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

Installation Restoration Program Records Search for Kingsley Field, Oregon.

DTIC Science & Technology

1982-06-01

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

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

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.

Traction patterns of tumor cells.

PubMed

Ambrosi, D; Duperray, A; Peschetola, V; Verdier, C

2009-01-01

The traction exerted by a cell on a planar deformable substrate can be indirectly obtained on the basis of the displacement field of the underlying layer. The usual methodology used to address this inverse problem is based on the exploitation of the Green tensor of the linear elasticity problem in a half space (Boussinesq problem), coupled with a minimization algorithm under force penalization. A possible alternative strategy is to exploit an adjoint equation, obtained on the basis of a suitable minimization requirement. The resulting system of coupled elliptic partial differential equations is applied here to determine the force field per unit surface generated by T24 tumor cells on a polyacrylamide substrate. The shear stress obtained by numerical integration provides quantitative insight of the traction field and is a promising tool to investigate the spatial pattern of force per unit surface generated in cell motion, particularly in the case of such cancer cells.

Transferable Coarse-Grained Models for Ionic Liquids.

PubMed

Wang, Yanting; Feng, Shulu; Voth, Gregory A

2009-04-14

The effective force coarse-graining (EF-CG) method was applied to the imidazolium-based nitrate ionic liquids with various alkyl side-chain lengths. The nonbonded EF-CG forces for the ionic liquid with a short side chain were extended to generate the nonbonded forces for the ionic liquids with longer side chains. The EF-CG force fields for the ionic liquids exhibit very good transferability between different systems at various temperatures and are suitable for investigating the mesoscopic structural properties of this class of ionic liquids. The good additivity and ease of manipulation of the EF-CG force fields can allow for an inverse design methodology of ionic liquids at the coarse-grained level. With the EF-CG force field, the molecular dynamics (MD) simulation at a very large scale has been performed to check the significance of finite size effects on the structural properties. From these MD simulation results, it can be concluded that the finite size effect on the phenomenon of ionic liquid spatial heterogeneity (Wang, Y.; Voth, G. A. J. Am. Chem. Soc. 2005, 127, 12192) is small and that this phenomenon is indeed a nanostructural behavior which leads to the experimentally observed mesoscopic heterogeneous structure of ionic liquids.

Safety Implications of High-Field MRI: Actuation of Endogenous Magnetic Iron Oxides in the Human Body

PubMed Central

Dobson, Jon; Bowtell, Richard; Garcia-Prieto, Ana; Pankhurst, Quentin

2009-01-01

Background Magnetic Resonance Imaging scanners have become ubiquitous in hospitals and high-field systems (greater than 3 Tesla) are becoming increasingly common. In light of recent European Union moves to limit high-field exposure for those working with MRI scanners, we have evaluated the potential for detrimental cellular effects via nanomagnetic actuation of endogenous iron oxides in the body. Methodology Theoretical models and experimental data on the composition and magnetic properties of endogenous iron oxides in human tissue were used to analyze the forces on iron oxide particles. Principal Finding and Conclusions Results show that, even at 9.4 Tesla, forces on these particles are unlikely to disrupt normal cellular function via nanomagnetic actuation. PMID:19412550

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.

A mathematical method for the turbulent behavior of crowds using agent particles

NASA Astrophysics Data System (ADS)

Ohnishi, Teruaki

2016-08-01

Among the people moving as a group there appear social and psychological forces together with physical forces such as friction and resistance. With the definition that the field of the crowd is the region of those forces continuously extending with varying strength, and with the pre-requisite that the spatial distribution of the crowd, i.e., the distribution of the field, varies according to the hydrodynamic rule by the Navier-Stokes equation, a methodology was proposed to describe the behavior of the crowd composed of many agent particles as the movement of a compressible, turbulent fluid. A numerical calculation was exemplified for the dynamic behavior and spatial distribution of crowds during movements when there appears a conflict between groups with different characters, imaging for instance the medieval battle of Breitenfeld.

Quantum theory of multiscale coarse-graining.

PubMed

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

2018-03-14

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

Canadian Air Force Establishment Analysis: Creating a meta-methodology to address integrated questions of force structure, workforce planning and organizational design

DTIC Science & Technology

2010-01-28

Considerations – Position categories: • Hard • Generic or “ soft ” • Advanced Training – Language requirements – Need for • military, combat and/or field...Analysis (DGMPRA) Presentation to MORS WG Personnel and National Security: A Quantitative Approach 25-28 January 2010 Defence Research and...SUPPLEMENTARY NOTES Personnel and National Security: A Quantitative Approach (Unclass), 25-28 January 2010, Johns Hopkins University Applied Physics

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.

Molecular Mechanics: The Method and Its Underlying Philosophy.

ERIC Educational Resources Information Center

Boyd, Donald B.; Lipkowitz, Kenny B.

1982-01-01

Molecular mechanics is a nonquantum mechanical method for solving problems concerning molecular geometries and energy. Methodology based on: the principle of combining potential energy functions of all structural features of a particular molecule into a total force field; derivation of basic equations; and use of available computer programs is…

The California Language Census Survey: Field Methodology Issues.

ERIC Educational Resources Information Center

Cornejo, Ricardo; Nadeau, Adel

This is the first in a series of papers on research, development, and training for bilingual/multicultural education. The first two sections of the paper describe Task Force findings specifying remedies available for eliminating past educational practices ruled unlawful under Lau v Nichols, particularly the section dealing with identification of…

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

PubMed

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

2015-07-15

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

Molecular simulation of caloric properties of fluids modelled by force fields with intramolecular contributions: Application to heat capacities

NASA Astrophysics Data System (ADS)

Smith, William R.; Jirsák, Jan; Nezbeda, Ivo; Qi, Weikai

2017-07-01

The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. We describe the correct methodology required to perform such calculations and illustrate it in this paper for the case of the internal energy and the enthalpy and their corresponding molar heat capacities. We provide numerical results for cP, one of the most important caloric properties. We also consider approximations to the correct calculation procedure previously used in the literature and illustrate their consequences for the examples of the relatively simple molecule 2-propanol, CH3CH(OH)CH3, and for the more complex molecule monoethanolamine, HO(CH2)2NH2, an important fluid used in carbon capture.

Magnetic Levitation of MC3T3 Osteoblast Cells as a Ground-Based Simulation of Microgravity

PubMed Central

Kidder, Louis S.; Williams, Philip C.; Xu, Wayne Wenzhong

2009-01-01

Diamagnetic samples placed in a strong magnetic field and a magnetic field gradient experience a magnetic force. Stable magnetic levitation occurs when the magnetic force exactly counter balances the gravitational force. Under this condition, a diamagnetic sample is in a simulated microgravity environment. The purpose of this study is to explore if MC3T3-E1 osteoblastic cells can be grown in magnetically simulated hypo-g and hyper-g environments and determine if gene expression is differentially expressed under these conditions. The murine calvarial osteoblastic cell line, MC3T3-E1, grown on Cytodex-3 beads, were subjected to a net gravitational force of 0, 1 and 2 g in a 17 T superconducting magnet for 2 days. Microarray analysis of these cells indicated that gravitational stress leads to up and down regulation of hundreds of genes. The methodology of sustaining long-term magnetic levitation of biological systems are discussed. PMID:20052306

Full-field modal analysis during base motion excitation using high-speed 3D digital image correlation

NASA Astrophysics Data System (ADS)

Molina-Viedma, Ángel J.; López-Alba, Elías; Felipe-Sesé, Luis; Díaz, Francisco A.

2017-10-01

In recent years, many efforts have been made to exploit full-field measurement optical techniques for modal identification. Three-dimensional digital image correlation using high-speed cameras has been extensively employed for this purpose. Modal identification algorithms are applied to process the frequency response functions (FRF), which relate the displacement response of the structure to the excitation force. However, one of the most common tests for modal analysis involves the base motion excitation of a structural element instead of force excitation. In this case, the relationship between response and excitation is typically based on displacements, which are known as transmissibility functions. In this study, a methodology for experimental modal analysis using high-speed 3D digital image correlation and base motion excitation tests is proposed. In particular, a cantilever beam was excited from its base with a random signal, using a clamped edge join. Full-field transmissibility functions were obtained through the beam and converted into FRF for proper identification, considering a single degree-of-freedom theoretical conversion. Subsequently, modal identification was performed using a circle-fit approach. The proposed methodology facilitates the management of the typically large amounts of data points involved in the DIC measurement during modal identification. Moreover, it was possible to determine the natural frequencies, damping ratios and full-field mode shapes without requiring any additional tests. Finally, the results were experimentally validated by comparing them with those obtained by employing traditional accelerometers, analytical models and finite element method analyses. The comparison was performed by using the quantitative indicator modal assurance criterion. The results showed a high level of correspondence, consolidating the proposed experimental methodology.

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

PubMed Central

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

2012-01-01

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

Force 2025 and Beyond Strategic Force Design Analytic Model

DTIC Science & Technology

2017-01-12

depiction of the core ideas of our force design model. Figure 1: Description of Force Design Model Figure 2 shows an overview of our methodology ...the F2025B Force Design Analytic Model research conducted by TRAC- MTRY and the Naval Postgraduate School. Our research develops a methodology for...designs. We describe a data development methodology that characterizes the data required to construct a force design model using our approach. We

Mass effects and internal space geometry in triatomic reaction dynamics

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.

2006-05-01

The effect of the distribution of mass in triatomic reaction dynamics is analyzed using the geometry of the associated internal space. Atomic masses are appropriately incorporated into internal coordinates as well as the associated non-Euclidean internal space metric tensor after a separation of the rotational degrees of freedom. Because of the non-Euclidean nature of the metric in the internal space, terms such as connection coefficients arise in the internal equations of motion, which act as velocity-dependent forces in a coordinate chart. By statistically averaging these terms, an effective force field is deduced, which accounts for the statistical tendency of geodesics in the internal space. This force field is shown to play a crucial role in determining mass-related branching ratios of isomerization and dissociation dynamics of a triatomic molecule. The methodology presented can be useful for qualitatively predicting branching ratios in general triatomic reactions, and may be applied to the study of isotope effects.

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

Topographic profiling and refractive-index analysis by use of differential interference contrast with bright-field intensity and atomic force imaging.

PubMed

Axelrod, Noel; Radko, Anna; Lewis, Aaron; Ben-Yosef, Nissim

2004-04-10

A methodology is described for phase restoration of an object function from differential interference contrast (DIC) images. The methodology involves collecting a set of DIC images in the same plane with different bias retardation between the two illuminating light components produced by a Wollaston prism. These images, together with one conventional bright-field image, allows for reduction of the phase deconvolution restoration problem from a highly complex nonlinear mathematical formulation to a set of linear equations that can be applied to resolve the phase for images with a relatively large number of pixels. Additionally, under certain conditions, an on-line atomic force imaging system that does not interfere with the standard DIC illumination modes resolves uncertainties in large topographical variations that generally lead to a basic problem in DIC imaging, i.e., phase unwrapping. Furthermore, the availability of confocal detection allows for a three-dimensional reconstruction with high accuracy of the refractive-index measurement of the object that is to be imaged. This has been applied to reconstruction of the refractive index of an arrayed waveguide in a region in which a defect in the sample is present. The results of this paper highlight the synergism of far-field microscopies integrated with scanned probe microscopies and restoration algorithms for phase reconstruction.

Numerical modelling of electromagnetic loads on fusion device structures

NASA Astrophysics Data System (ADS)

Bettini, Paolo; Furno Palumbo, Maurizio; Specogna, Ruben

2014-03-01

In magnetic confinement fusion devices, during abnormal operations (disruptions) the plasma begins to move rapidly towards the vessel wall in a vertical displacement event (VDE), producing plasma current asymmetries, vessel eddy currents and open field line halo currents, each of which can exert potentially damaging forces upon the vessel and in-vessel components. This paper presents a methodology to estimate electromagnetic loads, on three-dimensional conductive structures surrounding the plasma, which arise from the interaction of halo-currents associated to VDEs with a magnetic field of the order of some Tesla needed for plasma confinement. Lorentz forces, calculated by complementary formulations, are used as constraining loads in a linear static structural analysis carried out on a detailed model of the mechanical structures of a representative machine.

Heat transfer in aeropropulsion systems

NASA Astrophysics Data System (ADS)

Simoneau, R. J.

1985-07-01

Aeropropulsion heat transfer is reviewed. A research methodology based on a growing synergism between computations and experiments is examined. The aeropropulsion heat transfer arena is identified as high Reynolds number forced convection in a highly disturbed environment subject to strong gradients, body forces, abrupt geometry changes and high three dimensionality - all in an unsteady flow field. Numerous examples based on heat transfer to the aircraft gas turbine blade are presented to illustrate the types of heat transfer problems which are generic to aeropropulsion systems. The research focus of the near future in aeropropulsion heat transfer is projected.

Heat transfer in aeropropulsion systems

NASA Technical Reports Server (NTRS)

Simoneau, R. J.

1985-01-01

Aeropropulsion heat transfer is reviewed. A research methodology based on a growing synergism between computations and experiments is examined. The aeropropulsion heat transfer arena is identified as high Reynolds number forced convection in a highly disturbed environment subject to strong gradients, body forces, abrupt geometry changes and high three dimensionality - all in an unsteady flow field. Numerous examples based on heat transfer to the aircraft gas turbine blade are presented to illustrate the types of heat transfer problems which are generic to aeropropulsion systems. The research focus of the near future in aeropropulsion heat transfer is projected.

Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations.

PubMed

Vanegas, Juan M; Torres-Sánchez, Alejandro; Arroyo, Marino

2014-02-11

Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions. However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations (e.g. nonconstant normal stress profiles along an isotropic bilayer in equilibrium) is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations.

Extending the Range for Force Calibration in Magnetic Tweezers

PubMed Central

Daldrop, Peter; Brutzer, Hergen; Huhle, Alexander; Kauert, Dominik J.; Seidel, Ralf

2015-01-01

Magnetic tweezers are a wide-spread tool used to study the mechanics and the function of a large variety of biomolecules and biomolecular machines. This tool uses a magnetic particle and a strong magnetic field gradient to apply defined forces to the molecule of interest. Forces are typically quantified by analyzing the lateral fluctuations of the biomolecule-tethered particle in the direction perpendicular to the applied force. Since the magnetic field pins the anisotropy axis of the particle, the lateral fluctuations follow the geometry of a pendulum with a short pendulum length along and a long pendulum length perpendicular to the field lines. Typically, the short pendulum geometry is used for force calibration by power-spectral-density (PSD) analysis, because the movement of the bead in this direction can be approximated by a simple translational motion. Here, we provide a detailed analysis of the fluctuations according to the long pendulum geometry and show that for this direction, both the translational and the rotational motions of the particle have to be considered. We provide analytical formulas for the PSD of this coupled system that agree well with PSDs obtained in experiments and simulations and that finally allow a faithful quantification of the magnetic force for the long pendulum geometry. We furthermore demonstrate that this methodology allows the calibration of much larger forces than the short pendulum geometry in a tether-length-dependent manner. In addition, the accuracy of determination of the absolute force is improved. Our force calibration based on the long pendulum geometry will facilitate high-resolution magnetic-tweezers experiments that rely on short molecules and large forces, as well as highly parallelized measurements that use low frame rates. PMID:25992733

On the Role of Global Magnetic Field Configuration in Affecting Ring Current Dynamics

NASA Technical Reports Server (NTRS)

Zheng, Y.; Zaharia, S. G.; Fok, M. H.

2010-01-01

Plasma and field interaction is one important aspect of inner magnetospheric physics. The magnetic field controls particle motion through gradient, curvature drifts and E cross B drift. In this presentation, we show how the global magnetic field affects dynamics of the ring current through simulations of two moderate geomagnetic storms (20 November 2007 and 8-9 March 2008). Preliminary results of coupling the Comprehensive Ring Current Model (CRCM) with a three-dimensional plasma force balance code (to achieve self-consistency in both E and B fields) indicate that inclusion of self-consistency in B tends to mitigate the intensification of the ring current as other similar coupling efforts have shown. In our approach, self-consistency in the electric field is already an existing capability of the CRCM. The magnetic self-consistency is achieved by computing the three-dimensional magnetic field in force balance with anisotropic ring current ion distributions. We discuss the coupling methodology and its further improvement. In addition, comparative studies by using various magnetic field models will be shown. Simulation results will be put into a global context by analyzing the morphology of the ring current, its anisotropy and characteristics ofthe interconnected region 2 field-aligned currents.

Patterning in systems driven by nonlocal external forces.

PubMed

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

2016-11-01

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

Patterning in systems driven by nonlocal external forces

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Sample size in psychological research over the past 30 years.

PubMed

Marszalek, Jacob M; Barber, Carolyn; Kohlhart, Julie; Holmes, Cooper B

2011-04-01

The American Psychological Association (APA) Task Force on Statistical Inference was formed in 1996 in response to a growing body of research demonstrating methodological issues that threatened the credibility of psychological research, and made recommendations to address them. One issue was the small, even dramatically inadequate, size of samples used in studies published by leading journals. The present study assessed the progress made since the Task Force's final report in 1999. Sample sizes reported in four leading APA journals in 1955, 1977, 1995, and 2006 were compared using nonparametric statistics, while data from the last two waves were fit to a hierarchical generalized linear growth model for more in-depth analysis. Overall, results indicate that the recommendations for increasing sample sizes have not been integrated in core psychological research, although results slightly vary by field. This and other implications are discussed in the context of current methodological critique and practice.

A systems-based food safety evaluation: an experimental approach.

PubMed

Higgins, Charles L; Hartfield, Barry S

2004-11-01

Food establishments are complex systems with inputs, subsystems, underlying forces that affect the system, outputs, and feedback. Building on past exploration of the hazard analysis critical control point concept and Ludwig von Bertalanffy General Systems Theory, the National Park Service (NPS) is attempting to translate these ideas into a realistic field assessment of food service establishments and to use information gathered by these methods in efforts to improve food safety. Over the course of the last two years, an experimental systems-based methodology has been drafted, developed, and tested by the NPS Public Health Program. This methodology is described in this paper.

Conformational analysis of bis(methylthio)methane and diethyl sulfide molecules in the liquid phase: reverse Monte Carlo studies using classical interatomic potential functions.

PubMed

Gereben, Orsolya; Pusztai, László

2013-11-13

Series of flexible molecule reverse Monte Carlo calculations, using bonding and non-bonding interatomic potential functions (FMP-RMC), were performed starting from previous molecular dynamics results that had applied the OPLS-AA and EncadS force fields. During RMC modeling, the experimental x-ray total scattering structure factor was approached. The discrepancy between experimental and calculated structure factors, in comparison with the molecular dynamics results, decreased substantially in each case. The room temperature liquid structure of bis(methylthio)methane is excellently described by the FMP-RMC simulation that applied the EncadS force field parameters. The main conformer was found to be AG with 55.2%, followed by 37.2% of G(+)G(+) (G(-)G(-)) and 7.6% of AA; the stability of the G(+)G(+) (G(-)G(-)) conformer is most probably caused by the anomer effect. The liquid structure of diethyl sulfide can be best described by applying the OPLS-AA force field parameters during FMP-RMC simulation, although in this case the force field parameters were found to be not fully compatible with experimental data. Here, the two main conformers are AG (50.6%) and the AA (40%). In addition to findings on the actual real systems, a fairly detailed comparison between traditional and FMP-RMC methodology is provided.

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

Remote sensing of the correlation between breakpoint oscillations and infragravity waves in the surf and swash zone

NASA Astrophysics Data System (ADS)

Moura, T.; Baldock, T. E.

2017-04-01

A novel remote sensing methodology to determine the dominant infragravity mechanism in the inner surf and swash zone in the field is presented. Video observations of the breakpoint motion are correlated with the shoreline motion and inner surf zone water levels to determine the relationship between the time-varying breakpoint oscillations and the shoreline motion. The results of 13 field data sets collected from three different beaches indicate that, inside the surf zone, the dominance of bound wave or breakpoint forcing is strongly dependent on the surf zone width and the type of short wave breaking. Infragravity generation by bound wave release was stronger for conditions with relatively narrow surf zones and plunging waves; breakpoint forcing was dominant for wider surf zones and spilling breaker conditions.

Drawing Lessons from the Long War: What Operational Evaluation Methodology Should the Australian Army Use to Learn from Afghanistan and Iraq?

DTIC Science & Technology

2014-05-22

accessed August 2, 2013). 12 was established on the advice of Field Marshal Horatio Herbert Kitchener , 1st Earl Kitchener . The Australian Army’s...involvement in the First World War was an important companion to the subjective analysis to identify the lessons of the Australian Imperial Force. An

Total Quality Management (TQM) in Self-Financed Technical Institutions: A Quality Function Deployment (QFD) and Force Field Analysis Approach

ERIC Educational Resources Information Center

Thakkar, Jitesh; Deshmukh, S. G.; Shastree, Anil

2006-01-01

Purpose: To explore the potential for adoption of TQM in self-financed technical institutions in the light of new demands and challenges posed by customers/students and society. Design/methodology/approach: The paper presents use of quality function deployment (QFD) which prioritizes technical requirements and correlates them with various…

S4MPLE--Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking.

PubMed

Hoffer, Laurent; Chira, Camelia; Marcou, Gilles; Varnek, Alexandre; Horvath, Dragos

2015-05-19

This paper describes the development of the unified conformational sampling and docking tool called Sampler for Multiple Protein-Ligand Entities (S4MPLE). The main novelty in S4MPLE is the unified dealing with intra- and intermolecular degrees of freedom (DoF). While classically programs are either designed for folding or docking, S4MPLE transcends this artificial specialization. It supports folding, docking of a flexible ligand into a flexible site and simultaneous docking of several ligands. The trick behind it is the formal assimilation of inter-molecular to intra-molecular DoF associated to putative inter-molecular contact axes. This is implemented within the genetic operators powering a Lamarckian Genetic Algorithm (GA). Further novelty includes differentiable interaction fingerprints to control population diversity, and fitting a simple continuum solvent model and favorable contact bonus terms to the AMBER/GAFF force field. Novel applications-docking of fragment-like compounds, simultaneous docking of multiple ligands, including free crystallographic waters-were published elsewhere. This paper discusses: (a) methodology, (b) set-up of the force field energy functions and (c) their validation in classical redocking tests. More than 80% success in redocking was achieved (RMSD of top-ranked pose < 2.0 Å).

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions.

PubMed

Fischer, Nina M; van Maaren, Paul J; Ditz, Jonas C; Yildirim, Ahmet; van der Spoel, David

2015-07-14

In order to increase the accuracy of classical computer simulations, existing methodologies may need to be adapted. Hitherto, most force fields employ a truncated potential function to model van der Waals interactions, sometimes augmented with an analytical correction. Although such corrections are accurate for homogeneous systems with a long cutoff, they should not be used in inherently inhomogeneous systems such as biomolecular and interface systems. For such cases, a variant of the particle mesh Ewald algorithm (Lennard-Jones PME) was already proposed 20 years ago (Essmann et al. J. Chem. Phys. 1995, 103, 8577-8593), but it was implemented only recently (Wennberg et al. J. Chem. Theory Comput. 2013, 9, 3527-3537) in a major simulation code (GROMACS). The availability of this method allows surface tensions of liquids as well as bulk properties to be established, such as density and enthalpy of vaporization, without approximations due to truncation. Here, we report on simulations of ≈150 liquids (taken from a force field benchmark: Caleman et al. J. Chem. Theory Comput. 2012, 8, 61-74) using three different force fields and compare simulations with and without explicit long-range van der Waals interactions. We find that the density and enthalpy of vaporization increase for most liquids using the generalized Amber force field (GAFF, Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) and the Charmm generalized force field (CGenFF, Vanommeslaeghe et al. J. Comput. Chem. 2010, 31, 671-690) but less so for OPLS/AA (Jorgensen and Tirado-Rives, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665-6670), which was parametrized with an analytical correction to the van der Waals potential. The surface tension increases by ≈10(-2) N/m for all force fields. These results suggest that van der Waals attractions in force fields are too strong, in particular for the GAFF and CGenFF. In addition to the simulation results, we introduce a new version of a web server, http://virtualchemistry.org, aimed at facilitating sharing and reuse of input files for molecular simulations.

Gyration-radius dynamics in structural transitions of atomic clusters.

PubMed

Yanao, Tomohiro; Koon, Wang S; Marsden, Jerrold E; Kevrekidis, Ioannis G

2007-03-28

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Gyration-radius dynamics in structural transitions of atomic clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang S.; Marsden, Jerrold E.; Kevrekidis, Ioannis G.

2007-03-01

This paper is concerned with the structural transition dynamics of the six-atom Morse cluster with zero total angular momentum, which serves as an illustrative example of the general reaction dynamics of isolated polyatomic molecules. It develops a methodology that highlights the interplay between the effects of the potential energy topography and those of the intrinsic geometry of the molecular internal space. The method focuses on the dynamics of three coarse variables, the molecular gyration radii. By using the framework of geometric mechanics and hyperspherical coordinates, the internal motions of a molecule are described in terms of these three gyration radii and hyperangular modes. The gyration radii serve as slow collective variables, while the remaining hyperangular modes serve as rapidly oscillating "bath" modes. Internal equations of motion reveal that the gyration radii are subject to two different kinds of forces: One is the ordinary force that originates from the potential energy function of the system, while the other is an internal centrifugal force. The latter originates from the dynamical coupling of the gyration radii with the hyperangular modes. The effects of these two forces often counteract each other: The potential force generally works to keep the internal mass distribution of the system compact and symmetric, while the internal centrifugal force works to inflate and elongate it. Averaged fields of these two forces are calculated numerically along a reaction path for the structural transition of the molecule in the three-dimensional space of gyration radii. By integrating the sum of these two force fields along the reaction path, an effective energy curve is deduced, which quantifies the gross work necessary for the system to change its mass distribution along the reaction path. This effective energy curve elucidates the energy-dependent switching of the structural preference between symmetric and asymmetric conformations. The present methodology should be of wide use for the systematic reduction of dimensionality as well as for the identification of kinematic barriers associated with the rearrangement of mass distribution in a variety of molecular reaction dynamics in vacuum.

Adaptive accelerated ReaxFF reactive dynamics with validation from simulating hydrogen combustion.

PubMed

Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A; Sun, Huai

2014-07-02

We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H2 to form H2O product is ∼538 s, whereas the computational cost was just 1289 ps, a speed increase of ∼0.42 trillion (10(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF-OH2014 force field that was used in the simulations.

Human and Organizational Factors in the U.S. Naval Construction Force: A Qualitative Analysis of the U.S. Naval Mobile Construction Battalion Peacetime Deployment Construction Program

DTIC Science & Technology

2002-09-01

a program in its weapons systems acquisition program known as HARDMAN (Hardware/ Manpower Comparability Analysis Methodology) which combined...battalion-wide real-time training exercises out in the field each homeport. These field exercises are driven by tactical scenarios that tax the full range...received the proper training for your rating during A-School? q 1 q 2 q 3 q 4 q 5 q 6 q 7 If not, why not

Leadership at the Top: Some Insights from a Longitudinal Case Study of a UK Business School

ERIC Educational Resources Information Center

Williams, Allan P. O.

2009-01-01

A UK business school was researched to record its history and to account for its development. The data collection and interpretation were influenced by the flexible and iterative nature of the methodology. Theories and concepts used to make sense of the findings include: open systems, force fields, and power. The focus is on strategic leadership,…

A Methodology for the Determination of Contract Manpower Equivalents for the United States Air Force

DTIC Science & Technology

1975-05-28

ACKNOWLEDGMENTS The author would like to thank his committee members. Dr. Cooper Redwine, Dr. Jsck Byrd, and Dr. Arup Mallik ior their guidance and...Career Field upon completion of degree requirements. The author is married to o o 227 APPROVAL OF EXAMINING COMMITTEE Dr. fa. ’Byrd, or. Dr. A. K.. Mallik DATE Dr . C. N. Redwlne (Chairman)

On-demand Droplet Manipulation via Triboelectrification

NASA Astrophysics Data System (ADS)

Wang, Wei; Vahabi, Hamed; Cackovic, Matthew; Jiang, Rui; Kota, Arun

2017-11-01

Controlled manipulation of liquid droplets has attracted tremendous interest across different scientific fields over the past two decades. To date, a variety of external stimuli-mediated methods such as magnetic field, electric field, and light have been developed for manipulating droplets on surfaces. However, these methods usually have drawbacks such as complex fabrication of manipulation platform, low droplet motility, expensive actuation system and lack of precise control. In this work, we demonstrate the controlled manipulation of liquid droplet with both high (e.g., water) and low (e.g., n-hexadecane) dielectric strengths on a smooth, slippery surface via triboelectric effect. Our highly simple, facile and portable methodology enables on-demand, precise manipulation of droplets using solely the electrostatic attraction or repulsion force, which is exerted on the droplet by a simple charged actuator (e.g., Teflon film). We envision that our triboelectric effect enabled droplet manipulation methodology will open a new avenue for droplet based lab-on-a-chip systems, energy harvesting devices and biomedical applications.

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.

Static force field representation of environments based on agents' nonlinear motions

NASA Astrophysics Data System (ADS)

Campo, Damian; Betancourt, Alejandro; Marcenaro, Lucio; Regazzoni, Carlo

2017-12-01

This paper presents a methodology that aims at the incremental representation of areas inside environments in terms of attractive forces. It is proposed a parametric representation of velocity fields ruling the dynamics of moving agents. It is assumed that attractive spots in the environment are responsible for modifying the motion of agents. A switching model is used to describe near and far velocity fields, which in turn are used to learn attractive characteristics of environments. The effect of such areas is considered radial over all the scene. Based on the estimation of attractive areas, a map that describes their effects in terms of their localizations, ranges of action, and intensities is derived in an online way. Information of static attractive areas is added dynamically into a set of filters that describes possible interactions between moving agents and an environment. The proposed approach is first evaluated on synthetic data; posteriorly, the method is applied on real trajectories coming from moving pedestrians in an indoor environment.

A Methodology for Estimating the Full Cost of Replacing Trained Air Force Personnel

DTIC Science & Technology

1987-01-01

8217O S PROGRAM PROJECT TASK WORK UNIT IELEMENT NO I NO NO. NO. - ILE, t ),cl Udr.Iec u ,,I,( ’ I t C, IIct,o n ,A M e ’h o d o l o g y f o r E s t m a...force members. Since we can’t hire from the trained civilian pool, we have to wait four time periods as the newly enlisted member works his or her way...associated with these AFSCs. In order to validate our model we compared it with earlier work done in this field. The only comparable study we could find was

Dry-Surface Simulation Method for the Determination of the Work of Adhesion of Solid-Liquid Interfaces.

PubMed

Leroy, Frédéric; Müller-Plathe, Florian

2015-08-04

We introduce a methodology, referred to as the dry-surface method, to calculate the work of adhesion of heterogeneous solid-liquid interfaces by molecular simulation. This method employs a straightforward thermodynamic integration approach to calculate the work of adhesion as the reversible work to turn off the attractive part of the actual solid-liquid interaction potential. It is formulated in such a way that it may be used either to evaluate the ability of force fields to reproduce reference values of the work of adhesion or to optimize force-field parameters with reference values of the work of adhesion as target quantities. The methodology is tested in the case of water on a generic model of nonpolar substrates with the structure of gold. It is validated through a quantitative comparison to phantom-wall calculations and against a previous characterization of the thermodynamics of the gold-water interface. It is found that the work of adhesion of water on nonpolar substrates is a nonlinear function of the microscopic solid-liquid interaction energy parameter. We also comment on the ability of mean-field approaches to predict the work of adhesion of water on nonpolar substrates. In addition, we discuss in detail the information on the solid-liquid interfacial thermodynamics delivered by the phantom-wall approach. We show that phantom-wall calculations yield the solid-liquid interfacial tension relative to the solid surface tension rather than the absolute solid-liquid interfacial tension as previously believed.

The Development of a Methodology for Estimating the Cost of Air Force On-the-Job Training.

ERIC Educational Resources Information Center

Samers, Bernard N.; And Others

The Air Force uses a standardized costing methodology for resident technical training schools (TTS); no comparable methodology exists for computing the cost of on-the-job training (OJT). This study evaluates three alternative survey methodologies and a number of cost models for estimating the cost of OJT for airmen training in the Administrative…

Advances in free-energy-based simulations of protein folding and ligand binding.

PubMed

Perez, Alberto; Morrone, Joseph A; Simmerling, Carlos; Dill, Ken A

2016-02-01

Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: first, to fold small proteins with free-energy methods without knowing substructures and second, to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years--which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information. Copyright © 2015 Elsevier Ltd. All rights reserved.

Model Evaluation with Multi-wavelength Satellite Observations Using a Neural Network

NASA Astrophysics Data System (ADS)

Kolassa, Jana; Jimenez, Carlos; Aires, Filipe

2013-04-01

A methodology has been developed to evaluate fields of modelled parameters against a set of satellite observations. The method employs a Neural Network (NN) to construct a statistical model capturing the relationship between the satellite observations and the parameter from a land surface model, in this case the Soil Moisture (SM). This statistical model is then used to estimate the parameter of interest from the set of satellite observations. These estimates are compared to the modelled parameter in order to detect local deviations indicating a possible problem in the model or in the satellite observations. Several synthetic tests, during which an artificial error was added to the"true" soil moisture fields, showed that the methodology is able to correct the errors (Jimenez et al., submitted, 2012). This evaluation technique is very general and can be applied to any modelled parameter for which sensitive satellite observations are available. The use of NNs simplifies the evaluation of the model against satellite observations and is particularly well-suited to utilize the synergy from the observations at different wavelengths (Aires et al., 2005, 2012). In this study the proposed methodology has been applied to evaluate SM fields from a number of land surface models against a synergy of satellite observations from passive and active microwave, infrared and visible sensors. In an inter-comparison of the performance of several land surface models (ORCHIDEE (de Rosnay et al., 2002), HTESSEL (Balsamo et al., 2009), JULES (Best et al., 2011) ) it was found that the soil moisture fields from JULES, HTESSEL and ORCHIDEE are very consistent with the observations, but ORCHIDEE soil moisture shows larger local deviations close to some river basins (Kolassa et al., in press, 2012; Jimenez et al., submitted, 2012). Differences between all models and the observations could also be observed in the Eastern US and over mountainous regions, however, the errors here are more likely linked to the retrieved SM uncertainties. The proposed methodology can also be used to evaluate the quality of the model forcings: two soil moisture fields from ORCHIDEE using WATCH (Weedon et al., 2011) and ERA-interim (Balsamo et al., 2010) forcings were analysed. It was shown that the WATCH forcing data are more optimal, underlining the importance of forcing data for the accuracy of model predictions (Kolassa et al., in press, 2012). References Aires, F., Prigent, C., and Rossow, W.B. (2005), Sensitivity of satellite microwave and infrared observations to soil moisture at a global scale: 2. Global statistical relationships, J. Geophys. Res., 110, D11103, doi:10.1029/2004JD005094. Aires, F., O. Aznay, C. Prigent, M. Paul, F. Bernardo, Synergetic multi-wavelegnth remote sensing versus a posteriori combination of retrieved products: Application for the retrieval of atmospheric profiles using MetOp measurements, J. Geophys. Res., 2011 Balsamo, G., Viterbo, P., Beljaars, A., van den Hurk, B., Hirschi, M., Betts, A. and Scipa,l K. (2009) A Revised Hydrology for the ECMWF Model: Verification from Field Site to Terrestrial Water Storage and Impact in the Integrated Forecast System, J. Hydrol., 10, 623-643 Balsamo, G., Boussetta, S., Lopez, P., and Ferranti, L. (2010), Evaluation of ERA-Interim and ERA- Interim-GPCP-rescaled precipitation over the U.S.A., ERA-Report Series, 5, pp. 10. Best, M. J., M. Pryor, D. B. Clark, G. G. Rooney, R .L. H. Essery, C. B. Ménard, J. M. Edwards, M. A. Hendry, A. Porson, N. Gedney, L. M. Mercado, S. Sitch, E. Blyth, O. Boucher, P. M. Cox, C. S. B. Grimmond, and R. J. Harding (2011), The Joint UK Land Environment Simulator (JULES), model description - Part 1: Energy and water fluxes, Geosci. Model Dev., 4 Jimenez, C., Clark, D., Kolassa, J., Aires, F., Prigent, C., and Blyth, E. (2012), A joint analysis of modeled soil moisture fields and satellite observations (2012), J. Geophys. Res., Kolassa, J., Aires, F., Polcher, J., Prigent, C., and Pereira, J. (2012), Soil moisture Retrieval from Multi-instrument Observations: Information Content Analysis and Retrieval Methodology (2012), J. Geophys. Res., de Rosnay, P., Polcher, J., Bruen, M., Laval, K. (2002), Impact of a physically based soil water flow and soil-plant interaction representation for modeling large-scale land surface processes, J. Geophys. Res., 107, D11, 4118, 10.1029/2001JD000634 Weedon, G.P., Gomes, S., Viterbo, P., Shuttleworth, W.J., Blyth, E., O ̈sterle, H., Adam, J.C., Bellouin, N., Boucher, O., and Best, M. (2011), Creation of the WATCH Forcing Data and its use to assess global and regional reference crop evaporation over land during the twentieth century, J. Hydrometeorology,12, 5, pp. 823-848.

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)

Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles

NASA Astrophysics Data System (ADS)

Andersson, Magnus; Axner, Ove; Uhlin, Bernt Eric; Fällman, Erik

2006-08-01

Instrumentation and methodologies for single molecule force spectroscopy on bacterial adhesion organelles by the use of force measuring optical tweezers have been developed. A thorough study of the biomechanical properties of fimbrial adhesion organelles expressed by uropathogenic E. coli, so-called pili, is presented. Steady-state as well as dynamic force measurements on P pili, expressed by E. coli causing pyelonephritis, have revealed, among other things, various unfolding and refolding properties of the helical structure of P pili, the PapA rod. Based on these properties an energy landscape model has been constructed by which specific biophysical properties of the PapA rod have been extracted, e.g. the number of subunits, the length of a single pilus, bond lengths and activation energies for bond opening and closure. Moreover, long time repetitive measurements have shown that the rod can be unfolded and refolded repetitive times without losing its intrinsic properties. These properties are believed to be of importance for the bacteria's ability to maintain close contact with host cells during initial infections. The results presented are considered to be of importance for the field of biopolymers in general and the development of new pharmaceuticals towards urinary tract infections in particular. The results show furthermore that the methodology can be used to gain knowledge of the intrinsic biomechanical function of adhesion organelles. The instrumentation is currently used for characterization of type 1 pili, expressed by E. coli causing cystitis, i.e. infections in the bladder. The first force spectrometry investigations of these pili will be presented.

Comparison of ISRU Excavation System Model Blade Force Methodology and Experimental Results

NASA Technical Reports Server (NTRS)

Gallo, Christopher A.; Wilkinson, R. Allen; Mueller, Robert P.; Schuler, Jason M.; Nick, Andrew J.

2010-01-01

An Excavation System Model has been written to simulate the collection and transportation of regolith on the Moon. The calculations in this model include an estimation of the forces on the digging tool as a result of excavation into the regolith. Verification testing has been performed and the forces recorded from this testing were compared to the calculated theoretical data. A prototype lunar vehicle built at the NASA Johnson Space Center (JSC) was tested with a bulldozer type blade developed at the NASA Kennedy Space Center (KSC) attached to the front. This is the initial correlation of actual field test data to the blade forces calculated by the Excavation System Model and the test data followed similar trends with the predicted values. This testing occurred in soils developed at the NASA Glenn Research Center (GRC) which are a mixture of different types of sands and whose soil properties have been well characterized. Three separate analytical models are compared to the test data.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins.

PubMed

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-05

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

QM/MM Geometry Optimization on Extensive Free-Energy Surfaces for Examination of Enzymatic Reactions and Design of Novel Functional Properties of Proteins

NASA Astrophysics Data System (ADS)

Hayashi, Shigehiko; Uchida, Yoshihiro; Hasegawa, Taisuke; Higashi, Masahiro; Kosugi, Takahiro; Kamiya, Motoshi

2017-05-01

Many remarkable molecular functions of proteins use their characteristic global and slow conformational dynamics through coupling of local chemical states in reaction centers with global conformational changes of proteins. To theoretically examine the functional processes of proteins in atomic detail, a methodology of quantum mechanical/molecular mechanical (QM/MM) free-energy geometry optimization is introduced. In the methodology, a geometry optimization of a local reaction center is performed with a quantum mechanical calculation on a free-energy surface constructed with conformational samples of the surrounding protein environment obtained by a molecular dynamics simulation with a molecular mechanics force field. Geometry optimizations on extensive free-energy surfaces by a QM/MM reweighting free-energy self-consistent field method designed to be variationally consistent and computationally efficient have enabled examinations of the multiscale molecular coupling of local chemical states with global protein conformational changes in functional processes and analysis and design of protein mutants with novel functional properties.

Micro-resonator-based electric field sensors with long durations of sensitivity

NASA Astrophysics Data System (ADS)

Ali, Amir R.

2017-05-01

In this paper, we present a new fabrication method for the whispering gallery mode (WGM) micro-sphere based electric field sensor that which allows for longer time periods of sensitivity. Recently, a WGM-based photonic electric field sensor was proposed using a coupled dielectric microsphere-beam. The external electric field imposes an electrtrostriction force on the dielectric beam, deflecting it. The beam, in turn compresses the sphere causing a shift in its WGM. As part of the fabrication process, the PDMS micro-beams and the spheres are curied at high-temperature (100oC) and subsequently poled by exposing to strong external electric field ( 8 MV/m) for two hours. The poling process allows for the deposition of surface charges thereby increasing the electrostriction effect. This methodology is called curing-then-poling (CTP). Although the sensors do become sufficiently sensitive to electric field, they start de-poling after a short period (within 10 minutes) after poling, hence losing sensitivity. In an attempt to mitigate this problem and to lock the polarization for a longer period, we use an alternate methodology whereby the beam is poled and cured simultaneously (curing-while-poling or CWP). The new fabrication method allows for the retention of polarization (and hence, sensitivity to electric field) longer ( 1500 minutes). An analysis is carried out along with preliminary experiments. Results show that electric fields as small as 100 V/m can be detected with a 300 μm diameter sphere sensor a day after poling.

Acoustic manipulation of oscillating spherical bodies: Emergence of axial negative acoustic radiation force

NASA Astrophysics Data System (ADS)

Rajabi, Majid; Mojahed, Alireza

2016-11-01

In this paper, emergence of negative axial acoustic radiation force on a rigid oscillating spherical body is investigated for acoustic manipulation purposes. The problem of plane acoustic wave scattering from an oscillating spherical body submerged in an ideal acoustic fluid medium is solved. For the case of oscillating direction collinear with the wave propagation wave number vector (desired path), it has been shown that the acoustic radiation force, as a result of nonlinear acoustic wave interaction with bodies can be expressed as a linear function of incident wave field and the oscillation properties of the oscillator (i.e., amplitude and phase of oscillation). The negative (i.e., pulling effects) and positive (i.e., pushing effects) radiation force situations are divided in oscillation complex plane with a specific frequency-dependant straight line. This characteristic line defines the radiation force cancellation state. In order to investigate the stability of the mentioned manipulation strategy, the case of misaligned oscillation of sphere with the wave propagation direction is studied. The proposed methodology may suggest a novel concept of single-beam acoustic handling techniques based on smart carriers.

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.

Acoustic force measurements on polymer-coated microbubbles in a microfluidic device

PubMed Central

Memoli, Gianluca; Fury, Christopher R.; Baxter, Kate O.; Gélat, Pierre N.; Jones, Philip H.

2017-01-01

This work presents an acoustofluidic device for manipulating coated microbubbles, designed for the simultaneous use of optical and acoustical tweezers. A comprehensive characterization of the acoustic pressure in the device is presented, obtained by the synergic use of different techniques in the range of acoustic frequencies where visual observations showed aggregation of polymer-coated microbubbles. In absence of bubbles, the combined use of laser vibrometry and finite element modelling supported a non-invasive measurement of the acoustic pressure and an enhanced understanding of the system resonances. Calibrated holographic optical tweezers were used for direct measurements of the acoustic forces acting on an isolated microbubble, at low driving pressures, and to confirm the spatial distribution of the acoustic field. This allowed quantitative acoustic pressure measurements by particle tracking, using polystyrene beads, and an evaluation of the related uncertainties. This process facilitated the extension of tracking to microbubbles, which have a negative acoustophoretic contrast factor, allowing acoustic force measurements on bubbles at higher pressures than optical tweezers, highlighting four peaks in the acoustic response of the device. Results and methodologies are relevant to acoustofluidic applications requiring a precise characterization of the acoustic field and, in general, to biomedical applications with microbubbles or deformable particles. PMID:28599556

On a full Bayesian inference for force reconstruction problems

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

In a previous paper, the authors introduced a flexible methodology for reconstructing mechanical sources in the frequency domain from prior local information on both their nature and location over a linear and time invariant structure. The proposed approach was derived from Bayesian statistics, because of its ability in mathematically accounting for experimenter's prior knowledge. However, since only the Maximum a Posteriori estimate was computed, the posterior uncertainty about the regularized solution given the measured vibration field, the mechanical model and the regularization parameter was not assessed. To answer this legitimate question, this paper fully exploits the Bayesian framework to provide, from a Markov Chain Monte Carlo algorithm, credible intervals and other statistical measures (mean, median, mode) for all the parameters of the force reconstruction problem.

Future Combat System Spinout 1 Technical Field Test - Establishing and Implementing Models and Simulations System of Systems Verification, Validation and Accreditation Practices, Methodologies and Procedures

DTIC Science & Technology

2009-11-24

assisted by the Brigade Combat Team (BCT) Modernization effort, the use of Models and Simulations ( M &S) becomes more crucial in supporting major...in 2008 via a slice of the Current Force (CF) BCT structure. To ensure realistic operational context, a M &S System-of- Systems (SoS) level...messages, and constructive representation of platforms, vehicles, and terrain. The M &S federation also provided test control, data collection, and live

Fluid-dynamic design optimization of hydraulic proportional directional valves

NASA Astrophysics Data System (ADS)

Amirante, Riccardo; Catalano, Luciano Andrea; Poloni, Carlo; Tamburrano, Paolo

2014-10-01

This article proposes an effective methodology for the fluid-dynamic design optimization of the sliding spool of a hydraulic proportional directional valve: the goal is the minimization of the flow force at a prescribed flow rate, so as to reduce the required opening force while keeping the operation features unchanged. A full three-dimensional model of the flow field within the valve is employed to accurately predict the flow force acting on the spool. A theoretical analysis, based on both the axial momentum equation and flow simulations, is conducted to define the design parameters, which need to be properly selected in order to reduce the flow force without significantly affecting the flow rate. A genetic algorithm, coupled with a computational fluid dynamics flow solver, is employed to minimize the flow force acting on the valve spool at the maximum opening. A comparison with a typical single-objective optimization algorithm is performed to evaluate performance and effectiveness of the employed genetic algorithm. The optimized spool develops a maximum flow force which is smaller than that produced by the commercially available valve, mainly due to some major modifications occurring in the discharge section. Reducing the flow force and thus the electromagnetic force exerted by the solenoid actuators allows the operational range of direct (single-stage) driven valves to be enlarged.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

A Methodology for Identifying Cost Effective Strategic Force Mixes.

DTIC Science & Technology

1984-12-01

is not to say that the model could not be used to examine force increases. Given that the strategic force is already a mix of weapons, what is the...rules allow for the determination of what weapon mix to buy based on only the relative prices of the weapons and the parameters of the CES production...AD-A 151 773 AFIT/GOR/OS/84j /r A METHODOLOGY FOR IDENTIFYING COST EFFECTIVE STRATEGIC FORCE MIXES THESIS D I Thomas W. Manacapilli

Numerical Simulation of Flow in a Whirling Annular Seal and Comparison with Experiments

NASA Technical Reports Server (NTRS)

Athavale, M. M.; Hendricks, R. C.; Steinetz, B. M.

1995-01-01

The turbulent flow field in a simulated annular seal with a large clearance/radius ratio (0.015) and a whirling rotor was simulated using an advanced 3D CFD code SCISEAL. A circular whirl orbit with synchronous whirl was imposed on the rotor center. The flow field was rendered quasi-steady by making a transformation to a totaling frame. Standard k-epsilon model with wall functions was used to treat the turbulence. Experimentally measured values of flow parameters were used to specify the seal inlet and exit boundary conditions. The computed flow-field in terms of the velocity and pressure is compared with the experimental measurements inside the seal. The agreement between the numerical results and experimental data with correction is fair to good. The capability of current advanced CFD methodology to analyze this complex flow field is demonstrated. The methodology can also be extended to other whirl frequencies. Half- (or sub-) synchronous (fluid film unstable motion) and synchronous (rotor centrifugal force unbalance) whirls are the most unstable whirl modes in turbomachinery seals, and the flow code capability of simulating the flows in steady as well as whirling seals will prove to be extremely useful in the design, analyses, and performance predictions of annular as well as other types of seals.

Parallel computation with the force

NASA Technical Reports Server (NTRS)

Jordan, H. F.

1985-01-01

A methodology, called the force, supports the construction of programs to be executed in parallel by a force of processes. The number of processes in the force is unspecified, but potentially very large. The force idea is embodied in a set of macros which produce multiproceossor FORTRAN code and has been studied on two shared memory multiprocessors of fairly different character. The method has simplified the writing of highly parallel programs within a limited class of parallel algorithms and is being extended to cover a broader class. The individual parallel constructs which comprise the force methodology are discussed. Of central concern are their semantics, implementation on different architectures and performance implications.

Field emission microplasma actuation for microchannel flows

NASA Astrophysics Data System (ADS)

Sashank Tholeti, Siva; Shivkumar, Gayathri; Alexeenko, Alina A.

2016-06-01

Microplasmas offer attractive flow control methodology for gas transport in microsystems where large viscous losses make conventional pumping methods highly inefficient. We study microscale flow actuation by dielectric-barrier discharge (DBD) with field emission (FE) of electrons, which allows lowering the operational voltage from kV to a few hundred volts and below. A feasibility study of FE-DBD for flow actuation is performed using 2D particle-in-cell method with Monte Carlo collisions (PIC/MCC) at 10 MHz in nitrogen at atmospheric pressure. The free diffusion dominated, high velocity field emission electrons create a large positive space charge and a body force on the order of 106 N m-3. The body force and Joule heat decrease with increase in dielectric thickness and electrode thickness. The body force also decreases at lower pressures. The plasma body force distribution along with the Joule heating is then used in the Navier-Stokes simulations to quantify the flow actuation in a microchannel. Theoretical analysis and simulations for plasma actuated planar Poiseuille flow show that the gain in flow rate is inversely proportional to Reynolds number. This theoretical analysis is in good agreement with the simulations for a microchannel with closely placed actuators under incompressible conditions. Flow rate of FE-DBD driven 2D microchannel is around 100 ml min-1 mm-1 for an input power of 64 μW mm-1. The gas temperature rises by 1500 K due to the Joule heating, indicating FE-DBD’s potential for microcombustion, micropropulsion and chemical sensing in addition to microscale pumping and mixing applications.

Force on Force Modeling with Formal Task Structures and Dynamic Geometry

DTIC Science & Technology

2017-03-24

task framework, derived using the MMF methodology to structure a complex mission. It further demonstrated the integration of effects from a range of...application methodology was intended to support a combined developmental testing (DT) and operational testing (OT) strategy for selected systems under test... methodology to develop new or modify existing Models and Simulations (M&S) to: • Apply data from multiple, distributed sources (including test

Gravitational perturbation of irregular bodies modeled with regular polyhedra

NASA Astrophysics Data System (ADS)

Venditti, Flaviane; Prado, Antonio

In this work the study of the dynamics around bodies with non-spherical shapes is considered. The gravitational field of an irregular body, meaning that the mass distribution is asymmetric, generates orbits around this body to perform different from a keplerian orbit. In this case, there is a perturbation on the gravitational field that must be analyzed. To know the gravitational force of an irregular object, first it is necessary to model this body, which is not an easy thing to do, considering that, usually, they are not symmetric figures. To better model the irregular objects, a combination of several geometric figures can be used, like parallelepipeds. This can be applied to asteroids, which are objects with non-spherical shapes. The disturbing force generated by these bodies can then be obtained as the sum of the force on each figure. Here the equation for the potential of a cube is considered (MacMillan, 1930), which makes it possible to have analytical results. The main idea is to build a body with several cubes, and having the gravitational potential of each cube, it is possible to obtain the total perturbation as the sum of the forces acting on each piece. This methodology can be very helpful on space missions to small bodies, because when a spacecraft is in the vicinity of an irregular body, the gravitational perturbation generated by its shape must be considered to compensate this effect.

Optimizing Force Deployment and Force Structure for the Rapid Deployment Force

DTIC Science & Technology

1984-03-01

Analysis . . . . .. .. ... ... 97 Experimental Design . . . . . .. .. .. ... 99 IX. Use of a Flexible Response Surface ........ 10.2 Selection of a...setS . ere designe . arun, programming methodology , where the require: s.stem re..r is input and the model optimizes the num=er. :::pe, cargo. an...to obtain new computer outputs" (Ref 38:23). The methodology can be used with any decision model, linear or nonlinear. Experimental Desion Since the

The effect of inertia on the Dirac electron, the spin Hall current and the momentum space Berry curvature

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

Chowdhury, Debashree, E-mail: debashreephys@gmail.com; Basu, B., E-mail: sribbasu@gmail.com

2013-02-15

We have studied the spin dependent force and the associated momentum space Berry curvature in an accelerating system. The results are derived by taking into consideration the non-relativistic limit of a generally covariant Dirac equation with an electromagnetic field present, where the methodology of the Foldy-Wouthuysen transformation is applied to achieve the non-relativistic limit. Spin currents appear due to the combined action of the external electric field, the crystal field and the induced inertial electric field via the total effective spin-orbit interaction. In an accelerating frame, the crucial role of momentum space Berry curvature in the spin dynamics has alsomore » been addressed from the perspective of spin Hall conductivity. For time dependent acceleration, the expression for the spin polarization has been derived. - Highlights: Black-Right-Pointing-Pointer We study the effect of acceleration on the Dirac electron in the presence of an electromagnetic field, where the acceleration induces an electric field. Black-Right-Pointing-Pointer Spin currents appear due to the total effective electric field via the total spin-orbit interaction. Black-Right-Pointing-Pointer We derive the expression for the spin dependent force and the spin Hall current, which is zero for a particular acceleration. Black-Right-Pointing-Pointer The role of the momentum space Berry curvature in an accelerating system is discussed. Black-Right-Pointing-Pointer An expression for the spin polarization for time dependent acceleration is derived.« less

Improved characterization of heterogeneous permeability in saline aquifers from transient pressure data during freshwater injection

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

Kang, Peter K.; Lee, Jonghyun; Fu, Xiaojing

Managing recharge of freshwater into saline aquifers requires accurate estimation of the heterogeneous permeability field for maximizing injection and recovery efficiency. Here we present a methodology for subsurface characterization in saline aquifers that takes advantage of the density difference between the injected freshwater and the ambient saline groundwater. We combine high-resolution forward modeling of density-driven flow with an efficient Bayesian geostatistical inversion algorithm. In the presence of a density difference between the injected and ambient fluids due to differences in salinity, the pressure field is coupled to the spatial distribution of salinity. This coupling renders the pressure field transient: themore » time evolution of the salinity distribution controls the density distribution which then leads to a time-evolving pressure distribution. We exploit this coupling between pressure and salinity to obtain an improved characterization of the permeability field without multiple pumping tests or additional salinity measurements. We show that the inversion performance improves with an increase in the mixed convection ratio—the relative importance between viscous forces from injection and buoyancy forces from density difference. Thus, our work shows that measuring transient pressure data at multiple sampling points during freshwater injection into saline aquifers can be an effective strategy for aquifer characterization, key to the successful management of aquifer recharge.« less

Improved characterization of heterogeneous permeability in saline aquifers from transient pressure data during freshwater injection

DOE PAGES

Kang, Peter K.; Lee, Jonghyun; Fu, Xiaojing; ...

2017-05-31

Managing recharge of freshwater into saline aquifers requires accurate estimation of the heterogeneous permeability field for maximizing injection and recovery efficiency. Here we present a methodology for subsurface characterization in saline aquifers that takes advantage of the density difference between the injected freshwater and the ambient saline groundwater. We combine high-resolution forward modeling of density-driven flow with an efficient Bayesian geostatistical inversion algorithm. In the presence of a density difference between the injected and ambient fluids due to differences in salinity, the pressure field is coupled to the spatial distribution of salinity. This coupling renders the pressure field transient: themore » time evolution of the salinity distribution controls the density distribution which then leads to a time-evolving pressure distribution. We exploit this coupling between pressure and salinity to obtain an improved characterization of the permeability field without multiple pumping tests or additional salinity measurements. We show that the inversion performance improves with an increase in the mixed convection ratio—the relative importance between viscous forces from injection and buoyancy forces from density difference. Thus, our work shows that measuring transient pressure data at multiple sampling points during freshwater injection into saline aquifers can be an effective strategy for aquifer characterization, key to the successful management of aquifer recharge.« less

Rational Design Methodology.

DTIC Science & Technology

1978-09-01

This report describes an effort to specify a software design methodology applicable to the Air Force software environment . Available methodologies...of techniques for proof of correctness, design specification, and performance assessment of static designs. The rational methodology selected is a

Combining 3D Hydraulic Tomography with Tracer Tests for Improved Transport Characterization.

PubMed

Sanchez-León, E; Leven, C; Haslauer, C P; Cirpka, O A

2016-07-01

Hydraulic tomography (HT) is a method for resolving the spatial distribution of hydraulic parameters to some extent, but many details important for solute transport usually remain unresolved. We present a methodology to improve solute transport predictions by combining data from HT with the breakthrough curve (BTC) of a single forced-gradient tracer test. We estimated the three dimensional (3D) hydraulic-conductivity field in an alluvial aquifer by inverting tomographic pumping tests performed at the Hydrogeological Research Site Lauswiesen close to Tübingen, Germany, using a regularized pilot-point method. We compared the estimated parameter field to available profiles of hydraulic-conductivity variations from direct-push injection logging (DPIL), and validated the hydraulic-conductivity field with hydraulic-head measurements of tests not used in the inversion. After validation, spatially uniform parameters for dual-domain transport were estimated by fitting tracer data collected during a forced-gradient tracer test. The dual-domain assumption was used to parameterize effects of the unresolved heterogeneity of the aquifer and deemed necessary to fit the shape of the BTC using reasonable parameter values. The estimated hydraulic-conductivity field and transport parameters were subsequently used to successfully predict a second independent tracer test. Our work provides an efficient and practical approach to predict solute transport in heterogeneous aquifers without performing elaborate field tracer tests with a tomographic layout. © 2015, National Ground Water Association.

High Temperature, Permanent Magnet Biased, Fault Tolerant, Homopolar Magnetic Bearing Development

NASA Technical Reports Server (NTRS)

Palazzolo, Alan; Tucker, Randall; Kenny, Andrew; Kang, Kyung-Dae; Ghandi, Varun; Liu, Jinfang; Choi, Heeju; Provenza, Andrew

2008-01-01

This paper summarizes the development of a magnetic bearing designed to operate at 1,000 F. A novel feature of this high temperature magnetic bearing is its homopolar construction which incorporates state of the art high temperature, 1,000 F, permanent magnets. A second feature is its fault tolerance capability which provides the desired control forces with over one-half of the coils failed. The construction and design methodology of the bearing is outlined and test results are shown. The agreement between a 3D finite element, magnetic field based prediction for force is shown to be in good agreement with predictions at room and high temperature. A 5 axis test rig will be complete soon to provide a means to test the magnetic bearings at high temperature and speed.

Correlation of Descriptive Analysis and Instrumental Puncture Testing of Watermelon Cultivars.

PubMed

Shiu, J W; Slaughter, D C; Boyden, L E; Barrett, D M

2016-06-01

The textural properties of 5 seedless watermelon cultivars were assessed by descriptive analysis and the standard puncture test using a hollow probe with increased shearing properties. The use of descriptive analysis methodology was an effective means of quantifying watermelon sensory texture profiles for characterizing specific cultivars' characteristics. Of the 10 cultivars screened, 71% of the variation in the sensory attributes was measured using the 1st 2 principal components. Pairwise correlation of the hollow puncture probe and sensory parameters determined that initial slope, maximum force, and work after maximum force measurements all correlated well to the sensory attributes crisp and firm. These findings confirm that maximum force correlates well with not only firmness in watermelon, but crispness as well. The initial slope parameter also captures the sensory crispness of watermelon, but is not as practical to measure in the field as maximum force. The work after maximum force parameter is thought to reflect cellular arrangement and membrane integrity that in turn impact sensory firmness and crispness. Watermelon cultivar types were correctly predicted by puncture test measurements in heart tissue 87% of the time, although descriptive analysis was correct 54% of the time. © 2016 Institute of Food Technologists®

Creep force modelling for rail traction vehicles based on the Fastsim algorithm

NASA Astrophysics Data System (ADS)

Spiryagin, Maksym; Polach, Oldrich; Cole, Colin

2013-11-01

The evaluation of creep forces is a complex task and their calculation is a time-consuming process for multibody simulation (MBS). A methodology of creep forces modelling at large traction creepages has been proposed by Polach [Creep forces in simulations of traction vehicles running on adhesion limit. Wear. 2005;258:992-1000; Influence of locomotive tractive effort on the forces between wheel and rail. Veh Syst Dyn. 2001(Suppl);35:7-22] adapting his previously published algorithm [Polach O. A fast wheel-rail forces calculation computer code. Veh Syst Dyn. 1999(Suppl);33:728-739]. The most common method for creep force modelling used by software packages for MBS of running dynamics is the Fastsim algorithm by Kalker [A fast algorithm for the simplified theory of rolling contact. Veh Syst Dyn. 1982;11:1-13]. However, the Fastsim code has some limitations which do not allow modelling the creep force - creep characteristic in agreement with measurements for locomotives and other high-power traction vehicles, mainly for large traction creep at low-adhesion conditions. This paper describes a newly developed methodology based on a variable contact flexibility increasing with the ratio of the slip area to the area of adhesion. This variable contact flexibility is introduced in a modification of Kalker's code Fastsim by replacing the constant Kalker's reduction factor, widely used in MBS, by a variable reduction factor together with a slip-velocity-dependent friction coefficient decreasing with increasing global creepage. The proposed methodology is presented in this work and compared with measurements for different locomotives. The modification allows use of the well recognised Fastsim code for simulation of creep forces at large creepages in agreement with measurements without modifying the proven modelling methodology at small creepages.

Instrument response measurements of ion mobility spectrometers in situ: maintaining optimal system performance of fielded systems

NASA Astrophysics Data System (ADS)

Wallis, Eric; Griffin, Todd M.; Popkie, Norm, Jr.; Eagan, Michael A.; McAtee, Robert F.; Vrazel, Danet; McKinly, Jim

2005-05-01

Ion Mobility Spectroscopy (IMS) is the most widespread detection technique in use by the military for the detection of chemical warfare agents, explosives, and other threat agents. Moreover, its role in homeland security and force protection has expanded due, in part, to its good sensitivity, low power, lightweight, and reasonable cost. With the increased use of IMS systems as continuous monitors, it becomes necessary to develop tools and methodologies to ensure optimal performance over a wide range of conditions and extended periods of time. Namely, instrument calibration is needed to ensure proper sensitivity and to correct for matrix or environmental effects. We have developed methodologies to deal with the semi-quantitative nature of IMS and allow us to generate response curves that allow a gauge of instrument performance and maintenance requirements. This instrumentation communicates to the IMS systems via a software interface that was developed in-house. The software measures system response, logs information to a database, and generates the response curves. This paper will discuss the instrumentation, software, data collected, and initial results from fielded systems.

Constraint Force Equation Methodology for Modeling Multi-Body Stage Separation Dynamics

NASA Technical Reports Server (NTRS)

Toniolo, Matthew D.; Tartabini, Paul V.; Pamadi, Bandu N.; Hotchko, Nathaniel

2008-01-01

This paper discusses a generalized approach to the multi-body separation problems in a launch vehicle staging environment based on constraint force methodology and its implementation into the Program to Optimize Simulated Trajectories II (POST2), a widely used trajectory design and optimization tool. This development facilitates the inclusion of stage separation analysis into POST2 for seamless end-to-end simulations of launch vehicle trajectories, thus simplifying the overall implementation and providing a range of modeling and optimization capabilities that are standard features in POST2. Analysis and results are presented for two test cases that validate the constraint force equation methodology in a stand-alone mode and its implementation in POST2.

Closed Loop Control of a Tethered Magnetic Capsule Endoscope

PubMed Central

Taddese, Addisu Z.; Slawinski, Piotr R.; Obstein, Keith L.; Valdastri, Pietro

2017-01-01

Magnetic field gradients have repeatedly been shown to be the most feasible mechanism for gastrointestinal capsule endoscope actuation. An inverse quartic magnetic force variation with distance results in large force gradients induced by small movements of a driving magnet; this necessitates robotic actuation of magnets to implement stable control of the device. A typical system consists of a serial robot with a permanent magnet at its end effector that actuates a capsule with an embedded permanent magnet. We present a tethered capsule system where a capsule with an embedded magnet is closed loop controlled in 2 degree-of-freedom in position and 2 degree-of-freedom in orientation. Capitalizing on the magnetic field of the external driving permanent magnet, the capsule is localized in 6-D allowing for both position and orientation feedback to be used in a control scheme. We developed a relationship between the serial robot's joint parameters and the magnetic force and torque that is exerted onto the capsule. Our methodology was validated both in a dynamic simulation environment where a custom plug-in for magnetic interaction was written, as well as on an experimental platform. The tethered capsule was demonstrated to follow desired trajectories in both position and orientation with accuracy that is acceptable for colonoscopy. PMID:28286886

Closed Loop Control of a Tethered Magnetic Capsule Endoscope.

PubMed

Taddese, Addisu Z; Slawinski, Piotr R; Obstein, Keith L; Valdastri, Pietro

2016-06-01

Magnetic field gradients have repeatedly been shown to be the most feasible mechanism for gastrointestinal capsule endoscope actuation. An inverse quartic magnetic force variation with distance results in large force gradients induced by small movements of a driving magnet; this necessitates robotic actuation of magnets to implement stable control of the device. A typical system consists of a serial robot with a permanent magnet at its end effector that actuates a capsule with an embedded permanent magnet. We present a tethered capsule system where a capsule with an embedded magnet is closed loop controlled in 2 degree-of-freedom in position and 2 degree-of-freedom in orientation. Capitalizing on the magnetic field of the external driving permanent magnet, the capsule is localized in 6-D allowing for both position and orientation feedback to be used in a control scheme. We developed a relationship between the serial robot's joint parameters and the magnetic force and torque that is exerted onto the capsule. Our methodology was validated both in a dynamic simulation environment where a custom plug-in for magnetic interaction was written, as well as on an experimental platform. The tethered capsule was demonstrated to follow desired trajectories in both position and orientation with accuracy that is acceptable for colonoscopy.

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations

PubMed Central

Staritzbichler, René; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gómez, José D.

2014-01-01

As new atomic structures of membrane proteins are resolved, they reveal increasingly complex transmembrane topologies, and highly irregular surfaces with crevices and pores. In many cases, specific interactions formed with the lipid membrane are functionally crucial, as is the overall lipid composition. Compounded with increasing protein size, these characteristics pose a challenge for the construction of simulation models of membrane proteins in lipid environments; clearly, that these models are sufficiently realistic bears upon the reliability of simulation-based studies of these systems. Here, we introduce GRIFFIN, which uses a versatile framework to automate and improve a widely-used membrane-embedding protocol. Initially, GRIFFIN carves out lipid and water molecules from a volume equivalent to that of the protein, so as to conserve the system density. In the subsequent optimization phase GRIFFIN adds an implicit grid-based protein force-field to a molecular dynamics simulation of the pre-carved membrane. In this force-field, atoms inside the implicit protein volume experience an outward force that will expel them from that volume, whereas those outside are subject to electrostatic and van-der-Waals interactions with the implicit protein. At each step of the simulation, these forces are updated by GRIFFIN and combined with the intermolecular forces of the explicit lipid-water system. This procedure enables the construction of realistic and reproducible starting configurations of the protein-membrane interface within a reasonable timeframe and with minimal intervention. GRIFFIN is a standalone tool designed to work alongside any existing molecular dynamics package, such as NAMD or GROMACS. PMID:24707227

Vibration control of a ship engine system using high-load magnetorheological mounts associated with a new indirect fuzzy sliding mode controller

NASA Astrophysics Data System (ADS)

Phu, Do Xuan; Choi, Seung-Bok

2015-02-01

In this work, a new high-load magnetorheological (MR) fluid mount system is devised and applied to control vibration in a ship engine. In the investigation of vibration-control performance, a new modified indirect fuzzy sliding mode controller is formulated and realized. The design of the proposed MR mount is based on the flow mode of MR fluid, and it includes two separated coils for generating a magnetic field. An optimization process is carried out to achieve maximal damping force under certain design constraints, such as the allowable height of the mount. As an actuating smart fluid, a new plate-like iron-particle-based MR fluid is used, instead of the conventional spherical iron-particle-based MR fluid. After evaluating the field-dependent yield stress of the MR fluid, the field-dependent damping force required to control unwanted vibration in the ship engine is determined. Subsequently, an appropriate-sized MR mount is manufactured and its damping characteristics are evaluated. After confirming the sufficient damping force level of the manufactured MR mount, a medium-sized ship engine mount system consisting of eight MR mounts is established, and its dynamic governing equations are derived. A new modified indirect fuzzy sliding mode controller is then formulated and applied to the engine mount system. The displacement and velocity responses show that the unwanted vibrations of the ship engine system can be effectively controlled in both the axial and radial directions by applying the proposed control methodology.

A RLS-SVM Aided Fusion Methodology for INS during GPS Outages

PubMed Central

Yao, Yiqing; Xu, Xiaosu

2017-01-01

In order to maintain a relatively high accuracy of navigation performance during global positioning system (GPS) outages, a novel robust least squares support vector machine (LS-SVM)-aided fusion methodology is explored to provide the pseudo-GPS position information for the inertial navigation system (INS). The relationship between the yaw, specific force, velocity, and the position increment is modeled. Rather than share the same weight in the traditional LS-SVM, the proposed algorithm allocates various weights for different data, which makes the system immune to the outliers. Field test data was collected to evaluate the proposed algorithm. The comparison results indicate that the proposed algorithm can effectively provide position corrections for standalone INS during the 300 s GPS outage, which outperforms the traditional LS-SVM method. Historical information is also involved to better represent the vehicle dynamics. PMID:28245549

A RLS-SVM Aided Fusion Methodology for INS during GPS Outages.

PubMed

Yao, Yiqing; Xu, Xiaosu

2017-02-24

In order to maintain a relatively high accuracy of navigation performance during global positioning system (GPS) outages, a novel robust least squares support vector machine (LS-SVM)-aided fusion methodology is explored to provide the pseudo-GPS position information for the inertial navigation system (INS). The relationship between the yaw, specific force, velocity, and the position increment is modeled. Rather than share the same weight in the traditional LS-SVM, the proposed algorithm allocates various weights for different data, which makes the system immune to the outliers. Field test data was collected to evaluate the proposed algorithm. The comparison results indicate that the proposed algorithm can effectively provide position corrections for standalone INS during the 300 s GPS outage, which outperforms the traditional LS-SVM method. Historical information is also involved to better represent the vehicle dynamics.

Heart Rate Variability and Cardiac Vagal Tone in Psychophysiological Research – Recommendations for Experiment Planning, Data Analysis, and Data Reporting

PubMed Central

Laborde, Sylvain; Mosley, Emma; Thayer, Julian F.

2017-01-01

Psychophysiological research integrating heart rate variability (HRV) has increased during the last two decades, particularly given the fact that HRV is able to index cardiac vagal tone. Cardiac vagal tone, which represents the contribution of the parasympathetic nervous system to cardiac regulation, is acknowledged to be linked with many phenomena relevant for psychophysiological research, including self-regulation at the cognitive, emotional, social, and health levels. The ease of HRV collection and measurement coupled with the fact it is relatively affordable, non-invasive and pain free makes it widely accessible to many researchers. This ease of access should not obscure the difficulty of interpretation of HRV findings that can be easily misconstrued, however, this can be controlled to some extent through correct methodological processes. Standards of measurement were developed two decades ago by a Task Force within HRV research, and recent reviews updated several aspects of the Task Force paper. However, many methodological aspects related to HRV in psychophysiological research have to be considered if one aims to be able to draw sound conclusions, which makes it difficult to interpret findings and to compare results across laboratories. Those methodological issues have mainly been discussed in separate outlets, making difficult to get a grasp on them, and thus this paper aims to address this issue. It will help to provide psychophysiological researchers with recommendations and practical advice concerning experimental designs, data analysis, and data reporting. This will ensure that researchers starting a project with HRV and cardiac vagal tone are well informed regarding methodological considerations in order for their findings to contribute to knowledge advancement in their field. PMID:28265249

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

PubMed

Šponer, Jiří; Bussi, Giovanni; Krepl, Miroslav; Banáš, Pavel; Bottaro, Sandro; Cunha, Richard A; Gil-Ley, Alejandro; Pinamonti, Giovanni; Poblete, Simón; Jurečka, Petr; Walter, Nils G; Otyepka, Michal

2018-04-25

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

Determination of the Secondary Bjerknes Force in Acoustic Resonators on Ground and in Microgravity Conditions

NASA Astrophysics Data System (ADS)

Castro, Luz Angelica; Hoyos, Mauricio

2016-04-01

We propose an experimental methodology to determine the secondary Bjerknes force between rigid particles. Measurements done for different particles sizes showed acoustical inter particles interactions. We use and extend the methodology presented in a previous work. The determination of this force will lead us a better understanding of the aggregation process in acoustic resonators. We report in this work, the results of two parabolic flights campaigns performed at the Airbus A300 ZERO-G (Novespace, France).

Polarizable Molecular Dynamics in a Polarizable Continuum Solvent

PubMed Central

Lipparini, Filippo; Lagardère, Louis; Raynaud, Christophe; Stamm, Benjamin; Cancès, Eric; Mennucci, Benedetta; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip

2015-01-01

We present for the first time scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with non variational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real life systems, on standard cluster nodes; a scalable parallel implementation allows for further speed up in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable and long term energy conservation can be achieved. This paper is focused on the methodological developments, on the analysis of the algorithm and on the stability of the simulations; a proof-of-concept application is also presented to attest the possibilities of this newly developed technique. PMID:26516318

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

PubMed

Krupa, Paweł; Mozolewska, Magdalena A; Wiśniewska, Marta; Yin, Yanping; He, Yi; Sieradzan, Adam K; Ganzynkowicz, Robert; Lipska, Agnieszka G; Karczyńska, Agnieszka; Ślusarz, Magdalena; Ślusarz, Rafał; Giełdoń, Artur; Czaplewski, Cezary; Jagieła, Dawid; Zaborowski, Bartłomiej; Scheraga, Harold A; Liwo, Adam

2016-11-01

Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes. Freely available on the web at http://www.unres.pl/ CONTACT: has5@cornell.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Task III: Development of an Effective Computational Methodology for Body Force Representation of High-speed Rotor 37

NASA Technical Reports Server (NTRS)

Tan, Choon-Sooi; Suder, Kenneth (Technical Monitor)

2003-01-01

A framework for an effective computational methodology for characterizing the stability and the impact of distortion in high-speed multi-stage compressor is being developed. The methodology consists of using a few isolated-blade row Navier-Stokes solutions for each blade row to construct a body force database. The purpose of the body force database is to replace each blade row in a multi-stage compressor by a body force distribution to produce same pressure rise and flow turning. To do this, each body force database is generated in such a way that it can respond to the changes in local flow conditions. Once the database is generated, no hrther Navier-Stokes computations are necessary. The process is repeated for every blade row in the multi-stage compressor. The body forces are then embedded as source terms in an Euler solver. The method is developed to have the capability to compute the performance in a flow that has radial as well as circumferential non-uniformity with a length scale larger than a blade pitch; thus it can potentially be used to characterize the stability of a compressor under design. It is these two latter features as well as the accompanying procedure to obtain the body force representation that distinguish the present methodology from the streamline curvature method. The overall computational procedures have been developed. A dimensional analysis was carried out to determine the local flow conditions for parameterizing the magnitudes of the local body force representation of blade rows. An Euler solver was modified to embed the body forces as source terms. The results from the dimensional analysis show that the body forces can be parameterized in terms of the two relative flow angles, the relative Mach number, and the Reynolds number. For flow in a high-speed transonic blade row, they can be parameterized in terms of the local relative Mach number alone.

Topometry optimization of sheet metal structures for crashworthiness design using hybrid cellular automata

NASA Astrophysics Data System (ADS)

Mozumder, Chandan K.

The objective in crashworthiness design is to generate plastically deformable energy absorbing structures which can satisfy the prescribed force-displacement (FD) response. The FD behavior determines the reaction force, displacement and the internal energy that the structure should withstand. However, attempts to include this requirement in structural optimization problems remain scarce. The existing commercial optimization tools utilize models under static loading conditions because of the complexities associated with dynamic/impact loading. Due to the complexity of a crash event and the consequent time required to numerically analyze the dynamic response of the structure, classical methods (i.e., gradient-based and direct) are not well developed to solve this undertaking. This work presents an approach under the framework of the hybrid cellular automaton (HCA) method to solve the above challenge. The HCA method has been successfully applied to nonlinear transient topology optimization for crashworthiness design. In this work, the HCA algorithm has been utilized to develop an efficient methodology for synthesizing shell-based sheet metal structures with optimal material thickness distribution under a dynamic loading event using topometry optimization. This method utilizes the cellular automata (CA) computing paradigm and nonlinear transient finite element analysis (FEA) via ls-dyna. In this method, a set field variables is driven to their target states by changing a convenient set of design variables (e.g., thickness). These rules operate locally in cells within a lattice that only know local conditions. The field variables associated with the cells are driven to a setpoint to obtain the desired structure. This methodology is used to design for structures with controlled energy absorption with specified buckling zones. The peak reaction force and the maximum displacement are also constrained to meet the desired safety level according to passenger safety regulations. Design for prescribed FD response by minimizing the error between the actual response and desired FD curve is implemented. With the use of HCA rules, manufacturability constraints (e.g., rolling) and structures which can be manufactured by special techniques, such as, tailor-welded blanks (TWB), have also been implemented. This methodology is applied to shock-absorbing structural components for passengers in a crashing vehicle. These results are compared to previous designs showing the benefits of the method introduced in this work.

Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.

PubMed

Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma

2015-11-01

Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time. Copyright © 2015 Elsevier Inc. All rights reserved.

Magnetic resonant wireless power transfer for propulsion of implantable micro-robot

NASA Astrophysics Data System (ADS)

Kim, D.; Kim, M.; Yoo, J.; Park, H.-H.; Ahn, S.

2015-05-01

Recently, various types of mobile micro-robots have been proposed for medical and industrial applications. Especially in medical applications, a motor system for propulsion cannot easily be used in a micro-robot due to their small size. Therefore, micro-robots are usually actuated by controlling the magnitude and direction of an external magnetic field. However, for micro-robots, these methods in general are only applicable for moving and drilling operations, but not for the undertaking of various missions. In this paper, we propose a new micro-robot concept, which uses wireless power transfer to deliver the propulsion force and electric power simultaneously. The mechanism of Lorentz force generation and the coil design methodologies are explained, and validation of the proposed propulsion system for a micro-robot is discussed thorough a simulation and with actual measurements with up-scaled test vehicles.

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

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

Curriculum evaluation and revision in a nascent field: the utility of the retrospective pretest--posttest model in a homeland security program of study.

PubMed

Pelfrey, William V; Pelfrey, William V

2009-02-01

Although most academic disciplines evolve at a measured pace, the emerging field of homeland security must, for reasons of safety and security, evolve rapidly. The Department of Homeland Security sponsored the establishment of a graduate educational program for key officials holding homeland security roles. Because homeland security is a nascent field, the establishment of a program curriculum was forced to draw from a variety of disciplines. Curriculum evaluation was complicated by the rapid changes occurring in the emerging discipline, producing response shift bias, and interfering with the pre-post assessments. To compensate for the validity threat associated with response shift bias, a retrospective pretest-posttest evaluative methodology was used. Data indicate the program has evolved in a significant and orderly fashion and these data support the use of this innovative evaluation approach in the development of any discipline.

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

A methodology to condition distorted acoustic emission signals to identify fracture timing from human cadaver spine impact tests.

PubMed

Arun, Mike W J; Yoganandan, Narayan; Stemper, Brian D; Pintar, Frank A

2014-12-01

While studies have used acoustic sensors to determine fracture initiation time in biomechanical studies, a systematic procedure is not established to process acoustic signals. The objective of the study was to develop a methodology to condition distorted acoustic emission data using signal processing techniques to identify fracture initiation time. The methodology was developed from testing a human cadaver lumbar spine column. Acoustic sensors were glued to all vertebrae, high-rate impact loading was applied, load-time histories were recorded (load cell), and fracture was documented using CT. Compression fracture occurred to L1 while other vertebrae were intact. FFT of raw voltage-time traces were used to determine an optimum frequency range associated with high decibel levels. Signals were bandpass filtered in this range. Bursting pattern was found in the fractured vertebra while signals from other vertebrae were silent. Bursting time was associated with time of fracture initiation. Force at fracture was determined using this time and force-time data. The methodology is independent of selecting parameters a priori such as fixing a voltage level(s), bandpass frequency and/or using force-time signal, and allows determination of force based on time identified during signal processing. The methodology can be used for different body regions in cadaver experiments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Grade 10 Thai students' scientific argumentation in learning about electric field through science, technology, and society (STS) approach

NASA Astrophysics Data System (ADS)

Chitnork, Amporn; Yuenyong, Chokchai

2018-01-01

The research aimed to enhance Grade 10 Thai students' scientific argumentation in learning about electric field through science, technology, and society (STS) approach. The participants included 45 Grade 10 students who were studying in a school in Nongsonghong, Khon Kaen, Thailand. Methodology regarded interpretive paradigm. The intervention was the force unit which was provided based on Yuenyong (2006) STS approach. Students learned about the STS electric field unit for 4 weeks. The students' scientific argumentation was interpreted based on Toulmin's argument pattern or TAP. The TAP provided six components of argumentation including data, claim, warrants, qualifiers, rebuttals and backing. Tools of interpretation included students' activity sheets, conversation, journal writing, classroom observation and interview. The findings revealed that students held the different pattern of argumentation. Then, they change pattern of argumentation close to the TAP. It indicates that the intervention of STS electric field unit enhance students to develop scientific argumentation. This finding may has implication of further enhancing scientific argumentation in Thailand.

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD™, achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

PubMed

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Systemic Operational Design: Improving Operational Planning for the Netherlands Armed Forces

DTIC Science & Technology

2006-05-25

This methodology is called Soft Systems Methodology . His methodology is a structured way of thinking in which not only a perceived problematic...Many similarities exist between Systemic Operational Design and Soft Systems Methodology , their epistemology is related. Furthermore, they both have...Systems Thinking: Managing Chaos and Complexity. Boston: Butterworth Heinemann, 1999. Checkland, Peter, and Jim Scholes. Soft Systems Methodology in

Modeling Multibody Stage Separation Dynamics Using Constraint Force Equation Methodology

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.; Roithmayr, Carlos M.; Toniolo, Matthew D.; Karlgaard, Christopher D.; Pamadi, Bandu N.

2011-01-01

This paper discusses the application of the constraint force equation methodology and its implementation for multibody separation problems using three specially designed test cases. The first test case involves two rigid bodies connected by a fixed joint, the second case involves two rigid bodies connected with a universal joint, and the third test case is that of Mach 7 separation of the X-43A vehicle. For the first two cases, the solutions obtained using the constraint force equation method compare well with those obtained using industry- standard benchmark codes. For the X-43A case, the constraint force equation solutions show reasonable agreement with the flight-test data. Use of the constraint force equation method facilitates the analysis of stage separation in end-to-end simulations of launch vehicle trajectories

Improving Precipitation Forcings for the National Water Model

NASA Astrophysics Data System (ADS)

Fall, G. M.; Zhang, Z.; Miller, D.; Kitzmiller, D.; Patrick, N.; Sparrow, K.; Olheiser, C.; Szeliga, T.

2017-12-01

The National Weather Service's Office of Water Prediction (NWS/OWP) produces operational hydrologic products, many of which are generated by the National Water Model (NWM). NWM analysis cycles (also known as "near-real-time" or "update" cycles) are of key importance, since the land surface states and fluxes they produce are used to initialize all forecast cycles. Among all forcing fields (which include precipitation, temperature, humidity, radiation, and wind), precipitation is particularly important. Currently, NWM precipitation forcings for analysis cycles are generated by combining hourly radar-derived precipitation products from the Multi-Radar, Multi-Sensor (MRMS) system with short-term quantitative precipitation forecasts (QPF) from the Rapid Refresh (RAP) and High Resolution Rapid Refresh (HRRR) systems. Short term QPF is used in analysis cycles to fill coverage gaps in MRMS products, and its inclusion is necessary due to the short latency associated with NWM analysis cycles relative to the availability of other operational precipitation analyses. This presentation will describe the methodology used to remove QPF bias and to spatially merge MRMS, HRRR, and RAP into hourly forcing inputs for NWM version 2.0, expected to enter into operations in late 2018. The accuracy of version 2.0 precipitation forcings relative to reference data sources, and the degree to which these forcings will represent an improvement over those used to drive the previous NWM version (1.2), will be described.

A Maritime Phase Zero Force for the Year 2020

DTIC Science & Technology

2009-06-01

mind, the team constructed maritime forces and then evaluated them against the same scenarios to determine which ones performed better. The...120  1.  Project Methodology and Choice of Missions ...............................120  2.  Missions and Scenarios construction methodology... projects are designed to build tools that students in the Systems Engineering Analysis curriculum have learned over the 18 month enrollment in the program

A Delphi Study to Determine Variables for Predictive MICAP Modeling

DTIC Science & Technology

2013-06-01

design. Throughout literature it is common to find researchers that do not use qualitative study methodologies. Unlike quantitative methodologies...at Table 3. The researcher did note through a literature review that each questionnaire should be pretested on individuals who have not been involved... RESEARCH PROJECT Jeremy L. Pankoski, Major, USAF AFIT-ENS-GRP-13-J-21 DEPARTMENT OF THE AIR FORCE AIR UNIVERSITY AIR FORCE

System Interdependency Modeling in the Design of Prognostic and Health Management Systems in Smart Manufacturing.

PubMed

Malinowski, M L; Beling, P A; Haimes, Y Y; LaViers, A; Marvel, J A; Weiss, B A

2015-01-01

The fields of risk analysis and prognostics and health management (PHM) have developed in a largely independent fashion. However, both fields share a common core goal. They aspire to manage future adverse consequences associated with prospective dysfunctions of the systems under consideration due to internal or external forces. This paper describes how two prominent risk analysis theories and methodologies - Hierarchical Holographic Modeling (HHM) and Risk Filtering, Ranking, and Management (RFRM) - can be adapted to support the design of PHM systems in the context of smart manufacturing processes. Specifically, the proposed methodologies will be used to identify targets - components, subsystems, or systems - that would most benefit from a PHM system in regards to achieving the following objectives: minimizing cost, minimizing production/maintenance time, maximizing system remaining usable life (RUL), maximizing product quality, and maximizing product output. HHM is a comprehensive modeling theory and methodology that is grounded on the premise that no system can be modeled effectively from a single perspective. It can also be used as an inductive method for scenario structuring to identify emergent forced changes (EFCs) in a system. EFCs connote trends in external or internal sources of risk to a system that may adversely affect specific states of the system. An important aspect of proactive risk management includes bolstering the resilience of the system for specific EFCs by appropriately controlling the states. Risk scenarios for specific EFCs can be the basis for the design of prognostic and diagnostic systems that provide real-time predictions and recognition of scenario changes. The HHM methodology includes visual modeling techniques that can enhance stakeholders' understanding of shared states, resources, objectives and constraints among the interdependent and interconnected subsystems of smart manufacturing systems. In risk analysis, HHM is often paired with Risk Filtering, Ranking, and Management (RFRM). The RFRM process provides the users, (e.g., technology developers, original equipment manufacturers (OEMs), technology integrators, manufacturers), with the most critical risks to the objectives, which can be used to identify the most critical components and subsystems that would most benefit from a PHM system. A case study is presented in which HHM and RFRM are adapted for PHM in the context of an active manufacturing facility located in the United States. The methodologies help to identify the critical risks to the manufacturing process, and the major components and subsystems that would most benefit from a developed PHM system.

System Interdependency Modeling in the Design of Prognostic and Health Management Systems in Smart Manufacturing

PubMed Central

Malinowski, M.L.; Beling, P.A.; Haimes, Y.Y.; LaViers, A.; Marvel, J.A.; Weiss, B.A.

2017-01-01

The fields of risk analysis and prognostics and health management (PHM) have developed in a largely independent fashion. However, both fields share a common core goal. They aspire to manage future adverse consequences associated with prospective dysfunctions of the systems under consideration due to internal or external forces. This paper describes how two prominent risk analysis theories and methodologies – Hierarchical Holographic Modeling (HHM) and Risk Filtering, Ranking, and Management (RFRM) – can be adapted to support the design of PHM systems in the context of smart manufacturing processes. Specifically, the proposed methodologies will be used to identify targets – components, subsystems, or systems – that would most benefit from a PHM system in regards to achieving the following objectives: minimizing cost, minimizing production/maintenance time, maximizing system remaining usable life (RUL), maximizing product quality, and maximizing product output. HHM is a comprehensive modeling theory and methodology that is grounded on the premise that no system can be modeled effectively from a single perspective. It can also be used as an inductive method for scenario structuring to identify emergent forced changes (EFCs) in a system. EFCs connote trends in external or internal sources of risk to a system that may adversely affect specific states of the system. An important aspect of proactive risk management includes bolstering the resilience of the system for specific EFCs by appropriately controlling the states. Risk scenarios for specific EFCs can be the basis for the design of prognostic and diagnostic systems that provide real-time predictions and recognition of scenario changes. The HHM methodology includes visual modeling techniques that can enhance stakeholders’ understanding of shared states, resources, objectives and constraints among the interdependent and interconnected subsystems of smart manufacturing systems. In risk analysis, HHM is often paired with Risk Filtering, Ranking, and Management (RFRM). The RFRM process provides the users, (e.g., technology developers, original equipment manufacturers (OEMs), technology integrators, manufacturers), with the most critical risks to the objectives, which can be used to identify the most critical components and subsystems that would most benefit from a PHM system. A case study is presented in which HHM and RFRM are adapted for PHM in the context of an active manufacturing facility located in the United States. The methodologies help to identify the critical risks to the manufacturing process, and the major components and subsystems that would most benefit from a developed PHM system. PMID:28664162

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.

Doctoral training in statistics, measurement, and methodology in psychology: replication and extension of Aiken, West, Sechrest, and Reno's (1990) survey of PhD programs in North America.

PubMed

Aiken, Leona S; West, Stephen G; Millsap, Roger E

2008-01-01

In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD programs (86%) participated. This survey replicated and extended a previous survey (L. S. Aiken, S. G. West, L. B. Sechrest, & R. R. Reno, 1990), permitting examination of curriculum development. Most training supported laboratory and not field research. The median of 1.6 years of training in statistics and measurement was mainly devoted to the modally 1-year introductory statistics course, leaving little room for advanced study. Curricular enhancements were noted in statistics and to a minor degree in measurement. Additional coverage of both fundamental and innovative quantitative methodology is needed. The research design curriculum has largely stagnated, a cause for great concern. Elite programs showed no overall advantage in quantitative training. Forces that support curricular innovation are characterized. Human capital challenges to quantitative training, including recruiting and supporting young quantitative faculty, are discussed. Steps must be taken to bring innovations in quantitative methodology into the curriculum of PhD programs in psychology. PsycINFO Database Record (c) 2008 APA, all rights reserved.

Path planning in uncertain flow fields using ensemble method

NASA Astrophysics Data System (ADS)

Wang, Tong; Le Maître, Olivier P.; Hoteit, Ibrahim; Knio, Omar M.

2016-10-01

An ensemble-based approach is developed to conduct optimal path planning in unsteady ocean currents under uncertainty. We focus our attention on two-dimensional steady and unsteady uncertain flows, and adopt a sampling methodology that is well suited to operational forecasts, where an ensemble of deterministic predictions is used to model and quantify uncertainty. In an operational setting, much about dynamics, topography, and forcing of the ocean environment is uncertain. To address this uncertainty, the flow field is parametrized using a finite number of independent canonical random variables with known densities, and the ensemble is generated by sampling these variables. For each of the resulting realizations of the uncertain current field, we predict the path that minimizes the travel time by solving a boundary value problem (BVP), based on the Pontryagin maximum principle. A family of backward-in-time trajectories starting at the end position is used to generate suitable initial values for the BVP solver. This allows us to examine and analyze the performance of the sampling strategy and to develop insight into extensions dealing with general circulation ocean models. In particular, the ensemble method enables us to perform a statistical analysis of travel times and consequently develop a path planning approach that accounts for these statistics. The proposed methodology is tested for a number of scenarios. We first validate our algorithms by reproducing simple canonical solutions, and then demonstrate our approach in more complex flow fields, including idealized, steady and unsteady double-gyre flows.

Generating The Force: The Roundout Brigade

DTIC Science & Technology

1992-05-20

The Total Force Policy means the integration of planning, programming and budgeting for the manning, equipping, maintaining and training of a mix of...methodology for making force mix decisions: cost, force capability, training requirements, and personnel availability. The GAO did not 3 include political...considerations as part of its criteria for force mix determination. However, any examination of Active and Reserve Component force structure must

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

PubMed Central

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

Biological Parametric Mapping: A Statistical Toolbox for Multi-Modality Brain Image Analysis

PubMed Central

Casanova, Ramon; Ryali, Srikanth; Baer, Aaron; Laurienti, Paul J.; Burdette, Jonathan H.; Hayasaka, Satoru; Flowers, Lynn; Wood, Frank; Maldjian, Joseph A.

2006-01-01

In recent years multiple brain MR imaging modalities have emerged; however, analysis methodologies have mainly remained modality specific. In addition, when comparing across imaging modalities, most researchers have been forced to rely on simple region-of-interest type analyses, which do not allow the voxel-by-voxel comparisons necessary to answer more sophisticated neuroscience questions. To overcome these limitations, we developed a toolbox for multimodal image analysis called biological parametric mapping (BPM), based on a voxel-wise use of the general linear model. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in MATLAB with a user friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely-used T-field, has been implemented in the correlation analysis for more accurate results. An example with in-vivo data is presented demonstrating the potential of the BPM methodology as a tool for multimodal image analysis. PMID:17070709

The Methodology of Calculation of Cutting Forces When Machining Composite Materials

NASA Astrophysics Data System (ADS)

Rychkov, D. A.; Yanyushkin, A. S.

2016-08-01

Cutting of composite materials has specific features and is different from the processing of metals. When this characteristic intense wear of the cutting tool. An important criterion in the selection process parameters composite processing is the value of the cutting forces, which depends on many factors and is determined experimentally, it is not always appropriate. The study developed a method of determining the cutting forces when machining composite materials and the comparative evaluation of the calculated and actual values of cutting forces. The methodology for calculating cutting forces into account specific features of the cutting tool and the extent of wear, the strength properties of the processed material and cutting conditions. Experimental studies conducted with fiberglass milling cutter equipped with elements of hard metal VK3M. The discrepancy between the estimated and the actual values of the cutting force is not more than 10%.

Methods for estimating the labour force insured by the Ontario Workplace Safety and Insurance Board: 1990-2000.

PubMed

Smith, Peter M; Mustard, Cameron A; Payne, Jennifer I

2004-01-01

This paper presents a methodology for estimating the size and composition of the Ontario labour force eligible for coverage under the Ontario Workplace Safety & Insurance Act (WSIA). Using customized tabulations from Statistics Canada's Labour Force Survey (LFS), we made adjustments for self-employment, unemployment, part-time employment and employment in specific industrial sectors excluded from insurance coverage under the WSIA. Each adjustment to the LFS reduced the estimates of the insured labour force relative to the total Ontario labour force. These estimates were then developed for major occupational and industrial groups stratified by gender. Additional estimates created to test assumptions used in the methodology produced similar results. The methods described in this paper advance those previously used to estimate the insured labour force, providing researchers with a useful tool to describe trends in the rate of injury across differing occupational, industrial and gender groups in Ontario.

Surface-Controlled Properties of Myosin Studied by Electric Field Modulation.

PubMed

van Zalinge, Harm; Ramsey, Laurence C; Aveyard, Jenny; Persson, Malin; Mansson, Alf; Nicolau, Dan V

2015-08-04

The efficiency of dynamic nanodevices using surface-immobilized protein molecular motors, which have been proposed for diagnostics, drug discovery, and biocomputation, critically depends on the ability to precisely control the motion of motor-propelled, individual cytoskeletal filaments transporting cargo to designated locations. The efficiency of these devices also critically depends on the proper function of the propelling motors, which is controlled by their interaction with the surfaces they are immobilized on. Here we use a microfluidic device to study how the motion of the motile elements, i.e., actin filaments propelled by heavy mero-myosin (HMM) motor fragments immobilized on various surfaces, is altered by the application of electrical loads generated by an external electric field with strengths ranging from 0 to 8 kVm(-1). Because the motility is intimately linked to the function of surface-immobilized motors, the study also showed how the adsorption properties of HMM on various surfaces, such as nitrocellulose (NC), trimethylclorosilane (TMCS), poly(methyl methacrylate) (PMMA), poly(tert-butyl methacrylate) (PtBMA), and poly(butyl methacrylate) (PBMA), can be characterized using an external field. It was found that at an electric field of 5 kVm(-1) the force exerted on the filaments is sufficient to overcome the frictionlike resistive force of the inactive motors. It was also found that the effect of assisting electric fields on the relative increase in the sliding velocity was markedly higher for the TMCS-derivatized surface than for all other polymer-based surfaces. An explanation of this behavior, based on the molecular rigidity of the TMCS-on-glass surfaces as opposed to the flexibility of the polymer-based ones, is considered. To this end, the proposed microfluidic device could be used to select appropriate surfaces for future lab-on-a-chip applications as illustrated here for the almost ideal TMCS surface. Furthermore, the proposed methodology can be used to gain fundamental insights into the functioning of protein molecular motors, such as the force exerted by the motors under different operational conditions.

A shared position/force control methodology for teleoperation

NASA Technical Reports Server (NTRS)

Lee, Jin S.

1987-01-01

A flexible and computationally efficient shared position/force control concept and its implementation in the Robot Control C Library (RCCL) are presented form the point of teleoperation. This methodology enables certain degrees of freedom to be position-controlled through real time manual inputs and the remaining degrees of freedom to be force-controlled by computer. Functionally, it is a hybrid control scheme in that certain degrees of freedom are designated to be under position control, and the remaining degrees of freedom to be under force control. However, the methodology is also a shared control scheme because some degrees of freedom can be put under manual control and the other degrees of freedom put under computer control. Unlike other hybrid control schemes, which process position and force commands independently, this scheme provides a force control loop built on top of a position control inner loop. This feature minimizes the computational burden and increases disturbance rejection. A simple implementation is achieved partly because the joint control servos that are part of most robots can be used to provide the position control inner loop. Along with this control scheme, several menus were implemented for the convenience of the user. The implemented control scheme was successfully demonstrated for the tasks of hinged-panel opening and peg-in-hole insertion.

The Society for Implementation Research Collaboration Instrument Review Project: a methodology to promote rigorous evaluation.

PubMed

Lewis, Cara C; Stanick, Cameo F; Martinez, Ruben G; Weiner, Bryan J; Kim, Mimi; Barwick, Melanie; Comtois, Katherine A

2015-01-08

Identification of psychometrically strong instruments for the field of implementation science is a high priority underscored in a recent National Institutes of Health working meeting (October 2013). Existing instrument reviews are limited in scope, methods, and findings. The Society for Implementation Research Collaboration Instrument Review Project's objectives address these limitations by identifying and applying a unique methodology to conduct a systematic and comprehensive review of quantitative instruments assessing constructs delineated in two of the field's most widely used frameworks, adopt a systematic search process (using standard search strings), and engage an international team of experts to assess the full range of psychometric criteria (reliability, construct and criterion validity). Although this work focuses on implementation of psychosocial interventions in mental health and health-care settings, the methodology and results will likely be useful across a broad spectrum of settings. This effort has culminated in a centralized online open-access repository of instruments depicting graphical head-to-head comparisons of their psychometric properties. This article describes the methodology and preliminary outcomes. The seven stages of the review, synthesis, and evaluation methodology include (1) setting the scope for the review, (2) identifying frameworks to organize and complete the review, (3) generating a search protocol for the literature review of constructs, (4) literature review of specific instruments, (5) development of an evidence-based assessment rating criteria, (6) data extraction and rating instrument quality by a task force of implementation experts to inform knowledge synthesis, and (7) the creation of a website repository. To date, this multi-faceted and collaborative search and synthesis methodology has identified over 420 instruments related to 34 constructs (total 48 including subconstructs) that are relevant to implementation science. Despite numerous constructs having greater than 20 available instruments, which implies saturation, preliminary results suggest that few instruments stem from gold standard development procedures. We anticipate identifying few high-quality, psychometrically sound instruments once our evidence-based assessment rating criteria have been applied. The results of this methodology may enhance the rigor of implementation science evaluations by systematically facilitating access to psychometrically validated instruments and identifying where further instrument development is needed.

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

First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea

NASA Astrophysics Data System (ADS)

Masunov, Artëm E.; Tannu, Arman; Dyakov, Alexander A.; Matveeva, Anastasia D.; Freidzon, Alexandra Ya.; Odinokov, Alexey V.; Bagaturyants, Alexander A.

2017-06-01

The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature. Here we propose using global lattice energy minimization to predict the crystal packing from the first principles. We developed a methodology that includes the following: (1) parameter derivation for polarizable force field AMOEBA; (2) local minimizations of crystal structures with these parameters, combined with the evolutionary algorithm for a global minimum search, implemented in program USPEX; (3) filtering out duplicate polymorphs produced; (4) reoptimization and final ranking based on density functional theory (DFT) with many-body dispersion (MBD) correction; and (5) prediction of the second-order susceptibility tensor by finite field approach. This methodology was applied to predict virtual urea polymorphs. After filtering based on packing similarity, only two distinct packing modes were predicted: one experimental and one hypothetical. DFT + MBD ranking established non-centrosymmetric crystal packing as the global minimum, in agreement with the experiment. Finite field approach was used to predict nonlinear susceptibility, and H-bonding was found to account for a 2.5-fold increase in molecular hyperpolarizability to the bulk value.

All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

PubMed

Prior, C; Danilāne, L; Oganesyan, V S

2018-05-16

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

Molecular simulation of aqueous electrolyte solubility. 2. Osmotic ensemble Monte Carlo methodology for free energy and solubility calculations and application to NaCl.

PubMed

Moučka, Filip; Lísal, Martin; Škvor, Jiří; Jirsák, Jan; Nezbeda, Ivo; Smith, William R

2011-06-23

We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.

Optical tweezers force measurements to study parasites chemotaxis

NASA Astrophysics Data System (ADS)

de Thomaz, A. A.; Pozzo, L. Y.; Fontes, A.; Almeida, D. B.; Stahl, C. V.; Santos-Mallet, J. R.; Gomes, S. A. O.; Feder, D.; Ayres, D. C.; Giorgio, S.; Cesar, C. L.

2009-07-01

In this work, we propose a methodology to study microorganisms chemotaxis in real time using an Optical Tweezers system. Optical Tweezers allowed real time measurements of the force vectors, strength and direction, of living parasites under chemical or other kinds of gradients. This seems to be the ideal tool to perform observations of taxis response of cells and microorganisms with high sensitivity to capture instantaneous responses to a given stimulus. Forces involved in the movement of unicellular parasites are very small, in the femto-pico-Newton range, about the same order of magnitude of the forces generated in an Optical Tweezers. We applied this methodology to investigate the Leishmania amazonensis (L. amazonensis) and Trypanossoma cruzi (T. cruzi) under distinct situations.

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

Schoenbauer, B.; Bohac, D.; Huelman, P.

Combined space and water heater (combi or combo) systems are defined by their dual functionality. Combi systems provide both space heating and water heating capabilities with a single heat source. This guideline will focus on the installation and operation of residential systems with forced air heating and domestic hot water (DHW) functionality. Past NorthernSTAR research has used a combi system to replace a natural gas forced air distribution system furnace and tank type water heater (Schoenbauer et al. 2012; Schoenbauer, Bohac, and McAlpine 2014). The combi systems consisted of a water heater or boiler heating plant teamed with a hydronicmore » air handler that included an air handler, water coil, and water pump to circulate water between the heating plant and coil. The combi water heater or boiler had a separate circuit for DHW. Past projects focused on laboratory testing, field characterization, and control optimization of combi systems. Laboratory testing was done to fully characterize and test combi system components; field testing was completed to characterize the installed performance of combi systems; and control methodologies were analyzed to understand the potential of controls to simplify installation and design and to improve system efficiency and occupant comfort. This past work was relied upon on to create this measure guideline.« less

Tiny tweaks, big changes: An alternative strategy to empower ethical culture of human research in anesthesia (A Taiwan Acta Anesthesiologica Taiwanica-Ethics Review Task Force Report).

PubMed

Luk, Hsiang-Ning; Ennever, John F; Day, Yuan-Ji; Wong, Chih-Shung; Sun, Wei-Zen

2015-03-01

For this guidance article, the Ethics Review Task Force (ERTF) of the Journal reviewed and discussed the ethics issues related to publication of human research in the field of anesthesia. ERTF first introduced international ethics principles and minimal requirements of reporting of ethics practices, followed by discussing the universal problems of publication ethics. ERTF then compared the accountability and methodology of several medical journals in assuring authors' ethics compliance. Using the Taiwan Institutional Review Board system as an example, ERTF expressed the importance of institutional review board registration and accreditation to assure human participant protection. ERTF presented four major human research misconducts in the field of anesthesia in recent years. ERTF finally proposed a flow-chart to guide journal peer reviewers and editors in ethics review during the editorial process in publishing. Examples of template languages applied in the Ethics statement section in the manuscript are expected to strengthen the ethics compliance of the authors and to set an ethical culture for all the stakeholders involved in human research. Copyright © 2015. Published by Elsevier B.V.

Ligand- and receptor-based docking with LiBELa

NASA Astrophysics Data System (ADS)

dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

2015-08-01

Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Comprehensive Forced Response Analysis of J2X Turbine Bladed-Discs with 36- Degree Variation in CFD Loading

NASA Technical Reports Server (NTRS)

Elrod, David; Christensen, Eric; Brown, Andrew

2011-01-01

At NASA/MSFC, Structural Dynamics personnel continue to perform advanced analysis for the turbomachinery in the J2X Rocket Engine, which is under consideration for the new Space Launch System. One of the most challenging analyses in the program is predicting turbine blade structural capability. Resonance was predicted by modal analysis, so comprehensive forced response analyses using high fidelity cyclic symmetric finite element models were initiated as required. Analysis methodologies up to this point have assumed the flow field could be fully described by a sector, so the loading on every blade would be identical as it travelled through it. However, in the J2X the CFD flow field varied over the 360 deg of a revolution because of the flow speeds and tortuous axial path. MSFC therefore developed a complex procedure using Nastran Dmap's and Matlab scripts to apply this circumferentially varying loading onto the cyclically symmetric structural models to produce accurate dynamic stresses for every blade on the disk. This procedure is coupled with static, spin, and thermal loading to produce high cycle fatigue safety factors resulting in much more accurate analytical assessments of the blades.

Very empirical treatment of solvation and entropy: a force field derived from Log Po/w

NASA Astrophysics Data System (ADS)

Kellogg, Glen Eugene; Burnett, James C.; Abraham, Donald J.

2001-04-01

A non-covalent interaction force field model derived from the partition coefficient of 1-octanol/water solubility is described. This model, HINT for Hydropathic INTeractions, is shown to include, in very empirical and approximate terms, all components of biomolecular associations, including hydrogen bonding, Coulombic interactions, hydrophobic interactions, entropy and solvation/desolvation. Particular emphasis is placed on: (1) demonstrating the relationship between the total empirical HINT score and free energy of association, ΔG interaction; (2) showing that the HINT hydrophobic-polar interaction sub-score represents the energy cost of desolvation upon binding for interacting biomolecules; and (3) a new methodology for treating constrained water molecules as discrete independent small ligands. An example calculation is reported for dihydrofolate reductase (DHFR) bound with methotrexate (MTX). In that case the observed very tight binding, ΔG interaction≤-13.6 kcal mol-1, is largely due to ten hydrogen bonds between the ligand and enzyme with estimated strength ranging between -0.4 and -2.3 kcal mol-1. Four water molecules bridging between DHFR and MTX contribute an additional -1.7 kcal mol-1 stability to the complex. The HINT estimate of the cost of desolvation is +13.9 kcal mol-1.

ForC: a global database of forest carbon stocks and fluxes.

PubMed

Anderson-Teixeira, Kristina J; Wang, Maria M H; McGarvey, Jennifer C; Herrmann, Valentine; Tepley, Alan J; Bond-Lamberty, Ben; LeBauer, David S

2018-06-01

Forests play an influential role in the global carbon (C) cycle, storing roughly half of terrestrial C and annually exchanging with the atmosphere more than five times the carbon dioxide (CO 2 ) emitted by anthropogenic activities. Yet, scaling up from field-based measurements of forest C stocks and fluxes to understand global scale C cycling and its climate sensitivity remains an important challenge. Tens of thousands of forest C measurements have been made, but these data have yet to be integrated into a single database that makes them accessible for integrated analyses. Here we present an open-access global Forest Carbon database (ForC) containing previously published records of field-based measurements of ecosystem-level C stocks and annual fluxes, along with disturbance history and methodological information. ForC expands upon the previously published tropical portion of this database, TropForC (https://doi.org/10.5061/dryad.t516f), now including 17,367 records (previously 3,568) representing 2,731 plots (previously 845) in 826 geographically distinct areas. The database covers all forested biogeographic and climate zones, represents forest stands of all ages, and currently includes data collected between 1934 and 2015. We expect that ForC will prove useful for macroecological analyses of forest C cycling, for evaluation of model predictions or remote sensing products, for quantifying the contribution of forests to the global C cycle, and for supporting international efforts to inventory forest carbon and greenhouse gas exchange. A dynamic version of ForC is maintained at on GitHub (https://GitHub.com/forc-db), and we encourage the research community to collaborate in updating, correcting, expanding, and utilizing this database. ForC is an open access database, and we encourage use of the data for scientific research and education purposes. Data may not be used for commercial purposes without written permission of the database PI. Any publications using ForC data should cite this publication and Anderson-Teixeira et al. (2016a) (see Metadata S1). No other copyright or cost restrictions are associated with the use of this data set. © 2018 by the Ecological Society of America.

Soft tissue modelling through autowaves for surgery simulation.

PubMed

Zhong, Yongmin; Shirinzadeh, Bijan; Alici, Gursel; Smith, Julian

2006-09-01

Modelling of soft tissue deformation is of great importance to virtual reality based surgery simulation. This paper presents a new methodology for simulation of soft tissue deformation by drawing an analogy between autowaves and soft tissue deformation. The potential energy stored in a soft tissue as a result of a deformation caused by an external force is propagated among mass points of the soft tissue by non-linear autowaves. The novelty of the methodology is that (i) autowave techniques are established to describe the potential energy distribution of a deformation for extrapolating internal forces, and (ii) non-linear materials are modelled with non-linear autowaves other than geometric non-linearity. Integration with a haptic device has been achieved to simulate soft tissue deformation with force feedback. The proposed methodology not only deals with large-range deformations, but also accommodates isotropic, anisotropic and inhomogeneous materials by simply changing diffusion coefficients.

Quantum transport and the Wigner distribution function for Bloch electrons in spatially homogeneous electric and magnetic fields

NASA Astrophysics Data System (ADS)

Iafrate, G. J.; Sokolov, V. N.; Krieger, J. B.

2017-10-01

The theory of Bloch electron dynamics for carriers in homogeneous electric and magnetic fields of arbitrary time dependence is developed in the framework of the Liouville equation. The Wigner distribution function (WDF) is determined from the single-particle density matrix in the ballistic regime, i.e., collision effects are excluded. In the theory, the single-particle transport equation is established with the electric field described in the vector potential gauge, and the magnetic field is treated in the symmetric gauge. No specific assumptions are made concerning the form of the initial distribution in momentum or configuration space. The general approach is to employ the accelerated Bloch state representation (ABR) as a basis so that the dependence upon the electric field, including multiband Zener tunneling, is treated exactly. Further, in the formulation of the WDF, we transform to a new set of variables so that the final WDF is gauge invariant and is expressed explicitly in terms of the position, kinetic momentum, and time. The methodology for developing the WDF is illustrated by deriving the exact WDF equation for free electrons in homogeneous electric and magnetic fields resulting in the same form as given by the collisionless Boltzmann transport equation (BTE). The methodology is then extended to the case of electrons described by an effective Hamiltonian corresponding to an arbitrary energy band function; the exact WDF equation results for the effective Hamiltonian case are shown to approximate the free electron results when taken to second order in the magnetic field. As a corollary, in these cases, it is shown that if the WDF is a wave packet, then the time rate of change of the electron quasimomentum is given by the Lorentz force. In treating the problem of Bloch electrons in a periodic potential in the presence of homogeneous electric and magnetic fields, the methodology for deriving the WDF reveals a multiband character due to the inherent nature of the Bloch states. The K0 representation of the Bloch envelope functions is employed to express the multiband WDF in a useful form. In examining the single-band WDF, it is found that the collisionless WDF equation matches the equivalent BTE to first order in the magnetic field. These results are necessarily extended to second order in the magnetic field by employing a unitary transformation that diagonalizes the Hamiltonian using the ABR to second order. The unitary transformation process includes a discussion of the multiband WDF transport analysis and the identification of the combined Zener-magnetic-field induced tunneling.

Future in biomolecular computation

NASA Astrophysics Data System (ADS)

Wimmer, E.

1988-01-01

Large-scale computations for biomolecules are dominated by three levels of theory: rigorous quantum mechanical calculations for molecules with up to about 30 atoms, semi-empirical quantum mechanical calculations for systems with up to several hundred atoms, and force-field molecular dynamics studies of biomacromolecules with 10,000 atoms and more including surrounding solvent molecules. It can be anticipated that increased computational power will allow the treatment of larger systems of ever growing complexity. Due to the scaling of the computational requirements with increasing number of atoms, the force-field approaches will benefit the most from increased computational power. On the other hand, progress in methodologies such as density functional theory will enable us to treat larger systems on a fully quantum mechanical level and a combination of molecular dynamics and quantum mechanics can be envisioned. One of the greatest challenges in biomolecular computation is the protein folding problem. It is unclear at this point, if an approach with current methodologies will lead to a satisfactory answer or if unconventional, new approaches will be necessary. In any event, due to the complexity of biomolecular systems, a hierarchy of approaches will have to be established and used in order to capture the wide ranges of length-scales and time-scales involved in biological processes. In terms of hardware development, speed and power of computers will increase while the price/performance ratio will become more and more favorable. Parallelism can be anticipated to become an integral architectural feature in a range of computers. It is unclear at this point, how fast massively parallel systems will become easy enough to use so that new methodological developments can be pursued on such computers. Current trends show that distributed processing such as the combination of convenient graphics workstations and powerful general-purpose supercomputers will lead to a new style of computing in which the calculations are monitored and manipulated as they proceed. The combination of a numeric approach with artificial-intelligence approaches can be expected to open up entirely new possibilities. Ultimately, the most exciding aspect of the future in biomolecular computing will be the unexpected discoveries.

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.

Mechanical equilibrium of forces and moments applied on orthodontic brackets of a dental arch: Correlation with literature data on two and three adjacent teeth.

PubMed

Wagner, Delphine; Bolender, Yves; Rémond, Yves; George, Daniel

2017-01-01

Although orthodontics have greatly improved over the years, understanding of its associated biomechanics remains incomplete and is mainly based on two dimensional (2D) mechanical equilibrium and long-time clinical experience. Little experimental information exists in three dimensions (3D) about the forces and moments developed on orthodontic brackets over more than two or three adjacent teeth. We define here a simplified methodology to quantify 3D forces and moments applied on orthodontic brackets fixed on a dental arch and validate our methodology using existing results from the literature by means of simplified hypotheses.

Local Wind Influence on Freshwater Plume Behavior: Application to the Catalan Shelf.

NASA Astrophysics Data System (ADS)

Liste, Maria; Grifoll, Manel; Monbaliu, Jaak; Keupers, Ingrid; Komijani, Homayoon

2013-04-01

Introduction Freshwater fluxes are not always considered, and often their 3D character is neglected. The "distributed" continental run-off is seldom taken into consideration. The main aim of the EU-FP7 Field_Ac project (www.field_ac.eu), was to improve operational service for coastal areas and to generate added value for shelf and regional scale predictions including land discharge as a boundary condition. In this paper the dispersal of a fresh water plume in a small part of the Catalan Coast (NW Mediterranean Sea) caused by a flash flood event in March 2011 is presented in response to the local wind forcing. Observations and modeling results are shown for a short period but with a large impact on the receiving coastal waters. Methodology and aim For the coastal circulation model, version 3.0 of the Regional Ocean Modeling System [ROMS, Shchepetkin and McWilliams, 2005] has been chosen. ROMS solves the 3-D Reynolds-Averaged Navier-Stokes equations in sigma coordinates. The code design is modular, so that different choices for advection and mixing, for example, may be applied by simply modifying preprocessor flags. Nested increasing-resolution models have been implemented in order to reproduce with sufficient spatial resolution the coastal circulation and the river plume evolution in a small portion of the Catalan coastal area. The boundary conditions for the largest domain model are obtained from the MyOcean products. River and urban run-off are estimated based on measured or predicted rainfall in the contributing catchments areas. Conceptual models based on a reservoir-type schematization of the river and sewer network have been set up to allow for fast prediction of the different point source boundary conditions [Keupers et al., 2011]. Model output data are compared to in situ data from dedicated campaigns during the Field_AC Project and to data from operational buoys in the Catalan coastal area. Results Wind forcing leads to freshwater spreading. As expected, wind speed and direction and the magnitude of the fresh water discharge affect substantially the plume behavior. This case study illustrates clearly the need to consider both the wind forcing and the fresh water discharge as part of a single system. References Field_AC project (www.field_ac.eu), EU- FP7-SPACE-2009-1-242284. Keupers, I., Willems, P., Fernandez Sainz, J., Bricheno, L., Wolf, J., Polton, J., Howarth, J., Carniel, S., Staneva, J. (2011). Methodology (including best practice guidelines) on how to identify and incorporate 'concentrated' and 'distributed' run-off in pre-operational forecasts, based on the input and requirements from our users. FIELD_AC project, D3.1, 90 pp. MyOcean products (http://www.myocean.eu/). Shchepetkin and McWilliams, 2005. The Regional Ocean Modeling System (ROMS): A split-explicit, free-surface, topography-following coordinates ocean model. Ocean Modelling. Vol. 9 pp. 347-404.

Modeling apparent color for visual evaluation of camouflage fabrics

NASA Astrophysics Data System (ADS)

Ramsey, S.; Mayo, T.; Shabaev, A.; Lambrakos, S. G.

2017-08-01

As the U.S. Navy, Army, and Special Operations Forces progress towards fielding more advanced uniforms with multi-colored and highly detailed camouflage patterning, additional test methodologies are necessary in evaluating color in these types of camouflage textiles. The apparent color is the combination of all visible wavelengths (380-760 nm) of light reflected from large (>=1m2 ) fabric sample sizes for a given standoff distance (10-25ft). Camouflage patterns lose resolution with increasing standoff distance, and eventually all colors within the pattern appear monotone (the "apparent color" of the pattern). This paper presents an apparent color prediction model that can be used for evaluation of camouflage fabrics.

Surface Diagnostics in Tribology Technology and Advanced Coatings Development

NASA Technical Reports Server (NTRS)

Miyoshi, Kazuhisa

1999-01-01

This paper discusses the methodologies used for surface property measurement of thin films and coatings, lubricants, and materials in the field of tribology. Surface diagnostic techniques include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, stylus profilometry, x-ray diffraction, electron diffraction, Raman spectroscopy, Rutherford backscattering, elastic recoil spectroscopy, and tribology examination. Each diagnostic technique provides specific measurement results in its own unique way. In due course it should be possible to coordinate the different pieces of information provided by these diagnostic techniques into a coherent self-consistent description of the surface properties. Examples are given on the nature and character of thin diamond films.

Toward a Quantitative Comparison of Magnetic Field Extrapolations and Observed Coronal Loops

NASA Astrophysics Data System (ADS)

Warren, Harry P.; Crump, Nicholas A.; Ugarte-Urra, Ignacio; Sun, Xudong; Aschwanden, Markus J.; Wiegelmann, Thomas

2018-06-01

It is widely believed that loops observed in the solar atmosphere trace out magnetic field lines. However, the degree to which magnetic field extrapolations yield field lines that actually do follow loops has yet to be studied systematically. In this paper, we apply three different extrapolation techniques—a simple potential model, a nonlinear force-free (NLFF) model based on photospheric vector data, and an NLFF model based on forward fitting magnetic sources with vertical currents—to 15 active regions that span a wide range of magnetic conditions. We use a distance metric to assess how well each of these models is able to match field lines to the 12202 loops traced in coronal images. These distances are typically 1″–2″. We also compute the misalignment angle between each traced loop and the local magnetic field vector, and find values of 5°–12°. We find that the NLFF models generally outperform the potential extrapolation on these metrics, although the differences between the different extrapolations are relatively small. The methodology that we employ for this study suggests a number of ways that both the extrapolations and loop identification can be improved.

A combined theoretical and in vitro modeling approach for predicting the magnetic capture and retention of magnetic nanoparticles in vivo

PubMed Central

David, Allan E.; Cole, Adam J.; Chertok, Beata; Park, Yoon Shin; Yang, Victor C.

2011-01-01

Magnetic nanoparticles (MNP) continue to draw considerable attention as potential diagnostic and therapeutic tools in the fight against cancer. Although many interacting forces present themselves during magnetic targeting of MNP to tumors, most theoretical considerations of this process ignore all except for the magnetic and drag forces. Our validation of a simple in vitro model against in vivo data, and subsequent reproduction of the in vitro results with a theoretical model indicated that these two forces do indeed dominate the magnetic capture of MNP. However, because nanoparticles can be subject to aggregation, and large MNP experience an increased magnetic force, the effects of surface forces on MNP stability cannot be ignored. We accounted for the aggregating surface forces simply by measuring the size of MNP retained from flow by magnetic fields, and utilized this size in the mathematical model. This presumably accounted for all particle-particle interactions, including those between magnetic dipoles. Thus, our “corrected” mathematical model provided a reasonable estimate of not only fractional MNP retention, but also predicted the regions of accumulation in a simulated capillary. Furthermore, the model was also utilized to calculate the effects of MNP size and spatial location, relative to the magnet, on targeting of MNPs to tumors. This combination of an in vitro model with a theoretical model could potentially assist with parametric evaluations of magnetic targeting, and enable rapid enhancement and optimization of magnetic targeting methodologies. PMID:21295085

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.

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...

Magnetic fluid control for viscous loss reduction of high-speed MRF brakes and clutches with well-defined fail-safe behavior

NASA Astrophysics Data System (ADS)

Güth, Dirk; Schamoni, Markus; Maas, Jürgen

2013-09-01

No-load losses within brakes and clutches based on magnetorheological fluids are unavoidable and represent a major barrier towards their wide-spread commercial adoption. Completely torque free rotation is not yet possible due to persistent fluid contact within the shear gap. In this paper, a novel concept is presented that facilitates the controlled movement of the magnetorheological fluid from an active, torque-transmitting region into an inactive region of the shear gap. This concept enables complete decoupling of the fluid engaging surfaces such that viscous drag torque can be eliminated. In order to achieve the desired effect, motion in the magnetorheological fluid is induced by magnetic forces acting on the fluid, which requires an appropriate magnetic circuit design. In this investigation, we propose a methodology to determine suitable magnetic circuit designs with well-defined fail-safe behavior. The magnetically induced motion of magnetorheological fluids is modeled by the use of the Kelvin body force, and a multi-physics domain simulation is performed to elucidate various transitions between an engaged and disengaged operating mode. The modeling approach is validated by captured high-speed video frames which show the induced motion of the magnetorheological fluid due to the magnetic field. Finally, measurements performed with a prototype actuator prove that the induced viscous drag torque can be reduced significantly by the proposed magnetic fluid control methodology.

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

PubMed

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

2016-03-15

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

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

PubMed

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

2011-02-01

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

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.

Rocket-Based Combined Cycle Engine Technology Development: Inlet CFD Validation and Application

NASA Technical Reports Server (NTRS)

DeBonis, J. R.; Yungster, S.

1996-01-01

A CFD methodology has been developed for inlet analyses of Rocket-Based Combined Cycle (RBCC) Engines. A full Navier-Stokes analysis code, NPARC, was used in conjunction with pre- and post-processing tools to obtain a complete description of the flow field and integrated inlet performance. This methodology was developed and validated using results from a subscale test of the inlet to a RBCC 'Strut-Jet' engine performed in the NASA Lewis 1 x 1 ft. supersonic wind tunnel. Results obtained from this study include analyses at flight Mach numbers of 5 and 6 for super-critical operating conditions. These results showed excellent agreement with experimental data. The analysis tools were also used to obtain pre-test performance and operability predictions for the RBCC demonstrator engine planned for testing in the NASA Lewis Hypersonic Test Facility. This analysis calculated the baseline fuel-off internal force of the engine which is needed to determine the net thrust with fuel on.

Methodology for Examining Effects of Arms Control Reduction on Tactical Air Forces. An Example from Conventional Forces in Europe (CFE) Treaty Analysis

DTIC Science & Technology

1993-01-01

H. Wegner for developing the tactical air and ground force databases and producing the campaign results. Thanks are also due to Group Captain Michael ... Jackson , RAF, for developing the evaluation criteria for NATO’s tactical air force reductions during his stay at RAND. -xi. CONTENTS PREFACE

A Health Economics Approach to US Value Assessment Frameworks-Introduction: An ISPOR Special Task Force Report [1].

PubMed

Neumann, Peter J; Willke, Richard J; Garrison, Louis P

2018-02-01

Concerns about rising spending on prescription drugs and other areas of health care have led to multiple initiatives in the United States designed to measure and communicate the value of pharmaceuticals and other technologies for decision making. In this section we introduce the work of the International Society for Pharmacoeconomics and Outcomes Research Special Task Force on US Value Assessment Frameworks formed to review relevant perspectives and appropriate approaches and methods to support the definition and use of high-quality value frameworks. The Special Task Force was part of the International Society for Pharmacoeconomics and Outcomes Research Initiative on US Value Assessment Frameworks, which enlisted the expertise of leading health economists, concentrating on what the field of health economics can provide to help inform the development and use of value assessment frameworks. We focus on five value framework initiatives: the American College of Cardiology/American Heart Association, the American Society of Clinical Oncology, the Institute for Clinical and Economic Review, the Memorial Sloan Kettering Cancer Center, and the National Comprehensive Cancer Network. These entities differ in their missions, scope of activities, and methodological approaches. Because they are gaining visibility and some traction in the United States, it is essential to scrutinize whether the frameworks use approaches that are transparent as well as conceptually and methodologically sound. Our objectives were to describe the conceptual bases for value and its use in decision making, critically examine existing value frameworks, discuss the importance of sound conceptual underpinning, identify key elements of value relevant to specific decision contexts, and recommend good practice in value definition and implementation as well as areas for further research. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

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

Kinematic and neurophysiological consequences of an assisted-force-feedback brain-machine interface training: a case study.

PubMed

Silvoni, Stefano; Cavinato, Marianna; Volpato, Chiara; Cisotto, Giulia; Genna, Clara; Agostini, Michela; Turolla, Andrea; Ramos-Murguialday, Ander; Piccione, Francesco

2013-01-01

In a proof-of-principle prototypical demonstration we describe a new type of brain-machine interface (BMI) paradigm for upper limb motor-training. The proposed technique allows a fast contingent and proportionally modulated stimulation of afferent proprioceptive and motor output neural pathways using operant learning. Continuous and immediate assisted-feedback of force proportional to rolandic rhythm oscillations during actual movements was employed and illustrated with a single case experiment. One hemiplegic patient was trained for 2 weeks coupling somatosensory brain oscillations with force-field control during a robot-mediated center-out motor-task whose execution approaches movements of everyday life. The robot facilitated actual movements adding a modulated force directed to the target, thus providing a non-delayed proprioceptive feedback. Neuro-electric, kinematic, and motor-behavioral measures were recorded in pre- and post-assessments without force assistance. Patient's healthy arm was used as control since neither a placebo control was possible nor other control conditions. We observed a generalized and significant kinematic improvement in the affected arm and a spatial accuracy improvement in both arms, together with an increase and focalization of the somatosensory rhythm changes used to provide assisted-force-feedback. The interpretation of the neurophysiological and kinematic evidences reported here is strictly related to the repetition of the motor-task and the presence of the assisted-force-feedback. Results are described as systematic observations only, without firm conclusions about the effectiveness of the methodology. In this prototypical view, the design of appropriate control conditions is discussed. This study presents a novel operant-learning-based BMI-application for motor-training coupling brain oscillations and force feedback during an actual movement.

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.

Comparison of the ocean surface vector winds from atmospheric reanalysis and scatterometer-based wind products over the Nordic Seas and the northern North Atlantic and their application for ocean modeling

NASA Astrophysics Data System (ADS)

Dukhovskoy, Dmitry S.; Bourassa, Mark A.; Petersen, Gudrún Nína; Steffen, John

2017-03-01

Ocean surface vector wind fields from reanalysis data sets and scatterometer-derived gridded products are analyzed over the Nordic Seas and the northern North Atlantic for the time period from 2000 to 2009. The data sets include the National Center for Environmental Prediction Reanalysis 2 (NCEPR2), Climate Forecast System Reanalysis (CFSR), Arctic System Reanalysis (ASR), Cross-Calibrated Multiplatform (CCMP) wind product version 1.1 and recently released version 2.0, and QuikSCAT. The goal of the study is to assess discrepancies across the wind vector fields in the data sets and demonstrate possible implications of these differences for ocean modeling. Large-scale and mesoscale characteristics of winds are compared at interannual, seasonal, and synoptic timescales. A cyclone tracking methodology is developed and applied to the wind fields to compare cyclone characteristics in the data sets. Additionally, the winds are evaluated against observations collected from meteorological buoys deployed in the Iceland and Irminger Seas. The agreement among the wind fields is better for longer time and larger spatial scales. The discrepancies are clearly apparent for synoptic timescales and mesoscales. CCMP, ASR, and CFSR show the closest overall agreement with each other. Substantial biases are found in the NCEPR2 winds. Numerical sensitivity experiments are conducted with a coupled ice-ocean model forced by different wind fields. The experiments demonstrate differences in the net surface heat fluxes during storms. In the experiment forced by NCEPR2 winds, there are discrepancies in the large-scale wind-driven ocean dynamics compared to the other experiments.

Three Dimensional Numerical Simulation and Characterization of Crack Growth in the Weld Region of a Friction Stir Welded Structure

NASA Technical Reports Server (NTRS)

Seshadri, Banavara R.; Smith, Stephen W.; Newman, John A.

2013-01-01

Friction stir welding (FSW) fabrication technology is being adopted in aerospace applications. The use of this technology can reduce production cost, lead-times, reduce structural weight and need for fasteners and lap joints, which are typically the primary locations of crack initiation and multi-site fatigue damage in aerospace structures. FSW is a solid state welding process that is well-suited for joining aluminum alloy components; however, the process introduces residual stresses (both tensile and compressive) in joined components. The propagation of fatigue cracks in a residual stress field and the resulting redistribution of the residual stress field and its effect on crack closure have to be estimated. To insure the safe insertion of complex integral structures, an accurate understanding of the fatigue crack growth behavior and the complex crack path process must be understood. A life prediction methodology for fatigue crack growth through the weld under the influence of residual stresses in aluminum alloy structures fabricated using FSW will be detailed. The effects and significance of the magnitude of residual stress at a crack tip on the estimated crack tip driving force are highlighted. The location of the crack tip relative to the FSW and the effect of microstructure on fatigue crack growth are considered. A damage tolerant life prediction methodology accounting for microstructural variation in the weld zone and residual stress field will lead to the design of lighter and more reliable aerospace structures

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.

Validation of Vehicle Panel/Equipment Response from Diffuse Acoustic Field Excitation Using Spatially Correlated Transfer Function Approach

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Fulcher, Clay; Hunt, Ron

2012-01-01

An approach for predicting the vibration, strain, and force responses of a flight-like vehicle panel assembly to acoustic pressures is presented. Important validation for the approach is provided by comparison to ground test measurements in a reverberant chamber. The test article and the corresponding analytical model were assembled in several configurations to demonstrate the suitability of the approach for response predictions when the vehicle panel is integrated with equipment. Critical choices in the analysis necessary for convergence of the predicted and measured responses are illustrated through sensitivity studies. The methodology includes representation of spatial correlation of the pressure field over the panel surface. Therefore, it is possible to demonstrate the effects of hydrodynamic coincidence in the response. The sensitivity to pressure patch density clearly illustrates the onset of coincidence effects on the panel response predictions.

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.

Research Methodology in Second Language Studies: Trends, Concerns, and New Directions

ERIC Educational Resources Information Center

King, Kendall A.; Mackey, Alison

2016-01-01

The field of second language studies is using increasingly sophisticated methodological approaches to address a growing number of urgent, real-world problems. These methodological developments bring both new challenges and opportunities. This article briefly reviews recent ontological and methodological debates in the field, then builds on these…

ACHP | Working Together to Build a More Inclusive Preservation Program

Science.gov Websites

goal is to better position folklorists and folklore methodologies as central forces in historic . Folklore methodologies can help engage the local community and elicit their voices. As the National Park

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.

Substructuring of multibody systems for numerical transfer path analysis in internal combustion engines

NASA Astrophysics Data System (ADS)

Acri, Antonio; Offner, Guenter; Nijman, Eugene; Rejlek, Jan

2016-10-01

Noise legislations and the increasing customer demands determine the Noise Vibration and Harshness (NVH) development of modern commercial vehicles. In order to meet the stringent legislative requirements for the vehicle noise emission, exact knowledge of all vehicle noise sources and their acoustic behavior is required. Transfer path analysis (TPA) is a fairly well established technique for estimating and ranking individual low-frequency noise or vibration contributions via the different transmission paths. Transmission paths from different sources to target points of interest and their contributions can be analyzed by applying TPA. This technique is applied on test measurements, which can only be available on prototypes, at the end of the designing process. In order to overcome the limits of TPA, a numerical transfer path analysis methodology based on the substructuring of a multibody system is proposed in this paper. Being based on numerical simulation, this methodology can be performed starting from the first steps of the designing process. The main target of the proposed methodology is to get information of noise sources contributions of a dynamic system considering the possibility to have multiple forces contemporary acting on the system. The contributions of these forces are investigated with particular focus on distribute or moving forces. In this paper, the mathematical basics of the proposed methodology and its advantages in comparison with TPA will be discussed. Then, a dynamic system is investigated with a combination of two methods. Being based on the dynamic substructuring (DS) of the investigated model, the methodology proposed requires the evaluation of the contact forces at interfaces, which are computed with a flexible multi-body dynamic (FMBD) simulation. Then, the structure-borne noise paths are computed with the wave based method (WBM). As an example application a 4-cylinder engine is investigated and the proposed methodology is applied on the engine block. The aim is to get accurate and clear relationships between excitations and responses of the simulated dynamic system, analyzing the noise and vibrational sources inside a car engine, showing the main advantages of a numerical methodology.

Development of Magnetorheological Resistive Exercise Device for Rowing Machine

PubMed Central

Žiliukas, Pranas

2016-01-01

Training equipment used by professional sportsmen has a great impact on their sport performance. Most universal exercisers may help only to improve the general physical condition due to the specific kinematics and peculiar resistance generated by their loading units. Training of effective techniques and learning of psychomotor skills are possible only when exercisers conform to the movements and resistance typical for particular sports kinematically and dynamically. Methodology of developing a magnetorheological resistive exercise device for generating the desired law of passive resistance force and its application in a lever-type rowing machine are described in the paper. The structural parameters of a controllable hydraulic cylinder type device were found by means of the computational fluid dynamics simulation performed by ANSYS CFX software. Parameters describing the magnetorheological fluid as non-Newtonian were determined by combining numerical and experimental research of the resistance force generated by the original magnetorheological damper. A structural scheme of the device control system was developed and the variation of the strength of magnetic field that affects the magnetorheological fluid circulating in the device was determined, ensuring a variation of the resistance force on the oar handle adequate for the resistance that occurs during a real boat rowing stroke. PMID:27293479

Development of Magnetorheological Resistive Exercise Device for Rowing Machine.

PubMed

Grigas, Vytautas; Šulginas, Anatolijus; Žiliukas, Pranas

2015-01-01

Training equipment used by professional sportsmen has a great impact on their sport performance. Most universal exercisers may help only to improve the general physical condition due to the specific kinematics and peculiar resistance generated by their loading units. Training of effective techniques and learning of psychomotor skills are possible only when exercisers conform to the movements and resistance typical for particular sports kinematically and dynamically. Methodology of developing a magnetorheological resistive exercise device for generating the desired law of passive resistance force and its application in a lever-type rowing machine are described in the paper. The structural parameters of a controllable hydraulic cylinder type device were found by means of the computational fluid dynamics simulation performed by ANSYS CFX software. Parameters describing the magnetorheological fluid as non-Newtonian were determined by combining numerical and experimental research of the resistance force generated by the original magnetorheological damper. A structural scheme of the device control system was developed and the variation of the strength of magnetic field that affects the magnetorheological fluid circulating in the device was determined, ensuring a variation of the resistance force on the oar handle adequate for the resistance that occurs during a real boat rowing stroke.

Prerequisites and driving forces behind an extended working life among older workers.

PubMed

Hovbrandt, Pia; Håkansson, Carita; Albin, Maria; Carlsson, Gunilla; Nilsson, Kerstin

2017-11-28

Reforms are changing pension systems in many European countries, in order to both restrict early retirement and force people to extend their working life. From occupational therapy and occupational science perspectives, studies focusing on aspects of working life that motivate the older worker is urgent. The aim was to describe incentives behind an extended working life among people over age 65. Focus group methodology was used, with participants ages 66-71, from varying work fields: construction and technical companies and the municipal elderly care sector. Work was considered important and valuable to the degree of how challenging work was, the possibilities for inclusion in a team of colleagues and the chances for better personal finances. Amongst all, the participants expressed a feeling of a strengthened identity by being challenged and having the opportunity to manage working tasks. The finding showed the actual reasons behind an extended working life among older workers. However, a risk of rising social inequity may appear with increased working life if older people are forced to extend their working life due to a difficult financial situation as a pensioner. A variety of retirement options and initiatives in order to support older workers are justified.

Incorporating contact angles in the surface tension force with the ACES interface curvature scheme

NASA Astrophysics Data System (ADS)

Owkes, Mark

2017-11-01

In simulations of gas-liquid flows interacting with solid boundaries, the contact line dynamics effect the interface motion and flow field through the surface tension force. The surface tension force is directly proportional to the interface curvature and the problem of accurately imposing a contact angle must be incorporated into the interface curvature calculation. Many commonly used algorithms to compute interface curvatures (e.g., height function method) require extrapolating the interface, with defined contact angle, into the solid to allow for the calculation of a curvature near a wall. Extrapolating can be an ill-posed problem, especially in three-dimensions or when multiple contact lines are near each other. We have developed an accurate methodology to compute interface curvatures that allows for contact angles to be easily incorporated while avoiding extrapolation and the associated challenges. The method, known as Adjustable Curvature Evaluation Scale (ACES), leverages a least squares fit of a polynomial to points computed on the volume-of-fluid (VOF) representation of the gas-liquid interface. The method is tested by simulating canonical test cases and then applied to simulate the injection and motion of water droplets in a channel (relevant to PEM fuel cells).

Effective Swimmer’s Action during the Grab Start Technique

PubMed Central

Mourão, Luis; de Jesus, Karla; Roesler, Hélio; Machado, Leandro J.; Fernandes, Ricardo J.; Vilas-Boas, João Paulo; Vaz, Mário A. P.

2015-01-01

The external forces applied in swimming starts have been often studied, but using direct analysis and simple interpretation data processes. This study aimed to develop a tool for vertical and horizontal force assessment based on the swimmers’ propulsive and structural forces (passive forces due to dead weight) applied during the block phase. Four methodological pathways were followed: the experimented fall of a rigid body, the swimmers’ inertia effect, the development of a mathematical model to describe the outcome of the rigid body fall and its generalization to include the effects of the inertia, and the experimental swimmers’ starting protocol analysed with the inclusion of the developed mathematical tool. The first three methodological steps resulted in the description and computation of the passive force components. At the fourth step, six well-trained swimmers performed three 15 m maximal grab start trials and three-dimensional (3D) kinetic data were obtained using a six degrees of freedom force plate. The passive force contribution to the start performance obtained from the model was subtracted from the experimental force due to the swimmers resulting in the swimmers’ active forces. As expected, the swimmers’ vertical and horizontal active forces accounted for the maximum variability contribution of the experimental forces. It was found that the active force profile for the vertical and horizontal components resembled one another. These findings should be considered in clarifying the active swimmers’ force variability and the respective geometrical profile as indicators to redefine steering strategies. PMID:25978370

Network community-based model reduction for vortical flows

NASA Astrophysics Data System (ADS)

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

2018-06-01

A network community-based reduced-order model is developed to capture key interactions among coherent structures in high-dimensional unsteady vortical flows. The present approach is data-inspired and founded on network-theoretic techniques to identify important vortical communities that are comprised of vortical elements that share similar dynamical behavior. The overall interaction-based physics of the high-dimensional flow field is distilled into the vortical community centroids, considerably reducing the system dimension. Taking advantage of these vortical interactions, the proposed methodology is applied to formulate reduced-order models for the inter-community dynamics of vortical flows, and predict lift and drag forces on bodies in wake flows. We demonstrate the capabilities of these models by accurately capturing the macroscopic dynamics of a collection of discrete point vortices, and the complex unsteady aerodynamic forces on a circular cylinder and an airfoil with a Gurney flap. The present formulation is found to be robust against simulated experimental noise and turbulence due to its integrating nature of the system reduction.

Change Forces: Implementing Change in a Secondary School for the Common Good

ERIC Educational Resources Information Center

Melville, Wayne; Bartley, Anthony; Weinburgh, Molly

2012-01-01

In this article, we investigate the change forces that act on administrators, subject department chairpersons and teachers as they seek to implement a change in a Canadian secondary school. Using a case study methodology, our analysis of the data uses Sergiovanni's (1998) six change forces: bureaucratic, personal, market, professional, cultural,…

Evolution of Elemental Composition and Morphology in Fusion Reactor's First Wall

NASA Astrophysics Data System (ADS)

Kim, Yong W.

2007-11-01

Forcing of a multi-element alloy by a gradient field can modify the spatial profile of its elemental composition. The gradient field may be in the imposed temperature or the flux of impinging particles. In a fusion device, both scenarios apply. The consequences must be well understood because they change the thermal transport properties as well as the strength, corrosion and wear characteristics of the first wall materials. Given the large number of directions material evolution can take, new robust methods of near-surface composition analyses are needed. This paper presents a new measurement methodology and requisite instrumentation, which can provide measures of local elemental composition and transport properties simultaneously by time-resolved spectroscopy of laser-produced plasma (LPP) plume emissions from the specimen surfaces. The studies to date show that the composition profiles can be modified thermally in a reproducible manner; disparate thermal transport of constituent atoms can incur modifications of near-surface composition profiles.[Y.W. Kim, Int. J. Thermophysics 28, 732 (2007)] Also, disparate fluxes of fuel particles, fusion products and impurities force the first walls in myriad ways. Repetitive application of the LPP analysis can resolve the near-surface composition profile as well as transport properties over several microns with depth resolutions to 20 nm. Work supported in part by NSF-DMR.

Measure Guideline: Combined Space and Water Heating Installation and Optimization

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

Schoenbauer, B.; Bohac, D.; Huelman, P.

Combined space and water heater (combi or combo) systems are defined by their dual functionality. Combi systems provide both space heating and water heating capabilities with a single heat source. This guideline will focus on the installation and operation of residential systems with forced air heating and domestic hot water (DHW) functionality. Past NorthernSTAR research has used a combi system to replace a natural gas forced air distribution system furnace and tank type water heater (Schoenbauer et al. 2012; Schoenbauer, Bohac, and McAlpine 2014). The combi systems consisted of a water heater or boiler heating plant teamed with a hydronicmore » air handler that included an air handler, water coil, and water pump to circulate water between the heating plant and coil. The combi water heater or boiler had a separate circuit for DHW. Past projects focused on laboratory testing, field characterization, and control optimization of combi systems. Laboratory testing was done to fully characterize and test combi system components; field testing was completed to characterize the installed performance of combi systems; and control methodologies were analyzed to understand the potential of controls to simplify installation and design and to improve system efficiency and occupant comfort. This past work was relied upon on to create this measure guideline.« less

Progressive Stereo Locking (PSL): A Residual Dipolar Coupling Based Force Field Method for Determining the Relative Configuration of Natural Products and Other Small Molecules.

PubMed

Cornilescu, Gabriel; Ramos Alvarenga, René F; Wyche, Thomas P; Bugni, Tim S; Gil, Roberto R; Cornilescu, Claudia C; Westler, William M; Markley, John L; Schwieters, Charles D

2017-08-18

Establishing the relative configuration of a bioactive natural product represents the most challenging part in determining its structure. Residual dipolar couplings (RDCs) are sensitive probes of the relative spatial orientation of internuclear vectors. We adapted a force field structure calculation methodology to allow free sampling of both R and S configurations of the stereocenters of interest. The algorithm uses a floating alignment tensor in a simulated annealing protocol to identify the conformations and configurations that best fit experimental RDC and distance restraints (from NOE and J-coupling data). A unique configuration (for rigid molecules) or a very small number of configurations (for less rigid molecules) of the structural models having the lowest chiral angle energies and reasonable magnitudes of the alignment tensor are provided as the best predictions of the unknown configuration. For highly flexible molecules, the progressive locking of their stereocenters into their statistically dominant R or S state dramatically reduces the number of possible relative configurations. The result is verified by checking that the same configuration is obtained by initiating the locking from different regions of the molecule. For all molecules tested having known configurations (with conformations ranging from mostly rigid to highly flexible), the method accurately determined the correct configuration.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Determination of partial molar volumes from free energy perturbation theory†

PubMed Central

Vilseck, Jonah Z.; Tirado-Rives, Julian

2016-01-01

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343

Determination of partial molar volumes from free energy perturbation theory.

PubMed

Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L

2015-04-07

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

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

NASA Astrophysics Data System (ADS)

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

2008-01-01

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

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

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

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

The Literature Review of Analytical Support to Defence Transformation: Lessons Learned from Turkish Air Force Transformation Activities

DTIC Science & Technology

2010-04-01

available [11]. Additionally, Table-3 is a guide for DMAIC methodology including 29 different methods [12]. RTO-MP-SAS-081 6 - 4 NATO UNCLASSIFIED NATO...Table 3: DMAIC Methodology (5-Phase Methodology). Define Measure Analyze Improve Control Project Charter Prioritization Matrix 5 Whys Analysis...Methodology Scope [13] DMAIC PDCA Develop performance priorities This is a preliminary stage that precedes specific improvement projects, and the aim

VIII. THE PAST, PRESENT, AND FUTURE OF DEVELOPMENTAL METHODOLOGY.

PubMed

Little, Todd D; Wang, Eugene W; Gorrall, Britt K

2017-06-01

This chapter selectively reviews the evolution of quantitative practices in the field of developmental methodology. The chapter begins with an overview of the past in developmental methodology, discussing the implementation and dissemination of latent variable modeling and, in particular, longitudinal structural equation modeling. It then turns to the present state of developmental methodology, highlighting current methodological advances in the field. Additionally, this section summarizes ample quantitative resources, ranging from key quantitative methods journal articles to the various quantitative methods training programs and institutes. The chapter concludes with the future of developmental methodology and puts forth seven future innovations in the field. The innovations discussed span the topics of measurement, modeling, temporal design, and planned missing data designs. Lastly, the chapter closes with a brief overview of advanced modeling techniques such as continuous time models, state space models, and the application of Bayesian estimation in the field of developmental methodology. © 2017 The Society for Research in Child Development, Inc.

Assessment of historical masonry pillars reinforced by CFRP strips

NASA Astrophysics Data System (ADS)

Fedele, Roberto; Rosati, Giampaolo; Biolzi, Luigi; Cattaneo, Sara

2014-10-01

In this methodological study, the ultimate response of masonry pillars strengthened by externally bonded Carbon Fiber Reinforced Polymer (CFRP) was investigated. Historical bricks were derived from a XVII century rural building, whilst a high strength mortar was utilized for the joints. The conventional experimental information, concerning the overall reaction force and relative displacements provided by "point" sensors (LVDTs and clip gauge), were herein enriched with no-contact, full-field kinematic measurements provided by 2D Digital Image Correlation (2D DIC). Experimental information were critically compared with prediction provided by an advanced three-dimensional models, based on nonlinear finite elements under the simplifying assumption of perfect adhesion between the reinforcement and the support.

Structural partitioning of complex structures in the medium-frequency range. An application to an automotive vehicle

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2011-02-01

In a recent work [ Journal of Sound and Vibration 323 (2009) 849-863] the authors presented an energy-density field approach for the vibroacoustic analysis of complex structures in the low and medium frequency ranges. In this approach, a local vibroacoustic energy model as well as a simplification of this model were constructed. In this paper, firstly an extension of the previous theory is performed in order to include the case of general input forces and secondly, a structural partitioning methodology is presented along with a set of tools used for the construction of a partitioning. Finally, an application is presented for an automotive vehicle.

Spatial multibody modeling and vehicle dynamics analysis of advanced vehicle technologies

NASA Astrophysics Data System (ADS)

Letherwood, Michael D.; Gunter, David D.; Gorsich, David J.; Udvare, Thomas B.

2004-08-01

The US Army vision, announced in October of 1999, encompasses people, readiness, and transformation. The goal of the Army vision is to transition the entire Army into a force that is strategically responsive and dominant at every point of the spectrum of operations. The transformation component will be accomplished in three ways: the Objective Force, the Legacy (current) Force, and the Interim Force. The objective force is not platform driven, but rather the focus is on achieving capabilities that will operate as a "system of systems." As part of the Objective Force, the US Army plans to begin production of the Future Combat System (FCS) in FY08 and field the first unit by FY10 as currently defined in the FCS solicitation(1). As part of the FCS program, the Future Tactical Truck System (FTTS) encompasses all US Army tactical wheeled vehicles and its initial efforts will focus only on the heavy class. The National Automotive Center (NAC) is using modeling and simulation to demonstrate the feasibility and operational potential of advanced commercial and military technologies with application to new and existing tactical vehicles and to describe potential future vehicle capabilities. This document will present the results of computer-based, vehicle dynamics performance assessments of FTTS concepts with such features as hybrid power sources, active suspensions, skid steering, and in-hub electric drive motors. Fully three-dimensional FTTS models are being created using commercially available modeling and simulation methodologies such as ADAMS and DADS and limited vehicle dynamics validation studies are will be performed.

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.

Strategic Usefulness of Conventional Force/Special Operations Force Interdependence in Irregular Warfare

DTIC Science & Technology

2017-06-01

17  III.  METHODOLOGY ..............................................................................................19  A... CASE STUDY SELECTION ..................................................................19  B.  RESEARCH APPROACH...20  IV.  GLOBAL WAR ON TERRORISM CASE STUDY .........................................21  A.  AFGHANISTAN

Prediction of surface roughness and cutting force under MQL turning of AISI 4340 with nano fluid by using response surface methodology

NASA Astrophysics Data System (ADS)

Patole, Pralhad B.; Kulkarni, Vivek V.

2018-06-01

This paper presents an investigation into the minimum quantity lubrication mode with nano fluid during turning of alloy steel AISI 4340 work piece material with the objective of experimental model in order to predict surface roughness and cutting force and analyze effect of process parameters on machinability. Full factorial design matrix was used for experimental plan. According to design of experiment surface roughness and cutting force were measured. The relationship between the response variables and the process parameters is determined through the response surface methodology, using a quadratic regression model. Results show how much surface roughness is mainly influenced by feed rate and cutting speed. The depth of cut exhibits maximum influence on cutting force components as compared to the feed rate and cutting speed. The values predicted from the model and experimental values are very close to each other.

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

PubMed

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

2018-02-28

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

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

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

Kelley, Anne Myers

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

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

PubMed

Best, Robert B; Hummer, Gerhard

2009-07-02

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

Hydrofocusing Bioreactor Produces Anti-Cancer Alkaloids

NASA Technical Reports Server (NTRS)

Gonda, Steve R.; Valluri, Jagan V.

2011-01-01

A methodology for growing three-dimensional plant tissue models in a hydrodynamic focusing bioreactor (HFB) has been developed. The methodology is expected to be widely applicable, both on Earth and in outer space, as a means of growing plant cells and aggregates thereof under controlled conditions for diverse purposes, including research on effects of gravitation and other environmental factors upon plant growth and utilization of plant tissue cultures to produce drugs in quantities greater and at costs lower than those of conventional methodologies. The HFB was described in Hydro focus - ing Bioreactor for Three-Dimensional Cell Culture (MSC-22358), NASA Tech Briefs, Vol. 27, No. 3 (March 2003), page 66. To recapitulate: The HFB offers a unique hydrofocusing capability that enables the creation of a low-shear liquid culture environment simultaneously with the herding of suspended cells and tissue assemblies and removal of unwanted air bubbles. The HFB includes a rotating cell-culture vessel with a centrally located sampling port and an internal rotating viscous spinner attached to a rotating base. The vessel and viscous spinner can be made to rotate at the same speed and direction or different speeds and directions to tailor the flow field and the associated hydrodynamic forces in the vessel in order to obtain low-shear suspension of cells and control of the locations of cells and air bubbles. For research and pharmaceutical-production applications, the HFB offers two major benefits: low shear stress, which promotes the assembly of cells into tissue-like three-dimensional constructs; and randomization of gravitational vectors relative to cells, which affects production of medicinal compounds. Presumably, apposition of plant cells in the absence of shear forces promotes cell-cell contacts, cell aggregation, and cell differentiation. Only gentle mixing is necessary for distributing nutrients and oxygen. It has been postulated that inasmuch as cells in the simulated microgravitation of an HFB do not need to maintain the same surface forces as in normal Earth gravitation, they can divert more energy sources to growth and differentiation and, perhaps, to biosynthesis of greater quantities of desired medicinal compounds. Because one can adjust the HFB to vary effective gravitation, one can also test the effects of intermediate levels of gravitation on biosynthesis of various products. The potential utility of this methodology for producing drugs was demonstrated in experiments in which sandalwood and Madagascar periwinkle cells were grown in an HFB. The conditions in the HFB were chosen to induce the cells to form into aggregate cultures that produced anti-cancer indole alkaloids in amounts greater than do comparable numbers of cells of the same species cultured according to previously known methodologies. The observations made in these experiments were interpreted as suggesting that the aggregation of the cells might be responsible for the enhancement of production of alkaloids.

Application of CFE/POST2 for Simulation of Launch Vehicle Stage Separation

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Tartabini, Paul V.; Toniolo, Matthew D.; Roithmayr, Carlos M.; Karlgaard, Christopher D.; Samareh, Jamshid A.

2009-01-01

The constraint force equation (CFE) methodology provides a framework for modeling constraint forces and moments acting at joints that connect multiple vehicles. With implementation in Program to Optimize Simulated Trajectories II (POST 2), the CFE provides a capability to simulate end-to-end trajectories of launch vehicles, including stage separation. In this paper, the CFE/POST2 methodology is applied to the Shuttle-SRB separation problem as a test and validation case. The CFE/POST2 results are compared with STS-1 flight test data.

A Cross-Sectional Investigation of the Effects of Regional Labor Market Conditions on the Reenlistment Decisions of Air Force Enlistees

DTIC Science & Technology

1991-09-01

Baldwin, Robert H. and Thomas V. Daula. "Army Recruit Attrition and Force Manning Costs: Methodology and Analysis," Research in Labor Economics , ed. Ronald...Methodological Issues and a Proposed Specification," Research in Labor Economics , ed. Ronald Ehrenberg, 7:339-363 (1985b). Baldwin, Robert H. et al. "Military...Manpower Research: An Introduction," Research in Labor Economics , ed. Ronald Ehrenberg, L:257-260 (1985). Dalton, Dan R. et al. "Turnover Overstated: The

Improving Energy Security for Air Force Installations

NASA Astrophysics Data System (ADS)

Schill, David

Like civilian infrastructure, Air Force installations are dependent on electrical energy for daily operations. Energy shortages translate to decreased productivity, higher costs, and increased health risks. But for the United States military, energy shortages have the potential to become national security risks. Over ninety-five percent of the electrical energy used by the Air Force is supplied by the domestic grid, which is susceptible to shortages and disruptions. Many Air Force operations require a continuous source of energy, and while the Air Force has historically established redundant supplies of electrical energy, these back-ups are designed for short-term outages and may not provide sufficient supply for a longer, sustained power outage. Furthermore, it is the goal of the Department of Defense to produce or procure 25 percent of its facility energy from renewable sources by fiscal year 2025. In a government budget environment where decision makers are required to provide more capability with less money, it is becoming increasingly important for informed decisions regarding which energy supply options bear the most benefit for an installation. The analysis begins by exploring the field of energy supply options available to an Air Force installation. The supply options are assessed according to their ability to provide continuous and reliable energy, their applicability to unique requirements of Air Force installations, and their costs. Various methods of calculating energy usage by an installation are also addressed. The next step of this research develops a methodology and tool which assesses how an installation responds to various power outage scenarios. Lastly, various energy supply options are applied to the tool, and the results are reported in terms of cost and loss of installation capability. This approach will allow installation commanders and energy managers the ability to evaluate the cost and effectiveness of various energy investment options.

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.

Force Measurement on the GLAST Delta II Flight

NASA Technical Reports Server (NTRS)

Gordon, Scott; Kaufman, Daniel

2009-01-01

This viewgraph presentation reviews the interface force measurement at spacecraft separation of GLAST Delta II. The contents include: 1) Flight Force Measurement (FFM) Background; 2) Team Members; 3) GLAST Mission Overview; 4) Methodology Development; 5) Ground Test Validation; 6) Flight Data; 7) Coupled Loads Simulation (VCLA & Reconstruction); 8) Basedrive Simulation; 9) Findings; and 10) Summary and Conclusions.

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.

Design Methodology of a Dual-Halbach Array Linear Actuator with Thermal-Electromagnetic Coupling

PubMed Central

Eckert, Paulo Roberto; Flores Filho, Aly Ferreira; Perondi, Eduardo; Ferri, Jeferson; Goltz, Evandro

2016-01-01

This paper proposes a design methodology for linear actuators, considering thermal and electromagnetic coupling with geometrical and temperature constraints, that maximizes force density and minimizes force ripple. The method allows defining an actuator for given specifications in a step-by-step way so that requirements are met and the temperature within the device is maintained under or equal to its maximum allowed for continuous operation. According to the proposed method, the electromagnetic and thermal models are built with quasi-static parametric finite element models. The methodology was successfully applied to the design of a linear cylindrical actuator with a dual quasi-Halbach array of permanent magnets and a moving-coil. The actuator can produce an axial force of 120 N and a stroke of 80 mm. The paper also presents a comparative analysis between results obtained considering only an electromagnetic model and the thermal-electromagnetic coupled model. This comparison shows that the final designs for both cases differ significantly, especially regarding its active volume and its electrical and magnetic loading. Although in this paper the methodology was employed to design a specific actuator, its structure can be used to design a wide range of linear devices if the parametric models are adjusted for each particular actuator. PMID:26978370

Design Methodology of a Dual-Halbach Array Linear Actuator with Thermal-Electromagnetic Coupling.

PubMed

Eckert, Paulo Roberto; Flores Filho, Aly Ferreira; Perondi, Eduardo; Ferri, Jeferson; Goltz, Evandro

2016-03-11

This paper proposes a design methodology for linear actuators, considering thermal and electromagnetic coupling with geometrical and temperature constraints, that maximizes force density and minimizes force ripple. The method allows defining an actuator for given specifications in a step-by-step way so that requirements are met and the temperature within the device is maintained under or equal to its maximum allowed for continuous operation. According to the proposed method, the electromagnetic and thermal models are built with quasi-static parametric finite element models. The methodology was successfully applied to the design of a linear cylindrical actuator with a dual quasi-Halbach array of permanent magnets and a moving-coil. The actuator can produce an axial force of 120 N and a stroke of 80 mm. The paper also presents a comparative analysis between results obtained considering only an electromagnetic model and the thermal-electromagnetic coupled model. This comparison shows that the final designs for both cases differ significantly, especially regarding its active volume and its electrical and magnetic loading. Although in this paper the methodology was employed to design a specific actuator, its structure can be used to design a wide range of linear devices if the parametric models are adjusted for each particular actuator.

Image-based reconstruction of the Newtonian dynamics of solar coronal ejecta

NASA Astrophysics Data System (ADS)

Uritsky, Vadim M.; Thompson, Barbara J.

2016-10-01

We present a new methodology for analyzing rising and falling dynamics of unstable coronal material as represented by high-cadence SDO AIA images. The technique involves an adaptive spatiotemporal tracking of propagating intensity gradients and their characterization in terms of time-evolving areas swept out by the position vector originated from the Sun disk center. The measured values of the areal velocity and acceleration are used to obtain quantitative information on the angular momentum and acceleration along the paths of the rising and falling coronal plasma. In the absence of other forces, solar gravitation results in purely ballistic motions consistent with the Kepler's second law; non-central forces such as the Lorentz force introduce non-zero torques resulting in more complex motions. The developed algorithms enable direct evaluation of the line-of-sight component of the net torque applied to a unit mass of the ejected coronal material which is proportional to the image-plane projection of the observed areal acceleration. The current implementation of the method cannot reliably distinguish torque modulations caused by the coronal force field from those imposed by abrupt changes of plasma mass density and nontrivial projection effects. However, it can provide valid observational constraints on the evolution of large-scale unstable magnetic topologies driving major solar-coronal eruptions as demonstrated in the related talk by B. Thompson et al.

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

PubMed

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

2018-03-01

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

Catch trials in force field learning influence adaptation and consolidation of human motor memory

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

Force field studies are a common tool to investigate motor adaptation and consolidation. Thereby, subjects usually adapt their reaching movements to force field perturbations induced by a robotic device. In this context, so-called catch trials, in which the disturbing forces are randomly turned off, are commonly used to detect after-effects of motor adaptation. However, catch trials also produce sudden large motor errors that might influence the motor adaptation and the consolidation process. Yet, the detailed influence of catch trials is far from clear. Thus, the aim of this study was to investigate the influence of catch trials on motor adaptation and consolidation in force field experiments. Therefore, 105 subjects adapted their reaching movements to robot-generated force fields. The test groups adapted their reaching movements to a force field A followed by learning a second interfering force field B before retest of A (ABA). The control groups were not exposed to force field B (AA). To examine the influence of diverse catch trial ratios, subjects received catch trials during force field adaptation with a probability of either 0, 10, 20, 30, or 40%, depending on the group. First, the results on motor adaptation revealed significant differences between the diverse catch trial ratio groups. With increasing amount of catch trials, the subjects' motor performance decreased and subjects' ability to accurately predict the force field—and therefore internal model formation—was impaired. Second, our results revealed that adapting with catch trials can influence the following consolidation process as indicated by a partial reduction to interference. Here, the optimal catch trial ratio was 30%. However, detection of consolidation seems to be biased by the applied measure of performance. PMID:24795598

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane.

PubMed

Das, Arya; Ali, Sk Musharaf

2018-02-21

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology.

Molecular dynamics simulation for the test of calibrated OPLS-AA force field for binary liquid mixture of tri-iso-amyl phosphate and n-dodecane

NASA Astrophysics Data System (ADS)

Das, Arya; Ali, Sk. Musharaf

2018-02-01

Tri-isoamyl phosphate (TiAP) has been proposed to be an alternative for tri-butyl phosphate (TBP) in the Plutonium Uranium Extraction (PUREX) process. Recently, we have successfully calibrated and tested all-atom optimized potentials for liquid simulations using Mulliken partial charges for pure TiAP, TBP, and dodecane by performing molecular dynamics (MD) simulation. It is of immense importance to extend this potential for the various molecular properties of TiAP and TiAP/n-dodecane binary mixtures using MD simulation. Earlier, efforts were devoted to find out a suitable force field which can explain both structural and dynamical properties by empirical parameterization. Therefore, the present MD study reports the structural, dynamical, and thermodynamical properties with different mole fractions of TiAP-dodecane mixtures at the entire range of mole fraction of 0-1 employing our calibrated Mulliken embedded optimized potentials for liquid simulation (OPLS) force field. The calculated electric dipole moment of TiAP was seen to be almost unaffected by the TiAP concentration in the dodecane diluent. The calculated liquid densities of the TiAP-dodecane mixture are in good agreement with the experimental data. The mixture densities at different temperatures are also studied which was found to be reduced with temperature as expected. The plot of diffusivities for TiAP and dodecane against mole fraction in the binary mixture intersects at a composition in the range of 25%-30% of TiAP in dodecane, which is very much closer to the TBP/n-dodecane composition used in the PUREX process. The excess volume of mixing was found to be positive for the entire range of mole fraction and the excess enthalpy of mixing was shown to be endothermic for the TBP/n-dodecane mixture as well as TiAP/n-dodecane mixture as reported experimentally. The spatial pair correlation functions are evaluated between TiAP-TiAP and TiAP-dodecane molecules. Further, shear viscosity has been computed by performing the non-equilibrium molecular dynamics employing the periodic perturbation method. The calculated shear viscosity of the binary mixture is found to be in excellent agreement with the experimental values. The use of the newly calibrated OPLS force field embedding Mulliken charges is shown to be equally reliable in predicting the structural and dynamical properties for the mixture without incorporating any arbitrary scaling in the force field or Lennard-Jones parameters. Further, the present MD simulation results demonstrate that the Stokes-Einstein relation breaks down at the molecular level. The present methodology might be adopted to evaluate the liquid state properties of an aqueous-organic biphasic system, which is of great significance in the interfacial science and technology.

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

Field Test of the Methodology for Succession Planning for Technical Experts

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

Cain, Ronald A.; Kirk, Bernadette Lugue; Agreda, Carla L.

This report complements A Methodology for Succession Planning for Technical Experts (Ron Cain, Shaheen Dewji, Carla Agreda, Bernadette Kirk, July 2017), which describes a methodology for identifying and evaluating the loss of key technical skills at nuclear operations facilities. This report targets the methodology for identifying critical skills, hereafter referred to as “core competencies”. The methodology has been field tested by interviewing selected retiring subject matter experts (SMEs).

The electromagnetic force field, fluid flow field and temperature profiles in levitated metal droplets

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

A mathematical representation was developed for the electromagnetic force field, the flow field, the temperature field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was employed for the calculation of the electromagnetic force field, while the turbulent Navier - Stokes equations and the turbulent convective transport equations were used to represent the fluid flow field, the temperature field and the concentration field. The governing differential equations, written in spherical coordinates, were solved numerically. The computed results were in good agreement with measurements, regarding the lifting force, and the average temperature of the specimen and carburization rates, which were transport controlled.

Extracting the potential-well of a near-field optical trap using the Helmholtz-Hodge decomposition

NASA Astrophysics Data System (ADS)

Zaman, Mohammad Asif; Padhy, Punnag; Hansen, Paul C.; Hesselink, Lambertus

2018-02-01

The non-conservative nature of the force field generated by a near-field optical trap is analyzed. A plasmonic C-shaped engraving on a gold film is considered as the trap. The force field is calculated using the Maxwell stress tensor method. The Helmholtz-Hodge decomposition is used to extract the conservative and the non-conservative component of the force. Due to the non-negligible non-conservative component, it is found that the conventional approach of extracting the potential by direct integration of the force is not accurate. Despite the non-conservative nature of the force field, it is found that the statistical properties of a trapped nanoparticle can be estimated from the conservative component of the force field alone. Experimental and numerical results are presented to support the claims.

Muscle co-contraction patterns in robot-mediated force field learning to guide specific muscle group training.

PubMed

Pizzamiglio, Sara; Desowska, Adela; Shojaii, Pegah; Taga, Myriam; Turner, Duncan L

2017-01-01

Muscle co-contraction is a strategy of increasing movement accuracy and stability employed in dealing with force perturbation of movement. It is often seen in neuropathological populations. The direction of movement influences the pattern of co-contraction, but not all movements are easily achievable for populations with motor deficits. Manipulating the direction of the force instead, may be a promising rehabilitation protocol to train movement with use of a co-contraction reduction strategy. Force field learning paradigms provide a well described procedure to evoke and test muscle co-contraction. The aim of this study was to test the muscle co-contraction pattern in a wide range of arm muscles in different force-field directions utilising a robot-mediated force field learning paradigm of motor adaptation. Forty-two participants volunteered to participate in a study utilising robot-mediated force field motor adaptation paradigm with a clockwise or counter-clockwise force field. Kinematics and surface electromyography (EMG) of eight arm muscles were measured. Both muscle activation and co-contraction was earlier and stronger in flexors in the clockwise condition and in extensors in the counter-clockwise condition. Manipulating the force field direction leads to changes in the pattern of muscle co-contraction.

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

NASA Astrophysics Data System (ADS)

Cisneros, G. Andrés; Piquemal, Jean-Philip; Darden, Thomas A.

2006-11-01

The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H2O)n, n =64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs.

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

PubMed Central

Cisneros, G. Andrés; Piquemal, Jean-Philip; Darden, Thomas A.

2007-01-01

The simulation of biological systems by means of current empirical force fields presents shortcomings due to their lack of accuracy, especially in the description of the nonbonded terms. We have previously introduced a force field based on density fitting termed the Gaussian electrostatic model-0 (GEM-0) J.-P. Piquemal et al. [J. Chem. Phys. 124, 104101 (2006)] that improves the description of the nonbonded interactions. GEM-0 relies on density fitting methodology to reproduce each contribution of the constrained space orbital variation (CSOV) energy decomposition scheme, by expanding the electronic density of the molecule in s-type Gaussian functions centered at specific sites. In the present contribution we extend the Coulomb and exchange components of the force field to auxiliary basis sets of arbitrary angular momentum. Since the basis functions with higher angular momentum have directionality, a reference molecular frame (local frame) formalism is employed for the rotation of the fitted expansion coefficients. In all cases the intermolecular interaction energies are calculated by means of Hermite Gaussian functions using the McMurchie-Davidson [J. Comput. Phys. 26, 218 (1978)] recursion to calculate all the required integrals. Furthermore, the use of Hermite Gaussian functions allows a point multipole decomposition determination at each expansion site. Additionally, the issue of computational speed is investigated by reciprocal space based formalisms which include the particle mesh Ewald (PME) and fast Fourier-Poisson (FFP) methods. Frozen-core (Coulomb and exchange-repulsion) intermolecular interaction results for ten stationary points on the water dimer potential-energy surface, as well as a one-dimensional surface scan for the canonical water dimer, formamide, stacked benzene, and benzene water dimers, are presented. All results show reasonable agreement with the corresponding CSOV calculated reference contributions, around 0.1 and 0.15 kcal/mol error for Coulomb and exchange, respectively. Timing results for single Coulomb energy-force calculations for (H2O)n, n=64, 128, 256, 512, and 1024, in periodic boundary conditions with PME and FFP at two different rms force tolerances are also presented. For the small and intermediate auxiliaries, PME shows faster times than FFP at both accuracies and the advantage of PME widens at higher accuracy, while for the largest auxiliary, the opposite occurs. PMID:17115732

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields.

PubMed

Moučka, Filip; Nezbeda, Ivo; Smith, William R

2015-04-14

We describe a computationally efficient molecular simulation methodology for calculating the concentration dependence of the chemical potentials of both solute and solvent in aqueous electrolyte solutions, based on simulations of the salt chemical potential alone. We use our approach to study the predictions for aqueous NaCl solutions at ambient conditions of these properties by the recently developed polarizable force fields (FFs) AH/BK3 of Kiss and Baranyai (J. Chem. Phys. 2013, 138, 204507) and AH/SWM4-DP of Lamoureux and Roux (J. Phys. Chem. B 2006, 110, 3308 - 3322) and by the nonpolarizable JC FF of Joung and Cheatham tailored to SPC/E water (J. Phys. Chem. B 2008, 112, 9020 - 9041). We also consider their predictions of the concentration dependence of the electrolyte activity coefficient, the crystalline solid chemical potential, the electrolyte solubility, and the solution specific volume. We first highlight the disagreement in the literature concerning calculations of solubility by means of molecular simulation in the case of the JC FF and provide strong evidence of the correctness of our methodology based on recent independently obtained results for this important test case. We then compare the predictions of the three FFs with each other and with experiment and draw conclusions concerning their relative merits, with particular emphasis on the salt chemical potential and activity coefficient vs concentration curves and their derivatives. The latter curves have only previously been available from Kirkwood-Buff integrals, which require approximate numerical integrations over system pair correlation functions at each concentration. Unlike the case of the other FFs, the AH/BK3 curves are nearly parallel to the corresponding experimental curves at moderate and higher concentrations. This leads to an excellent prediction of the water chemical potential via the Gibbs-Duhem equation and enables the activity coefficient curve to be brought into excellent agreement with experiment by incorporating an appropriate value of the standard state chemical potential in the Henry Law convention.

Open and Shut: The Case for Optimizing Air Component Resilient Basing Strategies in an Anti-Access/Area Denial Operating Environment

DTIC Science & Technology

2018-04-09

The research focuses on gaps in current doctrine, command relationships, command and control, force structure of ABO forces, posture, training for...identifying conceptual challenges and methodologies to address them as well as describing areas for further research . 15. SUBJECT TERMS Airbase Opening...Denial environment. The research focuses on gaps in current doctrine, command relationships, command and control, force structure of ABO forces

Analysis of maintenance costing with emphasis on contracting versus using state forces.

DOT National Transportation Integrated Search

1982-01-01

The authors present the findings of a study to develop a methodology for analyzing decisions of whether to perform ordinary maintenance, maintenance replacement, and incidental construction with state forces or to let them to contract. In developing ...

Theoretical investigation of the force and dynamically coupled torsional-axial-lateral dynamic response of eared rotors

NASA Technical Reports Server (NTRS)

David, J. W.; Mitchell, L. D.

1982-01-01

Difficulties in solution methodology to be used to deal with the potentially higher nonlinear rotor equations when dynamic coupling is included. A solution methodology is selected to solve the nonlinear differential equations. The selected method was verified to give good results even at large nonlinearity levels. The transfer matrix methodology is extended to the solution of nonlinear problems.

Mining Predictors of Success in Air Force Flight Training Regiments via Semantic Analysis of Instructor Evaluations

DTIC Science & Technology

2018-03-01

We apply our methodology to the criticism text written in the flight-training program student evaluations in order to construct a model that...factors. We apply our methodology to the criticism text written in the flight-training program student evaluations in order to construct a model...9 D. BINARY CLASSIFICATION AND FEATURE SELECTION ..........11 III. METHODOLOGY

It is Time the United States Air Force Changes the way it Feeds its Airmen

DTIC Science & Technology

2008-03-01

narrative , phenomenology , ethnography , case study , and grounded theory . In purpose, these strategies are...methodology) the research will be analyzed. Methodology A qualitative research methodology and specifically a case study strategy for the...well as theory building in chapter five . Finally, in regards to reliability, Yin’s (2003) case study protocol guidance was used as a means to

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

DTIC Science & Technology

1968-03-01

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

Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

PubMed Central

2017-01-01

We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol). PAC-MAC shows a RMSE of 0.151 kBT with a calculation speed being potentially 1.0 × 104 times greater than TI. OPLS-AA force field parameters are optimized using PAC-MAC based on vapor–liquid equilibrium data, instead of enthalpies of vaporization or densities. The RMSE of PAC-MAC is reduced to 0.099 kBT by optimizing 50 force field parameters. The resulting OPLS-PM force field has a comparable accuracy as the OPLS-AA force field in the calculation of mixing free energies using TI. PMID:28418655

Magnetic moment of solar plasma and the Kelvin force: -The driving force of plasma up-flow -

NASA Astrophysics Data System (ADS)

Shibasaki, Kiyoto

2017-04-01

Thermal plasma in the solar atmosphere is magnetized (diamagnetic). The magnetic moment does not disappear by collisions because complete gyration is not a necessary condition to have magnetic moment. Magnetized fluid is subjected to Kelvin force in non-uniform magnetic field. Generally, magnetic field strength decreases upwards in the solar atmosphere, hence the Kelvin force is directed upwards along the field. This force is not included in the fluid treatment of MHD. By adding the Kelvin force to the MHD equation of motion, we can expect temperature dependent plasma flows along the field which are reported by many observations. The temperature dependence of the flow speed is explained by temperature dependence of magnetic moment. From the observed parameters, we can infer physical parameters in the solar atmosphere such as scale length of the magnetic field strength and the friction force acting on the flowing plasma. In case of closed magnetic field lines, loop-top concentration of hot plasma is expected which is frequently observed.

Methodology discourses as boundary work in the construction of engineering education.

PubMed

Beddoes, Kacey

2014-04-01

Engineering education research is a new field that emerged in the social sciences over the past 10 years. This analysis of engineering education research demonstrates that methodology discourses have played a central role in the construction and development of the field of engineering education, and that they have done so primarily through boundary work. This article thus contributes to science and technology studies literature by examining the role of methodology discourses in an emerging social science field. I begin with an overview of engineering education research before situating the case within relevant bodies of literature on methodology discourses and boundary work. I then identify two methodology discourses--rigor and methodological diversity--and discuss how they contribute to the construction and development of engineering education research. The article concludes with a discussion of how the findings relate to prior research on methodology discourses and boundary work and implications for future research.

Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA.

PubMed

Kubař, Tomáš; Elstner, Marcus

2013-04-28

In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated DNA. It turns out that the mean-field approach, where the wave function of the hole is driven into a superposition of adiabatic states, leads to over-delocalization of the hole charge. This problem is avoided using a surface hopping scheme, resulting in a smaller rate of hole transfer. The method is highly efficient due to the on-the-fly computation of the coarse-grained DFT Hamiltonian for the nucleobases, which is coupled to the environment using a QM/MM approach. The computational efficiency and partial parallel character of the methodology make it possible to simulate electron transfer in systems of relevant biochemical size on a nanosecond time scale. Since standard non-polarizable force fields are applied in the molecular-mechanics part of the calculation, a simple scaling scheme was introduced into the electrostatic potential in order to simulate the effect of electronic polarization. It is shown that electronic polarization has an important effect on the features of charge transfer. The methodology is applied to two kinds of DNA sequences, illustrating the features of transfer along a flat energy landscape as well as over an energy barrier. The performance and relative merit of the mean-field scheme and the surface hopping for this application are discussed.

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.

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

Item Response Modeling of Forced-Choice Questionnaires

ERIC Educational Resources Information Center

Brown, Anna; Maydeu-Olivares, Alberto

2011-01-01

Multidimensional forced-choice formats can significantly reduce the impact of numerous response biases typically associated with rating scales. However, if scored with classical methodology, these questionnaires produce ipsative data, which lead to distorted scale relationships and make comparisons between individuals problematic. This research…

Effects of AC/DC magnetic fields, frequency, and nanoparticle aspect ratio on cellular transfection of gene vectors

NASA Astrophysics Data System (ADS)

Ford, Kris; Mair, Lamar; Fisher, Mike; Rowshon Alam, Md.; Juliano, Rudolph; Superfine, Richard

2008-10-01

In order to make non-viral gene delivery a useful tool in the study and treatment of genetic disorders, it is imperative that these methodologies be further refined to yield optimal results. Transfection of magnetic nanoparticles and nanorods are used as non-viral gene vectors to transfect HeLa EGFP-654 cells that stably express a mutated enhanced green fluorescent protein (EGFP) gene. We deliver antisense oligonucleotides to these cells designed to correct the aberrant splicing caused by the mutation in the EGFP gene. We also transfect human bronchial endothelial cells and immortalized WI-38 lung cells with pEGFP-N1 vectors. To achieve this we bind the genes to magnetic nanoparticles and nanorods and introduce magnetic fields to effect transfection. We wish to examine the effects of magnetic fields on the transfection of these particles and the benefits of using alternating (AC) magnetic fields in improving transfection rates over direct (DC) magnetic fields. We specifically look at the frequency dependence of the AC field and particle aspect ratio as it pertains to influencing transfection rate. We posit that the increase in angular momentum brought about by the AC field and the high aspect ratio of the nanorod particles, is vital to generating the force needed to move the particle through the cell membrane.

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.

Dynamic identification of axial force and boundary restraints in tie rods and cables with uncertainty quantification using Set Inversion Via Interval Analysis

NASA Astrophysics Data System (ADS)

Kernicky, Timothy; Whelan, Matthew; Al-Shaer, Ehab

2018-06-01

A methodology is developed for the estimation of internal axial force and boundary restraints within in-service, prismatic axial force members of structural systems using interval arithmetic and contractor programming. The determination of the internal axial force and end restraints in tie rods and cables using vibration-based methods has been a long standing problem in the area of structural health monitoring and performance assessment. However, for structural members with low slenderness where the dynamics are significantly affected by the boundary conditions, few existing approaches allow for simultaneous identification of internal axial force and end restraints and none permit for quantifying the uncertainties in the parameter estimates due to measurement uncertainties. This paper proposes a new technique for approaching this challenging inverse problem that leverages the Set Inversion Via Interval Analysis algorithm to solve for the unknown axial forces and end restraints using natural frequency measurements. The framework developed offers the ability to completely enclose the feasible solutions to the parameter identification problem, given specified measurement uncertainties for the natural frequencies. This ability to propagate measurement uncertainty into the parameter space is critical towards quantifying the confidence in the individual parameter estimates to inform decision-making within structural health diagnosis and prognostication applications. The methodology is first verified with simulated data for a case with unknown rotational end restraints and then extended to a case with unknown translational and rotational end restraints. A laboratory experiment is then presented to demonstrate the application of the methodology to an axially loaded rod with progressively increased end restraint at one end.

Supporting the Future Total Force: A Methodology for Evaluating Potential Air National Guard Mission Assignments

DTIC Science & Technology

2007-01-01

practices. The Air Force continues to strive to align the total force with its primary function —to organize, train, and equip aviation forces primarily for...to include non -AOC command and control functions performed for the COMAFFOR and staff. Potential COMAFFOR Warfighting Operations Support Postures...representation of RAND intellectual property is provided for non -commercial use only. Unauthorized posting of RAND PDFs to a non -RAND Web site is

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

PubMed

Lemkul, Justin A; MacKerell, Alexander D

2017-05-09

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

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

Liu, Hao; Song, Dong; Lu, Hui; Luo, Ray; Chen, Hai-Feng

2018-05-28

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X-ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here we report our development for the CHARMM community. Our residue-specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections of for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J-couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

How accurately do force fields represent protein side chain ensembles?

PubMed

Petrović, Dušan; Wang, Xue; Strodel, Birgit

2018-05-23

Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

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

PubMed

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

2011-07-01

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

Swiss Armed Forces Organizational Level Leader Development: A Qualitative Case Study

DTIC Science & Technology

2017-06-09

chapter, divided in five distinct parts, describes the chosen research methodology , explain why the qualitative case study is appropriate to conduct...research study uses a qualitative methodology by performing a qualitative case study on the organizational level leader’s development process within...develop an in-depth understsanding of the phenomen.”82 Summary This research study uses a qualitative methodology by performing a case study on the

Coarse-graining errors and numerical optimization using a relative entropy framework

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2011-03-01

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, Srel, that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.

Simulating chemical reactions in ionic liquids using QM/MM methodology.

PubMed

Acevedo, Orlando

2014-12-18

The use of ionic liquids as a reaction medium for chemical reactions has dramatically increased in recent years due in large part to the numerous reported advances in catalysis and organic synthesis. In some extreme cases, ionic liquids have been shown to induce mechanistic changes relative to conventional solvents. Despite the large interest in the solvents, a clear understanding of the molecular factors behind their chemical impact is largely unknown. This feature article reviews our efforts developing and applying mixed quantum and molecular mechanical (QM/MM) methodology to elucidate the microscopic details of how these solvents operate to enhance rates and alter mechanisms for industrially and academically important reactions, e.g., Diels-Alder, Kemp eliminations, nucleophilic aromatic substitutions, and β-eliminations. Explicit solvent representation provided the medium dependence of the activation barriers and atomic-level characterization of the solute-solvent interactions responsible for the experimentally observed "ionic liquid effects". Technical advances are also discussed, including a linear-scaling pairwise electrostatic interaction alternative to Ewald sums, an efficient polynomial fitting method for modeling proton transfers, and the development of a custom ionic liquid OPLS-AA force field.

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

EAACI position paper for practical patch testing in allergic contact dermatitis in children.

PubMed

de Waard-van der Spek, Flora B; Darsow, Ulf; Mortz, Charlotte G; Orton, David; Worm, Margitta; Muraro, Antonella; Schmid-Grendelmeier, Peter; Grimalt, Ramon; Spiewak, Radoslaw; Rudzeviciene, Odilija; Flohr, Carsten; Halken, Susanne; Fiocchi, Alessandro; Borrego, Luis Miguel; Oranje, Arnold P

2015-11-01

Allergic contact dermatitis (ACD) in children appears to be on the increase, and contact sensitization may already begin in infancy. The diagnosis of contact dermatitis requires a careful evaluation of a patient's clinical history, physical examination, and skin testing. Patch testing is the gold standard diagnostic test. Based on consensus, the EAACI Task Force on Allergic Contact Dermatitis in Children produced this document to provide details on clinical aspects, the standardization of patch test methodology, and suggestions for future research in the field. We provide a baseline list of test allergens to be tested in children with suspected ACD. Additional tests should be performed only on specific indications. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The influence of war on the development of neurosurgery.

PubMed

Dowdy, Justin; Pait, T Glenn

2014-01-01

The treatment of craniospinal war wounds proved to be a significant driving force in the early growth of neurosurgery as a specialty. This publication explores the historical relationship between the evolution of combat methodology from antiquity through modern conflicts as it dovetails with and drives corresponding advancements in the field of neurosurgery. Whether it's the basic management principles for intracranial projectile wounds derived from World War I experiences, the drastic improvement in the outcomes and management of spinal cord injuries observed in World War II, or the fact that both of these wars played a crucial role in the development of a training system that is the origin of modern residency programs, the influence of wartime experiences is pervasive.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Post-assembly magnetization of a 100 kW high speed permanent magnet rotor.

PubMed

Lv, Yiliang; Wang, Guobin; Li, Liang

2015-03-01

A post-assembly magnetizing fixture has been designed and successfully used to magnetize the rotor of a 100 kW high speed permanent magnet synchronous motor. The rotor is a solid cylinder with outer diameter of 80 mm and total length of 515 mm. The permanent magnet material is samarium-cobalt (Sm2Co17) with saturation magnetizing field of 6 T. The mechanical stability of the magnetizing fixture has been studied as well as the general design methodology. The magnetizing coil is subdivided in order to reduce the electromagnetic force, and the coils are separately reinforced in different ways. The electromagnetic and structural optimization is performed by finite element analysis and verified by experiments.

Discovery of novel inhibitors of the NorA multidrug transporter of Staphylococcus aureus.

PubMed

Brincat, Jean Pierre; Carosati, Emanuele; Sabatini, Stefano; Manfroni, Giuseppe; Fravolini, Arnaldo; Raygada, Jose L; Patel, Diixa; Kaatz, Glenn W; Cruciani, Gabriele

2011-01-13

Four novel inhibitors of the NorA efflux pump of Staphylococcus aureus, discovered through a virtual screening process, are reported. The four compounds belong to different chemical classes and were tested for their in vitro ability to block the efflux of a well-known NorA substrate, as well as for their ability to potentiate the effect of ciprofloxacin (CPX) on several strains of S. aureus, including a NorA overexpressing strain. Additionally, the MIC values of each of the compounds individually are reported. A structure-activity relationship study was also performed on these novel chemotypes, revealing three new compounds that are also potent NorA inhibitors. The virtual screening procedure employed FLAP, a new methodology based on GRID force field descriptors.

Charge transfer interactions and nonlinear optical properties of push pull chromophore benzaldehyde phenylhydrazone: A vibrational approach

NASA Astrophysics Data System (ADS)

Ravikumar, C.; Joe, I. Hubert; Jayakumar, V. S.

2008-07-01

FT Raman and IR spectra of the crystallized nonlinear optic (NLO) molecule, benzaldehyde phenylhydrazone (BPH) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of BPH have been investigated with the help of B3LYP density functional theory (DFT) method. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). From the optimized geometry, the decrease in C-N bond length indicates the electron delocalization over the region of the molecule. The vibrational analysis confirm the charge transfer interaction between the phenyl rings through ≻Cdbnd N-N≺ skeleton.

Field significance of performance measures in the context of regional climate model evaluation. Part 2: precipitation

NASA Astrophysics Data System (ADS)

Ivanov, Martin; Warrach-Sagi, Kirsten; Wulfmeyer, Volker

2018-04-01

A new approach for rigorous spatial analysis of the downscaling performance of regional climate model (RCM) simulations is introduced. It is based on a multiple comparison of the local tests at the grid cells and is also known as `field' or `global' significance. The block length for the local resampling tests is precisely determined to adequately account for the time series structure. New performance measures for estimating the added value of downscaled data relative to the large-scale forcing fields are developed. The methodology is exemplarily applied to a standard EURO-CORDEX hindcast simulation with the Weather Research and Forecasting (WRF) model coupled with the land surface model NOAH at 0.11 ∘ grid resolution. Daily precipitation climatology for the 1990-2009 period is analysed for Germany for winter and summer in comparison with high-resolution gridded observations from the German Weather Service. The field significance test controls the proportion of falsely rejected local tests in a meaningful way and is robust to spatial dependence. Hence, the spatial patterns of the statistically significant local tests are also meaningful. We interpret them from a process-oriented perspective. While the downscaled precipitation distributions are statistically indistinguishable from the observed ones in most regions in summer, the biases of some distribution characteristics are significant over large areas in winter. WRF-NOAH generates appropriate stationary fine-scale climate features in the daily precipitation field over regions of complex topography in both seasons and appropriate transient fine-scale features almost everywhere in summer. As the added value of global climate model (GCM)-driven simulations cannot be smaller than this perfect-boundary estimate, this work demonstrates in a rigorous manner the clear additional value of dynamical downscaling over global climate simulations. The evaluation methodology has a broad spectrum of applicability as it is distribution-free, robust to spatial dependence, and accounts for time series structure.

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Improved side-chain torsion potentials for the Amber ff99SB protein force field

PubMed Central

Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

2010-01-01

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

Electron diamagnetic effect in a magnetic nozzle on a helicon plasma thruster performance

NASA Astrophysics Data System (ADS)

Takahashi, Kazunori; Lafleur, Trevor; Charles, Christine; Alexander, Peter; Boswell, Rod

2012-10-01

The axial force, which is called thrust sometimes, imparted from a magnetically expanding helicon plasma thruster is directly measured and the results are compared with a two-dimensional fluid theory. The force component solely transmitted to the expanding field is directly measured and identified as an axial force produced by the azimuthal current due to an electron diamagnetic drift and the radial component of the applied magnetic field. In this type of configuration, plasma diffusion in magnetic field affects a spatial profile of the plasma density and the resultant axial force onto the magnetic field. It is observed that the force component onto the magnetic field increases with an increase in the magnetic field strength, simultaneously with an increase in the plasma density downstream of the source exit, which could be due to suppression of the cross field diffusion in the magnetic nozzle.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle.

PubMed

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Three-Dimensional Measurement of the Helicity-Dependent Forces on a Mie Particle

NASA Astrophysics Data System (ADS)

Liu, Lulu; Di Donato, Andrea; Ginis, Vincent; Kheifets, Simon; Amirzhan, Arman; Capasso, Federico

2018-06-01

Recently, it was shown that a Mie particle in an evanescent field ought to experience optical forces that depend on the helicity of the totally internally reflected beam. As yet, a direct measurement of such helicity-dependent forces has been elusive, as the widely differing force magnitudes in the three spatial dimensions place stringent demands on a measurement's sensitivity and range. In this study, we report the simultaneous measurement of all components of this polarization-dependent optical force by using a 3D force spectroscopy technique with femtonewton sensitivity. The vector force fields are compared quantitatively with our theoretical calculations as the polarization state of the incident light is varied and show excellent agreement. By plotting the 3D motion of the Mie particle in response to the switched force field, we offer visual evidence of the effect of spin momentum on the Poynting vector of an evanescent optical field.

Force fields for describing the solution-phase synthesis of shape-selective metal nanoparticles

NASA Astrophysics Data System (ADS)

Zhou, Ya; Al-Saidi, Wissam; Fichthorn, Kristen

2013-03-01

Polyvinylpyrrolidone (PVP) and polyethylene oxide (PEO) are structure-directing agents that exhibit different performance in the polyol synthesis of Ag nanostructures. The success of these structure-directing agents in selective nanostructure synthesis is often attributed to their selective binding to Ag(100) facets. We use first-principles, density-functional theory (DFT) calculations in a vacuum environment to show that PVP has a stronger preference to bind to Ag(100) than to Ag(111), whereas PEO exhibits much weaker selectivity. To understand the role of solvent in the surface-sensitive binding, we develop classical force fields to describe the interactions of the structure-directing (PVP and PEO) and solvent (ethylene glycol) molecules with various Ag substrates. We parameterize the force fields through force-and-energy matching to DFT results using simulated annealing. We validate the force fields by comparisons to DFT and experimental binding energies. Our force fields reproduce the surface-sensitive binding predicted by DFT calculations. Molecular dynamics simulations based on these force fields can be used to reveal the role of solvent, polymer chain length, and polymer concentration in the selective synthesis of Ag nanostructures.

Magnetodynamic stability of a fluid cylinder under the Lundquist force-free magnetic field

NASA Astrophysics Data System (ADS)

Radwan, Ahmed E.; Halawa, Mohamed A.

1990-04-01

The magnetodynamic (in)stability of a conducting fluid cylinder subject to the capillarity and electromagnetic forces has been developed. The cylinder is pervaded by a uniform magnetic field but embedded in the Lundquist force-free varying field that allows for flowing a current surrounding the fluid. A general eigenvalue relation is derived based on a study of the equilibrium and perturbed states. The stability criterion is discussed analytically in general terms. The surface tension is destabilizing for small axisymmetric mode and stable for all others. The principle of the exchange of stability is allowed for the present problem due to the non-uniform behavior of the force-free field. Each of the axial and transverse force-free fields separately exerts a stabilizing influence in the most dangerous mode but the combined contribution of them is strongly destabilizing. Whether the model is acted upon the electromagnetic force (with the Lundquist field) the stability restrictions or/and the capillarity force are identified. Several reported works can be recovered as limiting cases with appropriate simplifications.

Strategic Choice: United States Special Forces’ Comparative Advantage in Irregular Warfare

DTIC Science & Technology

2017-03-01

UNITED STATES SPECIAL FORCES’ COMPARATIVE ADVANTAGE IN IRREGULAR WARFARE by Steven F. Payne March 2017 Thesis Advisor: Hy S. Rothstein...REPORT TYPE AND DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE STRATEGIC CHOICE: UNITED STATES SPECIAL FORCES’ COMPARATIVE ADVANTAGE IN...methodology, this thesis concludes that U.S. Army Special Forces have a comparative advantage over conventional forces to provide the National Command

Dynamic Loads Generation for Multi-Point Vibration Excitation Problems

NASA Technical Reports Server (NTRS)

Shen, Lawrence

2011-01-01

A random-force method has been developed to predict dynamic loads produced by rocket-engine random vibrations for new rocket-engine designs. The method develops random forces at multiple excitation points based on random vibration environments scaled from accelerometer data obtained during hot-fire tests of existing rocket engines. This random-force method applies random forces to the model and creates expected dynamic response in a manner that simulates the way the operating engine applies self-generated random vibration forces (random pressure acting on an area) with the resulting responses that we measure with accelerometers. This innovation includes the methodology (implementation sequence), the computer code, two methods to generate the random-force vibration spectra, and two methods to reduce some of the inherent conservatism in the dynamic loads. This methodology would be implemented to generate the random-force spectra at excitation nodes without requiring the use of artificial boundary conditions in a finite element model. More accurate random dynamic loads than those predicted by current industry methods can then be generated using the random force spectra. The scaling method used to develop the initial power spectral density (PSD) environments for deriving the random forces for the rocket engine case is based on the Barrett Criteria developed at Marshall Space Flight Center in 1963. This invention approach can be applied in the aerospace, automotive, and other industries to obtain reliable dynamic loads and responses from a finite element model for any structure subject to multipoint random vibration excitations.

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

Simulation of Human-induced Vibrations Based on the Characterized In-field Pedestrian Behavior

PubMed Central

Van Nimmen, Katrien; Lombaert, Geert; De Roeck, Guido; Van den Broeck, Peter

2016-01-01

For slender and lightweight structures, vibration serviceability is a matter of growing concern, often constituting the critical design requirement. With designs governed by the dynamic performance under human-induced loads, a strong demand exists for the verification and refinement of currently available load models. The present contribution uses a 3D inertial motion tracking technique for the characterization of the in-field pedestrian behavior. The technique is first tested in laboratory experiments with simultaneous registration of the corresponding ground reaction forces. The experiments include walking persons as well as rhythmical human activities such as jumping and bobbing. It is shown that the registered motion allows for the identification of the time variant pacing rate of the activity. Together with the weight of the person and the application of generalized force models available in literature, the identified time-variant pacing rate allows to characterize the human-induced loads. In addition, time synchronization among the wireless motion trackers allows identifying the synchronization rate among the participants. Subsequently, the technique is used on a real footbridge where both the motion of the persons and the induced structural vibrations are registered. It is shown how the characterized in-field pedestrian behavior can be applied to simulate the induced structural response. It is demonstrated that the in situ identified pacing rate and synchronization rate constitute an essential input for the simulation and verification of the human-induced loads. The main potential applications of the proposed methodology are the estimation of human-structure interaction phenomena and the development of suitable models for the correlation among pedestrians in real traffic conditions. PMID:27167309

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

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.

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

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.

Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

DOE PAGES

Borreguero Calvo, Jose M.; Lynch, Vickie E.

2015-11-23

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

PubMed

Kutateladze, Andrei G; Mukhina, Olga A

2014-09-05

Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

Development of a wave-induced forcing threshold for nearshore impact of Wave Energy Converter arrays

NASA Astrophysics Data System (ADS)

O'Dea, A.; Haller, M. C.; Ozkan-Haller, H. T.

2016-02-01

Wave-induced forcing is a function of spatial gradients in the wave radiation stresses and is the main driver of alongshore currents, rip currents, and nearshore sediment transport. The installation of nearshore Wave Energy Converter (WEC) arrays may cause significant changes in the surf zone radiation stresses and could therefore impact nearshore littoral processes. In the first part of this study, a new threshold for nearshore hydrodynamic impact due to the presence of WEC devices is established based on changes in the alongshore radiation stress gradients shoreward of WEC arrays. The threshold is defined based on the relationship between nearshore radiation stresses and alongshore currents as observed in field data. Next, we perform a parametric study of the nearshore impact of WEC arrays using the SWAN wave model. Trials are conducted on an idealized, alongshore-uniform beach with a range of WEC array configurations, locations, and incident wave conditions, and conditions that generate radiation stress gradients above the impact threshold are identified. Finally, the same methodology is applied to two wave energy test sites off the coast of Newport, OR with more complicated bathymetries. Although the trends at the field sites are similar to those seen in the parametric study, the location and extent of the changes in the alongshore radiation stress gradients appear to be heavily influenced by the local bathymetry.

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations

NASA Astrophysics Data System (ADS)

Monroe, Jacob I.; Shirts, Michael R.

2014-04-01

Molecular containers such as cucurbit[7]uril (CB7) and the octa-acid (OA) host are ideal simplified model test systems for optimizing and analyzing methods for computing free energies of binding intended for use with biologically relevant protein-ligand complexes. To this end, we have performed initially blind free energy calculations to determine the free energies of binding for ligands of both the CB7 and OA hosts. A subset of the selected guest molecules were those included in the SAMPL4 prediction challenge. Using expanded ensemble simulations in the dimension of coupling host-guest intermolecular interactions, we are able to show that our estimates in most cases can be demonstrated to fully converge and that the errors in our estimates are due almost entirely to the assigned force field parameters and the choice of environmental conditions used to model experiment. We confirm the convergence through the use of alternative simulation methodologies and thermodynamic pathways, analyzing sampled conformations, and directly observing changes of the free energy with respect to simulation time. Our results demonstrate the benefits of enhanced sampling of multiple local free energy minima made possible by the use of expanded ensemble molecular dynamics and may indicate the presence of significant problems with current transferable force fields for organic molecules when used for calculating binding affinities, especially in non-protein chemistries.

Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.

PubMed

Monroe, Jacob I; Shirts, Michael R

2014-04-01

Molecular containers such as cucurbit[7]uril (CB7) and the octa-acid (OA) host are ideal simplified model test systems for optimizing and analyzing methods for computing free energies of binding intended for use with biologically relevant protein-ligand complexes. To this end, we have performed initially blind free energy calculations to determine the free energies of binding for ligands of both the CB7 and OA hosts. A subset of the selected guest molecules were those included in the SAMPL4 prediction challenge. Using expanded ensemble simulations in the dimension of coupling host-guest intermolecular interactions, we are able to show that our estimates in most cases can be demonstrated to fully converge and that the errors in our estimates are due almost entirely to the assigned force field parameters and the choice of environmental conditions used to model experiment. We confirm the convergence through the use of alternative simulation methodologies and thermodynamic pathways, analyzing sampled conformations, and directly observing changes of the free energy with respect to simulation time. Our results demonstrate the benefits of enhanced sampling of multiple local free energy minima made possible by the use of expanded ensemble molecular dynamics and may indicate the presence of significant problems with current transferable force fields for organic molecules when used for calculating binding affinities, especially in non-protein chemistries.

The Three Stages of Critical Policy Methodology: An Example from Curriculum Analysis

ERIC Educational Resources Information Center

Rata, Elizabeth

2014-01-01

The article identifies and discusses three stages in the critical policy methodology used in the sociology of education. These are: firstly, employing a political economy theoretical framework that identifies causal links between global forces and local developments; secondly, analysing educational policy within that theoretically conceptualised…

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.

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

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.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

NASA Astrophysics Data System (ADS)

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

2017-02-01

A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results.

Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

DOE PAGES

Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; ...

2017-02-01

We developed a new modified embedded-atom method (MEAM) force field for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997)], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquidmore » density, self-diffusivity, viscosity, and vapor-liquid surface tension. We show that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.« less

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

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

75 FR 62403 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-08

... Project: 2011-2014 National Survey on Drug Use and Health: Methodological Field Tests (OMB No. 0930-0290..., SAMHSA received a three-year renewal of its generic clearance for methodological field tests. This will be a request for another renewal of the generic approval to continue methodological tests over the...

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.

The Social Attachment to Place

ERIC Educational Resources Information Center

Dahl, Michael S.; Sorenson, Olav

2010-01-01

Many theories either implicitly or explicitly assume that individuals readily move to places that improve their financial well-being. Other forces, however, offset these tendencies; for example, people often wish to remain close to family and friends. We introduce a methodology for determining how individuals weigh these countervailing forces, and…

Cave spiders choose optimal environmental factors with respect to the generated entropy when laying their cocoon

PubMed Central

Chiavazzo, Eliodoro; Isaia, Marco; Mammola, Stefano; Lepore, Emiliano; Ventola, Luigi; Asinari, Pietro; Pugno, Nicola Maria

2015-01-01

The choice of a suitable area to spiders where to lay eggs is promoted in terms of Darwinian fitness. Despite its importance, the underlying factors behind this key decision are generally poorly understood. Here, we designed a multidisciplinary study based both on in-field data and laboratory experiments focusing on the European cave spider Meta menardi (Araneae, Tetragnathidae) and aiming at understanding the selective forces driving the female in the choice of the depositional area. Our in-field data analysis demonstrated a major role of air velocity and distance from the cave entrance within a particular cave in driving the female choice. This has been interpreted using a model based on the Entropy Generation Minimization - EGM - method, without invoking best fit parameters and thanks to independent lab experiments, thus demonstrating that the female chooses the depositional area according to minimal level of thermo-fluid-dynamic irreversibility. This methodology may pave the way to a novel approach in understanding evolutionary strategies for other living organisms. PMID:25556697

Fluid Physics Under a Stochastic Acceleration Field

NASA Technical Reports Server (NTRS)

Vinals, Jorge

2001-01-01

The research summarized in this report has involved a combined theoretical and computational study of fluid flow that results from the random acceleration environment present onboard space orbiters, also known as g-jitter. We have focused on a statistical description of the observed g-jitter, on the flows that such an acceleration field can induce in a number of experimental configurations of interest, and on extending previously developed methodology to boundary layer flows. Narrow band noise has been shown to describe many of the features of acceleration data collected during space missions. The scale of baroclinically induced flows when the driving acceleration is random is not given by the Rayleigh number. Spatially uniform g-jitter induces additional hydrodynamic forces among suspended particles in incompressible fluids. Stochastic modulation of the control parameter shifts the location of the onset of an oscillatory instability. Random vibration of solid boundaries leads to separation of boundary layers. Steady streaming ahead of a modulated solid-melt interface enhances solute transport, and modifies the stability boundaries of a planar front.

Technical note: Simultaneous fully dynamic characterization of multiple input–output relationships in climate models

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

Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.

We introduce system identification techniques to climate science wherein multiple dynamic input–output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to thosemore » of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Moreover, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.« less

Technical note: Simultaneous fully dynamic characterization of multiple input–output relationships in climate models

DOE PAGES

Kravitz, Ben; MacMartin, Douglas G.; Rasch, Philip J.; ...

2017-02-17

We introduce system identification techniques to climate science wherein multiple dynamic input–output relationships can be simultaneously characterized in a single simulation. This method, involving multiple small perturbations (in space and time) of an input field while monitoring output fields to quantify responses, allows for identification of different timescales of climate response to forcing without substantially pushing the climate far away from a steady state. We use this technique to determine the steady-state responses of low cloud fraction and latent heat flux to heating perturbations over 22 regions spanning Earth's oceans. We show that the response characteristics are similar to thosemore » of step-change simulations, but in this new method the responses for 22 regions can be characterized simultaneously. Moreover, we can estimate the timescale over which the steady-state response emerges. The proposed methodology could be useful for a wide variety of purposes in climate science, including characterization of teleconnections and uncertainty quantification to identify the effects of climate model tuning parameters.« less

Hydrodynamic fractionation of finite size gold nanoparticle clusters.

PubMed

Tsai, De-Hao; Cho, Tae Joon; DelRio, Frank W; Taurozzi, Julian; Zachariah, Michael R; Hackley, Vincent A

2011-06-15

We demonstrate a high-resolution in situ experimental method for performing simultaneous size classification and characterization of functional gold nanoparticle clusters (GNCs) based on asymmetric-flow field flow fractionation (AFFF). Field emission scanning electron microscopy, atomic force microscopy, multi-angle light scattering (MALS), and in situ ultraviolet-visible optical spectroscopy provide complementary data and imagery confirming the cluster state (e.g., dimer, trimer, tetramer), packing structure, and purity of fractionated populations. An orthogonal analysis of GNC size distributions is obtained using electrospray-differential mobility analysis (ES-DMA). We find a linear correlation between the normalized MALS intensity (measured during AFFF elution) and the corresponding number concentration (measured by ES-DMA), establishing the capacity for AFFF to quantify the absolute number concentration of GNCs. The results and corresponding methodology summarized here provide the proof of concept for general applications involving the formation, isolation, and in situ analysis of both functional and adventitious nanoparticle clusters of finite size. © 2011 American Chemical Society

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

PubMed Central

2015-01-01

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

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.

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.

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

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.

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

Jornet, N; Carrasco de Fez, P; Jordi, O

Purpose: To evaluate the accuracy in total scatter factor (Sc,p) determination for small fields using commercial plastic scintillator detector (PSD). The manufacturer's spectral discrimination method to subtract Cerenkov light from the signal is discussed. Methods: Sc,p for field sizes ranging from 0.5 to 10 cm were measured using PSD Exradin (Standard Imaging) connected to two channel electrometer measuring the signals in two different spectral regions to subtract the Cerenkov signal from the PSD signal. A Pinpoint ionisation chamber 31006 (PTW) and a non-shielded semiconductor detector EFD (Scanditronix) were used for comparison. Measures were performed for a 6 MV X-ray beam.more » The Sc,p are measured at 10 cm depth in water for a SSD=100 cm and normalized to a 10'10 cm{sup 2} field size at the isocenter. All detectors were placed with their symmetry axis parallel to the beam axis.We followed the manufacturer's recommended calibration methodology to subtract the Cerenkov contribution to the signal as well as a modified method using smaller field sizes. The Sc,p calculated by using both calibration methodologies were compared. Results: Sc,p measured with the semiconductor and the PinPoint detectors agree, within 1.5%, for field sizes between 10'10 and 1'1 cm{sup 2}. Sc,p measured with the PSD using the manufacturer's calibration methodology were systematically 4% higher than those measured with the semiconductor detector for field sizes smaller than 5'5 cm{sup 2}. By using a modified calibration methodology for smalls fields and keeping the manufacturer calibration methodology for fields larger than 5'5cm{sup 2} field Sc,p matched semiconductor results within 2% field sizes larger than 1.5 cm. Conclusion: The calibration methodology proposed by the manufacturer is not appropriate for dose measurements in small fields. The calibration parameters are not independent of the incident radiation spectrum for this PSD. This work was partially financed by grant 2012 of Barcelona board of the AECC.« less

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 user's manual, revised

NASA Technical Reports Server (NTRS)

Jordan, Harry F.; Benten, Muhammad S.; Arenstorf, Norbert S.; Ramanan, Aruna V.

1987-01-01

A methodology for writing parallel programs for shared memory multiprocessors has been formalized as an extension to the Fortran language and implemented as a macro preprocessor. The extended language is known as the Force, and this manual describes how to write Force programs and execute them on the Flexible Computer Corporation Flex/32, the Encore Multimax and the Sequent Balance computers. The parallel extension macros are described in detail, but knowledge of Fortran is assumed.

Radiation Forces and Torques without Stress (Tensors)

ERIC Educational Resources Information Center

Bohren, Craig F.

2011-01-01

To understand radiation forces and torques or to calculate them does not require invoking photon or electromagnetic field momentum transfer or stress tensors. According to continuum electromagnetic theory, forces and torques exerted by radiation are a consequence of electric and magnetic fields acting on charges and currents that the fields induce…

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

PubMed Central

2016-01-01

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

Deep eutectic solvent formation: a structural view using molecular dynamics simulations with classical force fields

NASA Astrophysics Data System (ADS)

Mainberger, Sebastian; Kindlein, Moritz; Bezold, Franziska; Elts, Ekaterina; Minceva, Mirjana; Briesen, Heiko

2017-06-01

Deep eutectic solvents (DES) have gained a reputation as inexpensive and easy to handle ionic liquid analogues. This work employs molecular dynamics (MD) to simulate a variety of DES. The hydrogen bond acceptor (HBA) choline chloride was paired with the hydrogen bond donors (HBD) glycerol, 1,4-butanediol, and levulinic acid. Levulinic acid was also paired with the zwitterionic HBA betaine. In order to evaluate the reliability of data MD simulations can provide for DES, two force fields were compared: the Merck Molecular Force Field and the General Amber Force Field with two different sets of partial charges for the latter. The force fields were evaluated by comparing available experimental thermodynamic and transport properties against simulated values. Structural analysis was performed on the eutectic systems and compared to non-eutectic compositions. All force fields could be validated against certain experimental properties, but performance varied depending on the system and property in question. While extensive hydrogen bonding was found for all systems, details about the contribution of individual groups strongly varied among force fields. Interaction potentials revealed that HBA-HBA interactions weaken linearly with increasing HBD ratio, while HBD-HBD interactions grew disproportionally in magnitude, which might hint at the eutectic composition of a system.

Commensurability effects in the critical forces of a superconducting film with Kagomé pinning array at submatching fields

NASA Astrophysics Data System (ADS)

Vizarim, Nicolas P.; Carlone, Maicon; Verga, Lucas G.; Venegas, Pablo A.

2017-09-01

Using molecular dynamics simulations, we find the commensurability force peaks in a two-dimensional superconducting thin-film with a Kagomé pinning array. A transport force is applied in two mutually perpendicular directions, and the magnetic field is increased up to the first matching field. Usually the condition to have pronounced force peaks in systems with periodic pinning is associated to the rate between the applied magnetic field and the first matching field, it must be an integer or a rational fraction. Here, we show that another condition must be satisfied, the vortex ground state must be ordered. Our calculations show that the pinning size and strength may dramatically change the vortex ground state. Small pinning radius and high values of pinning strength may lead to disordered vortex configurations, which fade the critical force peaks. The critical forces show anisotropic behavior, but the same dependence on pinning strength and radius is observed for both driven force directions. Different to cases where the applied magnetic field is higher than the first matching field, here the depinning process begins with vortices weakly trapped on top of a pinning site and not with interstitial vortices. Our results are in good agreement with recent experimental results.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Scaling of wet granular flows in a rotating drum

NASA Astrophysics Data System (ADS)

Jarray, Ahmed; Magnanimo, Vanessa; Ramaioli, Marco; Luding, Stefan

2017-06-01

In this work, we investigate the effect of capillary forces and particle size on wet granular flows and we propose a scaling methodology that ensures the conservation of the bed flow. We validate the scaling law experimentally by using different size glass beads with tunable capillary forces. The latter is obtained using mixtures of ethanol-water as interstitial liquid and by increasing the hydrophobicity of glass beads with an ad-hoc silanization procedure. The scaling methodology in the flow regimes considered (slipping, slumping and rolling) yields similar bed flow for different particle sizes including the angle of repose that normally increases when decreasing the particle size.

Development of a robotic evaluation system for the ability of proprioceptive sensation in slow hand motion.

PubMed

Tanaka, Yoshiyuki; Mizoe, Genki; Kawaguchi, Tomohiro

2015-01-01

This paper proposes a simple diagnostic methodology for checking the ability of proprioceptive/kinesthetic sensation by using a robotic device. The perception ability of virtual frictional forces is examined in operations of the robotic device by the hand at a uniform slow velocity along the virtual straight/circular path. Experimental results by healthy subjects demonstrate that percentage of correct answers for the designed perceptual tests changes in the motion direction as well as the arm configuration and the HFM (human force manipulability) measure. It can be supposed that the proposed methodology can be applied into the early detection of neuromuscular/neurological disorders.

Faecal Parasitology: Concentration Methodology Needs to be Better Standardised

PubMed Central

Manser, Monika M.; Saez, Agatha Christie Santos; Chiodini, Peter L.

2016-01-01

Aim To determine whether variation in the preservative, pore size of the sieve, solvent, centrifugal force and centrifugation time used in the Ridley-Allen Concentration method for examining faecal specimens for parasite stages had any effect on their recovery in faecal specimens. Methods A questionnaire was sent to all participants in the UK NEQAS Faecal Parasitology Scheme. The recovery of parasite stages was compared using formalin diluted in water or formalin diluted in saline as the fixative, 3 different pore sizes of sieve, ether or ethyl acetate as a solvent, 7 different centrifugal forces and 6 different centrifugation times according to the methods described by participants completing the questionnaire. Results The number of parasite stages recovered was higher when formalin diluted in water was used as fixative, a smaller pore size of sieve was used, ethyl acetate along with Triton X 100 was used as a solvent and a centrifugal force of 3,000 rpm for 3 minutes were employed. Conclusions This study showed that differences in methodology at various stages of the concentration process affect the recovery of parasites from a faecal specimen and parasites present in small numbers could be missed if the recommended methodology is not followed. PMID:27073836

The influence of centrifugal forces on the B field structure of an axially symmetric equilibrium magnetosphere

NASA Technical Reports Server (NTRS)

Ye, Gang; Voigt, Gerd-Hannes

1989-01-01

A model is presented of an axially symmetric pole-on magnetosphere in MHD force balance, in which both plasma thermal pressure gradients and centrifugal force are taken into account. Assuming that planetary rotation leads to differentially rotating magnetotail field lines, the deformation of magnetotail field lines under the influence of both thermal plasma pressure and centrifugal forces was calculated. Analytic solutions to the Grad-Shafranov equation are presented, which include the centrifugal force term. It is shown that the nonrotational magnetosphere with hot thermal plasma leads to a field configuration without a toroidal B(phi) component and without field-aligned Birkeland currents. The other extreme, a rapidly rotating magnetosphere with cold plasma, leads to a configuration in which plasma must be confined within a thin disk in a plane where the radial magnetic field component B(r) vanishes locally.

Particles with nonlinear electric response: Suppressing van der Waals forces by an external field.

PubMed

Soo, Heino; Dean, David S; Krüger, Matthias

2017-01-01

We study the classical thermal component of Casimir, or van der Waals, forces between point particles with highly anharmonic dipole Hamiltonians when they are subjected to an external electric field. Using a model for which the individual dipole moments saturate in a strong field (a model that mimics the charges in a neutral, perfectly conducting sphere), we find that the resulting Casimir force depends strongly on the strength of the field, as demonstrated by analytical results. For a certain angle between the external field and center-to-center axis, the fluctuation force can be tuned and suppressed to arbitrarily small values. We compare the forces between these particles with those between particles with harmonic Hamiltonians and also provide a simple formula for asymptotically large external fields, which we expect to be generally valid for the case of saturating dipole moments.

Preface: Special Topic: From Quantum Mechanics to Force Fields.

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

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

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

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

Methodologies to determine forces on bones and muscles of body segments during exercise, employing compact sensors suitable for use in crowded space vehicles

NASA Technical Reports Server (NTRS)

Figueroa, Fernando

1995-01-01

Work under this grant was carried out by the author and by a graduate research assistant. An instrumented bicycle ergometer was implemented focusing on the stated objective: to estimate the forces exerted by each muscle of the feet, calf, and thigh of an individual while bicycling. The sensors used were light and compact. These were probes to measure muscle EMG activity, miniature accelerometers, miniature load sensors, and small encoders to measure angular positions of the pedal. A methodology was developed and implemented to completely describe the kinematics of the limbs using data from the sensors. This work has been published as a Master's Thesis by the Graduate student supported by the grant. The instrumented ergometer along with the sensors and instrumentation were tested during a KC-135 Zero-Gravity flight in July, 1994. A complete description of the system and the tests performed have been published as a report submitted to NASA Johnson Space Center. The data collected during the KC-135 flight is currently being processed so that a kinematic description of the bicycling experiment will be soon determined. A methodology to estimate the muscle forces has been formulated based on previous work. The methodology involves the use of optimization concepts so that the individual muscle forces that represent variables in dynamic equations of motion may be estimated. Optimization of a criteria (goal) function such as minimization of energy will be used along with constraint equations defined by rigid body equations of motion. Use of optimization principles is necessary, because the equations of motion alone constitute an indeterminate system of equations with respect to the large amount of muscle forces which constitute the variables in these equations. The number of variables is reduced somewhat by using forces measured by the load cells installed on the pedal. These load cells measure pressure and shear forces on the foot. The author and his collaborators at NASA and at the University of Alabama, Tuscaloosa, are continuing the work of reducing the experimental data from the KC-135 flight, and the implementation of the optimization methods to estimate muscle forces. As soon as results from these efforts are available, they will be published in reputable journals. Results of this work will impact studies addressing bone density loss and development of countermeasures to minimize bone loss in zero gravity conditions. By analyzing muscle forces on Earth and in Space during exercise, scientists could eventually formulate new exercises and machines to help maintain bone density. On Earth, this work will impact studies concerning arthritis, and will provide the means to study possible exercise countermeasures to minimize arthritis problems.

75 FR 78720 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-16

.... Proposed Project: 2011-2014 National Survey on Drug Use and Health: Methodological Field Tests (OMB No..., SAMHSA received a 3-year renewal of its generic clearance for methodological field tests. This will be a request for another renewal of the generic approval to continue methodological tests over the next 3 years...

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.

The Materiality of Fieldwork: An Ontology of Feminist Becoming

ERIC Educational Resources Information Center

Childers, Sara M.

2013-01-01

Through the materiality of fieldwork at a high-achieving high-poverty high school, I discuss how the collision between practices of feminist methodology and the materiality of fieldwork forced me to rethink the "feminist" in feminist research. Using the work of Karen Barad, this material-discursive account of methodology as ontology…

Stress-Strain Characterization for Reversed Loading Path and Constitutive Modeling for AHSS Springback Predictions

NASA Astrophysics Data System (ADS)

Zhu, Hong; Huang, Mai; Sadagopan, Sriram; Yao, Hong

2017-09-01

With increasing vehicle fuel economy standards, automotive OEMs are widely using various AHSS grades including DP, TRIP, CP and 3rd Gen AHSS to reduce vehicle weight due to their good combination of strength and formability. As one of enabling technologies for AHSS application, the requirement for requiring accurate prediction of springback for cold stamped AHSS parts stimulated a large number of investigations in the past decade with reversed loading path at large strains followed by constitutive modeling. With a spectrum of complex loading histories occurring in production stamping processes, there were many challenges in this field including issues of test data reliability, loading path representability, constitutive model robustness and non-unique constitutive parameter-identification. In this paper, various testing approaches and constitutive modeling will be reviewed briefly and a systematic methodology from stress-strain characterization, constitutive model parameter identification for material card generation will be presented in order to support automotive OEM’s need on virtual stamping. This systematic methodology features a tension-compression test at large strain with robust anti-buckling device with concurrent friction force correction, properly selected loading paths to represent material behavior during different springback modes as well as the 10-parameter Yoshida model with knowledge-based parameter-identification through nonlinear optimization. Validation cases for lab AHSS parts will also be discussed to check applicability of this methodology.

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.

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

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.

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

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.

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

Impact and Estimation of Balance Coordinate System Rotations and Translations in Wind-Tunnel Testing

NASA Technical Reports Server (NTRS)

Toro, Kenneth G.; Parker, Peter A.

2017-01-01

Discrepancies between the model and balance coordinate systems lead to biases in the aerodynamic measurements during wind-tunnel testing. The reference coordinate system relative to the calibration coordinate system at which the forces and moments are resolved is crucial to the overall accuracy of force measurements. This paper discusses sources of discrepancies and estimates of coordinate system rotation and translation due to machining and assembly differences. A methodology for numerically estimating the coordinate system biases will be discussed and developed. Two case studies are presented using this methodology to estimate the model alignment. Examples span from angle measurement system shifts on the calibration system to discrepancies in actual wind-tunnel data. The results from these case-studies will help aerodynamic researchers and force balance engineers to better the understand and identify potential differences in calibration systems due to coordinate system rotation and translation.

Learning a trajectory using adjoint functions and teacher forcing

NASA Technical Reports Server (NTRS)

Toomarian, Nikzad B.; Barhen, Jacob

1992-01-01

A new methodology for faster supervised temporal learning in nonlinear neural networks is presented which builds upon the concept of adjoint operators to allow fast computation of the gradients of an error functional with respect to all parameters of the neural architecture, and exploits the concept of teacher forcing to incorporate information on the desired output into the activation dynamics. The importance of the initial or final time conditions for the adjoint equations is discussed. A new algorithm is presented in which the adjoint equations are solved simultaneously (i.e., forward in time) with the activation dynamics of the neural network. We also indicate how teacher forcing can be modulated in time as learning proceeds. The results obtained show that the learning time is reduced by one to two orders of magnitude with respect to previously published results, while trajectory tracking is significantly improved. The proposed methodology makes hardware implementation of temporal learning attractive for real-time applications.

Pulsed field gradient magic angle spinning NMR self-diffusion measurements in liquids

NASA Astrophysics Data System (ADS)

Viel, Stéphane; Ziarelli, Fabio; Pagès, Guilhem; Carrara, Caroline; Caldarelli, Stefano

2008-01-01

Several investigations have recently reported the combined use of pulsed field gradient (PFG) with magic angle spinning (MAS) for the analysis of molecular mobility in heterogeneous materials. In contrast, little attention has been devoted so far to delimiting the role of the extra force field induced by sample rotation on the significance and reliability of self-diffusivity measurements. The main purpose of this work is to examine this phenomenon by focusing on pure liquids for which its impact is expected to be largest. Specifically, we show that self-diffusion coefficients can be accurately determined by PFG MAS NMR diffusion measurements in liquids, provided that specific experimental conditions are met. First, the methodology to estimate the gradient uniformity and to properly calibrate its absolute strength is briefly reviewed and applied on a MAS probe equipped with a gradient coil aligned along the rotor spinning axis, the so-called 'magic angle gradient' coil. Second, the influence of MAS on the outcome of PFG MAS diffusion measurements in liquids is investigated for two distinct typical rotors of different active volumes, 12 and 50 μL. While the latter rotor led to totally unreliable results, especially for low viscosity compounds, the former allowed for the determination of accurate self-diffusion coefficients both for fast and slowly diffusing species. Potential implications of this work are the possibility to measure accurate self-diffusion coefficients of sample-limited mixtures or to avoid radiation damping interferences in NMR diffusion measurements. Overall, the outlined methodology should be of interest to anyone who strives to improve the reliability of MAS diffusion studies, both in homogeneous and heterogeneous media.

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

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.

Modifications to give HOPE/MDC 2.0 the capability to solve for or consider vent forces: Mission planning, mission analysis, and software formulation

NASA Technical Reports Server (NTRS)

Zyla, L. V.

1979-01-01

The modifications are described as necessary to give the Houston Operations Predictor/Estimator (HOPE) program the capability to solve for or consider vent forces for orbit determination. The model implemented in solving for vent forces is described along with the integrator problems encountered. A summary derivation of the mathematical principles applicable to solve/consider methodology is provided.

Methodology for Constructing a Modernization Roadmap for Air Force Automatic Test Systems

DTIC Science & Technology

2012-01-01

Constructing a Modernization Roadmap for Air Force Automatic Test Systems Lionel A. Galway , Rachel Rue, James M. Masters, Ben D. Van Roo, Manuel...constructing a modernization roadmap for Air Force automatic test systems / Lionel A. Galway ... [et al.]. p. cm. Includes bibliographical...references. ISBN 978-0-8330-5899-7 (pbk. : alk. paper) 1. United States. Air Force—Weapons systems—Testing. I. Galway , Lionel A., 1950- UG633.M3445

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

Local deformation for soft tissue simulation

PubMed Central

Omar, Nadzeri; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2016-01-01

ABSTRACT This paper presents a new methodology to localize the deformation range to improve the computational efficiency for soft tissue simulation. This methodology identifies the local deformation range from the stress distribution in soft tissues due to an external force. A stress estimation method is used based on elastic theory to estimate the stress in soft tissues according to a depth from the contact surface. The proposed methodology can be used with both mass-spring and finite element modeling approaches for soft tissue deformation. Experimental results show that the proposed methodology can improve the computational efficiency while maintaining the modeling realism. PMID:27286482

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.

Determining the Ocean's Role on the Variable Gravity Field and Earth Rotation

NASA Technical Reports Server (NTRS)

Ponte, Rui M.

2000-01-01

Our three year investigation, carried out over the period 18-19 Nov 2000, focused on the study of the variability in ocean angular momentum and mass signals and their relation to the Earth's variable rotation and gravity field. This final report includes a summary description of our work and a list of related publications and presentations. One thrust of the investigation was to determine and interpret the changes in the ocean mass field, as they impact on the variable gravity field and Earth rotation. In this regard, the seasonal cycle in local vertically-integrated ocean mass was analyzed using two ocean models of different complexity: (1) the simple constant-density, coarse resolution model of Ponte; and (2) the fully stratified, eddy-resolving model of Semtner and Chervin. The dynamics and thermodynamics of the seasonal variability in ocean mass were examined in detail, as well as the methodologies to calculate those changes under different model formulations. Another thrust of the investigation was to examine signals in ocean angular momentum (OAM) in relation to Earth rotation changes. A number of efforts were undertaken in this regard. Sensitivity of the oceanic excitation to different assumptions about how the ocean is forced and how it dissipates its energy was explored.

Electric field stabilization of viscous liquid layers coating the underside of a surface

NASA Astrophysics Data System (ADS)

Anderson, Thomas G.; Cimpeanu, Radu; Papageorgiou, Demetrios T.; Petropoulos, Peter G.

2017-05-01

We investigate the electrostatic stabilization of a viscous thin film wetting the underside of a horizontal surface in the presence of an electric field applied parallel to the surface. The model includes the effect of bounding solid dielectric regions above and below the liquid-air system that are typically found in experiments. The competition between gravitational forces, surface tension, and the nonlocal effect of the applied electric field is captured analytically in the form of a nonlinear evolution equation. A semispectral solution strategy is employed to resolve the dynamics of the resulting partial differential equation. Furthermore, we conduct direct numerical simulations (DNS) of the Navier-Stokes equations using the volume-of-fluid methodology and assess the accuracy of the obtained solutions in the long-wave (thin-film) regime when varying the electric field strength from zero up to the point when complete stabilization occurs. We employ DNS to examine the limitations of the asymptotically derived behavior as the liquid layer thickness increases and find excellent agreement even beyond the regime of strict applicability of the asymptotic solution. Finally, the asymptotic and computational approaches are utilized to identify robust and efficient active control mechanisms allowing the manipulation of the fluid interface in light of engineering applications at small scales, such as mixing.

The Road to Information Dominance: "System of Systems" Concept for the United States Armed Forces.

DTIC Science & Technology

1998-04-06

information dominance through the U.S. Armed Forces "System of Systems" concept. It addresses and analyzes current and future strategic implications and requirements for U.S. warfighting communications and information systems. It proposes a more flexible, reliable, responsive, robust and survivable high capacity throughput communications and "bitways" system to support future force projection operations for the Force and/or Army After Next. Lastly, it concludes with a suggested methodology to implement the "System of Systems" concept to enable

Note: Thermal analog to atomic force microscopy force-displacement measurements for nanoscale interfacial contact resistance.

PubMed

Iverson, Brian D; Blendell, John E; Garimella, Suresh V

2010-03-01

Thermal diffusion measurements on polymethylmethacrylate-coated Si substrates using heated atomic force microscopy tips were performed to determine the contact resistance between an organic thin film and Si. The measurement methodology presented demonstrates how the thermal contrast signal obtained during a force-displacement ramp is used to quantify the resistance to heat transfer through an internal interface. The results also delineate the interrogation thickness beyond which thermal diffusion in the organic thin film is not affected appreciably by the underlying substrate.

A Decision Methodology and Organizational Structure for Determining the Mission Essentiality of Rail Service to U.S. Air Force Installations

DTIC Science & Technology

1983-09-01

and Director DLA, 4 May 1983. 128. Williams , Ernest W., Jr. ’A Critique cf the Staggers Rail Act of 1980," Transportation Journal, Spring 1992, pp.5...i3 unlim i-ted.L DEPARTMENT OF THE AIR FORCE W, .&•AIR UNIVERSITY FIN AIiR FORCE iNST irUTE OF TECHNOLOGY Wright- Patterson Air Force Base, Ohio 83...and reloaded on railcars for movement to German exercise sites (16:14). William Taylovr, President of the Illinois Central Gulf 33 Railroad, has

Toward Theory-Based Research in Political Communication.

ERIC Educational Resources Information Center

Simon, Adam F.; Iyengar, Shanto

1996-01-01

Praises the theoretical and methodological potential of the field of political communication. Calls for greater interaction and cross fertilization among the fields of political science, sociology, economics, and psychology. Briefly discusses relevant research methodologies. (MJP)

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.

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.

Artificial Intelligence Methodologies and Their Application to Diabetes

PubMed Central

Rigla, Mercedes; García-Sáez, Gema; Pons, Belén; Hernando, Maria Elena

2017-01-01

In the past decade diabetes management has been transformed by the addition of continuous glucose monitoring and insulin pump data. More recently, a wide variety of functions and physiologic variables, such as heart rate, hours of sleep, number of steps walked and movement, have been available through wristbands or watches. New data, hydration, geolocation, and barometric pressure, among others, will be incorporated in the future. All these parameters, when analyzed, can be helpful for patients and doctors’ decision support. Similar new scenarios have appeared in most medical fields, in such a way that in recent years, there has been an increased interest in the development and application of the methods of artificial intelligence (AI) to decision support and knowledge acquisition. Multidisciplinary research teams integrated by computer engineers and doctors are more and more frequent, mirroring the need of cooperation in this new topic. AI, as a science, can be defined as the ability to make computers do things that would require intelligence if done by humans. Increasingly, diabetes-related journals have been incorporating publications focused on AI tools applied to diabetes. In summary, diabetes management scenarios have suffered a deep transformation that forces diabetologists to incorporate skills from new areas. This recently needed knowledge includes AI tools, which have become part of the diabetes health care. The aim of this article is to explain in an easy and plane way the most used AI methodologies to promote the implication of health care providers—doctors and nurses—in this field. PMID:28539087

Artificial Intelligence Methodologies and Their Application to Diabetes.

PubMed

Rigla, Mercedes; García-Sáez, Gema; Pons, Belén; Hernando, Maria Elena

2018-03-01

In the past decade diabetes management has been transformed by the addition of continuous glucose monitoring and insulin pump data. More recently, a wide variety of functions and physiologic variables, such as heart rate, hours of sleep, number of steps walked and movement, have been available through wristbands or watches. New data, hydration, geolocation, and barometric pressure, among others, will be incorporated in the future. All these parameters, when analyzed, can be helpful for patients and doctors' decision support. Similar new scenarios have appeared in most medical fields, in such a way that in recent years, there has been an increased interest in the development and application of the methods of artificial intelligence (AI) to decision support and knowledge acquisition. Multidisciplinary research teams integrated by computer engineers and doctors are more and more frequent, mirroring the need of cooperation in this new topic. AI, as a science, can be defined as the ability to make computers do things that would require intelligence if done by humans. Increasingly, diabetes-related journals have been incorporating publications focused on AI tools applied to diabetes. In summary, diabetes management scenarios have suffered a deep transformation that forces diabetologists to incorporate skills from new areas. This recently needed knowledge includes AI tools, which have become part of the diabetes health care. The aim of this article is to explain in an easy and plane way the most used AI methodologies to promote the implication of health care providers-doctors and nurses-in this field.

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.

Methodological concerns for determining power output in the jump squat.

PubMed

Cormie, Prue; Deane, Russell; McBride, Jeffrey M

2007-05-01

The purpose of this study was to investigate the validity of power measurement techniques during the jump squat (JS) utilizing various combinations of a force plate and linear position transducer (LPT) devices. Nine men with at least 6 months of prior resistance training experience participated in this acute investigation. One repetition maximums (1RM) in the squat were determined, followed by JS testing under 2 loading conditions (30% of 1RM [JS30] and 90% of 1RM [JS90]). Three different techniques were used simultaneously in data collection: (a) 1 linear position transducer (1-LPT); (b) 1 linear position transducer and a force plate (1-LPT + FP); and (c) 2 linear position transducers and a force place (2-LPT + FP). Vertical velocity-, force-, and power-time curves were calculated for each lift using these methodologies and were compared. Peak force and peak power were overestimated by 1-LPT in both JS30 and JS90 compared with 2-LPT + FP and 1-LPT + FP (p

Force Exertion Capacity Measurements in Haptic Virtual Environments

ERIC Educational Resources Information Center

Munih, Marko; Bardorfer, Ales; Ceru, Bojan; Bajd, Tadej; Zupan, Anton

2010-01-01

An objective test for evaluating functional status of the upper limbs (ULs) in patients with muscular distrophy (MD) is presented. The method allows for quantitative assessment of the UL functional state with an emphasis on force exertion capacity. The experimental measurement setup and the methodology for the assessment of maximal exertable force…

The Revolutionary United Front and Child Soldiers during Sierra Leone’s Civil War

DTIC Science & Technology

2015-06-12

Armed Forces served as an ex post facto force during the internal conflict period between the APC and SLPP jockeying for the position of Prime Minister...civil war. Chapter 3, Research Methodology, addresses biases and the reliability of the study regarding the thesis findings. Chapter 4, Analysis

The environmental balance of the Alta Val d'Agri: a contribution to the evaluation of the industrial risk and strategic sustainable development

NASA Astrophysics Data System (ADS)

Loperte, S.; Cosmi, C.

2015-09-01

This study presents the preliminary environmental balance of the Alta Val d'Agri (Basilicata Region, Southern Italy), an area of great naturalistic interest characterized by the presence of huge oil and gas fields. The Driving Forces-Pressure-State-Impact-Responses (DPSIR) methodology was used to outline the background in terms of environmental impacts mainly caused by oil extraction activities, as well as potential existing responses. The study aims at providing stakeholders with an exhaustive framework to identify the existing data, the main sources of pollution, their potential impacts, the associated industrial risks and the existing policy strategies. Moreover, the DPSIR approach allows the identification of the vulnerable areas and the definition of targeted actions for a sustainable development of the area.

One-dimensional statistical parametric mapping in Python.

PubMed

Pataky, Todd C

2012-01-01

Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.

The application of the electrodynamic separator in minerals beneficiation

NASA Astrophysics Data System (ADS)

Skowron, M.; Syrek, P.; Surowiak, A.

2017-05-01

The aim of presented paper is elaboration of methodology of upgrading natural minerals in example of chalcocite and bornite sample. The results were obtained by means of laboratory drum separator. This device operates in accordance to properties of materials, which in this case was electrical conductivity. The study contains the analysis of the forces occurring inside of electrodynamic separator chamber, that act on the particles of various electrical properties. Both, the potential and electric field strength distributions were calculated, with set of separators setpoints. Theoretical analysis influenced on separator parameters, and hence impacted the empirical results too. Next, the authors conducted empirical research on chalcocite and bornite beneficiation by means of electrodynamic separation. The results of this process were shown graphically in form of upgrading curves of chalcocite considering elementary copper and lead.

Adjoint Airfoil Optimization of Darrieus-Type Vertical Axis Wind Turbine

NASA Astrophysics Data System (ADS)

Fuchs, Roman; Nordborg, Henrik

2012-11-01

We present the feasibility of using an adjoint solver to optimize the torque of a Darrieus-type vertical axis wind turbine (VAWT). We start with a 2D cross section of a symmetrical airfoil and restrict us to low solidity ratios to minimize blade vortex interactions. The adjoint solver of the ANSYS FLUENT software package computes the sensitivities of airfoil surface forces based on a steady flow field. Hence, we find the torque of a full revolution using a weighted average of the sensitivities at different wind speeds and angles of attack. The weights are computed analytically, and the range of angles of attack is given by the tip speed ratio. Then the airfoil geometry is evolved, and the proposed methodology is evaluated by transient simulations.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Social Gaming and Learning Applications: A Driving Force for the Future of Virtual and Augmented Reality?

NASA Astrophysics Data System (ADS)

Dörner, Ralf; Lok, Benjamin; Broll, Wolfgang

Backed by a large consumer market, entertainment and education applications have spurred developments in the fields of real-time rendering and interactive computer graphics. Relying on Computer Graphics methodologies, Virtual Reality and Augmented Reality benefited indirectly from this; however, there is no large scale demand for VR and AR in gaming and learning. What are the shortcomings of current VR/AR technology that prevent a widespread use in these application areas? What advances in VR/AR will be necessary? And what might future “VR-enhanced” gaming and learning look like? Which role can and will Virtual Humans play? Concerning these questions, this article analyzes the current situation and provides an outlook on future developments. The focus is on social gaming and learning.

Computational modeling of Metal-Organic Frameworks

NASA Astrophysics Data System (ADS)

Sung, Jeffrey Chuen-Fai

In this work, the metal-organic frameworks MIL-53(Cr), DMOF-2,3-NH 2Cl, DMOF-2,5-NH2Cl, and HKUST-1 were modeled using molecular mechanics and electronic structure. The effect of electronic polarization on the adsorption of water in MIL-53(Cr) was studied using molecular dynamics simulations of water-loaded MIL-53 systems with both polarizable and non-polarizable force fields. Molecular dynamics simulations of the full systems and DFT calculations on representative framework clusters were utilized to study the difference in nitrogen adsorption between DMOF-2,3-NH2Cl and DMOF-2,5-NH 2Cl. Finally, the control of proton conduction in HKUST-1 by complexation of molecules to the Cu open metal site was investigated using the MS-EVB methodology.

Silicon nanowires reliability and robustness investigation using AFM-based techniques

NASA Astrophysics Data System (ADS)

Bieniek, Tomasz; Janczyk, Grzegorz; Janus, Paweł; Grabiec, Piotr; Nieprzecki, Marek; Wielgoszewski, Grzegorz; Moczała, Magdalena; Gotszalk, Teodor; Buitrago, Elizabeth; Badia, Montserrat F.; Ionescu, Adrian M.

2013-07-01

Silicon nanowires (SiNWs) have undergone intensive research for their application in novel integrated systems such as field effect transistor (FET) biosensors and mass sensing resonators profiting from large surface-to-volume ratios (nano dimensions). Such devices have been shown to have the potential for outstanding performances in terms of high sensitivity, selectivity through surface modification and unprecedented structural characteristics. This paper presents the results of mechanical characterization done for various types of suspended SiNWs arranged in a 3D array. The characterization has been performed using techniques based on atomic force microscopy (AFM). This investigation is a necessary prerequisite for the reliable and robust design of any biosensing system. This paper also describes the applied investigation methodology and reports measurement results aggregated during series of AFM-based tests.

Ensuring safe operation and assessing the condition underground structures by the method of acoustic resonance flaw detection

NASA Astrophysics Data System (ADS)

Meskhi, Besarion; Pleshko, Mikhail; Buligin, Yuriy; Alexeenko, Lyudmila; Molev, Mikhail

2017-10-01

In the article the main results of theoretical and experimental research in the field of nondestructive testing and forecasting of the geomechanical state of the dome part of transport tunnels. It is shown that for this purpose it is possible to apply the acoustic resonance defectoscopy method. The method of mine measurements consisted in fixing the forced oscillations of a multilayer carbon-rock massif with the shock initiation of a seismoacoustic signal. The excitation and reception of acoustic standing waves were carried out in the lower rock layer. The actual characteristics of the efficiency of the acoustic assessment of the state of the geoenvironment provide the authors the opportunity to recommend the described methodology for mass practical application in the transport tunnels.

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

PubMed

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

2010-01-01

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

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...

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.

Modeling of intragranular misorientation and grain fragmentation in polycrystalline materials using the viscoplastic self-consistent formulation

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

Zecevic, Miroslav; Lebensohn, Ricardo A.; McCabe, Rodney J.

In this paper, the recently established methodology to use known algorithmic expressions of the second moments of the stress field in the grains of a polycrystalline aggregate for calculating average fluctuations of lattice rotation rates and the associated average intragranular misorientation distributions using the mean-field viscoplastic self-consistent (VPSC) formulation is extended to solve the coupled problem of considering the effect of intragranular misorientations on stress and rotation rate fluctuations. In turn, these coupled expressions are used to formulate and implement a grain fragmentation (GF) model in VPSC. Case studies, including tension and plane-strain compression of face-centered cubic polycrystals are usedmore » to illustrate the capabilities of the new model. GF-VPSC predictions of intragranular misorientation distributions and texture evolution are compared with experiments and full-field numerical simulations, showing good agreement. In particular, the inclusion of misorientation spreads reduced the intensity of the deformed texture and thus improved the texture predictions. Finally and moreover, considering that intragranular misorientations act as driving forces for recrystallization, the new GF-VPSC formulation is shown to enable modeling of microstructure evolution during deformation and recrystallization, in a computationally efficient manner.« less

Modeling of intragranular misorientation and grain fragmentation in polycrystalline materials using the viscoplastic self-consistent formulation

DOE PAGES

Zecevic, Miroslav; Lebensohn, Ricardo A.; McCabe, Rodney J.; ...

2018-06-15

In this paper, the recently established methodology to use known algorithmic expressions of the second moments of the stress field in the grains of a polycrystalline aggregate for calculating average fluctuations of lattice rotation rates and the associated average intragranular misorientation distributions using the mean-field viscoplastic self-consistent (VPSC) formulation is extended to solve the coupled problem of considering the effect of intragranular misorientations on stress and rotation rate fluctuations. In turn, these coupled expressions are used to formulate and implement a grain fragmentation (GF) model in VPSC. Case studies, including tension and plane-strain compression of face-centered cubic polycrystals are usedmore » to illustrate the capabilities of the new model. GF-VPSC predictions of intragranular misorientation distributions and texture evolution are compared with experiments and full-field numerical simulations, showing good agreement. In particular, the inclusion of misorientation spreads reduced the intensity of the deformed texture and thus improved the texture predictions. Finally and moreover, considering that intragranular misorientations act as driving forces for recrystallization, the new GF-VPSC formulation is shown to enable modeling of microstructure evolution during deformation and recrystallization, in a computationally efficient manner.« less

Haptic Technologies for MEMS Design

NASA Astrophysics Data System (ADS)

Calis, Mustafa; Desmulliez, Marc P. Y.

2006-04-01

This paper presents for the first time a design methodology for MEMS/NEMS based on haptic sensing technologies. The software tool created as a result of this methodology will enable designers to model and interact in real time with their virtual prototype. One of the main advantages of haptic sensing is the ability to bring unusual microscopic forces back to the designer's world. Other significant benefits for developing such a methodology include gain productivity and the capability to include manufacturing costs within the design cycle.

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

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.

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

Metaphor as a Methodological Tool: Identifying Teachers' Social Justice Dispositions across Diverse Secondary School Settings

ERIC Educational Resources Information Center

Mills, Carmen; Molla, Tebeje; Gale, Trevor; Cross, Russell; Parker, Stephen; Smith, Catherine

2017-01-01

This article investigates the social justice dispositions of teachers and principals in secondary schools as inferred from their metaphoric expressions. Drawing on a Bourdieuian account of disposition, our focus is the use of metaphor as a methodological tool to identify and reveal these otherwise latent forces within our data. Our analysis shows…

Psychological and Social Ramifications of Battering: Observations Leading to a Counseling Methodology for Victims of Domestic Violence.

ERIC Educational Resources Information Center

Wetzel, Laura; Ross, Mary Anne

1983-01-01

Presents a common set of characteristics observed among victims of battering and a profile of men who batter. Analyzes the destructive forces that keep victims captive and suggests a counseling methodology. Outlines stages through which a battered woman may progress in deciding to leave the battering situation. (Author/JAC)

Instructional System Development (ISD) in the Armed Services: Methodology and Application. Final Report, August 25, 1977 through March 19, 1979.

ERIC Educational Resources Information Center

Vineberg, Robert; Joyner, John N.

Instructional System Development (ISD) methodologies and practices were examined in the Army, Navy, Marine Corps, and Air Force, each of which prescribes the ISD system involving rigorous derivation of training requirements from job requirements, selection of instructional strategies to maximize training efficiency, and revision of instruction…

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.

Single-Vector Calibration of Wind-Tunnel Force Balances

NASA Technical Reports Server (NTRS)

Parker, P. A.; DeLoach, R.

2003-01-01

An improved method of calibrating a wind-tunnel force balance involves the use of a unique load application system integrated with formal experimental design methodology. The Single-Vector Force Balance Calibration System (SVS) overcomes the productivity and accuracy limitations of prior calibration methods. A force balance is a complex structural spring element instrumented with strain gauges for measuring three orthogonal components of aerodynamic force (normal, axial, and side force) and three orthogonal components of aerodynamic torque (rolling, pitching, and yawing moments). Force balances remain as the state-of-the-art instrument that provide these measurements on a scale model of an aircraft during wind tunnel testing. Ideally, each electrical channel of the balance would respond only to its respective component of load, and it would have no response to other components of load. This is not entirely possible even though balance designs are optimized to minimize these undesirable interaction effects. Ultimately, a calibration experiment is performed to obtain the necessary data to generate a mathematical model and determine the force measurement accuracy. In order to set the independent variables of applied load for the calibration 24 NASA Tech Briefs, October 2003 experiment, a high-precision mechanical system is required. Manual deadweight systems have been in use at Langley Research Center (LaRC) since the 1940s. These simple methodologies produce high confidence results, but the process is mechanically complex and labor-intensive, requiring three to four weeks to complete. Over the past decade, automated balance calibration systems have been developed. In general, these systems were designed to automate the tedious manual calibration process resulting in an even more complex system which deteriorates load application quality. The current calibration approach relies on a one-factor-at-a-time (OFAT) methodology, where each independent variable is incremented individually throughout its full-scale range, while all other variables are held at a constant magnitude. This OFAT approach has been widely accepted because of its inherent simplicity and intuitive appeal to the balance engineer. LaRC has been conducting research in a "modern design of experiments" (MDOE) approach to force balance calibration. Formal experimental design techniques provide an integrated view to the entire calibration process covering all three major aspects of an experiment; the design of the experiment, the execution of the experiment, and the statistical analyses of the data. In order to overcome the weaknesses in the available mechanical systems and to apply formal experimental techniques, a new mechanical system was required. The SVS enables the complete calibration of a six-component force balance with a series of single force vectors.

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.

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

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

PubMed

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

2018-04-10

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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.

Geomagnetic main field modeling using magnetohydrodynamic constraints

NASA Technical Reports Server (NTRS)

Estes, R. H.

1985-01-01

The influence of physical constraints are investigated which may be approximately satisfied by the Earth's liquid core on models of the geomagnetic main field and its secular variation. A previous report describes the methodology used to incorporate nonlinear equations of constraint into the main field model. The application of that methodology to the GSFC 12/83 field model to test the frozen-flux hypothesis and the usefulness of incorporating magnetohydrodynamic constraints for obtaining improved geomagnetic field models is described.

Self-Study as an Emergent Methodology in Career and Technical Education, Adult Education and Technology: An Invitation to Inquiry

ERIC Educational Resources Information Center

Hawley, Todd S.; Hostetler, Andrew L.

2017-01-01

In this manuscript, the authors explore self-study as an emerging research methodology with the potential to open up spaces of inquiry for researchers, graduate students, and teachers in a broad array of fields. They argue that the fields of career and technical education (CTE), adult education and technology can leverage self-study methodology in…

The force-free configuration of flux ropes in geomagnetotail: Cluster observations

NASA Astrophysics Data System (ADS)

Yang, Y. Y.; Shen, C.; Zhang, Y. C.; Rong, Z. J.; Li, X.; Dunlop, M.; Ma, Y. H.; Liu, Z. X.; Carr, C. M.; Rème, H.

2014-08-01

Unambiguous knowledge of magnetic field structure and the electric current distribution is critical for understanding the origin, evolution, and related dynamic properties of magnetic flux ropes (MFRs). In this paper, a survey of 13 MFRs in the Earth's magnetotail are conducted by Cluster multipoint analysis, so that their force-free feature, i.e., the kind of magnetic field structure satisfying J × B = 0, can be probed directly. It is showed that the selected flux ropes with the bipolar signature of the south-north magnetic field component generally lie near the equatorial plane, as expected, and that the magnetic field gradient is rather weak near the axis center, where the curvature radius is large. The current density (up to several tens of nA/m2) reaches their maximum values as the center is approached. It is found that the stronger the current density, the smaller the angles between the magnetic field and current in MFRs. The direct observations show that only quasi force-free structure is observed, and it tends to appear in the low plasma beta regime (in agreement with the theoretic results). The quasi force-free region is generally found to be embedded in the central portion of the MFRs, where the current is approximately field aligned and proportional to the strength of core field. It is shown that ~60% of surveyed MFRs can be globally approximated as force free. The force-free factor α is found to be nonconstantly varied through the quasi force-free MFR, suggesting that the force-free structure is nonlinear.

Evaluation of the attractive force of different types of new-generation magnetic attachment systems.

PubMed

Akin, Hakan; Coskun, M Emre; Akin, E Gulsah; Ozdemir, A Kemal

2011-03-01

Rare earth magnets have been used in prosthodontics, but their tendency for corrosion in the oral cavity and insufficient attractive forces limit long-term clinical application. The purpose of this study was to evaluate the attractive force of different types of new-generation magnetic attachment systems. The attractive force of the neodymium-iron-boron (Nd-Fe-B) and samarium-cobalt (Sm-Co) magnetic attachment systems, including closed-field (Hilop and Hicorex) and open-field (Dyna and Steco) systems, was measured in a universal testing machine (n=5). The data were statistically evaluated with 1-way ANOVA and post hoc Tukey-Kramer multiple comparison test (α=.05). The closed-field systems exhibited greater (P<.001) attractive force than the open-field systems. Moreover, there was a statistically significant difference in attractive force between Nd-Fe-B and Sm-Co magnets (P<.001). The strongest attractive force was found with the Hilop system (9.2 N), and the lowest force was found with the Steco system (2.3 N). The new generation of Nd-Fe-B closed-field magnets, along with improved technology, provides sufficient denture retention for clinical application. Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

NONLINEAR FORCE-FREE FIELD MODELING OF A SOLAR ACTIVE REGION USING SDO/HMI AND SOLIS/VSM DATA

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

Thalmann, J. K.; Wiegelmann, T.; Pietarila, A.

2012-08-15

We use SDO/HMI and SOLIS/VSM photospheric magnetic field measurements to model the force-free coronal field above a solar active region, assuming magnetic forces dominate. We take measurement uncertainties caused by, e.g., noise and the particular inversion technique, into account. After searching for the optimum modeling parameters for the particular data sets, we compare the resulting nonlinear force-free model fields. We show the degree of agreement of the coronal field reconstructions from the different data sources by comparing the relative free energy content, the vertical distribution of the magnetic pressure, and the vertically integrated current density. Though the longitudinal and transversemore » magnetic flux measured by the VSM and HMI is clearly different, we find considerable similarities in the modeled fields. This indicates the robustness of the algorithm we use to calculate the nonlinear force-free fields against differences and deficiencies of the photospheric vector maps used as an input. We also depict how much the absolute values of the total force-free, virial, and the free magnetic energy differ and how the orientation of the longitudinal and transverse components of the HMI- and VSM-based model volumes compare to each other.« less

The harmonic force field of benzene. A local density functional study

NASA Astrophysics Data System (ADS)

Bérces, Attila; Ziegler, Tom

1993-03-01

The harmonic force field of benzene has been calculated by a method based on local density functional theory (LDF). The calculations were carried out employing a triple zeta basis set with triple polarization on hydrogen and double polarization on carbon. The LDF force field was compared to the empirical field due to Ozkabak, Goodman, and Thakur [A. G. Ozkabak, L. Goodman, and S. N. Thakur, J. Phys. Chem. 95, 9044 (1991)], which has served as a benchmark for theoretical calculations as well as the theoretical field based on scaled Hartree-Fock ab initio calculation due to Pulay, Fogarasi, and Boggs [P. Pulay, G. Fogarasi, and J. E. Boggs, J. Chem. Phys. 74, 3999 (1981)]. The calculated LDF force field is in excellent qualitative and very good quantitative agreement with the theoretical field proposed by Pulay, Fogarasi, and Boggs as well as the empirical field due to Ozkabak, Goodman, and Thakur. The LDF field is closest to the values of Pulay and co-workers in those cases where the force constants due to Pulay, Fogarasi, and Boggs and to Ozkabak, Goodman, and Thakur differ in sign or magnitude. The accuracy of the LDF force field was investigated by evaluating a number of eigenvalue and eigenfunction dependent quantities from the the LDF force constants. The quantities under investigation include vibrational frequencies of seven isotopomers, isotopic shifts, as well as absorption intensities. The calculations were performed at both theoretical optimized and approximate equilibrium reference geometries. The predicted frequencies are usually within 1%-2% compared to the empirical harmonic frequencies. The least accurate frequency deviates by 5% from the experimental value. The average deviations from the empirical harmonic frequencies of C6H6 and C6D6 are 16.7 cm-1 (1.5%) and 15.2 cm-1 (1.7%), respectively, not including CH stretching frequencies, in the case where a theoretical reference geometry was used. The accuracy of the out-of-plane force field is especially remarkable; the average deviations for the C6H6 and C6D6 frequencies, based on the LDF force field, are 9.4 cm-1 (1.2%) and 7.3 cm-1 (1.2%), respectively. The absorption intensities were not predicted as accurately as it was expected based on the size of the basis set applied. An analysis is provided to ensure that the force constants are not significantly affected by numerical errors due to the numerical integration scheme employed.

Applicability of Performance Assessment Tools to Marine Corps Air Ground Task Force C4 System of Systems Performance Assessment

DTIC Science & Technology

2010-09-01

application of existing assessment tools that may be applicable to Marine Air Ground Task Force (MAGTF) Command, Control, Communications and...of existing assessment tools that may be applicable to Marine Air Ground Task Force (MAGTF) Command, Control, Communications and Computers (C4...assessment tools and analysis concepts that may be extended to the Marine Corps’ C4 System of Systems assessment methodology as a means to obtain a

Modeling and Simulation Behavior Validation Methodology and Extension Model Validation for the Individual Soldier

DTIC Science & Technology

2015-03-01

domains. Major model functions include: • Ground combat: Light and heavy forces. • Air mobile forces. • Future forces. • Fixed-wing and rotary-wing...Constraints: • Study must be completed no later than 31 December 2014. • Entity behavior limited to select COMBATXXI Mobility , Unmanned Aerial System...and SQL backend , as well as any open application programming interface API. • Allows data transparency and data driven navigation through the model

Supporting the Future Total Force. A Methodology for Evaluating Potential Air National Guard Mission Assignments

DTIC Science & Technology

2007-01-01

force with its primary function —to organize, train, and equip aviation forces primarily for prompt and sustained offen- sive and defensive air...staff. 4 The full warfighter headquarters end-to-end operation was considered in this study to include non -AOC command and control functions performed...representation of RAND intellectual property is provided for non -commercial use only. Unauthorized posting of RAND PDFs to a non -RAND Web site is

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

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

Lipid-converter, a framework for lipid manipulations in molecular dynamics simulations

PubMed Central

Larsson, Per; Kasson, Peter M.

2014-01-01

Construction of lipid membrane and membrane protein systems for molecular dynamics simulations can be a challenging process. In addition, there are few available tools to extend existing studies by repeating simulations using other force fields and lipid compositions. To facilitate this, we introduce lipidconverter, a modular Python framework for exchanging force fields and lipid composition in coordinate files obtained from simulations. Force fields and lipids are specified by simple text files, making it easy to introduce support for additional force fields and lipids. The converter produces simulation input files that can be used for structural relaxation of the new membranes. PMID:25081234

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

Folding Free Energy Landscape of the Decapeptide Chignolin

NASA Astrophysics Data System (ADS)

Dou, Xianghua; Wang, Jihua

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

Galerkin finite element scheme for magnetostrictive structures and composites

NASA Astrophysics Data System (ADS)

Kannan, Kidambi Srinivasan

The ever increasing-role of magnetostrictives in actuation and sensing applications is an indication of their importance in the emerging field of smart structures technology. As newer, and more complex, applications are developed, there is a growing need for a reliable computational tool that can effectively address the magneto-mechanical interactions and other nonlinearities in these materials and in structures incorporating them. This thesis presents a continuum level quasi-static, three-dimensional finite element computational scheme for modeling the nonlinear behavior of bulk magnetostrictive materials and particulate magnetostrictive composites. Models for magnetostriction must deal with two sources of nonlinearities-nonlinear body forces/moments in equilibrium equations governing magneto-mechanical interactions in deformable and magnetized bodies; and nonlinear coupled magneto-mechanical constitutive models for the material of interest. In the present work, classical differential formulations for nonlinear magneto-mechanical interactions are recast in integral form using the weighted-residual method. A discretized finite element form is obtained by applying the Galerkin technique. The finite element formulation is based upon three dimensional eight-noded (isoparametric) brick element interpolation functions and magnetostatic infinite elements at the boundary. Two alternative possibilities are explored for establishing the nonlinear incremental constitutive model-characterization in terms of magnetic field or in terms of magnetization. The former methodology is the one most commonly used in the literature. In this work, a detailed comparative study of both methodologies is carried out. The computational scheme is validated, qualitatively and quantitatively, against experimental measurements published in the literature on structures incorporating the magnetostrictive material Terfenol-D. The influence of nonlinear body forces and body moments of magnetic origin, on the response of magnetostrictive structures to complex mechanical and magnetic loading conditions, is carefully examined. While monolithic magnetostrictive materials have been commercially-available since the late eighties, attention in the smart structures research community has recently focussed upon building and using magnetostrictive particulate composite structures for conventional actuation applications and novel sensing methodologies in structural health monitoring. A particulate magnetostrictive composite element has been developed in the present work to model such structures. This composite element incorporates interactions between magnetostrictive particles by combining a numerical micromechanical analysis based on magneto-mechanical Green's functions, with a homogenization scheme based upon the Mori-Tanaka approach. This element has been applied to the simulation of particulate actuators and sensors reported in the literature. Simulation results are compared to experimental data for validation purposes. The computational schemes developed, for bulk materials and for composites, are expected to be of great value to researchers and designers of novel applications based on magnetostrictives.

The Introduction of Fields in Relation to Force

ERIC Educational Resources Information Center

Brunt, Marjorie; Brunt, Geoff

2012-01-01

The introduction of force at age 14-16 years is considered, starting with elementary student experiments using magnetic force fields. The meaningless use of terms such as "action" and "reaction", or "agent" and "receiver" is discussed. (Contains 6 figures.)

Calculation of Turbine Axial Thrust by Coupled CFD Simulations of the Main Flow Path and Secondary Cavity Flow in an SLI LOX Turbine

NASA Technical Reports Server (NTRS)

Dorney, D. J.; Marci, Bogdan; Tran, Ken; Sargent, Scott

2003-01-01

Each single reusable Space Launch Initiative (SLI) booster rocket is an engine operating at a record vacuum thrust level of over 730,000 Ibf using LOX and LH2. This thrust is more than 10% greater than that of the Delta IV rocket, resulting in relatively large LOX and LH2 turbopumps. Since the SLI rocket employs a staged combustion cycle the level of pressure is very high (thousands of psia). This high pressure creates many engineering challenges, including the balancing of axial-forces on the turbopumps. One of the main parameters in the calculation of the axial force is the cavity pressure upstream of the turbine disk. The flow in this cavity is very complex. The lack of understanding of this flow environment hinders the accurate prediction of axial thrust. In order to narrow down the uncertainty band around the actual turbine axial force, a coupled, unsteady computational methodology has been developed to simulate the interaction between the turbine main flow path and the cavity flow. The CORSAIR solver, an unsteady three- dimensional Navier-Stokes code for turbomachinery applications, was used to solve for both the main and the secondary flow fields. Turbine axial thrust values are presented in conjunction with the CFD simulation, together with several considerations regarding the turbine instrumentation for axial thrust estimations during test.

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

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

Afanas'ev, A A; Rubinov, A N; Gaida, L S

2015-10-31

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

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.

Driving Force of Plasma Bullet in Atmospheric-Pressure Plasma

NASA Astrophysics Data System (ADS)

Yambe, Kiyoyuki; Masuda, Seiya; Kondo, Shoma

2018-06-01

When plasma is generated by applying high-voltage alternating current (AC), the driving force of the temporally and spatially varying electric field is applied to the plasma. The strength of the driving force of the plasma at each spatial position is different because the electrons constituting the atmospheric-pressure nonequilibrium (cold) plasma move at a high speed in space. If the force applied to the plasma is accelerated only by the driving force, the plasma will be accelerated infinitely. The equilibrium between the driving force and the restricting force due to the collision between the plasma and neutral particles determines the inertial force and the drift velocity of the plasma. Consequently, the drift velocity depends on the strength of the time-averaged AC electric field. The pressure applied by the AC electric field equilibrates with the plasma pressure. From the law of conservation of energy, the pressure equilibrium is maintained by varying the drift velocity of the plasma.

Flows, Fields, and Forces in the Mars-Solar Wind Interaction

NASA Astrophysics Data System (ADS)

Halekas, J. S.; Brain, D. A.; Luhmann, J. G.; DiBraccio, G. A.; Ruhunusiri, S.; Harada, Y.; Fowler, C. M.; Mitchell, D. L.; Connerney, J. E. P.; Espley, J. R.; Mazelle, C.; Jakosky, B. M.

2017-11-01

We utilize suprathermal ion and magnetic field measurements from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, organized by the upstream magnetic field, to investigate the morphology and variability of flows, fields, and forces in the Mars-solar wind interaction. We employ a combination of case studies and statistical investigations to characterize the interaction in both quasi-parallel and quasi-perpendicular regions and under high and low solar wind Mach number conditions. For the first time, we include a detailed investigation of suprathermal ion temperature and anisotropy. We find that the observed magnetic fields and suprathermal ion moments in the magnetosheath, bow shock, and upstream regions have observable asymmetries controlled by the interplanetary magnetic field, with particularly large asymmetries found in the ion parallel temperature and anisotropy. The greatest temperature anisotropies occur in quasi-perpendicular regions of the magnetosheath and under low Mach number conditions. These results have implications for the growth and evolution of wave-particle instabilities and their role in energy transport and dissipation. We utilize the measured parameters to estimate the average ion pressure gradient, J × B, and v × B macroscopic force terms. The pressure gradient force maintains nearly cylindrical symmetry, while the J × B force has larger asymmetries and varies in magnitude in comparison to the pressure gradient force. The v × B force felt by newly produced planetary ions exceeds the other forces in magnitude in the magnetosheath and upstream regions for all solar wind conditions.

raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

NASA Astrophysics Data System (ADS)

Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

2017-03-01

We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

Improving the representation of clouds, radiation, and precipitation using spectral nudging in the Weather Research and Forecasting model

NASA Astrophysics Data System (ADS)

Spero, Tanya L.; Otte, Martin J.; Bowden, Jared H.; Nolte, Christopher G.

2014-10-01

Spectral nudging—a scale-selective interior constraint technique—is commonly used in regional climate models to maintain consistency with large-scale forcing while permitting mesoscale features to develop in the downscaled simulations. Several studies have demonstrated that spectral nudging improves the representation of regional climate in reanalysis-forced simulations compared with not using nudging in the interior of the domain. However, in the Weather Research and Forecasting (WRF) model, spectral nudging tends to produce degraded precipitation simulations when compared to analysis nudging—an interior constraint technique that is scale indiscriminate but also operates on moisture fields which until now could not be altered directly by spectral nudging. Since analysis nudging is less desirable for regional climate modeling because it dampens fine-scale variability, changes are proposed to the spectral nudging methodology to capitalize on differences between the nudging techniques and aim to improve the representation of clouds, radiation, and precipitation without compromising other fields. These changes include adding spectral nudging toward moisture, limiting nudging to below the tropopause, and increasing the nudging time scale for potential temperature, all of which collectively improve the representation of mean and extreme precipitation, 2 m temperature, clouds, and radiation, as demonstrated using a model-simulated 20 year historical period. Such improvements to WRF may increase the fidelity of regional climate data used to assess the potential impacts of climate change on human health and the environment and aid in climate change mitigation and adaptation studies.

A multidimensional approach for detecting species patterns in Malagasy vertebrates

PubMed Central

Yoder, Anne D.; Olson, Link E.; Hanley, Carol; Heckman, Kellie L.; Rasoloarison, Rodin; Russell, Amy L.; Ranivo, Julie; Soarimalala, Voahangy; Karanth, K. Praveen; Raselimanana, Achille P.; Goodman, Steven M.

2005-01-01

The biodiversity of Madagascar is extraordinarily distinctive, diverse, and endangered. It is therefore urgent that steps be taken to document, describe, interpret, and protect this exceptional biota. As a collaborative group of field and laboratory biologists, we employ a suite of methodological and analytical tools to investigate the vertebrate portion of Madagascar's fauna. Given that species are the fundamental unit of evolution, where micro- and macroevolutionary forces converge to generate biological diversity, a thorough understanding of species distribution and abundance is critical for understanding the evolutionary, ecological, and biogeographic forces that have shaped Malagasy vertebrate diversity. We illustrate the means by which we apply Mayr's “three basic tasks” of the systematist [Mayr, E. (1942) Systematics and the Origin of Species from the Viewpoint of a Zoologist (Harvard Univ. Press, Cambridge, MA)] to identify, classify, and study the organisms that together constitute Madagascar's vertebrate community. Using field inventory methods, specimen-based studies, and morphological and molecular analyses, we formulate hypotheses of species identity that then serve as the foundation for subsequent studies of biology and history. Our experience, as well as that of other investigators, has shown that much of the vertebrate species diversity in Madagascar is “cryptic” for both biological and practical reasons. Beyond issues of cryptic biological diversity, the resolution of species identity in Madagascar has been hampered because of a lack of vouchered comparative material at the population level. Through our activities, we are attempting to remedy these limitations while simultaneously enhancing research capacity in Madagascar. PMID:15851666

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

PubMed Central

Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

2013-01-01

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins

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

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

2015-08-06

Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna–Matthews–Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbitalmore » (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.« less

Coarse-graining errors and numerical optimization using a relative entropy framework.

PubMed

Chaimovich, Aviel; Shell, M Scott

2011-03-07

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework. © 2011 American Institute of Physics.

Groundwater pollution risk assessment. Application to different carbonate aquifers in south Spain

NASA Astrophysics Data System (ADS)

Jimenez Madrid, A.; Martinez Navarrete, C.; Carrasco Cantos, F.

2009-04-01

Water protection has been considered one of the most important environmental goals in the European politics since the 2000/60/CE Water Framework Directive came into force in 2000, and more specifically in 2006 with the 2006/118/CE Directive on groundwater protection. As one of the necessary requirements to tackle groundwater protection, a pollution risk assessment has been made through the analysis of both the existing hazard human activities map and the intrinsic aquifer vulnerability map, by applying the methodologies proposed by COST Action 620 in an experimental study site in south Spain containing different carbonated aquifers, which supply 8 towns ranging from 2000 to 2500 inhabitants. In order to generate both maps it was necessary to make a field inventory over a 1:10000 topographic base map, followed by Geographic Information System (GIS) processing. The outcome maps show a clear spatial distribution of both pollution risk and intrinsic vulnerability of the carbonated aquifers studied. As a final result, a map of the intensity of groundwater pollution risk is presented, representing and important base for the development of a proper methodology for the protection of groundwater resources for human consumption protection. Keywords. Hazard, Vulnerability, Risk, SIG, Protection

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, D.O.; Alexeff, I.; Sikka, V.K.

1987-08-10

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to ''float'' in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields. 6 figs.

Method and apparatus for removal of gaseous, liquid and particulate contaminants from molten metals

DOEpatents

Hobson, David O.; Alexeff, Igor; Sikka, Vinod K.

1988-01-01

Method and apparatus for removal of nonelectrically-conducting gaseous, liquid, and particulate contaminants from molten metal compositions by applying a force thereto. The force (commonly referred to as the Lorentz Force) exerted by simultaneous application of an electric field and a magnetic field on a molten conductor causes an increase, in the same direction as the force, in the apparent specific gravity thereof, but does not affect the nonconducting materials. This difference in apparent densities cause the nonconducting materials to "float" in the opposite direction from the Lorentz Force at a rapid rate. Means are further provided for removal of the contaminants and prevention of stirring due to rotational forces generated by the applied fields.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

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

Gao, Weimin; Niu, Haitao; Lin, Tong

2014-01-28

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform externalmore » electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.« less

Working Together for a Competitive Workforce. A Handbook for State Policy Teams. Investing in People Project.

ERIC Educational Resources Information Center

Zinser, Jana

This handbook describes the methodology of the Investing in People Project, conducted in Connecticut, Iowa, Kentucky, Washington, and West Virginia to help states in assessing their current work force and economic development systems and in building more comprehensive, integrated, and effective strategies for improving the work force. The handbook…

Internet Protocol Geolocation: Development of a Delay-Based Hybrid Methodology for Locating the Geographic Location of a Network Node

DTIC Science & Technology

2007-03-01

provides a means for anyone who has access to an Internet connection to collect or disseminate information on a global scale at a very low cost. The......AIR UNIVERSITY AIR FORCE INSTITUTE OF TECHNOLOGY Wright-Patterson Air Force Base, Ohio APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED

Upper limb joint forces and moments during underwater cyclical movements.

PubMed

Lauer, Jessy; Rouard, Annie Hélène; Vilas-Boas, João Paulo

2016-10-03

Sound inverse dynamics modeling is lacking in aquatic locomotion research because of the difficulty in measuring hydrodynamic forces in dynamic conditions. Here we report the successful implementation and validation of an innovative methodology crossing new computational fluid dynamics and inverse dynamics techniques to quantify upper limb joint forces and moments while moving in water. Upper limb kinematics of seven male swimmers sculling while ballasted with 4kg was recorded through underwater motion capture. Together with body scans, segment inertial properties, and hydrodynamic resistances computed from a unique dynamic mesh algorithm capable to handle large body deformations, these data were fed into an inverse dynamics model to solve for joint kinetics. Simulation validity was assessed by comparing the impulse produced by the arms, calculated by integrating vertical forces over a stroke period, to the net theoretical impulse of buoyancy and ballast forces. A resulting gap of 1.2±3.5% provided confidence in the results. Upper limb joint load was within 5% of swimmer׳s body weight, which tends to supports the use of low-load aquatic exercises to reduce joint stress. We expect this significant methodological improvement to pave the way towards deeper insights into the mechanics of aquatic movement and the establishment of practice guidelines in rehabilitation, fitness or swimming performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

PubMed

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

2017-04-11

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

Effect of ski geometry and standing height on kinetic energy: equipment designed to reduce risk of severe traumatic injuries in alpine downhill ski racing

PubMed Central

Gilgien, Matthias; Spörri, Jörg; Kröll, Josef; Müller, Erich

2016-01-01

Background Injuries in downhill (DH) are often related to high speed and, therefore, to high energy and forces which are involved in injury situations. Yet to date, no study has investigated the effect of ski geometry and standing height on kinetic energy (EKIN) in DH. This knowledge would be essential to define appropriate equipment rules that have the potential to protect the athletes’ health. Methods During a field experiment on an official World Cup DH course, 2 recently retired world class skiers skied on 5 different pairs of skis varying in width, length and standing height. Course characteristics, terrain and the skiers’ centre of mass position were captured by a differential Global Navigational Satellite System-based methodology. EKIN, speed, ski–snow friction force (FF), ground reaction force (FGRF) and ski–snow friction coefficient (CoeffF) were calculated and analysed in dependency of the used skis. Results In the steep terrain, longer skis with reduced width and standing height significantly decreased average EKIN by ∼3%. Locally, even larger reductions of EKIN were observed (up to 7%). These local decreases in EKIN were mainly explainable by higher FF. Moreover, CoeffF differences seem of greater importance for explaining local FF differences than the differences in FGRF. Conclusions Knowing that increased speed and EKIN likely lead to increased forces in fall/crash situations, the observed equipment-induced reduction in EKIN can be considered a reasonable measure to improve athlete safety, even though the achieved preventative gains are rather small and limited to steep terrain. PMID:26702013

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

Vertical microphysical profiles of convective clouds as a tool for obtaining aerosol cloud-mediated climate forcings

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

Rosenfeld, Daniel

Quantifying the aerosol/cloud-mediated radiative effect at a global scale requires simultaneous satellite retrievals of cloud condensation nuclei (CCN) concentrations and cloud base updraft velocities (Wb). Hitherto, the inability to do so has been a major cause of high uncertainty regarding anthropogenic aerosol/cloud-mediated radiative forcing. This can be addressed by the emerging capability of estimating CCN and Wb of boundary layer convective clouds from an operational polar orbiting weather satellite. Our methodology uses such clouds as an effective analog for CCN chambers. The cloud base supersaturation (S) is determined by Wb and the satellite-retrieved cloud base drop concentrations (Ndb), which ismore » the same as CCN(S). Developing and validating this methodology was possible thanks to the ASR/ARM measurements of CCN and vertical updraft profiles. Validation against ground-based CCN instruments at the ARM sites in Oklahoma, Manaus, and onboard a ship in the northeast Pacific showed a retrieval accuracy of ±25% to ±30% for individual satellite overpasses. The methodology is presently limited to boundary layer not raining convective clouds of at least 1 km depth that are not obscured by upper layer clouds, including semitransparent cirrus. The limitation for small solar backscattering angles of <25º restricts the satellite coverage to ~25% of the world area in a single day. This methodology will likely allow overcoming the challenge of quantifying the aerosol indirect effect and facilitate a substantial reduction of the uncertainty in anthropogenic climate forcing.« less

Development of Constraint Force Equation Methodology for Application to Multi-Body Dynamics Including Launch Vehicle Stage Seperation

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Toniolo, Matthew D.; Tartabini, Paul V.; Roithmayr, Carlos M.; Albertson, Cindy W.; Karlgaard, Christopher D.

2016-01-01

The objective of this report is to develop and implement a physics based method for analysis and simulation of multi-body dynamics including launch vehicle stage separation. The constraint force equation (CFE) methodology discussed in this report provides such a framework for modeling constraint forces and moments acting at joints when the vehicles are still connected. Several stand-alone test cases involving various types of joints were developed to validate the CFE methodology. The results were compared with ADAMS(Registered Trademark) and Autolev, two different industry standard benchmark codes for multi-body dynamic analysis and simulations. However, these two codes are not designed for aerospace flight trajectory simulations. After this validation exercise, the CFE algorithm was implemented in Program to Optimize Simulated Trajectories II (POST2) to provide a capability to simulate end-to-end trajectories of launch vehicles including stage separation. The POST2/CFE methodology was applied to the STS-1 Space Shuttle solid rocket booster (SRB) separation and Hyper-X Research Vehicle (HXRV) separation from the Pegasus booster as a further test and validation for its application to launch vehicle stage separation problems. Finally, to demonstrate end-to-end simulation capability, POST2/CFE was applied to the ascent, orbit insertion, and booster return of a reusable two-stage-to-orbit (TSTO) vehicle concept. With these validation exercises, POST2/CFE software can be used for performing conceptual level end-to-end simulations, including launch vehicle stage separation, for problems similar to those discussed in this report.

The eSurge-Venice project: how satellite data can improve the storm surge forecasting in the northern Adriatic Sea

NASA Astrophysics Data System (ADS)

Zecchetto, Stefano; Vignudelli, Stefano; Donlon, Craig; De Biasio, Francesco; Della Valle, Antonio; Umgiesser, Georg; Bajo, Marco

The Data User Element (DUE) program of the European Space Agency (ESA) is funding two projects (eSurge and eSurge-Venice) aimed to demonstrate the improvement of the storm surge forecasting through the use of Earth Observation (EO) data. eSurge-Venice (http://www.esurge-venice.eu/), is specifically focused on the Gulf of Venice, northern Adriatic Sea. The project objectives are: a) Select a number of Storm Surge Events occurred in the Venice lagoon since 1999; b) Provide the available satellite EO data related to the Storm Surge Events, mainly satellite winds and altimeter data, as well as all the available in-situ data and model forecasts; c) Provide a demonstration Near Real Time service (eSurge-Venice live) of EO data products and services in support of operational and experimental forecasting and warning services; d) Run a number of re-analysis cases, both for historical and contemporary storm surge events, to demonstrate the usefulness of EO data. Present storm surge models use atmospheric model wind fields as forcing. These are know to underestimate the wind in small basins like the Adriatic Sea (~1000 km by 300 km), where the orography plays an important role in shaping the winds. Therefore there is the need to verify and tune the atmospheric model wind fields used in the storm surge modeling, an activity which can easily done using satellite scatterometer winds. The project is now in the middle of his life, and promising preliminary results have been achieved using satellite scatterometer wind data to forge the atmospheric model wind fields forcing the storm surge model. This contribution will present the methodology adopted to tune the model wind fields according to the bias with scatterometer winds and the improvements induced in the storm surge model hindcast.

Angular momentum and torque described with the complex octonion

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

Weng, Zi-Hua, E-mail: xmuwzh@xmu.edu.cn

2014-08-15

The paper aims to adopt the complex octonion to formulate the angular momentum, torque, and force etc in the electromagnetic and gravitational fields. Applying the octonionic representation enables one single definition of angular momentum (or torque, force) to combine some physics contents, which were considered to be independent of each other in the past. J. C. Maxwell used simultaneously two methods, the vector terminology and quaternion analysis, to depict the electromagnetic theory. It motivates the paper to introduce the quaternion space into the field theory, describing the physical feature of electromagnetic and gravitational fields. The spaces of electromagnetic field andmore » of gravitational field can be chosen as the quaternion spaces, while the coordinate component of quaternion space is able to be the complex number. The quaternion space of electromagnetic field is independent of that of gravitational field. These two quaternion spaces may compose one octonion space. Contrarily, one octonion space can be separated into two subspaces, the quaternion space and S-quaternion space. In the quaternion space, it is able to infer the field potential, field strength, field source, angular momentum, torque, and force etc in the gravitational field. In the S-quaternion space, it is capable of deducing the field potential, field strength, field source, current continuity equation, and electric (or magnetic) dipolar moment etc in the electromagnetic field. The results reveal that the quaternion space is appropriate to describe the gravitational features, including the torque, force, and mass continuity equation etc. The S-quaternion space is proper to depict the electromagnetic features, including the dipolar moment and current continuity equation etc. In case the field strength is weak enough, the force and the continuity equation etc can be respectively reduced to that in the classical field theory.« less

Bilateral force reflection for teleoperators with masters and slaves with dissimilar and possibly redundant kinematics

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

Jansen, J.F.; Babcock, S.M.

1989-11-01

Several bilateral control techniques and methods for exploiting redundant slaves are investigated as a part of research to develop and analyze bilateral, force-reflecting control methodologies for teleoperator systems with kinematic dissimilar masters and slaves. The study indicates that, with force/torque sensing at the wrist, and an impedance type of controller with the appropriate joint compensation, a significant improvement in performance and controllability of a teleoperator system can be achieved. 32 refs., 6 figs., 2 tabs.

reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

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.

Mitigated-force carriage for high magnetic field environments

DOEpatents

Ludtka, Gerard M.; Ludtka, Gail M.; Wilgen, John B.; Murphy, Bart L.

2015-05-19

A carriage for high magnetic field environments includes a plurality of work-piece separators disposed in an operable relationship with a work-piece processing magnet having a magnetic field strength of at least 1 Tesla for supporting and separating a plurality of work-pieces by a preselected, essentially equal spacing, so that, as a first work-piece is inserted into the magnetic field, a second work-piece is simultaneously withdrawn from the magnetic field, so that an attractive magnetic force imparted on the first work-piece offsets a resistive magnetic force imparted on the second work-piece.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

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Search News Comments Updated 1 2 3 4 5 6 7 8 9 10 ... 188 Default Air Force Logo Air Force transitions to Field from May 2-4. (U.S. Air Force photo by Staff Sgt. Ryan Conroy) SECAF visits Hurlburt for AFSOC mission immersion Secretary of the Air Force Heather Wilson visited Hurlburt Field May 2-4 for her Air

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.

Numerical Investigation of Two-Phase Flows With Charged Droplets in Electrostatic Field

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook

1996-01-01

A numerical method to solve two-phase turbulent flows with charged droplets in an electrostatic field is presented. The ensemble-averaged Navier-Stokes equations and the electrostatic potential equation are solved using a finite volume method. The transitional turbulence field is described using multiple-time-scale turbulence equations. The equations of motion of droplets are solved using a Lagrangian particle tracking scheme, and the inter-phase momentum exchange is described by the Particle-In-Cell scheme. The electrostatic force caused by an applied electrical potential is calculated using the electrostatic field obtained by solving a Laplacian equation and the force exerted by charged droplets is calculated using the Coulombic force equation. The method is applied to solve electro-hydrodynamic sprays. The calculated droplet velocity distributions for droplet dispersions occurring in a stagnant surrounding are in good agreement with the measured data. For droplet dispersions occurring in a two-phase flow, the droplet trajectories are influenced by aerodynamic forces, the Coulombic force, and the applied electrostatic potential field.

Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.

PubMed

Kamath, Ganesh; Kurnikov, Igor; Fain, Boris; Leontyev, Igor; Illarionov, Alexey; Butin, Oleg; Olevanov, Michael; Pereyaslavets, Leonid

2016-11-01

We present the performance of blind predictions of water-cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF's are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.

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

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

PubMed

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

2017-09-05

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

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.

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

PubMed

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

2015-07-14

The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.

Host and adsorbate dynamics in silicates with flexible frameworks: Empirical force field simulation of water in silicalite

NASA Astrophysics Data System (ADS)

Bordat, Patrice; Cazade, Pierre-André; Baraille, Isabelle; Brown, Ross

2010-03-01

Molecular dynamics simulations are performed on the pure silica zeolite silicalite (MFI framework code), maintaining via a new force field both framework flexibility and realistic account of electrostatic interactions with adsorbed water. The force field is similar to the well-known "BKS" model [B. W. H. van Beest et al., Phys. Rev. Lett. 64, 1955 (1990)], but with reduced partial atomic charges and reoptimized covalent bond potential wells. The present force field reproduces the monoclinic to orthorhombic transition of silicalite. The force field correctly represents the hydrophobicity of pure silica silicalite, both the adsorption energy, and the molecular diffusion constants of water. Two types of adsorption, specific and weak unspecific, are predicted on the channel walls and at the channel intersection. We discuss molecular diffusion of water in silicalite, deducing a barrier to crossing between the straight and the zigzag channels. Analysis of the thermal motion shows that at room temperature, framework oxygen atoms incurring into the zeolite channels significantly influence the dynamics of adsorbed water.

Developing End-of-Training Entrustable Professional Activities for Psychiatry: Results and Methodological Lessons.

PubMed

Young, John Q; Hasser, Caitlin; Hung, Erick K; Kusz, Martin; O'Sullivan, Patricia S; Stewart, Colin; Weiss, Andrea; Williams, Nancy

2018-07-01

To develop entrustable professional activities (EPAs) for psychiatry and to demonstrate an innovative, validity-enhancing methodology that may be relevant to other specialties. A national task force employed a three-stage process from May 2014 to February 2017 to develop EPAs for psychiatry. In stage 1, the task force used an iterative consensus-driven process to construct proposed EPAs. Each included a title, full description, and relevant competencies. In stage 2, the task force interviewed four nonpsychiatric experts in EPAs and further revised the EPAs. In stage 3, the task force performed a Delphi study of national experts in psychiatric education and assessment. All survey participants completed a brief training program on EPAs. Quantitative and qualitative analysis led to further modifications. Essentialness was measured on a five-point scale. EPAs were included if the content validity index was at least 0.8 and the lower end of the asymmetric confidence interval was not lower than 4.0. Stages 1 and 2 yielded 24 and 14 EPAs, respectively. In stage 3, 31 of the 39 invited experts participated in both rounds of the Delphi study. Round 1 reduced the proposed EPAs to 13. Ten EPAs met the inclusion criteria in Round 2. The final EPAs provide a strong foundation for competency-based assessment in psychiatry. Methodological features such as critique by nonpsychiatry experts, a national Delphi study with frame-of-reference training, and stringent inclusion criteria strengthen the content validity of the findings and may serve as a model for future efforts in other specialties.

Force-controlled absorption in a fully-nonlinear numerical wave tank

NASA Astrophysics Data System (ADS)

Spinneken, Johannes; Christou, Marios; Swan, Chris

2014-09-01

An active control methodology for the absorption of water waves in a numerical wave tank is introduced. This methodology is based upon a force-feedback technique which has previously been shown to be very effective in physical wave tanks. Unlike other methods, an a-priori knowledge of the wave conditions in the tank is not required; the absorption controller being designed to automatically respond to a wide range of wave conditions. In comparison to numerical sponge layers, effective wave absorption is achieved on the boundary, thereby minimising the spatial extent of the numerical wave tank. In contrast to the imposition of radiation conditions, the scheme is inherently capable of absorbing irregular waves. Most importantly, simultaneous generation and absorption can be achieved. This is an important advance when considering inclusion of reflective bodies within the numerical wave tank. In designing the absorption controller, an infinite impulse response filter is adopted, thereby eliminating the problem of non-causality in the controller optimisation. Two alternative controllers are considered, both implemented in a fully-nonlinear wave tank based on a multiple-flux boundary element scheme. To simplify the problem under consideration, the present analysis is limited to water waves propagating in a two-dimensional domain. The paper presents an extensive numerical validation which demonstrates the success of the method for a wide range of wave conditions including regular, focused and random waves. The numerical investigation also highlights some of the limitations of the method, particularly in simultaneously generating and absorbing large amplitude or highly-nonlinear waves. The findings of the present numerical study are directly applicable to related fields where optimum absorption is sought; these include physical wavemaking, wave power absorption and a wide range of numerical wave tank schemes.

The Model of Complex Structure of Quark

NASA Astrophysics Data System (ADS)

Liu, Rongwu

2017-09-01

In Quantum Chromodynamics, quark is known as a kind of point-like fundamental particle which carries mass, charge, color, and flavor, strong interaction takes place between quarks by means of exchanging intermediate particles-gluons. An important consequence of this theory is that, strong interaction is a kind of short-range force, and it has the features of ``asymptotic freedom'' and ``quark confinement''. In order to reveal the nature of strong interaction, the ``bag'' model of vacuum and the ``string'' model of string theory were proposed in the context of quantum mechanics, but neither of them can provide a clear interaction mechanism. This article formulates a new mechanism by proposing a model of complex structure of quark, it can be outlined as follows: (1) Quark (as well as electron, etc) is a kind of complex structure, it is composed of fundamental particle (fundamental matter mass and electricity) and fundamental volume field (fundamental matter flavor and color) which exists in the form of limited volume; fundamental particle lies in the center of fundamental volume field, forms the ``nucleus'' of quark. (2) As static electric force, the color field force between quarks has classical form, it is proportional to the square of the color quantity carried by each color field, and inversely proportional to the area of cross section of overlapping color fields which is along force direction, it has the properties of overlap, saturation, non-central, and constant. (3) Any volume field undergoes deformation when interacting with other volume field, the deformation force follows Hooke's law. (4) The phenomena of ``asymptotic freedom'' and ``quark confinement'' are the result of color field force and deformation force.

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

NASA Astrophysics Data System (ADS)

Tamma, Venkata Ananth; Huang, Fei; Nowak, Derek; Kumar Wickramasinghe, H.

2016-06-01

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

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

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

Tamma, Venkata Ananth; Huang, Fei; Kumar Wickramasinghe, H., E-mail: hkwick@uci.edu

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

Nanosecond pulsed electric field induced changes in cell surface charge density.

PubMed

Dutta, Diganta; Palmer, Xavier-Lewis; Asmar, Anthony; Stacey, Michael; Qian, Shizhi

2017-09-01

This study reports that the surface charge density changes in Jurkat cells with the application of single 60 nanosecond pulse electric fields, using atomic force microscopy. Using an atomic force microscope tip and Jurkat cells on silica in a 0.01M KCl ionic concentration, we were able to measure the interfacial forces, while also predicting surface charge densities of both Jurkat cell and silica surfaces. The most important finding is that the pulsing conditions varyingly reduced the cells' surface charge density. This offers a novel way in which to examine cellular effects of pulsed electric fields that may lead to the identification of unique mechanical responses. Compared to a single low field strength NsPEF (15kV/cm) application, exposure of Jurkat cells to a single high field strength NsPEF (60kV/cm) resulted in a further reduction in charge density and major morphological changes. The structural, physical, and chemical properties of biological cells immensely influence their electrostatic force; we were able to investigate this through the use of atomic force microscopy by measuring the surface forces between the AFM's tip and the Jurkat cells under different pulsing conditions as well as the interfacial forces in ionic concentrations. Copyright © 2017 Elsevier Ltd. 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.

Methane Adsorption in Zr-Based MOFs: Comparison and Critical Evaluation of Force Fields

PubMed Central

2017-01-01

The search for nanoporous materials that are highly performing for gas storage and separation is one of the contemporary challenges in material design. The computational tools to aid these experimental efforts are widely available, and adsorption isotherms are routinely computed for huge sets of (hypothetical) frameworks. Clearly the computational results depend on the interactions between the adsorbed species and the adsorbent, which are commonly described using force fields. In this paper, an extensive comparison and in-depth investigation of several force fields from literature is reported for the case of methane adsorption in the Zr-based Metal–Organic Frameworks UiO-66, UiO-67, DUT-52, NU-1000, and MOF-808. Significant quantitative differences in the computed uptake are observed when comparing different force fields, but most qualitative features are common which suggests some predictive power of the simulations when it comes to these properties. More insight into the host–guest interactions is obtained by benchmarking the force fields with an extensive number of ab initio computed single molecule interaction energies. This analysis at the molecular level reveals that especially ab initio derived force fields perform well in reproducing the ab initio interaction energies. Finally, the high sensitivity of uptake predictions on the underlying potential energy surface is explored. PMID:29170687

Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

PubMed Central

Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, Bingbing; Zhang, John Z. H.; Mei, Ye

2015-01-01

A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. PMID:26039188

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.

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

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.

C6 GPMG and 40 mm AGL Weapon Integrated on RWS Mounted on TAPV Platform: Probability of Hit Methodology

DTIC Science & Technology

2010-09-01

nationale, 2010 DRDC Valcartier CR 2010-237 i Abstract …….. A probability of hit ( PHit ) methodology has been developed to characterize the...CFB (Canadian Forces Base). Résumé …..... Une méthodologie de probabilité d’impact ( PHit ) a été développée pour caractériser la performance globale...the crew commander and gunner from their respective crew stations inside the vehicle. A probability of hit ( PHit ) methodology has been developed to

Dynamic acoustic radiation force acting on cylindrical shells: theory and simulations.

PubMed

Mitri, F G; Fatemi, M

2005-05-01

An object placed in an acoustic field is known to experience a force due to the transfer of momentum from the wave to the object itself. This force is known to be steady when the incident field is considered to be continuous with constant amplitude. One may define the dynamic (oscillatory) radiation force for a continuous wave-field whose intensity varies slowly with time. This paper extends the theory of the dynamic acoustic radiation force resulting from an amplitude-modulated progressive plane wave-field incident on solid cylinders to the case of solid cylindrical shells with particular emphasis on their thickness and contents of their hollow regions. A new factor corresponding to the dynamic radiation force is defined as Y(d) and stands for the dynamic radiation force per unit energy density and unit cross sectional surface. The results of numerical calculations are presented, indicating the ways in which the form of the dynamic radiation force function curves are affected by variations in the material mechanical parameters and by changes in the interior fluid inside the shell's hollow region. It was shown that the dynamic radiation force function Y(d) deviates from the static radiation force function for progressive waves Y(p) when the modulation frequency increases. These results indicate that the theory presented here is broader than the existing theory on cylinders.

Optical tweezers for studying taxis in parasites

NASA Astrophysics Data System (ADS)

de Thomaz, A. A.; Fontes, A.; Stahl, C. V.; Pozzo, L. Y.; Ayres, D. C.; Almeida, D. B.; Farias, P. M. A.; Santos, B. S.; Santos-Mallet, J.; Gomes, S. A. O.; Giorgio, S.; Feder, D.; Cesar, C. L.

2011-04-01

In this work we present a methodology to measure force strengths and directions of living parasites with an optical tweezers setup. These measurements were used to study the parasites chemotaxis in real time. We observed behavior and measured the force of: (i) Leishmania amazonensis in the presence of two glucose gradients; (ii) Trypanosoma cruzi in the vicinity of the digestive system walls, and (iii) Trypanosoma rangeli in the vicinity of salivary glands as a function of distance. Our results clearly show a chemotactic behavior in every case. This methodology can be used to study any type of taxis, such as chemotaxis, osmotaxis, thermotaxis, phototaxis, of any kind of living microorganisms. These studies can help us to understand the microorganism sensory systems and their response function to these gradients.

Effects of robotically modulating kinematic variability on motor skill learning and motivation

PubMed Central

Reinkensmeyer, David J.

2015-01-01

It is unclear how the variability of kinematic errors experienced during motor training affects skill retention and motivation. We used force fields produced by a haptic robot to modulate the kinematic errors of 30 healthy adults during a period of practice in a virtual simulation of golf putting. On day 1, participants became relatively skilled at putting to a near and far target by first practicing without force fields. On day 2, they warmed up at the task without force fields, then practiced with force fields that either reduced or augmented their kinematic errors and were finally assessed without the force fields active. On day 3, they returned for a long-term assessment, again without force fields. A control group practiced without force fields. We quantified motor skill as the variability in impact velocity at which participants putted the ball. We quantified motivation using a self-reported, standardized scale. Only individuals who were initially less skilled benefited from training; for these people, practicing with reduced kinematic variability improved skill more than practicing in the control condition. This reduced kinematic variability also improved self-reports of competence and satisfaction. Practice with increased kinematic variability worsened these self-reports as well as enjoyment. These negative motivational effects persisted on day 3 in a way that was uncorrelated with actual skill. In summary, robotically reducing kinematic errors in a golf putting training session improved putting skill more for less skilled putters. Robotically increasing kinematic errors had no performance effect, but decreased motivation in a persistent way. PMID:25673732

Effects of robotically modulating kinematic variability on motor skill learning and motivation.

PubMed

Duarte, Jaime E; Reinkensmeyer, David J

2015-04-01

It is unclear how the variability of kinematic errors experienced during motor training affects skill retention and motivation. We used force fields produced by a haptic robot to modulate the kinematic errors of 30 healthy adults during a period of practice in a virtual simulation of golf putting. On day 1, participants became relatively skilled at putting to a near and far target by first practicing without force fields. On day 2, they warmed up at the task without force fields, then practiced with force fields that either reduced or augmented their kinematic errors and were finally assessed without the force fields active. On day 3, they returned for a long-term assessment, again without force fields. A control group practiced without force fields. We quantified motor skill as the variability in impact velocity at which participants putted the ball. We quantified motivation using a self-reported, standardized scale. Only individuals who were initially less skilled benefited from training; for these people, practicing with reduced kinematic variability improved skill more than practicing in the control condition. This reduced kinematic variability also improved self-reports of competence and satisfaction. Practice with increased kinematic variability worsened these self-reports as well as enjoyment. These negative motivational effects persisted on day 3 in a way that was uncorrelated with actual skill. In summary, robotically reducing kinematic errors in a golf putting training session improved putting skill more for less skilled putters. Robotically increasing kinematic errors had no performance effect, but decreased motivation in a persistent way. Copyright © 2015 the American Physiological Society.

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

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

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

PubMed Central

Vanommeslaeghe, K.; MacKerell, A. D.

2012-01-01

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF’s complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/. PMID:23146088

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

PubMed

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

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

Passive force balancing of an active magnetic regenerative liquefier

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

Teyber, R.; Meinhardt, K.; Thomsen, E.

Active magnetic regenerators (AMR) have the potential for high efficiency cryogen liquefaction. One active magnetic regenerative liquefier (AMRL) configuration consists of dual magnetocaloric regenerators that reciprocate in a persistent-mode superconducting solenoid. Issues with this configuration are the spatial and temporal magnetization gradients that induce large magnetic forces and winding currents. To solve the coupled problem, we present a force minimization approach using passive magnetic material to balance a dual-regenerator AMR. A magnetostatic model is developed and simulated force waveforms are compared with experimental measurements. A genetic algorithm identifies force-minimizing passive structures with virtually ideal balancing characteristics. Finally, implementation details aremore » investigated which affirm the potential of the proposed methodology.« less

Passive force balancing of an active magnetic regenerative liquefier

DOE PAGES

Teyber, R.; Meinhardt, K.; Thomsen, E.; ...

2017-11-02

Active magnetic regenerators (AMR) have the potential for high efficiency cryogen liquefaction. One active magnetic regenerative liquefier (AMRL) configuration consists of dual magnetocaloric regenerators that reciprocate in a persistent-mode superconducting solenoid. Issues with this configuration are the spatial and temporal magnetization gradients that induce large magnetic forces and winding currents. To solve the coupled problem, we present a force minimization approach using passive magnetic material to balance a dual-regenerator AMR. A magnetostatic model is developed and simulated force waveforms are compared with experimental measurements. A genetic algorithm identifies force-minimizing passive structures with virtually ideal balancing characteristics. Finally, implementation details aremore » investigated which affirm the potential of the proposed methodology.« less

Passive force balancing of an active magnetic regenerative liquefier

NASA Astrophysics Data System (ADS)

Teyber, R.; Meinhardt, K.; Thomsen, E.; Polikarpov, E.; Cui, J.; Rowe, A.; Holladay, J.; Barclay, J.

2018-04-01

Active magnetic regenerators (AMR) have the potential for high efficiency cryogen liquefaction. One active magnetic regenerative liquefier (AMRL) configuration consists of dual magnetocaloric regenerators that reciprocate in a persistent-mode superconducting solenoid. Issues with this configuration are the spatial and temporal magnetization gradients that induce large magnetic forces and winding currents. To solve the coupled problem, we present a force minimization approach using passive magnetic material to balance a dual-regenerator AMR. A magnetostatic model is developed and simulated force waveforms are compared with experimental measurements. A genetic algorithm identifies force-minimizing passive structures with virtually ideal balancing characteristics. Implementation details are investigated which affirm the potential of the proposed methodology.

Design of a piezoelectric inchworm actuator and compliant end effector for minimally invasive surgery

NASA Astrophysics Data System (ADS)

Canfield, Shawn; Edinger, Ben; Frecker, Mary I.; Koopmann, Gary H.

1999-06-01

Recent advances in robotics, tele-robotics, smart material actuators, and mechatronics raise new possibilities for innovative developments in millimeter-scale robotics capable of manipulating objects only fractions of a millimeter in size. These advances can have a wide range of applications in the biomedical community. A potential application of this technology is in minimally invasive surgery (MIS). The focus of this paper is the development of a single degree of freedom prototype to demonstrate the viability of smart materials, force feedback and compliant mechanisms for minimally invasive surgery. The prototype is a compliant gripper that is 7-mm by 17-mm, made from a single piece of titanium that is designed to function as a needle driver for small scale suturing. A custom designed piezoelectric `inchworm' actuator drives the gripper. The integrated system is computer controlled providing a user interface device capable of force feedback. The design methodology described draws from recent advances in three emerging fields in engineering: design of innovative tools for MIS, design of compliant mechanisms, and design of smart materials and actuators. The focus of this paper is on the design of a millimeter-scale inchworm actuator for use with a compliant end effector in MIS.

The effect of forced choice on facial emotion recognition: a comparison to open verbal classification of emotion labels

PubMed Central

Limbrecht-Ecklundt, Kerstin; Scheck, Andreas; Jerg-Bretzke, Lucia; Walter, Steffen; Hoffmann, Holger; Traue, Harald C.

2013-01-01

Objective: This article includes the examination of potential methodological problems of the application of a forced choice response format in facial emotion recognition. Methodology: 33 subjects were presented with validated facial stimuli. The task was to make a decision about which emotion was shown. In addition, the subjective certainty concerning the decision was recorded. Results: The detection rates are 68% for fear, 81% for sadness, 85% for anger, 87% for surprise, 88% for disgust, and 94% for happiness, and are thus well above the random probability. Conclusion: This study refutes the concern that the use of forced choice formats may not adequately reflect actual recognition performance. The use of standardized tests to examine emotion recognition ability leads to valid results and can be used in different contexts. For example, the images presented here appear suitable for diagnosing deficits in emotion recognition in the context of psychological disorders and for mapping treatment progress. PMID:23798981

Field significance of performance measures in the context of regional climate model evaluation. Part 1: temperature

NASA Astrophysics Data System (ADS)

Ivanov, Martin; Warrach-Sagi, Kirsten; Wulfmeyer, Volker

2018-04-01

A new approach for rigorous spatial analysis of the downscaling performance of regional climate model (RCM) simulations is introduced. It is based on a multiple comparison of the local tests at the grid cells and is also known as "field" or "global" significance. New performance measures for estimating the added value of downscaled data relative to the large-scale forcing fields are developed. The methodology is exemplarily applied to a standard EURO-CORDEX hindcast simulation with the Weather Research and Forecasting (WRF) model coupled with the land surface model NOAH at 0.11 ∘ grid resolution. Monthly temperature climatology for the 1990-2009 period is analysed for Germany for winter and summer in comparison with high-resolution gridded observations from the German Weather Service. The field significance test controls the proportion of falsely rejected local tests in a meaningful way and is robust to spatial dependence. Hence, the spatial patterns of the statistically significant local tests are also meaningful. We interpret them from a process-oriented perspective. In winter and in most regions in summer, the downscaled distributions are statistically indistinguishable from the observed ones. A systematic cold summer bias occurs in deep river valleys due to overestimated elevations, in coastal areas due probably to enhanced sea breeze circulation, and over large lakes due to the interpolation of water temperatures. Urban areas in concave topography forms have a warm summer bias due to the strong heat islands, not reflected in the observations. WRF-NOAH generates appropriate fine-scale features in the monthly temperature field over regions of complex topography, but over spatially homogeneous areas even small biases can lead to significant deteriorations relative to the driving reanalysis. As the added value of global climate model (GCM)-driven simulations cannot be smaller than this perfect-boundary estimate, this work demonstrates in a rigorous manner the clear additional value of dynamical downscaling over global climate simulations. The evaluation methodology has a broad spectrum of applicability as it is distribution-free, robust to spatial dependence, and accounts for time series structure.

Integrated vehicle-based safety systems heavy truck field operational test, methodology and results report.

DOT National Transportation Integrated Search

2010-12-01

"This document presents the methodology and results from the heavy-truck field operational test conducted as part of the Integrated Vehicle-Based Safety Systems program. These findings are the result of analyses performed by the University of Michiga...