effects of velocity and magnetic field on MREA performance. The analysis used to predict the MREA force as a function of piston velocity squared and applied field is presented. A conical fairing is mounted to the piston head of the MREA in order reduce predicted inlet flow loss by 9% at nominal velocity of 8 m/s, which resulted in a viscous force reduction of nominally 4%. The MREA behavior is experimentally measured using a high speed servo-hydraulic testing system for speeds up to 8 m/s. The measured MREA force is used to validate the analysis, which captures the transient force quite accurately, although the peak force is under-predicted at the peak speed of 8 m/s.

Design, analysis and test verification of advanced encapsulation systems

NASA Technical Reports Server (NTRS)

Garcia, A., III

1984-01-01

Investigations into transparent conductive polymers were begun. Polypyrrole was electrochemically deposited, but the film characteristics were poor. A proprietary polymer material supplied by Polaroid was evaluated and showed promise as a readily processable material. A method was developed for calculating the magnitude and location of the maximum electric field for the family of solar-cell-like shapes. A method for calculating the lines of force for three dimensional electric fields was developed and applied to a geometry of interest to the photovoltaic program.

Planning and management of the Nido Reef Complex Oil Field development, Philippines

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

Harry, R.Y.

1981-01-01

As Operator for the Northeast Palawan consortium, Philippines-Cities Service, Inc., commenced the Philippines first commercial offshore oil production from the Nido Reef Complex Oil Field on February 1, 1979, some 11 months after a decision by management to start development. The relative speed at which design, fabrication, and construction were accomplished is attributed to the use of the concepts of project planning, task force approach, and project management. This paper presents the above concepts as applied to the Nido Complex.

Volcano ecology: flourishing on the flanks of Mount St. Helens

Treesearch

Rhonda Mazza; Charlie Crisafulli

2016-01-01

Mount St. Helens’ explosive eruption on May 18, 1980, was a pivotal moment in the field of disturbance ecology. The subsequent sustained, integrated research effort has shaped the development of volcano ecology, an emerging field of focused research. Excessive heat, burial, and impact force are some of the disturbance mechanisms following an eruption. They are also...

Air Force Energy Program Policy Memorandum

DTIC Science & Technology

2009-06-16

Critical Asset Prioritization Methodology ( CAPM ) tool Manage costs. 3.4.2.5. Metrics Percentage of alternative/renewable fuel used for aviation fuel...supporting critical assets residing on military installations Field the Critical Asset Prioritization Methodology ( CAPM ) tool by Spring 2008. This CAPM ...Increase the number of flexible fuel systems • Identify/develop privately financed/operated energy production on Air Bases • Field the Critical

A physical model for low-frequency electromagnetic induction in the near field based on direct interaction between transmitter and receiver electrons

PubMed Central

Smith, Ray T.; Jjunju, Fred P. M.; Young, Iain S.; Taylor, Stephen

2016-01-01

A physical model of electromagnetic induction is developed which relates directly the forces between electrons in the transmitter and receiver windings of concentric coaxial finite coils in the near-field region. By applying the principle of superposition, the contributions from accelerating electrons in successive current loops are summed, allowing the peak-induced voltage in the receiver to be accurately predicted. Results show good agreement between theory and experiment for various receivers of different radii up to five times that of the transmitter. The limitations of the linear theory of electromagnetic induction are discussed in terms of the non-uniform current distribution caused by the skin effect. In particular, the explanation in terms of electromagnetic energy and Poynting’s theorem is contrasted with a more direct explanation based on variable filament induction across the conductor cross section. As the direct physical model developed herein deals only with forces between discrete current elements, it can be readily adapted to suit different coil geometries and is widely applicable in various fields of research such as near-field communications, antenna design, wireless power transfer, sensor applications and beyond. PMID:27493580

A physical model for low-frequency electromagnetic induction in the near field based on direct interaction between transmitter and receiver electrons.

PubMed

Smith, Ray T; Jjunju, Fred P M; Young, Iain S; Taylor, Stephen; Maher, Simon

2016-07-01

A physical model of electromagnetic induction is developed which relates directly the forces between electrons in the transmitter and receiver windings of concentric coaxial finite coils in the near-field region. By applying the principle of superposition, the contributions from accelerating electrons in successive current loops are summed, allowing the peak-induced voltage in the receiver to be accurately predicted. Results show good agreement between theory and experiment for various receivers of different radii up to five times that of the transmitter. The limitations of the linear theory of electromagnetic induction are discussed in terms of the non-uniform current distribution caused by the skin effect. In particular, the explanation in terms of electromagnetic energy and Poynting's theorem is contrasted with a more direct explanation based on variable filament induction across the conductor cross section. As the direct physical model developed herein deals only with forces between discrete current elements, it can be readily adapted to suit different coil geometries and is widely applicable in various fields of research such as near-field communications, antenna design, wireless power transfer, sensor applications and beyond.

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.

Controllable deformation of salt water-filled carbon nanotubes using an electric field with application to molecular sieving

NASA Astrophysics Data System (ADS)

Ye, Hongfei; Zheng, Yonggang; Zhang, Zhongqiang; Zhang, Hongwu; Chen, Zhen

2016-08-01

Precisely controlling the deformation of carbon nanotubes (CNTs) has practical application in the development of nanoscale functional devices, although it is a challenging task. Here, we propose a novel method to guide the deformation of CNTs through filling them with salt water and applying an electric field. With the electric field along the axial direction, the height of CNTs is enlarged by the axial electric force due to the internal ions and polar water molecules. Under an electric field with two mutually orthogonal components, the transverse electric force could further induce the bending deformation of CNTs. Based on the classical rod and beam theories, two mechanical models are constructed to verify and quantitatively describe the relationships between the tension and bending deformations of CNTs and the electric field intensity. Moreover, by means of the electric field-driven tension behavior of CNTs, we design a stretchable molecular sieve to control the flow rate of mixed gas and collect a single high-purity gas. The present work opens up new avenues in the design and fabrication of nanoscale controlling units.

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

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

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de; Kibies, Patrick

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

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

PubMed

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

2016-04-14

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

Spinmotive force due to domain wall motion in high field regime

NASA Astrophysics Data System (ADS)

Ieda, Jun'ichi; Yamane, Yuta; Maekawa, Sadamichi

2012-02-01

Spinmotive force associated with a moving vortex domain wall is investigated numerically. Dynamics of magnetization textures such as a domain wall exerts a non-conservative spin-force on conduction electrons [1], offering a new concept of magnetic devices [2]. This spinmotive force in permalloy nanowires has been detected by voltage measurement [3] where magnitude of the signal is limited less than 500 nV. Theoretically it is suggested that the spinmotive force signal increases as a function of external magnetic fields. At higher magnetic fields, however, the wall propagation mode becomes rather chaotic involving transformations of the wall structure and it remains to be seen how the spinmotive force appears. Numerical simulations show that the spinmotive force scales with the field even in a field range where the wall motion is no longer associated coherent precession. This feature has been tested in a recent experiment [4]. Further enhancement of the spinmotive force is explored by designing ferromagnetic nanostructures [5] and materials. [1] S. Barnes and S. Maekawa, PRL (2007). [2] S. Barnes, J. Ieda, and S. Maekawa, APL (2006). [3] S. A. Yang et al., PRL (2009). [4] M. Hayashi, J. Ieda et al., submitted. [5] Y. Yamane, J. Ieda et al., APEX (2011).

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

PubMed

Marston, Philip L; Zhang, Likun

2017-05-01

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

Systematic Validation of Protein Force Fields against Experimental Data

PubMed Central

Eastwood, Michael P.; Dror, Ron O.; Shaw, David E.

2012-01-01

Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field—the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins—one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins. PMID:22384157

77 FR 14006 - Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-08

... DEPARTMENT OF DEFENSE Department of the Air Force Record of Decision for the Military Housing Privatization Initiative Hurlburt Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement... Field and Eglin Air Force Base, Florida, Final Environmental Impact Statement (FEIS). The MHPI ROD...

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

Magnetic field exposure stiffens regenerating plant protoplast cell walls.

PubMed

Haneda, Toshihiko; Fujimura, Yuu; Iino, Masaaki

2006-02-01

Single suspension-cultured plant cells (Catharanthus roseus) and their protoplasts were anchored to a glass plate and exposed to a magnetic field of 302 +/- 8 mT for several hours. Compression forces required to produce constant cell deformation were measured parallel to the magnetic field by means of a cantilever-type force sensor. Exposure of intact cells to the magnetic field did not result in any changes within experimental error, while exposure of regenerating protoplasts significantly increased the measured forces and stiffened regenerating protoplasts. The diameters of intact cells or regenerating protoplasts were not changed after exposure to the magnetic field. Measured forces for regenerating protoplasts with and without exposure to the magnetic field increased linearly with incubation time, with these forces being divided into components based on the elasticity of synthesized cell walls and cytoplasm. Cell wall synthesis was also measured using a cell wall-specific fluorescent dye, and no changes were noted after exposure to the magnetic field. Analysis suggested that exposure to the magnetic field roughly tripled the Young's modulus of the newly synthesized cell wall without any lag.

Structural learning in feedforward and feedback control.

PubMed

Yousif, Nada; Diedrichsen, Jörn

2012-11-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control.

Structural learning in feedforward and feedback control

PubMed Central

Diedrichsen, Jörn

2012-01-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control. PMID:22896725

High Reynolds number turbulence model of rotating shear flows

NASA Astrophysics Data System (ADS)

Masuda, S.; Ariga, I.; Koyama, H. S.

1983-09-01

A Reynolds stress closure model for rotating turbulent shear flows is developed. Special attention is paid to keeping the model constants independent of rotation. First, general forms of the model of a Reynolds stress equation and a dissipation rate equation are derived, the only restrictions of which are high Reynolds number and incompressibility. The model equations are then applied to two-dimensional equilibrium boundary layers and the effects of Coriolis acceleration on turbulence structures are discussed. Comparisons with the experimental data and with previous results in other external force fields show that there exists a very close analogy between centrifugal, buoyancy and Coriolis force fields. Finally, the model is applied to predict the two-dimensional boundary layers on rotating plane walls. Comparisons with existing data confirmed its capability of predicting mean and turbulent quantities without employing any empirical relations in rotating fields.

The Russo-Japanese War of 1904-1905 and the Evolution of Operational Art

DTIC Science & Technology

2013-12-10

exhibited operational art as he could conceptualize the operation, and plan appropriate resources for an operation. The French army corps was able to...to manage massive forces and developed the corps under a Field Marshall that could maneuver and sustain until more French forces could arrive...Napoleon. Japan adopted the Western general staff model used by the French and Prussian armies to ensure effective management of armies at the

Annual Report to the President and the Congress

DTIC Science & Technology

2004-01-01

planning process has determined is needed to meet the military tasks as- signed to the Department by the President in his national security strategy...Commands" document, which formally as- signs forces to combatant commanders. The Global Force Management Process subsumes two developmen- tal measures...www.t2net.org), which was signed by Deputy Secretary of Defense Paul Wolfowitz on June 10, 2003, is a road map to developing and fielding dynamic

Task-Related Job Reading Inventory: Development and Field Trial of a Prototype.

DTIC Science & Technology

1983-07-01

or other data are used for any purpose other than in connection with a definitely Government -related procurement , the United States Government incurs...unlimited. C E S LABORATORY AIR FORCE SYSTEMS COMMAND BROOKS AIR FORCE BASE,TEXAS 78235 83 07 26 153 NOTICE When Government drawings, specifications...no responsibility or any obligation whatsoever. The fact that the Government may have formulated or in any way supplied the said drawings

Training Chrysalis: Applications of Special Forces Training in the Development of the Objective Force

DTIC Science & Technology

2003-06-06

refers constantly to an “adaptive enemy,” that is, one that will ferret out, analyze , and then exploit weaknesses within the OF systems , technologies...Department of the Army EAI Executive Agent Instruction FCS Future Combat System FTX Field Training Exercise G-chief Guerrilla Chief, leader of an...and lighter Army battle platforms will still have greater lethality and survivability than current systems . The information revolution will be

Electrorotation and levitation of cells and colloidal particles

PubMed Central

Foster, Kenneth R.; Sauer, Friedrich A.; Schwan, Herman P.

1992-01-01

We review dielectrophoretic forces on cells and colloidal particles, emphasizing their use for manipulating and characterizing the electrical properties of suspended particles. Compared with dielectric spectroscopy, these methods offer a measure of independence from electrode artifacts and mixture theory. On the assumption that the particles can be modeled as uniform dielectric objects with effective dielectric properties, a simple theory can be developed for the frequency variation in the field-induced forces. For particles exhibiting counterion polarization, dielectrophoretic forces differ considerably from predictions of this theory at low frequencies, apparently because of double layer phenomena. PMID:19431839

Improved treatment of nucleosides and nucleotides in the OPLS-AA force field

NASA Astrophysics Data System (ADS)

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.

2017-09-01

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.

Instrumentation and control of harmonic oscillators via a single-board microprocessor-FPGA device.

PubMed

Picone, Rico A R; Davis, Solomon; Devine, Cameron; Garbini, Joseph L; Sidles, John A

2017-04-01

We report the development of an instrumentation and control system instantiated on a microprocessor-field programmable gate array (FPGA) device for a harmonic oscillator comprising a portion of a magnetic resonance force microscope. The specific advantages of the system are that it minimizes computation, increases maintainability, and reduces the technical barrier required to enter the experimental field of magnetic resonance force microscopy. Heterodyne digital control and measurement yields computational advantages. A single microprocessor-FPGA device improves system maintainability by using a single programming language. The system presented requires significantly less technical expertise to instantiate than the instrumentation of previous systems, yet integrity of performance is retained and demonstrated with experimental data.

Impingement effect of service module reaction control system engine plumes. Results of service module reaction control system plume model force field application to an inflight Skylab mission proximity operation situation with the inflight Skylab response

NASA Technical Reports Server (NTRS)

Lobb, J. D., Jr.

1978-01-01

Plume impingement effects of the service module reaction control system thruster firings were studied to determine if previous flight experience would support the current plume impingement model for the orbiter reaction control system engines. The orbiter reaction control system is used for rotational and translational maneuvers such as those required during rendezvous, braking, docking, and station keeping. Therefore, an understanding of the characteristics and effects of the plume force fields generated by the reaction control system thruster firings were examined to develop the procedures for orbiter/payload proximity operations.

Instrumentation and control of harmonic oscillators via a single-board microprocessor-FPGA device

NASA Astrophysics Data System (ADS)

Picone, Rico A. R.; Davis, Solomon; Devine, Cameron; Garbini, Joseph L.; Sidles, John A.

2017-04-01

We report the development of an instrumentation and control system instantiated on a microprocessor-field programmable gate array (FPGA) device for a harmonic oscillator comprising a portion of a magnetic resonance force microscope. The specific advantages of the system are that it minimizes computation, increases maintainability, and reduces the technical barrier required to enter the experimental field of magnetic resonance force microscopy. Heterodyne digital control and measurement yields computational advantages. A single microprocessor-FPGA device improves system maintainability by using a single programming language. The system presented requires significantly less technical expertise to instantiate than the instrumentation of previous systems, yet integrity of performance is retained and demonstrated with experimental data.

Mixtures of amino-acid based ionic liquids and water.

PubMed

Chaban, Vitaly V; Fileti, Eudes Eterno

2015-09-01

New ionic liquids (ILs) involving increasing numbers of organic and inorganic ions are continuously being reported. We recently developed a new force field; in the present work, we applied that force field to investigate the structural properties of a few novel imidazolium-based ILs in aqueous mixtures via molecular dynamics (MD) simulations. Using cluster analysis, radial distribution functions, and spatial distribution functions, we argue that organic ions (imidazolium, deprotonated alanine, deprotonated methionine, deprotonated tryptophan) are well dispersed in aqueous media, irrespective of the IL content. Aqueous dispersions exhibit desirable properties for chemical engineering. The ILs exist as ion pairs in relatively dilute aqueous mixtures (10 mol%), while more concentrated mixtures feature a certain amount of larger ionic aggregates.

Links between the charge model and bonded parameter force constants in biomolecular force fields

NASA Astrophysics Data System (ADS)

Cerutti, David S.; Debiec, Karl T.; Case, David A.; Chong, Lillian T.

2017-10-01

The ff15ipq protein force field is a fixed charge model built by automated tools based on the two charge sets of the implicitly polarized charge method: one set (appropriate for vacuum) for deriving bonded parameters and the other (appropriate for aqueous solution) for running simulations. The duality is intended to treat water-induced electronic polarization with an understanding that fitting data for bonded parameters will come from quantum mechanical calculations in the gas phase. In this study, we compare ff15ipq to two alternatives produced with the same fitting software and a further expanded data set but following more conventional methods for tailoring bonded parameters (harmonic angle terms and torsion potentials) to the charge model. First, ff15ipq-Qsolv derives bonded parameters in the context of the ff15ipq solution phase charge set. Second, ff15ipq-Vac takes ff15ipq's bonded parameters and runs simulations with the vacuum phase charge set used to derive those parameters. The IPolQ charge model and associated protocol for deriving bonded parameters are shown to be an incremental improvement over protocols that do not account for the material phases of each source of their fitting data. Both force fields incorporating the polarized charge set depict stable globular proteins and have varying degrees of success modeling the metastability of short (5-19 residues) peptides. In this particular case, ff15ipq-Qsolv increases stability in a number of α -helices, correctly obtaining 70% helical character in the K19 system at 275 K and showing appropriately diminishing content up to 325 K, but overestimating the helical fraction of AAQAA3 by 50% or more, forming long-lived α -helices in simulations of a β -hairpin, and increasing the likelihood that the disordered p53 N-terminal peptide will also form a helix. This may indicate a systematic bias imparted by the ff15ipq-Qsolv parameter development strategy, which has the hallmarks of strategies used to develop other popular force fields, and may explain some of the need for manual corrections in this force fields' evolution. In contrast, ff15ipq-Vac incorrectly depicts globular protein unfolding in numerous systems tested, including Trp cage, villin, lysozyme, and GB3, and does not perform any better than ff15ipq or ff15ipq-Qsolv in tests on short peptides. We analyze the free energy surfaces of individual amino acid dipeptides and the electrostatic potential energy surfaces of each charge model to explain the differences.

Driving reconnection in sheared magnetic configurations with forced fluctuations

NASA Astrophysics Data System (ADS)

Pongkitiwanichakul, Peera; Makwana, Kirit D.; Ruffolo, David

2018-02-01

We investigate reconnection of magnetic field lines in sheared magnetic field configurations due to fluctuations driven by random forcing by means of numerical simulations. The simulations are performed with an incompressible, pseudo-spectral magnetohydrodynamics code in 2D where we take thick, resistively decaying, current-sheet like sheared magnetic configurations which do not reconnect spontaneously. We describe and test the forcing that is introduced in the momentum equation to drive fluctuations. It is found that the forcing does not change the rate of decay; however, it adds and removes energy faster in the presence of the magnetic shear structure compared to when it has decayed away. We observe that such a forcing can induce magnetic reconnection due to field line wandering leading to the formation of magnetic islands and O-points. These reconnecting field lines spread out as the current sheet decays with time. A semi-empirical formula is derived which reasonably explains the formation and spread of O-points. We find that reconnection spreads faster with stronger forcing and longer correlation time of forcing, while the wavenumber of forcing does not have a significant effect. When the field line wandering becomes large enough, the neighboring current sheets with opposite polarity start interacting, and then the magnetic field is rapidly annihilated. This work is useful to understand how forced fluctuations can drive reconnection in large scale current structures in space and astrophysical plasmas that are not susceptible to reconnection.

Development of a method to analyze single cell activity by using dielectrophoretic levitation.

PubMed

Hakoda, M; Hachisu, T; Wakizaka, Y; Mii, S; Kitajima, N

2005-01-01

In cell fusion and genetic recombination, although the activity of single cells is extremely important, there is no method to analyze single cell activity. Development of a quick analyzing method for single cell activity is desired in various fields. Dielectrophoresis (DEP) refers to the force exerted on the induced dipole moment of an uncharged dielectric and/or conductive particle by a nonuniform electric field. By applying DEP, we obtained experimentally a relationship between the cell activity and the dielectric property, Re[K(omega)], and examined how to evaluate the single cell activity by measuring Re[K(omega)] of a single cell. A cone and plate electrode geometry was adapted in order to achieve the feedback-controlled DEP levitation. The single cell is exposed to a nonuniform field induced by the cone and plate electrode, and a more polarizable cell is moved to the direction of the cone electrode by the DEP force. The cell settles in the position where the DEP force and gravity are balanced by controlling applied voltage. This settled position, measured on the center axis of the cone electrode, depended on the dielectric constant of the cell. From these results, the relationship between the specific growth rates in cell growth phase and the dielectric properties Re[K(omega)] was obtained. Furthermore, the effect on the cell activity of various stresses, such as concentration of carbon dioxide, temperature, etc., was examined.

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N'-diacetato)-chromium(III): development of vibrationally optimized force field (VOFF).

PubMed

Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W

2012-05-01

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.

Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

NASA Astrophysics Data System (ADS)

Neupane, Guru P.; Dhakal, Krishna P.; Lee, Hyunsoo; Guthold, Martin; Joseph, Vincent S.; Hong, Jong-Dal; Kim, Jeongyong

2013-05-01

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

A data-driven decomposition approach to model aerodynamic forces on flapping airfoils

NASA Astrophysics Data System (ADS)

Raiola, Marco; Discetti, Stefano; Ianiro, Andrea

2017-11-01

In this work, we exploit a data-driven decomposition of experimental data from a flapping airfoil experiment with the aim of isolating the main contributions to the aerodynamic force and obtaining a phenomenological model. Experiments are carried out on a NACA 0012 airfoil in forward flight with both heaving and pitching motion. Velocity measurements of the near field are carried out with Planar PIV while force measurements are performed with a load cell. The phase-averaged velocity fields are transformed into the wing-fixed reference frame, allowing for a description of the field in a domain with fixed boundaries. The decomposition of the flow field is performed by means of the POD applied on the velocity fluctuations and then extended to the phase-averaged force data by means of the Extended POD approach. This choice is justified by the simple consideration that aerodynamic forces determine the largest contributions to the energetic balance in the flow field. Only the first 6 modes have a relevant contribution to the force. A clear relationship can be drawn between the force and the flow field modes. Moreover, the force modes are closely related (yet slightly different) to the contributions of the classic potential models in literature, allowing for their correction. This work has been supported by the Spanish MINECO under Grant TRA2013-41103-P.

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.

Element Library for Three-Dimensional Stress Analysis by the Integrated Force Method

NASA Technical Reports Server (NTRS)

Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

1996-01-01

The Integrated Force Method, a recently developed method for analyzing structures, is extended in this paper to three-dimensional structural analysis. First, a general formulation is developed to generate the stress interpolation matrix in terms of complete polynomials of the required order. The formulation is based on definitions of the stress tensor components in term of stress functions. The stress functions are written as complete polynomials and substituted into expressions for stress components. Then elimination of the dependent coefficients leaves the stress components expressed as complete polynomials whose coefficients are defined as generalized independent forces. Such derived components of the stress tensor identically satisfy homogenous Navier equations of equilibrium. The resulting element matrices are invariant with respect to coordinate transformation and are free of spurious zero-energy modes. The formulation provides a rational way to calculate the exact number of independent forces necessary to arrive at an approximation of the required order for complete polynomials. The influence of reducing the number of independent forces on the accuracy of the response is also analyzed. The stress fields derived are used to develop a comprehensive finite element library for three-dimensional structural analysis by the Integrated Force Method. Both tetrahedral- and hexahedral-shaped elements capable of modeling arbitrary geometric configurations are developed. A number of examples with known analytical solutions are solved by using the developments presented herein. The results are in good agreement with the analytical solutions. The responses obtained with the Integrated Force Method are also compared with those generated by the standard displacement method. In most cases, the performance of the Integrated Force Method is better overall.

[The standardization of medical care and the training of medical personnel].

PubMed

Korbut, V B; Tyts, V V; Boĭshenko, V A

1997-09-01

The medical specialist training at all levels (medical orderly, doctor's assistant, general practitioner, doctors) should be based on the medical care standards. Preliminary studies in the field of military medicine standards have demonstrated that the medical service of the Armed Forces of Russia needs medical resources' standards, structure and organization standards, technology standards. Military medical service resources' standards should reflect the requisitions for: all medical specialists' qualification, equipment and material for medical set-ups, field medical systems, drugs, etc. Standards for structures and organization should include requisitions for: command and control systems in military formations' and task forces' medical services and their information support; health-care and evacuation functions, sanitary control and anti-epidemic measures and personnel health protection. Technology standards development could improve and regulate the health care procedures in the process of evacuation. Standards' development will help to solve the problem of the data-base for the military medicine education system and medical research.

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

PubMed

Kundu, Sangeeta

2018-02-01

The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

Dynamo Induced by Time-periodic Force

NASA Astrophysics Data System (ADS)

Wei, Xing

2018-03-01

To understand the dynamo driven by time-dependent flow, e.g., turbulence, we investigate numerically the dynamo induced by time-periodic force in rotating magnetohydrodynamic flow and focus on the effect of force frequency on the dynamo action. It is found that the dynamo action depends on the force frequency. When the force frequency is near resonance the force can drive dynamo, but when it is far away from resonance dynamo fails. In the frequency range near resonance to support dynamo, the force frequency at resonance induces a weak magnetic field and magnetic energy increases as the force frequency deviates from the resonant frequency. This is opposite to the intuition that a strong flow at resonance will induce a strong field. It is because magnetic field nonlinearly couples with fluid flow in the self-sustained dynamo and changes the resonance of driving force and inertial wave.

Recent advances on glass-forming systems driven far from equilibrium. Special issue marking the completion of the Research Unit FOR 1394 `Nonlinear response to probe vitrification'

NASA Astrophysics Data System (ADS)

Fuchs, Matthias

2017-08-01

The nature of the glass transition is one of the frontier questions in Statistical Physics and Materials Science. Highly cooperative structural processes develop in glass-forming melts exhibiting relaxational dynamics which is spread out over many decades in time. While considerable progress has been made in recent decades towards understanding dynamical slowing-down in quiescent systems, the interplay of glassy dynamics with external fields reveals a wealth of novel phenomena yet to be explored. This special issue focuses on recent results obtained by the Research Unit FOR 1394 `Nonlinear response to probe vitrification' which was funded by the German Science Foundation (DFG). In the projects of the research unit, strong external fields were used in order to gain insights into the complex structural and transport phenomena at the glass transition under far-from-equilibrium conditions. This aimed inter alia to test theories of the glass transition developed for quiescent systems by pushing them beyond their original regime. Combining experimental, simulational, and theoretical efforts, the eight projects within the FOR 1394 measured and determined aspects of the nonlinear response of supercooled metallic, polymeric, and silica melts, of colloidal dispersions, and of ionic liquids. Applied fields included electric and mechanic fields, and forced active probing (`micro-rheology'), where a single probe is forced through the glass-forming host. Nonlinear stress-strain and force-velocity relations as well as nonlinear dielectric susceptibilities and conductivities were observed. While the physical manipulation of melts and glasses is interesting in its own right, especially technologically, the investigations performed by the FOR 1394 suggest to use the response to strong homogeneous and inhomogeneous fields as technique to explore on the microscopic level the cooperative mechanisms in dense melts of strongly interacting constituents. Questions considered concern the (de-)coupling of different dynamical degrees of freedom in an external field, and the ensuing state diagrams. What forces are required to detach a localized probe particle from its initial environment in a supercooled liquid, in a glassy or granular system? Do metallic and colloidal glasses yield homogeneously or by strain localization under differently applied stresses? Which mechanisms determine field-dependent susceptibilities in dielectric and ionically conducting glass formers?

Determination of coronal magnetic fields from vector magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1992-01-01

The determination of coronal magnetic fields from vector magnetograms, including the development and application of algorithms to determine force-free coronal fields above selected observations of active regions is studied. Two additional active regions were selected and analyzed. The restriction of periodicity in the 3-D code which is used to determine the coronal field was removed giving the new code variable mesh spacing and is thus able to provide a more realistic description of coronal fields. The NOAA active region AR5747 of 20 Oct. 1989 was studied. A brief account of progress during the research performed is reported.

Implications of ICD-10 for Sarcopenia Clinical Practice and Clinical Trials: Report by the International Conference on Frailty and Sarcopenia Research Task Force.

PubMed

Vellas, B; Fielding, R A; Bens, C; Bernabei, R; Cawthon, P M; Cederholm, T; Cruz-Jentoft, A J; Del Signore, S; Donahue, S; Morley, J; Pahor, M; Reginster, J-Y; Rodriguez Mañas, L; Rolland, Y; Roubenoff, R; Sinclair, A; Cesari, M

2018-01-01

Establishment of an ICD-10-CM code for sarcopenia in 2016 was an important step towards reaching international consensus on the need for a nosological framework of age-related skeletal muscle decline. The International Conference on Frailty and Sarcopenia Research Task Force met in April 2017 to discuss the meaning, significance, and barriers to the implementation of the new code as well as strategies to accelerate development of new therapies. Analyses by the Sarcopenia Definitions and Outcomes Consortium are underway to develop quantitative definitions of sarcopenia. A consensus conference is planned to evaluate this analysis. The Task Force also discussed lessons learned from sarcopenia trials that could be applied to future trials, as well as lessons from the osteoporosis field, a clinical condition with many constructs similar to sarcopenia and for which ad hoc treatments have been developed and approved by regulatory agencies.

Predicting the melting temperature of ice-Ih with only electronic structure information as input.

PubMed

Pinnick, Eric R; Erramilli, Shyamsunder; Wang, Feng

2012-07-07

The melting temperature of ice-Ih was calculated with only electronic structure information as input by creating a problem-specific force field. The force field, Water model by AFM for Ice and Liquid (WAIL), was developed with the adaptive force matching (AFM) method by fitting to post-Hartree-Fock quality forces obtained in quantum mechanics∕molecular mechanics calculations. WAIL predicts the ice-Ih melting temperature to be 270 K. The model also predicts the densities of ice and water, the temperature of maximum density of water, the heat of vaporizations, and the radial distribution functions for both ice and water in good agreement with experimental measurements. The non-dissociative WAIL model is very similar to a flexible version of the popular TIP4P potential and has comparable computational cost. By customizing to problem-specific configurations with the AFM approach, the resulting model is remarkably more accurate than any variants of TIP4P for simulating ice-Ih and water in the temperature range from 253 K and 293 K under ambient pressure.

ELECTROMAGNETICALLY INDUCED DISTORTION OF A FIBRIN MATRIX WITH EMBEDDED MICROPARTICLES

PubMed Central

SCOGIN, TYLER; YESUDASAN, SUMITH; WALKER, MITCHELL L. R.

2018-01-01

Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the continued effort in developing fibrin therapies for potential life-saving solutions, more mechanical modeling is needed to understand the properties of fibrin structures with inclusions. In this study, a fibrin matrix embedded with magnetic micro particles (MMPs) was subjected to a magnetic field to determine the magnitude of the required force to create plastic deformation within the fibrin clot. Using finite element (FE) analysis, we estimated the magnetic force from an electromagnet at a sample space located approximately 3 cm away from the coil center. This electromagnetic force coupled with gravity was applied on a fibrin mechanical system with MMPs to calculate the stresses and displacements. Using appropriate coil parameters, it was determined that application of a magnetic field of 730 A/m on the fibrin surface was necessary to achieve an electromagnetic force of 36 nN (to engender plastic deformation). PMID:29628543

Development of fine-resolution analyses and expanded large-scale forcing properties. Part I: Methodology and evaluation

DOE PAGES

Li, Zhijin; Vogelmann, Andrew M.; Feng, Sha; ...

2015-01-20

We produce fine-resolution, three-dimensional fields of meteorological and other variables for the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Southern Great Plains site. The Community Gridpoint Statistical Interpolation system is implemented in a multiscale data assimilation (MS-DA) framework that is used within the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. The MS-DA algorithm uses existing reanalysis products and constrains fine-scale atmospheric properties by assimilating high-resolution observations. A set of experiments show that the data assimilation analysis realistically reproduces the intensity, structure, and time evolution of clouds and precipitation associated with a mesoscale convective system.more » Evaluations also show that the large-scale forcing derived from the fine-resolution analysis has an overall accuracy comparable to the existing ARM operational product. For enhanced applications, the fine-resolution fields are used to characterize the contribution of subgrid variability to the large-scale forcing and to derive hydrometeor forcing, which are presented in companion papers.« less

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.

Calculation of electromagnetic force in electromagnetic forming process of metal sheet

NASA Astrophysics Data System (ADS)

Xu, Da; Liu, Xuesong; Fang, Kun; Fang, Hongyuan

2010-06-01

Electromagnetic forming (EMF) is a forming process that relies on the inductive electromagnetic force to deform metallic workpiece at high speed. Calculation of the electromagnetic force is essential to understand the EMF process. However, accurate calculation requires complex numerical solution, in which the coupling between the electromagnetic process and the deformation of workpiece needs be considered. In this paper, an appropriate formula has been developed to calculate the electromagnetic force in metal work-piece in the sheet EMF process. The effects of the geometric size of coil, the material properties, and the parameters of discharge circuit on electromagnetic force are taken into consideration. Through the formula, the electromagnetic force at different time and in different positions of the workpiece can be predicted. The calculated electromagnetic force and magnetic field are in good agreement with the numerical and experimental results. The accurate prediction of the electromagnetic force provides an insight into the physical process of the EMF and a powerful tool to design optimum EMF systems.

Temperature regulation of bud-burst phenology within and among years in a young Douglas-fir (Pseudotsuga menziesii) plantation in western Washington, USA.

PubMed

Bailey, John D; Harrington, Constance A

2006-04-01

Past research has established that terminal buds of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings from many seed sources have a chilling requirement of about 1200 h at 0-5 degrees C; once chilled, temperatures > 5 degrees C force bud burst via accumulation of heat units. We tested this sequential bud-burst model in the field to determine whether terminal buds of trees in cooler microsites, which receive less heat forcing, develop more slowly than those in warmer microsites. For three years we monitored terminal bud development in young saplings as well as soil and air temperatures on large, replicated plots in a harvest unit; plots differed in microclimate based on amount of harvest residue and shade from neighboring stands. In two of three years, trees on cooler microsites broke bud 2 to 4 days earlier than those on warmer microsites, despite receiving less heat forcing from March to May each year. A simple sequential model did not predict cooler sites having earlier bud burst nor did it correctly predict the order of bud burst across the three years. We modified the basic heat-forcing model to initialize, or reset to zero, the accumulation of heat units whenever significant freezing temperature events (> or = 3 degree-hours day(-1) < 0 degrees C) occurred; this modified model correctly predicted the sequence of bud burst across years. Soil temperature alone or in combination with air temperature did not improve our predictions of bud burst. Past models of bud burst have relied heavily on data from controlled experiments with simple temperature patterns; analysis of more variable temperature patterns from our 3-year field trial, however, indicated that simple models of bud burst are inaccurate. More complex models that incorporate chilling hours, heat forcing, photoperiod and the occurrence of freeze events in the spring may be needed to predict effects of future silvicultural treatments as well to interpret the implications of climate-change scenarios. Developing and testing new models will require data from both field and controlled-environment experiments.

A Study of Laminar Compressible Viscous Pipe Flow Accelerated by an Axial Body Force, with Application to Magnetogasdynamics

NASA Technical Reports Server (NTRS)

Martin, E. Dale

1961-01-01

A study is made of the steady laminar flow of a compressible viscous fluid in a circular pipe when the fluid is accelerated by an axial body force. The application of the theory to the magnetofluidmechanics of an electrically conducting gas accelerated by electric and magnetic fields is discussed. Constant viscosity, thermal conductivity, and electrical conductivity are assumed. Fully developed flow velocity and temperature profiles are shown, and detailed results of the accelerating flow development, including velocity and pressure as functions of distance, are given for the case where the axial body force is constant and for the case where it is a linear function of velocity. From these results are determined the pipe entry length and the pressure difference required.

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.

PubMed

Zgarbová, Marie; Otyepka, Michal; Sponer, Jirí; Hobza, Pavel; Jurecka, Petr

2010-09-21

The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although comparing the empirical and non-empirical interaction energy components is in general problematic, it might bring insights useful for the construction of new force fields. Our results are relevant to often performed force-field-based interaction energy decompositions.

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2015-09-01

The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Passive scalar entrainment and mixing in a forced, spatially-developing mixing layer

NASA Technical Reports Server (NTRS)

Lowery, P. S.; Reynolds, W. C.; Mansour, N. N.

1987-01-01

Numerical simulations are performed for the forced, spatially-developing plane mixing layer in two and three dimensions. Transport of a passive scalar field is included in the computation. This, together with the allowance for spatial development in the simulations, affords the opportunity for study of the asymmetric entrainment of irrotational fluid into the layer. The inclusion of a passive scalar field provides a means for simulating the effect of this entrainment asymmetry on the generation of 'products' from a 'fast' chemical reaction. Further, the three-dimensional simulations provide useful insight into the effect of streamwise structures on these entrainment and 'fast' reaction processes. Results from a two-dimensional simulation indicate 1.22 parts high-speed fluid are entrained for every one part low-speed fluid. Inclusion of streamwise vortices at the inlet plane of a three-dimensional simulation indicate a further increase in asymmetric entrainment - 1.44:1. Results from a final three-dimensional simulation are presented. In this case, a random velocity perturbation is imposed at the inlet plane. The results indicate the 'natural' development of the large spanwise structures characteristic of the mixing layer.

Molecular dynamics simulations of methane hydrate using polarizable force fields

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

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

2007-06-14

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

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

Heat transfer enhancement of Fe3O4 ferrofluids in the presence of magnetic field

NASA Astrophysics Data System (ADS)

Fadaei, Farzad; Shahrokhi, Mohammad; Molaei Dehkordi, Asghar; Abbasi, Zeinab

2017-05-01

In this article, three-dimensional (3D) forced-convection heat transfer of magnetic nanofluids in a pipe subject to constant wall heat flux in the presence of single or double permanent magnet(s) or current-carrying wire has been investigated and compared. In this regard, laminar fluid flow and equilibrium magnetization for the ferrofluid were considered. In addition, variations of magnetic field in different media were taken into account and the assumption of having a linear relationship of magnetization with applied magnetic field intensity was also relaxed. Effects of magnetic field intensity, nanoparticle volume fraction, Reynolds number value, and the type of magnetic field source (i.e., a permanent magnet or current-carrying wire) on the forced-convection heat transfer of magnetic nanofluids were carefully investigated. It was found that by applying the magnetic field, the fluid mixing could be intensified that leads to an increase in the Nusselt number value along the pipe length. Moreover, the obtained simulation results indicate that applying the magnetic field induced by two permanent magnets with a magnetization of 3×105 (A/m) (for each one), the fully developed Nusselt number value can be increased by 196%.

Quantum Correlations of Light from a Room-Temperature Mechanical Oscillator

NASA Astrophysics Data System (ADS)

Sudhir, V.; Schilling, R.; Fedorov, S. A.; Schütz, H.; Wilson, D. J.; Kippenberg, T. J.

2017-07-01

When an optical field is reflected from a compliant mirror, its intensity and phase become quantum-correlated due to radiation pressure. These correlations form a valuable resource: the mirror may be viewed as an effective Kerr medium generating squeezed states of light, or the correlations may be used to erase backaction from an interferometric measurement of the mirror's position. To date, optomechanical quantum correlations have been observed in only a handful of cryogenic experiments, owing to the challenge of distilling them from thermomechanical noise. Accessing them at room temperature, however, would significantly extend their practical impact, with applications ranging from gravitational wave detection to chip-scale accelerometry. Here, we observe broadband quantum correlations developed in an optical field due to its interaction with a room-temperature nanomechanical oscillator, taking advantage of its high-cooperativity near-field coupling to an optical microcavity. The correlations manifest as a reduction in the fluctuations of a rotated quadrature of the field, in a frequency window spanning more than an octave below mechanical resonance. This is due to coherent cancellation of the two sources of quantum noise contaminating the measured quadrature—backaction and imprecision. Supplanting the backaction force with an off-resonant test force, we demonstrate the working principle behind a quantum-enhanced "variational" force measurement.