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.

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.

Self-consistent perturbed equilibrium with neoclassical toroidal torque in tokamaks

DOE PAGES

Park, Jong-Kyu; Logan, Nikolas C.

2017-03-01

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

Study on a new self-sensing magnetorheological elastomer bearing

NASA Astrophysics Data System (ADS)

Li, Rui; Zhou, Mengjiao; Wang, Minglian; Yang, Ping-an

2018-06-01

The complexity of a semi-active vibration isolation system results in the difficulty of realizing its role on impact load effectively. Thus, a new self-sensing bearing based on modified anisotropic magnetorheological elastomer (MRE) is proposed in this study. This self-sensing bearing was fabricated by dispersed multi-walled carbon nanotubes and carbonyl iron particles into polydimethylsiloxane matrix under a magnetic field. The working conditions of the bearing were analyzed and decoupled. An optimal structure size of the bearing was selected and used for setting up the experiment test system. The self-sensing characteristic of the MRE bearing under the multi-field coupling of load and magnetic fields was then investigated by this test system. Results showed that the resistance of the modified MRE, in which a preload was applied by the bearing, could change approximately 28%-56% under extrusion force, mechanical force, and external magnetic field. The vibration isolation performance was tested based on the self-sensing characteristic. The bearing had excellent mechanical properties, which could reduce at least 30% of vibration. Thus, the modified MRE of the magnetorheological elastomer bearing could be simultaneously used as an actuator and a sensor.

Casimir force in a Lorentz violating theory

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

Frank, Mariana; Turan, Ismail

2006-08-01

We study the effects of the minimal extension of the standard model including Lorentz violation on the Casimir force between two parallel conducting plates in the vacuum. We provide explicit solutions for the electromagnetic field using scalar field analogy, for both the cases in which the Lorentz violating terms come from the CPT-even or CPT-odd terms. We also calculate the effects of the Lorentz violating terms for a fermion field between two parallel conducting plates and analyze the modifications of the Casimir force due to the modifications of the Dirac equation. In all cases under consideration, the standard formulas formore » the Casimir force are modified by either multiplicative or additive correction factors, the latter case exhibiting different dependence on the distance between the plates.« less

Radiative corrections in the (varying power)-law modified gravity

NASA Astrophysics Data System (ADS)

Hammad, Fayçal

2015-06-01

Although the (varying power)-law modified gravity toy model has the attractive feature of unifying the early- and late-time expansions of the Universe, thanks to the peculiar dependence of the scalar field's potential on the scalar curvature, the model still suffers from the fine-tuning problem when used to explain the actually observed Hubble parameter. Indeed, a more correct estimate of the mass of the scalar field needed to comply with actual observations gives an unnaturally small value. On the other hand, for a massless scalar field the potential would have no minimum and hence the field would always remain massless. What solves these issues are the radiative corrections that modify the field's effective potential. These corrections raise the field's effective mass, rendering the model free from fine-tuning, immune against positive fifth-force tests, and better suited to tackle the dark matter sector.

An implicit divalent counterion force field for RNA molecular dynamics

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

Henke, Paul S.; Mak, Chi H., E-mail: cmak@usc.edu; Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grainedmore » models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.« less

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

PubMed

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

2018-04-05

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

Investigation of squeal noise under positive friction characteristics condition provided by friction modifiers

NASA Astrophysics Data System (ADS)

Liu, Xiaogang; Meehan, Paul A.

2016-06-01

Field application of friction modifiers on the top of rail has been shown to effectively curb squeal and reduce lateral forces, but performance can be variable, according to other relevant research. Up to now, most investigations of friction modifiers were conducted in the field, where it is difficult to control or measure important parameters such as angle of attack, rolling speed, adhesion ratio etc. In the present investigation, the effect of different friction modifiers on the occurrence of squeal was investigated on a rolling contact two disk test rig. In particular, friction-creep curves and squeal sound pressure levels were measured under different rolling speeds and friction modifiers. The results show friction modifiers can eliminate or reduce the negative slope of friction-creep curves, but squeal noise still exists. Theoretical modelling of instantaneous creep behaviours reveals a possible reason why wheel squeal still exists after the application of friction modifiers.

Sensitivity of Force Fields on Mechanical Properties of Metals Predicted by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

Increasing number of micro/nanoscale studies for scientific and engineering applications, leads to huge deployment of atomistic simulations such as molecular dynamics and Monte-Carlo simulation. Many complains from users in the simulation community arises for obtaining wrong results notwithstanding of correct simulation procedure and conditions. Improper choice of force field, known as interatomic potential is the likely causes. For the sake of users' assurance, convenience and time saving, several interatomic potentials are evaluated by molecular dynamics. Elastic properties of multiple FCC and BCC pure metallic species are obtained by LAMMPS, using different interatomic potentials designed for pure species and their alloys at different temperatures. The potentials created based on the Embedded Atom Method (EAM), Modified EAM (MEAM) and ReaX force fields, adopted from available open databases. Independent elastic stiffness constants of cubic single crystals for different metals are obtained. The results are compared with the experimental ones available in the literature and deviations for each force field are provided at each temperature. Using current work, users of these force fields can easily judge on the one they are going to designate for their problem.

Higher-order force moments of active particles

NASA Astrophysics Data System (ADS)

Nasouri, Babak; Elfring, Gwynn J.

2018-04-01

Active particles moving through fluids generate disturbance flows due to their activity. For simplicity, the induced flow field is often modeled by the leading terms in a far-field approximation of the Stokes equations, whose coefficients are the force, torque, and stresslet (zeroth- and first-order force moments) of the active particle. This level of approximation is quite useful, but may also fail to predict more complex behaviors that are observed experimentally. In this study, to provide a better approximation, we evaluate the contribution of the second-order force moments to the flow field and, by reciprocal theorem, present explicit formulas for the stresslet dipole, rotlet dipole, and potential dipole for an arbitrarily shaped active particle. As examples of this method, we derive modified Faxén laws for active spherical particles and resolve higher-order moments for active rod-like particles.

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.

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

Faster modified protocol for first order reversal curve measurements

NASA Astrophysics Data System (ADS)

De Biasi, Emilio

2017-10-01

In this work we present a faster modified protocol for first order reversal curve (FORC) measurements. The main idea of this procedure is to use the information of the ascending and descending branches constructed through successive sweeps of magnetic field. The new method reduces the number of field sweeps to almost one half as compared to the traditional method. The length of each branch is reduced faster than in the usual FORC protocol. The new method implies not only a new measurement protocol but also a new recipe for the previous treatment of the data. After of these pre-processing, the FORC diagram can be obtained by the conventional methods. In the present work we show that the new FORC procedure leads to results identical to the conventional method if the system under study follows the Stoner-Wohlfarth model with interactions that do not depend of the magnetic state (up or down) of the entities, as in the Preisach model. More specifically, if the coercive and interactions fields are not correlated, and the hysteresis loops have a square shape. Some numerical examples show the comparison between the usual FORC procedure and the propose one. We also discuss that it is possible to find some differences in the case of real systems, due to the magnetic interactions. There is no reason to prefer one FORC method over the other from the point of view of the information to be obtained. On the contrary, the use of both methods could open doors for a more accurate and deep analysis.

Martini straight: Boosting performance using a shorter cutoff and GPUs

NASA Astrophysics Data System (ADS)

de Jong, Djurre H.; Baoukina, Svetlana; Ingólfsson, Helgi I.; Marrink, Siewert J.

2016-02-01

In molecular dynamics simulations, sufficient sampling is of key importance and a continuous challenge in the field. The coarse grain Martini force field has been widely used to enhance sampling. In its original implementation, this force field applied a shifted Lennard-Jones potential for the non-bonded van der Waals interactions, to avoid problems related to a relatively short cutoff. Here we investigate the use of a straight cutoff Lennard-Jones potential with potential modifiers. Together with a Verlet neighbor search algorithm, the modified potential allows the use of GPUs to accelerate the computations in Gromacs. We find that this alternative potential has little influence on most of the properties studied, including partitioning free energies, bulk liquid properties and bilayer properties. At the same time, energy conservation is kept within reasonable bounds. We conclude that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs.

Modifying upper-limb inter-joint coordination in healthy subjects by training with a robotic exoskeleton.

PubMed

Proietti, Tommaso; Guigon, Emmanuel; Roby-Brami, Agnès; Jarrassé, Nathanaël

2017-06-12

The possibility to modify the usually pathological patterns of coordination of the upper-limb in stroke survivors remains a central issue and an open question for neurorehabilitation. Despite robot-led physical training could potentially improve the motor recovery of hemiparetic patients, most of the state-of-the-art studies addressing motor control learning, with artificial virtual force fields, only focused on the end-effector kinematic adaptation, by using planar devices. Clearly, an interesting aspect of studying 3D movements with a robotic exoskeleton, is the possibility to investigate the way the human central nervous system deals with the natural upper-limb redundancy for common activities like pointing or tracking tasks. We asked twenty healthy participants to perform 3D pointing or tracking tasks under the effect of inter-joint velocity dependant perturbing force fields, applied directly at the joint level by a 4-DOF robotic arm exoskeleton. These fields perturbed the human natural inter-joint coordination but did not constrain directly the end-effector movements and thus subjects capability to perform the tasks. As a consequence, while the participants focused on the achievement of the task, we unexplicitly modified their natural upper-limb coordination strategy. We studied the force fields direct effect on pointing movements towards 8 targets placed in the 3D peripersonal space, and we also considered potential generalizations on 4 distinct other targets. Post-effects were studied after the removal of the force fields (wash-out and follow up). These effects were quantified by a kinematic analysis of the pointing movements at both end-point and joint levels, and by a measure of the final postures. At the same time, we analysed the natural inter-joint coordination through PCA. During the exposition to the perturbative fields, we observed modifications of the subjects movement kinematics at every level (joints, end-effector, and inter-joint coordination). Adaptation was evidenced by a partial decrease of the movement deviations due to the fields, during the repetitions, but it occurred only on 21% of the motions. Nonetheless post-effects were observed in 86% of cases during the wash-out and follow up periods (right after the removal of the perturbation by the fields and after 30 minutes of being detached from the exoskeleton). Important inter-individual differences were observed but with small variability within subjects. In particular, a group of subjects showed an over-shoot with respect to the original unexposed trajectories (in 30% of cases), but the most frequent consequence (in 55% of cases) was the partial persistence of the modified upper-limb coordination, adopted at the time of the perturbation. Temporal and spatial generalizations were also evidenced by the deviation of the movement trajectories, both at the end-effector and at the intermediate joints and the modification of the final pointing postures towards targets which were never exposed to any field. Such results are the first quantified characterization of the effects of modification of the upper-limb coordination in healthy subjects, by imposing modification through viscous force fields distributed at the joint level, and could pave the way towards opportunities to rehabilitate pathological arm synergies with robots.

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

PubMed Central

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

2015-01-01

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

Reparameterization of Solute—Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

PubMed Central

Lay, Wesley K.; Miller, Mark S.

2018-01-01

AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ΔGtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose. PMID:28437100

Rarefaction shock waves and Hugoniot curve in the presence of free and trapped particles

NASA Astrophysics Data System (ADS)

Niknam, A. R.; Hashemzadeh, M.; Shokri, B.; Rouhani, M. R.

2009-12-01

The effects of the relativistic ponderomotive force and trapped particles in the presence of ponderomotive force on the rarefaction shock waves are investigated. The ponderomotive force alters the electron density distribution. This force and relativistic mass affect the plasma frequency. These physical parameters modify the total pressure and the existence condition of the rarefaction shock wave. Furthermore, the trapping of particles by the high frequency electromagnetic field considerably changes the existence condition of the rarefaction shock wave. The total pressure and Hugoniot curve are obtained by considering the relativistic ponderomotive force and trapped particles.

Analysis of eddy current induced in track on medium-low speed maglev train

NASA Astrophysics Data System (ADS)

Li, Guanchun; Jia, Zhen; He, Guang; Li, Jie

2017-06-01

Electromagnetic levitation (EMS) maglev train relies on the attraction between the electromagnets and rails which are mounted on the train to achieve suspension. During the movement, the magnetic field generated by the electromagnet will induce the eddy current in the orbit and the eddy current will weaken the suspended magnetic field. Which leads to the attenuation of the levitation force, the increases of suspension current and the degradation the suspension performance. In this paper, the influence of eddy current on the air gap magnetic field is solved by theoretical analysis, and the correction coefficient of air gap magnetic field is fitted according to the finite element data. The levitation force and current are calculated by the modified formula, and the velocity curves of the levitation force and current are obtained. The results show that the eddy current effect increases the load power by 61.9% in the case of heavy loads.

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

PubMed

Mitri, F G

2005-08-01

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

Simulations of Dynamical Friction Including Spatially-Varying Magnetic Fields

NASA Astrophysics Data System (ADS)

Bell, G. I.; Bruhwiler, D. L.; Litvinenko, V. N.; Busby, R.; Abell, D. T.; Messmer, P.; Veitzer, S.; Cary, J. R.

2006-03-01

A proposed luminosity upgrade to the Relativistic Heavy Ion Collider (RHIC) includes a novel electron cooling section, which would use ˜55 MeV electrons to cool fully-ionized 100 GeV/nucleon gold ions. We consider the dynamical friction force exerted on individual ions due to a relevant electron distribution. The electrons may be focussed by a strong solenoid field, with sensitive dependence on errors, or by a wiggler field. In the rest frame of the relativistic co-propagating electron and ion beams, where the friction force can be simulated for nonrelativistic motion and electrostatic fields, the Lorentz transform of these spatially-varying magnetic fields includes strong, rapidly-varying electric fields. Previous friction force simulations for unmagnetized electrons or error-free solenoids used a 4th-order Hermite algorithm, which is not well-suited for the inclusion of strong, rapidly-varying external fields. We present here a new algorithm for friction force simulations, using an exact two-body collision model to accurately resolve close interactions between electron/ion pairs. This field-free binary-collision model is combined with a modified Boris push, using an operator-splitting approach, to include the effects of external fields. The algorithm has been implemented in the VORPAL code and successfully benchmarked.

Alternative to particle dark matter

NASA Astrophysics Data System (ADS)

Khoury, Justin

2015-01-01

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

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

Free-energy landscape of the villin headpiece in an all-atom force field.

PubMed

Herges, Thomas; Wenzel, Wolfgang

2005-04-01

We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations started from random initial conditions converge to the folding funnel of the native conformation, but several competing low-energy metastable conformations were observed. From 76,000 independently generated conformations we derived a decoy tree which illustrates the topological structure of the entire low-energy part of the free-energy landscape and characterizes the ensemble of metastable conformations. These emerge as similar in secondary content, but differ in tertiary arrangement.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Force-free magnetic fields - The magneto-frictional method

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

Every Mass or Mass Group When Created Will have No Motion, Linear, Rotational or Vibratory Motion, Singly or in Some Combination, Which May Be Later Modified by External Forces--A Natural Law

NASA Astrophysics Data System (ADS)

Brekke, Stewart

2010-03-01

Every mass or mass group, from atoms and molecules to stars and galaxies,has no motion, is vibrating, rotating,or moving linearly, singularly or in some combination. When created, the excess energy of creation will generate a vibration, rotation and/or linear motion besides the mass or mass group. Curvilinear or orbital motion is linear motion in an external force field. External forces, such as photon, molecular or stellar collisions may over time modify the inital rotational, vibratory or linear motions of the mass of mass group. The energy equation for each mass or mass group is E=mc^2 + 1/2mv^2 + 1/2I2̂+ 1/2kx0^2 + WG+ WE+ WM.

The Role of the Upper Atmosphere for Dawn-Dusk and Interhemispheric Differences in the Coupled Magnetosphere-Ionosphere-Thermosphere System

NASA Astrophysics Data System (ADS)

Foerster, M.; Doornbos, E.; Haaland, S.

2016-12-01

Solar wind and IMF interaction with the geomagnetic field sets up a large-scale plasma circulation in the Earth's magnetosphere and the magnetically tightly connected ionosphere. The ionospheric ExB ion drift at polar latitudes accelerates the neutral gas as a nondivergent momentum source primarily in force balance with pressure gradients, while the neutral upper thermosphere circulation is essentially modified by apparent forces due to Earth's rotation (Coriolis and centrifugal forces) as well as advection and viscous forces. The apparent forces affect the dawn and dusk side asymmetrically, favouring a large dusk-side neutral wind vortex, while the non-dipolar portions of the Earth's magnetic field constitute significant hemispheric differences in magnetic flux and field configurations that lead to essential interhemispheric differences of the ion-neutral interaction. We present statistical studies of both the high-latitude ionospheric convection and the upper thermospheric circulation patterns based on measurements of the electron drift instrument (EDI) on board the Cluster satellites and by the accelerometer on board the CHAMP, GOCE, and Swarm spacecraft, respectively.

Toward structure prediction of cyclic peptides.

PubMed

Yu, Hongtao; Lin, Yu-Shan

2015-02-14

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

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Magnetic field effects and waves in complex plasmas

NASA Astrophysics Data System (ADS)

Kählert, Hanno; Melzer, André; Puttscher, Marian; Ott, Torben; Bonitz, Michael

2018-05-01

Magnetic fields can modify the physical properties of a complex plasma in various different ways. Weak magnetic fields in the mT range affect only the electrons while strong fields in the Tesla regime also magnetize the ions. In a rotating dusty plasma, the Coriolis force substitutes the Lorentz force and can be used to create an effective magnetization for the strongly coupled dust particles while leaving electrons and ions unaffected. Here, we present a summary of our recent experimental and theoretical work on magnetized complex plasmas. We discuss the dynamics of dust particles in magnetized discharges, the wave spectra of strongly coupled plasmas, and the excitations in confined plasmas. Contribution to the Topical Issue "Fundamentals of Complex Plasmas", edited by Jürgen Meichsner, Michael Bonitz, Holger Fehske, Alexander Piel.

A detailed analysis of open-field habituation and behavioral and neurochemical antidepressant-like effects in postweaning enriched rats.

PubMed

Brenes, Juan C; Padilla, Michael; Fornaguera, Jaime

2009-01-30

Our previous work has shown that male Sprague-Dawley rats reared in social isolation, standard housing and environmental enrichment differ in their spontaneous open-field activity and in some neurobehavioral depressive-like parameters. Here, we extended this evidence by using a shorter postweaning rearing period (1 month) and including additional evaluations. First, in order to obtain a better characterization of the exploratory strategies among rearing conditions we analyzed in detail the spontaneous activity at the first minute and during the 10-min session. Second, we asked whether the changes in open-field activity were related with basal anxiety levels in the elevated plus-maze. Third, behavior in the forced-swimming test was analyzed and afterward, the tissue levels of hippocampal norepinephrine and serotonin were assessed. The possible relationship between neurotransmitters and forced-swimming behavior were explored through correlation analyses. We found that rearing conditions (i) differed on locomotor habituation and on sensory-motor exploration at the first minute and during the 10-min session without modifying the plus-maze behavior; (ii) affected differentially the grooming time, its sequential components, and the relationship between grooming and locomotor parameters; (iii) modified forced-swimming behavior and the hippocampal concentration of norepinephrine, serotonin, and its turnover; and (iv) produced different correlation patterns between both neurotransmitters and forced-swimming behaviors. Overall, environmental enrichment accelerated open-field habituation and led to behavioral and neurochemical antidepressant-like effects. In contract, isolation rearing strongly impaired habituation and simple information processing, but showed marginal effects on depressive-like behavior and on hippocampal neurochemistry. The current results suggest that differential rearing is not only a useful procedure to study behavioral plasticity or rigidity in response to early experience, but also to modeling some developmental protective or risk factors underlying depressive disorders.

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

NASA Astrophysics Data System (ADS)

Eberhardt, Oliver; Wallmersperger, Thomas

2018-03-01

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

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.

Simulating the electrohydrodynamics of a viscous droplet

NASA Astrophysics Data System (ADS)

Theillard, Maxime; Saintillan, David

2016-11-01

We present a novel numerical approach for the simulation of viscous drop placed in an electric field in two and three spatial dimensions. Our method is constructed as a stable projection method on Quad/Octree grids. Using a modified pressure correction we were able to alleviate the standard time step restriction incurred by capillary forces. In weak electric fields, our results match remarkably well with the predictions from the Taylor-Melcher leaky dielectric model. In strong electric fields the so-called Quincke rotation is correctly reproduced.

Multiphysics modelling of the separation of suspended particles via frequency ramping of ultrasonic standing waves.

PubMed

Trujillo, Francisco J; Eberhardt, Sebastian; Möller, Dirk; Dual, Jurg; Knoerzer, Kai

2013-03-01

A model was developed to determine the local changes of concentration of particles and the formations of bands induced by a standing acoustic wave field subjected to a sawtooth frequency ramping pattern. The mass transport equation was modified to incorporate the effect of acoustic forces on the concentration of particles. This was achieved by balancing the forces acting on particles. The frequency ramping was implemented as a parametric sweep for the time harmonic frequency response in time steps of 0.1s. The physics phenomena of piezoelectricity, acoustic fields and diffusion of particles were coupled and solved in COMSOL Multiphysics™ (COMSOL AB, Stockholm, Sweden) following a three step approach. The first step solves the governing partial differential equations describing the acoustic field by assuming that the pressure field achieves a pseudo steady state. In the second step, the acoustic radiation force is calculated from the pressure field. The final step allows calculating the locally changing concentration of particles as a function of time by solving the modified equation of particle transport. The diffusivity was calculated as function of concentration following the Garg and Ruthven equation which describes the steep increase of diffusivity when the concentration approaches saturation. However, it was found that this steep increase creates numerical instabilities at high voltages (in the piezoelectricity equations) and high initial particle concentration. The model was simplified to a pseudo one-dimensional case due to computation power limitations. The predicted particle distribution calculated with the model is in good agreement with the experimental data as it follows accurately the movement of the bands in the centre of the chamber. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Positive and negative effective mass of classical particles in oscillatory and static fields.

PubMed

Dodin, I Y; Fisch, N J

2008-03-01

A classical particle oscillating in an arbitrary high-frequency or static field effectively exhibits a modified rest mass m(eff) derived from the particle averaged Lagrangian. Relativistic ponderomotive and diamagnetic forces, as well as magnetic drifts, are obtained from the m(eff) dependence on the guiding center location and velocity. The effective mass is not necessarily positive and can result in backward acceleration when an additional perturbation force is applied. As an example, adiabatic dynamics with m||>0 and m||<0 is demonstrated for a wave-driven particle along a dc magnetic field, m|| being the effective longitudinal mass derived from m(eff). Multiple energy states are realized in this case, yielding up to three branches of m|| for a given magnetic moment and parallel velocity.

Kansas Department of Transportation column expert : ultimate shear capacity of circular columns using the simplified modified compression field theory.

DOT National Transportation Integrated Search

2015-09-01

The importance of the analysis of circular columns to accurately predict their ultimate confined : capacity under shear-flexure-axial force interaction domain is recognized in light of the extreme load event : imposed by the current American Associat...

Moving force identification based on modified preconditioned conjugate gradient method

NASA Astrophysics Data System (ADS)

Chen, Zhen; Chan, Tommy H. T.; Nguyen, Andy

2018-06-01

This paper develops a modified preconditioned conjugate gradient (M-PCG) method for moving force identification (MFI) by improving the conjugate gradient (CG) and preconditioned conjugate gradient (PCG) methods with a modified Gram-Schmidt algorithm. The method aims to obtain more accurate and more efficient identification results from the responses of bridge deck caused by vehicles passing by, which are known to be sensitive to ill-posed problems that exist in the inverse problem. A simply supported beam model with biaxial time-varying forces is used to generate numerical simulations with various analysis scenarios to assess the effectiveness of the method. Evaluation results show that regularization matrix L and number of iterations j are very important influence factors to identification accuracy and noise immunity of M-PCG. Compared with the conventional counterpart SVD embedded in the time domain method (TDM) and the standard form of CG, the M-PCG with proper regularization matrix has many advantages such as better adaptability and more robust to ill-posed problems. More importantly, it is shown that the average optimal numbers of iterations of M-PCG can be reduced by more than 70% compared with PCG and this apparently makes M-PCG a preferred choice for field MFI applications.

Effect of thermal modification on rheological properties of polyethylene blends

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

Siriprumpoonthum, Monchai; Nobukawa, Shogo; Yamaguchi, Masayuki, E-mail: m-yama@jaist.ac.jp

2014-03-15

We examined the effects of thermal modification under flow field on the rheological properties of linear low-density polyethylene (LLDPE) with high molecular weight, low-density polyethylene (LDPE), and their blends, without thermal stabilizer. Although structural changes during processing are not detected by size extrusion chromatography or nuclear magnetic resonance spectroscopy, linear viscoelastic properties changed greatly, especially for the LLDPE. A cross-linking reaction took place, leading to, presumably, star-shaped long-chain branches. Consequently, the modified LLDPE, having high zero-shear viscosity, became a thermorheologically complex melt. Moreover, it should be noted that the drawdown force, defined as the uniaxial elongational force at a constantmore » draw ratio, was significantly enhanced for the blends. Enhancement of elongational viscosity was also detected. The drawdown force and elongational viscosity are marked for the thermally modified blend as compared with those for the blend of thermally modified pure components. Intermolecular cross-linking reactions between LDPE and LLDPE, yielding polymers with more than two branch points per chain, result in marked strain-hardening in the elongational viscosity behavior even at small strain. The recovery curve of the oscillatory modulus after the shear modification is further evidence of a branched structure.« less

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.

Vertical-probe-induced asymmetric dust oscillation in complex plasma.

PubMed

Harris, B J; Matthews, L S; Hyde, T W

2013-05-01

A complex plasma vertical oscillation experiment which modifies the bulk is presented. Spherical, micron-sized particles within a Coulomb crystal levitated in the sheath above the powered lower electrode in a GEC reference cell are perturbed using a probe attached to a Zyvex S100 Nanomanipulator. By oscillating the probe potential sinusoidally, particle motion is found to be asymmetric, exhibiting superharmonic response in one case. Using a simple electric field model for the plasma sheath, including a nonzero electric field at the sheath edge, dust particle charges are found by employing a balance of relevant forces and emission analysis. Adjusting the parameters of the electric field model allowed the change predicted in the levitation height to be compared with experiment. A discrete oscillator Green's function is applied using the derived force, which accurately predicts the particle's motion and allows the determination of the electric field at the sheath edge.

Non-Contact Thrust Stand Calibration Method for Repetitively-Pulsed Electric Thrusters

NASA Technical Reports Server (NTRS)

Wong, Andrea R.; Toftul, Alexandra; Polzin, Kurt A.; Pearson, J. Boise

2011-01-01

A thrust stand calibration technique for use in testing repetitively-pulsed electric thrusters for in-space propulsion has been developed and tested using a modified hanging pendulum thrust stand. In the implementation of this technique, current pulses are applied to a solenoidal coil to produce a pulsed magnetic field that acts against the magnetic field produced by a permanent magnet mounted to the thrust stand pendulum arm. The force on the magnet is applied in this non-contact manner, with the entire pulsed force transferred to the pendulum arm through a piezoelectric force transducer to provide a time-accurate force measurement. Modeling of the pendulum arm dynamics reveals that after an initial transient in thrust stand motion the quasisteady average deflection of the thrust stand arm away from the unforced or zero position can be related to the average applied force through a simple linear Hooke s law relationship. Modeling demonstrates that this technique is universally applicable except when the pulsing period is increased to the point where it approaches the period of natural thrust stand motion. Calibration data were obtained using a modified hanging pendulum thrust stand previously used for steady-state thrust measurements. Data were obtained for varying impulse bit at constant pulse frequency and for varying pulse frequency. The two data sets exhibit excellent quantitative agreement with each other as the constant relating average deflection and average thrust match within the errors on the linear regression curve fit of the data. Quantitatively, the error on the calibration coefficient is roughly 1% of the coefficient value.

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.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

PubMed

Khan, Hanif M; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D; Havenith, Remco W A; Reuter, Nathalie

2016-11-08

Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH 3 ) 3 ) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

Enhanced vertical mixing within mesoscale eddies due to high frequency winds in the South China Sea

NASA Astrophysics Data System (ADS)

Cardona, Yuley; Bracco, Annalisa

The South China Sea is a marginal basin with a complex circulation influenced by the East Asian Monsoon, river discharge and intricate bathymetry. As a result, both the mesoscale eddy field and the near-inertial energy distribution display large spatial variability and they strongly influence the oceanic transport and mixing. With an ensemble of numerical integrations using a regional ocean model, this work investigates how the temporal resolution of the atmospheric forcing fields modifies the horizontal and vertical velocity patterns and impacts the transport properties in the basin. The response of the mesoscale circulation in the South China Sea is investigated under three different forcing conditions: monthly, daily and 6-hourly momentum and heat fluxes. While the horizontal circulation does not display significant differences, the representation of the vertical velocity field displays high sensitivity to the frequency of the wind forcing. If the wind field contains energy at the inertial frequency or higher (daily and 6-hourly cases), then submesoscale fronts, vortex Rossby waves and near inertial waves are excited as ageostrophic expression of the vigorous eddy field. Those quasi- and near-inertial waves dominate the vertical velocity field in the mixed layer (vortex Rossby waves) and below the first hundred meters (near inertial waves) and they are responsible for the differences in the vertical transport properties under the various forcing fields as quantified by frequency spectra, vertical velocity profiles and vertical dispersion of Lagrangian tracers.

Mathematical Model for Collision-Coalescence Among Inclusions in the Bloom Continuous Caster with M-EMS

NASA Astrophysics Data System (ADS)

Lei, Hong; Jiang, Jimin; Yang, Bin; Zhao, Yan; Zhang, Hongwei; Wang, Weixian; Dong, Guiwen

2018-04-01

Mathematical simulation is an effective tool to analyze the fluid flow and the inclusion behavior in the bloom continuous caster with mold electromagnetic stirring (M-EMS). The mathematical model is applied to the modeling of magnetic field, flow field, and inclusion field. Due to the introduction of Archimedes force, the collision mechanism and inclusion's slipping velocity should be modified in the inclusion mass and population conservation model. Numerically predicted magnetic field, flow field, and the inclusion spatial distribution conform to the experimental results in the existing literature. Lorentz force plays an important role in the fluid flow, and Archimedes force plays an important role in the inclusion distribution in the continuous caster. Due to Brownian collision, Stokes collision, Archimedes collision, and turbulent collision, the coalescence among inclusions occurs in the bloom continuous caster with M-EMS. Among the four types of collisions, turbulent collision occurs most frequently, followed by Archimedes collision and Stokes collision. The frequency of Brownian collision is several orders of magnitudes smaller and is therefore negligible. The inclusion volume concentration, number density, and characteristic radius exhibit a U-shape in the continuous caster without M-EMS. However, with M-EMS, they exhibit an inverted U-shape.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis.

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

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

PubMed

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

2015-06-25

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

Kansas Department of Transportation column expert : ultimate shear capacity of circular columns using the simplified modified compression field theory : [technical summary].

DOT National Transportation Integrated Search

2015-09-01

Even though the behavior of concrete elements subjected to shear force has been : studied for many years, researchers do not have a full agreement on concrete : shear resistance. This is mainly because of the many different mechanisms : that affect t...

Nature of inclined growth in thin-layer electrodeposition under uniform magnetic fields.

PubMed

Soba, Alejandro; González, Graciela; Calivar, Lucas; Marshall, Guillermo

2012-11-01

Electrochemical deposition (ECD) in thin cells in a vertical position relative to gravity, subject to an external uniform magnetic field, yields a growth pattern formation with dense branched morphology with branches tilted in the direction of the magnetic force. We study the nature of the inclined growth through experiments and theory. Experiments in ECD, in the absence of magnetic forces, reveal that a branch grows by allowing fluid to penetrate its tip and to be ejected from the sides through a pair of symmetric vortices attached to the tip. The upper vortices zone defines an arch separating an inner zone ion depleted and an outer zone in a funnel-like form with a concentrated solution through which metal ions are carried into the tip. When a magnetic field is turned on, vortex symmetry is broken, one vortex becoming weaker than the other, inducing an inclination of the funnel. Consequently, particles entering the funnel give rise to branch growth tilted in the same direction. Theory predicts, in the absence of a magnetic force, funnel symmetry induced through symmetric vortices driven by electric and gravitational forces; when the magnetic force is on, it is composed with the pair of clockwise and counterclockwise vortices, reducing or amplifying one or the other. In turn, funnel tilting modifies particle trajectories, thus, growth orientation.

Navier-Stokes predictions of pitch damping for axisymmetric shell using steady coning motion

NASA Technical Reports Server (NTRS)

Weinacht, Paul; Sturek, Walter B.; Schiff, Lewis B.

1991-01-01

Previous theoretical investigations have proposed that the side force and moment acting on a body of revolution in steady coning motion could be related to the pitch-damping force and moment. In the current research effort, this approach is applied to produce predictions of the pitch damping for axisymmetric shell. The flow fields about these projectiles undergoing steady coning motion are successfully computed using a parabolized Navier-Stokes computational approach which makes use of a rotating coordinate frame. The governing equations are modified to include the centrifugal and Coriolis force terms due to the rotating coordinate frame. From the computed flow field, the side moments due to coning motion, spinning motion, and combined spinning and coning motion are used to determine the pitch-damping coefficients. Computations are performed for two generic shell configurations, a secant-ogive-cylinder and a secant-ogive-cylinder-boattail.

Guidance of magnetic space tug

NASA Astrophysics Data System (ADS)

Fabacher, Emilien; Lizy-Destrez, Stéphanie; Alazard, Daniel; Ankersen, Finn; Profizi, Alexandre

2017-07-01

Magnetic tugging of a target satellite without thrust capacity can be interesting in various contexts, as for example End-Of-Life management, or to complete launchers capabilities. The aim is to gradually modify the orbit of the target by constantly exerting on it a magnetic force. To do so, the chaser is assumed equipped with a steerable magnetic dipole, able to create both forces and torques on the magnetic torque rods carried by the target. The chaser is also supposed to carry electric thrusters, creating a continuous force which modifies the orbit of the whole formation composed of chaser and target. The relative motions of both satellites are derived, in order to assess the feasibility of such a concept. Relative configuration (attitudes and position) trajectories are derived, which are compliant with the dynamics, and enable the chaser to tug the target. Considering targets in Low Earth Orbit (LEO), the magnetic field of the Earth is taken into account, modeled by the International Geomagnetic Reference Field (IGRF). The position of the magnetic torque rod of the target may not be located at its center of mass. This lever-arm is taken into account in the dynamics. As for every Electro-Magnetic Formation Flight concept developed in the literature, satellites involved in magnetic tugging are constantly subjected to torques, created by the Earth magnetic field and by the magnetic fields created by the other satellites in the formation. In this study, the solution chosen to face this problem is to take into account the attitude equilibrium of the satellites early in the guidance phase, in order to avoid having to wave the dipole, as it is generally done. Promising results are presented for different types of orbit, showing that the concept could be feasible in many different scenarios.

Numerical investigation of hypersonic exhaust plume/afterbody flow fields

NASA Astrophysics Data System (ADS)

Edwards, T. A.

An upwind, implicit Navier-Stokes computer program has been applied to hypersonic exhaust plume/afterbody flowfields. The sensitivity of gross thrust to operating conditions has been assessed through parametric variations. Comparison of the numerical results with available experimental data shows good agreement in all cases investigated. Results show that, for moderately underexpanded jets, the afterbody force varies linearly with the nozzle exit pressure. Exhaust gases with low isentropic exponents (gamma) were found to contribute up to 25 percent more afterbody force than high-gamma exhaust gases. Modifying the nozzle geometry influenced the exhaust plume development, which had a significant effect on the afterbody force. Grid density, while important to resolving the initial plume/afterbody interaction, had only a minor impact on the resultant afterbody force.

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

PubMed

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

2015-02-10

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

Implementation of robotic force control with position accommodation

NASA Technical Reports Server (NTRS)

Ryan, Michael J.

1992-01-01

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

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

PubMed

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

2012-12-01

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

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

PubMed Central

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

2012-01-01

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

Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

PubMed Central

Wang, Lihua; Hingerty, Brian E; Srinivasan, A R; Olson, Wilma K; Broyde, Suse

2002-01-01

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance approximately 0.4 A greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands. PMID:12080128

KSC-2009-3466

NASA Image and Video Library

2009-06-01

CAPE CANAVERAL, Fla. – Hitching a ride on the Shuttle Carrier Aircraft, or SCA, a modified Boeing 747, space shuttle Atlantis has arrived in Lackland Air Force Base's Kelly Field Annex in Texas for a fuel stop on its journey back to Florida. Atlantis' next assignment is the STS-129 mission, targeted to launch in November 2009. Photo credit: NASA/Ben Smegelsky

KSC-2009-3464

NASA Image and Video Library

2009-06-01

CAPE CANAVERAL, Fla. – At Biggs Army Air Field in El Paso, Texas, the Shuttle Carrier Aircraft, or SCA, a modified Boeing 747, is ready to take off after an overnight stop at Biggs Army Air Field in El Paso, Texas. The shuttle and SCA left Edwards Air Force Base in California for its return to Florida.Atlantis is being returned to Florida on a ferry flight on the SCA. Atlantis' next assignment is the STS-129 mission, targeted to launch in November 2009. Photo credit: NASA/Ben Smegelsky

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

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

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

A new, simple electrostatic-acoustic hybrid levitator

NASA Technical Reports Server (NTRS)

Lierke, E. G.; Loeb, H.; Gross, D.

1990-01-01

Battelle has developed a hybrid levitator by combining the known single-axis acoustic standing wave levitator with a coaxial DC electric field. The resulting Coulomb forces on the charged liquid or solid sample support its weight and, together with the acoustic force, center the sample. Liquid samples with volumes approximately less than 100 micro-liters are deployed from a syringe reservoir into the acoustic pressure node. The sample is charged using a miniature high voltage power supply (approximately less than 20 kV) connected to the syringe needle. As the electric field, generated by a second miniature power supply, is increased, the acoustic intensity is reduced. The combination of both fields allows stable levitation of samples larger than either single technique could position on the ground. Decreasing the acoustic intensity reduces acoustic convection and sample deformation. Neither the electrostatic nor the acoustic field requires sample position sensing or active control. The levitator, now used for static and dynamic fluid physics investigations on the ground, can be easily modified for space operations.

Dynamics of elastic interactions in soft and biological matter.

PubMed

Yuval, Janni; Safran, Samuel A

2013-04-01

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

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

NASA Technical Reports Server (NTRS)

Gainer, Thomas G.

1990-01-01

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

Dielectrophoretic levitation in the presence of shear flow: implications for colloidal fouling of filtration membranes.

PubMed

Molla, Shahnawaz; Bhattacharjee, Subir

2007-10-09

The ability of dielectrophoretic (DEP) forces created using a microelectrode array to levitate particles in a colloidal suspension is studied experimentally and theoretically. The experimental system employs microfabricated electrode arrays on a glass substrate to apply repulsive DEP forces on polystyrene latex particles suspended in an aqueous medium. A numerical model based on the convection-diffusion-migration equation is presented to calculate the concentration distribution of colloidal particles in shear flow under the influence of a repulsive DEP force field. The results obtained from the numerical simulations are compared against trajectory analysis results and experimental data. The results indicate that by incorporating ac electric field-induced DEP forces in a shear flow, particle accumulation and deposition on the flow channel surfaces can be significantly reduced or even completely averted. The mathematical model is then used to indicate how the deposition behavior is modified in the presence of a permeable substrate, representative of tangential flow membrane filtration operations. The results indicate that the repulsive dielectrophoretic (DEP) forces imparted to the particles suspended in the feed can be employed to mitigate membrane fouling in a cross-flow filtration process.

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Solution of the exact equations for three-dimensional atmospheric entry using directly matched asymptotic expansions

NASA Technical Reports Server (NTRS)

Busemann, A.; Vinh, N. X.; Culp, R. D.

1976-01-01

The problem of determining the trajectories, partially or wholly contained in the atmosphere of a spherical, nonrotating planet, is considered. The exact equations of motion for three-dimensional, aerodynamically affected flight are derived. Modified Chapman variables are introduced and the equations are transformed into a set suitable for analytic integration using asymptotic expansions. The trajectory is solved in two regions: the outer region, where the force may be considered a gravitational field with aerodynamic perturbations, and the inner region, where the force is predominantly aerodynamic, with gravity as a perturbation. The two solutions are matched directly. A composite solution, valid everywhere, is constructed by additive composition. This approach of directly matched asymptotic expansions applied to the exact equations of motion couched in terms of modified Chapman variables yields an analytical solution which should prove to be a powerful tool for aerodynamic orbit calculations.

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Salt dependence of compression normal forces of quenched polyelectrolyte brushes

NASA Astrophysics Data System (ADS)

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

2001-03-01

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

Assessment of the air-soil partitioning of polycyclic aromatic hydrocarbons in a paddy field using a modified fugacity sampler.

PubMed

Wang, Yan; Luo, Chunling; Wang, Shaorui; Liu, Junwen; Pan, Suhong; Li, Jun; Ming, Lili; Zhang, Gan; Li, Xiangdong

2015-01-06

Rice, one of the most widely cultivated crops, has received great attention in contaminant uptake from soil and air, especially for the special approaches used for its cultivation. The dry-wet alternation method can influence the air-soil partitioning of semivolatile organic compounds (SVOCs) in the paddy ecosystem. Here, we modified a fugacity sampler to investigate the air-surface in situ partitioning of ubiquitous polycyclic aromatic hydrocarbons (PAHs) at different growth stages in a suburban paddy field in South China. The canopy of rice can form a closed space, which acts like a chamber that can force the air under the canopy to equilibrate with the field surface. When we compared the fugacities calculated using a fugacity model of the partition coefficients to the measured fugacities, we observed similar trends in the variation, but significantly different values between different growing stages, especially during the flooding stages. However, the measured and calculated fugacity fractions were comparable when uncertainties in our calculations were considered, with the exception of the high molecular weight (HMW) PAHs. The measured fugacity fractions suggested that the HMW PAHs were also closed to equilibrium between the paddy field and atmosphere. The modified fugacity sampler provided a novel way of accurately determining the in situ air-soil partitioning of SVOCs in a wet paddy field.

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

PubMed

Bailey, John D; Harrington, Constance A

2006-04-01

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

Non-contact thrust stand calibration method for repetitively pulsed electric thrusters.

PubMed

Wong, Andrea R; Toftul, Alexandra; Polzin, Kurt A; Pearson, J Boise

2012-02-01

A thrust stand calibration technique for use in testing repetitively pulsed electric thrusters for in-space propulsion has been developed and tested using a modified hanging pendulum thrust stand. In the implementation of this technique, current pulses are applied to a solenoid to produce a pulsed magnetic field that acts against a permanent magnet mounted to the thrust stand pendulum arm. The force on the magnet is applied in this non-contact manner, with the entire pulsed force transferred to the pendulum arm through a piezoelectric force transducer to provide a time-accurate force measurement. Modeling of the pendulum arm dynamics reveals that after an initial transient in thrust stand motion the quasi-steady average deflection of the thrust stand arm away from the unforced or "zero" position can be related to the average applied force through a simple linear Hooke's law relationship. Modeling demonstrates that this technique is universally applicable except when the pulsing period is increased to the point where it approaches the period of natural thrust stand motion. Calibration data were obtained using a modified hanging pendulum thrust stand previously used for steady-state thrust measurements. Data were obtained for varying impulse bit at constant pulse frequency and for varying pulse frequency. The two data sets exhibit excellent quantitative agreement with each other. The overall error on the linear regression fit used to determine the calibration coefficient was roughly 1%.

Frequency dependence of the acoustic radiation force acting on absorbing cylindrical shells.

PubMed

Mitri, Farid G

2005-02-01

The frequency dependence of the radiation force function Y(p) for absorbing cylindrical shells suspended in an inviscid fluid in a plane incident sound field is analysed, in relation to the thickness and the content of their interior hollow region. The theory is modified to include the effect of hysteresis type absorption of compressional and shear waves in the material. The results of numerical calculations are presented for two viscoelastic (lucite and phenolic polymer) materials, with the hollow region filled with water or air indicating how damping and change of the interior fluid inside the shell's hollow region affect the acoustic radiation force. The acoustic radiation force acting on cylindrical lucite shells immersed in a high density fluid (in this case mercury) and filled with water in their hollow region, is also studied.

Numerical simulation of velocity and temperature fields in natural circulation loop

NASA Astrophysics Data System (ADS)

Sukomel, L. A.; Kaban'kov, O. N.

2017-11-01

Low flow natural circulation regimes are realized in many practical applications and the existence of the reliable engineering and design calculation methods of flows driven exclusively by buoyancy forces is an actual problem. In particular it is important for the analysis of start up regimes of passive safety systems of nuclear power plants. In spite of a long year investigations of natural circulation loops no suitable predicting recommendations for heat transfer and friction for the above regimes have been proposed for engineering practice and correlations for forced flow are commonly used which considerably overpredicts the real flow velocities. The 2D numerical simulation of velocity and temperature fields in circular tubes for laminar flow natural circulation with reference to the laboratory experimental loop has been carried out. The results were compared with the 1D modified model and experimental data obtained on the above loop. The 1D modified model was still based on forced flow correlations, but in these correlations the physical properties variability and the existence of thermal and hydrodynamic entrance regions are taken into account. The comparison of 2D simulation, 1D model calculations and the experimental data showed that even subject to influence of liquid properties variability and entrance regions on heat transfer and friction the use of 1D model with forced flow correlations do not improve the accuracy of calculations. In general, according to 2D numerical simulation the wall shear stresses are mainly affected by the change of wall velocity gradient due to practically continuous velocity profiles deformation along the whole heated zone. The form of velocity profiles and the extent of their deformation in its turn depend upon the wall heat flux density and the hydraulic diameter.

Temperature of maximum density and excess thermodynamics of aqueous mixtures of methanol

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

González-Salgado, D.; Zemánková, K.; Noya, E. G.

In this work, we present a study of representative excess thermodynamic properties of aqueous mixtures of methanol over the complete concentration range, based on extensive computer simulation calculations. In addition to test various existing united atom model potentials, we have developed a new force-field which accurately reproduces the excess thermodynamics of this system. Moreover, we have paid particular attention to the behavior of the temperature of maximum density (TMD) in dilute methanol mixtures. The presence of a temperature of maximum density is one of the essential anomalies exhibited by water. This anomalous behavior is modified in a non-monotonous fashion bymore » the presence of fully miscible solutes that partly disrupt the hydrogen bond network of water, such as methanol (and other short chain alcohols). In order to obtain a better insight into the phenomenology of the changes in the TMD of water induced by small amounts of methanol, we have performed a new series of experimental measurements and computer simulations using various force fields. We observe that none of the force-fields tested capture the non-monotonous concentration dependence of the TMD for highly diluted methanol solutions.« less

Experimental and molecular dynamics simulation study of the sublimation energetics of cyclopentadienyltricarbonylmanganese (Cymantrene).

PubMed

Picciochi, Ricardo; Canongia Lopes, José N; Diogo, Hermínio P; Minas da Piedade, Manuel E

2008-10-16

The standard molar enthalpy of sublimation of monoclinic cyclopentadienyltricarbonylmanganese, Mn(eta (5)-C 5H 5)(CO) 3, at 298.15 K, was determined as Delta sub H m (o)[Mn(eta (5)-C 5H 5)(CO) 3] = 75.97 +/- 0.37 kJ x mol (-1) from Knudsen effusion and Calvet-drop microcalorimetry measurements, thus considerably improving the very large inaccuracy (>10 kJ x mol (-1)) of the published data. The obtained value was used to assess the extension of the OPLS-based all-atom force field we previously developed for iron metallocenes to manganese organometallic compounds. The modified force field was able to reproduce the volumetric properties (density and unit-cell volume) of crystalline Mn(eta (5)-C 5H 5)(CO) 3 with a deviation of 0.6% and the experimentally determined enthalpy of sublimation with an accuracy of 1 kJ x mol (-1). The interaction (epsilon) and atomic-diameter (sigma) parameters of the Lennard-Jones (12-6) potential function used to calculate dispersion contributions within the framework of the force field were found to be transferable from iron to manganese.

SOLAR MODULATION OF THE LOCAL INTERSTELLAR SPECTRUM WITH VOYAGER 1 , AMS-02, PAMELA , AND BESS

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

Corti, C.; Bindi, V.; Consolandi, C.

In recent years, the increasing precision of direct cosmic rays measurements opened the door to high-sensitivity indirect searches of dark matter and to more accurate predictions for radiation doses received by astronauts and electronics in space. The key ingredients in the study of these phenomena are the knowledge of the local interstellar spectrum (LIS) of galactic cosmic rays and the understanding of how the solar modulation affects the LIS inside the heliosphere. Voyager 1 , AMS-02, PAMELA , and BESS measurements of proton and helium fluxes provide valuable information, allowing us to shed light on the shape of the LISmore » and the details of the solar modulation during solar cycles 22-24. A new parametrization of the LIS is presented, based on the latest data from Voyager 1 and AMS-02. Using the framework of the force-field approximation, the solar modulation parameter is extracted from the time-dependent fluxes measured by PAMELA and BESS . A modified version of the force-field approximation with a rigidity-dependent modulation parameter is introduced, yielding better fits than the force-field approximation. The results are compared with the modulation parameter inferred by neutron monitors.« less

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

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

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Electrostatics of proteins in dielectric solvent continua. I. Newton's third law marries qE forces

NASA Astrophysics Data System (ADS)

Stork, Martina; Tavan, Paul

2007-04-01

The authors reformulate and revise an electrostatic theory treating proteins surrounded by dielectric solvent continua [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)] to make the resulting reaction field (RF) forces compatible with Newton's third law. Such a compatibility is required for their use in molecular dynamics (MD) simulations, in which the proteins are modeled by all-atom molecular mechanics force fields. According to the original theory the RF forces, which are due to the electric field generated by the solvent polarization and act on the partial charges of a protein, i.e., the so-called qE forces, can be quite accurately computed from Gaussian RF dipoles localized at the protein atoms. Using a slightly different approximation scheme also the RF energies of given protein configurations are obtained. However, because the qE forces do not account for the dielectric boundary pressure exerted by the solvent continuum on the protein, they do not obey the principle that actio equals reactio as required by Newton's third law. Therefore, their use in MD simulations is severely hampered. An analysis of the original theory has led the authors now to a reformulation removing the main difficulties. By considering the RF energy, which represents the dominant electrostatic contribution to the free energy of solvation for a given protein configuration, they show that its negative configurational gradient yields mean RF forces obeying the reactio principle. Because the evaluation of these mean forces is computationally much more demanding than that of the qE forces, they derive a suggestion how the qE forces can be modified to obey Newton's third law. Various properties of the thus established theory, particularly issues of accuracy and of computational efficiency, are discussed. A sample application to a MD simulation of a peptide in solution is described in the following paper [M. Stork and P. Tavan, J. Chem. Phys., 126, 165106 (2007).

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.

Tunneling magnetic force microscopy

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

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

PubMed Central

Siwy, Christopher M.

2017-01-01

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

EFFECTS OF A MODIFIED VITRECTOMY PROBE IN SMALL-GAUGE VITRECTOMY: An Experimental Study on the Flow and on the Traction Exerted on the Retina.

PubMed

Rizzo, Stanislao; Fantoni, Gualtiero; de Santis, Giovanni; Lue, Jaw-Chyng Lormen; Ciampi, Jonathan; Palla, Michele; Genovesi Ebert, Federica; Savastano, Alfonso; De Maria, Carmelo; Vozzi, Giovanni; Brant Fernandes, Rodrigo A; Faraldi, Francesco; Criscenti, Giuseppe

2017-09-01

Thorough this experimental study, the physic features of a modified 23-gauge vitrectomy probe were evaluated in vitro. A modified vitrectomy probe to increase vitreous outflow rate with a small-diameter probe, that also minimized tractional forces on the retina, was created and tested. The "new" probe was created by drilling an opening into the inner duct of a traditional 23-gauge probe with electrochemical or electrodischarge micromachining. Both vitreous outflow and tractional forces on the retina were examined using experimental models of vitreous surgery. The additional opening allowed the modified probe to have a cutting rate of 5,000 cuts per minute, while sustaining an outflow approximately 45% higher than in conventional 23-gauge probes. The modified probe performed two cutting actions per cycle, not one, as in standard probes. Because tractional force is influenced by cutting rate, retinal forces were 2.2 times lower than those observed with traditional cutters. The modified probe could be useful in vitreoretinal surgery. It allows for faster vitreous removal while minimizing tractional forces on the retina. Moreover, any available probe can be modified by creating a hole in the inner duct.

Repeated exposure to corticosterone increases depression-like behavior in two different versions of the forced swim test without altering nonspecific locomotor activity or muscle strength.

PubMed

Marks, Wendie; Fournier, Neil M; Kalynchuk, Lisa E

2009-08-04

We have recently shown that repeated high dose injections of corticosterone (CORT) reliably increase depression-like behavior on a modified one-day version of the forced swim test. The main purpose of this experiment was to compare the effect of these CORT injections on our one-day version of the forced swim test and the more traditional two-day version of the test. A second purpose was to determine whether altered behavior in the forced swim test could be due to nonspecific changes in locomotor activity or muscle strength. Separate groups of rats received a high dose CORT injection (40 mg/kg) or a vehicle injection once per day for 21 consecutive days. Then, half the rats from each group were exposed to the traditional two-day forced swim test and the other half were exposed to our one-day forced swim test. After the forced swim testing, all the rats were tested in an open field and in a wire suspension grip strength test. The CORT injections significantly increased the time spent immobile and decreased the time spent swimming in both versions of the forced swim test. However, they had no significant effect on activity in the open field or grip strength in the wire suspension test. These results show that repeated CORT injections increase depression-like behavior regardless of the specific parameters of forced swim testing, and that these effects are independent of changes in locomotor activity or muscle strength.

Centrifuges in gravitational physiology research

NASA Technical Reports Server (NTRS)

Ballard, Rodney W.; Davies, Phil; Fuller, Charles A.

1993-01-01

Data from space flight and ground based experiments have clearly demonstrated the importance of Earth gravity for normal physiological function in man and animals. Gravitational Physiology is concerned with the role and influence of gravity on physiological systems. Research in this field examines how we perceive and respond to gravity and the mechanisms underlying these responses. Inherent in our search for answers to these questions is the ability to alter gravity, which is not physically possible without leaving Earth. However, useful experimental paradigms have been to modify the perceived force of gravity by changing either the orientation of subjects to the gravity vector (i.e., postural changes) or by applying inertial forces to augment the magnitude of the gravity vector. The later technique has commonly been used by applying centripetal force via centrifugation.

A Novel Metal-Ferroelectric-Semiconductor Field-Effect Transistor Memory Cell Design

NASA Technical Reports Server (NTRS)

Phillips, Thomas A.; Bailey, Mark; Ho, Fat Duen

2004-01-01

The use of a Metal-Ferroelectric-Semiconductor Field-Effect Transistor (MFSFET) in a resistive-load SRAM memory cell has been investigated A typical two-transistor resistive-load SRAM memory cell architecture is modified by replacing one of the NMOS transistors with an n-channel MFSFET. The gate of the MFSFET is connected to a polling voltage pulse instead of the other NMOS transistor drain. The polling voltage pulses are of sufficient magnitude to saturate the ferroelectric gate material and force the MFSFET into a particular logic state. The memory cell circuit is further modified by the addition of a PMOS transistor and a load resistor in order to improve the retention characteristics of the memory cell. The retention characteristics of both the "1" and "0" logic states are simulated. The simulations show that the MFSFET memory cell design can maintain both the "1" and "0" logic states for a long period of time.

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.

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

PubMed Central

Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

2013-01-01

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 microseconds of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations. PMID:23477537

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

PubMed

Henriksen, Niel M; Roe, Daniel R; Cheatham, Thomas E

2013-04-18

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

On the synchrotron radiation reaction in external magnetic field

NASA Astrophysics Data System (ADS)

Tursunov, Arman; Kološ, Martin

2017-12-01

We study the dynamics of point electric charges undergoing radiation reaction force due to synchrotron radiation in the presence of external uniform magnetic field. The radiation reaction force cannot be neglected in many physical situations and its presence modifies the equations of motion significantly. The exact form of the equation of motion known as the Lorentz-Dirac equation contains higher order Schott term which leads to the appearance of the runaway solutions. We demonstrate effective computational ways to avoid such unphysical solutions and perform numerical integration of the dynamical equations. We show that in the ultrarelativistic case the Schott term is small and does not have considerable effect to the trajectory of a particle. We compare results with the covariant Landau-Lifshitz equation which is the first iteration of the Lorentz-Dirac equation. Even though the Landau-Lifshitz equation is thought to be approximative solution, we show that in realistic scenarios both approaches lead to identical results.

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Thermo-Electric-Magnetic Hydrodynamics in Solidification: In Situ Observations and Theory

NASA Astrophysics Data System (ADS)

Fautrelle, Y.; Wang, J.; Salloum-Abou-Jaoude, G.; Abou-Khalil, L.; Reinhart, G.; Li, X.; Ren, Z. M.; Nguyen-Thi, H.

2018-02-01

Solidification of liquid metals contains all the ingredients for the development of the thermo-electric (TE) effect, namely liquid-solid interface and temperature gradients. The combination of TE currents with a superimposed magnetic field gives rise to thermo-electromagnetic (TEM) volume forces acting on both liquid and solid. This results in the generation of fluid flows, which considerably modifies the morphology of the solidification front as well as that of the mushy zone. TEM forces also act on the solid and cause both fragmentation of dendrite branches and a movement of equiaxed grains in suspension. These phenomena have already been unveiled by post-mortem analysis of samples, but they can be analyzed in more detail by using x-ray in situ and real-time observations. Here, we present conclusive evidence of all the aforementioned effects thanks to in situ observations of Al-Cu alloy solidification under static magnetic field.

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

PubMed

Trevethan, Thomas; Shluger, Alexander

2009-07-01

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

Transferable Pseudo-Classical Electrons for Aufbau of Atomic Ions

PubMed Central

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith

2014-01-01

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species. PMID:24752384

Transferable pseudoclassical electrons for aufbau of atomic ions.

PubMed

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith

2014-06-05

Generalizing the LEWIS reactive force field from electron pairs to single electrons, we present LEWIS• in which explicit valence electrons interact with each other and with nuclear cores via pairwise interactions. The valence electrons are independently mobile particles, following classical equations of motion according to potentials modified from Coulombic as required to capture quantum characteristics. As proof of principle, the aufbau of atomic ions is described for diverse main group elements from the first three rows of the periodic table, using a single potential for interactions between electrons of like spin and another for electrons of unlike spin. The electrons of each spin are found to distribute themselves in a fashion akin to the major lobes of the hybrid atomic orbitals, suggesting a pointillist description of the electron density. The broader validity of the LEWIS• force field is illustrated by predicting the vibrational frequencies of diatomic and triatomic hydrogen species. Copyright © 2014 Wiley Periodicals, Inc.

Development of criteria for the use of asphalt-rubber as a Stress-Absorbing Membrane Interlayer (SAMI)

NASA Astrophysics Data System (ADS)

Newcomb, D. E.; McKeen, R. G.

1983-12-01

This report documents over 2 years of research efforts to characterize asphalt-rubber mixtures to be used in Stress-Absorbing Membrane Interlayers (SAMI). The purpose of these SAMIs is to retard or prevent reflection cracking in asphalt-concrete overlays. Several laboratory experiments and one field trial were conducted to define significant test methods and parameters for incorporation into construction design and specification documents. Test methods used in this study included a modified softening point test, force-ductility, and Schweyer viscosity. Variables investigated included (1) Laboratory-mixing temperature; (2) Rubber type; (3) Laboratory storage time; (4) Laboratory storage condition; (5) Laboratory batch replication; (6) Laboratory mixing time; (7) Field mixing time; (8) Laboratory test temperature; (9) Force-Ductility elongation rates; and (10) Asphalt grade. It was found that mixing temperature, mixing time, rubber type, and asphalt grade all have significant effects upon the behavior of asphalt-rubber mixtures. Significant variability was also noticed in different laboratory batch replications. Varying laboratory test temperature and force-ductility elongation rate revealed further differences in asphalt-rubber mixtures.

Plasma Component of Self-gravitating Disks and Relevant Magnetic Configurations

NASA Astrophysics Data System (ADS)

Bertin, G.; Coppi, B.

2006-04-01

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

The role of electro-osmosis and dielectrophoresis in collection of micro/nano size particles in low frequency AC electric field

NASA Astrophysics Data System (ADS)

Wei, Chehung; Hsu, Che-Wei; Wang, Ching-Chieh

2007-09-01

The collecting and sorting micro size particles by electric force is easy to integrate with other bioassays. There are many forms of electric forces such as electrophoresis, dielectrophoresis and electroosmosis which can be used to manipulate particles. In an attempt to understand the role of electroosmosis and dielectrophoresis in the collection of micro size particles, a small device made of two parallel plates is used to study the particle movement under AC electric field. The device is fabricated by a top electrode and a bottom electrode separated by a spacer. The top electrode is made from an ITO glass where the bottom electrode is made of Corning 1737 glass sputtered with chromium. A dielectric layer is fabricated by spin coating a thin photo-resist (0.5~1μm) on the bottom electrode and a spacer made of curing PDMS is utilized to separate these electrodes. A 900μm × 900μm collecting chamber is fabricated on the bottom electrode via photolithography. The amine-modified polystyrene fluorescent particles whose average size is 1 μm were used for collection experiments. Different frequency and power were applied to generate the non-uniform electric field. It was found that frequency is the critical factor for electroosmotic velocity. There seems to be an optimum frequency that leads to largest particle velocity. The underlying mechanism is believed to the competing forces among dielectrophoresis and electroosmosis. This device demonstrates that the electroosmosis force is suitable for collecting bio-particles in AC electric field.

Modified Mason number for charged paramagnetic colloidal suspensions

NASA Astrophysics Data System (ADS)

Du, Di; Hilou, Elaa; Biswal, Sibani Lisa

2016-06-01

The dynamics of magnetorheological fluids have typically been described by the Mason number, a governing parameter defined as the ratio between viscous and magnetic forces in the fluid. For most experimental suspensions of magnetic particles, surface forces, such as steric and electrostatic interactions, can significantly influence the dynamics. Here we propose a theory of a modified Mason number that accounts for surface forces and show that this modified Mason number is a function of interparticle distance. We demonstrate that this modified Mason number is accurate in describing the dynamics of a rotating pair of paramagnetic colloids of identical or mismatched sizes in either high or low salt solutions. The modified Mason number is confirmed to be pseudoconstant for particle pairs and particle chains undergoing a stable-metastable transition during rotation. The interparticle distance term can be calculated using theory or can be measured experimentally. This modified Mason number is more applicable to magnetorheological systems where surface forces are not negligible.

Effects of Traveling Magnetic Field on Dynamics of Solidification

NASA Technical Reports Server (NTRS)

2003-01-01

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

Experimental Study of Tool Wear and Grinding Forces During BK-7 Glass Micro-grinding with Modified PCD Tool

NASA Astrophysics Data System (ADS)

Pratap, A.; Sahoo, P.; Patra, K.; Dyakonov, A. A.

2017-09-01

This study focuses on the improvement in grinding performance of BK-7 glass using polycrystalline diamond micro-tool. Micro-tools are modified using wire EDM and performance of modified tools is compared with that of as received tool. Tool wear of different types of tools are observed. To quantify the tool wear, a method based on weight loss of tool is introduced in this study. Modified tools significantly reduce tool wear in comparison to the normal tool. Grinding forces increase with machining time due to tool wear. However, modified tools produce lesser forces thus can improve life of the PCD micro-grinding tool.

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

NASA Astrophysics Data System (ADS)

Wu, Xiangyang

1999-07-01

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

Optically controlled electrophoresis with a photoconductive substrate

NASA Astrophysics Data System (ADS)

Inami, Wataru; Nagashima, Taiki; Kawata, Yoshimasa

2018-05-01

A photoconductive substrate is used to perform electrophoresis. Light-induced micro-particle flow manipulation is demonstrated without using a fabricated flow channel. The path along which the particles were moved was formed by an illuminated light pattern on the substrate. Because the substrate conductivity and electric field distribution can be modified by light illumination, the forces acting on the particles can be controlled. This technique has potential applications as a high functionality analytical device.

New cellular automaton model for magnetohydrodynamics

NASA Technical Reports Server (NTRS)

Chen, Hudong; Matthaeus, William H.

1987-01-01

A new type of two-dimensional cellular automation method is introduced for computation of magnetohydrodynamic fluid systems. Particle population is described by a 36-component tensor referred to a hexagonal lattice. By appropriate choice of the coefficients that control the modified streaming algorithm and the definition of the macroscopic fields, it is possible to compute both Lorentz-force and magnetic-induction effects. The method is local in the microscopic space and therefore suited to massively parallel computations.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

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

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

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

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

Effect of chromium picolinate on modified forced swimming test in diabetic rats: involvement of serotonergic pathways and potassium channels.

PubMed

Khanam, Razia; Pillai, K K

2006-02-01

Depression occurs frequently in patients with diabetes mellitus. Chromium picolinate, an essential trace element is recommended for diabetes and also has been reported to benefit depression, but its mechanism is still debated. To investigate the mechanism, we studied its effects on serum insulin, serum glucose and on modified forced swimming test, a behavioural paradigm for depression in rats. The study involving co-administration of sub-active doses of glimepiride, a K(+) channel blocker and chromium picolinate on blood glucose levels and modified forced swimming test was also performed to probe any role of K(+) channels in its antidiabetic and antidepressants effects. Streptozotocin (55 mg/kg, intraperitoneally) was injected in rats to induce diabetes (Type 1). After a week, chromium picolinate (8 microg/ml in drinking water) was administered for 4 weeks. Normal rats received similar drug treatment. The sub-active doses of chromium picolinate (4 microg/ml in drinking water) and glimeperide (2.5 mg/kg, orally) were co-administered and their effects on modified forced swimming test and on glucose levels were measured. Chromium picolinate (8 microg/ml in drinking water) produced hypoglycaemia in diabetic and normal rats. It had no effects on the streptozotocin-induced reduction in insulin levels. Chromium picolinate (8 microg/ml in drinking water) increased swimming with subsequent decrease in immobility. The sub-active doses of chromium picolinate and glimeperide showed significant additive effects in modified forced swimming test and reduction in serum glucose concentrations, though statistically insignificant. In conclusion chromium picolinate shows antidepressant action on modified forced swimming test affecting only swimming that suggests serotonergic pathways involvement. The additive effects on swimming in modified forced swimming test and reduction in serum glucose levels shows involvement of K(+) channels in antidiabetic and antidepressant actions of chromium picolinate.

Dynamical properties of nematic liquid crystals subjected to shear flow and magnetic fields: tumbling instability and nonequilibrium fluctuations.

PubMed

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2013-07-01

We investigate the dynamical properties of monodomain nematic liquid crystals under shear flow and magnetic fields on the basis of the Ericksen-Leslie theory. Stable and unstable states appear depending on the magnetic field and the shear rate. The trajectory of the unstable state shows tumbling motion. The phase diagram of these states is plotted as a function of the three components of the magnetic field at a constant shear rate. The phase diagram changes depending on the viscous properties of different types of nematic liquid crystals. In this nonequilibrium steady state, we calculate the correlation function of director fluctuations and the response function, and discuss the nonequilibrium fluctuations and the modified fluctuation-dissipation relation in connection with nonconservative forces due to shear flow.

Chiral magnetic effect in the presence of electroweak interactions as a quasiclassical phenomenon

NASA Astrophysics Data System (ADS)

Dvornikov, Maxim; Semikoz, Victor B.

2018-03-01

We elaborate the quasiclassical approach to obtain the modified chiral magnetic effect (CME) in the case when the massless charged fermions interact with electromagnetic fields and the background matter by the electroweak forces. The derivation of the anomalous current along the external magnetic field involves the study of the energy density evolution of chiral particles in parallel electric and magnetic fields. We consider both the particle acceleration by the external electric field and the contribution of the Adler anomaly. The condition of the validity of this method for the derivation of the CME is formulated. We obtain the expression for the electric current along the external magnetic field, which appears to coincide with our previous results based on the purely quantum approach. Our results are compared with the findings of other authors.

Atomic force measurements of 16-mercaptohexadecanoic acid and its salt with CH 3, OH, and CONHCH 3 functionalized self-assembled monolayers

NASA Astrophysics Data System (ADS)

Morales-Cruz, Angel L.; Tremont, Rolando; Martínez, Ramón; Romañach, Rodolfo; Cabrera, Carlos R.

2005-03-01

Chemical and mechanical properties of different compounds can be elucidated by measuring fundamental forces such as adhesion, attraction and repulsion, between modified surfaces by means of atomic force microscopy (AFM) in force mode calibration. This work presents a combination of AFM, self-assembled monolayers (SAMs), and crystallization techniques to study the forces of interaction between excipients and active ingredients used in pharmaceutical formulations. SAMs of 16-mercaptohexadecanoate, which represent magnesium stereate, were used to modify the probe tip, whereas CH3-, OH- and CONHCH3-functional SAMs were formed on a gold-coated mica substrate, and used as examples of the surfaces of lactose and theophylline. The crystals of lactose and theophylline were characterized by scanning electron microscopy (SEM) and X-ray diffraction (XRD). The modification of gold surfaces with 16-mercaptohexadecanoate, 10-mercapto-1-decanol (OH-functional SAM), 1-decanethiol (CH3-functional) and N-methyl-11-mercaptoundecanamide (CONHCH3-functional SAM) was studied by X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and Fourier transform-infrared spectroscopy (FT-IR) in specular reflectance mode. XPS and AES results of the modified surfaces showed the presence of sulfur binding, and kinetic energies that correspond to the presence of 10-mercapto-1-decanol, 1-decanethiol, N-methyl-11-mercaptoundecanamide and the salt of 16-mercaptohexadecanoic acid. The absorption bands in the IR spectra further confirm the modification of the gold-coated substrates with these compounds. Force versus distance measurements were performed between the modified tip and the modified gold-coated mica substrates. The mean adhesion forces between the COO-Ca2+ functionalized tip and the CH3-, OH-, and CONHCH3-modified substrates were determined to be 4.5, 8.9 and 6.3 nN, respectively. The magnitude of the adhesion force (ion-dipole) interaction between the modified tip and substrate decreases in the following order: COO-Ca2+/OH > COO-Ca2+/CONHCH3 > COO-Ca2+/CH3.

Nonlinear resonance of the rotating circular plate under static loads in magnetic field

NASA Astrophysics Data System (ADS)

Hu, Yuda; Wang, Tong

2015-11-01

The rotating circular plate is widely used in mechanical engineering, meanwhile the plates are often in the electromagnetic field in modern industry with complex loads. In order to study the resonance of a rotating circular plate under static loads in magnetic field, the nonlinear vibration equation about the spinning circular plate is derived according to Hamilton principle. The algebraic expression of the initial deflection and the magneto elastic forced disturbance differential equation are obtained through the application of Galerkin integral method. By mean of modified Multiple scale method, the strongly nonlinear amplitude-frequency response equation in steady state is established. The amplitude frequency characteristic curve and the relationship curve of amplitude changing with the static loads and the excitation force of the plate are obtained according to the numerical calculation. The influence of magnetic induction intensity, the speed of rotation and the static loads on the amplitude and the nonlinear characteristics of the spinning plate are analyzed. The proposed research provides the theory reference for the research of nonlinear resonance of rotating plates in engineering.

General virial theorem for modified-gravity MOND

NASA Astrophysics Data System (ADS)

Milgrom, Mordehai

2014-01-01

An important and useful relation is known to hold in two specific MOND theories. It pertains to low-acceleration, isolated systems of pointlike masses, mp, at positions rp, subject to gravitational forces Fp. It reads ∑prp·Fp=-(2/3)(Ga0)1/2 [(∑pmp)3/2-∑p mp3/2]; a0 is the MOND acceleration constant. Here I show that this relation holds in the nonrelativistic limit of any modified-gravity MOND theory. It follows from only the basic tenets of MOND, which include departure from standard dynamics at accelerations below a0, and space-time scale invariance in the nonrelativistic, low-acceleration limit. This implies space-dilatation invariance of the static, gravitational-field equations, which, in turn, leads to the above point-mass virial relation. Thus, the various MOND predictions and tests based on this relation hold in any modified-gravity MOND theory. Since we do not know that any of the existing MOND theories point in the right direction, it is important to identify such predictions that hold in a much larger class of theories. Among these predictions are the MOND two-body force for arbitrary masses, and a general mass-velocity-dispersion relation of the form σ2=(2/3)(MGa0)1/2[1-∑p(mp/M)3/2], where M = ∑p mp.

Concurrent Validity of a Portable Force Plate Using Vertical Jump Force-Time Characteristics.

PubMed

Lake, Jason; Mundy, Peter; Comfort, Paul; McMahon, John J; Suchomel, Timothy J; Carden, Patrick

2018-05-29

This study examined concurrent validity of countermovement vertical jump (CMJ) reactive strength index modified and force-time characteristics recorded using a one dimensional portable and laboratory force plate system. Twenty-eight men performed bilateral CMJs on two portable force plates placed on top of two in-ground force plates, both recording vertical ground reaction force at 1000 Hz. Time to take-off, jump height, reactive strength index modified, braking and propulsion impulse, mean net force, and duration were calculated from the vertical force from both force plate systems. Results from both systems were highly correlated (r≥.99). There were small (d<.12) but significant differences between their respective braking impulse, braking mean net force, propulsion impulse, and propulsion mean net force (p<.001). However, limits of agreement yielded a mean value of 1.7% relative to the laboratory force plate system (95% CL: .9% to 2.5%), indicating very good agreement across all of the dependent variables. The largest limits of agreement belonged to jump height (2.1%), time to take-off (3.4%), and reactive strength index modified (3.8%). The portable force plate system provides a valid method of obtaining reactive strength measures, and several underpinning force-time variables, from unloaded CMJ and practitioners can use both force plates interchangeably.

Laboratory study of low-β forces in arched, line-tied magnetic flux ropes

NASA Astrophysics Data System (ADS)

Myers, C. E.; Yamada, M.; Ji, H.; Yoo, J.; Jara-Almonte, J.; Fox, W.

2016-11-01

The loss-of-equilibrium is a solar eruption mechanism whereby a sudden breakdown of the magnetohydrodynamic force balance in the Sun's corona ejects a massive burst of particles and energy into the heliosphere. Predicting a loss-of-equilibrium, which has more recently been formulated as the torus instability, relies on a detailed understanding of the various forces that hold the pre-eruption magnetic flux rope in equilibrium. Traditionally, idealized analytical force expressions are used to derive simplified eruption criteria that can be compared to solar observations and modeling. What is missing, however, is a validation that these idealized analytical force expressions can be applied to the line-tied, low-aspect-ratio conditions of the corona. In this paper, we address this shortcoming by using a laboratory experiment to study the forces that act on long-lived, arched, line-tied magnetic flux ropes. Three key force terms are evaluated over a wide range of experimental conditions: (1) the upward hoop force; (2) the downward strapping force; and (3) the downward toroidal field tension force. First, the laboratory force measurements show that, on average, the three aforementioned force terms cancel to produce a balanced line-tied equilibrium. This finding validates the laboratory force measurement techniques developed here, which were recently used to identify a dynamic toroidal field tension force that can prevent flux rope eruptions [Myers et al., Nature 528, 526 (2015)]. The verification of magnetic force balance also confirms the low-β assumption that the plasma thermal pressure is negligible in these experiments. Next, the measured force terms are directly compared to corresponding analytical expressions. While the measured and analytical forces are found to be well correlated, the low-aspect-ratio, line-tied conditions in the experiment are found to both reduce the measured hoop force and increase the measured tension force with respect to analytical expectations. These two co-directed effects combine to generate laboratory flux rope equilibria at lower altitudes than are predicted analytically. Such considerations are expected to modify the loss-of-equilibrium eruption criteria for analogous flux ropes in the solar corona.

Laboratory study of low- β forces in arched, line-tied magnetic flux ropes

DOE PAGES

Myers, C. E.; Yamada, M.; Ji, H.; ...

2016-11-04

Here, the loss-of-equilibrium is a solar eruption mechanism whereby a sudden breakdown of the magnetohydrodynamic force balance in the Sun's corona ejects a massive burst of particles and energy into the heliosphere. Predicting a loss-of-equilibrium, which has more recently been formulated as the torus instability, relies on a detailed understanding of the various forces that hold the pre-eruption magnetic flux rope in equilibrium. Traditionally, idealized analytical force expressions are used to derive simplified eruption criteria that can be compared to solar observations and modeling. What is missing, however, is a validation that these idealized analytical force expressions can be appliedmore » to the line-tied, low-aspect-ratio conditions of the corona. In this paper, we address this shortcoming by using a laboratory experiment to study the forces that act on long-lived, arched, line-tied magnetic flux ropes. Three key force terms are evaluated over a wide range of experimental conditions: (1) the upward hoop force; (2) the downward strapping force; and (3) the downward toroidal field tension force. First, the laboratory force measurements show that, on average, the three aforementioned force terms cancel to produce a balanced line-tied equilibrium. This finding validates the laboratory force measurement techniques developed here, which were recently used to identify a dynamic toroidal field tension force that can prevent flux rope eruption. The verification of magnetic force balance also confirms the low-beta assumption that the plasma thermal pressure is negligible in these experiments. Next, the measured force terms are directly compared to corresponding analytical expressions. While the measured and analytical forces are found to be well correlated, the low-aspect-ratio, line-tied conditions in the experiment are found to both reduce the measured hoop force and increase the measured tension force with respect to analytical expectations. These two co-directed effects combine to generate laboratory flux rope equilibria at lower altitudes than are predicted analytically. Such considerations are expected to modify the loss-of-equilibrium eruption criteria for analogous flux ropes in the solar corona.« less

Laboratory study of low- β forces in arched, line-tied magnetic flux ropes

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

Myers, C. E.; Yamada, M.; Ji, H.

Here, the loss-of-equilibrium is a solar eruption mechanism whereby a sudden breakdown of the magnetohydrodynamic force balance in the Sun's corona ejects a massive burst of particles and energy into the heliosphere. Predicting a loss-of-equilibrium, which has more recently been formulated as the torus instability, relies on a detailed understanding of the various forces that hold the pre-eruption magnetic flux rope in equilibrium. Traditionally, idealized analytical force expressions are used to derive simplified eruption criteria that can be compared to solar observations and modeling. What is missing, however, is a validation that these idealized analytical force expressions can be appliedmore » to the line-tied, low-aspect-ratio conditions of the corona. In this paper, we address this shortcoming by using a laboratory experiment to study the forces that act on long-lived, arched, line-tied magnetic flux ropes. Three key force terms are evaluated over a wide range of experimental conditions: (1) the upward hoop force; (2) the downward strapping force; and (3) the downward toroidal field tension force. First, the laboratory force measurements show that, on average, the three aforementioned force terms cancel to produce a balanced line-tied equilibrium. This finding validates the laboratory force measurement techniques developed here, which were recently used to identify a dynamic toroidal field tension force that can prevent flux rope eruption. The verification of magnetic force balance also confirms the low-beta assumption that the plasma thermal pressure is negligible in these experiments. Next, the measured force terms are directly compared to corresponding analytical expressions. While the measured and analytical forces are found to be well correlated, the low-aspect-ratio, line-tied conditions in the experiment are found to both reduce the measured hoop force and increase the measured tension force with respect to analytical expectations. These two co-directed effects combine to generate laboratory flux rope equilibria at lower altitudes than are predicted analytically. Such considerations are expected to modify the loss-of-equilibrium eruption criteria for analogous flux ropes in the solar corona.« less

KSC-07pd2044

NASA Image and Video Library

2007-07-03

OFFUTT FIELD, NEB. -- The shuttle carrier aircraft, or SCA, and its piggyback passenger Atlantis are captured in the light of a full moon after landing at Offutt Field on the ferry flight from California to Florida. Atlantis landed at Edwards Air Force Base in California to end mission STS-117. Touchdown was at 8:27 a.m. EDT. The SCA is a modified Boeing 747 jetliner. The return to KSC began July 1 and took three days after stops across the country for fuel. The last stop was at Ft. Campbell in Kentucky. Weather conditions over the last leg postponed the return trip until July 3. Photo credit: NASA/Casey Wood

Statistical field theory with constraints: Application to critical Casimir forces in the canonical ensemble.

PubMed

Gross, Markus; Gambassi, Andrea; Dietrich, S

2017-08-01

The effect of imposing a constraint on a fluctuating scalar order parameter field in a system of finite volume is studied within statistical field theory. The canonical ensemble, corresponding to a fixed total integrated order parameter (e.g., the total number of particles), is obtained as a special case of the theory. A perturbative expansion is developed which allows one to systematically determine the constraint-induced finite-volume corrections to the free energy and to correlation functions. In particular, we focus on the Landau-Ginzburg model in a film geometry (i.e., in a rectangular parallelepiped with a small aspect ratio) with periodic, Dirichlet, or Neumann boundary conditions in the transverse direction and periodic boundary conditions in the remaining, lateral directions. Within the expansion in terms of ε=4-d, where d is the spatial dimension of the bulk, the finite-size contribution to the free energy of the confined system and the associated critical Casimir force are calculated to leading order in ε and are compared to the corresponding expressions for an unconstrained (grand canonical) system. The constraint restricts the fluctuations within the system and it accordingly modifies the residual finite-size free energy. The resulting critical Casimir force is shown to depend on whether it is defined by assuming a fixed transverse area or a fixed total volume. In the former case, the constraint is typically found to significantly enhance the attractive character of the force as compared to the grand canonical case. In contrast to the grand canonical Casimir force, which, for supercritical temperatures, vanishes in the limit of thick films, in the canonical case with fixed transverse area the critical Casimir force attains for thick films a negative value for all boundary conditions studied here. Typically, the dependence of the critical Casimir force both on the temperaturelike and on the fieldlike scaling variables is different in the two ensembles.

Statistical field theory with constraints: Application to critical Casimir forces in the canonical ensemble

NASA Astrophysics Data System (ADS)

Gross, Markus; Gambassi, Andrea; Dietrich, S.

2017-08-01

The effect of imposing a constraint on a fluctuating scalar order parameter field in a system of finite volume is studied within statistical field theory. The canonical ensemble, corresponding to a fixed total integrated order parameter (e.g., the total number of particles), is obtained as a special case of the theory. A perturbative expansion is developed which allows one to systematically determine the constraint-induced finite-volume corrections to the free energy and to correlation functions. In particular, we focus on the Landau-Ginzburg model in a film geometry (i.e., in a rectangular parallelepiped with a small aspect ratio) with periodic, Dirichlet, or Neumann boundary conditions in the transverse direction and periodic boundary conditions in the remaining, lateral directions. Within the expansion in terms of ɛ =4 -d , where d is the spatial dimension of the bulk, the finite-size contribution to the free energy of the confined system and the associated critical Casimir force are calculated to leading order in ɛ and are compared to the corresponding expressions for an unconstrained (grand canonical) system. The constraint restricts the fluctuations within the system and it accordingly modifies the residual finite-size free energy. The resulting critical Casimir force is shown to depend on whether it is defined by assuming a fixed transverse area or a fixed total volume. In the former case, the constraint is typically found to significantly enhance the attractive character of the force as compared to the grand canonical case. In contrast to the grand canonical Casimir force, which, for supercritical temperatures, vanishes in the limit of thick films, in the canonical case with fixed transverse area the critical Casimir force attains for thick films a negative value for all boundary conditions studied here. Typically, the dependence of the critical Casimir force both on the temperaturelike and on the fieldlike scaling variables is different in the two ensembles.

Tomography of a Probe Potential Using Atomic Sensors on Graphene.

PubMed

Wyrick, Jonathan; Natterer, Fabian D; Zhao, Yue; Watanabe, Kenji; Taniguchi, Takashi; Cullen, William G; Zhitenev, Nikolai B; Stroscio, Joseph A

2016-12-27

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2016-06-01

The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein-protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density Nbulk; and relative solvent molecular density g. For a molecular solute, 4πr2p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss's law of Maxwell's equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

The battalion medical platoon: a flawed scalpel.

PubMed

Cannon, M W; Stoute, J A

1992-08-01

This article discusses the current organization and doctrine for a medical platoon in an armour-heavy task force in light of experience gained in Operations Desert Shield and Desert Storm. The organization of and doctrine for the use of the platoon is covered first. This is followed by a discussion of how doctrine was modified based on field exercises, and projected, and actual, combat operations. It concludes with a presentation of lessons learned and recommendations for changes.

Transformation optics beyond the manipulation of light trajectories.

PubMed

Ginis, Vincent; Tassin, Philippe

2015-08-28

Since its inception in 2006, transformation optics has become an established tool to understand and design electromagnetic systems. It provides a geometrical perspective into the properties of light waves without the need for a ray approximation. Most studies have focused on modifying the trajectories of light rays, e.g. beam benders, lenses, invisibility cloaks, etc. In this contribution, we explore transformation optics beyond the manipulation of light trajectories. With a few well-chosen examples, we demonstrate that transformation optics can be used to manipulate electromagnetic fields up to an unprecedented level. In the first example, we introduce an electromagnetic cavity that allows for deep subwavelength confinement of light. The cavity is designed with transformation optics even though the concept of trajectory ceases to have any meaning in a structure as small as this cavity. In the second example, we show that the properties of Cherenkov light emitted in a transformation-optical material can be understood and modified from simple geometric considerations. Finally, we show that optical forces--a quadratic function of the fields--follow the rules of transformation optics too. By applying a folded coordinate transformation to a pair of waveguides, optical forces can be enhanced just as if the waveguides were closer together. With these examples, we open up an entirely new spectrum of devices that can be conceived using transformation optics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Influence of Idealized Heterogeneity on Wet and Dry Planetary Boundary Layers Coupled to the Land Surface. 1; Instantaneous Fields and Statistics

NASA Technical Reports Server (NTRS)

Houser, Paul (Technical Monitor); Patton, Edward G.; Sullivan, Peter P.; Moeng, Chin-Hoh

2003-01-01

This is the first in a two-part series of manuscripts describing numerical experiments on the influence of 2-30 km striplike heterogeneity on wet and dry boundary layers coupled to the land surface. The strip-like heterogeneity is shown to dramatically alter the structure of the free-convective boundary layer by inducing significant organized circulations that modify turbulent statistics. The coupling with the land-surface modifies the circulations compared to previous studies using fixed surface forcing. Total boundary layer turbulence kinetic energy increases significantly for surface heterogeneity at scales between Lambda/z(sub i) = 4 and 9, however entrainment rates for all cases are largely unaffected by the strip-like heterogeneity.

A diagnostic approach to obtaining planetary boundary layer winds using satellite-derived thermal data

NASA Technical Reports Server (NTRS)

Belt, Carol L.; Fuelberg, Henry E.

1984-01-01

The feasibility of using satellite derived thermal data to generate realistic synoptic scale winds within the planetary boundary layer (PBL) is examined. Diagnostic modified Ekman wind equations from the Air Force Global Weather Central (AFGWC) Boundary Layer Model are used to compute winds at seven levels within the PBL transition layer (50 m to 1600 m AGL). Satellite derived winds based on 62 predawn TIROS-N soundings are compared to similarly derived wind fields based on 39 AVE-SESAME II rawinsonde (RAOB) soundings taken 2 h later. Actual wind fields are also used as a basis for comparison. Qualitative and statistical comparisons show that the Ekman winds from both sources are in very close agreement, with an average vector correlation coefficient of 0.815. Best results are obtained at 300 m AGL. Satellite winds tend to be slightly weaker than their RAOB counterparts and exhibit a greater degree of cross-isobaric flow. The modified Ekman winds show a significant improvement over geostrophic values at levels nearest the surface.

Theoretical approach to oxygen atom degradation of silver

NASA Technical Reports Server (NTRS)

Fromhold, Albert T., Jr.; Noh, Seung; Beshears, Ronald; Whitaker, Ann F.; Little, Sally A.

1987-01-01

Based on available Rutherford backscattering spectrometry (RBS), proton induced X-ray emission (PIXE) and ellipsometry data obtained on silver specimens subjected to atomic oxygen attack in low Earth orbit STS flight 41-G, a theory was developed to model the oxygen atom degradation of silver. The diffusion of atomic oxygen in a microscopically nonuniform medium is an essential constituent of the theory. The driving force for diffusion is the macroscopic electrochemical potential gradient developed between the specimen surface exposed to the ambient and the bulk of the silver specimen. The longitudinal electric effect developed parallel to the gradient is modified by space charge of the diffusing charged species. Lateral electric fields and concentration differences also exist due to the nonuniform nature of the medium. The lateral concentration differences are found to be more important than the lateral electric fields in modifying the diffusion rate. The model was evaluated numerically. Qualitative agreement exists between the kinetics predicted by the theory and kinetic data taken in ground-based experiments utilizing a plasma asher.

Electroosmosis modulated biomechanical transport through asymmetric microfluidics channel

NASA Astrophysics Data System (ADS)

Jhorar, R.; Tripathi, D.; Bhatti, M. M.; Ellahi, R.

2018-05-01

This article addresses the electrokinetically modulated biomechanical transport through a two-dimensional asymmetric microchannel induced by peristaltic waves. Electrokinetic transport with peristaltic phenomena grabbed a significant attention due to its novel applications in engineering. Electrical fields also provide an excellent mode for regulating flows. The electrohydrodynamics problem is modified by means of Debye-Hückel linearization. Firstly, the governing flow problem is described by continuity and momentum equations in the presence of electrokinetic forces in Cartesian coordinates, then long wavelength and low/zero Reynolds ("neglecting the inertial forces") approximations are applied to modify the governing flow problem. The resulting differential equations are solved analytically in order to obtain exact solutions for velocity profile whereas the numerical integration is carried out to analyze the pumping characteristics. The physical behaviour of sundry parameters is discussed for velocity profile, pressure rise and volume flow rate. In particular, the behaviour of electro-osmotic parameter, phase difference, and Helmholtz-Smoluchowski velocity is examined and discussed. The trapping mechanism is also visualized by drawing streamlines against the governing parameters. The present study offers various interesting results that warrant further study on electrokinetic transport with peristalsis.

Self-organization processes in polysiloxane block copolymers, initiated by modifying fullerene additives

NASA Astrophysics Data System (ADS)

Voznyakovskii, A. P.; Kudoyarova, V. Kh.; Kudoyarov, M. F.; Patrova, M. Ya.

2017-08-01

Thin films of a polyblock polysiloxane copolymer and their composites with a modifying fullerene C60 additive are studied by atomic force microscopy, Rutherford backscattering, and neutron scattering. The data of atomic force microscopy show that with the addition of fullerene to the bulk of the polymer matrix, the initial relief of the film surface is leveled more, the larger the additive. This trend is associated with the processes of self-organization of rigid block sequences, which are initiated by the field effect of the surface of fullerene aggregates and lead to an increase in the number of their domains in the bulk of the polymer matrix. The data of Rutherford backscattering and neutron scattering indicate the formation of additional structures with a radius of 60 nm only in films containing fullerene, and their fraction increases with increasing fullerene concentration. A comparative analysis of the data of these methods has shown that such structures are, namely, the domains of a rigid block and are not formed by individual fullerene aggregates. The interrelation of the structure and mechanical properties of polymer films is considered.

A comparative work on vibration control of a quarter car suspension system with two different magneto-rheological dampers

NASA Astrophysics Data System (ADS)

Park, Jhin Ha; Kim, Wan Ho; Shin, Cheol Soo; Choi, Seung-Bok

2017-01-01

This work compares the ride comfort of a passenger vehicle whose suspension system is equipped with two different magneto-rheological (MR) dampers: with and without bypass holes in the piston. In order to achieve this goal, two cylindrical type MR dampers, which otherwise have the same such geometrical dimensions as radius of piston, length of pole and distance between two poles, are designed based on a mathematical model and subsequently manufactured. One of MR dampers is then modified by making bypass holes in the piston bobbin structure to obtain a relatively low slope of damping force in the pre-yield region. The field-dependent damping force characteristics are investigated through both simulation and experiment. After characterizing the field-dependent damping force of the two MR dampers, a quarter car model is established to evaluate the ride comfort. In this work, a simple but very effective sky-hook controller is adopted, and vibration control performance is evaluated under two road profiles: bump and random road excitations. It is demonstrated through simulation and experiment that the MR damper with bypass holes provides better ride comfort to the car so equipped than that without.

Accurate force field for molybdenum by machine learning large materials data

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

A corrected model for static and dynamic electromechanical instability of narrow nanotweezers: Incorporation of size effect, surface layer and finite dimensions

NASA Astrophysics Data System (ADS)

Koochi, Ali; Hosseini-Toudeshky, Hossein; Abadyan, Mohamadreza

2018-03-01

Herein, a corrected theoretical model is proposed for modeling the static and dynamic behavior of electrostatically actuated narrow-width nanotweezers considering the correction due to finite dimensions, size dependency and surface energy. The Gurtin-Murdoch surface elasticity in conjunction with the modified couple stress theory is employed to consider the coupling effect of surface stresses and size phenomenon. In addition, the model accounts for the external force corrections by incorporating the impact of narrow width on the distribution of Casimir attraction, van der Waals (vdW) force and the fringing field effect. The proposed model is beneficial for the precise modeling of the narrow nanotweezers in nano-scale.

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Interaction and dynamics of ionic liquids based on choline and amino acid anions

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

Campetella, M.; Bodo, E., E-mail: enrico.bodo@uniroma1.it; Caminiti, R., E-mail: ruggero.caminiti@uniroma1.it

2015-06-21

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial inmore » establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.« less

Interaction and dynamics of ionic liquids based on choline and amino acid anions

NASA Astrophysics Data System (ADS)

Campetella, M.; Bodo, E.; Caminiti, R.; Martino, A.; D'Apuzzo, F.; Lupi, S.; Gontrani, L.

2015-06-01

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial in establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.

About improving efficiency of the P3 M algorithms when computing the inter-particle forces in beam dynamics

NASA Astrophysics Data System (ADS)

Kozynchenko, Alexander I.; Kozynchenko, Sergey A.

2017-03-01

In the paper, a problem of improving efficiency of the particle-particle- particle-mesh (P3M) algorithm in computing the inter-particle electrostatic forces is considered. The particle-mesh (PM) part of the algorithm is modified in such a way that the space field equation is solved by the direct method of summation of potentials over the ensemble of particles lying not too close to a reference particle. For this purpose, a specific matrix "pattern" is introduced to describe the spatial field distribution of a single point charge, so the "pattern" contains pre-calculated potential values. This approach allows to reduce a set of arithmetic operations performed at the innermost of nested loops down to an addition and assignment operators and, therefore, to decrease the running time substantially. The simulation model developed in C++ substantiates this view, showing the descent accuracy acceptable in particle beam calculations together with the improved speed performance.

Performance Improvement of Diagonal Type MHD Generator by Modification of PTO Electrode Configuration

NASA Astrophysics Data System (ADS)

Takahashi, Toru; Fujino, Takayasu; Ishikawa, Motoo

Time dependent three-dimensional numerical analysis is carried out in order to clarify causes of voltage loss occurring near power takeoff regions and to suggest how to reduce the voltage loss for the scramjet engine driven MHD generator which was developed under the hypersonic vehicle electric power system program in USA. The numerical results under the experimental condition show that the local positive electric field is induced near the power takeoff electrodes. The phenomenon is due to the electric field loss by the high electric current through the weakly ionized plasma with low temperature and also by the low electromotive force near the power takeoff electrodes. When the configuration of power takeoff electrodes is modified, the current density near the power takeoff electrodes becomes small and the electromotive force becomes strong. The electric power output under the optimum electrode configuration of power takeoff is improved by 22 percent, compared with the value under the experimental condition.

Surface Modulation of Graphene Field Effect Transistors on Periodic Trench Structure.

PubMed

Jin, Jun Eon; Choi, Jun Hee; Yun, Hoyeol; Jang, Ho-Kyun; Lee, Byung Chul; Choi, Ajeong; Joo, Min-Kyu; Dettlaff-Weglikowska, Urszula; Roth, Siegmar; Lee, Sang Wook; Lee, Jae Woo; Kim, Gyu Tae

2016-07-20

In this work, graphene field effect transistors (FETs) were fabricated on a trench structure made by carbonized poly(methylmethacrylate) to modify the graphene surface. The trench-structured devices showed different characteristics depending on the channel orientation and the pitch size of the trenches as well as channel area in the FETs. Periodic corrugations and barriers of suspended graphene on the trench structure were measured by atomic force microscopy and electrostatic force microscopy. Regular barriers of 160 mV were observed for the trench structure with graphene. To confirm the transfer mechanism in the FETs depending on the channel orientation, the ratio of experimental mobility (3.6-3.74) was extracted from the current-voltage characteristics using equivalent circuit simulation. It is shown that the number of barriers increases as the pitch size decreases because the number of corrugations increases from different trench pitches. The noise for the 140 nm pitch trench is 1 order of magnitude higher than that for the 200 nm pitch trench.

Single ricin detection by atomic force microscopy chemomechanical mapping

NASA Astrophysics Data System (ADS)

Chen, Guojun; Zhou, Jianfeng; Park, Bosoon; Xu, Bingqian

2009-07-01

The authors report on a study of detecting ricin molecules immobilized on chemically modified Au (111) surface by chemomechanically mapping the molecular interactions with a chemically modified atomic force microscopy (AFM) tip. AFM images resolved the different fold-up conformations of single ricin molecule as well as their intramolecule structure of A- and B-chains. AFM force spectroscopy study of the interaction indicates that the unbinding force has a linear relation with the logarithmic force loading rate, which agrees well with calculations using one-barrier bond dissociation model.

Multiscale Modeling of Non-crystalline Ceramics (Glass)

DTIC Science & Technology

2011-02-01

4). 5.3 Approach: We will produce high silica glasses with additions of up to 10 wt% of network formers and modifiers using Momentive’s lab scale...Aij , rij , ρ, and Cij are constants, which are provided by van Beest et al. (16); we refer to equation 2 as the BKS potential. 7.2 Generating...Optischer und Elektrostatischer Gitterpotentiale. Ann. Phys. 1921, 369, 253–287. 16. van Beest , B. W. H.; Kramer, G. J.; van Santen, R. A. Force-fields for

Oxide nanoelectronics on demand.

PubMed

Cen, Cheng; Thiel, Stefan; Mannhart, Jochen; Levy, Jeremy

2009-02-20

Electronic confinement at nanoscale dimensions remains a central means of science and technology. We demonstrate nanoscale lateral confinement of a quasi-two-dimensional electron gas at a lanthanum aluminate-strontium titanate interface. Control of this confinement using an atomic force microscope lithography technique enabled us to create tunnel junctions and field-effect transistors with characteristic dimensions as small as 2 nanometers. These electronic devices can be modified or erased without the need for complex lithographic procedures. Our on-demand nanoelectronics fabrication platform has the potential for widespread technological application.

Control of locomotor stability in stabilizing and destabilizing environments.

PubMed

Wu, Mengnan/Mary; Brown, Geoffrey; Gordon, Keith E

2017-06-01

To develop effective interventions targeting locomotor stability, it is crucial to understand how people control and modify gait in response to changes in stabilization requirements. Our purpose was to examine how individuals with and without incomplete spinal cord injury (iSCI) control lateral stability in haptic walking environments that increase or decrease stabilization demands. We hypothesized that people would adapt to walking in a predictable, stabilizing viscous force field and unpredictable destabilizing force field by increasing and decreasing feedforward control of lateral stability, respectively. Adaptations in feedforward control were measured using after-effects when fields were removed. Both groups significantly (p<0.05) decreased step width in the stabilizing field. When the stabilizing field was removed, narrower steps persisted in both groups and subjects with iSCI significantly increased movement variability (p<0.05). The after-effect of walking in the stabilizing field was a suppression of ongoing general stabilization mechanisms. In the destabilizing field, subjects with iSCI took faster steps and increased lateral margins of stability (p<0.05). Step frequency increases persisted when the destabilizing field was removed (p<0.05), suggesting that subjects with iSCI made feedforward adaptions to increase control of lateral stability. In contrast, in the destabilizing field, non-impaired subjects increased movement variability (p<0.05) and did not change step width, step frequency, or lateral margin of stability (p>0.05). When the destabilizing field was removed, increases in movement variability persisted (p<0.05), suggesting that non-impaired subjects made feedforward decreases in resistance to perturbations. Published by Elsevier B.V.

Electrons in strong electromagnetic fields: spin effects and radiation reaction (Conference Presentation)

NASA Astrophysics Data System (ADS)

Bauke, Heiko; Wen, Meng; Keitel, Christoph H.

2017-05-01

Various different classical models of electrons including their spin degree of freedom are commonly applied to describe the coupled dynamics of relativistic electron motion and spin precession in strong electromagnetic fields. The spin dynamics is usually governed by the Thomas-Bargmann-Michel-Telegdi equation [1, 2] in these models, while the electron's orbital motion follows the (modified) Lorentz force and a spin-dependent Stern-Gerlach force. Various classical models can lead to different or even contradicting predictions how the spin degree of freedom modifies the electron's orbital motion when the electron moves in strong electromagnetic fields. This discrepancy is rooted in the model-specific energy dependency of the spin induced relativistic Stern-Gerlach force acting on the electron. The Frenkel model [3, 4] and the classical Foldy-Wouthuysen model 5 are compared exemplarily against each other and against the quantum mechanical Dirac equation in order to identify parameter regimes where these classical models make different predictions [6, 7]. Our theoretical results allow for experimental tests of these models. In the setup of the longitudinal Stern-Gerlach effect, the Frenkel model and classical Foldy-Wouthuysen model lead in the relativistic limit to qualitatively different spin effects on the electron trajectory. Furthermore, it is demonstrated that in tightly focused beams in the near infrared the effect of the Stern-Gerlach force of the Frenkel model becomes sufficiently large to be potentially detectable in an experiment. Among the classical spin models, the Frenkel model is certainly prominent for its long history and its wide application. Our results, however, suggest that the classical Foldy-Wouthuysen model is superior as it is qualitatively in better agreement with the quantum mechanical Dirac equation. In ultra strong laser setups at parameter regimes where effects of the Stern-Gerlach force become relevant also radiation reaction effects are expected to set in. We incorporate radiation reaction classically via the Landau-Lifshitz equation and demonstrate that although radiation reaction effects can have a significant effect on the electron trajectory, the Frenkel model and the classical Foldy-Wouthuysen model remain distinguishable also if radiation reaction effects are taken into account. Our calculations are also suitable to verify the Landau-Lifshitz equation for the radiation reaction of electrons and other spin one-half particles. 1. Thomas, L. H., "I. The kinematics of an electron with an axis," The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science 3(13), 1-22 (1927). 2. Bargmann, V., Michel, L., and Telegdi, V. L., "Precession of the polarization of particles moving in a homogeneous electromagnetic field," Phys. Rev. Lett. 2(10), 435-436 (1959). 3. Frenkel, J., "Die Elektrodynamik des rotierenden Elektrons," Z. Phys. 37(4-5), 243-262 (1926). 4. Frenkel, J., "Spinning electrons," Nature (London) 117(2949), 653-654 (1926). 5. Silenko, A. J., "Foldy-Wouthyusen transformation and semiclassical limit for relativistic particles in strong external fields," Phys. Rev. A 77(1), 012116 (2008). 6. Wen, M., Bauke, H., and Keitel, C. H., "Identifying the Stern-Gerlach force of classical electron dynamics," Sci. Rep. 6, 31624 (2016). 7. Wen, M., Keitel, C. H., and Bauke, H., "Spin one-half particles in strong electromagnetic fields: spin effects and radiation reaction," arXiv:1610.08951 (2016).

Comparative study of generalized born models: Born radii and peptide folding.

PubMed

Zhu, Jiang; Alexov, Emil; Honig, Barry

2005-02-24

In this study, we have implemented four analytical generalized Born (GB) models and investigated their performance in conjunction with the GROMOS96 force field. The four models include that of Still and co-workers, the HCT model of Cramer, Truhlar, and co-workers, a modified form of the AGB model of Levy and co-workers, and the GBMV2 model of Brooks and co-workers. The models were coded independently and implemented in the GROMOS software package and in TINKER. They were compared in terms of their ability to reproduce the results of Poisson-Boltzmann (PB) calculations and in their performance in the ab initio peptide folding of two peptides, one that forms a beta-hairpin in solution and one that forms an alpha-helix. In agreement with previous work, the GBMV2 model is most successful in reproducing PB results while the other models tend to underestimate the effective Born radii of buried atoms. In contrast, stochastic dynamics simulations on the folding of the two peptides, the C-terminus beta-hairpin of the B1 domain of protein G and the alanine-based alpha-helical peptide 3K(I), suggest that the simpler GB models are more effective in sampling conformational space. Indeed, the Still model used in conjunction with the GROMOS96 force field is able to fold the hairpin peptide to a native-like structure without the benefit of enhanced sampling techniques. This is due in part to the properties of the united-atom GROMOS96 force field which appears to be more flexible, and hence to sample more efficiently, than force fields such as OPLSAA. Our results suggest a general strategy which involves using different combinations of force fields and solvent models in different applications, for example, using GROMOS96 and a simple GB model in sampling and OPLSAA and a more accurate GB model in refinement. The fact that various methods have been implemented in a unified way should facilitate the testing and subsequent use of different methods to evaluate conformational free energies in different applications. Our results also bear on some general issues involved in peptide folding and structure prediction which are addressed in the Discussion.

Implementation and modification of a three-dimensional radiation stress formulation for surf zone and rip-current applications

USGS Publications Warehouse

Kumar, N.; Voulgaris, G.; Warner, John C.

2011-01-01

Regional Ocean Modeling System (ROMS v 3.0), a three-dimensional numerical ocean model, was previously enhanced for shallow water applications by including wave-induced radiation stress forcing provided through coupling to wave propagation models (SWAN, REF/DIF). This enhancement made it suitable for surf zone applications as demonstrated using examples of obliquely incident waves on a planar beach and rip current formation in longshore bar trough morphology (Haas and Warner, 2009). In this contribution, we present an update to the coupled model which implements a wave roller model and also a modified method of the radiation stress term based on Mellor (2008, 2011a,b,in press) that includes a vertical distribution which better simulates non-conservative (i.e., wave breaking) processes and appears to be more appropriate for sigma coordinates in very shallow waters where wave breaking conditions dominate. The improvements of the modified model are shown through simulations of several cases that include: (a) obliquely incident spectral waves on a planar beach; (b) obliquely incident spectral waves on a natural barred beach (DUCK'94 experiment); (c) alongshore variable offshore wave forcing on a planar beach; (d) alongshore varying bathymetry with constant offshore wave forcing; and (e) nearshore barred morphology with rip-channels. Quantitative and qualitative comparisons to previous analytical, numerical, laboratory studies and field measurements show that the modified model replicates surf zone recirculation patterns (onshore drift at the surface and undertow at the bottom) more accurately than previous formulations based on radiation stress (Haas and Warner, 2009). The results of the model and test cases are further explored for identifying the forces operating in rip current development and the potential implication for sediment transport and rip channel development. Also, model analysis showed that rip current strength is higher when waves approach at angles of 5?? to 10?? in comparison to normally incident waves. ?? 2011 Elsevier B.V.

Investigating Plasma Motion of Magnetic Clouds at 1 AU through a Velocity-modified Cylindrical Force-free Flux Rope Model

NASA Astrophysics Data System (ADS)

Wang, Y.; Shen, C.; Liu, R.; Zhou, Z.

2014-12-01

Magnetic clouds (MCs) are the interplanetary counterparts of coronal mass ejections (CMEs). Due to the very low value of Can't connect to bucket.int.confex.com:4201 (Connection refused) LWP::Protocol::http::Socket: connect: Connection refused at /usr/local/lib/perl5/site_perl/5.8.8/LWP/Protocol/http.pm line 51. in MCs, they are believed to be in a nearly force-free state and therefore are able to be modeled by a cylindrical force-free flux rope. However, the force-free state only describes the magnetic field topology but not the plasma motion of a MC. For a MC propagating in interplanetary space, the global plasma motion has three possible components: linear propagating motion of a MC away from the Sun, expanding motion and circular motion with respect to the axis of the MC. By assuming the quasi-steady evolution and self-similar expansion, we introduced the three-component motion into the cylindrical force-free flux rope model, and developed a velocity-modified model. Then we applied the model to 73 MCs observed by Wind spacecraft to investigate the properties of the plasma motion of MCs. It is found that (1) some MCs did not propagate along the Sun-Earth line, suggesting the direct evidence of the CME's deflected propagation and/or rotation in interplanetary space, (2) the expansion speed is correlated with the radial propagation speed and 62%/17% of MCs underwent a under/over-expansion at 1 AU, and (3) the circular motion does exists though it is only on the order of 10 km s-1. These findings advance our understanding of the MC's properties at 1 AU as well as the dynamic evolution of CMEs from the Sun to interplanetary space.

Weight, gravitation, inertia, and tides

NASA Astrophysics Data System (ADS)

Pujol, Olivier; Lagoute, Christophe; Pérez, José-Philippe

2015-11-01

This paper deals with the factors that influence the weight of an object near the Earth's surface. They are: (1) the Earth's gravitational force, (2) the centrifugal force due to the Earth's diurnal rotation, and (3) tidal forces due to the gravitational field of the Moon and Sun, and other solar system bodies to a lesser extent. Each of these three contributions is discussed and expressions are derived. The relationship between weight and gravitation is thus established in a direct and pedagogical manner readily understandable by undergraduate students. The analysis applies to the Newtonian limit of gravitation. The derivation is based on an experimental (or operational) definition of weight, and it is shown that it coincides with the Earth’s gravitational force modified by diurnal rotation around a polar axis and non-uniformity of external gravitational bodies (tidal term). Two examples illustrate and quantify these modifications, respectively the Eötvös effect and the oceanic tides; tidal forces due to differential gravitation on a spacecraft and an asteroid are also proposed as examples. Considerations about inertia are also given and some comments are made about a widespread, yet confusing, explanation of tides based on a centrifugal force. Finally, the expression of the potential energy of the tide-generating force is established rigorously in the appendix.

A modification of Einstein-Schrödinger theory that contains both general relativity and electrodynamics

NASA Astrophysics Data System (ADS)

Shifflett, J. A.

2008-08-01

We modify the Einstein-Schrödinger theory to include a cosmological constant Λ z which multiplies the symmetric metric, and we show how the theory can be easily coupled to additional fields. The cosmological constant Λ z is assumed to be nearly cancelled by Schrödinger’s cosmological constant Λ b which multiplies the nonsymmetric fundamental tensor, such that the total Λ = Λ z + Λ b matches measurement. The resulting theory becomes exactly Einstein-Maxwell theory in the limit as | Λ z | → ∞. For | Λ z | ~ 1/(Planck length)2 the field equations match the ordinary Einstein and Maxwell equations except for extra terms which are < 10-16 of the usual terms for worst-case field strengths and rates-of-change accessible to measurement. Additional fields can be included in the Lagrangian, and these fields may couple to the symmetric metric and the electromagnetic vector potential, just as in Einstein-Maxwell theory. The ordinary Lorentz force equation is obtained by taking the divergence of the Einstein equations when sources are included. The Einstein-Infeld-Hoffmann (EIH) equations of motion match the equations of motion for Einstein-Maxwell theory to Newtonian/Coulombian order, which proves the existence of a Lorentz force without requiring sources. This fixes a problem of the original Einstein-Schrödinger theory, which failed to predict a Lorentz force. An exact charged solution matches the Reissner-Nordström solution except for additional terms which are ~10-66 of the usual terms for worst-case radii accessible to measurement. An exact electromagnetic plane-wave solution is identical to its counterpart in Einstein-Maxwell theory.

An immersed boundary method for simulating vesicle dynamics in three dimensions

NASA Astrophysics Data System (ADS)

Seol, Yunchang; Hu, Wei-Fan; Kim, Yongsam; Lai, Ming-Chih

2016-10-01

We extend our previous immersed boundary (IB) method for 3D axisymmetric inextensible vesicle in Navier-Stokes flows (Hu et al., 2014 [17]) to general three dimensions. Despite a similar spirit in numerical algorithms to the axisymmetric case, the fully 3D numerical implementation is much more complicated and is far from straightforward. A vesicle membrane surface is known to be incompressible and exhibits bending resistance. As in 3D axisymmetric case, instead of keeping the vesicle locally incompressible, we adopt a modified elastic tension energy to make the vesicle surface patch nearly incompressible so that solving the unknown tension (Lagrange multiplier for the incompressible constraint) can be avoided. Nevertheless, the new elastic force derived from the modified tension energy has exactly the same mathematical form as the original one except the different definitions of tension. The vesicle surface is discretized on a triangular mesh where the elastic tension and bending force are calculated on each vertex (Lagrangian marker in the IB method) of the triangulation. A series of numerical tests on the present scheme are conducted to illustrate the robustness and applicability of the method. We perform the convergence study for the immersed boundary forces and the fluid velocity field. We then study the vesicle dynamics in various flows such as quiescent, simple shear, and gravitational flows. Our numerical results show good agreements with those obtained in previous theoretical, experimental and numerical studies.

Effect of short range hydrodynamic on bimodal colloidal gel systems

NASA Astrophysics Data System (ADS)

Boromand, Arman; Jamali, Safa; Maia, Joao

2015-03-01

Colloidal Gels and disordered arrested systems has been studied extensively during the past decades. Although, they have found their place in multiple industries such as cosmetic, food and so on, their physical principals are still far beyond being understood. The interplay between different types of interactions from quantum scale, Van der Waals interaction, to short range interactions, depletion interaction, and long range interactions such as electrostatic double layer makes this systems challenging from simulation point of view. Many authors have implemented different simulation techniques such as molecular dynamics (MD) and Brownian dynamics (BD) to capture better picture during phase separation of colloidal system with short range attractive force. However, BD is not capable to include multi-body hydrodynamic interaction and MD is limited by the computational resources and is limited to short time and length scales. In this presentation we used Core-modified dissipative particle dynamics (CM-DPD) with modified depletion potential, as a coarse-grain model, to address the gel formation process in short ranged-attractive colloidal suspensions. Due to the possibility to include and separate short and long ranged-hydrodynamic forces in this method we studied the effect of each of those forces on the final morphology and report one of the controversial question in this field on the effect of hydrodynamics on the cluster formation process on bimodal, soft-hard colloidal mixtures.

Forces of Commonly Used Chiropractic Techniques for Children: A Review of the Literature.

PubMed

Todd, Angela J; Carroll, Matthew T; Mitchell, Eleanor K L

2016-01-01

The purpose of this study is to review the available literature that describes forces of the most commonly used chiropractic techniques for children. Review of the English-language literature using search terms Chiropract* and technique, protocol, or approach in databases PubMed, Cumulative Index to Nursing and Allied Health Literature, Allied and Complementary Medicine, and Index to Chiropractic Literature and direct contact with authors of articles and book chapters. Eleven articles that discussed the 7 most commonly used pediatric chiropractic techniques and the forces applied were identified. Chiropractic techniques reviewed described forces that were modified based on the age of the patient. Force data for mechanically assisted devices were varied, with the minimum force settings for some devices outside the age-specific safe range recommended in the literature when not modified in some way. This review found that technique selection and application by chiropractors treating infants and young children are typically modified in force and speed to suit the age and development of the child. Copyright © 2016. Published by Elsevier Inc.

Influence of the turbulent motion on the chiral magnetic effect in the early universe

NASA Astrophysics Data System (ADS)

Dvornikov, Maxim; Semikoz, Victor B.

2017-02-01

We study the magnetohydrodynamics of relativistic plasmas accounting for the chiral magnetic effect (CME). To take into account the evolution of the plasma velocity, obeying the Navier-Stokes equation, we approximate it by the Lorentz force accompanied by the phenomenological drag time parameter. On the basis of this ansatz, we obtain the contributions of both the turbulence effects, resulting from the dynamo term, and the magnetic field instability, caused by the CME, to the evolution of the magnetic field governed by the modified Faraday equation. In this way, we explore the evolution of the magnetic field energy and the magnetic helicity density spectra in the early Universe plasma. We find that the right-left electron asymmetry is enhanced by the turbulent plasma motion in a strong seed magnetic field compared to the pure CME case studied earlier for the hot Universe plasma in the same broken phase.

Magnetic field effects on the crust structure of neutron stars

NASA Astrophysics Data System (ADS)

Franzon, B.; Negreiros, R.; Schramm, S.

2017-12-01

We study the effects of high magnetic fields on the structure and on the geometry of the crust in neutron stars. We find that the crust geometry is substantially modified by the magnetic field inside the star. We build stationary and axis-symmetric magnetized stellar models by using well-known equations of state to describe the neutron star crust, namely, the Skyrme model for the inner crust and the Baym-Pethick-Sutherland equation of state for the outer crust. We show that the magnetic field has a dual role, contributing to the crust deformation via the electromagnetic interaction (manifested in this case as the Lorentz force) and by contributing to curvature due to the energy stored in it. We also study a direct consequence of the crust deformation due to the magnetic field: the thermal relaxation time. This quantity, which is of great importance to the thermal evolution of neutron stars, is sensitive to the crust properties, and, as such, we show that it may be strongly affected by the magnetic field.

Geologic map of the Zarkashan-Anguri copper and gold deposits, Ghazni Province, Afghanistan, modified from the 1968 original map compilation of E.P. Meshcheryakov and V.P. Sayapin

USGS Publications Warehouse

Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geological map of the area of Zarkashan-Anguri gold deposits, scale 1:50,000, which was compiled by E.P. Meshcheryakov and V.P. Sayapin in 1968. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original document and related reports and also visited the field area in April 2010. This modified map, which includes a cross section, illustrates the geologic setting of the Zarkashan-Anguri copper and gold deposits. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross section and includes modifications based on our examination of that and other documents, and based on observations made and sampling undertaken during our field visit. (Refer to the Introduction and the References in the Map PDF for an explanation of our methodology and for complete citations of the original map and related reports.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map.

EBSD Study of the Influence of a High Magnetic Field on the Microstructure and Orientation of the Al-Si Eutectic During Directional Solidification

NASA Astrophysics Data System (ADS)

Li, Xi; Fautrelle, Yves; Gagnoud, Annie; Ren, Zhongming; Moreau, Rene

2016-06-01

The effect of a high magnetic field on the morphology of the Al-Si eutectic was investigated using EBSD technology. The results revealed that the application of the magnetic field modified the morphology of the Al-Si eutectic significantly. Indeed, the magnetic field destroyed the coupled growth of the Al-Si eutectic and caused the formation of the divorced α-Al and Si dendrites at low growth speeds (≤1 μm/s). The magnetic field was also found to refine the eutectic grains and reduce the eutectic spacing at the initial growth stage. Moreover, the magnetic field caused the occurrence of the columnar-to-equiaxed transition of the α-Al phase in the Al-Si eutectic. The abovementioned effects were enhanced as the magnetic field increased. This result should be attributed to the magnetic field restraining the interdiffusion of Si and Al atoms in liquid ahead of the liquid/solid interface and the thermoelectric magnetic force acting on the eutectic lamellae under the magnetic field.

Ground crewmen prepare to load the crated SOFIA primary mirror assembly into an Air Force C-17 for shipment to NASA Ames Research Center for finish coating

NASA Image and Video Library

2008-05-01

Technicians at NASA's Dryden Aircraft Operations Facility in Palmdale, Calif., loaded the German-built primary mirror assembly of the Stratospheric Observatory for Infrared Astronomy, or SOFIA, onto an Air Force C-17 for shipment to NASA's Ames Research Center on May 1, 2008. In preparation for the final finish coating of the mirror, the more than two-ton mirror assembly had been removed from its cavity in the rear fuselage of the highly modified SOFIA Boeing 747SP two weeks earlier. After arrival at NASA Ames at Moffett Field near Mountain View, Calif., the mirror would receive its aluminized finish coating before being re-installed in the SOFIA aircraft.

Frequency shift, damping, and tunneling current coupling with quartz tuning forks in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Nony, Laurent; Bocquet, Franck; Para, Franck; Loppacher, Christian

2016-09-01

A combined experimental and theoretical approach to the coupling between frequency-shift (Δ f ) , damping, and tunneling current (It) in combined noncontact atomic force microscopy/scanning tunneling microscopy using quartz tuning forks (QTF)-based probes is reported. When brought into oscillating tunneling conditions, the tip located at the QTF prong's end radiates an electromagnetic field which couples to the QTF prong motion via its piezoelectric tensor and loads its electrodes by induction. Our approach explains how those It-related effects ultimately modify the Δ f and the damping measurements. This paradigm to the origin of the coupling between It and the nc-AFM regular signals relies on both the intrinsic piezoelectric nature of the quartz constituting the QTF and its electrodes design.

Application of Landsat imagery to problems of petroleum exploration in Qaidam Basin, China

USGS Publications Warehouse

Bailey, G.B.; Anderson, P.D.

1982-01-01

Tertiary and Quaternary nonmarine, petroleum-bearing sedimentary rocks have been extensively deformed by compressive forces. These forces created many folds which are current targets of Chinese exploration programs. Image-derived interpretations of folds, strike-slip faults, thrust faults, normal or reverse faults, and fractures compared very favorably, in terms of locations and numbers mapped, with Chinese data compiled from years of extensive field mapping. Many potential hydrocarbon trapping structures were precisely located. Orientations of major structural trends defined from Landsat imagery correlate well with those predicted for the area based on global tectonic theory. These correlations suggest that similar orientations exist in the eastern half of the basin where folded rocks are mostly obscured by unconsolidated surface sediments and where limited exploration has occurred.--Modified journal abstract.

Stresses in curved nematic membranes.

PubMed

Santiago, J A

2018-05-01

Ordering configurations of a director field on a curved membrane induces stress. In this work, we present a theoretical framework to calculate the stress tensor and the torque as a consequence of the nematic ordering; we use the variational principle and invariance of the energy under Euclidean motions. Euler-Lagrange equations of the membrane as well as the corresponding boundary conditions also appear as natural results. The stress tensor found includes attraction-repulsion forces between defects; likewise, defects are attracted to patches with the same sign in Gaussian curvature. These forces are mediated by the Green function of the Laplace-Beltrami operator of the surface. In addition, we find nonisotropic forces that involve derivatives of the Green function and the Gaussian curvature, even in the normal direction to the membrane. We examine the case of axial membranes to analyze the spherical one. For spherical vesicles we find the modified Young-Laplace law as a consequence of the nematic texture. In the case of spherical cap with defect at the north pole, we find that the force is repulsive with respect to the north pole, indicating that it is an unstable equilibrium point.

The Capture of Interstellar Dust: The Pure Poynting-Robertson Case

NASA Technical Reports Server (NTRS)

Jackson, A. A.

2001-01-01

Ulysses and Galileo spacecraft have discovered interstellar dust particles entering the solar system. In general, particles trajectories not altered by Lorentz forces or radiation pressure should encounter the sun on open orbits. Under Newtonian forces alone these particles return to the interstellar medium. Dissipative forces, such as Poynting Robertson (PR) and corpuscular drag and non-dissipative Lorentz forces can modify open orbits to become closed. In particular, it is possible for the orbits of particles that pass close to the Sun to become closed due to PR drag. Further, solar irradiation will cause modification of the size of the dust particle by evaporation. The combination of these processes gives rise a class of capture orbits and bound orbits with evaporation. Considering only the case of pure PR drag a minimum impact parameter is derived for initial capture by Poynting-Robertson drag. Orbits in the solar radiation field are computed numerically accounting for evaporation with optical and material properties for ideal interstellar particles modeled. The properties of this kind of particle capture are discussed for the Sun but is applicable to other stars.

Stresses in curved nematic membranes

NASA Astrophysics Data System (ADS)

Santiago, J. A.

2018-05-01

Ordering configurations of a director field on a curved membrane induces stress. In this work, we present a theoretical framework to calculate the stress tensor and the torque as a consequence of the nematic ordering; we use the variational principle and invariance of the energy under Euclidean motions. Euler-Lagrange equations of the membrane as well as the corresponding boundary conditions also appear as natural results. The stress tensor found includes attraction-repulsion forces between defects; likewise, defects are attracted to patches with the same sign in Gaussian curvature. These forces are mediated by the Green function of the Laplace-Beltrami operator of the surface. In addition, we find nonisotropic forces that involve derivatives of the Green function and the Gaussian curvature, even in the normal direction to the membrane. We examine the case of axial membranes to analyze the spherical one. For spherical vesicles we find the modified Young-Laplace law as a consequence of the nematic texture. In the case of spherical cap with defect at the north pole, we find that the force is repulsive with respect to the north pole, indicating that it is an unstable equilibrium point.

Cosmological bounds on non-Abelian dark forces

NASA Astrophysics Data System (ADS)

Forestell, Lindsay; Morrissey, David E.; Sigurdson, Kris

2018-04-01

Non-Abelian dark gauge forces that do not couple directly to ordinary matter may be realized in nature. The minimal form of such a dark force is a pure Yang-Mills theory. If the dark sector is reheated in the early Universe, it will be realized as a set of dark gluons at high temperatures and as a collection of dark glueballs at lower temperatures, with a cosmological phase transition from one form to the other. Despite being dark, the gauge fields of the new force can connect indirectly to the standard model through nonrenormalizable operators. These operators will transfer energy between the dark and visible sectors, and they allow some or all of the dark glueballs to decay. In this work we investigate the cosmological evolution and decays of dark glueballs in the presence of connector operators to the standard model. Dark glueball decays can modify cosmological and astrophysical observables, and we use these considerations to put very strong limits on the existence of pure non-Abelian dark forces. On the other hand, if one or more of the dark glueballs are stable, we find that they can potentially make up the dark matter of the Universe.

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA

PubMed Central

2015-01-01

Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson–Crick/Watson–Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)2 [Biochemistry, 1996, 35, 9677–9689] and (GCGGAUGC)2 [Biochemistry, 2007, 46, 1511–1522] demonstrate imino and sheared conformations for the two central GA pairs, respectively. These systems were studied using molecular dynamics and free energy change calculations for conformational changes, using umbrella sampling. For the structures to maintain their native conformations during molecular dynamics simulations, a modification to the standard Amber ff10 force field was required, which allowed the amino group of guanine to leave the plane of the base [J. Chem. Theory Comput., 2009, 5, 2088–2100] and form out-of-plane hydrogen bonds with a cross-strand cytosine or uracil. The requirement for this modification suggests the importance of out-of-plane hydrogen bonds in stabilizing the native structures. Free energy change calculations for each sequence demonstrated the correct conformational preference when the force field modification was used, but the extent of the preference is underestimated. PMID:24803859

Characterization of the liquid Li-solid Mo (1 1 0) interface from classical molecular dynamics for plasma-facing applications

NASA Astrophysics Data System (ADS)

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

2017-11-01

An understanding of the wetting properties and a characterization of the interface between liquid lithium (Li) and solid molybdenum (Mo) are relevant to assessing the efficacy of Li as a plasma-facing component in fusion reactors. In this work, a new second-nearest neighbor modified embedded-atom method (2NN MEAM) force field is parameterized to describe the interactions between Li and Mo. The new force field reproduces several benchmark properties obtained from first-principles quantum mechanics simulations, including binding curves for Li at three different adsorption sites and the corresponding forces on Li atoms adsorbed on the Mo (1 1 0) surface. This force field is then used to study the wetting of liquid Li on the (1 1 0) surface of Mo and to examine the Li-Mo interface using molecular dynamics simulations. From droplet simulations, we find that liquid Li tends to completely wet the perfect Mo (1 1 0) surface, in contradiction with previous experimental measurements that found non-zero contact angles for liquid Li on a Mo substrate. However, these experiments were not carried out under ultra-high vacuum conditions or with a perfect (1 1 0) Mo surface, suggesting that the presence of impurities, such as oxygen, and surface structure play a crucial role in this wetting process. From thin-film simulations, it is observed that the first layer of Li on the Mo (1 1 0) surface has many solid-like properties such as a low mobility and a larger degree of ordering when compared to layers further away from the surface, even at temperatures well above the bulk melting temperature of Li. These findings are consistent with temperature-programmed desorption experiments.

Imaging ballistic carrier trajectories in graphene using scanning gate microscopy

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

Morikawa, Sei; Masubuchi, Satoru; Dou, Ziwei

2015-12-14

We use scanning gate microscopy to map out the trajectories of ballistic carriers in high-mobility graphene encapsulated by hexagonal boron nitride and subject to a weak magnetic field. We employ a magnetic focusing geometry to image carriers that emerge ballistically from an injector, follow a cyclotron path due to the Lorentz force from an applied magnetic field, and land on an adjacent collector probe. The local electric field generated by the scanning tip in the vicinity of the carriers deflects their trajectories, modifying the proportion of carriers focused into the collector. By measuring the voltage at the collector while scanningmore » the tip, we are able to obtain images with arcs that are consistent with the expected cyclotron motion. We also demonstrate that the tip can be used to redirect misaligned carriers back to the collector.« less

KSC-2009-3469

NASA Image and Video Library

2009-06-01

CAPE CANAVERAL, Fla. – Hitching a ride on the Shuttle Carrier Aircraft, or SCA, a modified Boeing 747, space shuttle Atlantis has arrived at Biggs Armuy Air Field in El Paso, Texas. Atlantis landed at Edwards Air Force Base in California on May 24, which concluded mission STS-125, after two landing opportunities at Kennedy were waved off due to weather concerns. Atlantis is being returned to Florida on a ferry flight on the SCA. Atlantis' next assignment is the STS-129 mission, targeted to launch in November 2009. Photo credit: NASA/Ben Smegelsky

Electrical and optical properties of sol-gel derived La modified PbTiO 3 thin films

NASA Astrophysics Data System (ADS)

Chopra, Sonalee; Sharma, Seema; Goel, T. C.; Mendiratta, R. G.

2004-09-01

Lanthanum modified lead titanate (Pb 1- xLa xTi 1- x/4 O 3) PLT x ( x=0.08 i.e. PLT8) sol-gel derived thin films have been prepared on indium tin oxide (ITO) coated glass and quartz substrates using lead acetate trihydrate, lanthanum acetate hydrate and titanium isopropoxide as precursors along with 2-methoxyethanol as solvent and acetic acid as catalyst by spin coating method. The microstructure and surface morphology of the films annealed at 650 °C have been studied by X-ray diffraction technique and atomic force microscope (AFM). XRD has shown a single phase with tetragonal structure and AFM images have confirmed a smooth and crack-free surface with low surface roughness. The dependence of leakage current on applied voltage show ohmic behavior at low field region with a space charge conduction mechanism at high fields. The wavelength dispersion curve of thin films obtained from the transmission spectrum of thin films show that the films have high optical transparency in the visible region.

Contact-free calibration of an asymmetric multi-layer interferometer for the surface force balance

NASA Astrophysics Data System (ADS)

Balabajew, Marco; van Engers, Christian D.; Perkin, Susan

2017-12-01

The Surface Force Balance (SFB, also known as Surface Force Apparatus, SFA) has provided important insights into many phenomena within the field of colloid and interface science. The technique relies on using white light interferometry to measure the distance between surfaces with sub-nanometer resolution. Up until now, the determination of the distance between the surfaces required a so-called "contact calibration," an invasive procedure during which the surfaces are brought into mechanical contact. This requirement for a contact calibration limits the range of experimental systems that can be investigated with SFB, for example, it precludes experiments with substrates that would be irreversibly modified or damaged by mechanical contact. Here we present a non-invasive method to measure absolute distances without performing a contact calibration. The method can be used for both "symmetric" and "asymmetric" systems. We foresee many applications for this general approach including, most immediately, experiments using single layer graphene electrodes in the SFB which may be damaged when brought into mechanical contact.

Digital holographic microscopy long-term and real-time monitoring of cell division and changes under simulated zero gravity.

PubMed

Pan, Feng; Liu, Shuo; Wang, Zhe; Shang, Peng; Xiao, Wen

2012-05-07

The long-term and real-time monitoring the cell division and changes of osteoblasts under simulated zero gravity condition were succeed by combing a digital holographic microscopy (DHM) with a superconducting magnet (SM). The SM could generate different magnetic force fields in a cylindrical cavity, where the gravitational force of biological samples could be canceled at a special gravity position by a high magnetic force. Therefore the specimens were levitated and in a simulated zero gravity environment. The DHM was modified to fit with SM by using single mode optical fibers and a vertically-configured jig designed to hold specimens and integrate optical device in the magnet's bore. The results presented the first-phase images of living cells undergoing dynamic divisions and changes under simulated zero gravity environment for a period of 10 hours. The experiments demonstrated that the SM-compatible DHM setup could provide a highly efficient and versatile method for research on the effects of microgravity on biological samples.

Metric-affine f (R ,T ) theories of gravity and their applications

NASA Astrophysics Data System (ADS)

Barrientos, E.; Lobo, Francisco S. N.; Mendoza, S.; Olmo, Gonzalo J.; Rubiera-Garcia, D.

2018-05-01

We study f (R ,T ) theories of gravity, where T is the trace of the energy-momentum tensor Tμ ν, with independent metric and affine connection (metric-affine theories). We find that the resulting field equations share a close resemblance with their metric-affine f (R ) relatives once an effective energy-momentum tensor is introduced. As a result, the metric field equations are second-order and no new propagating degrees of freedom arise as compared to GR, which contrasts with the metric formulation of these theories, where a dynamical scalar degree of freedom is present. Analogously to its metric counterpart, the field equations impose the nonconservation of the energy-momentum tensor, which implies nongeodesic motion and consequently leads to the appearance of an extra force. The weak field limit leads to a modified Poisson equation formally identical to that found in Eddington-inspired Born-Infeld gravity. Furthermore, the coupling of these gravity theories to perfect fluids, electromagnetic, and scalar fields, and their potential applications are discussed.

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

KSC00pp0887

NASA Image and Video Library

2000-06-19

In a hangar at Cape Canaveral Air Force Station, a weather researcher checks a field mill measuring device on the Cessna Citation. The aircraft is being used for NASA’s airborne field mill study. The plane also carries cloud physics probes (under the body and wings) that measure the size, shape and number of ice and water particles in clouds. The plane is being flown into anvil clouds in the KSC area as part of a study to review and possibly modify lightning launch commit criteria. The weather study could lead to improved lightning avoidance rules and fewer launch scrubs for the Space Shuttle and other launch vehicles on the Eastern and Western ranges.; More information about the study can be found in Release No. 56-00

KSC-00pp0887

NASA Image and Video Library

2000-06-19

In a hangar at Cape Canaveral Air Force Station, a weather researcher checks a field mill measuring device on the Cessna Citation. The aircraft is being used for NASA’s airborne field mill study. The plane also carries cloud physics probes (under the body and wings) that measure the size, shape and number of ice and water particles in clouds. The plane is being flown into anvil clouds in the KSC area as part of a study to review and possibly modify lightning launch commit criteria. The weather study could lead to improved lightning avoidance rules and fewer launch scrubs for the Space Shuttle and other launch vehicles on the Eastern and Western ranges.; More information about the study can be found in Release No. 56-00

An axion-like scalar field environment effect on binary black hole merger

NASA Astrophysics Data System (ADS)

Yang, Qing; Ji, Li-Wei; Hu, Bin; Cao, Zhou-Jian; Cai, Rong-Gen

2018-06-01

The environment, such as an accretion disk, could modify the signal of the gravitational wave from astrophysical black hole binaries. In this article, we model the matter field around intermediate-mass binary black holes by means of an axion-like scalar field and investigate their joint evolution. In detail, we consider equal mass binary black holes surrounded by a shell of axion-like scalar field both in spherically symmetric and non-spherically symmetric cases, and with different strengths of the scalar field. Our result shows that the environmental scalar field could essentially modify the dynamics. Firstly, in the spherically symmetric case, with increase of the scalar field strength, the number of circular orbits for the binary black hole is reduced. This means that the scalar field could significantly accelerate the merger process. Secondly, once the scalar field strength exceeds a certain critical value, the scalar field could collapse into a third black hole with its mass being larger than that of the binary. Consequently, the new black hole that collapses from the environmental scalar field could accrete the binary promptly and the binary collides head-on with each other. In this process, there is almost no quadrupole signal produced, and, consequently, the gravitational wave is greatly suppressed. Thirdly, when the scalar field strength is relatively smaller than the critical value, the black hole orbit could develop eccentricity through accretion of the scalar field. Fourthly, during the initial stage of the inspiral, the gravitational attractive force from the axion-like scalar field could induce a sudden turn in the binary orbits, hence resulting in a transient wiggle in the gravitational waveform. Finally, in the non-spherical case, the scalar field could gravitationally attract the binary moving toward the center of mass for the scalar field and slow down the merger process.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Rock riprap design for protection of stream channels near highway structures; Volume 2, Evaluation of Riprap design procedures

USGS Publications Warehouse

Blodgett, J.C.; McConaughy, C.E.

1986-01-01

In volume 2, seven procedures now being used for design of rock riprap installations were evaluated using data from 26 field sites. Four basic types of riprap failures were identified: Particle erosion, translational slide, modified slump, and slump. Factors associated with riprap failure include stone size , bank side slope, size gradation, thickness, insufficient toe or endwall, failure of the bank material, overtopping during floods, and geomorphic changes in the channel. A review of field data and the design procedures suggests that estimates of hydraulic forces acting on the boundary based on flow velocity rather than shear stress are more reliable. Several adjustments for local conditions, such as channel curvature, superelevation, or boundary roughness, may be unwarranted in view of the difficulty in estimating critical hydraulic forces for which the riprap is to be designed. Success of the riprap is related not only to the appropriate procedure for selecting stone size, but also to the reliability of estimated hydraulic and channel factors applicable to the site. (See also W89-04910) (Author 's abstract)

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

PubMed

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

2018-04-05

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

More evidence for azimuthal ion spin in HiPIMS discharges

NASA Astrophysics Data System (ADS)

Poolcharuansin, P.; Liebig, B.; Bradley, J. W.

2012-02-01

The velocity and energy distribution functions of ions escaping radially from the magnetic trap region of a HiPIMS discharge have been measured using a retarding field analyzer (RFA). Spatially and angularly resolved measurements recorded at a representative time show more energetic ions detected along a line-of-sight coincident with an oncoming rotating ion fluid, which circulates above the racetrack in the same direction as the electron E × B drift. The difference in the mean ion energies between measurements made into and against the direction of rotation is ~5 eV. Numerical solutions of the equation of motion for the ions accounting for azimuthal acceleration (modified two-stream instability model used by Lundin et al) have been found. The centripetal force caused by the radial electric field and a drag force term accounting for ion collisions revealed that only a small fraction (typically <5%) of the circulating ion flux can leave the discharge tangentially. Operating the discharge at different background pressures revealed an interplay between the azimuthal acceleration of ions, dominating under low pressure conditions and the scattering of ions into the RFA at higher pressure.

Adhesion mapping of chemically modified and poly(ethylene oxide)-grafted glass surfaces.

PubMed

Jogikalmath, G; Stuart, J K; Pungor, A; Hlady, V

1999-08-01

Two-dimensional mapping of the adhesion pull-off forces was used to study the origin of surface heterogeneity in the grafted poly(ethylene oxide) (PEO) layer. The variance of the pull-off forces measured over the μm-sized regions after each chemical step of modifying glass surfaces was taken to be a measure of the surface chemical heterogeneity. The attachment of γ-glycidoxypropyltrimethoxy silane (GPS) to glass decreased the pull-off forces relative to the clean glass and made the surface more uniform. The subsequent hydrolysis of the terminal epoxide groups resulted in a larger surface heterogeneity which was modeled by two populations of the terminal hydroxyl groups, each with its own distribution of adhesion forces and force variance. The activation of the hydroxyls with carbonyldiimmidazole (CDI) healed the surface and lowered its adhesion, however, the force variance remained rather large. Finally, the grafting of the α,ω-diamino poly(ethyleneoxide) chains to the CDI-activated glass largely eliminated adhesion except at a few discrete regions. The adhesion on the PEO grafted layer followed the Poisson distribution of the pull-off forces. With the exception of the glass surface, a correlation between the water contact angles and the mean pull-off forces measured with the Si(3)N(4) tip surfaces was found for all modified glass surfaces.

Surface morphology of a modified ballistic deposition model.

PubMed

Banerjee, Kasturi; Shamanna, J; Ray, Subhankar

2014-08-01

The surface and bulk properties of a modified ballistic deposition model are investigated. The deposition rule interpolates between nearest- and next-nearest-neighbor ballistic deposition and the random deposition models. The stickiness of the depositing particle is controlled by a parameter and the type of interparticle force. Two such forces are considered: Coulomb and van der Waals type. The interface width shows three distinct growth regions before eventual saturation. The rate of growth depends more strongly on the stickiness parameter than on the type of interparticle force. However, the porosity of the deposits is strongly influenced by the interparticle force.

Processing of DMSP magnetic data and its use in geomagnetic field modeling

NASA Technical Reports Server (NTRS)

Ridgway, J. R.; Sabaka, T. J.; Chinn, D.; Langel, R. A.

1989-01-01

The DMSP F-7 satellite is an operational Air Force meteorological satellite which carried a magnetometer for geophysical measurements. The magnetometer was located within the body of the spacecraft in the presence of large spacecraft fields. In addition to stray magnetic fields, the data have inherent position and time inaccuracies. Algorithms were developed to identify and remove time varying magnetic field noise from the data. Techniques developed for Magsat were then modified and used to attempt determination of the spacecraft fields, of any rotation between the magnetometer axes and the spacecraft axes, and of any scale changes within the magnetometer itself. The corrected data were then used to attempt to model the geomagnetic field. This was done in combination with data from Magsat, from the standard magnetic observatories, from aeromagnetic and other survey data, and from DE-2 spacecraft field data. Future DMSP missions can be upgraded in terms of geomagnetic measurements by upgrading the time and position information furnished with the data, placing the magnetometer at the end of the boom, upgrading the attitude determination at the magnetometer, and increasing the accuracy of the magnetometer.

Which is the optimal risk stratification system for surgically treated localized primary GIST? Comparison of three contemporary prognostic criteria in 171 tumors and a proposal for a modified Armed Forces Institute of Pathology risk criteria.

PubMed

Goh, Brian K P; Chow, Pierce K H; Yap, Wai-Ming; Kesavan, Sittampalam M; Song, In-Chin; Paul, Pradeep G; Ooi, Boon-Swee; Chung, Yaw-Fui A; Wong, Wai-Keong

2008-08-01

This study aims to validate and compare the performance of the National Institute of Health (NIH) criteria, Huang modified NIH criteria, and Armed Forces Institute of Pathology (AFIP) risk criteria for gastrointestinal stromal tumors (GISTs) in a large series of localized primary GISTs surgically treated at a single institution to determine the ideal risk stratification system for GIST. The clinicopathological features of 171 consecutive patients who underwent surgical resection for GISTs were retrospectively reviewed. Statistical analyses were performed to compare the prognostic value of the three risk criteria by analyzing the discriminatory ability linear trend, homogeneity, monotonicity of gradients, and Akaike information criteria. The median actuarial recurrence-free survival (RFS) for all 171 patients was 70%. On multivariate analyses, size >10 cm, mitotic count >5/50 high-power field, tumor necrosis, and serosal involvement were independent prognostic factors of RFS. All three risk criteria demonstrated a statistically significant difference in the recurrence rate, median actuarial RFS, actuarial 5-year RFS, and tumor-specific death across the different stages. Comparison of the various risk-stratification systems demonstrated that our proposed modified AFIP criteria had the best independent predictive value of RFS when compared with the other systems. The NIH, modified NIH, and AFIP criteria are useful in the prognostication of GIST, and the AFIP risk criteria provided the best prognostication among the three systems for primary localized GIST. However, remarkable prognostic heterogeneity exists in the AFIP high-risk category, and with our proposed modification, this system provides the most accurate prognostic information.

Dynamic response of porous functionally graded material nanobeams subjected to moving nanoparticle based on nonlocal strain gradient theory

NASA Astrophysics Data System (ADS)

Barati, Mohammad Reza

2017-11-01

Up to now, nonlocal strain gradient theory (NSGT) is broadly applied to examine free vibration, static bending and buckling of nanobeams. This theory captures nonlocal stress field effects together with the microstructure-dependent strain gradient effects. In this study, forced vibrations of NSGT nanobeams on elastic substrate subjected to moving loads are examined. The nanobeam is made of functionally graded material (FGM) with even and uneven porosity distributions inside the material structure. The graded material properties with porosities are described by a modified power-law model. Dynamic deflection of the nanobeam is obtained via Galerkin and inverse Laplace transform methods. The importance of nonlocal parameter, strain gradient parameter, moving load velocity, porosity volume fraction, type of porosity distribution and elastic foundation on forced vibration behavior of nanobeams are discussed.

Flux pinning characteristics in cylindrical ingot niobium used in superconducting radio frequency cavity fabrication

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

Dhavale Ashavai, Pashupati Dhakal, Anatolii A Polyanskii, Gianluigi Ciovati

We present the results of from DC magnetization and penetration depth measurements of cylindrical bulk large-grain (LG) and fine-grain (FG) niobium samples used for the fabrication of superconducting radio frequency (SRF) cavities. The surface treatment consisted of electropolishing and low temperature baking as they are typically applied to SRF cavities. The magnetization data were fitted using a modified critical state model. The critical current density Jc and pinning force Fp are calculated from the magnetization data and their temperature dependence and field dependence are presented. The LG samples have lower critical current density and pinning force density compared to FGmore » samples which implies a lower flux trapping efficiency. This effect may explain the lower values of residual resistance often observed in LG cavities than FG cavities.« less

Mixed formulation for frictionless contact problems

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Kim, Kyun O.

1989-01-01

Simple mixed finite element models and a computational precedure are presented for the solution of frictionless contact problems. The analytical formulation is based on a form of Reissner's large rotation theory of the structure with the effects of transverse shear deformation included. The contact conditions are incorporated into the formulation by using a perturbed Lagrangian approach with the fundamental unknowns consisting of the internal forces (stress resultants), the generalized displacements, and the Lagrange multipliers associated with the contact conditions. The element characteristic array are obtained by using a modified form of the two-field Hellinger-Reissner mixed variational principle. The internal forces and the Lagrange multipliers are allowed to be discontinuous at interelement boundaries. The Newton-Raphson iterative scheme is used for the solution of the nonlinear algebraic equations, and the determination of the contact area and the contact pressures.

Photogravimagnetic assists of light sails: a mixed blessing for Breakthrough Starshot?

NASA Astrophysics Data System (ADS)

Forgan, Duncan H.; Heller, René; Hippke, Michael

2018-03-01

Upon entering a star system, light sails are subject to both gravitational forces and radiation pressure, and can use both in concert to modify their trajectory. Moreover, stars possess significant magnetic fields, and if the sail is in any way charged, it will feel the Lorentz force also. We investigate the dynamics of so-called `photogravimagnetic assists' of sailcraft around α Centauri A, a potential first destination en route to Proxima Centauri (the goal of the Breakthrough Starshot programme). We find that a 10-m2 sail with a charge-to-mass ratio of around 10 μC g-1 or higher will need to take account of magnetic field effects during orbital manoeuvres. The magnetic field can provide an extra source of deceleration and deflection, and allow capture on to closer orbits around a target star. However, flipping the sign of the sailcraft's charge can radically change resulting trajectories, resulting in complex loop-de-loops around magnetic field lines and essentially random ejection from the star system. Even on well-behaved trajectories, the field can generate off-axis deflections at α Centauri that, while minor, can result in very poor targeting of the final destination (Proxima) post-assist. Fortunately for Breakthrough Starshot, nanosails are less prone to charging en route than their heavier counterparts, but can still accrue relatively high charge at both the origin and destination, when travelling at low speeds. Photogravimagnetic assists are highly non-trivial, and require careful course correction to mitigate against unwanted changes in trajectory.

Physical stress modifies top-down and bottom-up forcing on plant growth and reproduction in a coastal ecosystem.

PubMed

Daleo, Pedro; Alberti, Juan; Bruschetti, Carlos Martin; Pascual, Jesos; Iribarne, Oscar; Silliman, Brian R

2015-08-01

Bottom-up and top-down effects act together to exert strong control over plant growth and reproduction, but how physical stress modifies those interactive forces remains unclear. Even though empirical evidence is scarce, theory predicts that the importance of both top-down- and bottom-up forces may decrease as physical stress increases. Here, we experimentally evaluate in the field the separate and interactive effect of salinity, nutrient availability, and crab herbivory on plant above- and belowground biomass, as well as on sexual and clonal reproduction in the salt marsh plant Spartina densiflora. Results show that the outcome of the interaction between nutrient availability and herbivory is highly context dependent, not only varying with the abiotic context (i.e., with or without increased salinity stress), but also with the dependent variable considered. Contrary to theoretical predictions, our results show that, consistently across different measured variables, salinity stress did not cancel bottom-up (i.e., nutrients) or top-down (i.e., consumers) control, but has additive effects. Our results support emerging theory by highlighting that, under many conditions, physical stress can act additively with, or even stimulate, consumer control, especially in cases where the physical stress is only experienced by basal levels of the trophic chain. Abiotic stress, as well as bottom-up and top-down factors, can affect salt marsh structure and function not only by affecting biomass production but also by having other indirect effects, such as changing patterns in plant biomass allocation and reproduction.

The Influence of Joint Distraction Force on the Soft-Tissue Balance Using Modified Gap-Balancing Technique in Posterior-Stabilized Total Knee Arthroplasty.

PubMed

Nagai, Kanto; Muratsu, Hirotsugu; Takeoka, Yoshiki; Tsubosaka, Masanori; Kuroda, Ryosuke; Matsumoto, Tomoyuki

2017-10-01

During modified gap-balancing technique, there is no consensus on the best method for obtaining appropriate soft-tissue balance and determining the femoral component rotation. Sixty-five varus osteoarthritic patients underwent primary posterior-stabilized total knee arthroplasty using modified gap-balancing technique. The influence of joint distraction force on the soft-tissue balance measurement during the modified gap-balancing technique was evaluated with Offset Repo-Tensor between the osteotomized surfaces at extension, and between femoral posterior condyles and tibial osteotomized surface at flexion of the knee before the resection of femoral posterior condyles. The joint center gap (millimeters) and varus ligament balance (°) were measured under 20, 40, and 60 pounds of joint distraction forces, and the differences in these values at extension and flexion (the value at flexion minus the value at extension) were also calculated. The differences in joint center gap (-6.7, -6.8, and -6.9 mm for 20, 40, and 60 pounds, respectively) and varus ligament balance (3.5°, 3.8°, and 3.8°) at extension and flexion were not significantly different among different joint distraction forces, although the joint center gap and varus ligament balance significantly increased stepwise at extension and flexion as the joint distraction force increased. The difference in joint center gap and varus ligament balance at extension and flexion were consistent even among the different joint distraction forces. This novel index would be useful for the determination of femoral component rotation during the modified gap-balancing technique. Copyright © 2017 Elsevier Inc. All rights reserved.

Separation of Single-Walled Carbon Nanotubes with DEP-FFF

NASA Technical Reports Server (NTRS)

Schmidt, Howard K.; Peng, Haiqing; Alvarez, Noe; Mendes, Manuel; Pasquali, Matteo

2011-01-01

A process using a modified dielectrophoresis device separates single-walled carbon nanotubes (SWNTs) according to their polarizability in electric fields. This depends on the size and dielectric constant of individual nanotubes and easily separates metallic from semiconducting nanotubes. Separation by length has also been demonstrated. Partial separation (enrichment) according to bandgap (which is linked to polarizability) has also been shown and can be improved to full separation of individual types of semiconducting SWNTs with better control over operational parameters and the length of SWNT starting material. This process and device can be scaled affordably to generate useful amounts of semiconducting SWNTs for electronic device development and production. In this study, a flow injection dielectrophoresis technique was used with a modified dielectrophoresis device. The length, width, and height of the modified chamber were 28, 2.5, and 0.025 cm, respectively. On the bottom of the chamber, there are two arrays of 50-m-wide, 2-m-thick gold electrodes, which are connected to an AC voltage generator and are alternately arranged so that every electrode is adjacent to two electrodes of the opposite polar. There is an additional plate electrode on the top of the chamber that is negatively biased. During the experiment, a syringe pump constantly pumps in the mobile phase, 1-percent sodium dodecylbenzene sulfonate (SDBS) solution, into the chamber. The frequency and voltage are set to 1 MHz and 10 V peak-to-peak, respectively. About 150 micro-L of SWNTs in 1- percent SDBS decanted solution are injected to the mobile phase through a septum near the entrance of the chamber. The flow rate of the mobile phase is set to 0.02 cu cm/min. The injected SWNTs sample flows through the chamber before it is lead into a fluorescence flow-through cell and collected for further analysis. The flow-through cell has three windows, thus allowing the fluorometer to collect fluorescence spectrum and visible absorption spectrums simultaneously. Dielectrophoresis field-flow fractionation (DEP-FFF) generally depends on interaction of a sedimentation force and DEP force for particle separation, and SWNTs are neutrally buoyant in water. In this innovation, the third electrode was added to create a sedimentation force based on DC electrophoresis. This makes this particular device applicable to separations on any neutrally buoyant particles in solution and a more general process for a broad range of nanomaterials sorting and separations.

Active Control of Sound Radiation due to Subsonic Wave Scattering from Discontinuities on Thin Elastic Beams.

NASA Astrophysics Data System (ADS)

Guigou, Catherine Renee J.

1992-01-01

Much progress has been made in recent years in active control of sound radiation from vibrating structures. Reduction of the far-field acoustic radiation can be obtained by directly modifying the response of the structure by applying structural inputs rather than by adding acoustic sources. Discontinuities, which are present in many structures are often important in terms of sound radiation due to wave scattering behavior at their location. In this thesis, an edge or boundary type discontinuity (clamped edge) and a point discontinuity (blocking mass) are analytically studied in terms of sound radiation. When subsonic vibrational waves impinge on these discontinuities, large scattered sound levels are radiated. Active control is then achieved by applying either control forces, which approximate shakers, or pairs of control moments, which approximate piezoelectric actuators, near the discontinuity. Active control of sound radiation from a simply-supported beam is also examined. For a single frequency, the flexural response of the beam subject to an incident wave or an input force (disturbance) and to control forces or control moments is expressed in terms of waves of both propagating and near-field types. The far-field radiated pressure is then evaluated in terms of the structural response, using Rayleigh's formula or a stationary phase approach, depending upon the application. The control force and control moment magnitudes are determined by optimizing a quadratic cost function, which is directly related to the control performance. On determining the optimal control complex amplitudes, these can be resubstituted in the constitutive equations for the system under study and the minimized radiated fields can be evaluated. High attenuation in radiated sound power and radiated acoustic pressure is found to be possible when one or two active control actuators are located near the discontinuity, as is shown to be mostly associated with local changes in beam response near the discontinuity. The effect of the control actuators on the far-field radiated pressure, the wavenumber spectrum, the flexural displacement and the near-field time averaged intensity and pressure distributions are studied in order to further understand the control mechanisms. The influence of the near-field structural waves is investigated as well. Some experimental results are presented for comparison.

Microstructure evolution and tribological properties of acrylonitrile-butadiene rubber surface modified by atmospheric plasma treatment

NASA Astrophysics Data System (ADS)

Shen, Ming-xue; Zhang, Zhao-xiang; Peng, Xu-dong; Lin, Xiu-zhou

2017-09-01

For the purpose of prolonging the service life for rubber sealing elements, the frictional behavior of acrylonitrile-butadiene rubber (NBR) surface by dielectric barrier discharge plasma treatments was investigated in this paper. Surface microstructure and chemical composition were measured by atomic force microscopy, field-emission scanning electron microscopy, and X-ray photoelectron spectroscopy, respectively. Water contact angles of the modified rubber surface were also measured to evaluate the correlation between surface wettability and tribological properties. The results show that plasma treatments can improve the properties of the NBR against friction and wear effectively, the surface microstructure and roughness of plasma-modified NBR surface had an important influence on the surface tribological behavior, and the wear depth first decreased and then increased along with the change of plasma treatment time. It was found that the wettability of the modified surface was gradually improved, which was mainly due to the change of the chemical composition after the treatment. This study suggests that the plasma treatment could effectively improve the tribological properties of the NBR surface, and also provides information for developing wear-resistant NBR for industrial applications.

Conceptual design of a high-speed electromagnetic switch for a modified flux-coupling-type SFCL and its application in renewable energy system.

PubMed

Chen, Lei; Chen, Hongkun; Yang, Jun; Shu, Zhengyu; He, Huiwen; Shu, Xin

2016-01-01

The modified flux-coupling-type superconducting fault current (SFCL) is a high-efficient electrical auxiliary device, whose basic function is to suppress the short-circuit current by controlling the magnetic path through a high-speed switch. In this paper, the high-speed switch is based on electromagnetic repulsion mechanism, and its conceptual design is carried out to promote the application of the modified SFCL. Regarding that the switch which is consisting of a mobile copper disc, two fixed opening and closing coils, the computational method for the electromagnetic force is discussed, and also the dynamic mathematical model including circuit equation, magnetic field equation as well as mechanical motion equation is theoretically deduced. According to the mathematical modeling and calculation of characteristic parameters, a feasible design scheme is presented, and the high-speed switch's response time can be less than 0.5 ms. For that the modified SFCL is equipped with this high-speed switch, the SFCL's application in a 10 kV micro-grid system with multiple renewable energy sources are assessed in the MATLAB software. The simulations are well able to affirm the SFCL's performance behaviors.

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.

Theoretical analysis of non-linear Joule heating effects over an electro-thermal patterned flow

NASA Astrophysics Data System (ADS)

Sanchez, Salvador; Ascanio, Gabriel; Mendez, Federico; Bautista, Oscar

2017-11-01

In this work, non-linear Joule heating effects for electro-thermal patterned flows driven inside of a slit microchannel are analyzed. Here, the movement of fluids is controlled by placing electro-thermal forces, which are generated through an imposed longitudinal electric field, E0, and the wall electric potential produced by electrodes inserted along the surface of the microchannel wall, ζ. For this analysis, viscosity and electrical conductivity of fluids are included as known functions, which depend on the temperature; therefore, in order to determine the flow, temperature and electric potential fields together with its simultaneous interactions, the equations of continuity, momentum, energy, charges distribution and electrical current have to be solved in a coupled manner. The main results obtained in the study reveal that with the presence of thermal gradients along of the microchannel, local electro-thermal forces, Fχ, are affected in a sensible manner, and consequently, the flow field is modified substantially, causing the interruption or intensification of recirculations along of the microchannel. This work was supported by the Fondo SEP-CONACYT through research Grants No. 220900 and 20171181 from SIP-IPN. F. Mendez acknowledges support from PAPIIT-UNAM under Contract Number IN112215. S. Sanchez thanks to DGAPA-UNAM for the postdoctoral fellowship.

The study of VOPc thin film transistors on modified substrates

NASA Astrophysics Data System (ADS)

Song, De; Xu, Qi; Cheng, Hongcang; Li, Bao-zeng; Shang, Yubin

2018-02-01

The vanadyl phthalocyanine (VOPc) organic thin film transistors (OTFTs) were fabricated on the various organosilane self-assembled monolayer (SAM) modified substrates. And the effect of the surface properties on the performance of these transistors was studied. The atomic force morphologies and X-ray diffraction (XRD) spectrums of vanadyl phthalocyanine films on different SAM-modified surfaces were studied. They reveal that the terminal functional groups of organosilane affect the growth of VOPc film and device performance. The VOPc film on octadecyltrichlorosilane (OTS) modified substrate has larger crystal size and effective crystal thickness than those on phenyltrichlorosilane (PTS), 1H,1H,2H,2H-Perfluorodec-yltrichlorosilane (FDTS) as well as non-modified substrate, which contributes the mobility of corresponding device several and several dozen times relative to other ones. The effective crystal thickness and crystal grain size of VOPc film on PTS is between that on OTS treated and that on non-modified substrate due to the stronger attractive force between VOPc and SiO2. The VOPc films' performance and effective crystal thickness on FDTS treated are worse than that on PTS due to the existents of attractive force between -CF3 and VOPc.

Multiscale Analysis of Rapidly Rotating Dynamo Simulations

NASA Astrophysics Data System (ADS)

Orvedahl, R.; Calkins, M. A.; Featherstone, N. A.

2017-12-01

The magnetic field of the planets and stars are generated by dynamo action in their electrically conducting fluid interiors. Numerical models of this process solve the fundamental equations of magnetohydrodynamics driven by convection in a rotating spherical shell. Rotation plays an important role in modifying the resulting convective flows and the self-generated magnetic field. We present results of simulating rapidly rotating systems that are unstable to dynamo action. We use the pseudo-spectral code Rayleigh to generate a suite of direct numerical simulations. Each simulation uses the Boussinesq approximation and is characterized by an Ekman number (Ek=ν /Ω L2) of 10-5. We vary the degree of convective forcing to obtain a range of convective Rossby numbers. The resulting flows and magnetic structures are analyzed using a Reynolds decomposition. We determine the relative importance of each term in the scale-separated governing equations and estimate the relevant spatial scales responsible for generating the mean magnetic field.

SNOM and AFM microscopy techniques to study the effect of non-ionizing radiation on the morphological and biochemical properties of human keratinocytes cell line (HaCaT).

PubMed

Rieti, S; Manni, V; Lisi, A; Giuliani, L; Sacco, D; D'Emilia, E; Cricenti, A; Generosi, R; Luce, M; Grimaldi, S

2004-01-01

In this study we have employed atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM) techniques to study the effect of the interaction between human keratinocytes (HaCaT) and electromagnetic fields at low frequency. HaCaT cells were exposed to a sinusoidal magnetic field at a density of 50 Hz, 1 mT. AFM analysis revealed modification in shape and morphology in exposed cells with an increase in the areas of adhesion between cells. This latter finding was confirmed by SNOM indirect immunofluorescence analysis performed with a fluorescent antibody against the adhesion marker beta4 integrin, which revealed an increase of beta4 integrin segregation in the cell membrane of 50-Hz exposed cells, suggesting that a higher percentage of these cells shows a modified pattern of this adhesion marker.

Evaluation of knee joint forces during kneeling work with different kneepads.

PubMed

Xu, Hang; Jampala, Sree; Bloswick, Donald; Zhao, Jie; Merryweather, Andrew

2017-01-01

The main purpose of this study is to determine knee joint forces resulting from kneeling work with and without kneepads to quantify how different kneepads redistribute force. Eleven healthy males simulated a tile setting task to different locations during six kneepad states (five different kneepad types and without kneepad). Peak and average forces on the anatomical landmarks of both knees were obtained by custom force sensors. The results revealed that kneepad design can significantly modify the forces on the knee joint through redistribution. The Professional Gel design was preferred among the five tested kneepads which was confirmed with both force measurements and participants' responses. The extreme reaching locations induced significantly higher joint forces on left knee or right knee depending on task. The conclusion of this study is that a properly selected kneepad for specific tasks and a more neutral working posture can modify the force distribution on the knees and likely decrease the risk of knee disorders from kneeling work. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-12-01

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

Perceived causality, force, and resistance in the absence of launching.

PubMed

Hubbard, Timothy L; Ruppel, Susan E

2017-04-01

In the launching effect, a moving object (the launcher) contacts a stationary object (the target), and upon contact, the launcher stops and the target begins moving in the same direction and at the same or slower velocity as previous launcher motion (Michotte, 1946/1963). In the study reported here, participants viewed a modified launching effect display in which the launcher stopped before or at the moment of contact and the target remained stationary. Participants rated perceived causality, perceived force, and perceived resistance of the launcher on the target or the target on the launcher. For launchers and for targets, increases in the size of the spatial gap between the final location of the launcher and the location of the target decreased ratings of perceived causality and ratings of perceived force and increased ratings of perceived resistance. Perceived causality, perceived force, and perceived resistance exhibited gradients or fields extending from the launcher and from the target and were not dependent upon contact of the launcher and target. Causal asymmetries and force asymmetries reported in previous studies did not occur, and this suggests that such asymmetries might be limited to typical launching effect stimuli. Deviations from Newton's laws of motion are noted, and the existence of separate radii of action extending from the launcher and from the target is suggested.

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

Testing chameleon gravity with the Coma cluster

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

Terukina, Ayumu; Yamamoto, Kazuhiro; Lombriser, Lucas

2014-04-01

We propose a novel method to test the gravitational interactions in the outskirts of galaxy clusters. When gravity is modified, this is typically accompanied by the introduction of an additional scalar degree of freedom, which mediates an attractive fifth force. The presence of an extra gravitational coupling, however, is tightly constrained by local measurements. In chameleon modifications of gravity, local tests can be evaded by employing a screening mechanism that suppresses the fifth force in dense environments. While the chameleon field may be screened in the interior of the cluster, its outer region can still be affected by the extramore » force, introducing a deviation between the hydrostatic and lensing mass of the cluster. Thus, the chameleon modification can be tested by combining the gas and lensing measurements of the cluster. We demonstrate the operability of our method with the Coma cluster, for which both a lensing measurement and gas observations from the X-ray surface brightness, the X-ray temperature, and the Sunyaev-Zel'dovich effect are available. Using the joint observational data set, we perform a Markov chain Monte Carlo analysis of the parameter space describing the different profiles in both the Newtonian and chameleon scenarios. We report competitive constraints on the chameleon field amplitude and its coupling strength to matter. In the case of f(R) gravity, corresponding to a specific choice of the coupling, we find an upper bound on the background field amplitude of |f{sub R0}| < 6 × 10{sup −5}, which is currently the tightest constraint on cosmological scales.« less

Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field

PubMed Central

2015-01-01

A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. PMID:25691830

Processing of DMSP magnetic data: Handbook of programs, tapes, and datasets

NASA Technical Reports Server (NTRS)

Langel, R. A.; Sabaka, T. J.; Ridgway, J. R.

1990-01-01

The DMSP F-7 satellite was an operational Air Force meteorological satellite which carried a magnetometer for geophysical measurements. The magnetometer was located within the body of the spacecraft in the presence of large spacecraft fields. In addition to stray magnetic fields, the data have inherent position and time inaccuracies. Algorithms were developed to identify and remove time varying magnetic field noise from the data. These algorithms are embodied in an automated procedure which fits a smooth curve through the data and then identifies outliers and which filters the predominant Fourier component of noise from the data. Techniques developed for Magsat were then modified and used to attempt determination of the spacecraft fields, of any rotation between the magnetometer axes and the spacecraft axes, and of any scale changes within the magnetometer itself. Software setup and usage are documented and program listings are included in the Appendix. The initial and resulting data are archived on magnetic cartridge and the formats are documented.

Toric focusing for radiation force applications using a toric lens coupled to a spherically focused transducer.

PubMed

Arnal, Bastien; Nguyen, Thu-Mai; O'Donnell, Matthew

2014-12-01

Dynamic elastography using radiation force requires that an ultrasound field be focused during hundreds of microseconds at a pressure of several megapascals. Here, we address the importance of the focal geometry. Although there is usually no control of the elevational focal width in generating a tissue mechanical response, we propose a tunable approach to adapt the focus geometry that can significantly improve radiation force efficiency. Several thin, in-house-made polydimethylsiloxane lenses were designed to modify the focal spot of a spherical transducer. They exhibited low absorption and the focal spot widths were extended up to 8-fold in the elevation direction. Radiation force experiments demonstrated an 8-fold increase in tissue displacements using the same pressure level in a tissue-mimicking phantom with a similar shear wave spectrum, meaning it does not affect elastography resolution. Our results demonstrate that larger tissue responses can be obtained for a given pressure level, or that similar response can be reached at a much lower mechanical index (MI). We envision that this work will impact 3-D elastography using 2-D phased arrays, where such shaping can be achieved electronically with the potential for adaptive optimization.

Radiation reaction on a classical charged particle: a modified form of the equation of motion.

PubMed

Alcaine, Guillermo García; Llanes-Estrada, Felipe J

2013-09-01

We present and numerically solve a modified form of the equation of motion for a charged particle under the influence of an external force, taking into account the radiation reaction. This covariant equation is integro-differential, as Dirac-Röhrlich's, but has several technical improvements. First, the equation has the form of Newton's second law, with acceleration isolated on the left hand side and the force depending only on positions and velocities: Thus, the equation is linear in the highest derivative. Second, the total four-force is by construction perpendicular to the four-velocity. Third, if the external force vanishes for all future times, the total force and the acceleration automatically vanish at the present time. We show the advantages of this equation by solving it numerically for several examples of external force.

Radiation reaction on a classical charged particle: A modified form of the equation of motion

NASA Astrophysics Data System (ADS)

Alcaine, Guillermo García; Llanes-Estrada, Felipe J.

2013-09-01

We present and numerically solve a modified form of the equation of motion for a charged particle under the influence of an external force, taking into account the radiation reaction. This covariant equation is integro-differential, as Dirac-Röhrlich's, but has several technical improvements. First, the equation has the form of Newton's second law, with acceleration isolated on the left hand side and the force depending only on positions and velocities: Thus, the equation is linear in the highest derivative. Second, the total four-force is by construction perpendicular to the four-velocity. Third, if the external force vanishes for all future times, the total force and the acceleration automatically vanish at the present time. We show the advantages of this equation by solving it numerically for several examples of external force.

Simulation model of fatigue crack opening/closing phenomena for predicting RPG load under arbitrary stress distribution field

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

Toyosada, M.; Niwa, T.

1995-12-31

In this paper, Newman`s calculation model is modified to solve his neglected effect of the change of stress distribution ahead of a crack, and to leave elastic plastic materials along the crack surface because of the compatibility of Dugdale model. In addition to above treatment, the authors introduce plastic shrinkage at an immediate generation of new crack surfaces due to emancipation of internal force with the magnitude of yield stress level during unloading process in the model. Moreover, the model is expanded to arbitrary stress distribution field. By using the model, RPG load is simulated for a center notched specimenmore » under constant amplitude loading with various stress ratios and decreased maximum load while keeping minimum load.« less

Topology, Geometry, and Mechanics of Z -Plasty

NASA Astrophysics Data System (ADS)

Matsumoto, Elisabetta A.; Liang, Haiyi; Mahadevan, L.

2018-02-01

Reconstructive surgeries often use topological manipulation of tissue to minimize postoperative scarring. The most common version of this, Z -plasty, involves modifying a straight line cut into a Z shape, followed by a rotational transposition of the resulting triangular pedicle flaps, and a final restitching of the wound. This locally reorients the anisotropic stress field and reduces the potential for scarring. We analyze the planar geometry and mechanics of the Z -plasty to quantify the rotation of the overall stress field and the local forces on the restitched cut using theory, simulations, and simple physical Z -plasty experiments with foam sheets that corroborate each other. Our study rationalizes the most typical surgical choice of this angle, and opens the way for a range of surgical decisions by characterizing the stresses along the cut.

Vibration Control via Stiffness Switching of Magnetostrictive Transducers

NASA Technical Reports Server (NTRS)

Scheidler, Justin J.; Asnani, Vivake M.; Dapino, Marcelo J.

2016-01-01

This paper presents a computational study of structural vibration control that is realized by switching a magnetostrictive transducer between high and low stiffness states. Switching is accomplished by either changing the applied magnetic field with a voltage excitation or changing the shunt impedance on the transducer's coil (i.e., the magnetostrictive material's magnetic boundary condition). Switched-stiffness vibration control is simulated using a lumped mass supported by a damper and the magnetostrictive transducer (mount), which is represented by a nonlinear, electromechanical model. Free vibration of the mass is calculated while varying the mount's stiffness according to a reference switched-stiffness vibration control law. The results reveal that switching the magnetic field produces the desired change in stiffness, but also an undesired actuation force that can significantly degrade the vibration control. Hence, a modified switched-stiffness control law that accounts for the actuation force is proposed and implemented for voltage-controlled stiffness switching. The influence of the magnetomechanical bias condition is also discussed. Voltage-controlled stiffness switching is found to introduce damping equivalent to a viscous damping factor up to about 0.25; this is shown to primarily result from active vibration reduction caused by the actuation force. The merit of magnetostrictive switched-stiffness vibration control is then quantified by comparing the results of voltage- and shunt-controlled stiffness switching to the performance of optimal magnetostrictive shunt damping.

Non-linear, non-monotonic effect of nano-scale roughness on particle deposition in absence of an energy barrier: Experiments and modeling

PubMed Central

Jin, Chao; Glawdel, Tomasz; Ren, Carolyn L.; Emelko, Monica B.

2015-01-01

Deposition of colloidal- and nano-scale particles on surfaces is critical to numerous natural and engineered environmental, health, and industrial applications ranging from drinking water treatment to semi-conductor manufacturing. Nano-scale surface roughness-induced hydrodynamic impacts on particle deposition were evaluated in the absence of an energy barrier to deposition in a parallel plate system. A non-linear, non-monotonic relationship between deposition surface roughness and particle deposition flux was observed and a critical roughness size associated with minimum deposition flux or “sag effect” was identified. This effect was more significant for nanoparticles (<1 μm) than for colloids and was numerically simulated using a Convective-Diffusion model and experimentally validated. Inclusion of flow field and hydrodynamic retardation effects explained particle deposition profiles better than when only the Derjaguin-Landau-Verwey-Overbeek (DLVO) force was considered. This work provides 1) a first comprehensive framework for describing the hydrodynamic impacts of nano-scale surface roughness on particle deposition by unifying hydrodynamic forces (using the most current approaches for describing flow field profiles and hydrodynamic retardation effects) with appropriately modified expressions for DLVO interaction energies, and gravity forces in one model and 2) a foundation for further describing the impacts of more complicated scales of deposition surface roughness on particle deposition. PMID:26658159

Non-linear, non-monotonic effect of nano-scale roughness on particle deposition in absence of an energy barrier: Experiments and modeling

NASA Astrophysics Data System (ADS)

Jin, Chao; Glawdel, Tomasz; Ren, Carolyn L.; Emelko, Monica B.

2015-12-01

Deposition of colloidal- and nano-scale particles on surfaces is critical to numerous natural and engineered environmental, health, and industrial applications ranging from drinking water treatment to semi-conductor manufacturing. Nano-scale surface roughness-induced hydrodynamic impacts on particle deposition were evaluated in the absence of an energy barrier to deposition in a parallel plate system. A non-linear, non-monotonic relationship between deposition surface roughness and particle deposition flux was observed and a critical roughness size associated with minimum deposition flux or “sag effect” was identified. This effect was more significant for nanoparticles (<1 μm) than for colloids and was numerically simulated using a Convective-Diffusion model and experimentally validated. Inclusion of flow field and hydrodynamic retardation effects explained particle deposition profiles better than when only the Derjaguin-Landau-Verwey-Overbeek (DLVO) force was considered. This work provides 1) a first comprehensive framework for describing the hydrodynamic impacts of nano-scale surface roughness on particle deposition by unifying hydrodynamic forces (using the most current approaches for describing flow field profiles and hydrodynamic retardation effects) with appropriately modified expressions for DLVO interaction energies, and gravity forces in one model and 2) a foundation for further describing the impacts of more complicated scales of deposition surface roughness on particle deposition.

The double-layer of penetrable ions: an alternative route to charge reversal.

PubMed

Frydel, Derek; Levin, Yan

2013-05-07

We investigate a double-layer of penetrable ions near a charged wall. We find a new mechanism for charge reversal that occurs in the weak-coupling regime and, accordingly, the system is suitable for the mean-field analysis. The penetrability is achieved by smearing-out the ionic charge inside a sphere, so there is no need to introduce non-electrostatic forces and the system in the low coupling limit can be described by a modified version of the Poisson-Boltzmann equation. The predictions of the theory are compared with the Monte Carlo simulations.

Radiatively driven winds from magnetic, fast-rotating stars

NASA Technical Reports Server (NTRS)

Nerney, S.

1986-01-01

An analytical procedure is developed to solve the magnetohydrodynamic equations for the stellar wind problem in the strong-magnetic field, optically thick limit for hot stars. The slow-mode, Alfven, and fast-mode critical points are modified by the radiation terms in the force equation but in a manner that can be treated relatively easily. Once the velocities at the critical points and the distances to the points are known, the streamline constants are determined in a straight-forward manner. This allows the structure of the wind to be elucidated without recourse to complicated computational schemes.

Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

PubMed

Schug, Alexander; Herges, Thomas; Verma, Abhinav; Lee, Kyu Hwan; Wenzel, Wolfgang

2005-12-09

The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.

KSC-2009-3462

NASA Image and Video Library

2009-05-31

CAPE CANAVERAL, Fla. – Bolted onto the Shuttle Carrier Aircraft, or SCA, a modified Boeing 747, space shuttle Atlantis gets ready for takeoff from Edwards Air Force Base in California, headed for its first stop at Biggs Army Air Field in El Paso, Texas. Atlantis landed at Edwards on May 24, which concluded mission STS-125, after two landing opportunities at Kennedy were waved off due to weather concerns. Atlantis is being returned to Florida on a ferry flight on the SCA. Atlantis' next assignment is the STS-129 mission, targeted to launch in November 2009. Photo credit: NASA/Ben Smegelsky

Control of microstructure in soldered, brazed, welded, plated, cast or vapor deposited manufactured components

DOEpatents

Ripley, Edward B.; Hallman, Russell L.

2015-11-10

Disclosed are methods and systems for controlling of the microstructures of a soldered, brazed, welded, plated, cast, or vapor deposited manufactured component. The systems typically use relatively weak magnetic fields of either constant or varying flux to affect material properties within a manufactured component, typically without modifying the alloy, or changing the chemical composition of materials or altering the time, temperature, or transformation parameters of a manufacturing process. Such systems and processes may be used with components consisting of only materials that are conventionally characterized as be uninfluenced by magnetic forces.

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

PubMed Central

Vanommeslaeghe, K.

2014-01-01

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

[Characteristics of electroosmotic flow in open-tubular capillary electrochromatography with magnetic nanoparticle coating as mixed-mode stationary phase].

PubMed

Qin, Sasa; Zhou, Chaoran; Zhu, Yaxian; Ren, Zhiyu; Zhang, Lingyi; Fu, Honggang; Zhang, Weibing

2011-09-01

A novel open-tubular capillary electrochromatography (OT-CEC) column with magnetic nanoparticle coating as mixed-mode stationary phase was prepared. The mixed-mode stationary phases were obtained by mixing C18 and amino modified magnetic nanoparticles with different ratios. The mixed modified magnetic nanoparticles as stationary phase were introduced into the capillary by using external magnetic force. The magnetic nanoparticle coating can be easily regenerated by removing the external magnetic field, and applied to other separation modes. The characteristics of electroosmotic flow (EOF) were theoretically investigated through the effect of physicochemical properties of different stationary phases on EOF. The experiment was conducted under different ratios of mixed-mode stationary phases and coating lengths, and it was verified that the theoretical conclusions accorded with the experimental results. It was shown that the EOF can be easily adjusted by changing the ratio of stationary phases or the number of permanent magnets.

Nonlinear analysis of thermally and electrically actuated functionally graded material microbeam.

PubMed

Li, Yingli; Meguid, S A; Fu, Yiming; Xu, Daolin

2014-02-08

In this paper, we provide a unified and self-consistent treatment of a functionally graded material (FGM) microbeam with varying thermal conductivity subjected to non-uniform or uniform temperature field. Specifically, it is our objective to determine the effect of the microscopic size of the beam, the electrostatic gap, the temperature field and material property on the pull-in voltage of the microbeam under different boundary conditions. The non-uniform temperature field is obtained by integrating the steady-state heat conduction equation. The governing equations account for the microbeam size by introducing an internal material length-scale parameter that is based on the modified couple stress theory. Furthermore, it takes into account Casimir and van der Waals forces, and the associated electrostatic force with the first-order fringing field effects. The resulting nonlinear differential equations were converted to a coupled system of algebraic equations using the differential quadrature method. The outcome of our work shows the dramatic effect and dependence of the pull-in voltage of the FGM microbeam upon the temperature field, its gradient for a given boundary condition. Specifically, both uniform and non-uniform thermal loading can actuate the FGM microbeam even without an applied voltage. Our work also reveals that the non-uniform temperature field is more effective than the uniform temperature field in actuating a FGM cantilever-type microbeam. For the clamped-clamped case, care must be taken to account for the effective use of thermal loading in the design of microbeams. It is also observed that uniform thermal loading will lead to a reduction in the pull-in voltage of a FGM microbeam for all the three boundary conditions considered.

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

PubMed

Vanommeslaeghe, K; MacKerell, A D

2015-05-01

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

Effects of modified short-leg walkers on ground reaction force characteristics.

PubMed

Keefer, Maria; King, Jon; Powell, Douglas; Krusenklaus, John H; Zhang, Songning

2008-11-01

Although short-leg walkers are often used in the treatment of lower extremity injuries (ankle and foot fractures and severe ankle sprains), little is known about the effect the short-leg walker on gait characteristics. The purpose was to examine how heel height modifications in different short-leg walkers and shoe side may affect ground reaction forces in walking. Force platforms were used to collect ground reaction force data on 10 healthy participants. Five trials were performed in each of six conditions: lab shoes, gait walker, gait walker with heel insert on shoe side, gait walker modified with insert on walker side, equalizer walker, and equalizer walker with heel insert on shoe side. Conditions were randomized and walking speed was standardized between conditions. A 2x6 (sidexcondition) repeated analysis of variance was used on selected ground reaction force variables (P<0.05). The application of a walker created peak vertical and anteroposterior ground reaction forces prior to the normal peaks associated with the loading response. Wearing a walker introduced an elevated minimum vertical ground reaction force in all conditions except the equalizer walker when compared to shoe on the shoe side. Peak propulsive anteroposterior ground reaction forces were smaller in all walker conditions compared to shoe on walker side. The application of heel insert in gait walker with heel insert (on shoe side) and gait walker modified (on walker side) does not diminish the minimum vertical ground reaction force as hypothesized. Wearing a walker decreases the peak propulsive anteroposterior ground reaction force on the walker side and induces asymmetrical loading.

Enhanced heat transfer with full circumferential ribs in helical pipe

NASA Astrophysics Data System (ADS)

Chang, S. W.; Su, L. M.; Yang, T. L.

2002-08-01

This paper describes an experimental study of heat transfers in the smooth-walled and rib-roughened helical pipes with reference to the design of enhanced cooling passages in the cylinder head and liner of a marine propulsive diesel engine. The manner in which the repeated ribs modify the forced heat convection in the helical pipe is considered for the case where the flow is turbulent upon entering the coil but laminar in further downstream. A selection of experimental results illustrates the individual and interactive effects of Dean vortices and rib-flows on heat transfer along the inner and outer helixes of coils. The experimental-based observations reveal that the centrifugal force modifies the heat transfer in a manner to generate circumferential heat transfer variation with better cooling performance on the outer edge relative to its inner counterpart even with the agitated flow field caused by the repeated ribs. Heat transfer augmentation factor in the range of 1.3 - 3 times of the smooth-walled level is achieved using the present ribbing geometry. A set of empirical correlations based on the experimental data has been developed to permit the evaluation of heat transfers along the inner and outer helixes of the smooth-walled and rib-roughened helical pipes.

Phoretic drag reduction of chemically active homogeneous spheres under force fields and shear flows

NASA Astrophysics Data System (ADS)

Yariv, Ehud; Kaynan, Uri

2017-01-01

Surrounded by a spherically symmetric solute cloud, chemically active homogeneous spheres do not undergo conventional autophoresis when suspended in an unbounded liquid domain. When exposed to external flows, solute advection deforms that cloud, resulting in a generally asymmetric distribution of diffusio-osmotic slip which, in turn, modifies particle motion. Inspired by classical forced-convection analyses [Acrivos and Taylor, Phys. Fluids 5, 387 (1962), 10.1063/1.1706630; Frankel and Acrivos, Phys. Fluids 11, 1913 (1968), 10.1063/1.1692218] we illustrate this phoretic phenomenon using two prototypic configurations, one where the particle sediments under a uniform force field and one where it is subject to a simple shear flow. In addition to the Péclet number Pe associated with the imposed flow, the governing nonlinear problem also depends upon α , the intrinsic Péclet number associated with the chemical activity of the particle. As in the forced-convection problems, the small-Péclet-number limit is nonuniform, breaking down at large distances away from the particle. Calculation of the leading-order autophoretic effects thus requires use of matched asymptotic expansions, the outer region being at distances that scale inversely with Pe and Pe1 /2 in the respective sedimentation and shear problems. In the sedimentation problem we find an effective drag reduction of fractional amount α /8 ; in the shear problem we find that the magnitude of the stresslet is decreased by a fractional amount α /4 . For a dilute particle suspension the latter result is manifested by a reduction of the effective viscosity.

Aerodynamic Simulation of the MARINTEK Braceless Semisubmersible Wave Tank Tests

NASA Astrophysics Data System (ADS)

Stewart, Gordon; Muskulus, Michael

2016-09-01

Model scale experiments of floating offshore wind turbines are important for both platform design for the industry as well as numerical model validation for the research community. An important consideration in the wave tank testing of offshore wind turbines are scaling effects, especially the tension between accurate scaling of both hydrodynamic and aerodynamic forces. The recent MARINTEK braceless semisubmersible wave tank experiment utilizes a novel aerodynamic force actuator to decouple the scaling of the aerodynamic forces. This actuator consists of an array of motors that pull on cables to provide aerodynamic forces that are calculated by a blade-element momentum code in real time as the experiment is conducted. This type of system has the advantage of supplying realistically scaled aerodynamic forces that include dynamic forces from platform motion, but does not provide the insights into the accuracy of the aerodynamic models that an actual model-scale rotor could provide. The modeling of this system presents an interesting challenge, as there are two ways to simulate the aerodynamics; either by using the turbulent wind fields as inputs to the aerodynamic model of the design code, or by surpassing the aerodynamic model and using the forces applied to the experimental turbine as direct inputs to the simulation. This paper investigates the best practices of modeling this type of novel aerodynamic actuator using a modified wind turbine simulation tool, and demonstrates that bypassing the dynamic aerodynamics solver of design codes can lead to erroneous results.

Experimental and Numerical Studies of Mechanically- and Convectively-Driven Turbulence in Planetary Interiors

NASA Astrophysics Data System (ADS)

Grannan, Alexander Michael

2017-08-01

The energy for driving turbulent flows in planetary fluid layers comes from a combination of thermocompositional sources and the motion of the boundary in contact with the fluid through mechanisms like precessional, tidal, and librational forcing. Characterizing the resulting turbulent fluid motions are necessary for understanding many aspects of the planet's dynamics and evolution including the generation of magnetic fields in the electrically conducting fluid layers and dissipation in the oceans. Although such flows are strongly inertial they are also strongly influenced by the Coriolis force whose source is in the rotation of the body and tends to constrain the inertial effects and provide support for fluid instabilities that might in-turn generate turbulence. Furthermore, the magnetic fields generated by the electrically conducting fluids act back on the fluid through the Lorentz force that also tends to constrain the flow. The goal of this dissertation is to investigate the characteristics of turbulent flows under the influence of mechanical, convective, rotational and magnetic forcing. In order to investigate the response of the fluid to mechanical forcing, I have modified a unique set of laboratory experiments that allows me to quantify the generation of turbulence driven by the periodic oscillations of the fluid containing boundary through tides and libration. These laboratory experiments replicate the fundamental ingredients found in planetary environments and are necessary for the excitation of instabilities that drive the turbulent fluid motions. For librational forcing, a rigid ellipsoidal container and ellipsoidal shell of isothermal unstratified fluid is made to rotate with a superimposed oscillation while, for tidal forcing, an elastic ellipsoidal container of isothermal unstratified fluid is made to rotate while an independently rotating perturbance also flexes the elastic container. By varying the strength and frequencies of these oscillations the characteristics of the resulting turbulence are investigated using meridional views to identify the dominate modes and spatial location of the turbulence. For the first time, measurements of the velocity in the equatorial plane are coupled with high resolution numerical simulations of the full flow field in identical geometry to characterize the instability mechanism, energy deposited into the fluid layer, and long-term evolution of the flow. The velocities determined through laboratory and numerical simulations when extrapolated to planets allow me to argue that the dynamics of mechanical forcing in low viscosity fluids may an important role as new and potentially large source of dissipation in planetary interiors. To study convective forcing, I have modified and performed a set of rotating and non-rotating hydrodynamic convection experiments using water as well as rotating and non-rotating magnetohydrodynamic convection in gallium. These studies are performed in a cylindrical geometry representing a model of high latitude planetary core style convection wherein the axis of rotation and gravity are aligned. For the studies using water, the steady columns that are characteristic of rotating convection and present in the dynamo models are likely to destabilize at the more extreme planetary parameters giving way to transitions to more complex styles of rotating turbulent flow. In the studies of liquid metal where the viscosity is lower, the onset of rotating convection occurs through oscillatory columnar convection well below the onset of steady columns. Such oscillatory modes are not represented at the parameters used by current dynamo models. Furthermore a suite of laboratory experiments shows that the imposition of rotational forces and magnetic forces both separately and together generate zeroeth order flow transitions that change the fundamental convective modes and heat transfer. Such regimes are more easily accessible to laboratory experiments then to numerical simulations but demonstrate the need for a new generation of dynamo simulations capable of including the fundamental properties of liquid metals as are relevant for understanding the dynamics of planetary interiors.

Recent Developments and Applications of the CHARMM force fields

PubMed Central

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

2011-01-01

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

22 CFR 126.12 - Continuation in force.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Continuation in force. 126.12 Section 126.12... PROVISIONS § 126.12 Continuation in force. All determinations, authorizations, licenses, approvals of... previous provisions of this subchapter, continue in full force and effect until or unless modified, revoked...

Adsorption of Wine Constituents on Functionalized Surfaces.

PubMed

Mierczynska-Vasilev, Agnieszka; Smith, Paul A

2016-10-18

The adsorption of macromolecules on solid surfaces is of great importance in the field of nanotechnology, biomaterials, biotechnological, and food processes. In the field of oenology adsorption of wine macromolecules such as polyphenols, polysaccharides, and proteins is much less desirable on membrane materials because of fouling and reduced filtering performance. On the other hand, adsorption of these molecules on processing aids is very beneficial for achieving wine clarity and stability. In this article, the effect of surface chemical functionalities on the adsorption of white, rosé, and red wine constituents was evaluated. Allylamine, acrylic acid, and ethanol were selected as precursors for plasma polymerization in order to generate coatings rich in amine, carboxyl, and hydroxyl chemical groups, respectively. The surface chemical functionalities were characterized by X-ray photoelectron spectroscopy (XPS) and the ability of different surface chemical functionalities to adsorb wine constituents were characterized by quartz crystal microbalance with dissipation (QCM-D) and atomic force microscopy (AFM). The results demonstrated that the amine and carboxyl modified surfaces encourage adsorption of constituents from white wine. The hydroxyl modified surfaces have the ability to preferentially adsorb rosé wine constituents, whereas red wine adsorbed to the highest extent on acrylic acid surface.

The Space Shuttle Endeavour, mounted securely atop one of NASA's modified Boeing 747 Shuttle Carrier Aircraft, left NASA's Dryden Flight Research Center at Edwards Air Force Base in Southern California at sunrise on Friday, June 28

NASA Image and Video Library

2002-06-28

The Space Shuttle Endeavour, mounted securely atop one of NASA's modified Boeing 747 Shuttle Carrier Aircraft, left NASA's Dryden Flight Research Center at Edwards Air Force Base in Southern California at sunrise on Friday, June 28.

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

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

PubMed

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

2014-09-01

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

Measurements of Induced-Charge Electroosmotic Flow Around a Metallic Rod

NASA Astrophysics Data System (ADS)

Beskok, Ali; Canpolat, Cetin

2012-11-01

A cylindrical gold-coated stainless steel rod was positioned at the center of a straight microchannel connecting two fluid reservoirs on either end. The microchannel was filled with 1 mM KCl containing 0.5 micron diameter carboxylate-modified spherical particles. Induced-charge electro-osmotic (ICEO) flow occurred around the metallic rod under a sinusoidal AC electric field applied using two platinum electrodes. The ICEO flows around the metallic rod were measured using micro particle image velocimetry (micro-PIV) technique as functions of the AC electric field strength and frequency. The present study provides experimental data about ICEO flow in the weakly nonlinear limit of thin double layers, in which, the charging dynamics of the double layer cannot be presented analytically. Flow around the rod is quadrupolar, driving liquid towards the rod along the electric field and forcing it away from the rod in the direction perpendicular to the imposed electric field. The measured ICEO flow velocity is proportional to the square of the electric field strength, and depends on the applied AC frequency.

Modeling contamination of shallow unconfined aquifers through infiltration beds

USGS Publications Warehouse

Ostendorf, D.W.

1986-01-01

We model the transport of a simply reactive contaminant through an infiltration bed and underlying shallow, one-dimensional, unconfined aquifer with a plane, steeply sloping bottom in the assumed absence of dispersion and downgradient dilution. The effluent discharge and ambient groundwater flow under the infiltration beds are presumed to form a vertically mixed plume marked by an appreciable radial velocity component in the near field flow region. The near field analysis routes effluent contamination as a single linear reservoir whose output forms a source plane for the one-dimensional, far field flow region downgradient of the facility; the location and width of the source plane reflect the relative strengths of ambient flow and effluent discharge. We model far field contaminant transport, using an existing method of characteristics solution with frame speeds modified by recharge, bottom slope, and linear adsorption, and concentrations reflecting first-order reaction kinetics. The near and far field models simulate transport of synthetic detergents, chloride, total nitrogen, and boron in a contaminant plume at the Otis Air Force Base sewage treatment plant in Barnstable County, Massachusetts, with reasonable accuracy.

The Dynamics of Oblate Drop Between Heterogeneous Plates Under Alternating Electric Field. Non-uniform Field

NASA Astrophysics Data System (ADS)

Kashina, M. A.; Alabuzhev, A. A.

2018-02-01

The dynamics of the incompressible fluid drop under the non-uniform electric field are considered. The drop is bounded axially by two parallel solid planes and the case of heterogeneous plates is investigated. The external electric field acts as an external force that causes motion of the contact line. We assume that the electric current is alternative current and the AC filed amplitude is a spatially non-uniform function. In equilibrium, the drop has the form of a circular cylinder. The equilibrium contact angle is 0.5 π. In order to describe this contact line motion the modified Hocking boundary condition is applied: the velocity of the contact line is proportional to the deviation of the contact angle and the speed of the fast relaxation processes, which frequency is proportional to twice the frequency of the electric field. The Hocking parameter depends on the polar angle, i.e. the coefficient of the interaction between the plate and the fluid (the contact line) is a function of the plane coordinates. This function is expanded in a series of the Laplace operator eigenfunctions.

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.

The forced-choice paradigm and the perception of facial expressions of emotion.

PubMed

Frank, M G; Stennett, J

2001-01-01

The view that certain facial expressions of emotion are universally agreed on has been challenged by studies showing that the forced-choice paradigm may have artificially forced agreement. This article addressed this methodological criticism by offering participants the opportunity to select a none of these terms are correct option from a list of emotion labels in a modified forced-choice paradigm. The results show that agreement on the emotion label for particular facial expressions is still greater than chance, that artifactual agreement on incorrect emotion labels is obviated, that participants select the none option when asked to judge a novel expression, and that adding 4 more emotion labels does not change the pattern of agreement reported in universality studies. Although the original forced-choice format may have been prone to artifactual agreement, the modified forced-choice format appears to remedy that problem.

Correlation of the Capacity Factor in Vesicular Electrokinetic Chromatography with the Octanol:Water Partition Coefficient for Charged and Neutral Analytes

PubMed Central

Razak, J. L.; Cutak, B. J.; Larive, C. K.; Lunte, C. E.

2008-01-01

Purpose The aim of this study was to develop a method based upon electrokinetic chromatography (EKC) using oppositely charged surfactant vesicles as a buffer modifier to estimate hydrophobicity (log P) for a range of neutral and charged compounds. Methods Vesicles were formed from cetyltrimethylammonium bromide (CTAB) and sodium n-octyl sulfate (SOS). The size and polydispersity of the vesicles were characterized by electron microscopy, dynamic light scattering, and pulsed-field gradient NMR (PFG-NMR). PFG-NMR was also used to determine if ion-pairing between cationic analytes and free SOS monomer occurred. The CTAB/SOS vesicles were used as a buffer modifier in capillary electrophoresis (CE). The capacity factor (log k′) was calculated by determining the mobility of the analytes both in the presence and absence of vesicles. Log k′ was determined for 29 neutral and charged analytes. Results There was a linear relationship between the log of capacity factor (log k′) and octanol/water partition coefficient (log P) for both neutral and basic species at pH 6.0, 7.3, and 10.2. This indicated that interaction between the cation and vesicle was dominated by hydrophobic forces. At pH 4.3, the log k′ values for the least hydrophobic basic analytes were higher than expected, indicating that electrostatic attraction as well as hydrophobic forces contributed to the overall interaction between the cation and vesicle. Anionic compounds could not be evaluated using this system. Conclusion Vesicular electrokinetic chromatography (VEKC) using surfactant vesicles as buffer modifiers is a promising method for the estimation of hydrophobicity. PMID:11336344

Meso-beta scale numerical simulation studies of terrain-induced jet streak mass/momentum perturbations

NASA Technical Reports Server (NTRS)

Lin, Yuh-Lang; Kaplan, Michael L.

1995-01-01

Mesoscale model simulations provide insight into the complex jet streak adjustments on 11-12 July 1981 that preceded the first of two significant gravity wave events to have been generated over the Rocky Mountains in Montana. Simulations employing a variety of terrain treatments indicate that prior to wave formation, geostrophic adjustment processes modified the structure of the mid-upper tropospheric jet streak by creating secondary jetlets to the southeast of the polar jet streak in proximity to the gravity wave generation region. This simulated restructuring of the mid-upper tropospheric jet streak is the result of a four stage process. During stage 1, the wind adjusts to the mass field as the jet streak exit region propagates into the inflection point between the upstream trough and downstream ridge in the height field. Stage 2 is initiated as the mass field is forced to adjust to the new ageostrophic wind field created during stage 1. Stage 3 is defined by a second geostrophic adjustment process occurring in a similar manner but to the south and east of the adjustment which occurs during stage 1. A low-level mesoscale jetlet is formed during stage 4 in response to the low-level pressure falls that are established during stage 3. The perturbation of this jetlet, caused by orographically-induced adiabatic and diabatic physical processes, is the likely mechanism responsible for the generation of the first and second episode of observed gravity waves. The dynamics responsible for this wave episode are discussed as differential surface sensible heating inducing an orographically-forced mountain-plains solenoid, resulting in the formation of additional mesoscale jetlets and internal gravity waves. Also discussed is how convective latent heating modifies the numerically simulated terrain-induced internal gravity waves, especially their amplitude and phase velocities, which provide better agreement with those wave characteristics observed in nature. Finally, the three-dimensional linear response of a zonally uniform barotropic flow in a vertically unbounded, continuously stratified, Boussinesq atmosphere which is perturbed from geostrophic equilibrium is investigated.

The effect of an external electric field on the growth of incongruent-melting material

NASA Astrophysics Data System (ADS)

Uda, Satoshi; Huang, Xinming; Wang, Shou-Qi

2005-02-01

The significance of an electric field on the crystallization process is differentiated into two consequences; (i) thermodynamic effect and (ii) growth-dynamic effect. The former modifies the chemical potential of the associated phases which changes the equilibrium phase relationship while the latter influences the solute transport, growth kinetics, surface creation and defect generation during growth. The intrinsic electric field generating during growth is attributed to the crystallization-related electromotive force and the thermoelectric power driven by the temperature gradient at the interface which influences the solute transport and solute partitioning. The external electric field was applied to the growth apparatus in the ternary system of La2O3- Ga2O3- SiO2 so that the chemical potential of both solid and liquid phases changed leading to the variation of the equilibrium phase relationship. Imposing a 500 V/cm electric field on the system moved the boundary of primary phase field of lanthanum gallate ( LaGaO3) and Ga-bearing lanthanum silicate ( La14GaxSi9-xO) toward the SiO2 apex by 5 mol% which clearly demonstrated the change of the phase relationship by the external electric field.

5 CFR 930.210 - Reduction in force.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Reduction in force. 930.210 Section 930... § 930.210 Reduction in force. (a) Retention preference regulations. Except as modified by this section, the reduction in force regulations in part 351 of this chapter apply to administrative law judges. (b...

Modified cantilevers to probe unambiguously out-of-plane piezoresponse

NASA Astrophysics Data System (ADS)

Alyabyeva, Natalia; Ouvrard, Aimeric; Lindfors-Vrejoiu, Ionela; Kolomiytsev, Alexey; Solodovnik, Maxim; Ageev, Oleg; McGrouther, Damien

2018-06-01

We demonstrate and investigate the coupling of contributions from both in-plane (IP) polarization and out-of-plane (OP) components in BiFeO3 (BFO) thin-film polarization probed by piezoresponse force microscopy (PFM). Such coupling leads to image artifacts which prevent the correct determination of OP polarization vector directions and the corresponding piezoelectric coefficient d33. Using material strength theory with a one-dimensional modeling of the cantilever oscillation amplitude under electrostatic and elastic forces as a function of the tip length, we have evidenced the impact of IP piezoresponse to the OP signal for tip length longer than 4 μm. The IP polarization vector induces a significant longitudinal bending of the cantilever, due to the small spring constant of long tips, which provokes a normal deviation superimposed to the OP piezoresponse. These artifacts can be reduced by increasing the longitudinal spring constant of the cantilever by shortening the tip length. Standard cantilevers with 15-μm-long tips were modified to reach the desired tip length, using focused ion-beam techniques and tested using PFM on the same BFO thin film. Tip length shortening has strongly reduced IP artifacts as expected, while the impact of nonlocal electrostatic forces, becoming predominant for tips shorter than 1 μm, has led to a non-negligible deflection offset. For shorter tips, a strong electric field from a cantilever beam can induce polarization switching as observed for a 0.5-μm-long tip. Tip length ranging from 1 to 4 μm allowed minimizing both artifacts to probe unambiguously OP piezoresponse and quantify the d33 piezoelectric coefficient.

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

PubMed

Narth, Christophe; Lagardère, Louis; Polack, Étienne; Gresh, Nohad; Wang, Qiantao; Bell, David R; Rackers, Joshua A; Ponder, Jay W; Ren, Pengyu Y; Piquemal, Jean-Philip

2016-02-15

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. Copyright © 2016 Wiley Periodicals, Inc.

Magneto-elastic modeling of composites containing chain-structured magnetostrictive particles

NASA Astrophysics Data System (ADS)

Yin, H. M.; Sun, L. Z.; Chen, J. S.

2006-05-01

Magneto-elastic behavior is investigated for two-phase composites containing chain-structured magnetostrictive particles under both magnetic and mechanical loading. To derive the local magnetic and elastic fields, three modified Green's functions are derived and explicitly integrated for the infinite domain containing a spherical inclusion with a prescribed magnetization, body force, and eigenstrain. A representative volume element containing a chain of infinite particles is introduced to solve averaged magnetic and elastic fields in the particles and the matrix. Effective magnetostriction of composites is derived by considering the particle's magnetostriction and the magnetic interaction force. It is shown that there exists an optimal choice of the Young's modulus of the matrix and the volume fraction of the particles to achieve the maximum effective magnetostriction. A transversely isotropic effective elasticity is derived at the infinitesimal deformation. Disregarding the interaction term, this model provides the same effective elasticity as Mori-Tanaka's model. Comparisons of model results with the experimental data and other models show the efficacy of the model and suggest that the particle interactions have a considerable effect on the effective magneto-elastic properties of composites even for a low particle volume fraction.

SENSITIVITY OF HELIOSEISMIC TRAVEL TIMES TO THE IMPOSITION OF A LORENTZ FORCE LIMITER IN COMPUTATIONAL HELIOSEISMOLOGY

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

Moradi, Hamed; Cally, Paul S., E-mail: hamed.moradi@monash.edu

The rapid exponential increase in the Alfvén wave speed with height above the solar surface presents a serious challenge to physical modeling of the effects of magnetic fields on solar oscillations, as it introduces a significant Courant-Friedrichs-Lewy time-step constraint for explicit numerical codes. A common approach adopted in computational helioseismology, where long simulations in excess of 10 hr (hundreds of wave periods) are often required, is to cap the Alfvén wave speed by artificially modifying the momentum equation when the ratio between the Lorentz and hydrodynamic forces becomes too large. However, recent studies have demonstrated that the Alfvén wave speedmore » plays a critical role in the MHD mode conversion process, particularly in determining the reflection height of the upwardly propagating helioseismic fast wave. Using numerical simulations of helioseismic wave propagation in constant inclined (relative to the vertical) magnetic fields we demonstrate that the imposition of such artificial limiters significantly affects time-distance travel times unless the Alfvén wave-speed cap is chosen comfortably in excess of the horizontal phase speeds under investigation.« less

Spreading of a liquid film on a substrate by the evaporation-adsorption process

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

Wayner, P.C. Jr.; Schonberg, J.

1992-09-01

The importance of evaporation followed by multilayer adsorption in comparison to liquid flow at the leading edge of a volatile spreading film is analyzed. Presuming that both flows are functions of the same chemical potential gradient, a dimensionless group (N) which delineates the relative importance of vapor diffusion flow to viscous flow on the surface is obtained: N = [rho][sub i]D[nu]x/([minus][bar A][pi]). The relative importance of vapor flow increases with the vapor-pressure dependent partial density, [rho][sub i], and diffusivity, D, of the diffusing vapor, the kinematic viscosity of the liquid, [nu], and the distance downstream from the bulk liquid region,more » x, and decreases with the Hamaker constant, 6[pi][bar A]. Using physical properties the modifiers volatile'' and nonvolatile'' can thereby be put in perspective. Changes in the interfacial force field are a function of [bar A]. The spreading velocity due to the vapor diffusion process is obtained and is found to decrease with a decrease in the interfacial force field and the bulk vapor pressure. The infinite stress at the contact line can be easily relieved by evaporation-adsorption in many systems.« less

Lyapunov Orbits in the Jupiter System Using Electrodynamic Tethers

NASA Technical Reports Server (NTRS)

Bokelmann, Kevin; Russell, Ryan P.; Lantoine, Gregory

2013-01-01

Various researchers have proposed the use of electrodynamic tethers for power generation and capture from interplanetary transfers. The effect of tether forces on periodic orbits in Jupiter-satellite systems are investigated. A perturbation force is added to the restricted three-body problem model and a series of simplifications allows development of a conservative system that retains the Jacobi integral. Expressions are developed to find modified locations of equilibrium positions. Modified families of Lyapunov orbits are generated as functions of tether size and Jacobi integral. Zero velocity curves and stability analyses are used to evaluate the dynamical properties of tether-modified orbits.

Vibrational properties of TaW alloy using modified embedded atom method potential

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

Chand, Manesh, E-mail: maneshchand@gmail.com; Uniyal, Shweta; Joshi, Subodh

2016-05-06

Force-constants up to second neighbours of pure transition metal Ta and TaW alloy are determined using the modified embedded atom method (MEAM) potential. The obtained force-constants are used to calculate the phonon dispersion of pure Ta and TaW alloy. As a further application of MEAM potential, the force-constants are used to calculate the local vibrational density of states and mean square thermal displacements of pure Ta and W impurity atoms with Green’s function method. The calculated results are found to be in agreement with the experimental measurements.

Enhancing the Detection of Dysmorphic Red Blood Cells and Renal Tubular Epithelial Cells with a Modified Urinalysis Protocol.

PubMed

Chu-Su, Yu; Shukuya, Kenichi; Yokoyama, Takashi; Lin, Wei-Chou; Chiang, Chih-Kang; Lin, Chii-Wann

2017-01-11

Urinary sediment is used to evaluate patients with possible urinary tract diseases. Currently, numerous protocols are applied to detect dysmorphic red blood cells (RBCs) and renal tubular epithelial cells (RTECs) in urinary sediment. However, distinct protocols are used by nephrologists and medical technologists for specimen concentration and observation, which leads to major discrepancies in the differential counts of formed elements such as dysmorphic RBCs and RTECs and might interfere with an accurate clinical diagnosis. To resolve these problems, we first tested a modified urinalysis protocol with an increased relative centrifuge force and concentration factor in 20 biopsy-confirmed glomerulonephritis patients with haematuria. We successfully improved the recovery ratio of dysmorphic RBCs in clinical specimens from 34.7% to 42.0% (P < 0.001). Furthermore, we confirmed the correlation between counts by the modified urinary protocol and Sysmex UF-1000i urinary flow cytometer (r ≥ 0.898, P < 0.001). A total of 28 types of isomorphic and dysmorphic RBCs were detected using a bright field microscope, with results comparable to those using a standard phase contrast microscope. Finally, we applied Sternheimer stain to enhance the contrast of RTECs in the urinary sediments. We concluded that this modified urinalysis protocol significantly enhanced the quality of urinalysis.

Enhancing the Detection of Dysmorphic Red Blood Cells and Renal Tubular Epithelial Cells with a Modified Urinalysis Protocol

PubMed Central

Chu-Su, Yu; Shukuya, Kenichi; Yokoyama, Takashi; Lin, Wei-Chou; Chiang, Chih-Kang; Lin, Chii-Wann

2017-01-01

Urinary sediment is used to evaluate patients with possible urinary tract diseases. Currently, numerous protocols are applied to detect dysmorphic red blood cells (RBCs) and renal tubular epithelial cells (RTECs) in urinary sediment. However, distinct protocols are used by nephrologists and medical technologists for specimen concentration and observation, which leads to major discrepancies in the differential counts of formed elements such as dysmorphic RBCs and RTECs and might interfere with an accurate clinical diagnosis. To resolve these problems, we first tested a modified urinalysis protocol with an increased relative centrifuge force and concentration factor in 20 biopsy-confirmed glomerulonephritis patients with haematuria. We successfully improved the recovery ratio of dysmorphic RBCs in clinical specimens from 34.7% to 42.0% (P < 0.001). Furthermore, we confirmed the correlation between counts by the modified urinary protocol and Sysmex UF-1000i urinary flow cytometer (r ≥ 0.898, P < 0.001). A total of 28 types of isomorphic and dysmorphic RBCs were detected using a bright field microscope, with results comparable to those using a standard phase contrast microscope. Finally, we applied Sternheimer stain to enhance the contrast of RTECs in the urinary sediments. We concluded that this modified urinalysis protocol significantly enhanced the quality of urinalysis. PMID:28074941

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

USDA-ARS?s Scientific Manuscript database

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

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

PubMed

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

2016-03-15

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

Impact of spectral nudging on the downscaling of tropical cyclones in regional climate simulations

NASA Astrophysics Data System (ADS)

Choi, Suk-Jin; Lee, Dong-Kyou

2016-06-01

This study investigated the simulations of three months of seasonal tropical cyclone (TC) activity over the western North Pacific using the Advanced Research WRF Model. In the control experiment (CTL), the TC frequency was considerably overestimated. Additionally, the tracks of some TCs tended to have larger radii of curvature and were shifted eastward. The large-scale environments of westerly monsoon flows and subtropical Pacific highs were unreasonably simulated. The overestimated frequency of TC formation was attributed to a strengthened westerly wind field in the southern quadrants of the TC center. In comparison with the experiment with the spectral nudging method, the strengthened wind speed was mainly modulated by large-scale flow that was greater than approximately 1000 km in the model domain. The spurious formation and undesirable tracks of TCs in the CTL were considerably improved by reproducing realistic large-scale atmospheric monsoon circulation with substantial adjustment between large-scale flow in the model domain and large-scale boundary forcing modified by the spectral nudging method. The realistic monsoon circulation took a vital role in simulating realistic TCs. It revealed that, in the downscaling from large-scale fields for regional climate simulations, scale interaction between model-generated regional features and forced large-scale fields should be considered, and spectral nudging is a desirable method in the downscaling method.

Fluidic Spacetime and Representation of Fields in the Tri-Space Model of the Universe

NASA Astrophysics Data System (ADS)

Meholic, Gregory V.

2009-03-01

The Tri-Space Model of the universe (see Meholic, 1998 and 2004) is based upon the premise that the governing mathematics of special relativity describe a symmetrical continuum that supports not just one, but three, independent spacetimes each with a unique set of physical laws founded on the velocity v to light speed c ratio. These realms are subluminal space (where v/c<1), luminal spacetime (where v/c = 1), and superluminal space (where v/c>1) together comprising the `tri-space' universe. Although real, measurable mass can exist in both the sub- and superluminal spaces, the adjacent luminal spacetime shared by the two spaces is the realm in which all electromagnetic and gravitational fields exist. Determining the true nature of spacetime, and hence the true nature of the fundamental forces, has been the driving objective for ideas such as string theory and quantum mechanics. The Tri-Space approach, however, merges the basic premises of these ideas with the philosophy that the three spatial realms, especially luminal spacetime, can be represented as a quasi-fluidic continuum whose behavior can be approximated through modified classical fluid-dynamic analogies with flow field structure and fluid properties. If the fluid-like properties of spacetime can be sufficiently defined, then a graphical representation of the fundamental structure and characterization of the basic forces in nature can be developed.

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.

What is the force on a magnetic dipole?

NASA Astrophysics Data System (ADS)

Franklin, Jerrold

2018-05-01

This paper will be of interest to physics graduate students and faculty. We show that attempts to modify the force on a magnetic dipole by introducing either hidden momentum or internal forces are not correct. The standard textbook result {F}={{\

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.

Investigation of impingement region and wall jets formed by the interaction of high aspect ratio lift jets and a ground plane

NASA Technical Reports Server (NTRS)

Kotansky, D. R.; Glaze, L. W.

1978-01-01

Flow characteristics of impinging jets emanating from rectangular exit area converging nozzles of exit area aspect ratio four, six, and eight were investigated. Azimuthal distributions of wall jet radial momentum flux in the ground plane were strongly directional and sensitive to rectangular nozzle exit area aspect ratio, jet impingement angle, and height above ground, H/D. Effects of jet exit velocity profile nonuniformities were also investigated. Data from the single nozzle rectangular jet impringement investigations were incorporated into an existing VTOL aircraft ground flow field computer program. It is suggested that this program together with the Douglas Neumann program modified for V/STOL applications may be used for the analysis and prediction of flow fields and resulting forces and moments on multijet V/STOL aircraft hovering in ground effect.

Scanning hall probe microscopy (SHPM) using quartz crystal AFM feedback.

PubMed

Dede, M; Urkmen, K; Girişen, O; Atabak, M; Oral, A; Farrer, I; Ritchie, D

2008-02-01

Scanning Hall Probe Microscopy (SHPM) is a quantitative and non-invasive technique for imaging localized surface magnetic field fluctuations such as ferromagnetic domains with high spatial and magnetic field resolution of approximately 50 nm and 7 mG/Hz(1/2) at room temperature. In the SHPM technique, scanning tunneling microscope (STM) or atomic force microscope (AFM) feedback is used to keep the Hall sensor in close proximity of the sample surface. However, STM tracking SHPM requires conductive samples; therefore the insulating substrates have to be coated with a thin layer of gold. This constraint can be eliminated with the AFM feedback using sophisticated Hall probes that are integrated with AFM cantilevers. However it is very difficult to micro fabricate these sensors. In this work, we have eliminated the difficulty in the cantilever-Hall probe integration process, just by gluing a Hall Probe chip to a quartz crystal tuning fork force sensor. The Hall sensor chip is simply glued at the end of a 32.768 kHz or 100 kHz Quartz crystal, which is used as force sensor. An LT-SHPM system is used to scan the samples. The sensor assembly is dithered at the resonance frequency using a digital Phase Locked Loop circuit and frequency shifts are used for AFM tracking. SHPM electronics is modified to detect AFM topography and the frequency shift, along with the magnetic field image. Magnetic domains and topography of an Iron Garnet thin film crystal, NdFeB demagnetised magnet and hard disk samples are presented at room temperature. The performance is found to be comparable with the SHPM using STM feedback.

Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pK(a) shifts of protein residues.

PubMed

Sharma, Ity; Kaminski, George A

2017-01-15

Our Fuzzy-Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second-order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK a value of 7.37 units. Thus, the presented model is capable or reproducing pK a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors

NASA Astrophysics Data System (ADS)

Santos-Filho, Osvaldo A.; Mishra, Rama K.; Hopfinger, A. J.

2001-09-01

Free energy force field (FEFF) 3D-QSAR analysis was used to construct ligand-receptor binding models for a set of 18 structurally diverse antifolates including pyrimethamine, cycloguanil, methotrexate, aminopterin and trimethoprim, and 13 pyrrolo[2,3-d]pyrimidines. The molecular target (`receptor') used was a 3D-homology model of a specific mutant type of Plasmodium falciparum (Pf) dihydrofolate reductase (DHFR). The dependent variable of the 3D-QSAR models is the IC50 inhibition constant for the specific mutant type of PfDHFR. The independent variables of the 3D-QSAR models (the descriptors) are scaled energy terms of a modified first-generation AMBER force field combined with a hydration shell aqueous solvation model and a collection of 2D-QSAR descriptors often used in QSAR studies. Multiple temperature molecular dynamics simulation (MDS) and the genetic function approximation (GFA) were employed using partial least square (PLS) and multidimensional linear regressions as the fitting functions to develop FEFF 3D-QSAR models for the binding process. The significant FEFF energy terms in the best 3D-QSAR models include energy contributions of the direct ligand-receptor interaction. Some changes in conformational energy terms of the ligand due to binding to the enzyme are also found to be important descriptors. The FEFF 3D-QSAR models indicate some structural features perhaps relevant to the mechanism of resistance of the PfDHFR to current antimalarials. The FEFF 3D-QSAR models are also compared to receptor-independent (RI) 4D-QSAR models developed in an earlier study and subsequently refined using recently developed generalized alignment rules.

A Smart Magnetically Active Nanovehicle for on-Demand Targeted Drug Delivery: Where van der Waals Force Balances the Magnetic Interaction.

PubMed

Panja, Sudipta; Maji, Somnath; Maiti, Tapas K; Chattopadhyay, Santanu

2015-11-04

The magnetic field is a promising external stimulus for controlled and targeted delivery of therapeutic agents. Here, we focused on the preparation of a novel magnetically active polymeric micelle (MAPM) for magnetically targeted controlled drug delivery. To accomplish this, a number of superparamagnetic as well as biocompatible hybrid micelles were prepared by grafting four armed pentaerythretol poly(ε-caprolactone) (PE-PCL) onto the surface of Fe3O4 magnetic nanoparticles (MNPs) of two different ranges of size (∼5 nm and ∼15 nm). PE-PCL (four-armed) was synthesized by ring-opening polymerization, and it has been subsequently grafted onto the surface of modified MNP through urethane (-NHCO-) linkage. Polymer-immobilized MNP (5 and 15 nm) showed peculiar dispersion behavior. One displayed uniform dispersion of MNP (5 nm), while the other (15 nm) revealed associated structure. This type of size dependent contradictory dispersion behavior was realized by taking the van der Waals force as well as magnetic dipole-dipole force into consideration. The uniformly dispersed polymer immobilized MNP (5 nm) was used for the preparation of MAPM. The hydrodynamic size and bulk morphology of MAPM were studied by dynamic light scattering and high-resolution transmission electron microscopy. The anticancer drug (DOX) was encapsulated into the MAPM. The magnetic field triggers cell uptake of MAPM micelles preferentially toward targeted cells compare to untargeted ones. The cell viabilities of MAMP, DOX-encapsulated MAPM, and free DOX were studied against HeLa cell by MTT assay. In vitro release profile displayed about 51.5% release of DOX from MAPM (just after 1 h) under the influence of high frequency alternating magnetic field (HFAMF; prepared in-house device). The DOX release rate has also been tailored by on-demand application of HFAMF.

Restoration of the contact surface in FORCE-type centred schemes I: Homogeneous two-dimensional shallow water equations

NASA Astrophysics Data System (ADS)

Canestrelli, Alberto; Toro, Eleuterio F.

2012-10-01

Recently, the FORCE centred scheme for conservative hyperbolic multi-dimensional systems has been introduced in [34] and has been applied to Euler and relativistic MHD equations, solved on unstructured meshes. In this work we propose a modification of the FORCE scheme, named FORCE-Contact, that provides improved resolution of contact and shear waves. This paper presents the technique in full detail as applied to the two-dimensional homogeneous shallow water equations. The improvements due to the new method are particularly evident when an additional equation is solved for a tracer, since the modified scheme exactly resolves isolated and steady contact discontinuities. The improvement is considerable also for slowly moving contact discontinuities, for shear waves and for steady states in meandering channels. For these types of flow fields, the numerical results provided by the new FORCE-Contact scheme are comparable with, and sometimes better than, the results obtained from upwind schemes, such as Roes scheme for example. In a companion paper, a similar approach to restoring the missing contact wave and preserving well-balanced properties for non-conservative one- and two-layer shallow water equations is introduced. However, the procedure is general and it is in principle applicable to other multidimensional hyperbolic systems in conservative and non-conservative form, such as the Euler equations for compressible gas dynamics.

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

MEAM interatomic force calculation subroutine for LAMMPS

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

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

Modified two-layer social force model for emergency earthquake evacuation

NASA Astrophysics Data System (ADS)

Zhang, Hao; Liu, Hong; Qin, Xin; Liu, Baoxi

2018-02-01

Studies of crowd behavior with related research on computer simulation provide an effective basis for architectural design and effective crowd management. Based on low-density group organization patterns, a modified two-layer social force model is proposed in this paper to simulate and reproduce a group gathering process. First, this paper studies evacuation videos from the Luan'xian earthquake in 2012, and extends the study of group organization patterns to a higher density. Furthermore, taking full advantage of the strength in crowd gathering simulations, a new method on grouping and guidance is proposed while using crowd dynamics. Second, a real-life grouping situation in earthquake evacuation is simulated and reproduced. Comparing with the fundamental social force model and existing guided crowd model, the modified model reduces congestion time and truly reflects group behaviors. Furthermore, the experiment result also shows that a stable group pattern and a suitable leader could decrease collision and allow a safer evacuation process.

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.

Ghost Condensation and Modification of Gravity at Long distances

NASA Astrophysics Data System (ADS)

Luty, Markus

2004-05-01

This talk will describe the physics of a "ghost condensate", a new kind of cosmological fluid that can fill the universe and give rise to novel gravitational effects. The fluid has a preferred rest frame, but is nonetheless compatible with maximally symmetric spacetimes such as flat space or de Sitter. In the presence of a ghost condensate, gravity is modified in a nontrivial way at large distances and late times. New phenomena include new contributions to dark energy and dark matter, antigravity, new spin-dependent forces, and oscillatory potentials. All of this new physics can be described by a completely explicit and consistent effective field theory.

Control of hydrodynamic cavitation using ultrasonic

NASA Astrophysics Data System (ADS)

Chatterjee, Dhiman; Arakeri, Vijay H.

2003-11-01

Hydrodynamic cavitation is known to have many harmful effects like surface damage and generation of noise. We investigated the use of ultrasonics to control traveling bubble cavitation. Ultrasonic pressure field, produced by a piezoelectric crystal, was applied to modify the nuclei size distribution. Effects of continuous-wave (CW) and pulsed excitations were studied. At low dissolved gas content the CW-mode performed better than the pulsed one, whereas for high gas content the pulsed one was more effective. The dominant mechanisms were Bjerknes force and rectified diffusion in these two cases. Simultaneous excitation by two crystals in CW and pulsed modes was seen to control cavitation better.

Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

NASA Astrophysics Data System (ADS)

Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

2008-10-01

We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

Cavitation on Hydrofoils with Leading Edge Protuberances

NASA Astrophysics Data System (ADS)

Custodio, Derrick; Henoch, Charles; Johari, Hamid; Office of Naval Research Collaboration

2012-11-01

The effects of spanwise-uniform sinusoidal leading edge protuberances on the flow characteristics and forces of finite-span hydrofoils under vaporous cavitation conditions were examined experimentally over angles of attack ranging from -9° α <= 27°. Two planforms were studied, rectangular and swept, at a Reynolds number of ~ 720,000. Two protuberance wavelengths, λ = 0.25 c and 0.50 c, and three amplitudes, A = 0.025 c, 0.05 c, and 0.12 c, were examined as they resemble the humpback whale flipper morphology. All hydrofoils retain a mean NACA 634-021 profile. The forces and moments were measured at a freestream velocity of 7.2 m/s, and high-speed digital photography was used to capture flow field images at several angles of attack. The cavitation number corresponding to incipient leading edge cavitation was also calculated. As far as forces and cavitation number are concerned, results show that the baseline hydrofoil tends to have nearly equal or improved performance over the modified hydrofoils at most angles of attack tested. Flow images reveal that it is possible that the extent of sheet and tip vortex cavitation can be reduced with the introduction of leading edge protuberances. The forces and cavitation characteristics will be presented. Sponsored by the ONR-ULI program.

Thermal stability and gel quality of myofibrillar protein as affected by soy protein isolates subjected to an acidic pH and mild heating.

PubMed

Niu, Haili; Xia, Xiufang; Wang, Chao; Kong, Baohua; Liu, Qian

2018-03-01

Thermal stability and gel quality of myofibrillar protein were evaluated with regard to the addition of native soy protein isolates (SPI) and SPI subjected to acidic pH and mild heating (modified SPI). Compared with the control, the addition of modified SPI increased the compression force of the protein gel and decreased water loss (P<0.05). Differential scanning calorimetry results showed that an addition of 0.75% native SPI decreased the first transition temperature (P<0.05), and addition of 0.5% and 0.75% modified SPI exhibited no appreciable changes on it (P>0.05), indicating that a higher concentration of modified SPI would not damage the protein thermal stability. Moreover, the addition of modified SPI enhanced hydrogen bonding and disulphide linkages. Atomic force microscopy analysis revealed that the addition of modified SPI decreased the roughness of the mixed myofibrillar protein gels. Overall, modified SPI has the potential to improve myofibrillar protein gel texture and water holding capacity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Vibration Control via Stiffness Switching of Magnetostrictive Transducers

NASA Technical Reports Server (NTRS)

Scheidler, Justin J.; Asnani, Vivake M.; Dapino, Marcelo J.

2016-01-01

In this paper, a computational study is presented of structural vibration control that is realized by switching a magnetostrictive transducer between high and low stiffness states. Switching is accomplished by either changing the applied magnetic field with a voltage excitation or changing the shunt impedance on the transducer's coil (i.e., the magnetostrictive material's magnetic boundary condition). Switched-stiffness vibration control is simulated using a lumped mass supported by a damper and the magnetostrictive transducer (mount), which is represented by a nonlinear, electromechanical model. Free vibration of the mass is calculated while varying the mount's stiffness according to a reference switched-stiffness vibration control law. The results reveal that switching the magnetic field produces the desired change in stiffness, but also an undesired actuation force that can significantly degrade the vibration control. Hence, a modified switched-stiffness control law that accounts for the actuation force is proposed and implemented for voltage-controlled stiffness switching. The influence of the magneto-mechanical bias condition is also discussed. Voltage-controlled stiffness switching is found to introduce damping equivalent to a viscous damping factor up to about 0.13; this is shown to primarily result from active vibration reduction caused by the actuation force. The merit of magnetostrictive switched-stiffness vibration control is then quantified by comparing the results of voltage- and shunt-controlled stiffness switching to the performance of optimal magnetostrictive shunt damping. For the cases considered, optimal resistive shunt damping performed considerably better than both voltage- and shunt-controlled stiffness switching.

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.

Multiscale Analysis of Rapidly Rotating Dynamo Simulations

NASA Astrophysics Data System (ADS)

Orvedahl, Ryan; Calkins, Michael; Featherstone, Nicholas

2017-11-01

The magnetic field of the planets and stars are generated by dynamo action in their electrically conducting fluid interiors. Numerical models of this process solve the fundamental equations of magnetohydrodynamics driven by convection in a rotating spherical shell. Rotation plays an important role in modifying the resulting convective flows and the self-generated magnetic field. We present results of simulating rapidly rotating systems that are unstable to dynamo action. We use the pseudo-spectral code Rayleigh to generate a suite of direct numerical simulations. Each simulation uses the Boussinesq approximation and is characterized by an Ekman number (Ek = ν / ΩL2) of 10-5. We vary the degree of convective forcing to obtain a range of convective Rossby numbers. The resulting flows and magnetic structures are analyzed using a Reynolds decomposition. We determine the relative importance of each term in the scale-separated governing equations and estimate the relevant spatial scales responsible for generating the mean magnetic field.

Evaluation of Turner relaxed state as a model of long-lived ion-trapping structures in plasma focus and Z-pinches

NASA Astrophysics Data System (ADS)

Auluck, S. K. H.

2011-03-01

Relatively long-lived spheroidal structures coincident with the neutron emission phase have been observed in frozen deuterium fiber Z-pinch and some plasma focus devices. Existence of energetic ion-trapping mechanism in plasma focus has also been inferred from experimental data. It has been conjectured that these are related phenomena. This paper applies Turner's theory [L. Turner, IEEE Trans. Plasma Sci. 14, 849 (1986)] of relaxation of a Hall magnetofluid to construct a model of these structures and ion-trapping mechanism. Turner's solution modified for a finite-length plasma is used to obtain expressions for the magnetic field, velocity, and equilibrium pressure fields and is shown to represent an entity which is simultaneously a fluid vortex, a force-free magnetic field, a confined finite-pressure plasma, a charged object, and a trapped energetic ion beam. Characteristic features expected from diagnostic experiments are evaluated and shown to resemble experimental observations.

Goldstone models of modified gravity

NASA Astrophysics Data System (ADS)

Brax, Philippe; Valageas, Patrick

2017-02-01

We investigate scalar-tensor theories where matter couples to the scalar field via a kinetically dependent conformal coupling. These models can be seen as the low-energy description of invariant field theories under a global Abelian symmetry. The scalar field is then identified with the Goldstone mode of the broken symmetry. It turns out that the properties of these models are very similar to the ones of ultralocal theories where the scalar-field value is directly determined by the local matter density. This leads to a complete screening of the fifth force in the Solar System and between compact objects, through the ultralocal screening mechanism. On the other hand, the fifth force can have large effects in extended structures with large-scale density gradients, such as galactic halos. Interestingly, it can either amplify or damp Newtonian gravity, depending on the model parameters. We also study the background cosmology and the linear cosmological perturbations. The background cosmology is hardly different from its Λ -CDM counterpart while cosmological perturbations crucially depend on whether the coupling function is convex or concave. For concave functions, growth is hindered by the repulsiveness of the fifth force while it is enhanced in the convex case. In both cases, the departures from the Λ -CDM cosmology increase on smaller scales and peak for galactic structures. For concave functions, the formation of structure is largely altered below some characteristic mass, as smaller structures are delayed and would form later through fragmentation, as in some warm dark matter scenarios. For convex models, small structures form more easily than in the Λ -CDM scenario. This could lead to an over-abundance of small clumps. We use a thermodynamic analysis and show that although convex models have a phase transition between homogeneous and inhomogeneous phases, on cosmological scales the system does not enter the inhomogeneous phase. On the other hand, for galactic halos, the coexistence of small and large substructures in their outer regions could lead to observational signatures of these models.

Application of the STROBE statement to the hypospadias literature: Report of the international pediatric urology task force on hypospadias.

PubMed

Braga, Luis H; Lorenzo, Armando J; Bagli, Darius J; Pippi Salle, Joao L; Caldamone, Anthony

2016-12-01

Observational studies, particularly case series, represent the majority of the current hypospadias research. As a result, this literature lacks standardization of surgical techniques, uniform definitions of hypospadias complications, and consistency of outcome reporting, which may make it difficult to compare results across studies. A modified version of the STROBE statement, containing 20 items, was presented at the International Pediatric Urology Task Force on Hypospadias meeting to assist with clear and transparent reporting of hypospadias studies. The adoption and implementation of this modified tool will allow investigators and health care providers to critically evaluate quality and identify bias within the literature. In addition this instrument will ensure consistency of reporting, improving objective comparisons between studies, unification of results, and development of evidence-based clinical guidelines. In this article, we have applied the modified STROBE statement to the hypospadias literature, aiming to create a guide on study reporting for pediatric urologists, and ultimately improve the quality of research in our field. We present itemized recommendations for adequate reporting of hypospadias studies and case series, ranging from drafting the abstract to addressing biases and potential sources of confounding. Included with each item is a brief explanation of its importance and potential effect on the study, as well as pertinent examples of hypospadias articles. A modified STROBE summary table containing 20 items is presented in (Supplementary Table 1). If properly conducted and reported, hypospadias studies have the potential to provide useful information to clinicians and surgeons. However, authors should recognize the inherent limitations of these observational studies, especially in the form of bias, which may introduce invalid data or limit generalizability. Thus, we expect that the use of this guiding tool will not only improve transparency of hypospadias reporting, but also improve its methodological quality, allowing proper comparison and interpretation of data across different institutions. Copyright © 2016 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

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.

Experiments evaluating compliance and force feedback effect on manipulator performance

NASA Technical Reports Server (NTRS)

Kugath, D. A.

1972-01-01

The performance capability was assessed of operators performing simulated space tasks using manipulator systems which had compliance and force feedback varied. Two manipulators were used, the E-2 electromechanical man-equivalent (force, reach, etc.) master-slave system and a modified CAM 1400 hydraulic master-slave with 100 lbs force capability at reaches of 24 ft. The CAM 1400 was further modified to operate without its normal force feedback. Several experiments and simulations were performed. The first two involved the E-2 absorbing the energy of a moving mass and secondly, guiding a mass thru a maze. Thus, both work and self paced tasks were studied as servo compliance was varied. Three simulations were run with the E-2 mounted on the CAM 1400 to evaluate the concept of a dexterous manipulator as an end effector of a boom-manipulator. Finally, the CAM 1400 performed a maze test and also simulated the capture of a large mass as the servo compliance was varied and with force feedback included and removed.

Flextime: A Modified Work Force Scheduling Technique for Selected Headquarters Air Force Logistics Command Organizations.

ERIC Educational Resources Information Center

Kimzey, Reed T.; Prince, Samuel M. O.

The thesis discusses the advantages and disadvantages of one work force scheduling technique--flextime. The authors were interested in determining if a flextime schedule could be put into effect in a governmental organization such as Headquarters Air Force Logistics Command (AFLC). The study objectives were to determine the feasibility,…

Tailoring magnetostriction with various directions for directional solidification Fe82Ga15Al3 alloy by magnetic field heat treatment

NASA Astrophysics Data System (ADS)

Li, Xiaolong; Bao, Xiaoqian; Liu, Yangyang; Yu, Linhua; Li, Jiheng; Gao, Xuexu

2017-10-01

The magnetostriction of the Fe82Ga15Al3 alloy, along the length and width, can be tailored by applying a magnetic field heat treatment. In this work, the Fe82Ga15Al3 sheet was cut from the directional solidified Fe82Ga15Al3 alloy with the ⟨100⟩ preferred orientation and was annealed at 720 °C for 30 min under a magnetic field of 800 Oe along the length direction with a heating and cooling rate of 100 °C/min. The magnetostrictive properties along the length and width directions were modified to λ// = 7 ppm and λ⊥ = -210 ppm from λ// = 210 ppm and λ⊥ = -10 ppm for the initial sample prior to the magnetic field heat treatment. The cellular-like magnetic domain structure was composed of parallel 180° stripe domains and vertical 90° domains observed using a magnetic-force microscope. The change in magnetostriction along parallel and perpendicular directions was mainly resulted from the rotation of the magnetic domain units.

Transport and attenuation of carboxylate-modified latex microspheres in fractured rock laboratory and field tracer tests

USGS Publications Warehouse

Becker, M.W.; Reimus, P.W.; Vilks, P.

1999-01-01

Understanding colloid transport in ground water is essential to assessing the migration of colloid-size contaminants, the facilitation of dissolved contaminant transport by colloids, in situ bioremediation, and the health risks of pathogen contamination in drinking water wells. Much has been learned through laboratory and field-scale colloid tracer tests, but progress has been hampered by a lack of consistent tracer testing methodology at different scales and fluid velocities. This paper presents laboratory and field tracer tests in fractured rock that use the same type of colloid tracer over an almost three orders-of-magnitude range in scale and fluid velocity. Fluorescently-dyed carboxylate-modified latex (CML) microspheres (0.19 to 0.98 ??m diameter) were used as tracers in (1) a naturally fractured tuff sample, (2) a large block of naturally fractured granite, (3) a fractured granite field site, and (4) another fractured granite/schist field site. In all cases, the mean transport time of the microspheres was shorter than the solutes, regardless of detection limit. In all but the smallest scale test, only a fraction of the injected microsphere mass was recovered, with the smaller microspheres being recovered to a greater extent than the larger microspheres. Using existing theory, we hypothesize that the observed microsphere early arrival was due to volume exclusion and attenuation was due to aggregation and/or settling during transport. In most tests, microspheres were detected using flow cytometry, which proved to be an excellent method of analysis. CML microspheres appear to be useful tracers for fractured rock in forced gradient and short-term natural gradient tests, but longer residence times may result in small microsphere recoveries.Understanding colloid transport in ground water is essential to assessing the migration of colloid-size contaminants, the facilitation of dissolved contaminant transport by colloids, in situ bioremediation, and the health risks of pathogen contamination in drinking water wells. Much has been learned through laboratory and field-scale colloid tracer tests, but progress has been hampered by a lack of consistent tracer testing methodology at different scales and fluid velocities. This paper presents laboratory and field tracer tests in fractured rock that use the same type of colloid tracer over an almost three orders-of-magnitude range in scale and fluid velocity. Fluorescently-dyed carboxylate-modified latex (CML) microspheres (0.19 to 0.98 ??m diameter) were used as tracers in (1) a naturally fractured tuff sample, (2) a large block of naturally fractured granite, (3) a fractured granite field site, and (4) another fractured granite/schist field site. In all cases, the mean transport time of the microspheres was shorter than the solutes, regardless of detection limit. In all but the smallest scale test, only a fraction of the injected microsphere mass was recovered, with the smaller microspheres being recovered to a greater extent than the larger microspheres. Using existing theory, we hypothesize that the observed microsphere early arrival was due to volume exclusion and attenuation was due to aggregation and/or settling during transport. In most tests, microspheres were detected using flow cytometry, which proved to be an excellent method of analysis. CML microspheres appear to be useful tracers for fractured rock in forced gradient and short-term natural gradient tests, but longer residence times may result in small microsphere recoveries.

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.

Influence of electrical double-layer dispersion forces and size dependency on pull-in instability of clamped microplate immersed in ionic liquid electrolytes

NASA Astrophysics Data System (ADS)

Karimipour, I.; Beni, Yaghoub Tadi; Taheri, N.

2017-10-01

Plate-type clamped microplate is of the most common constructive elements for developing in-liquid-operating devices. While the electromechanical behavior of clamped microplate in non-liquid environments has exclusively been addressed in the literature, no theoretical studies have yet been conducted on precise modeling of the clamped microplate in electrolyte liquid. Herein, the electromechanical response and instability of the clamped microplate immersed in ionic electrolyte media are investigated. The electrochemical force field is determined using double layer theory and linearized Poisson-Boltzmann equation. The presence of dispersion forces, i.e., Casimir and van der Waals attractions, are included in the theoretical model considering the correction due to the presence of liquid media between the interacting surfaces (three-layer model). To this end, a kind of microplate has been designed, i.e., a square microplate with all edges clamped supported. The strain gradient elasticity is employed to model the size-dependent structural behavior of the clamped microplate. To solve the nonlinear constitutive equation of the system, Extended Kantorovich Method, is employed and the pull-in parameter of the microplate are extracted. Impacts of the dispersion forces and size effect on the instability characteristics are discussed as well as the effect of ion concentration and potential ratio. It is found that the significant difference between the pull-in instability parameters in the modified strain gradient theory and the classical theory for thin microplates is merely due to the consideration of size effect parameter in the modified strain gradient theory. To confirm the validity of formulations, the numerical values of the results are compared. The results predicted via the aforementioned approach are in excellent agreement with those in the literature. Some new examples are solved to demonstrate the applicability of the procedure.

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

PubMed Central

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R.; Benítez, Mariana

2014-01-01

Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes. PMID:24959170

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

PubMed

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R; Benítez, Mariana

2014-01-01

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

Tripodal penta(p-phenylene) for the biofunctionalization of alkynyl-modified silicon surfaces

NASA Astrophysics Data System (ADS)

Sánchez-Molina, María; Díaz, Amelia; Valpuesta, María; Contreras-Cáceres, Rafael; López-Romero, J. Manuel; López-Ramírez, M. Rosa

2018-07-01

Here we report the optimization on the covalent grafting methodology of a tripod-shaped penta(p-phenylene), 1, on alkynyl-terminated silicon surfaces, and the incorporation of an active theophylline derivative, 2, for the specific immobilization of proteins. The tripodal molecule presents azide-terminal groups to be attached onto a silicon surface containing an alkynyl monolayer. Initially, compound 1 has been covalently incorporated on alkynyl-terminated Si wafers, by the copper catalyzed alkyne-azide 1,3-dipolar cycloaddition (CuAAC, a click reaction). The tripod density on the silicon surface is tuned by performing the CuAAC reaction at different concentrations of 1, as well as under different experimental conditions (T, base, copper source, shaking). Then, tripod 1-modified surface has also been biofunctionalized with 2. The effective preparation of this silicon-modified surface allowed us to study the streptavidin immobilization on the surface. Characterization of the different surfaces has been carried out by X-ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM) and Bright-Field Optical Transmission Microscopy (Confocal) techniques. We also include density functional theory (DFT) analysis of the organic structures to confirm the height-profile and the tripod-surface relative configuration extracted from AFM images.

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.

Astrophysical tests of modified gravity: Constraints from distance indicators in the nearby universe

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

Jain, Bhuvnesh; Vikram, Vinu; Sakstein, Jeremy

2013-12-10

We use distance measurements in the nearby universe to carry out new tests of gravity, surpassing other astrophysical tests by over two orders of magnitude for chameleon theories. The three nearby distance indicators—cepheids, tip of the red giant branch (TRGB) stars, and water masers—operate in gravitational fields of widely different strengths. This enables tests of scalar-tensor gravity theories because they are screened from enhanced forces to different extents. Inferred distances from cepheids and TRGB stars are altered (in opposite directions) over a range of chameleon gravity theory parameters well below the sensitivity of cosmological probes. Using published data, we havemore » compared cepheid and TRGB distances in a sample of unscreened dwarf galaxies within 10 Mpc. We use a comparable set of screened galaxies as a control sample. We find no evidence for the order unity force enhancements expected in these theories. Using a two-parameter description of the models (the coupling strength and background field value), we obtain constraints on both the chameleon and symmetron screening scenarios. In particular we show that f(R) models with background field values f {sub R0} above 5 × 10{sup –7} are ruled out at the 95% confidence level. We also compare TRGB and maser distances to the galaxy NGC 4258 as a second test for larger field values. While there are several approximations and caveats in our study, our analysis demonstrates the power of gravity tests in the local universe. We discuss the prospects for additional improved tests with future observations.« less

Orienting movements in area 9 identified by long-train ICMS.

PubMed

Lanzilotto, M; Perciavalle, V; Lucchetti, C

2015-03-01

The effect of intracortical microstimulation has been studied in several cortical areas from motor to sensory areas. The frontal pole has received particular attention, and several microstimulation studies have been conducted in the frontal eye field, supplementary eye field, and the premotor ear-eye field, but no microstimulation studies concerning area 9 are currently available in the literature. In the present study, to fill up this gap, electrical microstimulation was applied to area 9 in two macaque monkeys using long-train pulses of 500-700-800 and 1,000 ms, during two different experimental conditions: a spontaneous condition, while the animals were not actively fixating on a visual target, and during a visual fixation task. In these experiments, we identified backward ear movements, goal-directed eye movements, and the development of head forces. Kinematic parameters for ear and eye movements overlapped in the spontaneous condition, but they were different during the visual fixation task. In this condition, ear and eye kinematics have an opposite behavior: movement amplitude, duration, and maximal and mean velocities increase during a visual fixation task for the ear, while they decrease for the eye. Therefore, a top-down visual attention engagement could modify the kinematic parameters for these two effectors. Stimulation with the longest train durations, i.e., 800/1,000 ms, evokes not only the highest eye amplitude, but also a significant development of head forces. In this research article, we propose a new vision of the frontal oculomotor fields, speculating a role for area 9 in the control of goal-directed orienting behaviors and gaze shift control.

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.

Anomalous dielectric relaxation with linear reaction dynamics in space-dependent force fields.

PubMed

Hong, Tao; Tang, Zhengming; Zhu, Huacheng

2016-12-28

The anomalous dielectric relaxation of disordered reaction with linear reaction dynamics is studied via the continuous time random walk model in the presence of space-dependent electric field. Two kinds of modified reaction-subdiffusion equations are derived for different linear reaction processes by the master equation, including the instantaneous annihilation reaction and the noninstantaneous annihilation reaction. If a constant proportion of walkers is added or removed instantaneously at the end of each step, there will be a modified reaction-subdiffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps, there will be a standard linear reaction kinetics term but a fractional order temporal derivative operating on an anomalous diffusion term. The dielectric polarization is analyzed based on the Legendre polynomials and the dielectric properties of both reactions can be expressed by the effective rotational diffusion function and component concentration function, which is similar to the standard reaction-diffusion process. The results show that the effective permittivity can be used to describe the dielectric properties in these reactions if the chemical reaction time is much longer than the relaxation time.

Associative polymers bridging between layers of multilamellar vesicles.

NASA Astrophysics Data System (ADS)

Choi, Seo; Bhatia, Surita

2006-03-01

Multilamellar vesicles can be found in a variety of pharmaceutical formulations, personal care products, and home care products. Hydrophobically modified associative polymers are often used to stabilize the vesicles or to control the rheological properties of these formulations. The hydrophobic groups are expected to insert themselves into the vesicle bilayers. Recent experimental work shows that hydrophobically modified polymers may from bridges between vesicles or may bridge between layers of a single vesicle. The latter configuration forces an interlayer spacing roughly equal to the radius of gyration of the backbone between associative groups. We have performed simple mean-field calculations on ideal telechelic associative polymers between concentric spherical surfaces. We find that the free energy per chain has an attractive minimum when the layer spacing is approximately N^1/2l, which is consistent with experimental results. The depth of the minimum depends on both chain length and curvature, and as expected when the curvature becomes small, the result for telechelic chains between flat surfaces is recovered.

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent

PubMed Central

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding. PMID:29081606

Facile Preparation of a Platinum Silicide Nanoparticle-Modified Tip Apex for Scanning Kelvin Probe Microscopy.

PubMed

Lin, Chun-Ting; Chen, Yu-Wei; Su, James; Wu, Chien-Ting; Hsiao, Chien-Nan; Shiao, Ming-Hua; Chang, Mao-Nan

2015-12-01

In this study, we propose an ultra-facile approach to prepare a platinum silicide nanoparticle-modified tip apex (PSM tip) used for scanning Kelvin probe microscopy (SKPM). We combined a localized fluoride-assisted galvanic replacement reaction (LFAGRR) and atmospheric microwave annealing (AMA) to deposit a single platinum silicide nanoparticle with a diameter of 32 nm on the apex of a bare silicon tip of atomic force microscopy (AFM). The total process was completed in an ambient environment in less than 3 min. The improved potential resolution in the SKPM measurement was verified. Moreover, the resolution of the topography is comparable to that of a bare silicon tip. In addition, the negative charges found on the PSM tips suggest the possibility of exploring the use of current PSM tips to sense electric fields more precisely. The ultra-fast and cost-effective preparation of the PSM tips provides a new direction for the preparation of functional tips for scanning probe microscopy.

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent.

PubMed

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding.

Simulating the interplay between plasma transport, electric field, and magnetic field in the near-earth nightside magnetosphere

NASA Astrophysics Data System (ADS)

Gkioulidou, Malamati

The convection electric field resulting from the coupling of the Earth's magnetosphere with the solar wind and interplanetary magnetic field (IMF) drives plasma in the tail plasma sheet earthward. This transport and the resulting energy storage in the near Earth plasma sheet are important for setting up the conditions that lead to major space weather disturbances, such as storms and substorms. Penetration of plasma sheet particles into the near-Earth magnetosphere in response to enhanced convection is crucial to the development of the Region 2 field-aligned current system and large-scale magnetosphere-ionosphere (M-I) coupling, which results in the shielding of the convection electric field. In addition to the electric field, plasma transport is also strongly affected by the magnetic field, which is distinctly different from dipole field in the inner plasma sheet and changes with plasma pressure in maintaining force balance. The goal of this dissertation is to investigate how the plasma transport into the inner magnetosphere is affected by the interplay between plasma, electric field and magnetic field. For this purpose, we conduct simulations using the Rice Convection Model (RCM), which self-consistently calculates the electric field resulting from M-I coupling. In order to quantitatively evaluate the interplay, we improved the RCM simulations by establishing realistic plasma sheet particle sources, by incorporating it with a modified Dungey force balance magnetic field solver (RCM-Dungey runs), and by adopting more realistic electron loss rates. We found that plasma sheet particle sources strongly affect the shielding of the convection electric field, with a hotter and more tenuous plasma sheet resulting in less shielding than a colder and denser one and thus in more earthward penetration of the plasma sheet. The Harang reversal, which is closely associated with the shielding of the convection electric field and the earthward penetration of low-energy protons, is found to be located at lower latitudes and extend more dawnward for a hotter and more tenuous plasma sheet. In comparison with simulation runs under an empirical but not force balance magnetic field from the Tsyganenko 96 model, the simulation results show that transport under force-balanced magnetic field results in weaker pressure gradients and thus weaker R2 FAC in the near-earth region, weaker shielding of the penetration electric field and, as a result, more earthward penetration of plasma sheet protons and electrons with their inner edges being closer together and more azimuthally symmetric. To evaluate the effect of electron loss rate on ionospheric conductivity, a major contributing factor to M-I coupling, we run RCM-Dungey with a more realistic, MLT dependent electron loss rate established from observed wave activity. Comparing our results with those using a strong diffusion everywhere rate, we found that under the MLT dependent loss rate, the dawn-dusk asymmetry in the precipitating electron energy fluxes agrees better with statistical DMSP observations. The more realistic loss rate is much weaker than the strong diffusion limit in the inner magnetosphere. This allows high-energy electrons in the inner magnetosphere to remain much longer and produce substantial conductivity at lower latitudes. The higher conductivity at lower latitudes under the MLT dependent loss rate results in less efficient shielding in response to an enhanced convection electric field, and thus to deeper penetration of the ion plasma sheet into the inner magnetosphere than under the strong diffusion everywhere rate.

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.

The Flow Field on Hydrofoils with Leading Edge Protuberances

NASA Astrophysics Data System (ADS)

Custodio, Derrick; Henoch, Charles; Johari, Hamid

2009-11-01

The exceptional mobility of the humpback whale has been linked to the use of its unique pectoral flippers. Biologists speculate that the flippers leading edge protuberances are a form of passive flow control. Force measurements on 2D hydrofoils with spanwise uniform leading edge protuberances, resembling those seen on the humpback whale flipper, were taken in a water tunnel and have revealed performance modifications when compared to a baseline NACA 63(4)-021 hydrofoil model. Qualitative flow visualization techniques and Particle Image Velocimetry (PIV) flow field measurements on the modified hydrofoils have shown that streamwise vortices originating from the shoulders of the protuberances are the likely cause of performance changes. Varying levels of interaction among adjacent streamwise vortices have been observed as a function of angle of attack and chord location. The circulation of these vortices as a function of angle of attack and spatial location was measured and an analysis of the vortex interactions will be presented.

Marine Layer Stratus Study

NASA Astrophysics Data System (ADS)

Wells, Leonard A.

2007-06-01

The intent of this study is to develop a better understanding of the behavior of late spring through early fall marine layer stratus and fog at Vandenberg Air Force Base, which accounts for a majority of aviation forecasting difficulties. The main objective was to use Leipper (1995) study as a starting point to evaluate synoptic and mesoscale processes involved, and identify specific meteorological parameters that affected the behavior of marine layer stratus and fog. After identifying those parameters, the study evaluates how well the various weather models forecast them. The main conclusion of this study is that weak upper-air dynamic features work with boundary layer motions to influence marine layer behavior. It highlights the importance of correctly forecasting the surface temperature by showing how it ties directly to the wind field. That wind field, modified by the local terrain, establishes the low-level convergence and divergence pattern and the resulting marine layer cloud thicknesses and visibilities.

Electrowetting of Weak Polyelectrolyte-Coated Surfaces.

PubMed

Sénéchal, Vincent; Saadaoui, Hassan; Rodriguez-Hernandez, Juan; Drummond, Carlos

2017-05-23

Polymer coatings are commonly used to modify interfacial properties like wettability, lubrication, or biocompatibility. These properties are determined by the conformation of polymer molecules at the interface. Polyelectrolytes are convenient elementary bricks to build smart materials, given that polyion chain conformation is very sensitive to different environmental variables. Here we discuss the effect of an applied electric field on the properties of surfaces coated with poly(acrylic acid) brushes. By combining atomic force microscopy, quartz crystal microbalance, and contact angle experiments, we show that it is possible to precisely tune polyion chain conformation, surface adhesion, and surface wettability using very low applied voltages if the polymer grafting density and environmental conditions (pH and ionic strength) are properly formulated. Our results indicate that the effective ionization degree of the grafted weak polyacid can be finely controlled with the externally applied field, with important consequences for the macroscopic surface properties.

Long-term stability assessment of AlGaN/GaN field effect transistors modified with peptides: Device characteristics vs. surface properties

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

Rohrbaugh, Nathaniel; Bryan, Isaac; Bryan, Zachary

AlGaN/GaN Field Effect Transistors (FETs) are promising biosensing devices. Functionalization of these devices is explored in this study using an in situ approach with phosphoric acid etchant and a phosphonic acid derivative. Devices are terminated on peptides and soaked in water for up to 168 hrs to examine FETs for both device responses and surface chemistry changes. Measurements demonstrated threshold voltage shifting after the functionalization and soaking processes, but demonstrated stable FET behavior throughout. X-ray photoelectron spectroscopy and atomic force microscopy confirmed peptides attachment to device surfaces before and after water soaking. Results of this work point to the stabilitymore » of peptide coated functionalized AlGaN/GaN devices in solution and support further research of these devices as disposable, long term, in situ biosensors.« less

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-08-02

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

Vibrational analysis of vertical axis wind turbine blades

NASA Astrophysics Data System (ADS)

Kapucu, Onur

The goal of this research is to derive a vibration model for a vertical axis wind turbine blade. This model accommodates the affects of varying relative flow angle caused by rotating the blade in the flow field, uses a simple aerodynamic model that assumes constant wind speed and constant rotation rate, and neglects the disturbance of wind due to upstream blade or post. The blade is modeled as elastic Euler-Bernoulli beam under transverse bending and twist deflections. Kinetic and potential energy equations for a rotating blade under deflections are obtained, expressed in terms of assumed modal coordinates and then plugged into Lagrangian equations where the non-conservative forces are the lift and drag forces and moments. An aeroelastic model for lift and drag forces, approximated with third degree polynomials, on the blade are obtained assuming an airfoil under variable angle of attack and airflow magnitudes. A simplified quasi-static airfoil theory is used, in which the lift and drag coefficients are not dependent on the history of the changing angle of attack. Linear terms on the resulting equations of motion will be used to conduct a numerical analysis and simulation, where numeric specifications are modified from the Sandia-17m Darrieus wind turbine by Sandia Laboratories.

The Space Shuttle Endeavour, mounted securely atop one of NASA's modified Boeing 747 Shuttle Carrier Aircraft, left NASA's Dryden Flight Research Center at Edwards Air Force Base in Southern California at sunrise on Friday, June 28, nine days after conclu

NASA Image and Video Library

2002-06-28

The Space Shuttle Endeavour, mounted securely atop one of NASA's modified Boeing 747 Shuttle Carrier Aircraft, left NASA's Dryden Flight Research Center at Edwards Air Force Base in Southern California at sunrise on Friday, June 28, nine days after concluding mission STS-111 to the International Space Station with a landing at Edwards.

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

PubMed

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

2018-03-01

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

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

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

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

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

PubMed Central

Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

2008-01-01

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

ECN-3931

NASA Image and Video Library

1974-01-28

This photograph shows a modified General Dynamics TACT/F-111A Aardvaark with supercritical wings installed. The aircraft, with flaps and landing gear down, is in a decending turn over Rogers Dry Lakebed at Edwards Air Force Base. Starting in 1971 the NASA Flight Research Center and the Air Force undertook a major research and flight testing program, using F-111A (#63-9778), which would span almost 20 years before completion. Intense interest over the results coming from the NASA F-8 supercritical wing program spurred NASA and the Air Force to modify the General Dynamics-Convair F-111A to explore the application of supercritical wing technology to maneuverable military aircraft. This flight program was called Transonic Aircraft Technology (TACT).

QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

PubMed

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

PubMed

Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

2016-11-09

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol -1 . For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol -1 and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol -1 ) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol -1 ). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

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

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

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

Manipulating nanoparticle transport within blood flow through external forces: an exemplar of mechanics in nanomedicine

PubMed Central

Ye, Huilin; Shen, Zhiqiang; Wei, Mei; Li, Ying

2018-01-01

A large number of nanoparticles (NPs) have been raised for diverse biomedical applications and some of them have shown great potential in treatment and imaging of diseases. Design of NPs is essential for delivery efficacy due to a number of biophysical barriers, which prevents the circulation of NPs in vascular flow and their accumulation at tumour sites. The physiochemical properties of NPs, so-called ‘4S’ parameters, such as size, shape, stiffness and surface functionalization, play crucial roles in their life journey to be delivered to tumour sites. NPs can be modified in various ways to extend their blood circulation time and avoid their clearance by phagocytosis, and efficiently diffuse into tumour cells. However, it is difficult to overcome these barriers simultaneously by a simple combination of ‘4S’ parameters for NPs. At this moment, external triggerings are necessary to guide the movement of NPs, which include light, ultrasound, magnetic field, electrical field and chemical interaction. The delivery system can be constructed to be sensitive to these external stimuli which can reduce the non-specific toxicity and improve the efficacy of the drug-delivery system. From a mechanics point of view, we discuss how different forces play their roles in the margination of NPs in blood flow and tumour microvasculature. PMID:29662344

Magnetic concentration of a retroviral vector using magnetite cationic liposomes.

PubMed

Ito, Akira; Takahashi, Tetsuya; Kameyama, Yujiro; Kawabe, Yoshinori; Kamihira, Masamichi

2009-03-01

For tissue engineering purposes, retroviral vectors represent an efficient method of delivering exogenous genes such as growth factors to injured tissues because gene-transduced cells can produce stable and constant levels of the gene product. However, retroviral vector technology suffers from low yields. In the present study, we used magnetite nanoparticles and magnetic force to concentrate the retroviral vectors to enhance the transduction efficiency and to enable their magnetic manipulation. Magnetite nanoparticles modified with cationic liposomes were added to a solution containing a retroviral vector pseudotyped with vesicular stomatitis virus glycoprotein. The magnetic particles that captured the viral vectors were collected using a magnetic force and seeded into mouse neuroblastoma Neuro2a cells. The viral titer was up to 55 times greater (up to 3 x 10(8) infectious units/mL). Additionally, the magnetically labeled retroviral vectors can be directed to the desired regions for infection by applying magnetic fields, and micro-patterns of gene-transduced cell regions could be created on a cellular monolayer using micro-patterned magnetic concentrators. These results suggest that this technique provides a promising approach to capturing and concentrating viral vectors, thus achieving high transduction efficiency and the ability to deliver genes to a specific injured site by applying a magnetic field.

Tactile directional sensibility: peripheral neural mechanisms in man.

PubMed

Olausson, H; Wessberg, J; Kakuda, N

2000-06-02

Tactile directional sensibility, i.e. the ability to tell the direction of an object's motion across the skin, is an easily observed sensory function that is highly sensitive to disturbances of the somatosensory system. Based on previous psychophysical experiments on healthy subjects it was concluded that directional sensibility depends on two kinds of information from cutaneous mechanoreceptors; spatio-temporal information and information about friction-induced changes in skin stretch. In the present study responses to similar probe movements as in the psychophysical experiments were recorded from human single mechanoreceptors in the forearm skin. All slowly adapting type 2 (SA2) units were spontaneously active, and with increasing force of friction their discharge rates were modified by probe movements at increasing distances from the Ruffini end-organ, reflecting the high stretch-sensitivity of these units. Slowly adapting type 1 (SA1) and field units responded to the moving probe within well-defined skin areas directly overlying the individual receptor terminals, and compared to the SA2 units their response properties were less dependent on the force of friction. The results suggest that SA1 and field units have the capacity to signal spatio-temporal information, whereas a population of SA2 units have the capacity to signal direction-specific information about changes in lateral skin stretch.

Manipulating nanoparticle transport within blood flow through external forces: an exemplar of mechanics in nanomedicine

NASA Astrophysics Data System (ADS)

Ye, Huilin; Shen, Zhiqiang; Yu, Le; Wei, Mei; Li, Ying

2018-03-01

A large number of nanoparticles (NPs) have been raised for diverse biomedical applications and some of them have shown great potential in treatment and imaging of diseases. Design of NPs is essential for delivery efficacy due to a number of biophysical barriers, which prevents the circulation of NPs in vascular flow and their accumulation at tumour sites. The physiochemical properties of NPs, so-called `4S' parameters, such as size, shape, stiffness and surface functionalization, play crucial roles in their life journey to be delivered to tumour sites. NPs can be modified in various ways to extend their blood circulation time and avoid their clearance by phagocytosis, and efficiently diffuse into tumour cells. However, it is difficult to overcome these barriers simultaneously by a simple combination of `4S' parameters for NPs. At this moment, external triggerings are necessary to guide the movement of NPs, which include light, ultrasound, magnetic field, electrical field and chemical interaction. The delivery system can be constructed to be sensitive to these external stimuli which can reduce the non-specific toxicity and improve the efficacy of the drug-delivery system. From a mechanics point of view, we discuss how different forces play their roles in the margination of NPs in blood flow and tumour microvasculature.

Molecular-dynamic simulations of the thermophysical properties of hexanitrohexaazaisowurtzitane single crystal at high pressures and temperatures

NASA Astrophysics Data System (ADS)

Kozlova, S. A.; Gubin, S. A.; Maklashova, I. V.; Selezenev, A. A.

2017-11-01

Molecular dynamic simulations of isothermal compression parameters are performed for a hexanitrohexaazaisowurtzitane single crystal (C6H6O12N12) using a modified ReaxFF-log reactive force field. It is shown that the pressure-compression ratio curve for a single C6H6O12N12 crystal at constant temperature T = 300 K in pressure range P = 0.05-40 GPa is in satisfactory agreement with experimental compression isotherms obtained for a single C6H6O12N12 crystal. Hugoniot molecular-dynamic simulations of the shock-wave hydrostatic compression of a single C6H6O12N12 crystal are performed. Along with Hugoniot temperature-pressure curves, calculated shock-wave pressure-compression ratios for a single C6H6O12N12 crystal are obtained for a wide pressure range of P = 1-40 GPa. It is established that the percussive adiabat obtained for a single C6H6O12N12 crystal is in a good agreement with the experimental data. All calculations are performed using a LAMMPS molecular dynamics simulation software package that provides a ReaxFF-lg reactive force field to support the approach.

Magnetic Beads Enhance Adhesion of NIH 3T3 Fibroblasts: A Proof-of-Principle In Vitro Study for Implant-Mediated Long-Term Drug Delivery to the Inner Ear

PubMed Central

Aliuos, Pooyan; Schulze, Jennifer; Schomaker, Markus; Reuter, Günter; Stolle, Stefan R. O.; Werner, Darja; Ripken, Tammo; Lenarz, Thomas; Warnecke, Athanasia

2016-01-01

Introduction Long-term drug delivery to the inner ear may be achieved by functionalizing cochlear implant (CI) electrodes with cells providing neuroprotective factors. However, effective strategies in order to coat implant surfaces with cells need to be developed. Our vision is to make benefit of electromagnetic field attracting forces generated by CI electrodes to bind BDNF-secreting cells that are labelled with magnetic beads (MB) onto the electrode surfaces. Thus, the effect of MB-labelling on cell viability and BDNF production were investigated. Materials and Methods Murine NIH 3T3 fibroblasts—genetically modified to produce BDNF—were labelled with MB. Results Atomic force and bright field microscopy illustrated the internalization of MB by fibroblasts after 24 h of cultivation. Labelling cells with MB did not expose cytotoxic effects on fibroblasts and allowed adhesion on magnetic surfaces with sufficient BDNF release. Discussion Our data demonstrate a novel approach for mediating enhanced long-term adhesion of BDNF-secreting fibroblasts on model electrode surfaces for cell-based drug delivery applications in vitro and in vivo. This therapeutic strategy, once transferred to cells suitable for clinical application, may allow the biological modifications of CI surfaces with cells releasing neurotrophic or other factors of interest. PMID:26918945

Experimental and molecular dynamics simulation study of the sublimation and vaporization energetics of iron metalocenes. crystal structures of Fe(eta5-C5H4CH3)2 and Fe[(eta5-(C5H5)(eta5-C5H4CHO)].

PubMed

Lousada, Claudio M; Pinto, Susana S; Lopes, José N Canongia; da Piedade, M Fatima Minas; Diogo, Hermínio P; da Piedade, Manuel E Minas

2008-04-03

The standard molar enthalpies of sublimation of ferrocene, 1,1'-dimethylferrocene, decamethylferrocene, ferrocenecarboxaldehyde and alpha-methylferrocenemethanol, and the enthalpy of vaporization of N,N-dimethyl(aminomethyl)ferrocene, at 298.15 K, were determined by Calvet-drop microcalorimetry and/or the Knudsen effusion method. The obtained values were used to assess and refine our previously developed force field for metallocenes. The modified force field was able to reproduce the deltasubHdegreesm and deltavapHdegreesm values of the test-set with an accuracy better than 5 kJ.mol-1, except for decamethylferrocene, in which case the deviation between the calculated and experimental deltasubHdegreesm values was 16.1 kJ.mol-1. The origin of the larger error found in the prediction of the sublimation energetics of decamethylferrocene, and which was also observed in the estimation of structural properties (e.g., density and unit cell dimensions), is discussed. Finally, the crystal structures of Fe(eta5-C5H4CH3)2 and Fe[(eta5-(C5H5)(eta5-C5H4CHO)] at 293 and 150 K, respectively, are reported.

A modified Brownian force for ultrafine particle penetration through building crack modeling

NASA Astrophysics Data System (ADS)

Chen, Chen; Zhao, Bin

2017-12-01

Combustion processes related to industry, traffic, agriculture, and waste treatment and disposal increase the amount of outdoor ultrafine particles (UFPs), which have adverse effects on human health. Given that people spend the majority of their time indoors, it is critical to understand the penetration of outdoor UFPs through building cracks in order to estimate human exposure to outdoor-originated UFPs. Lagrangian tracking is an efficient approach for modeling particle penetration. However, the Brownian motion for Lagrangian tracking in ANSYS Fluent®, a widely used software for particle dispersion modeling, is not able to model UFP dispersion accurately. In this study, we modified the Brownian force by rewriting the Brownian diffusion coefficient and particle integration time step with a user-defined function in ANSYS Fluent® to model particle penetration through building cracks. The results obtained using the modified model agree much better with the experimental results, with the averaged relative error less than 14% for the smooth crack cases and 21% for the rough crack case. We expect the modified Brownian force model proposed herein to be applied for UFP dispersion modeling in more indoor air quality studies.

Suppressing Crack Formation in Particulate Systems by Utilizing Capillary Forces

PubMed Central

Schneider, Monica; Maurath, Johannes; Fischer, Steffen B.; Weiß, Moritz; Willenbacher, Norbert; Koos, Erin

2017-01-01

Cracks, formed during the drying of particulate films, can reduce the effectiveness or even render products useless. We present a novel, generic approach to suppress crack formation in thin films made from hard particle suspensions, which are otherwise highly susceptible to cracking, using the capillary force between particles present when a trace amount of an immiscible liquid is added to a suspension. This secondary liquid preserves the particle cohesion, modifying the structure and increasing the drying rate. Crack-free films can be produced at thicknesses much greater than the critical cracking thickness for a suspension without capillary interactions, and even persists after sintering. This capillary suspension strategy is applicable to a broad range of materials including suspensions of metals, semiconductive and ceramic oxides or glassy polymeric particles and can be easily implemented in many industrial processes since it is based on well-established unit operations. Promising fields of application include ceramic foils and printed electronic devices. PMID:28263554

Proposal for an observational test of the Vainshtein mechanism.

PubMed

Hui, Lam; Nicolis, Alberto

2012-08-03

Modified gravity theories capable of genuine self-acceleration typically invoke a Galileon scalar which mediates a long-range force but is screened by the Vainshtein mechanism on small scales. In such theories, nonrelativistic stars carry the full scalar charge (proportional to their mass), while black holes carry none. Thus, for a galaxy free falling in some external gravitational field, its central massive black hole is expected to lag behind the stars. To look for this effect, and to distinguish it from other astrophysical effects, one can correlate the gravitational pull from the surrounding structure with the offset between the stellar center and the black hole. The expected offset depends on the central density of the galaxy and ranges up to ∼0.1 kpc for small galaxies. The observed offset in M87 cannot be explained by this effect unless the scalar force is significantly stronger than gravity. We also discuss the systematic offset of compact objects from the galactic plane as another possible signature.

Effect of perfluorodecyltrichlorosilane on the surface properties and anti-corrosion behavior of poly(dimethylsiloxane)-ZnO coatings

NASA Astrophysics Data System (ADS)

Arukalam, Innocent O.; Meng, Meijiang; Xiao, Haigang; Ma, Yuantai; Oguzie, Emeka E.; Li, Ying

2018-03-01

Poly(dimethylsiloxane)-ZnO coatings modified with different amounts of perfluorodecyltrichlorosilane (FDTS) were prepared using sol-gel technique. The results of field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) examinations showed that the surface structures and roughness of the coatings were respectively influenced by the increasing addition of FDTS. The water contact angle measurements showed maximum value of 130.52° with the 0.10 g FDTS-modified coating sample. The X-ray photoelectron spectroscopy (XPS) results indicated the coatings' hydrophobicity was also influenced by surface chemistry. The FTIR-ATR characterization results showed there was remarkable increase in the crystallinity of 0.10 g FDTS-modified coating after modification, and was confirmed by differential scanning calorimetry (DSC) analysis of crystallization temperature and the X-ray diffraction (XRD) results with an estimation of 71.29% percent crystallinity. The mechanical properties of the coatings were also conducted. The EIS measurements for anti-corrosion behavior showed that 0.10 g FDTS-modified coating had the highest barrier performance and lowest rate of degradation. Indeed, the obtained data have demonstrated that 0.10 g (≈ 0.18%) FDTS produced the most significantly effect on the surface and barrier properties of the coatings and thus, can effectively be used for anti-corrosion application in the marine environments.

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.

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.

An investigation into the use of two polyacid-modified composite resins (compomers) and a resin-modified glass poly(alkenoate) cement used to retain orthodontic bands.

PubMed

Williams, P H; Sherriff, M; Ireland, A J

2005-06-01

The aim of this investigation was to determine the effectiveness of a conventional glass poly(alkenoate) cement (Intact) and newer polyacid-modified composite resin cements (Transbond Plus and Ultra Band-Lok) to retain orthodontic bands. In the in vitro part of this study, stainless steel bands were cemented to 240 extracted third molar teeth in three test groups comprising Intact, Transbond Plus and Ultra Band-Lok. The force to deband (N) for all three cements was recorded using an Instron universal testing machine after the following observation periods: 20 minutes and 3, 6 and 12 months. The results indicated that all three cements increased their median force to deband after 12 months. Of the two compomers, Transbondtrade mark Plus demonstrated the highest median force to deband at all four time intervals. In the in vivo part of the study, 30 patients participated in a randomized cross-mouth clinical trial where the molar bands were cemented in place using either Intact or Transbond Plus. Ultra Band-Lok was not used in the clinical part of the study. The results showed there to be no clinically significant difference in band failure rates between the two cements. When patients were asked to score each for taste, there was a significant difference, with the glass poly(alkenoate) cement (Intact) being more acceptable than the polyacid-modified composite Transbond Plus (P < 0.001). No significant differences were observed in the in vitro median force to deband or in vivo band failure rates between the glass poly(alkenoate) cement and the polyacid-modified composite resins. The choice of cementing agent can therefore be made on patient factors, e.g. taste, or operator factors, e.g. ease of handling, cost and shelf life.

Procedures for offline grid nesting in regional ocean models

NASA Astrophysics Data System (ADS)

Mason, Evan; Molemaker, Jeroen; Shchepetkin, Alexander F.; Colas, Francois; McWilliams, James C.; Sangrà, Pablo

One-way offline nesting of a primitive-equation regional ocean numerical model (ROMS) is investigated, with special attention to the boundary forcing file creation process. The model has a modified open boundary condition which minimises false wave reflections, and is optimised to utilise high-frequency boundary updates. The model configuration features a previously computed solution which supplies boundary forcing data to an interior domain with an increased grid resolution. At the open boundaries of the interior grid (the child) the topography is matched to that of the outer grid (the parent), over a narrow transition region. A correction is applied to the normal baroclinic and barotropic velocities at the open boundaries of the child to ensure volume conservation. It is shown that these steps, together with a carefully constructed interpolation of the parent data, lead to a high-quality child solution, with minimal artifacts such as persistent rim currents and wave reflections at the boundaries. Sensitivity experiments provide information about the robustness of the model open boundary condition to perturbations in the surface wind stress forcing field, to the perturbation of the volume conservation enforcement in the boundary forcing, and to perturbation of the vertical density structure in the boundary forcing. This knowledge is important when extending the nesting technique to include external data from alien sources, such as ocean models with physics and/or numerics different from ROMS, or from observed climatologies of temperature, salinity and sea level.

Adhesive and morphological characteristics of surface chemically modified polytetrafluoroethylene films

NASA Astrophysics Data System (ADS)

Hopp, B.; Kresz, N.; Kokavecz, J.; Smausz, T.; Schieferdecker, H.; Döring, A.; Marti, O.; Bor, Z.

2004-01-01

In the present paper, we report an experimental determination of adhesive and topographic characteristics of chemically modified surface of polytetrafluoroethylene (PTFE) films. The surface chemistry was modified by ArF excimer laser irradiation in presence of triethylene-tetramine photoreagent. The applied laser fluence was varied in the range of 0.4-9 mJ/cm 2, and the number of laser pulses incident on the same area was 1500. To detect the changes in the adhesive features of the treated Teflon samples, we measured receding contact angle for distilled water and adhesion strength, respectively. It was found that the receding contact angle decreased from 96° to 30-37° and the adhesion strength of two-component epoxy glue to the treated sample surface increased from 0.03 to 9 MPa in the applied laser fluence range. Additionally, it was demonstrated that the adhesion of human cells to the modified Teflon samples is far better than to the untreated ones. The contact mode and pulsed force mode atomic force microscopic investigations of the treated samples demonstrated that the measured effective contact area of the irradiated films does not differ significantly from that of the original films, but the derived adhesion force is stronger on the modified samples than on the untreated ones. Hence, the increased adhesion of the treated Teflon films is caused by the higher surface energy.

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.

Field test method to determine presence and quantity of modifiers in liquid asphalt.

DOT National Transportation Integrated Search

2015-05-01

Asphalt modified with styrene butadiene styrene (SBS) polymer and/or ground tire rubber (GTR) is widely used in the U.S. : to enhance its performance. However, there are very few field tests developed to verify the content of modifier(s) in asphalt :...

Liquid film drag out in the presence of molecular forces

NASA Astrophysics Data System (ADS)

Schmidhalter, I.; Cerro, R. L.; Giavedoni, M. D.; Saita, F. A.

2013-03-01

From a practical as well as a conceptual point of view, one of the most interesting problems of physicochemical hydrodynamics is the drag out of a liquid film by a moving solid out of a pool of liquid. The basic problem, sometimes denoted the Landau-Levich problem [L. Landau and B. Levich, "Dragging of a liquid by a moving plate," Acta Physicochim. USSR 17, 42-54 (1942)], involves an interesting blend of capillary and viscous forces plus a matching of the static solution for capillary rise with a numerical solution of the film evolution equation, neglecting gravity, on the downstream region of the flow field. The original solution describes experimental data for a wide range of Capillary numbers but fails to match results for large and very small Capillary numbers. Molecular level forces are introduced to create an augmented version of the film evolution equation to show the effect of van der Waals forces at the lower range of Capillary numbers. A closed form solution for static capillary rise, including molecular forces, was matched with a numerical solution of the augmented film evolution equation in the dynamic meniscus region. Molecular forces do not sensibly modify the static capillary rise region, since film thicknesses are larger than the range of influence of van der Waals forces, but are determinant in shaping the downstream dynamic meniscus of the very thin liquid films. As expected, a quantitatively different level of disjoining pressure for different values of molecular constants remains in the very thin liquid film far downstream. Computational results for a wide range of Capillary numbers and Hamaker constants show a clear transition towards a region where the film thickness becomes independent of the coating speed.

Assessment of dual-point drag reduction for an executive-jet modified airfoil section

NASA Technical Reports Server (NTRS)

Allison, Dennis O.; Mineck, Raymond E.

1996-01-01

This paper presents aerodynamic characteristics and pressure distributions for an executive-jet modified airfoil and discusses drag reduction relative to a baseline airfoil for two cruise design points. A modified airfoil was tested in the adaptive-wall test section of the NASA Langley 0.3-Meter Transonic Cryogenic Tunnel (0.3-m TCT) for Mach numbers ranging from 0.250 to 0.780 and chord Reynolds numbers ranging from 3.0 x 10(exp 6) to 18.0 x 10(exp 6). The angle of attack was varied from minus 2 degrees to almost 10 degrees. Boundary-layer transition was fixed at 5 percent of chord on both the upper and lower surfaces of the model for most of the test. The two design Mach numbers were 0.654 and 0.735, chord Reynolds numbers were 4.5 x 10(exp 6) and 8.9 x 10(exp 6), and normal-force coefficients were 0.98 and 0.51. Test data are presented graphically as integrated force and moment coefficients and chordwise pressure distributions. The maximum normal-force coefficient decreases with increasing Mach number. At a constant normal-force coefficient in the linear region, as Mach number increases an increase occurs in the slope of normal-force coefficient versus angle of attack, negative pitching-moment coefficient, and drag coefficient. With increasing Reynolds number at a constant normal-force coefficient, the pitching-moment coefficient becomes more negative and the drag coefficient decreases. The pressure distributions reveal that when present, separation begins at the trailing edge as angle of attack is increased. The modified airfoil, which is designed with pitching moment and geometric constraints relative to the baseline airfoil, achieved drag reductions for both design points (12 and 22 counts). The drag reductions are associated with stronger suction pressures in the first 10 percent of the upper surface and weakened shock waves.

Gas dynamics in strong centrifugal fields

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

Bogovalov, S.V.; Kislov, V.A.; Tronin, I.V.

2015-03-10

Dynamics of waves generated by scopes in gas centrifuges (GC) for isotope separation is considered. The centrifugal acceleration in the GC reaches values of the order of 106g. The centrifugal and Coriolis forces modify essentially the conventional sound waves. Three families of the waves with different polarisation and dispersion exist in these conditions. Dynamics of the flow in the model GC Iguasu is investigated numerically. Comparison of the results of the numerical modelling of the wave dynamics with the analytical predictions is performed. New phenomena of the resonances in the GC is found. The resonances occur for the waves polarizedmore » along the rotational axis having the smallest dumping due to the viscosity.« less

Application of ceramic superconductors in high speed turbines

NASA Technical Reports Server (NTRS)

Mcmichael, C. K.; Lamb, M. A.; Lin, M. W.; Ma, K. B.; Chu, W. K.

1992-01-01

A turbine system was modified to adapt melt textured YBa2Cu3O(7-delta) (YBCO) with high energy permanent magnets to form a hybrid superconducting magnetic bearing (HSMB). The HSMB/turbine prototype has achieved a static axial thrust capacity exceeding 41 N/sq cm (60 psi) and a radial magnetic stiffness of 7 N/mm in a field cooled state at 77 K. A comparison was made between different configurations of magnets and superconductor for radial stability, axial instability, and force hystereses. This systematic study lead to a greater understanding of the interactions between YBCO and high energy permanent magnets to define design parameters for high rotational devices using the HSMB design.

Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems

NASA Astrophysics Data System (ADS)

Ding, Yun-Qiao; Chen, Cheng-Lung; Gu, Qi-Rui; Liao, Jun-Min; Chuang, Po-Hsiang

2014-04-01

Molecular dynamics simulation with a modified CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field was carried out to investigate the properties of chrome-tanned collagen in comparison with chrome-free collagen under hydrated and dehydrated conditions. An attempt has been made to explain the microcosmic origins of the various properties of the chromium(III)-crosslinked collagen. The present simulation describes the clear crosslinking topology of polychromiums to peptide chains, identifies the linking site and the capacity of the linkage, explains why the efficiency is not 100% in a practical tanning process and provides a new viewpoint on the crosslinking of the polychromium with the side chains of the collagen.

KSC-00pp0886

NASA Image and Video Library

2000-06-19

In a hangar at Cape Canaveral Air Force Station, a Cessna Citation aircraft has been fitted on the wings with devices that measure electric fields (black circles shown behind the open door) and with cloud physics probes (under the body and wings) that measure the size, shape and number of ice and water particles in clouds. The plane is being flown into anvil clouds in the KSC area as part of a study to review and possibly modify lightning launch commit criteria. The weather study could lead to improved lightning avoidance rules and fewer launch scrubs for the Space Shuttle and other launch vehicles on the Eastern and Western ranges.; More information about the study can be found in Release No. 56-00

KSC00pp0886

NASA Image and Video Library

2000-06-19

In a hangar at Cape Canaveral Air Force Station, a Cessna Citation aircraft has been fitted on the wings with devices that measure electric fields (black circles shown behind the open door) and with cloud physics probes (under the body and wings) that measure the size, shape and number of ice and water particles in clouds. The plane is being flown into anvil clouds in the KSC area as part of a study to review and possibly modify lightning launch commit criteria. The weather study could lead to improved lightning avoidance rules and fewer launch scrubs for the Space Shuttle and other launch vehicles on the Eastern and Western ranges.; More information about the study can be found in Release No. 56-00

Carbon nanotube modified probes for stable and high sensitivity conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Slattery, Ashley D.; Shearer, Cameron J.; Gibson, Christopher T.; Shapter, Joseph G.; Lewis, David A.; Stapleton, Andrew J.

2016-11-01

Conductive atomic force microscopy (C-AFM) is used to characterise the nanoscale electrical properties of many conducting and semiconducting materials. We investigate the effect of single walled carbon nanotube (SWCNT) modification of commercial Pt/Ir cantilevers on the sensitivity and image stability during C-AFM imaging. Pt/Ir cantilevers were modified with small bundles of SWCNTs via a manual attachment procedure and secured with a conductive platinum pad. AFM images of topography and current were collected from heterogeneous polymer and nanomaterial samples using both standard and SWCNT modified cantilevers. Typically, achieving a good current image comes at the cost of reduced feedback stability. In part, this is due to electrostatic interaction and increased tip wear upon applying a bias between the tip and the sample. The SWCNT modified tips displayed superior current sensitivity and feedback stability which, combined with superior wear resistance of SWCNTs, is a significant advancement for C-AFM.

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.

Forced swimming and imipramine modify plasma and brain amino acid concentrations in mice.

PubMed

Murakami, Tatsuro; Yamane, Haruka; Tomonaga, Shozo; Furuse, Mitsuhiro

2009-01-05

The relationships between monoamine metabolism and forced swimming or antidepressants have been well studied, however information is lacking regarding amino acid metabolism under these conditions. Therefore, the aim of the present study was to investigate the effects of forced swimming and imipramine on amino acid concentrations in plasma, the cerebral cortex and the hypothalamus in mice. Forced swimming caused cerebral cortex concentrations of L-glutamine, L-alanine, and taurine to be increased, while imipramine treatment caused decreased concentrations of L-glutamate, L-alanine, L-tyrosine, L-methionine, and L-ornithine. In the hypothalamus, forced swimming decreased the concentration of L-serine while imipramine treatment caused increased concentration of beta-alanine. Forced swimming caused increased plasma concentration of taurine, while concentrations of L-serine, L-asparagine, L-glutamine and beta-alanine were decreased. Imipramine treatment caused increased plasma concentration of all amino acid, except for L-aspartate and taurine. In conclusion, forced swimming and imipramine treatment modify central and peripheral amino acid metabolism. These results may aid in the identification of amino acids that have antidepressant-like effects, or may help to refine the dosages of antidepressant drugs.

Comparisons Between Experimental and Semi-theoretical Cutting Forces of CCS Disc Cutters

NASA Astrophysics Data System (ADS)

Xia, Yimin; Guo, Ben; Tan, Qing; Zhang, Xuhui; Lan, Hao; Ji, Zhiyong

2018-05-01

This paper focuses on comparisons between the experimental and semi-theoretical forces of CCS disc cutters acting on different rocks. The experimental forces obtained from LCM tests were used to evaluate the prediction accuracy of a semi-theoretical CSM model. The results show that the CSM model reliably predicts the normal forces acting on red sandstone and granite, but underestimates the normal forces acting on marble. Some additional LCM test data from the literature were collected to further explore the ability of the CSM model to predict the normal forces acting on rocks of different strengths. The CSM model underestimates the normal forces acting on soft rocks, semi-hard rocks and hard rocks by approximately 38, 38 and 10%, respectively, but very accurately predicts those acting on very hard and extremely hard rocks. A calibration factor is introduced to modify the normal forces estimated by the CSM model. The overall trend of the calibration factor is characterized by an exponential decrease with increasing rock uniaxial compressive strength. The mean fitting ratios between the normal forces estimated by the modified CSM model and the experimental normal forces acting on soft rocks, semi-hard rocks and hard rocks are 1.076, 0.879 and 1.013, respectively. The results indicate that the prediction accuracy and the reliability of the CSM model have been improved.

Effect of External Loading on Force and Power Production During Plyometric Push-ups.

PubMed

Hinshaw, Taylour J; Stephenson, Mitchell L; Sha, Zhanxin; Dai, Boyi

2018-04-01

Hinshaw, TJ, Stephenson, ML, Sha, Z, and Dai, B. Effect of external loading on force and power production during plyometric push-ups. J Strength Cond Res 32(4): 1099-1108, 2018-One common exercise to train upper-body strength and power is the push-up. Training at the loads that would produce the greatest power is an effective way to increase peak power. The purpose of the current study was to quantify the changes in peak force, peak power, and peak velocity among a modified plyometric push-up and plyometric push-ups with or without external loading in physically active young adults. Eighteen male and 17 female participants completed 4 push-ups: (a) modified plyometric push-up on the knees, (b) plyometric push-up without external loading, (c) plyometric push-up with an external load of 5% of body weight, and (d) plyometric push-up with an external load of 10% of body weight. Two force platforms were set up to collect vertical ground reaction forces at the hands and feet. The modified plyometric push-up demonstrated the lowest force, power, and velocity (5.4≥ Cohen's dz ≥1.2). Peak force and force at peak velocity increased (3.8≥ Cohen's dz ≥0.3) and peak velocity and velocity at peak power decreased (1.4≥ Cohen's dz ≥0.8) for the push-up without external loading compared with the 2 push-ups with external loading. No significant differences were observed for peak power among the push-ups with or without external loading (0.4≥ Cohen's dz ≥0.1). Although peak power is similar with or without external loading, push-ups without external loading may be more beneficial for a quick movement, and push-ups with external loading may be more beneficial for a greater force production.

The Layered Structure of The Universe

NASA Astrophysics Data System (ADS)

Kursunoglu, Behram N.

2003-06-01

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

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

Integrated analysis on static/dynamic aeroelasticity of curved panels based on a modified local piston theory

NASA Astrophysics Data System (ADS)

Yang, Zhichun; Zhou, Jian; Gu, Yingsong

2014-10-01

A flow field modified local piston theory, which is applied to the integrated analysis on static/dynamic aeroelastic behaviors of curved panels, is proposed in this paper. The local flow field parameters used in the modification are obtained by CFD technique which has the advantage to simulate the steady flow field accurately. This flow field modified local piston theory for aerodynamic loading is applied to the analysis of static aeroelastic deformation and flutter stabilities of curved panels in hypersonic flow. In addition, comparisons are made between results obtained by using the present method and curvature modified method. It shows that when the curvature of the curved panel is relatively small, the static aeroelastic deformations and flutter stability boundaries obtained by these two methods have little difference, while for curved panels with larger curvatures, the static aeroelastic deformation obtained by the present method is larger and the flutter stability boundary is smaller compared with those obtained by the curvature modified method, and the discrepancy increases with the increasing of curvature of panels. Therefore, the existing curvature modified method is non-conservative compared to the proposed flow field modified method based on the consideration of hypersonic flight vehicle safety, and the proposed flow field modified local piston theory for curved panels enlarges the application range of piston theory.

The role of large-scale eddies in the climate equilibrium. Part 2: Variable static stability

NASA Technical Reports Server (NTRS)

Zhou, Shuntai; Stone, Peter H.

1993-01-01

Lorenz's two-level model on a sphere is used to investigate how the results of Part 1 are modified when the interaction of the vertical eddy heat flux and static stability is included. In general, the climate state does not depend very much on whether or not this interaction is included, because the poleward eddy heat transport dominates the eddy forcing of mean temperature and wind fields. However, the climatic sensitivity is significantly affected. Compared to two-level model results with fixed static stability, the poleward eddy heat flux is less sensitive to the meridional temperature gradient and the gradient is more sensitive to the forcing. For example, the logarithmic derivative of the eddy flux with respect to the gradient has a slope that is reduced from approximately 15 on a beta-plane with fixed static stability and approximately 6 on a sphere with fixed static stability, to approximately 3 to 4 in the present model. This last result is more in line with analyses from observations. The present model also has a stronger baroclinic adjustment than that in Part 1, more like that in two-level beta-plane models with fixed static stability, that is, the midlatitude isentropic slope is very insensitive to the forcing, the diabatic heating, and the friction, unless the forcing is very weak.

Magnetically modified bioсells in constant magnetic field

NASA Astrophysics Data System (ADS)

Abramov, E. G.; Panina, L. K.; Kolikov, V. A.; Bogomolova, E. V.; Snetov, V. N.; Cherepkova, I. A.; Kiselev, A. A.

2017-02-01

Paper addresses the inverse problem in determining the area, where the external constant magnetic field captures the biological cells modified by the magnetic nanoparticles. Zero velocity isolines, in area where the modified cells are captured by the magnetic field were determined by numerical method for two locations of the magnet. The problem was solved taking into account the gravitational field, magnetic induction, density of medium, concentration and size of cells, and size and magnetization of nanoparticles attached to the cell. Increase in the number of the nanoparticles attached to the cell and decrease in the cell' size, enlarges the area, where the modified cells are captured and concentrated by the magnet. Solution is confirmed by the visible pattern formation of the modified cells Saccharomyces cerevisiae.

Evaluation of an operational ocean model configuration at 1/12° spatial resolution for the Indonesian seas (NEMO2.3/INDO12) - Part 1: Ocean physics

NASA Astrophysics Data System (ADS)

Tranchant, Benoît; Reffray, Guillaume; Greiner, Eric; Nugroho, Dwiyoga; Koch-Larrouy, Ariane; Gaspar, Philippe

2016-03-01

INDO12 is a 1/12° regional version of the NEMO physical ocean model covering the whole Indonesian EEZ (Exclusive Economic Zone). It has been developed and is now running every week in the framework of the INDESO (Infrastructure Development of Space Oceanography) project implemented by the Indonesian Ministry of Marine Affairs and Fisheries. The initial hydrographic conditions as well as open-boundary conditions are derived from the operational global ocean forecasting system at 1/4° operated by Mercator Océan. Atmospheric forcing fields (3-hourly ECMWF (European Centre for Medium-Range Weather Forecast) analyses) are used to force the regional model. INDO12 is also forced by tidal currents and elevations, and by the inverse barometer effect. The turbulent mixing induced by internal tides is taken into account through a specific parameterisation. In this study we evaluate the model skill through comparisons with various data sets including outputs of the parent model, climatologies, in situ temperature and salinity measurements, and satellite data. The biogeochemical model results assessment is presented in a companion paper (Gutknecht et al., 2015). The simulated and altimeter-derived Eddy Kinetic Energy fields display similar patterns and confirm that tides are a dominant forcing in the area. The volume transport of the Indonesian throughflow (ITF) is in good agreement with the INSTANT estimates while the transport through Luzon Strait is, on average, westward but probably too weak. Compared to satellite data, surface salinity and temperature fields display marked biases in the South China Sea. Significant water mass transformation occurs along the main routes of the ITF and compares well with observations. Vertical mixing is able to modify the South and North Pacific subtropical water-salinity maximum as seen in T-S diagrams. In spite of a few weaknesses, INDO12 proves to be able to provide a very realistic simulation of the ocean circulation and water mass transformation through the Indonesian Archipelago. Work is ongoing to reduce or eliminate the remaining problems in the second INDO12 version.

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.

Nongyrotropic Electrons in Guide Field Reconnection

NASA Technical Reports Server (NTRS)

Wendel, D. E.; Hesse, M.; Bessho, N.; Adrian, M. L.; Kuznetsova, M.

2016-01-01

We apply a scalar measure of nongyrotropy to the electron pressure tensor in a 2D particle-in-cell simulation of guide field reconnection and assess the corresponding electron distributions and the forces that account for the nongyrotropy. The scalar measure reveals that the nongyrotropy lies in bands that straddle the electron diffusion region and the separatrices, in the same regions where there are parallel electric fields. Analysis of electron distributions and fields shows that the nongyrotropy along the inflow and outflow separatrices emerges as a result of multiple populations of electrons influenced differently by large and small-scale parallel electric fields and by gradients in the electric field. The relevant parallel electric fields include large-scale potential ramps emanating from the x-line and sub-ion inertial scale bipolar electron holes. Gradients in the perpendicular electric field modify electrons differently depending on their phase, thus producing nongyrotropy. Magnetic flux violation occurs along portions of the separatrices that coincide with the parallel electric fields. An inductive electric field in the electron EB drift frame thus develops, which has the effect of enhancing nongyrotropies already produced by other mechanisms and under certain conditions producing their own nongyrotropy. Particle tracing of electrons from nongyrotropic populations along the inflows and outflows shows that the striated structure of nongyrotropy corresponds to electrons arriving from different source regions. We also show that the relevant parallel electric fields receive important contributions not only from the nongyrotropic portion of the electron pressure tensor but from electron spatial and temporal inertial terms as well.

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

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

Measuring the force of punches and kicks among combat sport athletes using a modified punching bag with an embedded accelerometer.

PubMed

Buśko, Krzysztof; Staniak, Zbigniew; Szark-Eckardt, Mirosława; Nikolaidis, Pantelis Theodoros; Mazur-Różycka, Joanna; Łach, Patrycja; Michalski, Radosław; Gajewski, Jan; Górski, Michał

2016-01-01

The main aim of the study was to design a new system to measure punching and kicking forces as well as reaction times in combat sport athletes. In addition, the study examined whether there were any intergender differences in the force of punches thrown by boxers and kicking forces delivered by taekwondo athletes. Boxers (male, n = 13; female, n = 7) were examined for the force of single straight punches and taekwondo athletes (male, n = 14; female, n = 14) for force of single Apdolio and Dwit Chagi kicks. The punching bag was equipped with acceleration transducers and gyroscopes embedded in a cylinder covered with a layer to absorb shock as well as a set of colour signal diodes. Value of the punching bag's acceleration was used for calculating: strike force; the punching location on the bag; and time of a strike. The relative error of force calculation was 3%; the relative error in acceleration measurement was less than 1%. The force of a straight rear-hand punch was greater than the force of a lead-hand punch among male and female boxers. The force of Apdolio kick delivered with a rear leg was greater compared to a lead leg among female and male taekwondo athletes. Significant gender differences were noticed in the force in both types of kicks. In boxers, intergender differences were reported only for the force of a punch thrown with the rear hand. Based on these findings, it was concluded that the modified punching bag is a good diagnostic tool for combat sports.

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.

Thermal force induced by the presence of a particle near a solidifying interface.

PubMed

Hadji, L

2001-11-01

The presence of a foreign particle in the melt, ahead of a solid-liquid interface, leads to the onset of interfacial deformations if the thermal conductivity of the particle, k(p), differs from that of the melt, k(l). In this paper, the influence of the thermal conductivity contrast on the interaction between the solidifying interface and the particle is quantified. We show that the interface distortion gives rise to a thermal force whose expression is given by F(th)=2piLGa3(1-alpha)/(2+alpha)T(m), where L is the latent heat of fusion per unit volume, T(m) is the melting point, a is the particle's radius, G the thermal gradient in the liquid phase and alpha=k(p)/k(l). The derivation makes use of the following assumptions: (i) the particle is small compared to the horizontal extent of the interface, (ii) the particle is placed in the near proximity of the deformable solid-liquid interface, and (iii) the interface is practically immobile in the calculation of the thermal field, i.e., V

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

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

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

NASA Astrophysics Data System (ADS)

Radwan, Ahmed E.; Halawa, Mohamed A.

1990-04-01

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

Validation and Application of the ReaxFF Reactive Force Field to Hydrocarbon Oxidation Kinetics

DTIC Science & Technology

2016-06-23

AFRL-AFOSR-VA-TR-2016-0278 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics Adrianus Van Duin...application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-14-1-0355 5c.  PROGRAM...Chenoweth Dec14 Validation and application of the ReaxFF reactive force field to hydrocarbon oxidation kinetics DISTRIBUTION A: Distribution approved for

Bubble induced flow field modulation for pool boiling enhancement over a tubular surface

NASA Astrophysics Data System (ADS)

Raghupathi, P. A.; Joshi, I. M.; Jaikumar, A.; Emery, T. S.; Kandlikar, S. G.

2017-06-01

We demonstrate the efficacy of using a strategically placed enhancement feature to modify the trajectory of bubbles nucleating on a horizontal tubular surface to increase both the critical heat flux (CHF) and the heat transfer coefficient (HTC). The CHF on a plain tube is shown to be triggered by a local dryout at the bottom of the tube due to vapor agglomeration. To mitigate this effect and delay CHF, the nucleating bubble trajectory is modified by incorporating a bubble diverter placed axially at the bottom of the tube. The nucleating bubble at the base of the diverter experiences a tangential evaporation momentum force (EMF) which causes the bubble to grow sideways away from the tube and avoid localized bubble patches that are responsible for CHF initiation. High speed imaging confirmed the lateral displacement of the bubbles away from the diverter closely matched with the theoretical predictions using EMF and buoyancy forces. Since the EMF is stronger at higher heat fluxes, bubble displacement increases with heat flux and results in the formation of separate liquid-vapor pathways wherein the liquid enters almost unobstructed at the bottom and the vapor bubble leaves sideways. Experimental results yielded CHF and HTC enhancements of ˜60% and ˜75%, respectively, with the diverter configuration when compared to a plain tube. This work can be used for guidance in developing enhancement strategies to effectively modulate the liquid-vapor flow around the heater surface at various locations to enhance HTC and CHF.

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.

Particle-in-cell simulation study of a lower-hybrid shock

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

Dieckmann, M. E.; Ynnerman, A.; Sarri, G.

2016-06-15

The expansion of a magnetized high-pressure plasma into a low-pressure ambient medium is examined with particle-in-cell simulations. The magnetic field points perpendicular to the plasma's expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by the lower-hybrid (LH) wave. The ambipolar electric field points in the expansion direction and it induces together with the background magnetic field a fast E cross B drift of electrons. The drifting electrons modify the background magnetic field, resulting in its pile-up by the LH shock. The magnetic pressure gradient force accelerates the ambientmore » ions ahead of the LH shock, reducing the relative velocity between the ambient plasma and the LH shock to about the phase speed of the shocked LH wave, transforming the LH shock into a nonlinear LH wave. The oscillations of the electrostatic potential have a larger amplitude and wavelength in the magnetized plasma than in an unmagnetized one with otherwise identical conditions. The energy loss to the drifting electrons leads to a noticeable slowdown of the LH shock compared to that in an unmagnetized plasma.« less

Convolutional virtual electric field for image segmentation using active contours.

PubMed

Wang, Yuanquan; Zhu, Ce; Zhang, Jiawan; Jian, Yuden

2014-01-01

Gradient vector flow (GVF) is an effective external force for active contours; however, it suffers from heavy computation load. The virtual electric field (VEF) model, which can be implemented in real time using fast Fourier transform (FFT), has been proposed later as a remedy for the GVF model. In this work, we present an extension of the VEF model, which is referred to as CONvolutional Virtual Electric Field, CONVEF for short. This proposed CONVEF model takes the VEF model as a convolution operation and employs a modified distance in the convolution kernel. The CONVEF model is also closely related to the vector field convolution (VFC) model. Compared with the GVF, VEF and VFC models, the CONVEF model possesses not only some desirable properties of these models, such as enlarged capture range, u-shape concavity convergence, subject contour convergence and initialization insensitivity, but also some other interesting properties such as G-shape concavity convergence, neighboring objects separation, and noise suppression and simultaneously weak edge preserving. Meanwhile, the CONVEF model can also be implemented in real-time by using FFT. Experimental results illustrate these advantages of the CONVEF model on both synthetic and natural images.

A theoretical Deduction from the Hubble law based on a Modified Newtonian Dynamics with field of Yukawa inverse

NASA Astrophysics Data System (ADS)

Falcon, N.

2017-07-01

At cosmic scales the dynamics of the Universe are almost exclusively prescribed by the force of gravity; however the assumption of the law of gravitation, depending on the inverse of the distance, leads to the known problems of the rotation curves of galaxies and missing mass (dark matter). The problem of the coupling of gravity to changes in scale and deviations from the law of the inverse square is an old problem (Laplace, 1805; Seeliger 1898), which has motivated alternatives to Newtonian dynamics compatible with observations. The present paper postulates a modified Newtonian dynamics by adding an inverse Yukawa potential: U(r)≡U0(M)(r-r0)e-α/r is the the potential per unit mass (in N/kg) as a function of the barionic mass that causes the field, r0 is of the order of 50h-1 Mpc and alpha is a coupling constant of the order of 2.5 h-1 Mpc. This potential is zero within the solar system, slightly attractive at interstellar distances, very attractive in galactic range and repulsive at cosmic scales. Its origin is the barionic matter, it allows to include the Milgrow MoND theory to explain the rotation curves, it is compatible with the experiments Eovos type, and allows to deduce the law of Hubble to cosmic scales, in the form H0=100h km/s Mpc≍U0(M)/c, where U0(M)≍ 4pi×6.67 10-11m/s2, is obtained from the Laplace's equation, assuming that the gravitational force is the law of the inverse of the square plus a non-linear term type Yukawa inverse. It is concluded that the modification of the law of gravity with nonlinear terms, allows to model the dynamics of the Universe on a large scale and include non-locality without dark matter. (See Falcon et al. 2014, International Journal of Astronomy and Astrophysics, 4, 551-559).

Polyethylenimine functionalized magnetic nanoparticles as a potential non-viral vector for gene delivery.

PubMed

Zhou, Yangbo; Tang, Zhaomin; Shi, Chunli; Shi, Shuai; Qian, Zhiyong; Zhou, Shaobing

2012-11-01

Polyethylenimine (PEI) functionalized magnetic nanoparticles were synthesized as a potential non-viral vector for gene delivery. The nanoparticles could provide the magnetic-targeting, and the cationic polymer PEI could condense DNA and avoid in vitro barriers. The magnetic nanoparticles were characterized by Fourier transform infrared spectroscopy, X-ray powder diffraction, dynamic light scattering measurements, transmission electron microscopy, vibrating sample magnetometer and atomic force microscopy. Agarose gel electrophoresis was used to asses DNA binding and perform a DNase I protection assay. The Alamar blue assay was used to evaluate negative effects on the metabolic activity of cells incubated with PEI modified magnetic nanoparticles and their complexes with DNA both in the presence or absence of an external magnetic field. Flow cytometry and fluorescent microscopy were also performed to investigate the transfection efficiency of the DNA-loaded magnetic nanoparticles in A549 and B16-F10 tumor cells with (+M) or without (-M) the magnetic field. The in vitro transfection efficiency of magnetic nanoparticles was improved obviously in a permanent magnetic field. Therefore, the magnetic nanoparticles show considerable potential as nanocarriers for gene delivery.

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.

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

PubMed

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

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.

Bespoke optical springs and passive force clamps from shaped dielectric particles

NASA Astrophysics Data System (ADS)

Simpson, S. H.; Phillips, D. B.; Carberry, D. M.; Hanna, S.

2013-09-01

By moulding optical fields, holographic optical tweezers are able to generate structured force fields with magnitudes and length scales of great utility for experiments in soft matter and biological physics. It has recently been noted that optically induced force fields are determined not only by the incident optical field, but by the shape and composition of the particles involved [Gluckstad J. Optical manipulation: sculpting the object. Nat Photonics 2011;5:7-8]. Indeed, there are desirable but simple attributes of a force field, such as orientational control, that cannot be introduced by sculpting optical fields alone. With this insight in mind, we show, theoretically, how relationships between force and displacement can be controlled by optimizing particle shapes. We exhibit a constant force optical spring, made from a tapered microrod and discuss methods by which it could be fabricated. In addition, we investigate the optical analogue of streamlining, and show how objects can be shaped so as to reduce the effects of radiation pressure, and hence switch from non-trapping to trapping regimes.

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

NASA Astrophysics Data System (ADS)

Unan, Hulya; Yildirim, Ahmet; Tekpinar, Mustafa

2015-07-01

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

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

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

2003-01-01

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

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

Development of agribiotechnology and biosafety regulations used to assess safety of genetically modified crops in Bangladesh.

PubMed

Nasiruddin, Khondoker M; Nasim, Anwar

2007-01-01

Bangladesh is on the verge of adopting genetically modified (GM) crops for commercial cultivation and consumption as feed and food. Most of the laboratories are engaged in tissue culture and molecular characterization on plants, whereas some have started living modified organism research with shortages of trained manpower, infrastructure, and funding. Nutritionally improved Golden Rice, biotech brinjal, and late blight-resistant potato are in contained trials in a greenhouse, and potato ring spot virus-resistant papaya is in the process of approval for a field trial. The government has taken some initiative in support of GM organism research, which include the formation of a Biotechnology Department in all institutes and the formation of the apex body, the National Task Force Committee on Biotechnology of Bangladesh under the chairpersonship of the Prime Minister. Biosafety policy guidelines and related aspects of biotechnology issues have been approved, and the laws are in the process of being promulgated. Being a party to the Cartagena Protocol, proper biosafety measures are regulated by the appropriate authority as stated. Although there are no laws made yet directly for biosafety of GM crops/foods, the relevant laws on agriculture, medicine, food, import, trade, environment, etc. may suffice and explain the situation.

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.

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.

Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom.

PubMed

Schappals, Michael; Mecklenfeld, Andreas; Kröger, Leif; Botan, Vitalie; Köster, Andreas; Stephan, Simon; García, Edder J; Rutkai, Gabor; Raabe, Gabriele; Klein, Peter; Leonhard, Kai; Glass, Colin W; Lenhard, Johannes; Vrabec, Jadran; Hasse, Hans

2017-09-12

Thermodynamic properties are often modeled by classical force fields which describe the interactions on the atomistic scale. Molecular simulations are used for retrieving thermodynamic data from such models, and many simulation techniques and computer codes are available for that purpose. In the present round robin study, the following fundamental question is addressed: Will different user groups working with different simulation codes obtain coinciding results within the statistical uncertainty of their data? A set of 24 simple simulation tasks is defined and solved by five user groups working with eight molecular simulation codes: DL_POLY, GROMACS, IMC, LAMMPS, ms2, NAMD, Tinker, and TOWHEE. Each task consists of the definition of (1) a pure fluid that is described by a force field and (2) the conditions under which that property is to be determined. The fluids are four simple alkanes: ethane, propane, n-butane, and iso-butane. All force fields consider internal degrees of freedom: OPLS, TraPPE, and a modified OPLS version with bond stretching vibrations. Density and potential energy are determined as a function of temperature and pressure on a grid which is specified such that all states are liquid. The user groups worked independently and reported their results to a central instance. The full set of results was disclosed to all user groups only at the end of the study. During the study, the central instance gave only qualitative feedback. The results reveal the challenges of carrying out molecular simulations. Several iterations were needed to eliminate gross errors. For most simulation tasks, the remaining deviations between the results of the different groups are acceptable from a practical standpoint, but they are often outside of the statistical errors of the individual simulation data. However, there are also cases where the deviations are unacceptable. This study highlights similarities between computer experiments and laboratory experiments, which are both subject not only to statistical error but also to systematic error.

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.

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.

Muscle activity patterns altered during pedaling at different body orientations.

PubMed

Brown, D A; Kautz, S A; Dairaghi, C A

1996-10-01

Gravity is a contributing force that is believed to influence strongly the control of limb movements since it affects sensory input and also contributes to task mechanics. By altering the relative contribution of gravitational force to the overall forces used to control pedaling at different body orientations, we tested the hypothesis that joint torque and muscle activation patterns would be modified to generate steady-state pedaling at altered body orientations. Eleven healthy subjects pedaled a modified ergometer at different body orientations (from horizontal to vertical), maintaining the same workload (80 J), cadence (60 rpm), and hip and knee kinematics. Pedal reaction forces and crank and pedal kinematics were measured and used to calculate joint torques and angles. EMG was recorded from four muscles (tibialis anterior, triceps surae, rectus femoris, biceps femoris). Measures of muscle activation (joint torque and EMG activity) showed strong dependence on body orientation, indicating that muscle activity is not fixed and is modified in response to altered body orientation. Simulations confirmed that, while joint torque changes were not necessary to pedal at different body orientations, observed changes were necessary to maintain consistent crank angular velocity profiles. Dependence of muscle activity on body orientation may be due to neural integration of sensory information with an internal model that includes characteristics of the endpoint, to produce consistent pedaling trajectories. Thus, both sensory consequences and mechanical aspects of gravitational forces are important determinants of locomotor tasks such as pedaling.

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.

NASA's modified Boeing 747 Shuttle Carrier Aircraft with the Space Shuttle Endeavour on top lifts of

NASA Technical Reports Server (NTRS)

2001-01-01

NASA's modified Boeing 747 Shuttle Carrier Aircraft with the Space Shuttle Endeavour on top lifts off from Edwards Air Force Base to begin its ferry flight back to the Kennedy Space Center in Florida.

75 FR 30689 - Modification of Class C Airspace; Beale Air Force Base, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-02

...-0367; Airspace Docket No. 10-AWA-2] RIN 2120-AA66 Modification of Class C Airspace; Beale Air Force... modifies the legal description of the Beale Air Force Base (AFB), CA, Class C airspace area by allowing the... Beale AFB Class C airspace area will be consistent with the actual hours of operation of the Beale AFB...

Computational Methods of Studying the Binding of Toxins From Venomous Animals to Biological Ion Channels: Theory and Applications

PubMed Central

Chen, Rong; Chung, Shin-Ho

2013-01-01

The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, Brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field. PMID:23589832

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.

Geologic map of the Shaida deposit and Misgaran prospect, Herat Province, Afghanistan, modified from the 1973 original map compilation of V.I. Tarasenko and others

USGS Publications Warehouse

Tucker, Robert D.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2014-01-01

This map is a modified version of Geological map and map of useful minerals, Shaida area, scale 1:50,000, which was compiled by V.I. Tarasenko, N.I. Borozenets, and others in 1973. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original document and related reports and also visited the field area in August 2010.This modified map illustrates the geological structure of the Shaida copper-lead-zinc deposit and Misgaran copper-lead-zinc prospect in western Afghanistan and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of these documents and on observations made during our field visit. Elevations on the cross sections are derived from the original Soviet topography and might not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map.The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

Geologic map of the Khanneshin carbonatite complex, Helmand Province, Afghanistan, modified from the 1976 original map compilation of V.G. Cheremytsin

USGS Publications Warehouse

Tucker, Robert D.; Peters, Stephen G.; Schulz, Klaus J.; Renaud, Karine M.; Stettner, Will R.; Masonic, Linda M.; Packard, Patricia H.

2011-01-01

This map is a modified version of the Geological map of the Khanneshin carbonatite complex, scale 1:10,000, which was compiled by V.G. Cheremytsin in 1976. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original map and also visited the field area in September 2009, August 2010, and February 2011. This modified map, which includes cross sections, illustrates the geologic structure of the Khanneshin carbonatite complex. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of that map and a related report, and based on observations made during our field visits. (Refer to the References section in the Map PDF for complete citations of the original map and related report.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

Transverse forces versus modified ashworth scale for upper limb flexion/extension in para-sagittal plane.

PubMed

Seth, Nitin; Johnson, Denise; Abdullah, Hussein A

2017-07-01

Spasticity is a common impairment following an upper motor neuron lesion in conditions such as stroke and brain injury. A clinical issue is how to best quantify and measure spasticity. Recently, research has been performed to develop new methods of spasticity quantification using various systems. This paper follows up on previous work taking a closer look at the role of transversal forces obtained via rehabilitation robot for motions in the para-sagittal plane. Results from 45 healthy individuals and 40 individuals with acquired brain injury demonstrate that although the passive upper motions are vertical, horizontal forces into and away from the individual's body demonstrate a relationship with the Modified Ashworth Scale. This finding leads the way to new avenues of spasticity quantification and monitoring.

Modified KdV equation for trapped ions in polarized dusty plasma

NASA Astrophysics Data System (ADS)

Singh, K.; Kaur, N.; Sethi, P.; Saini, N. S.

2018-01-01

In this investigation, the effect of polarization force on dust acoustic solitary waves (DASWs) has been presented in a dusty plasma composed of Maxwellian electrons, vortex-like (trapped) ions, and negatively charged mobile dust grains. It has been found that from the Maxwellian ions distribution to a vortex-like one, the dynamics of small but finite amplitude DA solitary waves is governed by a nonlinear equation of modified Korteweg-de Vries (mKdV) type instead of KdV. The combined effect of trapped ions and polarization force strongly influence the characteristics of DASWs. Only rarefactive solitary structures are formed under the influence of ions trapping and polarization force. The implications of our results are useful in real astrophysical situations of space and laboratory dusty plasmas.

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.

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.

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.

Frictional forces in material removal for glasses and ceramics using magnetorheological finishing

NASA Astrophysics Data System (ADS)

Miao, Chunlin

Magnetorheological finishing (MRF) spotting experiments on stationary parts are conducted in this work to understand the material removal mechanism in MRF. Drag force and normal force are measured in situ, simultaneously for the first time for a variety of optical materials in MRF. We study material removal process in MRF as a function of material mechanical properties. We experimentally demonstrate that material removal in MRF is strongly related to shear stress. Shear stress is predominantly determined by material mechanical properties. A modified Preston's equation is proposed to estimate the material removal in MRF by combining shear stress and material mechanical properties. We investigate extensively the effect of various MRF process parameters, including abrasive concentration, magnetic field strength, penetration depth and wheel speed, on material removal efficiency. Material removal rate model is expanded to include these parameters. We develop a nonaqueous magnetorheological (MR) fluid for examining the mechanical contribution in MRF material removal. This fluid is based on a combination of two CI particles and a combination of two organic liquids. Material removal with this nonaqueous MR fluid is discussed. We formulate a new corrosion resistant MR fluid which is based on metal oxide coated carbonyl iron (CI) particles. The rheological behavior, stability and corrosion resistance are examined.

Active control of sound radiation from a vibrating rectangular panel by sound sources and vibration inputs - An experimental comparison

NASA Technical Reports Server (NTRS)

Fuller, C. R.; Hansen, C. H.; Snyder, S. D.

1991-01-01

Active control of sound radiation from a rectangular panel by two different methods has been experimentally studied and compared. In the first method a single control force applied directly to the structure is used with a single error microphone located in the radiated acoustic field. Global attenuation of radiated sound was observed to occur by two main mechanisms. For 'on-resonance' excitation, the control force had the effect of increasing the total panel input impedance presented to the nosie source, thus reducing all radiated sound. For 'off-resonance' excitation, the control force tends not significantly to modify the panel total response amplitude but rather to restructure the relative phases of the modes leading to a more complex vibration pattern and a decrease in radiation efficiency. For acoustic control, the second method, the number of acoustic sources required for global reduction was seen to increase with panel modal order. The mechanism in this case was that the acoustic sources tended to create an inverse pressure distribution at the panel surface and thus 'unload' the panel by reducing the panel radiation impedance. In general, control by structural inputs appears more effective than control by acoustic sources for structurally radiated noise.

Self-consistent Simulation of Microparticle and Ion Wakefield Configuration

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Co-current Doping Effect of Nanoscale Carbon and Aluminum Nitride on Critical Current Density and Flux Pinning Properties of Bulk MgB2 Superconductors

NASA Astrophysics Data System (ADS)

Tripathi, D.; Dey, T. K.

2018-05-01

The effect of nanoscale aluminum nitride (n-AlN) and carbon (n-C) co-doping on superconducting properties of polycrystalline bulk MgB2 superconductor has been investigated. Polycrystalline pellets of MgB2, MgB2 + 0.5 wt% AlN (nano), MgB_{1.99}C_{0.01} and MgB_{1.99}C_{0.01} + 0.5 wt% AlN (nano) have been synthesized by a solid reaction process under inert atmosphere. The transition temperature (TC) estimated from resistivity measurement indicates only a small decrease for C (nano) and co-doped MgB2 samples. The magnetic field response of investigated samples has been measured at 4, 10, and 20 K in the field range ± 6 T. MgB2 pellets co-doped with 0.5 wt% n-AlN and 1 wt% n-C display appreciable enhancement in critical current density (J_C) of MgB2 in both low (≥ 3 times), as well as, high-field region (≥ 15 times). J_C versus H behavior of both pristine and doped MgB2 pellets is well explained in the light of the collective pinning model. Further, the normalized pinning force density f_p(= F_p/F_{pmax}) displays a fair correspondence with the scaling procedure proposed by Eisterer et al. Moreover, the scaled data of the pinning force density (i.e., f_p{-}h data) of the investigated pellets at different temperature are well interpreted by a modified Dew-Hughes expression reported by Sandu and Chee.

Magnetic fields in giant planet formation and protoplanetary discs

NASA Astrophysics Data System (ADS)

Keith, Sarah Louise

2015-12-01

Protoplanetary discs channel accretion onto their host star. How this is achieved is critical to the growth of giant planets which capture their massive gaseous atmosphere from the surrounding flow. Theoretical studies find that an embedded magnetic field could power accretion by hydromagnetic turbulence or torques from a large-scale field. This thesis presents a study of the inuence of magnetic fields in three key aspects of this process: circumplanetary disc accretion, gas flow across gaps in protoplanetary discs, and magnetic-braking in accretion discs. The first study examines the conditions needed for self-consistent accretion driven by magnetic fields or gravitational instability. Models of these discs typically rely on hydromagnetic turbulence as the source of effective viscosity. However, magnetically coupled,accreting regions may be so limited that the disc may not support sufficient inflow. An improved Shakura-Sunyaev ? disc is used to calculate the ionisation fraction and strength of non-ideal effects. Steady magnetically-driven accretion is limited to the thermally ionised, inner disc so that accretion in the remainder of the disc is time-dependent. The second study addresses magnetic flux transport in an accretion gap evacuated by a giant planet. Assuming the field is passively drawn along with the gas, the hydrodynamical simulation of Tanigawa, Ohtsuki & Machida (2012) is used for an a posteriori analysis of the gap field structure. This is used to post-calculate magnetohydrodynamical quantities. This assumption is self-consistent as magnetic forces are found to be weak, and good magnetic coupling ensures the field is frozen into the gas. Hall drift dominates across much of the gap, with the potential to facilitate turbulence and modify the toroidal field according to the global field orientation. The third study considers the structure and stability of magnetically-braked accretion discs. Strong evidence for MRI dead-zones has renewed interest in accretion powered by large-scale fields. An equilibrium model is presented for the radial structure of an axisymmetric, magnetically-braked accretion disc connected to a force-free external field. The accretion rate is multivalued at protoplanetary disc column densities, featuring an `S-curve' associated with models of accretion outbursting. A local, linear analysis of the stability of radial modes finds that the rapidly accreting, middle and upper solution branches are unstable, further highlighting the potential for eruptive accretion events.

Development of a novel electric field-assisted modified hydrodynamic cavitation system for disintegration of waste activated sludge.

PubMed

Jung, Kyung-Won; Hwang, Min-Jin; Yun, Yeo-Myeong; Cha, Min-Jung; Ahn, Kyu-Hong

2014-09-01

In this current study, we present a modified hydrodynamic cavitation device that combines an electric field to substitute for the chemical addition. A modified HC system is basically an orifice plate and crisscross pipe assembly, in which the crisscross pipe imparts some turbulence, which creates collision events. This study shows that for maximizing disintegration, combining HC system, which called electric field-assisted modified orifice plate hydrodynamic cavitation (EFM-HC) in this study, with an electric field is important. Various HC systems were compared in terms of disintegration of WAS, and, among them, the EFM-HC system exhibited the best performance with the highest disintegration efficiency of 47.0±2.0% as well as the destruction of WAS morphological characteristics. The experimental results clearly show that a conventional HC system was successfully modified. In addition, electric field has a great potential for efficient disintegration of WAS for as a additional option in a combination treatment. This study suggests continued research in this field may lead to an appropriate design for commercial use. Copyright © 2014 Elsevier B.V. All rights reserved.

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

PubMed

Edwards, Devin T; Faulk, Jaevyn K; LeBlanc, Marc-André; Perkins, Thomas T

2017-12-19

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm 2 cantilever into one terminated with a gold-coated, 4 × 4 μm 2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM. Published by Elsevier Inc.

Application of Remote Sensing to Assess the Impact of Short Term Climate Variability on Coastal Sedimentation

NASA Technical Reports Server (NTRS)

Moeller, Christopher C.; Gunshor, Mathew M.; Menzel, W. Paul; Huh, Oscar K.; Walker, Nan D.; Rouse, Lawrence J.; Frey, Herbert V. (Technical Monitor)

2001-01-01

The University of Wisconsin and Louisiana State University have teamed to study the forcing of winter season cold frontal wind systems on sediment distribution patterns and geomorphology in the Louisiana coastal zone. Wind systems associated with cold fronts have been shown to modify coastal circulation and resuspend sediments along the microtidal Louisiana coast. The assessment includes quantifying the influence of cumulative winter season atmospheric forcing (through surface wind observations) from year to year in response to short term climate variability, such as El Nino events. A correlation between winter cyclone frequency and the strength of El Nino events has been suggested. The atmospheric forcing data are being correlated to geomorphic measurements along western Louisiana's prograding muddy coast. Remote sensing data is being used to map and track sediment distribution patterns for various wind conditions. Transferring a suspended sediment concentration (SSC) algorithm to EOS MODIS observations will enable estimates of SSC in case 2 waters over the global domain. Progress in Year 1 of this study has included data collection and analysis of wind observations for atmospheric forcing characterization, a field activity (TX-2001) to collect in situ water samples with co-incident remote sensing measurements from the NASA ER-2 based MODIS Airborne Simulator (MAS) and the EOS Terra based MODerate resolution Imaging Spectroradiometer (MODIS) instruments, aerial photography and of sediment burial pipe field measurements along the prograding muddy Chenier Plain coast of western Louisiana for documenting coastal change in that dynamic region, and routine collection of MODIS 250 in resolution data for monitoring coastal sediment patterns. The data sets are being used in a process to transfer an SSC estimation algorithm to the MODIS platform. Work is underway on assessing coastal transport for the winter 2000-01 season. Water level data for use in a Geomorphic Impact Index, which relates wind energy, water level conditions, and geomorphic change along the microtidal western Louisiana coastline is being assembled.

Charge patterns as templates for the assembly of layered biomolecular structures.

PubMed

Naujoks, Nicola; Stemmer, Andreas

2006-08-01

Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

Every Heavenly Body When Created Will Have No Motion, Linear, Rotational and/or Vibratory Motion, Singly or in Some Combination

NASA Astrophysics Data System (ADS)

Brekke, Stewart

2010-02-01

Each galaxy, star and planet is in a state of no motion, linear, rotational and/or vibratory motion. Orbital motion is linear motion in a force field such as gravity. These motions were created in the formation of the galaxy, star or planet unless modified by external events such as colliding galaxies or impacts such as meteors. Some motions, such as rotations and vibrations may be differential such as in the cases of our sun and the Milky Way galaxy. The basic equation for each heavenly body is as follows. E = mc^2 + 1/2mv^2 + 1/2I2̂+ 1/2Kx^2 + WG+ WE+ WM. )

A NASA Technician directs loading of the crated SOFIA primary mirror assembly into a C-17 for shipment to NASA Ames Research Center for finish coating

NASA Image and Video Library

2008-05-01

Technicians at NASA's Dryden Aircraft Operations Facility in Palmdale, Calif., loaded the German-built primary mirror assembly of the Stratospheric Observatory for Infrared Astronomy, or SOFIA, onto an Air Force C-17 for shipment to NASA's Ames Research Center on May 1, 2008. In preparation for the final finish coating of the mirror, the more than two-ton mirror assembly had been removed from its cavity in the rear fuselage of the highly modified SOFIA Boeing 747SP two weeks earlier. After arrival at NASA Ames at Moffett Field near Mountain View, Calif., the mirror would receive its aluminized finish coating before being re-installed in the SOFIA aircraft.

Dimensionless Analysis and Numerical Modeling of Rebalancing Phenomena During Levitation

NASA Astrophysics Data System (ADS)

Gao, Lei; Shi, Zhe; Li, Donghui; McLean, Alexander; Chattopadhyay, Kinnor

2016-06-01

Electromagnetic levitation (EML) has proved to be a powerful tool for research activities in areas pertaining to materials physics and engineering. The customized EML setups in various fields, ranging from solidification to nanomaterial manufacturing, require the designing of stable levitation systems. Since the elevated droplet is opaque, the most effective way to research on EML is mathematical modeling. In the present study, a 3D model was built to investigate the rebalancing phenomenon causing instabilities during droplet melting. A mathematical model modified based on Hooke's law (spring) was proposed to describe the levitation system. This was combined with dimensionless analysis to investigate the generation of levitation forces as it will significantly affect the behavior of the spring model.

Portable gas chromatograph-mass spectrometer

DOEpatents

Andresen, Brian D.; Eckels, Joel D.; Kimmons, James F.; Myers, David W.

1996-01-01

A gas chromatograph-mass spectrometer (GC-MS) for use as a field portable organic chemical analysis instrument. The GC-MS is designed to be contained in a standard size suitcase, weighs less than 70 pounds, and requires less than 600 watts of electrical power at peak power (all systems on). The GC-MS includes: a conduction heated, forced air cooled small bore capillary gas chromatograph, a small injector assembly, a self-contained ion/sorption pump vacuum system, a hydrogen supply, a dual computer system used to control the hardware and acquire spectrum data, and operational software used to control the pumping system and the gas chromatograph. This instrument incorporates a modified commercial quadrupole mass spectrometer to achieve the instrument sensitivity and mass resolution characteristic of laboratory bench top units.

Computational algorithms for simulations in atmospheric optics.

PubMed

Konyaev, P A; Lukin, V P

2016-04-20

A computer simulation technique for atmospheric and adaptive optics based on parallel programing is discussed. A parallel propagation algorithm is designed and a modified spectral-phase method for computer generation of 2D time-variant random fields is developed. Temporal power spectra of Laguerre-Gaussian beam fluctuations are considered as an example to illustrate the applications discussed. Implementation of the proposed algorithms using Intel MKL and IPP libraries and NVIDIA CUDA technology is shown to be very fast and accurate. The hardware system for the computer simulation is an off-the-shelf desktop with an Intel Core i7-4790K CPU operating at a turbo-speed frequency up to 5 GHz and an NVIDIA GeForce GTX-960 graphics accelerator with 1024 1.5 GHz processors.

Thermodynamics of surface defects at the aspirin/water interface

NASA Astrophysics Data System (ADS)

Schneider, Julian; Zheng, Chen; Reuter, Karsten

2014-09-01

We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics simulations. To this end, we adopt and modify existing approaches to calculate binding free energies of biological ligand/receptor complexes to be applicable to common surface defects, such as step edges and kink sites. We obtain statistically accurate and reliable free energy values for the aspirin/water interface, which can be applied to estimate the distribution of defects using well-established thermodynamic relations. As a show case we calculate the free energy upon dissolving molecules from kink sites at the interface. This free energy can be related to the solubility concentration and we obtain solubility values in excellent agreement with experimental results.

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.

Theoretical model of gravitational perturbation of current collector axisymmetric flow field

NASA Astrophysics Data System (ADS)

Walker, John S.; Brown, Samuel H.; Sondergaard, Neal A.

1989-03-01

Some designs of liquid metal collectors in homopolar motors and generators are essentially rotating liquid metal fluids in cylindrical channels with free surfaces and will, at critical rotational speeds, become unstable. The role of gravity in modifying this ejection instability is investigated. Some gravitational effects can be theoretically treated by perturbation techniques on the axisymmetric base flow of the liquid metal. This leads to a modification of previously calculated critical current collector ejection values neglecting gravity effects. The derivation of the mathematical model which determines the perturbation of the liquid metal base flow due to gravitational effects is documented. Since gravity is a small force compared with the centrifugal effects, the base flow solutions can be expanded in inverse powers of the Froude number and modified liquid flow profiles can be determined as a function of the azimuthal angle. This model will be used in later work to theoretically study the effects of gravity on the ejection point of the current collector. A rederivation of the hydrodynamic instability threshold of a liquid metal current collector is presented.

Theoretical model of gravitational perturbation of current collector axisymmetric flow field

NASA Astrophysics Data System (ADS)

Walker, John S.; Brown, Samuel H.; Sondergaard, Neal A.

1990-05-01

Some designs of liquid-metal current collectors in homopolar motors and generators are essentially rotating liquid-metal fluids in cylindrical channels with free surfaces and will, at critical rotational speeds, become unstable. An investigation at David Taylor Research Center is being performed to understand the role of gravity in modifying this ejection instability. Some gravitational effects can be theoretically treated by perturbation techniques on the axisymmetric base flow of the liquid metal. This leads to a modification of previously calculated critical-current-collector ejection values neglecting gravity effects. The purpose of this paper is to document the derivation of the mathematical model which determines the perturbation of the liquid-metal base flow due to gravitational effects. Since gravity is a small force compared with the centrifugal effects, the base flow solutions can be expanded in inverse powers of the Froude number and modified liquid-flow profiles can be determined as a function of the azimuthal angle. This model will be used in later work to theoretically study the effects of gravity on the ejection point of the current collector.

Fabrication of SrTiO3 Layer on Pt Electrode for Label-Free Capacitive Biosensors

PubMed Central

Carapella, Giovanni; Pilloton, Roberto; Di Matteo, Marisa

2018-01-01

Due to their interesting ferroelectric, conductive and dielectric properties, in recent years, perovskite-structured materials have begun to attract increasing interest in the biosensing field. In this study, a strontium titanate perovskite layer (SrTiO3) has been synthesized on a platinum electrode and exploited for the development of an impedimetric label-free immunosensor for Escherichia coli O157:H7 detection. The electrochemical characterization of the perovskite-modified electrode during the construction of the immunosensor, as well as after the interaction with different E. coli O157:H7 concentrations, showed a reproducible decrease of the total capacitance of the system that was used for the analytical characterization of the immunosensor. Under optimized conditions, the capacitive immunosensor showed a linear relationship from to 1 to 7 log cfu/mL with a low detection limit of 1 log cfu/mL. Moreover, the atomic force microscopy (AFM) technique underlined the increase in roughness of the SrTiO3-modified electrode surface after antibody immobilization, as well as the effective presence of cells with the typical size of E. coli. PMID:29547521

Conductive properties of switchable photoluminescence thermosetting systems based on liquid crystals.

PubMed

Tercjak, Agnieszka; Gutierrez, Junkal; Ocando, Connie; Mondragon, Iñaki

2010-03-16

Conductive properties of different thermosetting materials modified with nematic 4'-(hexyl)-4-biphenyl-carbonitrile (HBC) liquid crystal and rutile TiO(2) nanoparticles were successfully studied by means of tunneling atomic force miscroscopy (TUNA). Taking into account the liquid crystal state of the HBC at room temperature, depending on both the HBC content and the presence of TiO(2) nanoparticles, designed materials showed different TUNA currents passed through the sample. The addition of TiO(2) nanoparticles into the systems multiply the detected current if compared to the thermosetting systems without TiO(2) nanoparticles and simultaneously stabilized the current passed through the sample, making the process reversible since the absolute current values were almost the same applying both negative and positive voltage. Moreover, thermosetting systems modified with liquid crystals with and without TiO(2) nanoparticles are photoluminescence switchable materials as a function of temperature gradient during repeatable heating/cooling cycle. Conductive properties of switchable photoluminescence thermosetting systems based on liquid crystals can allow them to find potential application in the field of photoresponsive devices, with a high contrast ratio between transparent and opaque states.

Simulated molecular-scale interaction of supercritical fluid mobile and stationary phases.

PubMed

Siders, Paul D

2017-12-08

In supercritical fluid chromatography, molecules from the mobile phase adsorb on the stationary phase. Stationary-phase alkylsilane-terminated silica surfaces might adsorb molecules at the silica, among the silanes, on a silane layer, or in pore space between surfaces. Mobile phases of carbon dioxide, pure and modified with methanol, and stationary phases were simulated at the molecular scale. Classical atomistic force fields were used in Gibbs-ensemble hybrid Monte Carlo calculations. Excess adsorption of pure carbon dioxide mobile phase peaked at fluid densities of 0.002-0.003Å -3 . Mobile phase adsorption from 7% methanol in carbon dioxide peaked at lower fluid density. Methanol was preferentially adsorbed from the mixed fluid. Surface silanes prevented direct interaction of fluid-phase molecules with silica. Some adsorbed molecules mixed with tails of bonded silanes; some formed layers above the silanes. Much adsorption occurred by filling the space between surfaces in the stationary-phase model. The distribution in the stationary phase of methanol molecules from a modified fluid phase varied with pressure. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis and numerical modelling of eddy current damper for vibration problems

NASA Astrophysics Data System (ADS)

Irazu, L.; Elejabarrieta, M. J.

2018-07-01

This work discusses a contactless eddy current damper, which is used to attenuate structural vibration. Eddy currents can remove energy from dynamic systems without any contact and, thus, without adding mass or modifying the rigidity of the structure. An experimental modal analysis of a cantilever beam in the absence of and under a partial magnetic field is conducted in the bandwidth of 01 kHz. The results show that the eddy current phenomenon can attenuate the vibration of the entire structure without modifying the natural frequencies or the mode shapes of the structure itself. In this study, a new inverse method to numerically determine the dynamic properties of the contactless eddy current damper is proposed. The proposed inverse method and the eddy current model based on a lineal viscous force are validated by a practical application. The numerically obtained transfer function correlates with the experimental one, thus showing good agreement in the entire bandwidth of 01 kHz. The proposed method provides an easy and quick tool to model and predict the dynamic behaviour of the contactless eddy current damper, thereby avoiding the use of complex analytical models.

Numerical and Analytical Investigation of the Energy and Momentum Exchange Between the Shocked Solar Wind and Topside Ionosphere for Non-Magnetic Planets and Moons

NASA Astrophysics Data System (ADS)

Dobe, Z.; Shapiro, V. D.; Quest, K.; Szego, K.; Huba, J.

1998-11-01

Previously[1], we proposed a model of the planetary ions pick-up by the shocked solar wind flow developing in the mantle-turbulent boundary region surrounding the ionospheres of non-magnetic planets-Mars and Venus. In the present paper we are modifying this model taking into account the flow of the planetary elections immediately pick-up by E x B forces of the shocked solar wind. It is shown that flow of the cold planetary electrons drives a strong hydrodynamical instability of the electrostatic whistlers efficiently coupling planetary ions with the flow of the solar wind. The linear stage of the instability is investigated both analytically and numerically, and results are found to be in a good agreement. Nonlunear stage of the instability is investigated with the modified numerical hybrid code[2], and demonstrates both effects of acceleration and heating of the planetary ions by the solar wind. Field aligned electron acceleration is also investigated in a test particle approximation using wave power spectrum obtained in a self-consistent numerical simulation.

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.

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

Mapping the Influence of Prior Tectonism on Seismicity in the Central and Eastern US

NASA Astrophysics Data System (ADS)

Boyd, O. S.; Levandowski, W.; Ramirez-Guzman, L.; Zellman, M.; Briggs, R.

2015-12-01

From the Atlantic margin to the Rockies, most earthquakes in the central and eastern U.S. occur in ancient tectonic zones, yet many such features have been historically quiescent. If all intraplate stress were transferred from plate boundaries or bases, the stress field would be broadly uniform, with all well-oriented faults equally likely to slip. But faults are not the only product of tectonism; intrusions, metamorphism, or any number of other alterations may modify crustal and/or upper mantle density, leaving behind lithostatic pressure gradients that can locally elevate or reduce stress on faults. With data provided by Earthscope, we are working to map lithospheric density across the U.S. and to quantify gravitational body-forces using analytical and finite-element methods. Regional-scale 3D models show that gravitational forces focus seismicity and reorient principal stress both in the New Madrid seismic zone and the western Great Plains. Sedimentary fill and low elevation encourage Reelfoot Rift-normal contraction, yet along-strike variations in lower crustal density rotate body-forces beneath New Madrid to interfere constructively with far-field compression, augmenting differential stress by 5-10 MPa. On the plains of SE Colorado and SE Wyoming, the Cheraw and Wheatland/Whalen faults collocate with multiply reactivated Proterozoic sutures, enigmatic Quaternary extension, and focused seismicity with regionally anomalous NW-SE moment tensor T-axes. Earthscope data help reveal anomalously buoyant lower crust beneath each suture -­- which we hypothesize reflects hydration by Farallon slab-derived fluids that have preferentially migrated along ancient fracture networks -- that generates 10 MPa of localized suture-normal tension, consistent with geomorphic strain- and seismic stress-indicators. As continent-wide seismic models emerge from Earthscope data, we will continue to map regions where inherited structures encourage intraplate seismicity.

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.

Open and closed loop manipulation of charged microchiplets in an electric field

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

Lu, J. P., E-mail: jplu@parc.com; Thompson, J. D.; Whiting, G. L.

We demonstrate the ability to orient, position, and transport microchips (“chiplets”) with electric fields. In an open-loop approach, modified four phase traveling wave potential patterns manipulate chiplets in a dielectric solution using dynamic template agitation techniques. Repeatable parallel assembly of chiplets is demonstrated to a positional accuracy of 6.5 μm using electrodes of 200 μm pitch. Chiplets with dipole surface charge patterns are used to show that orientation can be controlled by adding unique charge patterns on the chiplets. Chip path routing is also demonstrated. With a closed-loop control system approach using video feedback, dielectric, and electrophoretic forces are used to achievemore » positioning accuracy of better than 1 μm with 1 mm pitch driving electrodes. These chip assembly techniques have the potential to enable future printer systems where inputs are electronic chiplets and the output is a functional electronic system.« less

DUHOCAMIS: a dual hollow cathode ion source for metal ion beams.

PubMed

Zhao, W J; Müller, M W O; Janik, J; Liu, K X; Ren, X T

2008-02-01

In this paper we describe a novel ion source named DUHOCAMIS for multiply charged metal ion beams. This ion source is derived from the hot cathode Penning ion gauge ion source (JINR, Dubna, 1957). A notable characteristic is the modified Penning geometry in the form of a hollow sputter electrode, coaxially positioned in a compact bottle-magnetic field along the central magnetic line of force. The interaction of the discharge geometry with the inhomogeneous but symmetrical magnetic field enables this device to be operated as hollow cathode discharge and Penning discharge as well. The main features of the ion source are the very high metal ion efficiency (up to 25%), good operational reproducibility, flexible and efficient operations for low charged as well as highly charged ions, compact setup, and easy maintenance. For light ions, e.g., up to titanium, well-collimated beams in the range of several tens of milliamperes of pulsed ion current (1 ms, 10/s) have been reliably performed in long time runs.

Experimental investigation of a throttlable 15 cm hollow cathode ion thruster

NASA Technical Reports Server (NTRS)

Wilbur, P. J.

1972-01-01

The use of dished high perveance grids on a 15 cm modified SERT 2 thruster is shown to facilitate throttled operation over a beam current range from 60 to 600 mA. Effects of increasing the radial component of the magnetic field in the main discharge chamber and decreasing the dimensions of the cathode discharge region are examined and found to degrade performance to the extent that primary electrons are forced in toward the center-line of the thruster. Studies of the baffle aperture region of two thrusters indicate that the electric potential gradient vector is perpendicular to the local magnetic field lines when the thruster is operating properly. The correlation between the shape of the ion beam current density and that of the ion density at the screen grid within the thruster is shown to be 94%. Additional experimental studies on maximum propellant utilization, plasma ion production cost, neutral density in the cathode discharge region, double ion production in hollow cathode thrusters and thermal flow meter performance are discussed.

Spontaneous scalarization with an extremely massive field and heavy neutron stars

NASA Astrophysics Data System (ADS)

Morisaki, Soichiro; Suyama, Teruaki

2017-10-01

We investigate the internal structure and the mass-radius relation of neutron stars in a recently proposed scalar-tensor theory dubbed asymmetron in which a massive scalar field undergoes spontaneous scalarization inside neutron stars. We focus on the case where the Compton wavelength is shorter than 10 km, which has not been investigated in the literature. By solving the modified Einstein equations, either purely numerically or by partially using a semianalytic method, we find that not only the weakening of gravity by spontaneous scalarization but also the scalar force affect the internal structure significantly in the massive case. We also find that the maximum mass of neutron stars is larger for certain parameter sets than that in general relativity and reaches 2 M⊙ even if the effect of strange hadrons is taken into account. There is even a range of parameters where the maximum mass of neutron stars largely exceeds the threshold that violates the causality bound in general relativity.

Reconfigurable paramagnetic microswimmers: Brownian motion affects non-reciprocal actuation.

PubMed

Du, Di; Hilou, Elaa; Biswal, Sibani Lisa

2018-05-09

Swimming at low Reynolds number is typically dominated by a large viscous drag, therefore microscale swimmers require non-reciprocal body deformation to generate locomotion. Purcell described a simple mechanical swimmer at the microscale consisting of three rigid components connected together with two hinges. Here we present a simple microswimmer consisting of two rigid paramagnetic particles with different sizes. When placed in an eccentric magnetic field, this simple microswimmer exhibits non-reciprocal body motion and its swimming locomotion can be directed in a controllable manner. Additional components can be added to create a multibody microswimmer, whereby the particles act cooperatively and translate in a given direction. For some multibody swimmers, the stochastic thermal forces fragment the arm, which therefore modifies the swimming strokes and changes the locomotive speed. This work offers insight into directing the motion of active systems with novel time-varying magnetic fields. It also reveals that Brownian motion not only affects the locomotion of reciprocal swimmers that are subject to the Scallop theorem, but also affects that of non-reciprocal swimmers.

Process parameter effects on material removal in magnetorheological finishing of borosilicate glass.

PubMed

Miao, Chunlin; Lambropoulos, John C; Jacobs, Stephen D

2010-04-01

We investigate the effects of processing parameters on material removal for borosilicate glass. Data are collected on a magnetorheological finishing (MRF) spot taking machine (STM) with a standard aqueous magnetorheological (MR) fluid. Normal and shear forces are measured simultaneously, in situ, with a dynamic dual load cell. Shear stress is found to be independent of nanodiamond concentration, penetration depth, magnetic field strength, and the relative velocity between the part and the rotating MR fluid ribbon. Shear stress, determined primarily by the material mechanical properties, dominates removal in MRF. The addition of nanodiamond abrasives greatly enhances the material removal efficiency, with the removal rate saturating at a high abrasive concentration. The volumetric removal rate (VRR) increases with penetration depth but is insensitive to magnetic field strength. The VRR is strongly correlated with the relative velocity between the ribbon and the part, as expected by the Preston equation. A modified removal rate model for MRF offers a better estimation of MRF removal capability by including nanodiamond concentration and penetration depth.

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.

The Coulomb based magneto-electric coupling in multiferroic tunnel junctions and granular multiferroics

NASA Astrophysics Data System (ADS)

Udalov, O. G.; Beloborodov, I. S.

2018-05-01

We study magneto-electric effect in two systems: i) multiferroic tunnel junction (MFTJ) - magnetic tunnel junction with ferroelectric barrier and ii) granular multiferroic (GMF) in which ferromagnetic (FM) metallic grains embedded into ferroelectric matrix. We show that the Coulomb interaction influences the magnetic state of the system in several ways: i) through the spin-dependent part of the Coulomb interaction; ii) due to the Coulomb blockade effect suppressing electron hopping and therefore reducing magnetic coupling; and iii) through image forces and polarization screening that modify the barrier for electrons in MFTJ and GMF. We show that in the absence of spin-orbit or strain-mediated coupling magneto-electric effect appears in GMF and MFTJ. The Coulomb interaction depends on the dielectric properties of the system. For GMF it depends on the dielectric constant of FE matrix and for MFTJ on the dielectric constant of the FE barrier. Applying external electric field one can tune the dielectric constant and the Coulomb interaction. Thus, one can control magnetic state with electric field.

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

Observations of nonlinear and nonuniform kink dynamics in a laboratory flux rope

NASA Astrophysics Data System (ADS)

Sears, J.; Intrator, T.; Feng, Y.; Swan, H.; Gao, K.; Chapdelaine, L.

2013-12-01

A plasma column with axial magnetic field and current has helically twisted field lines. When current density in the column exceeds the kink instability threshold this magnetic configuration becomes unstable. Flux ropes in the solar wind and some solar prominences exhibit this topology, with their dynamics strongly and nonlinearly coupled to the ratio of axial current to magnetic field. The current-driven kink mode is ubiquitous in laboratory plasmas and well suited to laboratory study. In the Reconnection Scaling Experiment (RSX), nonlinear stability properties beyond the simple perturbative kink model are observed and readily diagnosed. We use a plasma gun to generate a single plasma column 0.50 m in length, in which we then drive an axial plasma current at the limit of marginal kink stability. With plasma current maintained at this threshold, we observe a deformation to a new dynamic equilibrium with finite gyration amplitude, where the currents and magnetic fields that support the force balance have surprising axial structure. Three dimensional measurements of magnetic field, plasma density, plasma potential, and ion flow velocity in the deformed plasma column show variation in the axial direction of the instability parameter and in the terms of the momentum equation. Likewise the pitch of the kink is measured to be nonuniform over the column length. In addition there is a return current antiparallel to the driven plasma current at distances up to 0.30 m from the gun that also modifies the force balance. These axial inhomogeneities, which are not considered in the model of an ideal kink, may be the terms that allow the deformed equilibrium of the RSX plasma to exist. Supported by DOE Office of Fusion Energy Sciences under LANS contract DE-AC52-06NA25369, NASA Geospace NNHIOA044I, Basic. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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.

Modified social force model based on information transmission toward crowd evacuation simulation

NASA Astrophysics Data System (ADS)

Han, Yanbin; Liu, Hong

2017-03-01

In this paper, the information transmission mechanism is introduced into the social force model to simulate pedestrian behavior in an emergency, especially when most pedestrians are unfamiliar with the evacuation environment. This modified model includes a collision avoidance strategy and an information transmission model that considers information loss. The former is used to avoid collision among pedestrians in a simulation, whereas the latter mainly describes how pedestrians obtain and choose directions appropriate to them. Simulation results show that pedestrians can obtain the correct moving direction through information transmission mechanism and that the modified model can simulate actual pedestrian behavior during an emergency evacuation. Moreover, we have drawn four conclusions to improve evacuation based on the simulation results; and these conclusions greatly contribute in optimizing a number of efficient emergency evacuation schemes for large public places.

Acoustic levitator for structure measurements on low temperature liquid droplets.

PubMed

Weber, J K R; Rey, C A; Neuefeind, J; Benmore, C J

2009-08-01

A single-axis acoustic levitator was constructed and used to levitate liquid and solid drops of 1-3 mm in diameter at temperatures in the range -40 to +40 degrees C. The levitator comprised (i) two acoustic transducers mounted on a rigid vertical support that was bolted to an optical breadboard, (ii) an acoustic power supply that controlled acoustic intensity, relative phase of the drive to the transducers, and could modulate the acoustic forces at frequencies up to 1 kHz, (iii) a video camera, and (iv) a system for providing a stream of controlled temperature gas flow over the sample. The acoustic transducers were operated at their resonant frequency of approximately 22 kHz and could produce sound pressure levels of up to 160 dB. The force applied by the acoustic field could be modulated to excite oscillations in the sample. Sample temperature was controlled using a modified Cryostream Plus and measured using thermocouples and an infrared thermal imager. The levitator was installed at x-ray beamline 11 ID-C at the Advanced Photon Source and used to investigate the structure of supercooled liquids.

Compensation for loads during arm movements using equilibrium-point control.

PubMed

Gribble, P L; Ostry, D J

2000-12-01

A significant problem in motor control is how information about movement error is used to modify control signals to achieve desired performance. A potential source of movement error and one that is readily controllable experimentally relates to limb dynamics and associated movement-dependent loads. In this paper, we have used a position control model to examine changes to control signals for arm movements in the context of movement-dependent loads. In the model, based on the equilibrium-point hypothesis, equilibrium shifts are adjusted directly in proportion to the positional error between desired and actual movements. The model is used to simulate multi-joint movements in the presence of both "internal" loads due to joint interaction torques, and externally applied loads resulting from velocity-dependent force fields. In both cases it is shown that the model can achieve close correspondence to empirical data using a simple linear adaptation procedure. An important feature of the model is that it achieves compensation for loads during movement without the need for either coordinate transformations between positional error and associated corrective forces, or inverse dynamics calculations.

Swimming Back and Forth Using Planar Flagellar Propulsion at Low Reynolds Numbers.

PubMed

Khalil, Islam S M; Tabak, Ahmet Fatih; Hamed, Youssef; Mitwally, Mohamed E; Tawakol, Mohamed; Klingner, Anke; Sitti, Metin

2018-02-01

Peritrichously flagellated Escherichia coli swim back and forth by wrapping their flagella together in a helical bundle. However, other monotrichous bacteria cannot swim back and forth with a single flagellum and planar wave propagation. Quantifying this observation, a magnetically driven soft two-tailed microrobot capable of reversing its swimming direction without making a U-turn trajectory or actively modifying the direction of wave propagation is designed and developed. The microrobot contains magnetic microparticles within the polymer matrix of its head and consists of two collinear, unequal, and opposite ultrathin tails. It is driven and steered using a uniform magnetic field along the direction of motion with a sinusoidally varying orthogonal component. Distinct reversal frequencies that enable selective and independent excitation of the first or the second tail of the microrobot based on their tail length ratio are found. While the first tail provides a propulsive force below one of the reversal frequencies, the second is almost passive, and the net propulsive force achieves flagellated motion along one direction. On the other hand, the second tail achieves flagellated propulsion along the opposite direction above the reversal frequency.

Past, present, and future of epigenetics applied to livestock breeding

PubMed Central

González-Recio, Oscar; Toro, Miguel A.; Bach, Alex

2015-01-01

This article reviews the concept of Lamarckian inheritance and the use of the term epigenetics in the field of animal genetics. Epigenetics was first coined by Conrad Hal Waddington (1905–1975), who derived the term from the Aristotelian word epigenesis. There exists some controversy around the word epigenetics and its broad definition. It includes any modification of the expression of genes due to factors other than mutation in the DNA sequence. This involves DNA methylation, post-translational modification of histones, but also linked to regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. There is little evidence of the existence of transgenerational epigenetic inheritance in mammals, which may commonly be confounded with environmental forces acting simultaneously on an individual, her developing fetus and the germ cell lines of the latter, although it could have an important role in the cellular energetic status of cells. Finally, we review some of the scarce literature on the use of epigenetics in animal breeding programs. PMID:26442117

The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene.

PubMed

Mackie, Cameron J; Candian, Alessandra; Huang, Xinchuan; Maltseva, Elena; Petrignani, Annemieke; Oomens, Jos; Buma, Wybren Jan; Lee, Timothy J; Tielens, Alexander G G M

2015-12-14

Current efforts to characterize and study interstellar polycyclic aromatic hydrocarbons (PAHs) rely heavily on theoretically predicted infrared (IR) spectra. Generally, such studies use the scaled harmonic frequencies for band positions and double harmonic approximation for intensities of species, and then compare these calculated spectra with experimental spectra obtained under matrix isolation conditions. High-resolution gas-phase experimental spectroscopic studies have recently revealed that the double harmonic approximation is not sufficient for reliable spectra prediction. In this paper, we present the anharmonic theoretical spectra of three PAHs: naphthalene, anthracene, and tetracene, computed with a locally modified version of the SPECTRO program using Cartesian derivatives transformed from Gaussian 09 normal coordinate force constants. Proper treatments of Fermi resonances lead to an impressive improvement on the agreement between the observed and theoretical spectra, especially in the C-H stretching region. All major IR absorption features in the full-scale matrix-isolated spectra, the high-temperature gas-phase spectra, and the most recent high-resolution gas-phase spectra obtained under supersonically cooled molecular beam conditions in the CH-stretching region are assigned.

The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene

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

Mackie, Cameron J., E-mail: mackie@strw.leidenuniv.nl; Candian, Alessandra; Tielens, Alexander G. G. M.

2015-12-14

Current efforts to characterize and study interstellar polycyclic aromatic hydrocarbons (PAHs) rely heavily on theoretically predicted infrared (IR) spectra. Generally, such studies use the scaled harmonic frequencies for band positions and double harmonic approximation for intensities of species, and then compare these calculated spectra with experimental spectra obtained under matrix isolation conditions. High-resolution gas-phase experimental spectroscopic studies have recently revealed that the double harmonic approximation is not sufficient for reliable spectra prediction. In this paper, we present the anharmonic theoretical spectra of three PAHs: naphthalene, anthracene, and tetracene, computed with a locally modified version of the SPECTRO program using Cartesianmore » derivatives transformed from Gaussian 09 normal coordinate force constants. Proper treatments of Fermi resonances lead to an impressive improvement on the agreement between the observed and theoretical spectra, especially in the C–H stretching region. All major IR absorption features in the full-scale matrix-isolated spectra, the high-temperature gas-phase spectra, and the most recent high-resolution gas-phase spectra obtained under supersonically cooled molecular beam conditions in the CH-stretching region are assigned.« less

Prediction of forces and moments for hypersonic flight vehicle control effectors

NASA Technical Reports Server (NTRS)

Maughmer, Mark D.; Long, Lyle N.; Guilmette, Neal; Pagano, Peter

1993-01-01

This research project includes three distinct phases. For completeness, all three phases of the work are briefly described in this report. The goal was to develop methods of predicting flight control forces and moments for hypersonic vehicles which could be used in a preliminary design environment. The first phase included a preliminary assessment of subsonic/supersonic panel methods and hypersonic local flow inclination methods for such predictions. While these findings clearly indicated the usefulness of such methods for conceptual design activities, deficiencies exist in some areas. Thus, a second phase of research was conducted in which a better understanding was sought for the reasons behind the successes and failures of the methods considered, particularly for the cases at hypersonic Mach numbers. This second phase involved using computational fluid dynamics methods to examine the flow fields in detail. Through these detailed predictions, the deficiencies in the simple surface inclination methods were determined. In the third phase of this work, an improvement to the surface inclination methods was developed. This used a novel method for including viscous effects by modifying the geometry to include the viscous/shock layer.

Acoustic levitator for structure measurements on low temperature liquid droplets

NASA Astrophysics Data System (ADS)

Weber, J. K. R.; Rey, C. A.; Neuefeind, J.; Benmore, C. J.

2009-08-01

A single-axis acoustic levitator was constructed and used to levitate liquid and solid drops of 1-3 mm in diameter at temperatures in the range -40 to +40 °C. The levitator comprised (i) two acoustic transducers mounted on a rigid vertical support that was bolted to an optical breadboard, (ii) an acoustic power supply that controlled acoustic intensity, relative phase of the drive to the transducers, and could modulate the acoustic forces at frequencies up to 1 kHz, (iii) a video camera, and (iv) a system for providing a stream of controlled temperature gas flow over the sample. The acoustic transducers were operated at their resonant frequency of ˜22 kHz and could produce sound pressure levels of up to 160 dB. The force applied by the acoustic field could be modulated to excite oscillations in the sample. Sample temperature was controlled using a modified Cryostream Plus and measured using thermocouples and an infrared thermal imager. The levitator was installed at x-ray beamline 11 ID-C at the Advanced Photon Source and used to investigate the structure of supercooled liquids.