Uncertainties in forces extracted from non-contact atomic force microscopy measurements by fitting of long-range background forces.

PubMed

Sweetman, Adam; Stannard, Andrew

2014-01-01

In principle, non-contact atomic force microscopy (NC-AFM) now readily allows for the measurement of forces with sub-nanonewton precision on the atomic scale. In practice, however, the extraction of the often desired 'short-range' force from the experimental observable (frequency shift) is often far from trivial. In most cases there is a significant contribution to the total tip-sample force due to non-site-specific van der Waals and electrostatic forces. Typically, the contribution from these forces must be removed before the results of the experiment can be successfully interpreted, often by comparison to density functional theory calculations. In this paper we compare the 'on-minus-off' method for extracting site-specific forces to a commonly used extrapolation method modelling the long-range forces using a simple power law. By examining the behaviour of the fitting method in the case of two radically different interaction potentials we show that significant uncertainties in the final extracted forces may result from use of the extrapolation method.

Daniell method for power spectral density estimation in atomic force microscopy

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

Labuda, Aleksander

An alternative method for power spectral density (PSD) estimation—the Daniell method—is revisited and compared to the most prevalent method used in the field of atomic force microscopy for quantifying cantilever thermal motion—the Bartlett method. Both methods are shown to underestimate the Q factor of a simple harmonic oscillator (SHO) by a predictable, and therefore correctable, amount in the absence of spurious deterministic noise sources. However, the Bartlett method is much more prone to spectral leakage which can obscure the thermal spectrum in the presence of deterministic noise. By the significant reduction in spectral leakage, the Daniell method leads to amore » more accurate representation of the true PSD and enables clear identification and rejection of deterministic noise peaks. This benefit is especially valuable for the development of automated PSD fitting algorithms for robust and accurate estimation of SHO parameters from a thermal spectrum.« less

Numerical investigation of the pseudopotential lattice Boltzmann modeling of liquid-vapor for multi-phase flows

NASA Astrophysics Data System (ADS)

Nemati, Maedeh; Shateri Najaf Abady, Ali Reza; Toghraie, Davood; Karimipour, Arash

2018-01-01

The incorporation of different equations of state into single-component multiphase lattice Boltzmann model is considered in this paper. The original pseudopotential model is first detailed, and several cubic equations of state, the Redlich-Kwong, Redlich-Kwong-Soave, and Peng-Robinson are then incorporated into the lattice Boltzmann model. A comparison of the numerical simulation achievements on the basis of density ratios and spurious currents is used for presentation of the details of phase separation in these non-ideal single-component systems. The paper demonstrates that the scheme for the inter-particle interaction force term as well as the force term incorporation method matters to achieve more accurate and stable results. The velocity shifting method is demonstrated as the force term incorporation method, among many, with accuracy and stability results. Kupershtokh scheme also makes it possible to achieve large density ratio (up to 104) and to reproduce the coexistence curve with high accuracy. Significant reduction of the spurious currents at vapor-liquid interface is another observation. High-density ratio and spurious current reduction resulted from the Redlich-Kwong-Soave and Peng-Robinson EOSs, in higher accordance with the Maxwell construction results.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Cascaded lattice Boltzmann method with improved forcing scheme for large-density-ratio multiphase flow at high Reynolds and Weber numbers.

PubMed

Lycett-Brown, Daniel; Luo, Kai H

2016-11-01

A recently developed forcing scheme has allowed the pseudopotential multiphase lattice Boltzmann method to correctly reproduce coexistence curves, while expanding its range to lower surface tensions and arbitrarily high density ratios [Lycett-Brown and Luo, Phys. Rev. E 91, 023305 (2015)PLEEE81539-375510.1103/PhysRevE.91.023305]. Here, a third-order Chapman-Enskog analysis is used to extend this result from the single-relaxation-time collision operator, to a multiple-relaxation-time cascaded collision operator, whose additional relaxation rates allow a significant increase in stability. Numerical results confirm that the proposed scheme enables almost independent control of density ratio, surface tension, interface width, viscosity, and the additional relaxation rates of the cascaded collision operator. This allows simulation of large density ratio flows at simultaneously high Reynolds and Weber numbers, which is demonstrated through binary collisions of water droplets in air (with density ratio up to 1000, Reynolds number 6200 and Weber number 440). This model represents a significant improvement in multiphase flow simulation by the pseudopotential lattice Boltzmann method in which real-world parameters are finally achievable.

Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

PubMed

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

2013-08-28

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

Finding the Density of Objects without Measuring Mass and Volume

ERIC Educational Resources Information Center

Mumba, Frackson; Tsige, Mesfin

2007-01-01

A simple method based on the moment of forces and Archimedes' principle is described for finding density without measuring the mass and volume of an object. The method involves balancing two unknown objects of masses M[subscript 1] and M[subscript 2] on each side of a pivot on a metre rule and measuring their corresponding moment arms. The object…

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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.

Why Density Dependent Propulsion?

NASA Technical Reports Server (NTRS)

Robertson, Glen A.

2011-01-01

In 2004 Khoury and Weltman produced a density dependent cosmology theory they call the Chameleon, as at its nature, it is hidden within known physics. The Chameleon theory has implications to dark matter/energy with universe acceleration properties, which implies a new force mechanism with ties to the far and local density environment. In this paper, the Chameleon Density Model is discussed in terms of propulsion toward new propellant-less engineering methods.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

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

DOEpatents

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

1987-08-10

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

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

DOEpatents

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

1988-01-01

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

An isometric muscle force estimation framework based on a high-density surface EMG array and an NMF algorithm

NASA Astrophysics Data System (ADS)

Huang, Chengjun; Chen, Xiang; Cao, Shuai; Qiu, Bensheng; Zhang, Xu

2017-08-01

Objective. To realize accurate muscle force estimation, a novel framework is proposed in this paper which can extract the input of the prediction model from the appropriate activation area of the skeletal muscle. Approach. Surface electromyographic (sEMG) signals from the biceps brachii muscle during isometric elbow flexion were collected with a high-density (HD) electrode grid (128 channels) and the external force at three contraction levels was measured at the wrist synchronously. The sEMG envelope matrix was factorized into a matrix of basis vectors with each column representing an activation pattern and a matrix of time-varying coefficients by a nonnegative matrix factorization (NMF) algorithm. The activation pattern with the highest activation intensity, which was defined as the sum of the absolute values of the time-varying coefficient curve, was considered as the major activation pattern, and its channels with high weighting factors were selected to extract the input activation signal of a force estimation model based on the polynomial fitting technique. Main results. Compared with conventional methods using the whole channels of the grid, the proposed method could significantly improve the quality of force estimation and reduce the electrode number. Significance. The proposed method provides a way to find proper electrode placement for force estimation, which can be further employed in muscle heterogeneity analysis, myoelectric prostheses and the control of exoskeleton devices.

Titan Density Reconstruction Using Radiometric and Cassini Attitude Control Flight Data

NASA Technical Reports Server (NTRS)

Andrade, Luis G., Jr.; Burk, Thomas A.

2015-01-01

This paper compares three different methods of Titan atmospheric density reconstruction for the Titan 87 Cassini flyby. T87 was a unique flyby that provided independent Doppler radiometric measurements on the ground throughout the flyby including at Titan closest approach. At the same time, the onboard accelerometer provided an independent estimate of atmospheric drag force and density during the flyby. These results are compared with the normal method of reconstructing atmospheric density using thruster on-time and angular momentum accumulation. Differences between the estimates are analyzed and a possible explanation for the differences is evaluated.

Eigenmode resonance in a two-layer stratification

NASA Astrophysics Data System (ADS)

Kanda, Isao; Linden, P. F.

2002-06-01

In this paper, we study the velocity field at the density interface of a two-layer stratification system when the flow is forced at the mid-depth of the lower layer by the source sink forcing method. It is known that, in a sufficiently strong linear stratification, the source sink forcing in certain configurations produces a single-vortex pattern which corresponds to the lowest eigenmode of the Helmholtz equation (Kanda & Linden 2001). Two types of forcing configuration are used for the two-layer experiments: one that leads to a steady single-vortex pattern in a linear stratification, and one that results in an unsteady irregular state. Strong single-vortex patterns appear intermittently for the former configurations despite the absence of stratification at the forcing height. When the single-vortex pattern occurs at the density interface, a similar flow field extends down to the forcing height. The behaviour is explained as the coupling of the resonant eigenmode at the interface with the horizontal component of the forcing jets. The results show that stratification can organise a flow, even though it is forced by an apparently random three-dimensional forcing.

Forces on a segregating particle

NASA Astrophysics Data System (ADS)

Lueptow, Richard M.; Shankar, Adithya; Fry, Alexander M.; Ottino, Julio M.; Umbanhowar, Paul B.

2017-11-01

Size segregation in flowing granular materials is not well understood at the particle level. In this study, we perform a series of 3D Discrete Element Method (DEM) simulations to measure the segregation force on a single spherical test particle tethered to a spring in the vertical direction in a shearing bed of particles with gravity acting perpendicular to the shear. The test particle is the same size or larger than the bed particles. At equilibrium, the downward spring force and test particle weight are offset by the upward buoyancy-like force and a size ratio dependent force. We find that the buoyancy-like force depends on the bed particle density and the Voronoi volume occupied by the test particle. By changing the density of the test particle with the particle size ratio such that the buoyancy force matches the test particle weight, we show that the upward size segregation force is a quadratic function of the particle size ratio. Based on this, we report an expression for the net force on a single particle as the sum of a size ratio dependent force, a buoyancy-like force, and the weight of the particle. Supported by NSF Grant CBET-1511450 and the Procter and Gamble Company.

Microfluidic devices, systems, and methods for quantifying particles using centrifugal force

DOEpatents

Schaff, Ulrich Y.; Sommer, Gregory J.; Singh, Anup K.

2015-11-17

Embodiments of the present invention are directed toward microfluidic systems, apparatus, and methods for measuring a quantity of cells in a fluid. Examples include a differential white blood cell measurement using a centrifugal microfluidic system. A method may include introducing a fluid sample containing a quantity of cells into a microfluidic channel defined in part by a substrate. The quantity of cells may be transported toward a detection region defined in part by the substrate, wherein the detection region contains a density media, and wherein the density media has a density lower than a density of the cells and higher than a density of the fluid sample. The substrate may be spun such that at least a portion of the quantity of cells are transported through the density media. Signals may be detected from label moieties affixed to the cells.

Quasi-One-Dimensional Particle-in-Cell Simulation of Magnetic Nozzles

NASA Technical Reports Server (NTRS)

Ebersohn, Frans H.; Sheehan, J. P.; Gallimore, Alec D.; Shebalin, John V.

2015-01-01

A method for the quasi-one-dimensional simulation of magnetic nozzles is presented and simulations of a magnetic nozzle are performed. The effects of the density variation due to plasma expansion and the magnetic field forces on ion acceleration are investigated. Magnetic field forces acting on the electrons are found to be responsible for the formation of potential structures which accelerate ions. The effects of the plasma density variation alone are found to only weakly affect ion acceleration. Strongly diverging magnetic fields drive more rapid potential drops.

Fusion reaction cross-sections using the Wong model within Skyrme energy density based semiclassical extended Thomas Fermi approach

NASA Astrophysics Data System (ADS)

Kumar, Raj; Sharma, Manoj K.; Gupta, Raj K.

2011-11-01

First, the nuclear proximity potential, obtained by using the semiclassical extended Thomas Fermi (ETF) approach in Skyrme energy density formalism (SEDF), is shown to give more realistic barriers in frozen density approximation, as compared to the sudden approximation. Then, taking advantage of the fact that, in ETF method, different Skyrme forces give different barriers (height, position and curvature), we use the ℓ-summed extended-Wong model of Gupta and collaborators (2009) [1] under frozen densities approximation for calculating the cross-sections, where the Skyrme force is chosen with proper barrier characteristics, not-requiring additional "barrier modification" effects (lowering or narrowing, etc.), for a best fit to data at sub-barrier energies. The method is applied to capture cross-section data from 48Ca + 238U, 244Pu, and 248Cm reactions and to fusion-evaporation cross-sections from 58Ni + 58Ni, 64Ni + 64Ni, and 64Ni + 100Mo reactions, with effects of deformations and orientations of nuclei included, wherever required. Interestingly, whereas the capture cross-sections in Ca-induced reactions could be fitted to any force, such as SIII, SV and GSkI, by allowing a small change of couple of units in deduced ℓ-values at below-barrier energies, the near-barrier data point of 48Ca + 248Cm reaction could not be fitted to ℓ-values deduced for below-barrier energies, calling for a check of data. On the other hand, the fusion-evaporation cross-sections in Ni-induced reactions at sub-barrier energies required different Skyrme forces, representing "modifications of the barrier", for the best fit to data at all incident center-of-mass energies E's, displaying a kind of fusion hindrance at sub-barrier energies. This barrier modification effect is taken into care here by using different Skyrme forces for reactions belonging to different regions of the periodic table. Note that more than one Skyrme force (with identical barrier characteristics) could equally well fit the same data.

Nanoscale hydrodynamics near solids

NASA Astrophysics Data System (ADS)

Camargo, Diego; de la Torre, J. A.; Duque-Zumajo, D.; Español, Pep; Delgado-Buscalioni, Rafael; Chejne, Farid

2018-02-01

Density Functional Theory (DFT) is a successful and well-established theory for the study of the structure of simple and complex fluids at equilibrium. The theory has been generalized to dynamical situations when the underlying dynamics is diffusive as in, for example, colloidal systems. However, there is no such a clear foundation for Dynamic DFT (DDFT) for the case of simple fluids in contact with solid walls. In this work, we derive DDFT for simple fluids by including not only the mass density field but also the momentum density field of the fluid. The standard projection operator method based on the Kawasaki-Gunton operator is used for deriving the equations for the average value of these fields. The solid is described as featureless under the assumption that all the internal degrees of freedom of the solid relax much faster than those of the fluid (solid elasticity is irrelevant). The fluid moves according to a set of non-local hydrodynamic equations that include explicitly the forces due to the solid. These forces are of two types, reversible forces emerging from the free energy density functional, and accounting for impenetrability of the solid, and irreversible forces that involve the velocity of both the fluid and the solid. These forces are localized in the vicinity of the solid surface. The resulting hydrodynamic equations should allow one to study dynamical regimes of simple fluids in contact with solid objects in isothermal situations.

Quantum Field Energy Sensor based on the Casimir Effect

NASA Astrophysics Data System (ADS)

Ludwig, Thorsten

The Casimir effect converts vacuum fluctuations into a measurable force. Some new energy technologies aim to utilize these vacuum fluctuations in commonly used forms of energy like electricity or mechanical motion. In order to study these energy technologies it is helpful to have sensors for the energy density of vacuum fluctuations. In today's scientific instrumentation and scanning microscope technologies there are several common methods to measure sub-nano Newton forces. While the commercial atomic force microscopes (AFM) mostly work with silicon cantilevers, there are a large number of reports on the use of quartz tuning forks to get high-resolution force measurements or to create new force sensors. Both methods have certain advantages and disadvantages over the other. In this report the two methods are described and compared towards their usability for Casimir force measurements. Furthermore a design for a quantum field energy sensor based on the Casimir force measurement will be described. In addition some general considerations on extracting energy from vacuum fluctuations will be given.

Method and apparatus for simultaneous determination of fluid mass flow rate, mean velocity and density

DOEpatents

Hamel, William R.

1984-01-01

This invention relates to a new method and new apparatus for determining fluid mass flowrate and density. In one aspect of the invention, the fluid is passed through a straight cantilevered tube in which transient oscillation has been induced, thus generating Coriolis damping forces on the tube. The decay rate and frequency of the resulting damped oscillation are measured, and the fluid mass flowrate and density are determined therefrom. In another aspect of the invention, the fluid is passed through the cantilevered tube while an electrically powered device imparts steady-state harmonic excitation to the tube. This generates Coriolis tube-damping forces which are dependent on the mass flowrate of the fluid. Means are provided to respond to incipient flow-induced changes in the amplitude of vibration by changing the power input to the excitation device as required to sustain the original amplitude of vibration. The fluid mass flowrate and density are determined from the required change in power input. The invention provides stable, rapid, and accurate measurements. It does not require bending of the fluid flow.

An Immersed Boundary-Lattice Boltzmann Method for Simulating Particulate Flows

NASA Astrophysics Data System (ADS)

Zhang, Baili; Cheng, Ming; Lou, Jing

2013-11-01

A two-dimensional momentum exchange-based immersed boundary-lattice Boltzmann method developed by X.D. Niu et al. (2006) has been extended in three-dimensions for solving fluid-particles interaction problems. This method combines the most desirable features of the lattice Boltzmann method and the immersed boundary method by using a regular Eulerian mesh for the flow domain and a Lagrangian mesh for the moving particles in the flow field. The non-slip boundary conditions for the fluid and the particles are enforced by adding a force density term into the lattice Boltzmann equation, and the forcing term is simply calculated by the momentum exchange of the boundary particle density distribution functions, which are interpolated by the Lagrangian polynomials from the underlying Eulerian mesh. This method preserves the advantages of lattice Boltzmann method in tracking a group of particles and, at the same time, provides an alternative approach to treat solid-fluid boundary conditions. Numerical validations show that the present method is very accurate and efficient. The present method will be further developed to simulate more complex problems with particle deformation, particle-bubble and particle-droplet interactions.

A grouping method based on grid density and relationship for crowd evacuation simulation

NASA Astrophysics Data System (ADS)

Li, Yan; Liu, Hong; Liu, Guang-peng; Li, Liang; Moore, Philip; Hu, Bin

2017-05-01

Psychological factors affect the movement of people in the competitive or panic mode of evacuation, in which the density of pedestrians is relatively large and the distance among them is small. In this paper, a crowd is divided into groups according to their social relations to simulate the actual movement of crowd evacuation more realistically and increase the attractiveness of the group based on social force model. The force of group attraction is the synthesis of two forces; one is the attraction of the individuals generated by their social relations to gather, and the other is that of the group leader to the individuals within the group to ensure that the individuals follow the leader. The synthetic force determines the trajectory of individuals. The evacuation process is demonstrated using the improved social force model. In the improved social force model, the individuals with close social relations gradually present a closer and coordinated action while following the leader. In this paper, a grouping algorithm is proposed based on grid density and relationship via computer simulation to illustrate the features of the improved social force model. The definition of the parameters involved in the algorithm is given, and the effect of relational value on the grouping is tested. Reasonable numbers of grids and weights are selected. The effectiveness of the algorithm is shown through simulation experiments. A simulation platform is also established using the proposed grouping algorithm and the improved social force model for crowd evacuation simulation.

Study of 11Li+p elastic scattering using BHF formalism with three body force

NASA Astrophysics Data System (ADS)

Sharma, Manjari; Haider, W.

2018-04-01

In the present work we have analyzed the elastic scattering data of 11Li + p at 62, 68.4 and 75 MeV/nucleon, using the microscopic optical potential calculated within the framework of Brueckner-Hartree-Fock formalism (BHF). The calculation uses Argonne v18 and Urbana v14 inter-nucleon potentials and the Urbana IX (UVIX) model of three body force. The required nucleon-density distributions for 11Li are obtained using the semi-phenomenological model for nuclear density distributions. The optical potential has been obtained by folding the g-matrices as calculated in BHF (with and without three body forces) over the nucleon density distributions. We have used the exact method for calculating both the direct and the exchange parts of the spin-orbit potential. Our results reveal that the spin-orbit potential significantly contributes to 11Li+p elastic scattering at all three incident energies. Further, the calculated spin-orbit potential in BHF is much smaller and more diffused as compared with the phenomenological spin-orbit potential. The analysis reveals that the calculated microscopic optical potentials, with and without three body force using BHF approach with phenomenological form of density distribution, provides satisfactory agreement with the elastic scattering data for 11Li+p.

Investigating the effect of tablet thickness and punch curvature on density distribution using finite elements method.

PubMed

Diarra, Harona; Mazel, Vincent; Busignies, Virginie; Tchoreloff, Pierre

2015-09-30

Finite elements method was used to study the influence of tablet thickness and punch curvature on the density distribution inside convex faced (CF) tablets. The modeling of the process was conducted on 2 pharmaceutical excipients (anhydrous calcium phosphate and microcrystalline cellulose) by using Drucker-Prager Cap model in Abaqus(®) software. The parameters of the model were obtained from experimental tests. Several punch shapes based on industrial standards were used. A flat-faced (FF) punch and 3 convex faced (CF) punches (8R11, 8R8 and 8R6) with a diameter of 8mm were chosen. Different tablet thicknesses were studied at a constant compression force. The simulation of the compaction of CF tablets with increasing thicknesses showed an important change on the density distribution inside the tablet. For smaller thicknesses, low density zones are located toward the center. The density is not uniform inside CF tablets and the center of the 2 faces appears with low density whereas the distribution inside FF tablets is almost independent of the tablet thickness. These results showed that FF and CF tablets, even obtained at the same compression force, do not have the same density at the center of the compact. As a consequence differences in tensile strength, as measured by diametral compression, are expected. This was confirmed by experimental tests. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparing the statistics of interstellar turbulence in simulations and observations. Solenoidal versus compressive turbulence forcing

NASA Astrophysics Data System (ADS)

Federrath, C.; Roman-Duval, J.; Klessen, R. S.; Schmidt, W.; Mac Low, M.-M.

2010-03-01

Context. Density and velocity fluctuations on virtually all scales observed with modern telescopes show that molecular clouds (MCs) are turbulent. The forcing and structural characteristics of this turbulence are, however, still poorly understood. Aims: To shed light on this subject, we study two limiting cases of turbulence forcing in numerical experiments: solenoidal (divergence-free) forcing and compressive (curl-free) forcing, and compare our results to observations. Methods: We solve the equations of hydrodynamics on grids with up to 10243 cells for purely solenoidal and purely compressive forcing. Eleven lower-resolution models with different forcing mixtures are also analysed. Results: Using Fourier spectra and Δ-variance, we find velocity dispersion-size relations consistent with observations and independent numerical simulations, irrespective of the type of forcing. However, compressive forcing yields stronger compression at the same rms Mach number than solenoidal forcing, resulting in a three times larger standard deviation of volumetric and column density probability distributions (PDFs). We compare our results to different characterisations of several observed regions, and find evidence of different forcing functions. Column density PDFs in the Perseus MC suggest the presence of a mainly compressive forcing agent within a shell, driven by a massive star. Although the PDFs are close to log-normal, they have non-Gaussian skewness and kurtosis caused by intermittency. Centroid velocity increments measured in the Polaris Flare on intermediate scales agree with solenoidal forcing on that scale. However, Δ-variance analysis of the column density in the Polaris Flare suggests that turbulence is driven on large scales, with a significant compressive component on the forcing scale. This indicates that, although likely driven with mostly compressive modes on large scales, turbulence can behave like solenoidal turbulence on smaller scales. Principal component analysis of G216-2.5 and most of the Rosette MC agree with solenoidal forcing, but the interior of an ionised shell within the Rosette MC displays clear signatures of compressive forcing. Conclusions: The strong dependence of the density PDF on the type of forcing must be taken into account in any theory using the PDF to predict properties of star formation. We supply a quantitative description of this dependence. We find that different observed regions show evidence of different mixtures of compressive and solenoidal forcing, with more compressive forcing occurring primarily in swept-up shells. Finally, we emphasise the role of the sonic scale for protostellar core formation, because core formation close to the sonic scale would naturally explain the observed subsonic velocity dispersions of protostellar cores. A movie is only available in electronic form at http://www.aanda.org

Spatial averaging of a dissipative particle dynamics model for active suspensions

NASA Astrophysics Data System (ADS)

Panchenko, Alexander; Hinz, Denis F.; Fried, Eliot

2018-03-01

Starting from a fine-scale dissipative particle dynamics (DPD) model of self-motile point particles, we derive meso-scale continuum equations by applying a spatial averaging version of the Irving-Kirkwood-Noll procedure. Since the method does not rely on kinetic theory, the derivation is valid for highly concentrated particle systems. Spatial averaging yields stochastic continuum equations similar to those of Toner and Tu. However, our theory also involves a constitutive equation for the average fluctuation force. According to this equation, both the strength and the probability distribution vary with time and position through the effective mass density. The statistics of the fluctuation force also depend on the fine scale dissipative force equation, the physical temperature, and two additional parameters which characterize fluctuation strengths. Although the self-propulsion force entering our DPD model contains no explicit mechanism for aligning the velocities of neighboring particles, our averaged coarse-scale equations include the commonly encountered cubically nonlinear (internal) body force density.

Absorption, scattering, and radiation force efficiencies in the longitudinal wave scattering by a small viscoelastic particle in an isotropic solid.

PubMed

Lopes, J H; Leão-Neto, J P; Silva, G T

2017-11-01

Analytical expressions of the absorption, scattering, and elastic radiation force efficiency factors are derived for the longitudinal plane wave scattering by a small viscoelastic particle in a lossless solid matrix. The particle is assumed to be much smaller than the incident wavelength, i.e., the so-called long-wavelength (Rayleigh) approximation. The efficiencies are dimensionless quantities that represent the absorbed and scattering powers and the elastic radiation force on the particle. In the quadrupole approximation, they are expressed in terms of contrast functions (bulk and shear moduli, and density) between the particle and solid matrix. The results for a high-density polyethylene particle embedded in an aluminum matrix agree with those obtained with the partial wave expansion method. Additionally, the connection between the elastic radiation force and forward scattering function is established through the optical theorem. The present results should be useful for ultrasound characterization of particulate composites, and the development of implanted devices activated by radiation force.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

Method and apparatus for determining fluid mass flowrates

DOEpatents

Hamel, W.R.

1982-10-07

This invention relates to a new method and new apparatus for determining fluid mass flowrate and density. In one aspect of the invention, the fluid is passed through a straight cantilevered tube in which transient oscillation has been induced, thus generating Coriolis damping forces on the tube. The decay rate and frequency of the resulting damped oscillation are measured, and the fluid mass flowrate and density are determined therefrom. In another aspect of the invention, the fluid is passed through the cantilevered tube while an electrically powered device imparts steady-state harmonic excitation to the tube. This generates Coriolis tube-damping forces which are dependent on the mass flowrate of the fluid. Means are provided to respond to incipient flow-induced changes in the amplitude of vibration by changing the power input to the excitation device as required to sustain the original amplitude of vibration. The fluid mass flowrate and density are determined from the required bending of the fluid flow.

A relationship between three-dimensional surface hydration structures and force distribution measured by atomic force microscopy.

PubMed

Miyazawa, Keisuke; Kobayashi, Naritaka; Watkins, Matthew; Shluger, Alexander L; Amano, Ken-ichi; Fukuma, Takeshi

2016-04-07

Hydration plays important roles in various solid-liquid interfacial phenomena. Very recently, three-dimensional scanning force microscopy (3D-SFM) has been proposed as a tool to visualise solvated surfaces and their hydration structures with lateral and vertical (sub) molecular resolution. However, the relationship between the 3D force map obtained and the equilibrium water density, ρ(r), distribution above the surface remains an open question. Here, we investigate this relationship at an interface of an inorganic mineral, fluorite, and water. The force maps measured in pure water are directly compared to force maps generated using the solvent tip approximation (STA) model and from explicit molecular dynamics simulations. The results show that the simulated STA force map describes the major features of the experimentally obtained force image. The agreement between the STA data and the experiment establishes the correspondence between the water density used as an input to the STA model and the experimental hydration structure and thus provides a tool to bridge the experimental force data and atomistic solvation structures. Further applications of this method should improve the accuracy and reliability of both interpretation of 3D-SFM force maps and atomistic simulations in a wide range of solid-liquid interfacial phenomena.

A mathematical method for quantifying in vivo mechanical behaviour of heel pad under dynamic load.

PubMed

Naemi, Roozbeh; Chatzistergos, Panagiotis E; Chockalingam, Nachiappan

2016-03-01

Mechanical behaviour of the heel pad, as a shock attenuating interface during a foot strike, determines the loading on the musculoskeletal system during walking. The mathematical models that describe the force deformation relationship of the heel pad structure can determine the mechanical behaviour of heel pad under load. Hence, the purpose of this study was to propose a method of quantifying the heel pad stress-strain relationship using force-deformation data from an indentation test. The energy input and energy returned densities were calculated by numerically integrating the area below the stress-strain curve during loading and unloading, respectively. Elastic energy and energy absorbed densities were calculated as the sum of and the difference between energy input and energy returned densities, respectively. By fitting the energy function, derived from a nonlinear viscoelastic model, to the energy density-strain data, the elastic and viscous model parameters were quantified. The viscous and elastic exponent model parameters were significantly correlated with maximum strain, indicating the need to perform indentation tests at realistic maximum strains relevant to walking. The proposed method showed to be able to differentiate between the elastic and viscous components of the heel pad response to loading and to allow quantifying the corresponding stress-strain model parameters.

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

PubMed

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

2016-05-10

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

Dynamic Loads Generation for Multi-Point Vibration Excitation Problems

NASA Technical Reports Server (NTRS)

Shen, Lawrence

2011-01-01

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

Effective charges of ionic liquid determined self-consistently through combination of molecular dynamics simulation and density-functional theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2017-11-15

A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly]). It was found that the double-zeta valence polarized or larger size of basis set is required for the convergence of the effective charge of the ion. The choice of the XC functional was further not influential as far as the generalized gradient approximation is used. The charge-fitting method and force field govern the accuracy of the MD/DFT scheme, on the other hand. We examined the charge-fitting methods of Blöchl, the iterative Hirshfeld (Hirshfeld-I), and REPEAT in combination with Lopes et al.'s force field and general AMBER force field. There is no single combination of charge fitting and force field that provides good agreements with the experiments, while the MD/DFT scheme reduces the effective charges of the ions and leads to better description of energetics and dynamics compared to the original force field with unit charges. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Laser reflection method for determination of shear stress in low density transitional flows

NASA Astrophysics Data System (ADS)

Sathian, Sarith P.; Kurian, Job

2006-03-01

The details of laser reflection method (LRM) for the determination of shear stress in low density transitional flows are presented. The method is employed to determine the shear stress due to impingement of a low density supersonic free jet issuing out from a convergent divergent nozzle on a flat plate. The plate is smeared with a thin oil film and kept parallel to the nozzle axis. For a thin oil film moving under the action of aerodynamic boundary layer, the shear stress at the air-oil interface is equal to the shear stress between the surface and air. A direct and dynamic measurement of the oil film slope generated by the shear force is done using a position sensing detector (PSD). The thinning rate of the oil film is directly measured which is the major advantage of the LRM. From the oil film slope history, calculation of the shear stress is done using a three-point formula. The range of Knudsen numbers investigated is from 0.028 to 0.516. Pressure ratio across the nozzle varied from 3,500 to 8,500 giving highly under expanded free jets. The measured values of shear, in the overlapping region of experimental parameters, show fair agreement with those obtained by force balance method and laser interferometric method.

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

PubMed

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

2012-01-10

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

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

PubMed Central

2011-01-01

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

Diamond tool wear detection method using cutting force and its power spectrum analysis in ultra-precision fly cutting

NASA Astrophysics Data System (ADS)

Zhang, G. Q.; To, S.

2014-08-01

Cutting force and its power spectrum analysis was thought to be an effective method monitoring tool wear in many cutting processes and a significant body of research has been conducted on this research area. However, relative little similar research was found in ultra-precision fly cutting. In this paper, a group of experiments were carried out to investigate the cutting forces and its power spectrum characteristics under different tool wear stages. Result reveals that the cutting force increases with the progress of tool wear. The cutting force signals under different tool wear stages were analyzed using power spectrum analysis. The analysis indicates that a characteristic frequency does exist in the power spectrum of the cutting force, whose power spectral density increases with the increasing of tool wear level, this characteristic frequency could be adopted to monitor diamond tool wear in ultra-precision fly cutting.

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

Aerodynamic characteristics of the upper stages of a launch vehicle in low-density regime

NASA Astrophysics Data System (ADS)

Oh, Bum Seok; Lee, Joon Ho

2016-11-01

Aerodynamic characteristics of the orbital block (remaining configuration after separation of nose fairing and 1st and 2nd stages of the launch vehicle) and the upper 2-3stage (configuration after separation of 1st stage) of the 3 stages launch vehicle (KSLV-II, Korea Space Launch Vehicle) at high altitude of low-density regime are analyzed by SMILE code which is based on DSMC (Direct Simulation Monte-Carlo) method. To validating of the SMILE code, coefficients of axial force and normal forces of Apollo capsule are also calculated and the results agree very well with the data predicted by others. For the additional validations and applications of the DSMC code, aerodynamic calculation results of simple shapes of plate and wedge in low-density regime are also introduced. Generally, aerodynamic characteristics in low-density regime differ from those of continuum regime. To understand those kinds of differences, aerodynamic coefficients of the upper stages (including upper 2-3 stage and the orbital block) of the launch vehicle in low-density regime are analyzed as a function of Mach numbers and altitudes. The predicted axial force coefficients of the upper stages of the launch vehicle are very high compared to those in continuum regime. In case of the orbital block which flies at very high altitude (higher than 250km), all aerodynamic coefficients are more dependent on velocity variations than altitude variations. In case of the upper 2-3 stage which flies at high altitude (80km-150km), while the axial force coefficients and the locations of center of pressure are less changed with the variations of Knudsen numbers (altitudes), the normal force coefficients and pitching moment coefficients are more affected by variations of Knudsen numbers (altitude).

Spectral Quadrature method for accurate O ( N ) electronic structure calculations of metals and insulators

DOE PAGES

Pratapa, Phanisri P.; Suryanarayana, Phanish; Pask, John E.

2015-12-02

We present the Clenshaw–Curtis Spectral Quadrature (SQ) method for real-space O(N) Density Functional Theory (DFT) calculations. In this approach, all quantities of interest are expressed as bilinear forms or sums over bilinear forms, which are then approximated by spatially localized Clenshaw–Curtis quadrature rules. This technique is identically applicable to both insulating and metallic systems, and in conjunction with local reformulation of the electrostatics, enables the O(N) evaluation of the electronic density, energy, and atomic forces. The SQ approach also permits infinite-cell calculations without recourse to Brillouin zone integration or large supercells. We employ a finite difference representation in order tomore » exploit the locality of electronic interactions in real space, enable systematic convergence, and facilitate large-scale parallel implementation. In particular, we derive expressions for the electronic density, total energy, and atomic forces that can be evaluated in O(N) operations. We demonstrate the systematic convergence of energies and forces with respect to quadrature order as well as truncation radius to the exact diagonalization result. In addition, we show convergence with respect to mesh size to established O(N 3) planewave results. In conclusion, we establish the efficiency of the proposed approach for high temperature calculations and discuss its particular suitability for large-scale parallel computation.« less

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

DOE PAGES

Mones, Letif; Jones, Andrew; Götz, Andreas W.; ...

2015-02-03

We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

PubMed Central

Mones, Letif; Jones, Andrew; Götz, Andreas W; Laino, Teodoro; Walker, Ross C; Leimkuhler, Ben; Csányi, Gábor; Bernstein, Noam

2015-01-01

The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25649827

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

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

Mones, Letif; Jones, Andrew; Götz, Andreas W.

We present the implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis usingmore » various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.« less

Expectation-Based Control of Noise and Chaos

NASA Technical Reports Server (NTRS)

Zak, Michael

2006-01-01

A proposed approach to control of noise and chaos in dynamic systems would supplement conventional methods. The approach is based on fictitious forces composed of expectations governed by Fokker-Planck or Liouville equations that describe the evolution of the probability densities of the controlled parameters. These forces would be utilized as feedback control forces that would suppress the undesired diffusion of the controlled parameters. Examples of dynamic systems in which the approach is expected to prove beneficial include spacecraft, electronic systems, and coupled lasers.

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

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

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

Low temperature ablation models made by pressure/vacuum application

NASA Technical Reports Server (NTRS)

Fischer, M. C.; Heier, W. C.

1970-01-01

Method developed employs high pressure combined with strong vacuum force to compact ablation models into desired conical shape. Technique eliminates vapor hazard and results in high material density providing excellent structural integrity.

Implicit Incompressible SPH.

PubMed

Ihmsen, Markus; Cornelis, Jens; Solenthaler, Barbara; Horvath, Christopher; Teschner, Matthias

2013-07-25

We propose a novel formulation of the projection method for Smoothed Particle Hydrodynamics (SPH). We combine a symmetric SPH pressure force and an SPH discretization of the continuity equation to obtain a discretized form of the pressure Poisson equation (PPE). In contrast to previous projection schemes, our system does consider the actual computation of the pressure force. This incorporation improves the convergence rate of the solver. Furthermore, we propose to compute the density deviation based on velocities instead of positions as this formulation improves the robustness of the time-integration scheme. We show that our novel formulation outperforms previous projection schemes and state-of-the-art SPH methods. Large time steps and small density deviations of down to 0.01% can be handled in typical scenarios. The practical relevance of the approach is illustrated by scenarios with up to 40 million SPH particles.

Implicit incompressible SPH.

PubMed

Ihmsen, Markus; Cornelis, Jens; Solenthaler, Barbara; Horvath, Christopher; Teschner, Matthias

2014-03-01

We propose a novel formulation of the projection method for Smoothed Particle Hydrodynamics (SPH). We combine a symmetric SPH pressure force and an SPH discretization of the continuity equation to obtain a discretized form of the pressure Poisson equation (PPE). In contrast to previous projection schemes, our system does consider the actual computation of the pressure force. This incorporation improves the convergence rate of the solver. Furthermore, we propose to compute the density deviation based on velocities instead of positions as this formulation improves the robustness of the time-integration scheme. We show that our novel formulation outperforms previous projection schemes and state-of-the-art SPH methods. Large time steps and small density deviations of down to 0.01 percent can be handled in typical scenarios. The practical relevance of the approach is illustrated by scenarios with up to 40 million SPH particles.

A Semi-Analytical Method for the PDFs of A Ship Rolling in Random Oblique Waves

NASA Astrophysics Data System (ADS)

Liu, Li-qin; Liu, Ya-liu; Xu, Wan-hai; Li, Yan; Tang, You-gang

2018-03-01

The PDFs (probability density functions) and probability of a ship rolling under the random parametric and forced excitations were studied by a semi-analytical method. The rolling motion equation of the ship in random oblique waves was established. The righting arm obtained by the numerical simulation was approximately fitted by an analytical function. The irregular waves were decomposed into two Gauss stationary random processes, and the CARMA (2, 1) model was used to fit the spectral density function of parametric and forced excitations. The stochastic energy envelope averaging method was used to solve the PDFs and the probability. The validity of the semi-analytical method was verified by the Monte Carlo method. The C11 ship was taken as an example, and the influences of the system parameters on the PDFs and probability were analyzed. The results show that the probability of ship rolling is affected by the characteristic wave height, wave length, and the heading angle. In order to provide proper advice for the ship's manoeuvring, the parametric excitations should be considered appropriately when the ship navigates in the oblique seas.

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

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

Nemchinsky, V.; Khrabry, A.

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE PAGES

Nemchinsky, V.; Khrabry, A.

2018-02-01

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Trunk density profile estimates from dual X-ray absorptiometry.

PubMed

Wicke, Jason; Dumas, Geneviève A; Costigan, Patrick A

2008-01-01

Accurate body segment parameters are necessary to estimate joint loads when using biomechanical models. Geometric methods can provide individualized data for these models but the accuracy of the geometric methods depends on accurate segment density estimates. The trunk, which is important in many biomechanical models, has the largest variability in density along its length. Therefore, the objectives of this study were to: (1) develop a new method for modeling trunk density profiles based on dual X-ray absorptiometry (DXA) and (2) develop a trunk density function for college-aged females and males that can be used in geometric methods. To this end, the density profiles of 25 females and 24 males were determined by combining the measurements from a photogrammetric method and DXA readings. A discrete Fourier transformation was then used to develop the density functions for each sex. The individual density and average density profiles compare well with the literature. There were distinct differences between the profiles of two of participants (one female and one male), and the average for their sex. It is believed that the variations in these two participants' density profiles were a result of the amount and distribution of fat they possessed. Further studies are needed to support this possibility. The new density functions eliminate the uniform density assumption associated with some geometric models thus providing more accurate trunk segment parameter estimates. In turn, more accurate moments and forces can be estimated for the kinetic analyses of certain human movements.

Systems, devices, and methods for agglutination assays using sedimentation

DOEpatents

Schaff, Ulrich Y.; Sommer, Gregory J.; Singh, Anup K.

2016-01-26

Embodiments of the present invention include methods for conducting agglutination assays using sedimentation. Aggregates may be exposed to sedimentation forces and travel through a density medium to a detection area. Microfluidic devices, such as microfluidic disks, are described for conducting the agglutination assays, as are systems for conducting the assays.

Non-lead, environmentally safe projectiles and method of making same

DOEpatents

Lowden, Richard A.; McCoig, Thomas M.; Dooley, Joseph B.

1998-01-01

A projectile, such as a bullet, is made by combining two different metals in proportions calculated to achieve a desired density, without using lead. A base constituent, made of a material having density greater than lead, is combined with a binder constituent having less density. The binder constituent is malleable and ductile metallic phase material that forms projectile shapes when subjected to a consolidation force, such as compression. The metal constituents can be selected, rationed, and consolidated to achieve desired frangibility characteristics.

Non-lead, environmentally safe projectiles and method of making same

DOEpatents

Lowden, Richard A.; McCoig, Thomas M.; Dooley, Joseph B.

2000-01-01

A projectile, such as a bullet, is made by combining two different metals in proportions calculated to achieve a desired density, without using lead. A base constituent, made of a material having density greater than lead, is combined with a binder constituent having less density. The binder constituent is malleable and ductile metallic phase material that forms projectile shapes when subjected to a consolidation force, such as compression. The metal constituents can be selected, rationed, and consolidated to achieve desired frangibility characteristics.

Non-lead environmentally safe projectiles and method of making same

DOEpatents

Lowden, Richard A.; McCoig, Thomas M.; Dooley, Joseph B.

1999-01-01

A projectile, such as a bullet, is made by combining two different metals in proportions calculated to achieve a desired density, without using lead. A base constituent, made of a material having density greater than lead, is combined with a binder constituent having less density. The binder constituent is malleable and ductile metallic base material that forms projectile shapes when subjected to a consolidation force, such as compression. The metal constituents can be selected, rationed, and consolidated to achieve desired frangibility characteristics.

Non-lead, environmentally safe projectiles and method of making same

DOEpatents

Lowden, R.A.; McCoig, T.M.; Dooley, J.B.

1998-06-02

A projectile, such as a bullet, is made by combining two different metals in proportions calculated to achieve a desired density, without using lead. A base constituent, made of a material having density greater than lead, is combined with a binder constituent having less density. The binder constituent is malleable and ductile metallic phase material that forms projectile shapes when subjected to a consolidation force, such as compression. The metal constituents can be selected, rationed, and consolidated to achieve desired frangibility characteristics. 7 figs.

An innovative methodology for measurement of stress distribution of inflatable membrane structures

NASA Astrophysics Data System (ADS)

Zhao, Bing; Chen, Wujun; Hu, Jianhui; Chen, Jianwen; Qiu, Zhenyu; Zhou, Jinyu; Gao, Chengjun

2016-02-01

The inflatable membrane structure has been widely used in the fields of civil building, industrial building, airship, super pressure balloon and spacecraft. It is important to measure the stress distribution of the inflatable membrane structure because it influences the safety of the structural design. This paper presents an innovative methodology for the measurement and determination of the stress distribution of the inflatable membrane structure under different internal pressures, combining photogrammetry and the force-finding method. The shape of the inflatable membrane structure is maintained by the use of pressurized air, and the internal pressure is controlled and measured by means of an automatic pressure control system. The 3D coordinates of the marking points pasted on the membrane surface are acquired by three photographs captured from three cameras based on photogrammetry. After digitizing the markings on the photographs, the 3D curved surfaces are rebuilt. The continuous membrane surfaces are discretized into quadrilateral mesh and simulated by membrane links to calculate the stress distributions using the force-finding method. The internal pressure is simplified to the external node forces in the normal direction according to the contributory area of the node. Once the geometry x, the external force r and the topology C are obtained, the unknown force densities q in each link can be determined. Therefore, the stress distributions of the inflatable membrane structure can be calculated, combining the linear adjustment theory and the force density method based on the force equilibrium of inflated internal pressure and membrane internal force without considering the mechanical properties of the constitutive material. As the use of the inflatable membrane structure is attractive in the field of civil building, an ethylene-tetrafluoroethylene (ETFE) cushion is used with the measurement model to validate the proposed methodology. The comparisons between the obtained results and numerical simulation for the inflation process of the ETFE cushion are performed, and the strong agreements demonstrate that the proposed methodology is feasible and accurate.

Flux-Feedback Magnetic-Suspension Actuator

NASA Technical Reports Server (NTRS)

Groom, Nelson J.

1990-01-01

Flux-feedback magnetic-suspension actuator provides magnetic suspension and control forces having linear transfer characteristics between force command and force output over large range of gaps. Hall-effect devices used as sensors for electronic feedback circuit controlling currents flowing in electromagnetic windings to maintain flux linking suspended element at substantially constant value independent of changes in length of gap. Technique provides effective method for maintenance of constant flux density in gap and simpler than previous methods. Applications include magnetic actuators for control of shapes and figures of antennas and of precise segmented reflectors, magnetic suspensions in devices for storage of angular momentum and/or kinetic energy, and systems for control, pointing, and isolation of instruments.

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

NASA Astrophysics Data System (ADS)

Patel, Sandeep; Brooks, Charles L.

2005-01-01

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

Optimization of radial-type superconducting magnetic bearing using the Taguchi method

NASA Astrophysics Data System (ADS)

Ai, Liwang; Zhang, Guomin; Li, Wanjie; Liu, Guole; Liu, Qi

2018-07-01

It is important and complicated to model and optimize the levitation behavior of superconducting magnetic bearing (SMB). That is due to the nonlinear constitutive relationships of superconductor and ferromagnetic materials, the relative movement between the superconducting stator and PM rotor, and the multi-parameter (e.g., air-gap, critical current density, and remanent flux density, etc.) affecting the levitation behavior. In this paper, we present a theoretical calculation and optimization method of the levitation behavior for radial-type SMB. A simplified model of levitation force calculation is established using 2D finite element method with H-formulation. In the model, the boundary condition of superconducting stator is imposed by harmonic series expressions to describe the traveling magnetic field generated by the moving PM rotor. Also, experimental measurements of the levitation force are performed and validate the model method. A statistical method called Taguchi method is adopted to carry out an optimization of load capacity for SMB. Then the factor effects of six optimization parameters on the target characteristics are discussed and the optimum parameters combination is determined finally. The results show that the levitation behavior of SMB is greatly improved and the Taguchi method is suitable for optimizing the SMB.

Finding the Density of a Liquid Using a Metre Rule

ERIC Educational Resources Information Center

Chattopadhyay, K. N.

2008-01-01

A simple method, which is based on the principle of moment of forces only, is described for the determination of the density of liquids without measuring the mass and volume. At first, an empty test tube and a solid substance, which are hung on each side of a metre rule, are balanced and the moment arm of the test tube is measured. Keeping the…

Line length dependence of threshold current density and driving force in eutectic SnPb and SnAgCu solder electromigration

NASA Astrophysics Data System (ADS)

Yoon, Min-Seung; Ko, Min-Ku; Kim, Bit-Na; Kim, Byung-Joon; Park, Yong-Bae; Joo, Young-Chang

2008-04-01

The relationship between the threshold current density and the critical line length in eutectic SnPb and SnAgCu electromigrations were examined using solder lines with the various lengths ranging from 100to1000μm. When the electron wind-force was balanced by the back-stress gradient force, the net flux of electromigration is zero, at which the current density and line length are defined as the threshold current density and the critical length, respectively. It was found that in SnAgCu electromigration, the 1/L dependence on the threshold current density showed good agreement, whereas the threshold current densities of the eutectic SnPb deviated from the 1/L dependence. The balance between the electron wind-force and the back-stress gradient force was the main factor determining the threshold product of SnAgCu electromigration. On the other hand, in the case of eutectic SnPb, the chemical driving force is contributed as a back-flux force in addition to the back-stress gradient force. The existence of the chemical driving force was caused by the nonequilibrium Pb concentration inside the Pb-rich phases between the cathode and anode during the electromigration procedure.

A mean-density model of ionic surfactants for the dispersion of carbon nanotubes in aqueous solutions

NASA Astrophysics Data System (ADS)

Joung, Young Soo

2018-05-01

We propose a new analytical model of ionic surfactants used for the dispersion of carbon nanotubes (CNTs) in aqueous solutions. Although ionic surfactants are commonly used to facilitate the dispersion of CNTs in aqueous solutions, understanding the dispersion process is challenging and time-consuming owing to its complexity and nonlinearity. In this work, we develop a mean-density model of ionic surfactants to simplify the calculation of interaction forces between CNTs stabilized by ionic surfactants. Using this model, we can evaluate various interaction forces between the CNTs and ionic surfactants under different conditions. The dispersion mechanism is investigated by estimating the potential of mean force (PMF) as a function of van der Waals forces, electrostatic forces, interfacial tension, and osmotic pressure. To verify the proposed model, we compare the PMFs derived using our method with those derived from molecular dynamics simulations using comparable CNTs and ionic surfactants. Notably, for stable dispersions, the osmotic pressure and interfacial energy are important for long-range and short-range interactions, respectively, in comparison with the effect of electrostatic forces. Our model effectively prescribes specific surfactants and their concentrations to achieve stable aqueous suspensions of CNTs.

Revised Chapman-Enskog analysis for a class of forcing schemes in the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Li, Q.; Zhou, P.; Yan, H. J.

2016-10-01

In the lattice Boltzmann (LB) method, the forcing scheme, which is used to incorporate an external or internal force into the LB equation, plays an important role. It determines whether the force of the system is correctly implemented in an LB model and affects the numerical accuracy. In this paper we aim to clarify a critical issue about the Chapman-Enskog analysis for a class of forcing schemes in the LB method in which the velocity in the equilibrium density distribution function is given by u =∑αeαfα / ρ , while the actual fluid velocity is defined as u ̂=u +δtF / (2 ρ ) . It is shown that the usual Chapman-Enskog analysis for this class of forcing schemes should be revised so as to derive the actual macroscopic equations recovered from these forcing schemes. Three forcing schemes belonging to the above class are analyzed, among which Wagner's forcing scheme [A. J. Wagner, Phys. Rev. E 74, 056703 (2006), 10.1103/PhysRevE.74.056703] is shown to be capable of reproducing the correct macroscopic equations. The theoretical analyses are examined and demonstrated with two numerical tests, including the simulation of Womersley flow and the modeling of flat and circular interfaces by the pseudopotential multiphase LB model.

A Simplified Model for the Optical Force exerted on a Vertically Oriented Cilium by an Optical Trap and the Resulting Deformation

NASA Astrophysics Data System (ADS)

Lofgren, Ian; Resnick, Andrew

2014-03-01

Eukaryotic cilia are essentially whiplike structures extending from the cell body. Although their existence has been long known, their mechanical and functional properties are poorly understood. Optical traps are a non-contact method of applying a localized force to microscopic objects and an ideal tool for the study of ciliary mechanics. Starting with the discrete dipole approximation, a common means of calculating the optical force on an object that is not spherical, we tackle the problem of the optical force on a cilium. Treating the cilium as a homogeneous nonmagnetic cylinder and the electric field of the laser beam as linearly polarized results in a force applied in the direction of polarization. The force density in the polarization direction is derived from the force on an individual dipole within the cilium, which can be integrated over the volume of the cilium in order to find the total force. Utilizing Euler-Bernoulli beam theory, we integrate the force density over a cross section of the cilium and numerically solve a fourth order differential equation to obtain the final deformation of the cilium. This prediction will later be compared with experimental results to infer the mechanical stiffness of the cilium. Support from the National Institutes of Health, 1R15DK092716 is gratefully acknowledged.

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control.

PubMed

Johnson, Keith C; Clemmens, Emilie; Mahmoud, Hani; Kirkpatrick, Robin; Vizcarra, Juan C; Thomas, Wendy E

2017-01-01

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately. Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads. Here we describe the instrument and its ability to apply 2-260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli ( E. coli ) bacteria, and see similar results to previous studies. This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

One-dimensional Vlasov-Maxwell equilibrium for the force-free Harris sheet.

PubMed

Harrison, Michael G; Neukirch, Thomas

2009-04-03

In this Letter, the first nonlinear force-free Vlasov-Maxwell equilibrium is presented. One component of the equilibrium magnetic field has the same spatial structure as the Harris sheet, but whereas the Harris sheet is kept in force balance by pressure gradients, in the force-free solution presented here force balance is maintained by magnetic shear. Magnetic pressure, plasma pressure and plasma density are constant. The method used to find the equilibrium is based on the analogy of the one-dimensional Vlasov-Maxwell equilibrium problem to the motion of a pseudoparticle in a two-dimensional conservative potential. The force-free solution can be generalized to a complete family of equilibria that describe the transition between the purely pressure-balanced Harris sheet to the force-free Harris sheet.

Simultaneous constraint and phase conversion processing of oxide superconductors

DOEpatents

Li, Qi; Thompson, Elliott D.; Riley, Jr., Gilbert N.; Hellstrom, Eric E.; Larbalestier, David C.; DeMoranville, Kenneth L.; Parrell, Jeffrey A.; Reeves, Jodi L.

2003-04-29

A method of making an oxide superconductor article includes subjecting an oxide superconductor precursor to a texturing operation to orient grains of the oxide superconductor precursor to obtain a highly textured precursor; and converting the textured oxide superconducting precursor into an oxide superconductor, while simultaneously applying a force to the precursor which at least matches the expansion force experienced by the precursor during phase conversion to the oxide superconductor. The density and the degree of texture of the oxide superconductor precursor are retained during phase conversion. The constraining force may be applied isostatically.

The analysis of tensegrity structures for the design of a morphing wing

NASA Astrophysics Data System (ADS)

Moored, Keith W., III; Bart-Smith, Hilary

2005-05-01

Tensegrity structures have become of engineering interest in recent years, but very few have found practical use. This lack of integration is attributed to the lack of a well formulated design procedure. In this paper, a preliminary procedure is presented for developing morphing tensegrity structures that include actuating elements. To do this, the virtual work method has been modified to allow for individual actuation of struts and cables. A generalized connectivity matrix for a cantilever beam constructed from either a single 4-strut cell or multiple 4-strut cells has been developed. Global deflections resulting from actuation of specific elements have been calculated. Furthermore, the force density method is expanded to include a necessary upper bound condition such that a physically feasible structure can be designed. Finally, the importance of relative force density values on the overall shape of a structure comprising of multiple unit cells is discussed.

Simultaneous determination of the residual stress, elastic modulus, density and thickness of ultrathin film utilizing vibrating doubly clamped micro-/nanobeams

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

Stachiv, Ivo, E-mail: stachiv@fzu.cz; Institute of Physics, Czech Academy of Sciences, Prague; Kuo, Chih-Yun

2016-04-15

Measurement of ultrathin film thickness and its basic properties can be highly challenging and time consuming due to necessity of using several very sophisticated devices. Here, we report an easy accessible resonant based method capable to simultaneously determinate the residual stress, elastic modulus, density and thickness of ultrathin film coated on doubly clamped micro-/nanobeam. We show that a general dependency of the resonant frequencies on the axial load is also valid for in-plane vibrations, and the one depends only on the considered vibrational mode. As a result, we found that the film elastic modulus, density and thickness can be evaluatedmore » from two measured in-plane and out-plane fundamental resonant frequencies of micro-/nanobeam with and without film under different prestress forces. Whereas, the residual stress can be determined from two out-plane (in-plane) measured consecutive resonant frequencies of beam with film under different prestress forces without necessity of knowing film and substrate properties and dimensions. Moreover, we also reveal that the common uncertainties in force (and thickness) determination have a negligible (and minor) impact on the determined film properties. The application potential of the present method is illustrated on the beam made of silicon and SiO{sub 2} with deposited 20 nm thick AlN and 40 nm thick Au thin films, respectively.« less

Adhesive behavior of micro/nano-textured surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yuyan; Wang, Xiaoli; Li, Hanqing; Wang, Ben

2015-02-01

A numerical model of the adhesive contact between a rigid smooth sphere and an elastic textured surface based on the Lennard-Jones interatomic potential law and the Hamaker summation method is established. Textures are considered by introducing the texture height distribution into the gap equation. Simulation results show that the pull-off force on textured surfaces decreases compared to that on smooth surfaces. Furthermore, effects of sphere-shaped textures on reducing adhesion are more obvious than cylinder-shaped or cube-shaped textures when the coverage area ratio, maximum height and interval of textures are fixed. For surfaces with sphere-shaped textures, variation trends of the mean pull-off force with texture density are not monotonous, and there exists a certain range of texture densities in which the mean pull-off force is small and its variation is insignificant. In addition, the pull-off force depends also on the maximum height and radius of textures. On one hand, if the texture radius is fixed, larger maximum height results in smaller pull-off force, and if the maximum height is fixed, the pull-off force tends to increase almost linearly with increases in texture radius. On the other hand, if the height-diameter ratio of textures is fixed, the pull-off force reaches a minimum at an optimum texture radius or maximum height.

NMR imaging of density distributions in tablets.

PubMed

Djemai, A; Sinka, I C

2006-08-17

This paper describes the use of (1)H nuclear magnetic resonance (NMR) for 3D mapping of the relative density distribution in pharmaceutical tablets manufactured under controlled conditions. The tablets are impregnated with a compatible liquid. The technique involves imaging of the presence of liquid which occupies the open pore space. The method does not require special calibration as the signal is directly proportional to the porosity for the imaging conditions used. The NMR imaging method is validated using uniform density flat faced tablets and also by direct comparison with X-ray computed tomography. The results illustrate (1) the effect of die wall friction on density distribution by compressing round, curved faced tablets using clean and pre-lubricated tooling, (2) the evolution of density distribution during compaction for both clean and pre-lubricated die wall conditions, by imaging tablets compressed to different compaction forces, and (3) the effect of tablet image on density distribution by compressing two complex shape tablets in identical dies to the same average density using punches with different geometries.

Global analysis of Skyrme forces with higher-order density dependencies

NASA Astrophysics Data System (ADS)

Zuo, Zhi-Wei; Pei, Jun-Chen; Xiong, Xue-Yu; Zhu, Yi

2018-05-01

The density-dependent term in Skyrme forces is essential to simulate three-body and many-body correlations beyond the low-momentum two-body interaction. We speculate that a single density term may be insufficient and a higher-order density dependent term is added. The present work investigates the influence of higher-order density dependencies based on extended UNEDF0 and SkM* forces. Global descriptions of nuclear masses and charge radii are presented. The extended UNEDF0 force gives a global rms error on binding energies of 1.29 MeV. The influence on fission barriers and equation of state are also investigated. Perspectives to improve Skyrme forces are discussed, including global center-of-mass corrections and Lipkin-Nogami pairing corrections. Supported by National Natural Science Foundation of China (11522538)

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

PubMed Central

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

2011-01-01

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

Measuring atmospheric density using GPS-LEO tracking data

NASA Astrophysics Data System (ADS)

Kuang, D.; Desai, S.; Sibthorpe, A.; Pi, X.

2014-01-01

We present a method to estimate the total neutral atmospheric density from precise orbit determination of Low Earth Orbit (LEO) satellites. We derive the total atmospheric density by determining the drag force acting on the LEOs through centimeter-level reduced-dynamic precise orbit determination (POD) using onboard Global Positioning System (GPS) tracking data. The precision of the estimated drag accelerations is assessed using various metrics, including differences between estimated along-track accelerations from consecutive 30-h POD solutions which overlap by 6 h, comparison of the resulting accelerations with accelerometer measurements, and comparison against an existing atmospheric density model, DTM-2000. We apply the method to GPS tracking data from CHAMP, GRACE, SAC-C, Jason-2, TerraSAR-X and COSMIC satellites, spanning 12 years (2001-2012) and covering orbital heights from 400 km to 1300 km. Errors in the estimates, including those introduced by deficiencies in other modeled forces (such as solar radiation pressure and Earth radiation pressure), are evaluated and the signal and noise levels for each satellite are analyzed. The estimated density data from CHAMP, GRACE, SAC-C and TerraSAR-X are identified as having high signal and low noise levels. These data all have high correlations with anominal atmospheric density model and show common features in relative residuals with respect to the nominal model in related parameter space. On the contrary, the estimated density data from COSMIC and Jason-2 show errors larger than the actual signal at corresponding altitudes thus having little practical value for this study. The results demonstrate that this method is applicable to data from a variety of missions and can provide useful total neutral density measurements for atmospheric study up to altitude as high as 715 km, with precision and resolution between those derived from traditional special orbital perturbation analysis and those obtained from onboard accelerometers.

van der Waals forces in density functional theory: a review of the vdW-DF method.

PubMed

Berland, Kristian; Cooper, Valentino R; Lee, Kyuho; Schröder, Elsebeth; Thonhauser, T; Hyldgaard, Per; Lundqvist, Bengt I

2015-06-01

A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

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.

Force Limited Random Vibration Test of TESS Camera Mass Model

NASA Technical Reports Server (NTRS)

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

2015-01-01

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

Numerical Study of Hydrothermal Wave Suppression in Thermocapillary Flow Using a Predictive Control Method

NASA Astrophysics Data System (ADS)

Muldoon, F. H.

2018-04-01

Hydrothermal waves in flows driven by thermocapillary and buoyancy effects are suppressed by applying a predictive control method. Hydrothermal waves arise in the manufacturing of crystals, including the "open boat" crystal growth process, and lead to undesirable impurities in crystals. The open boat process is modeled using the two-dimensional unsteady incompressible Navier-Stokes equations under the Boussinesq approximation and the linear approximation of the surface thermocapillary force. The flow is controlled by a spatially and temporally varying heat flux density through the free surface. The heat flux density is determined by a conjugate gradient optimization algorithm. The gradient of the objective function with respect to the heat flux density is found by solving adjoint equations derived from the Navier-Stokes ones in the Boussinesq approximation. Special attention is given to heat flux density distributions over small free-surface areas and to the maximum admissible heat flux density.

Ponderomotive force on solitary structures created during radiation pressure acceleration of thin foils

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

Tripathi, Vipin K.; Sharma, Anamika

2013-05-15

We estimate the ponderomotive force on an expanded inhomogeneous electron density profile, created in the later phase of laser irradiated diamond like ultrathin foil. When ions are uniformly distributed along the plasma slab and electron density obeys the Poisson's equation with space charge potential equal to negative of ponderomotive potential, φ=−φ{sub p}=−(mc{sup 2}/e)(γ−1), where γ=(1+|a|{sup 2}){sup 1/2}, and |a| is the normalized local laser amplitude inside the slab; the net ponderomotive force on the slab per unit area is demonstrated analytically to be equal to radiation pressure force for both overdense and underdense plasmas. In case electron density is takenmore » to be frozen as a Gaussian profile with peak density close to relativistic critical density, the ponderomotive force has non-monotonic spatial variation and sums up on all electrons per unit area to equal radiation pressure force at all laser intensities. The same result is obtained for the case of Gaussian ion density profile and self consistent electron density profile, obeying Poisson's equation with φ=−φ{sub p}.« less

High-Sensitivity Measurement of Density by Magnetic Levitation.

PubMed

Nemiroski, Alex; Kumar, A A; Soh, Siowling; Harburg, Daniel V; Yu, Hai-Dong; Whitesides, George M

2016-03-01

This paper presents methods that use Magnetic Levitation (MagLev) to measure very small differences in density of solid diamagnetic objects suspended in a paramagnetic medium. Previous work in this field has shown that, while it is a convenient method, standard MagLev (i.e., where the direction of magnetization and gravitational force are parallel) cannot resolve differences in density <10(-4) g/cm(3) for macroscopic objects (>mm) because (i) objects close in density prevent each other from reaching an equilibrium height due to hard contact and excluded volume, and (ii) using weaker magnets or reducing the magnetic susceptibility of the medium destabilizes the magnetic trap. The present work investigates the use of weak magnetic gradients parallel to the faces of the magnets as a means of increasing the sensitivity of MagLev without destabilization. Configuring the MagLev device in a rotated state (i.e., where the direction of magnetization and gravitational force are perpendicular) relative to the standard configuration enables simple measurements along the axes with the highest sensitivity to changes in density. Manipulating the distance of separation between the magnets or the lengths of the magnets (along the axis of measurement) enables the sensitivity to be tuned. These modifications enable an improvement in the resolution up to 100-fold over the standard configuration, and measurements with resolution down to 10(-6) g/cm(3). Three examples of characterizing the small differences in density among samples of materials having ostensibly indistinguishable densities-Nylon spheres, PMMA spheres, and drug spheres-demonstrate the applicability of rotated Maglev to measuring the density of small (0.1-1 mm) objects with high sensitivity. This capability will be useful in materials science, separations, and quality control of manufactured objects.

Use of Subsonic Kernel Function in an Influence-Coefficient Method of Aeroelastic Analysis and some Comparisons with Experiment

NASA Technical Reports Server (NTRS)

Sewall, John L.; Herr, Robert W.; Watkins, Charles E.

1960-01-01

This paper illustrates the development and application of an influence-coefficient method of analysis for calculating the response of a flexible wing in an airstream to an oscillating disturbing force and for treating such aeroelastic instabilities as flutter and divergence. Aerodynamic coefficients are derived on the basis of lifting - surface theory for subsonic compressible flow by use of the method presented in NASA Technical Report R-48. Application of the analysis is made to a uniform cantilever wing- tip tank configuration for which responses to a sinusoidal disturbing force and flutter speeds were measured over a range of subsonic Mach numbers and densities. Calculated responses and flutter speeds based on flexibility influence coefficients measured at nine stations are in good agreement with experiment, provided the aerodynamic load is distributed over the wing so that local centers of pressure very nearly coincide with these nine influence stations. The use of experimental values of bending and torsional structural damping coefficients in the analysis generally improved the agreement between calculated and experimental responses. Some calculations were made to study the effects on density on responses near the flutter conditions, and linear response trends were obtained over a wide range of densities.

Force Density Function Relationships in 2-D Granular Media

NASA Technical Reports Server (NTRS)

Youngquist, Robert C.; Metzger, Philip T.; Kilts, Kelly N.

2004-01-01

An integral transform relationship is developed to convert between two important probability density functions (distributions) used in the study of contact forces in granular physics. Developing this transform has now made it possible to compare and relate various theoretical approaches with one another and with the experimental data despite the fact that one may predict the Cartesian probability density and another the force magnitude probability density. Also, the transforms identify which functional forms are relevant to describe the probability density observed in nature, and so the modified Bessel function of the second kind has been identified as the relevant form for the Cartesian probability density corresponding to exponential forms in the force magnitude distribution. Furthermore, it is shown that this transform pair supplies a sufficient mathematical framework to describe the evolution of the force magnitude distribution under shearing. Apart from the choice of several coefficients, whose evolution of values must be explained in the physics, this framework successfully reproduces the features of the distribution that are taken to be an indicator of jamming and unjamming in a granular packing. Key words. Granular Physics, Probability Density Functions, Fourier Transforms

Relationship of forces acting on implant rods and degree of scoliosis correction.

PubMed

Salmingo, Remel Alingalan; Tadano, Shigeru; Fujisaki, Kazuhiro; Abe, Yuichiro; Ito, Manabu

2013-02-01

Adolescent idiopathic scoliosis is a complex spinal pathology characterized as a three-dimensional spine deformity combined with vertebral rotation. Various surgical techniques for correction of severe scoliotic deformity have evolved and became more advanced in applying the corrective forces. The objective of this study was to investigate the relationship between corrective forces acting on deformed rods and degree of scoliosis correction. Implant rod geometries of six adolescent idiopathic scoliosis patients were measured before and after surgery. An elasto-plastic finite element model of the implant rod before surgery was reconstructed for each patient. An inverse method based on Finite Element Analysis was used to apply forces to the implant rod model such that it was deformed the same after surgery. Relationship between the magnitude of corrective forces and degree of correction expressed as change of Cobb angle was evaluated. The effects of screw configuration on the corrective forces were also investigated. Corrective forces acting on rods and degree of correction were not correlated. Increase in number of implant screws tended to decrease the magnitude of corrective forces but did not provide higher degree of correction. Although greater correction was achieved with higher screw density, the forces increased at some level. The biomechanics of scoliosis correction is not only dependent to the corrective forces acting on implant rods but also associated with various parameters such as screw placement configuration and spine stiffness. Considering the magnitude of forces, increasing screw density is not guaranteed as the safest surgical strategy. Copyright © 2012 Elsevier Ltd. All rights reserved.

Mapping the distribution of specific antibody interaction forces on individual red blood cells

NASA Astrophysics Data System (ADS)

Yeow, Natasha; Tabor, Rico F.; Garnier, Gil

2017-02-01

Current blood typing methods rely on the agglutination of red blood cells (RBCs) to macroscopically indicate a positive result. An indirect agglutination mechanism is required when blood typing with IgG forms of antibodies. To date, the interaction forces between anti-IgG and IgG antibodies have been poorly quantified, and blood group related antigens have never been quantified with the atomic force microscope (AFM). Instead, the total intensity resulting from fluorescent-tagged antibodies adsorbed on RBC has been measured to calculate an average antigen density on a series of RBCs. In this study we mapped specific antibody interaction forces on the RBC surface. AFM cantilever tips functionalized with anti-IgG were used to probe RBCs incubated with specific IgG antibodies. This work provides unique insight into antibody-antigen interactions in their native cell-bound location, and crucially, on a per-cell basis rather than an ensemble average set of properties. Force profiles obtained from the AFM directly provide not only the anti-IgG - IgG antibody interaction force, but also the spatial distribution and density of antigens over a single cell. This new understanding might be translated into the development of very selective and quantitative interactions that underpin the action of drugs in the treatment of frontier illnesses.

Forced unfolding of single-chain polymeric nanoparticles.

PubMed

Hosono, Nobuhiko; Kushner, Aaron M; Chung, Jaeyoon; Palmans, Anja R A; Guan, Zhibin; Meijer, E W

2015-06-03

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is applied to single-chain polymeric nanoparticles (SCPNs) to acquire information about the internal folding structure of SCPNs and inherent kinetic parameters of supramolecular self-assembling motifs embedded into the SCPNs. The SCPNs used here are polyacrylate-based polymers carrying 2-ureido-4-[1H]-pyrimidinone (UPy) or benzene-1,3,5-tricarboxamide (BTA) pendants that induce an intramolecular chain collapse into nanoparticles consisting of one polymer chain only via internal supramolecular cross-linking. The SCPN is stretched by an AFM cantilever to unfold mechanically, which allows measuring of force-extension profiles of the SCPNs. Consecutive peaks observed in the force profiles are attributed to rupture events of self-assembled UPy/BTA units in the SCPNs. The force profiles have been analyzed statistically for a series of polymers with different UPy/BTA incorporation densities. The results provide insights into the internal conformation of SCPNs, where the folding structure can be changed with the incorporation density of UPy/BTA. In addition, dynamic loading rate analysis allows the determination of kinetic parameters of BTA self-assembly, which has not been accessible by any other method. This study offers a rational tool for understanding the folding structure, kinetics, and pathway of two series of SCPNs.

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

NASA Astrophysics Data System (ADS)

Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M.

1999-06-01

We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

van der Waals forces in density functional theory: a review of the vdW-DF method

DOE PAGES

Berland, Kristian; Cooper, Valentino R.; Lee, Kyuho; ...

2015-05-15

We review a density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology. The insights that led to the construction of the Rutgers–Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only formore » dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible.« less

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation

DOEpatents

Schaff, Ulrich Y.; Koh, Chung-Yan; Sommer, Gregory J.

2016-04-05

Embodiments of the present invention are directed toward devices, systems, and method for conducting assays using sedimentation. In one example, a method includes layering a mixture on a density medium, subjecting sedimentation particles in the mixture to sedimentation forces to cause the sedimentation particles to move to a detection area through a density medium, and detecting a target analyte in a detection region of the sedimentation channel. In some examples, the sedimentation particles and labeling agent may have like charges to reduce non-specific binding of labeling agent and sedimentation particles. In some examples, the density medium is provided with a separation layer for stabilizing the assay during storage and operation. In some examples, the sedimentation channel may be provided with a generally flat sedimentation chamber for dispersing the particle pellet over a larger surface area.

Devices, systems, and methods for conducting assays with improved sensitivity using sedimentation

DOEpatents

Schaff, Ulrich Y; Koh, Chung-Yan; Sommer, Gregory J

2015-02-24

Embodiments of the present invention are directed toward devices, systems, and method for conducting assays using sedimentation. In one example, a method includes layering a mixture on a density medium, subjecting sedimentation particles in the mixture to sedimentation forces to cause the sedimentation particles to move to a detection area through a density medium, and detecting a target analyte in a detection region of the sedimentation channel. In some examples, the sedimentation particles and labeling agent may have like charges to reduce non-specific binding of labeling agent and sedimentation particles. In some examples, the density medium is provided with a separation layer for stabilizing the assay during storage and operation. In some examples, the sedimentation channel may be provided with a generally flat sedimentation chamber for dispersing the particle pellet over a larger surface area.

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model.

PubMed

Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir

2018-04-10

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

DOE PAGES

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco; ...

2018-03-15

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

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

PubMed

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

2012-07-07

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

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

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

Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco

Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

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

PubMed Central

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

2009-01-01

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

Characterization of forced response of density stratified reacting wake

NASA Astrophysics Data System (ADS)

Pawar, Samadhan A.; Sujith, Raman I.; Emerson, Benjamin; Lieuwen, Tim

2018-02-01

The hydrodynamic stability of a reacting wake depends primarily on the density ratio [i.e., ratio of unburnt gas density (ρu) to burnt gas density (ρb)] of the flow across the wake. The variation of the density ratio from high to low value, keeping ρ u / ρ b > 1 , transitions dynamical characteristics of the reacting wake from a linearly globally stable (or convectively unstable) to a globally unstable mode. In this paper, we propose a framework to analyze the effect of harmonic forcing on the deterministic and synchronization characteristics of reacting wakes. Using the recurrence quantification analysis of the forced wake response, we show that the deterministic behaviour of the reacting wake increases as the amplitude of forcing is increased. Furthermore, for different density ratios, we found that the synchronization of the top and bottom branches of the wake with the forcing signal is dependent on whether the mean frequency of the natural oscillations of the wake (fn) is lesser or greater than the frequency of external forcing (ff). We notice that the response of both branches (top and bottom) of the reacting wake to the external forcing is asymmetric and symmetric for the low and high density ratios, respectively. Furthermore, we characterize the phase-locking behaviour between the top and bottom branches of the wake for different values of density ratios. We observe that an increase in the density ratio results in a gradual decrease in the relative phase angle between the top and bottom branches of the wake, which leads to a change in the vortex shedding pattern from a sinuous (anti-phase) to a varicose (in-phase) mode of the oscillations.

Accelerating large scale Kohn-Sham density functional theory calculations with semi-local functionals and hybrid functionals

NASA Astrophysics Data System (ADS)

Lin, Lin

The computational cost of standard Kohn-Sham density functional theory (KSDFT) calculations scale cubically with respect to the system size, which limits its use in large scale applications. In recent years, we have developed an alternative procedure called the pole expansion and selected inversion (PEXSI) method. The PEXSI method solves KSDFT without solving any eigenvalue and eigenvector, and directly evaluates physical quantities including electron density, energy, atomic force, density of states, and local density of states. The overall algorithm scales as at most quadratically for all materials including insulators, semiconductors and the difficult metallic systems. The PEXSI method can be efficiently parallelized over 10,000 - 100,000 processors on high performance machines. The PEXSI method has been integrated into a number of community electronic structure software packages such as ATK, BigDFT, CP2K, DGDFT, FHI-aims and SIESTA, and has been used in a number of applications with 2D materials beyond 10,000 atoms. The PEXSI method works for LDA, GGA and meta-GGA functionals. The mathematical structure for hybrid functional KSDFT calculations is significantly different. I will also discuss recent progress on using adaptive compressed exchange method for accelerating hybrid functional calculations. DOE SciDAC Program, DOE CAMERA Program, LBNL LDRD, Sloan Fellowship.

Label-free density difference amplification-based cell sorting.

PubMed

Song, Jihwan; Song, Minsun; Kang, Taewook; Kim, Dongchoul; Lee, Luke P

2014-11-01

The selective cell separation is a critical step in fundamental life sciences, translational medicine, biotechnology, and energy harvesting. Conventional cell separation methods are fluorescent activated cell sorting and magnetic-activated cell sorting based on fluorescent probes and magnetic particles on cell surfaces. Label-free cell separation methods such as Raman-activated cell sorting, electro-physiologically activated cell sorting, dielectric-activated cell sorting, or inertial microfluidic cell sorting are, however, limited when separating cells of the same kind or cells with similar sizes and dielectric properties, as well as similar electrophysiological phenotypes. Here we report a label-free density difference amplification-based cell sorting (dDACS) without using any external optical, magnetic, electrical forces, or fluidic activations. The conceptual microfluidic design consists of an inlet, hydraulic jump cavity, and multiple outlets. Incoming particles experience gravity, buoyancy, and drag forces in the separation chamber. The height and distance that each particle can reach in the chamber are different and depend on its density, thus allowing for the separation of particles into multiple outlets. The separation behavior of the particles, based on the ratio of the channel heights of the inlet and chamber and Reynolds number has been systematically studied. Numerical simulation reveals that the difference between the heights of only lighter particles with densities close to that of water increases with increasing the ratio of the channel heights, while decreasing Reynolds number can amplify the difference in the heights between the particles considered irrespective of their densities.

StarSmasher: Smoothed Particle Hydrodynamics code for smashing stars and planets

NASA Astrophysics Data System (ADS)

Gaburov, Evghenii; Lombardi, James C., Jr.; Portegies Zwart, Simon; Rasio, F. A.

2018-05-01

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle method that approximates a continuous fluid as discrete nodes, each carrying various parameters such as mass, position, velocity, pressure, and temperature. In an SPH simulation the resolution scales with the particle density; StarSmasher is able to handle both equal-mass and equal number-density particle models. StarSmasher solves for hydro forces by calculating the pressure for each particle as a function of the particle's properties - density, internal energy, and internal properties (e.g. temperature and mean molecular weight). The code implements variational equations of motion and libraries to calculate the gravitational forces between particles using direct summation on NVIDIA graphics cards. Using a direct summation instead of a tree-based algorithm for gravity increases the accuracy of the gravity calculations at the cost of speed. The code uses a cubic spline for the smoothing kernel and an artificial viscosity prescription coupled with a Balsara Switch to prevent unphysical interparticle penetration. The code also implements an artificial relaxation force to the equations of motion to add a drag term to the calculated accelerations during relaxation integrations. Initially called StarCrash, StarSmasher was developed originally by Rasio.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Conductance of AFM Deformed Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Maiti, Amitesh; Anatram, M. P.; Biegel, Bryan (Technical Monitor)

2002-01-01

This viewgraph presentation provides information on the electrical conductivity of carbon nanotubes upon deformation by atomic force microscopy (AFM). The density of states and conductance were computed using four orbital tight-binding method with various parameterizations. Different chiralities develop bandgap that varies with chirality.

Growth method for AIIIBV and AIVBVI heterostructures

NASA Astrophysics Data System (ADS)

Fedorchenko, I. V.; Kushkov, A. R.; Gaev, D. S.; Rabinovich, O. I.; Marenkin, S. F.; Didenko, S. I.; Legotin, S. A.; Orlova, M. N.; Krasnov, A. A.

2018-02-01

The results of nanoscale islet films grown by AIIIBV and AIVBVI incongruent evaporation compounds are discussed. The surface morphology structure was studied by atomic-force microscopy. It is shown that the distribution density and the characteristic dimensions of nanostructures depend on the evaporation temperature.

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.

Modeling and analysis of a novel planar eddy current damper

NASA Astrophysics Data System (ADS)

Zhang, He; Kou, Baoquan; Jin, Yinxi; Zhang, Lu; Zhang, Hailin; Li, Liyi

2014-05-01

In this paper, a novel 2-DOF permanent magnet planar eddy current damper is proposed, of which the stator is made of a copper plate and the mover is composed of two orthogonal 1-D permanent magnet arrays with a double sided structure. The main objective of the planar eddy current damper is to provide two orthogonal damping forces for dynamic systems like the 2-DOF high precision positioning system. Firstly, the basic structure and the operating principle of the planar damper are introduced. Secondly, the analytical model of the planar damper is established where the magnetic flux density distribution of the permanent magnet arrays is obtained by using the equivalent magnetic charge method and the image method. Then, the analytical expressions of the damping force and damping coefficient are derived. Lastly, to verify the analytical model, the finite element method (FEM) is adopted for calculating the flux density and a planar damper prototype is manufactured and thoroughly tested. The results from FEM and experiments are in good agreement with the ones from the analytical expressions indicating that the analytical model is reasonable and correct.

An efficient mass-preserving interface-correction level set/ghost fluid method for droplet suspensions under depletion forces

NASA Astrophysics Data System (ADS)

Ge, Zhouyang; Loiseau, Jean-Christophe; Tammisola, Outi; Brandt, Luca

2018-01-01

Aiming for the simulation of colloidal droplets in microfluidic devices, we present here a numerical method for two-fluid systems subject to surface tension and depletion forces among the suspended droplets. The algorithm is based on an efficient solver for the incompressible two-phase Navier-Stokes equations, and uses a mass-conserving level set method to capture the fluid interface. The four novel ingredients proposed here are, firstly, an interface-correction level set (ICLS) method; global mass conservation is achieved by performing an additional advection near the interface, with a correction velocity obtained by locally solving an algebraic equation, which is easy to implement in both 2D and 3D. Secondly, we report a second-order accurate geometric estimation of the curvature at the interface and, thirdly, the combination of the ghost fluid method with the fast pressure-correction approach enabling an accurate and fast computation even for large density contrasts. Finally, we derive a hydrodynamic model for the interaction forces induced by depletion of surfactant micelles and combine it with a multiple level set approach to study short-range interactions among droplets in the presence of attracting forces.

Bayesian calibration of coarse-grained forces: Efficiently addressing transferability

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Rosch, Thomas W.; Phelan, Frederick R.

2016-04-01

Generating and calibrating forces that are transferable across a range of state-points remains a challenging task in coarse-grained (CG) molecular dynamics. In this work, we present a coarse-graining workflow, inspired by ideas from uncertainty quantification and numerical analysis, to address this problem. The key idea behind our approach is to introduce a Bayesian correction algorithm that uses functional derivatives of CG simulations to rapidly and inexpensively recalibrate initial estimates f0 of forces anchored by standard methods such as force-matching. Taking density-temperature relationships as a running example, we demonstrate that this algorithm, in concert with various interpolation schemes, can be used to efficiently compute physically reasonable force curves on a fine grid of state-points. Importantly, we show that our workflow is robust to several choices available to the modeler, including the interpolation schemes and tools used to construct f0. In a related vein, we also demonstrate that our approach can speed up coarse-graining by reducing the number of atomistic simulations needed as inputs to standard methods for generating CG forces.

Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.

PubMed

Demerdash, Omar N A; Mitchell, Julie C

2012-07-01

Normal mode analysis has emerged as a useful technique for investigating protein motions on long time scales. This is largely due to the advent of coarse-graining techniques, particularly Hooke's Law-based potentials and the rotational-translational blocking (RTB) method for reducing the size of the force-constant matrix, the Hessian. Here we present a new method for domain decomposition for use in RTB that is based on hierarchical clustering of atomic density gradients, which we call Density-Cluster RTB (DCRTB). The method reduces the number of degrees of freedom by 85-90% compared with the standard blocking approaches. We compared the normal modes from DCRTB against standard RTB using 1-4 residues in sequence in a single block, with good agreement between the two methods. We also show that Density-Cluster RTB and standard RTB perform well in capturing the experimentally determined direction of conformational change. Significantly, we report superior correlation of DCRTB with B-factors compared with 1-4 residue per block RTB. Finally, we show significant reduction in computational cost for Density-Cluster RTB that is nearly 100-fold for many examples. Copyright © 2012 Wiley Periodicals, Inc.

Phonon dispersion and local density of states in NiPd alloy using modified embedded atom method potential

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

Joshi, Subodh, E-mail: subodhssgk@gmail.com; Chand, Manesh, E-mail: maneshchand@gmail.com; Dabral, Krishna, E-mail: kmkrishna.dabral@gmail.com

2016-05-06

A modified embedded atom method (MEAM) potential model up to second neighbours has been used to calculate the phonon dispersions for Ni{sub 0.55}Pd{sub 0.45} alloy in which Pd is introduced as substitutional impurity. Using the force-constants obtained from MEAM potential, the local vibrational density of states in host Ni and substitutional Pd atoms using Green’s function method has been calculated. The calculation of phonon dispersions of NiPd alloy shows a good agreement with the experimental results. Condition of resonance mode has also been investigated and resonance mode in the frequency spectrum of impurity atom at low frequency is observed.

Inertial particle focusing in serpentine channels on a centrifugal platform

NASA Astrophysics Data System (ADS)

Shamloo, Amir; Mashhadian, Ali

2018-01-01

Inertial particle focusing as a powerful passive method is widely used in diagnostic test devices. It is common to use a curved channel in this approach to achieve particle focusing through balancing of the secondary flow drag force and the inertial lift force. Here, we present a focusing device on a disk based on the interaction of secondary flow drag force, inertial lift force, and centrifugal forces to focus particles. By choosing a channel whose cross section has a low aspect ratio, the mixing effect of the secondary flow becomes negligible. To calculate inertial lift force, which is exerted on the particle from the fluid, the interaction between the fluid and particle is investigated accurately through implementation of 3D Direct Numerical Solution (DNS) method. The particle focusing in three serpentine channels with different corner angles of 75°, 85°, and 90° is investigated for three polystyrene particles with diameters of 8 μm, 9.9 μm, and 13 μm. To show the simulation reliability, the results obtained from the simulations of two examples, namely, particle focusing and centrifugal platform, are verified against experimental counterparts. The effects of angular velocity of disk on the fluid velocity and on the focusing parameters are studied. Fluid velocity in a channel with corner angle of 75° is greater than two other channels. Furthermore, the particle equilibrium positions at the cross section of channel are obtained at the outlet. There are two equilibrium positions located at the centers of the long walls. Finally, the effect of particle density on the focusing length is investigated. A particle with a higher density and larger diameter is focused in a shorter length of the channel compared to its counterpart with a lower density and shorter diameter. The channel with a corner angle of 90° has better focusing efficiency compared to other channels. This design focuses particles without using any pump or sheath flow. Inertial particle focusing on centrifugal platform, which rarely has been studied, can be used for a wide range of diagnostic lab-on-a-disk device.

Method and apparatus for forming billets from metallic chip scraps

DOEpatents

Girshov, Vladimir Leonidovich [St. Petersburg, RU; Treschevskiy, Arnold Nikolayevich [St. Petersburg, RU; Kochkin, Victor Georgievich [St. Petersburg, RU; Abramov, Alexey Alexandrovich [St. Petersburg, RU; Sidenko, Natalja Semenovna [St. Petersburg, RU

2006-05-02

After recycled titanium alloy chips are crushed and cleaned, they are pressed into cylindrically briquettes with a relative density of 0.6, and placed into capsules. The capsules are heated and placed into a preheated pressing rig. The pressing rig repetitively applies axial force to the capsule, resulting in a relative density of at least 0.95. The product billets are used for consumable electrodes, secondary casting alloys, forgings, extruded semi-finished products and the like.

DAMQT: A package for the analysis of electron density in molecules

NASA Astrophysics Data System (ADS)

López, Rafael; Rico, Jaime Fernández; Ramírez, Guillermo; Ema, Ignacio; Zorrilla, David

2009-09-01

DAMQT is a package for the analysis of the electron density in molecules and the fast computation of the density, density deformations, electrostatic potential and field, and Hellmann-Feynman forces. The method is based on the partition of the electron density into atomic fragments by means of a least deformation criterion. Each atomic fragment of the density is expanded in regular spherical harmonics times radial factors, which are piecewise represented in terms of analytical functions. This representation is used for the fast evaluation of the electrostatic potential and field generated by the electron density and nuclei, as well as for the computation of the Hellmann-Feynman forces on the nuclei. An analysis of the atomic and molecular deformations of the density can be also carried out, yielding a picture that connects with several concepts of the empirical structural chemistry. Program summaryProgram title: DAMQT1.0 Catalogue identifier: AEDL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv3 No. of lines in distributed program, including test data, etc.: 278 356 No. of bytes in distributed program, including test data, etc.: 31 065 317 Distribution format: tar.gz Programming language: Fortran90 and C++ Computer: Any Operating system: Linux, Windows (Xp, Vista) RAM: 190 Mbytes Classification: 16.1 External routines: Trolltech's Qt (4.3 or higher) ( http://www.qtsoftware.com/products), OpenGL (1.1 or higher) ( http://www.opengl.org/), GLUT 3.7 ( http://www.opengl.org/resources/libraries/glut/). Nature of problem: Analysis of the molecular electron density and density deformations, including fast evaluation of electrostatic potential, electric field and Hellmann-Feynman forces on nuclei. Solution method: The method of Deformed Atoms in Molecules, reported elsewhere [1], is used for partitioning the molecular electron density into atomic fragments, which are further expanded in spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated to density. Restrictions: The current version is limited to 120 atoms, 2000 contracted functions, and l=5 in basis functions. Density must come from a LCAO calculation (any level) with spherical (not Cartesian) Gaussian functions. Unusual features: The program contains an OPEN statement to binary files (stream) in file GOPENMOL.F90. This statement has not a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel's ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance). Additional comments: The distribution file for this program is over 30 Mbytes and therefore is not delivered directly when download or e-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Largely dependent on the system size and the module run (from fractions of a second to hours). References: [1] J. Fernández Rico, R. López, I. Ema, G. Ramírez, J. Mol. Struct. (Theochem) 727 (2005) 115.

Identification of modal parameters including unmeasured forces and transient effects

NASA Astrophysics Data System (ADS)

Cauberghe, B.; Guillaume, P.; Verboven, P.; Parloo, E.

2003-08-01

In this paper, a frequency-domain method to estimate modal parameters from short data records with known input (measured) forces and unknown input forces is presented. The method can be used for an experimental modal analysis, an operational modal analysis (output-only data) and the combination of both. A traditional experimental and operational modal analysis in the frequency domain starts respectively, from frequency response functions and spectral density functions. To estimate these functions accurately sufficient data have to be available. The technique developed in this paper estimates the modal parameters directly from the Fourier spectra of the outputs and the known input. Instead of using Hanning windows on these short data records the transient effects are estimated simultaneously with the modal parameters. The method is illustrated, tested and validated by Monte Carlo simulations and experiments. The presented method to process short data sequences leads to unbiased estimates with a small variance in comparison to the more traditional approaches.

Microscopically based energy density functionals for nuclei using the density matrix expansion. II. Full optimization and validation

NASA Astrophysics Data System (ADS)

Navarro Pérez, R.; Schunck, N.; Dyhdalo, A.; Furnstahl, R. J.; Bogner, S. K.

2018-05-01

Background: Energy density functional methods provide a generic framework to compute properties of atomic nuclei starting from models of nuclear potentials and the rules of quantum mechanics. Until now, the overwhelming majority of functionals have been constructed either from empirical nuclear potentials such as the Skyrme or Gogny forces, or from systematic gradient-like expansions in the spirit of the density functional theory for atoms. Purpose: We seek to obtain a usable form of the nuclear energy density functional that is rooted in the modern theory of nuclear forces. We thus consider a functional obtained from the density matrix expansion of local nuclear potentials from chiral effective field theory. We propose a parametrization of this functional carefully calibrated and validated on selected ground-state properties that is suitable for large-scale calculations of nuclear properties. Methods: Our energy functional comprises two main components. The first component is a non-local functional of the density and corresponds to the direct part (Hartree term) of the expectation value of local chiral potentials on a Slater determinant. Contributions to the mean field and the energy of this term are computed by expanding the spatial, finite-range components of the chiral potential onto Gaussian functions. The second component is a local functional of the density and is obtained by applying the density matrix expansion to the exchange part (Fock term) of the expectation value of the local chiral potential. We apply the UNEDF2 optimization protocol to determine the coupling constants of this energy functional. Results: We obtain a set of microscopically constrained functionals for local chiral potentials from leading order up to next-to-next-to-leading order with and without three-body forces and contributions from Δ excitations. These functionals are validated on the calculation of nuclear and neutron matter, nuclear mass tables, single-particle shell structure in closed-shell nuclei, and the fission barrier of 240Pu. Quantitatively, they perform noticeably better than the more phenomenological Skyrme functionals. Conclusions: The inclusion of higher-order terms in the chiral perturbation expansion seems to produce a systematic improvement in predicting nuclear binding energies while the impact on other observables is not really significant. This result is especially promising since all the fits have been performed at the single-reference level of the energy density functional approach, where important collective correlations such as center-of-mass correction, rotational correction, or zero-point vibrational energies have not been taken into account yet.

Modeling and analysis of a magnetically levitated synchronous permanent magnet planar motor

NASA Astrophysics Data System (ADS)

Kou, Baoquan; Zhang, Lu; Li, Liyi; Zhang, Hailin

2012-04-01

In this paper, a new magnetically levitated synchronous permanent magnet planar motor (MLSPMPM) driven by composite-current is proposed, of which the mover is made of a copper coil array and the stator are magnets and magnetic conductor. The coil pitch τt and permanent magnet pole pitch τp satisfy the following relationship 3nτt = (3n ± 1)τp. Firstly, an analytical model of the planar motor is established, flux density distribution of the two-dimensional magnet array is obtained by solving the equations of the scalar magnetic potential. Secondly, the expressions of the electromagnetic forces induced by magnetic field and composite current are derived. To verify the analytical model and the electromagnetic forces, finite element method (FEM) is used for calculating the flux density and electromagnetic forces of the MLSPMPM. And the results from FEM are in good agreement with the results from the analytical equations. This indicates that the analytical model is reasonable.

Response of a semiconducting infinite medium under two temperature theory with photothermal excitation due to laser pulses

NASA Astrophysics Data System (ADS)

Lotfy, Kh.; Gabr, M. E.

2017-12-01

A novel model of two-dimensional deformations for two-temperature theory at the free surface under the excitation of thermoelastic wave by pulsed laser for a semi-infinite semiconducting medium is studied. The effect of mechanical force during a photothermal process is investigated. The mathematical methods of the Lord-Shulman (LS includes one relaxation time) and Green-Lindsay (GL with two relaxation times) theories as well as the classical dynamical coupled theory (CD) are used. An exact expression for displacement components, force stresses, carrier density and distribution of temperature are obtained using the harmonic wave analysis. Combinations of two-temperature and photothermal theories are obtained analytically. Comparisons of the results are made between the three theories also. The effects of thermoelectric coupling parameter, two-temperature parameter on the displacement component, force stress, carrier density, and distribution of temperature for silicon (Si) medium have been illustrated graphically. The variations of the considered variables with the horizontal distance have been discussed.

Quantification of Cyclic Ground Reaction Force Histories During Daily Activity in Humans

NASA Technical Reports Server (NTRS)

Breit, G. A.; Whalen, R. T.; Wade, Charles E. (Technical Monitor)

1994-01-01

Theoretical models and experimental studies of bone remodeling suggest that bone density and structure are influenced by local cyclic skeletal tissue stress and strain histories. Estimation of long-term loading histories in humans is usually achieved by assessment of physical activity level by questionnaires, logbooks, and pedometers, since the majority of lower limb cyclic loading occurs during walking and running. These methods provide some indication of the mechanical loading history, but fail to consider the true magnitude of the lower limb skeletal forces generated by various daily activities. These techniques cannot account for individual gait characteristics, gait speed, and unpredictable high loading events that may influence bone mass significantly. We have developed portable instrumentation to measure and record the vertical component of the ground reaction force (GRFz) during normal daily activity. This equipment allows long-term quantitative monitoring of musculoskeletal loads, which in conjunction with bone mineral density assessments, promises to elucidate the relationship between skeletal stresses and bone remodeling.

Thermal properties of nuclear matter in a variational framework with relativistic corrections

NASA Astrophysics Data System (ADS)

Zaryouni, S.; Hassani, M.; Moshfegh, H. R.

2014-01-01

The properties of hot symmetric nuclear matter for a wide range of densities and temperatures are investigated by employing the AV14 potential within the lowest order constrained variational (LOCV) method with the inclusion of a phenomenological three-body force as well as relativistic corrections. The relativistic corrections of many-body kinetic energies as well as the boot interaction corrections are presented for a wide range of densities and temperatures. The free energy, pressure, incompressibility, and other thermodynamic quantities of symmetric nuclear matter are obtained and discussed. The critical temperature is found, and the liquid-gas phase transition is analyzed both with and without the inclusion of three-body forces and relativistic corrections in the LOCV approach. It is shown that the critical temperature is strongly affected by the three-body forces but does not depend on the relativistic corrections. Finally, the results obtained in the present study are compared with other many-body calculations and experimental predictions.

Children with Heavy Prenatal Alcohol Exposure have Different Frequency Domain Signal Characteristics when Producing Isometric Force

PubMed Central

Nguyen, Tanya T.; Ashrafi, Ashkan; Thomas, Jennifer D.; Riley, Edward P.; Simmons, Roger W.

2013-01-01

To extend our current understanding of the teratogenic effects of prenatal alcohol exposure on the control of isometric force, the present study investigated the signal characteristics of power spectral density functions resulting from sustained control of isometric force by children with and without heavy prenatal exposure to alcohol. It was predicted that the functions associated with the force signals would be fundamentally different for the two groups. Twenty-five children aged between 7 and 17 years with heavy prenatal alcohol exposure and 21 non-alcohol exposed control children attempted to duplicate a visually represented target force by pressing on a load cell. The level of target force (5 and 20% of maximum voluntary contraction) and the time interval between visual feedback (20ms, 320ms and 740ms) were manipulated. A multivariate spectral estimation method with sinusoidal windows was applied to individual isometric force-time signals. Analysis of the resulting power spectral density functions revealed that the alcohol-exposed children had a lower mean frequency, less spectral variability, greater peak power and a lower frequency at which peak power occurred. Furthermore, mean frequency and spectral variability produced by the alcohol-exposed group remained constant across target load and visual feedback interval, suggesting that these children were limited to making long-time scale corrections to the force signal. In contrast, the control group produced decreased mean frequency and spectral variability as target force and the interval between visual feedback increased, indicating that when feedback was frequently presented these children used the information to make short-time scale adjustments to the ongoing force signal. Knowledge of these differences could facilitate the design of motor rehabilitation exercises that specifically target isometric force control deficits in alcohol-exposed children. PMID:23238099

A Finite-Element Method Model of Soft Tissue Response to Impulsive Acoustic Radiation Force

PubMed Central

Palmeri, Mark L.; Sharma, Amy C.; Bouchard, Richard R.; Nightingale, Roger W.; Nightingale, Kathryn R

2010-01-01

Several groups are studying acoustic radiation force and its ability to image the mechanical properties of tissue. Acoustic radiation force impulse (ARFI) imaging is one modality using standard diagnostic ultrasound scanners to generate localized, impulsive, acoustic radiation forces in tissue. The dynamic response of tissue is measured via conventional ultrasonic speckle-tracking methods and provides information about the mechanical properties of tissue. A finite-element method (FEM) model has been developed that simulates the dynamic response of tissues, with and without spherical inclusions, to an impulsive acoustic radiation force excitation from a linear array transducer. These FEM models were validated with calibrated phantoms. Shear wave speed, and therefore elasticity, dictates tissue relaxation following ARFI excitation, but Poisson’s ratio and density do not significantly alter tissue relaxation rates. Increased acoustic attenuation in tissue increases the relative amount of tissue displacement in the near field compared with the focal depth, but relaxation rates are not altered. Applications of this model include improving image quality, and distilling material and structural information from tissue’s dynamic response to ARFI excitation. Future work on these models includes incorporation of viscous material properties and modeling the ultrasonic tracking of displaced scatterers. PMID:16382621

DGDFT: A massively parallel method for large scale density functional theory calculations.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

The atmospheric emission method of calculating the neutral atmosphere and charged particle densities in the upper atmosphere

NASA Astrophysics Data System (ADS)

McElroy, Kenneth L., Jr.

1992-12-01

A method is presented for the determination of neutral gas densities in the ionosphere from rocket-borne measurements of UV atmospheric emissions. Computer models were used to calculate an initial guess for the neutral atmosphere. Using this neutral atmosphere, intensity profiles for the N2 (0,5) Vegard-Kaplan band, the N2 Lyman-Birge-Hopfield band system, and the OI2972 A line were calculated and compared with the March 1990 NPS MUSTANG data. The neutral atmospheric model was modified and the intensity profiles recalculated until a fit with the data was obtained. The neutral atmosphere corresponding to the intensity profile that fit the data was assumed to be the atmospheric composition prevailing at the time of the observation. The ion densities were then calculated from the neutral atmosphere using a photochemical model. The electron density profile calculated by this model was compared with the electron density profile measured by the U.S. Air Force Geophysics Laboratory at a nearby site.

An Implementation of Hydrostatic Boundary Conditions for Variable Density Lattice Boltzmann Methods

NASA Astrophysics Data System (ADS)

Bardsley, K. J.; Thorne, D. T.; Lee, J. S.; Sukop, M. C.

2006-12-01

Lattice Boltzmann Methods (LBMs) have been under development for the last two decades and have become another capable numerical method for simulating fluid flow. Recent advances in lattice Boltzmann applications involve simulation of density-dependent fluid flow in closed (Dixit and Babu, 2006; D'Orazio et al., 2004) or periodic (Guo and Zhao, 2005) domains. However, standard pressure boundary conditions (BCs) are incompatible with concentration-dependent density flow simulations that use a body force for gravity. An implementation of hydrostatic BCs for use under these conditions is proposed here. The basis of this new implementation is an additional term in the pressure BC. It is derived to account for the incorporation of gravity as a body force and the effect of varying concentration in the fluid. The hydrostatic BC expands the potential of density-dependent LBM to simulate domains with boundaries other than the closed or periodic boundaries that have appeared in previous literature on LBM simulations. With this new implementation, LBM will be able to simulate complex concentration-dependent density flows, such as salt water intrusion in the classic Henry and Henry-Hilleke problems. This is demonstrated using various examples, beginning with a closed box system, and ending with a system containing two solid walls, one velocity boundary and one pressure boundary, as in the Henry problem. References Dixit, H. N., V. Babu, (2006), Simulation of high Rayleigh number natural convection in a square cavity using the lattice Boltzmann method, Int. J. Heat Mass Transfer, 49, 727-739. D'Orazio, A., M. Corcione, G.P. Celata, (2004), Application to natural convection enclosed flows of a lattice Boltzmann BGK model coupled with a general purpose thermal boundary conditions, Int. J. Thermal Sci., 43, 575-586. Gou, Z., T.S. Zhao, (2005), Lattice Boltzmann simulation of natural convection with temperature-dependant viscosity in a porous cavity, Numerical Heat Transfer, Part B, 47, 157-177.

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.

A free energy-based surface tension force model for simulation of multiphase flows by level-set method

NASA Astrophysics Data System (ADS)

Yuan, H. Z.; Chen, Z.; Shu, C.; Wang, Y.; Niu, X. D.; Shu, S.

2017-09-01

In this paper, a free energy-based surface tension force (FESF) model is presented for accurately resolving the surface tension force in numerical simulation of multiphase flows by the level set method. By using the analytical form of order parameter along the normal direction to the interface in the phase-field method and the free energy principle, FESF model offers an explicit and analytical formulation for the surface tension force. The only variable in this formulation is the normal distance to the interface, which can be substituted by the distance function solved by the level set method. On one hand, as compared to conventional continuum surface force (CSF) model in the level set method, FESF model introduces no regularized delta function, due to which it suffers less from numerical diffusions and performs better in mass conservation. On the other hand, as compared to the phase field surface tension force (PFSF) model, the evaluation of surface tension force in FESF model is based on an analytical approach rather than numerical approximations of spatial derivatives. Therefore, better numerical stability and higher accuracy can be expected. Various numerical examples are tested to validate the robustness of the proposed FESF model. It turns out that FESF model performs better than CSF model and PFSF model in terms of accuracy, stability, convergence speed and mass conservation. It is also shown in numerical tests that FESF model can effectively simulate problems with high density/viscosity ratio, high Reynolds number and severe topological interfacial changes.

Study on magnetic circuit of moving magnet linear compressor

NASA Astrophysics Data System (ADS)

Xia, Ming; Chen, Xiaoping; Chen, Jun

2015-05-01

The moving magnet linear compressors are very popular in the tactical miniature stirling cryocoolers. The magnetic circuit of LFC3600 moving magnet linear compressor, manufactured by Kunming institute of Physics, was studied in this study. Three methods of the analysis theory, numerical calculation and experiment study were applied in the analysis process. The calculated formula of magnetic reluctance and magnetomotive force were given in theoretical analysis model. The magnetic flux density and magnetic flux line were analyzed in numerical analysis model. A testing method was designed to test the magnetic flux density of the linear compressor. When the piston of the motor was in the equilibrium position, the value of the magnetic flux density was at the maximum of 0.27T. The results were almost equal to the ones from numerical analysis.

Modeling of nanoscale liquid mixture transport by density functional hydrodynamics

NASA Astrophysics Data System (ADS)

Dinariev, Oleg Yu.; Evseev, Nikolay V.

2017-06-01

Modeling of multiphase compositional hydrodynamics at nanoscale is performed by means of density functional hydrodynamics (DFH). DFH is the method based on density functional theory and continuum mechanics. This method has been developed by the authors over 20 years and used for modeling in various multiphase hydrodynamic applications. In this paper, DFH was further extended to encompass phenomena inherent in liquids at nanoscale. The new DFH extension is based on the introduction of external potentials for chemical components. These potentials are localized in the vicinity of solid surfaces and take account of the van der Waals forces. A set of numerical examples, including disjoining pressure, film precursors, anomalous rheology, liquid in contact with heterogeneous surface, capillary condensation, and forward and reverse osmosis, is presented to demonstrate modeling capabilities.

Effects of particle-fluid density ratio on the interactions between the turbulent channel flow and finite-size particles

NASA Astrophysics Data System (ADS)

Yu, Zhaosheng; Lin, Zhaowu; Shao, Xueming; Wang, Lian-Ping

2017-09-01

A parallel direct-forcing fictitious domain method is employed to perform fully resolved numerical simulations of turbulent channel flow laden with finite-size particles. The effects of the particle-fluid density ratio on the turbulence modulation in the channel flow are investigated at the friction Reynolds number of 180, the particle volume fraction of 0.84 % , and the particle-fluid density ratio ranging from 1 to 104.2. The results show that the variation of the flow drag with the particle-fluid density ratio is not monotonic, with a larger flow drag for the density ratio of 10.42, compared to those of unity and 104.2. A significant drag reduction by the particles is observed for large particle-fluid density ratios during the transient stage, but not at the statistically stationary stage. The intensity of particle velocity fluctuations generally decreases with increasing particle inertia, except that the particle streamwise root-mean-square velocity and streamwise-transverse velocity correlation in the near-wall region are largest at the density ratio of the order of 10. The averaged momentum equations are derived with the spatial averaging theorem and are used to analyze the mechanisms for the effects of the particles on the flow drag. The results indicate that the drag-reduction effect due to the decrease in the fluid Reynolds shear stress is counteracted by the drag-enhancement effect due to the increase in the total particle stress or the interphase drag force for the large particle-inertia case. The sum of the total Reynolds stress and particle inner stress contributions to the flow drag is largest at the density ratio of the order of 10, which is the reason for the largest flow drag at this density ratio. The interphase drag force obtained from the averaged momentum equation (the balance theory) is significantly smaller than (but agrees qualitatively with) that from the empirical drag formula based on the phase-averaged slip velocity for large density ratios. For the neutrally buoyant case, the balance theory predicts a positive interphase force on the particles arising from the negative gradient of the particle inner stress, which cannot be predicted by the drag formula based on the phase-averaged slip velocity. In addition, our results show that both particle collision and particle-turbulence interaction play roles in the formation of the inhomogeneous distribution of the particles at the density ratio of the order of 10.

Effects of particle-fluid density ratio on the interactions between the turbulent channel flow and finite-size particles.

PubMed

Yu, Zhaosheng; Lin, Zhaowu; Shao, Xueming; Wang, Lian-Ping

2017-09-01

A parallel direct-forcing fictitious domain method is employed to perform fully resolved numerical simulations of turbulent channel flow laden with finite-size particles. The effects of the particle-fluid density ratio on the turbulence modulation in the channel flow are investigated at the friction Reynolds number of 180, the particle volume fraction of 0.84%, and the particle-fluid density ratio ranging from 1 to 104.2. The results show that the variation of the flow drag with the particle-fluid density ratio is not monotonic, with a larger flow drag for the density ratio of 10.42, compared to those of unity and 104.2. A significant drag reduction by the particles is observed for large particle-fluid density ratios during the transient stage, but not at the statistically stationary stage. The intensity of particle velocity fluctuations generally decreases with increasing particle inertia, except that the particle streamwise root-mean-square velocity and streamwise-transverse velocity correlation in the near-wall region are largest at the density ratio of the order of 10. The averaged momentum equations are derived with the spatial averaging theorem and are used to analyze the mechanisms for the effects of the particles on the flow drag. The results indicate that the drag-reduction effect due to the decrease in the fluid Reynolds shear stress is counteracted by the drag-enhancement effect due to the increase in the total particle stress or the interphase drag force for the large particle-inertia case. The sum of the total Reynolds stress and particle inner stress contributions to the flow drag is largest at the density ratio of the order of 10, which is the reason for the largest flow drag at this density ratio. The interphase drag force obtained from the averaged momentum equation (the balance theory) is significantly smaller than (but agrees qualitatively with) that from the empirical drag formula based on the phase-averaged slip velocity for large density ratios. For the neutrally buoyant case, the balance theory predicts a positive interphase force on the particles arising from the negative gradient of the particle inner stress, which cannot be predicted by the drag formula based on the phase-averaged slip velocity. In addition, our results show that both particle collision and particle-turbulence interaction play roles in the formation of the inhomogeneous distribution of the particles at the density ratio of the order of 10.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Nonequilibrium forces following quenches in active and thermal matter.

PubMed

Rohwer, Christian M; Solon, Alexandre; Kardar, Mehran; Krüger, Matthias

2018-03-01

Nonequilibrium systems with conserved quantities like density or momentum are known to exhibit long-ranged correlations. This, in turn, leads to long-ranged fluctuation-induced (Casimir) forces, predicted to arise in a variety of nonequilibrium settings. Here, we study such forces, which arise transiently between parallel plates or compact inclusions in a gas of particles, following a change ("quench") in temperature or activity of the medium. Analytical calculations, as well as numerical simulations of passive or active Brownian particles, indicate two distinct forces: (i) The immediate effect of the quench is adsorption or desorption of particles of the medium to the immersed objects, which in turn initiates a front of relaxing (mean) density. This leads to time-dependent density-induced forces. (ii) A long-term effect of the quench is that density fluctuations are modified, manifested as transient (long-ranged) (pair-)correlations that relax diffusively to their (short-ranged) steady-state limit. As a result, transient fluctuation-induced forces emerge. We discuss the properties of fluctuation-induced and density-induced forces as regards universality, relaxation as a function of time, and scaling with distance between objects. Their distinct signatures allow us to distinguish the two types of forces in simulation data. Our simulations also show that a quench of the effective temperature of an active medium gives rise to qualitatively similar effects to a temperature quench in a passive medium. Based on this insight, we propose several scenarios for the experimental observation of the forces described here.

Nonequilibrium forces following quenches in active and thermal matter

NASA Astrophysics Data System (ADS)

Rohwer, Christian M.; Solon, Alexandre; Kardar, Mehran; Krüger, Matthias

2018-03-01

Nonequilibrium systems with conserved quantities like density or momentum are known to exhibit long-ranged correlations. This, in turn, leads to long-ranged fluctuation-induced (Casimir) forces, predicted to arise in a variety of nonequilibrium settings. Here, we study such forces, which arise transiently between parallel plates or compact inclusions in a gas of particles, following a change ("quench") in temperature or activity of the medium. Analytical calculations, as well as numerical simulations of passive or active Brownian particles, indicate two distinct forces: (i) The immediate effect of the quench is adsorption or desorption of particles of the medium to the immersed objects, which in turn initiates a front of relaxing (mean) density. This leads to time-dependent density-induced forces. (ii) A long-term effect of the quench is that density fluctuations are modified, manifested as transient (long-ranged) (pair-)correlations that relax diffusively to their (short-ranged) steady-state limit. As a result, transient fluctuation-induced forces emerge. We discuss the properties of fluctuation-induced and density-induced forces as regards universality, relaxation as a function of time, and scaling with distance between objects. Their distinct signatures allow us to distinguish the two types of forces in simulation data. Our simulations also show that a quench of the effective temperature of an active medium gives rise to qualitatively similar effects to a temperature quench in a passive medium. Based on this insight, we propose several scenarios for the experimental observation of the forces described here.

Hierarchical optimization for neutron scattering problems

DOE PAGES

Bao, Feng; Archibald, Rick; Bansal, Dipanshu; ...

2016-03-14

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Hierarchical optimization for neutron scattering problems

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

Bao, Feng; Archibald, Rick; Bansal, Dipanshu

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Calculating Free Energies Using Average Force

NASA Technical Reports Server (NTRS)

Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

Comparative study of methods to calibrate the stiffness of a single-beam gradient-force optical tweezers over various laser trapping powers

PubMed Central

Sarshar, Mohammad; Wong, Winson T.; Anvari, Bahman

2014-01-01

Abstract. Optical tweezers have become an important instrument in force measurements associated with various physical, biological, and biophysical phenomena. Quantitative use of optical tweezers relies on accurate calibration of the stiffness of the optical trap. Using the same optical tweezers platform operating at 1064 nm and beads with two different diameters, we present a comparative study of viscous drag force, equipartition theorem, Boltzmann statistics, and power spectral density (PSD) as methods in calibrating the stiffness of a single beam gradient force optical trap at trapping laser powers in the range of 0.05 to 1.38 W at the focal plane. The equipartition theorem and Boltzmann statistic methods demonstrate a linear stiffness with trapping laser powers up to 355 mW, when used in conjunction with video position sensing means. The PSD of a trapped particle’s Brownian motion or measurements of the particle displacement against known viscous drag forces can be reliably used for stiffness calibration of an optical trap over a greater range of trapping laser powers. Viscous drag stiffness calibration method produces results relevant to applications where trapped particle undergoes large displacements, and at a given position sensing resolution, can be used for stiffness calibration at higher trapping laser powers than the PSD method. PMID:25375348

Nanosecond pulsed electric field induced changes in cell surface charge density.

PubMed

Dutta, Diganta; Palmer, Xavier-Lewis; Asmar, Anthony; Stacey, Michael; Qian, Shizhi

2017-09-01

This study reports that the surface charge density changes in Jurkat cells with the application of single 60 nanosecond pulse electric fields, using atomic force microscopy. Using an atomic force microscope tip and Jurkat cells on silica in a 0.01M KCl ionic concentration, we were able to measure the interfacial forces, while also predicting surface charge densities of both Jurkat cell and silica surfaces. The most important finding is that the pulsing conditions varyingly reduced the cells' surface charge density. This offers a novel way in which to examine cellular effects of pulsed electric fields that may lead to the identification of unique mechanical responses. Compared to a single low field strength NsPEF (15kV/cm) application, exposure of Jurkat cells to a single high field strength NsPEF (60kV/cm) resulted in a further reduction in charge density and major morphological changes. The structural, physical, and chemical properties of biological cells immensely influence their electrostatic force; we were able to investigate this through the use of atomic force microscopy by measuring the surface forces between the AFM's tip and the Jurkat cells under different pulsing conditions as well as the interfacial forces in ionic concentrations. Copyright © 2017 Elsevier Ltd. All rights reserved.

An efficient and economical way to enhance the performance of present HTS Maglev systems by utilizing the anisotropy property of bulk superconductors

NASA Astrophysics Data System (ADS)

Deng, Zigang; Wang, Jiasu; Zheng, Jun; Zhang, Ya; Wang, Suyu

2013-02-01

We report a simple, efficient and economical way to enhance the levitation or guidance performance of present high-temperature superconducting (HTS) Maglev systems by exploring the anisotropic properties of the critical current density in the a-b plane and along the c-axis of bulk superconductors. In the method, the bulk laying mode with different c-axis directions is designed to match with the magnetic field configuration of the applied permanent magnet guideway (PMG). Experimental results indicate that more than a factor of two improvement in the levitation force or guidance force is achieved when changing the laying mode of bulk superconductors from the traditional fashion of keeping the c-axis vertical to the PMG surface to the studied one of keeping the c-axis parallel to the PMG surface, at the maximum horizontal and vertical magnetic field positions of the PMG, respectively. These phenomena resulted from the physical nature of the generated levitation force and guidance force (electromagnetic forces) and the fact that there are different critical current densities in the a-b plane and along the c axis. Based on the experimental results, new HTS Maglev systems can be designed to meet the requirements of practical heavy-load or curved-route applications.

Acoustic particle separation

NASA Technical Reports Server (NTRS)

Barmatz, M. B.; Stoneburner, J. D.; Jacobi, N.; Wang, T. (Inventor)

1985-01-01

A method is described which uses acoustic energy to separate particles of different sizes, densities, or the like. The method includes applying acoustic energy resonant to a chamber containing a liquid of gaseous medium to set up a standing wave pattern that includes a force potential well wherein particles within the well are urged towards the center, or position of minimum force potential. A group of particles to be separated is placed in the chamber, while a non-acoustic force such as gravity is applied, so that the particles separate with the larger or denser particles moving away from the center of the well to a position near its edge and progressively smaller lighter particles moving progressively closer to the center of the well. Particles are removed from different positions within the well, so that particles are separated according to the positions they occupy in the well.

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

PubMed

Szalewicz, Krzysztof

2014-11-18

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

A Lagrangian discontinuous Galerkin hydrodynamic method

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

Liu, Xiaodong; Morgan, Nathaniel Ray; Burton, Donald E.

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for solving the two-dimensional gas dynamic equations on unstructured hybrid meshes. The physical conservation laws for the momentum and total energy are discretized using a DG method based on linear Taylor expansions. Three different approaches are investigated for calculating the density variation over the element. The first approach evolves a Taylor expansion of the specific volume field. The second approach follows certain finite element methods and uses the strong mass conservation to calculate the density field at a location inside the element or on the element surface. The thirdmore » approach evolves a Taylor expansion of the density field. The nodal velocity, and the corresponding forces, are explicitly calculated by solving a multidirectional approximate Riemann problem. An effective limiting strategy is presented that ensures monotonicity of the primitive variables. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. Results from a suite of test problems are presented to demonstrate the robustness and expected second-order accuracy of this new method.« less

A Lagrangian discontinuous Galerkin hydrodynamic method

DOE PAGES

Liu, Xiaodong; Morgan, Nathaniel Ray; Burton, Donald E.

2017-12-11

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for solving the two-dimensional gas dynamic equations on unstructured hybrid meshes. The physical conservation laws for the momentum and total energy are discretized using a DG method based on linear Taylor expansions. Three different approaches are investigated for calculating the density variation over the element. The first approach evolves a Taylor expansion of the specific volume field. The second approach follows certain finite element methods and uses the strong mass conservation to calculate the density field at a location inside the element or on the element surface. The thirdmore » approach evolves a Taylor expansion of the density field. The nodal velocity, and the corresponding forces, are explicitly calculated by solving a multidirectional approximate Riemann problem. An effective limiting strategy is presented that ensures monotonicity of the primitive variables. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. Results from a suite of test problems are presented to demonstrate the robustness and expected second-order accuracy of this new method.« less

Comparison of accelerometer data calibration methods used in thermospheric neutral density estimation

NASA Astrophysics Data System (ADS)

Vielberg, Kristin; Forootan, Ehsan; Lück, Christina; Löcher, Anno; Kusche, Jürgen; Börger, Klaus

2018-05-01

Ultra-sensitive space-borne accelerometers on board of low Earth orbit (LEO) satellites are used to measure non-gravitational forces acting on the surface of these satellites. These forces consist of the Earth radiation pressure, the solar radiation pressure and the atmospheric drag, where the first two are caused by the radiation emitted from the Earth and the Sun, respectively, and the latter is related to the thermospheric density. On-board accelerometer measurements contain systematic errors, which need to be mitigated by applying a calibration before their use in gravity recovery or thermospheric neutral density estimations. Therefore, we improve, apply and compare three calibration procedures: (1) a multi-step numerical estimation approach, which is based on the numerical differentiation of the kinematic orbits of LEO satellites; (2) a calibration of accelerometer observations within the dynamic precise orbit determination procedure and (3) a comparison of observed to modeled forces acting on the surface of LEO satellites. Here, accelerometer measurements obtained by the Gravity Recovery And Climate Experiment (GRACE) are used. Time series of bias and scale factor derived from the three calibration procedures are found to be different in timescales of a few days to months. Results are more similar (statistically significant) when considering longer timescales, from which the results of approach (1) and (2) show better agreement to those of approach (3) during medium and high solar activity. Calibrated accelerometer observations are then applied to estimate thermospheric neutral densities. Differences between accelerometer-based density estimations and those from empirical neutral density models, e.g., NRLMSISE-00, are observed to be significant during quiet periods, on average 22 % of the simulated densities (during low solar activity), and up to 28 % during high solar activity. Therefore, daily corrections are estimated for neutral densities derived from NRLMSISE-00. Our results indicate that these corrections improve model-based density simulations in order to provide density estimates at locations outside the vicinity of the GRACE satellites, in particular during the period of high solar/magnetic activity, e.g., during the St. Patrick's Day storm on 17 March 2015.

Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory

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

Ghosh, Swarnava; Suryanarayana, Phanish, E-mail: phanish.suryanarayana@ce.gatech.edu

2016-02-15

We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we develop a generalized framework for performing OF-DFT simulations with different variants of the electronic kinetic energy. In particular, we propose a self-consistent field (SCF) type fixed-point method for calculations involving linear-response kinetic energy functionals. In this framework, evaluation of both the electronic ground-state and forces on the nuclei are amenable to computations that scale linearly with the number of atoms. We develop a parallel implementation of this formulation using the finite-difference discretization.more » We demonstrate that higher-order finite-differences can achieve relatively large convergence rates with respect to mesh-size in both the energies and forces. Additionally, we establish that the fixed-point iteration converges rapidly, and that it can be further accelerated using extrapolation techniques like Anderson's mixing. We validate the accuracy of the results by comparing the energies and forces with plane-wave methods for selected examples, including the vacancy formation energy in Aluminum. Overall, the suitability of the proposed formulation for scalable high performance computing makes it an attractive choice for large-scale OF-DFT calculations consisting of thousands of atoms.« less

Physical Activity and Bone Density in Women

NASA Technical Reports Server (NTRS)

Bowley, Susan M.; Whalen, R. T.

2000-01-01

A mathematical model of bone density regulation as a function of the daily tissue "effective" stress has been derived. Using the model, the influence of daily activity in the form of a daily loading history has been related to bone density of the calcaneus. The theory incorporates a stress exponent m to account for differences in the importance of magnitude and number of load cycles experienced during daily activity. We have derived a parameter from the model, the "Bone Density Index" (BDI). We have developed a method of collecting daily habitual loading histories using an insole force sensor interfaced to a portable digital data logger carried in a fanny pack. Our goal for this study was to determine a stress exponent, m, relating GRFz history to Calcaneal Bone Mineral Density (CBMD).

Thermal nanostructure: An order parameter multiscale ensemble approach

NASA Astrophysics Data System (ADS)

Cheluvaraja, S.; Ortoleva, P.

2010-02-01

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

Optimizing Cubature for Efficient Integration of Subspace Deformations

PubMed Central

An, Steven S.; Kim, Theodore; James, Doug L.

2009-01-01

We propose an efficient scheme for evaluating nonlinear subspace forces (and Jacobians) associated with subspace deformations. The core problem we address is efficient integration of the subspace force density over the 3D spatial domain. Similar to Gaussian quadrature schemes that efficiently integrate functions that lie in particular polynomial subspaces, we propose cubature schemes (multi-dimensional quadrature) optimized for efficient integration of force densities associated with particular subspace deformations, particular materials, and particular geometric domains. We support generic subspace deformation kinematics, and nonlinear hyperelastic materials. For an r-dimensional deformation subspace with O(r) cubature points, our method is able to evaluate subspace forces at O(r2) cost. We also describe composite cubature rules for runtime error estimation. Results are provided for various subspace deformation models, several hyperelastic materials (St.Venant-Kirchhoff, Mooney-Rivlin, Arruda-Boyce), and multimodal (graphics, haptics, sound) applications. We show dramatically better efficiency than traditional Monte Carlo integration. CR Categories: I.6.8 [Simulation and Modeling]: Types of Simulation—Animation, I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—Physically based modeling G.1.4 [Mathematics of Computing]: Numerical Analysis—Quadrature and Numerical Differentiation PMID:19956777

Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy

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

Lyapunova, Elena, E-mail: lyapunova@icmm.ru; Ural Federal University, Kuibyishev Str. 48, Ekaterinburg, 620000; Nikituk, Alexander, E-mail: nas@icmm.ru

Mechanical properties of living cancer and normal thyroidal cells were investigated by atomic force microscopy (AFM). Cell mechanics was compared before and after treatment with ML7, which is known to reduce myosin activity and induce softening of cell structures. We recorded force curves with extended dwell time of 6 seconds in contact at maximum forces from 500 pN to 1 nN. Data were analyzed within different frameworks: Hertz fit was applied in order to evaluate differences in Young’s moduli among cell types and conditions, while the fluctuations of the cantilever in contact with cells were analyzed with both conventional algorithmsmore » (probability density function and power spectral density) and multifractal detrended fluctuation analysis (MF-DFA). We found that cancer cells were softer than normal cells and ML7 had a substantial softening effect on normal cells, but only a marginal one on cancer cells. Moreover, we observed that all recorded signals for normal and cancer cells were monofractal with small differences between their scaling parameters. Finally, the applicability of wavelet-based methods of data analysis for the discrimination of different cell types is discussed.« less

Dynamics of an acoustically levitated particle using the lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Barrios, G.; Rechtman, R.

When the acoustic force inside a cavity balances the gravitational force on a particle the result is known as acoustic levitation. Using the lattice Boltzmann equation method we find the acoustic force acting on a rounded particle for two different single-axis acoustic levitators in two dimensions, the first with plane waves, the second with a rounded reflector that enhances the acoustic force. With no gravitational force, a particle oscillates around a pressure node; in the presence of gravity the oscillation is shifted a small vertical distance below the pressure node. This distance increases linearly as the density ratio between the solid particle and fluid grows. For both cavities, the particle oscillates with the frequency of the sound source and its harmonics and in some cases there is a much smaller second dominant frequency. When the momentum of the acoustic source changes, the oscillation around the average vertical position can have both frequencies mentioned above. However, if this quantity is large enough, the oscillations of the particle are aperiodic in the cavity with a rounded reflector.

On mapping subangstrom electron clouds with force microscopy.

PubMed

Wright, C Alan; Solares, Santiago D

2011-11-09

In 2004 Hembacher et al. (Science 2004, 305, 380-383) reported simultaneous higher-harmonics atomic force mocroscopy (AFM)/scanning tunneling microscopy (STM) images acquired while scanning a graphite surface with a tungsten tip. They interpreted the observed subatomic features in the AFM images as the signature of lobes of increased electron density at the tungsten tip apex. Although these intriguing images have stirred controversy, an in-depth theoretical feasibility study has not yet been produced. Here we report on the development of a method for simulating higher harmonics AFM images and its application to the same system. Our calculations suggest that four lobes of increased electron density are expected to be present at a W(001) tip apex atom and that the corresponding higher harmonics AFM images of graphite can exhibit 4-fold symmetry features. Despite these promising results, open questions remain since the calculated amplitudes of the higher harmonics generated by the short-range forces are on the order of hundredths of picometers, leading to very small corrugations in the theoretical images. Additionally, the complex, intermittent nature of the tip-sample interaction, which causes constant readjustment of the tip and sample orbitals as the tip approaches and retracts from the surface, prevents a direct quantitative connection between the electron density and the AFM image features.

Development of a united-atom force field for 1-ethyl-3-methylimidazolium tetracyanoborate ionic liquid

NASA Astrophysics Data System (ADS)

Koller, Thomas; Ramos, Javier; Garrido, Nuno M.; Fröba, Andreas P.; Economou, Ioannis G.

2012-06-01

Three united-atom (UA) force fields are presented for the ionic liquid 1-ethyl-3-methylimidazolium tetracyanoborate, abbreviated as [EMIM]+[B(CN)4]-. The atomistic charges were calculated based on the restrained electrostatic potential (RESP) of the isolated ions (abbreviated as force field 1, FF-1) and the ensemble averaged RESP (EA-RESP) method from the most stable ion pair configurations obtained by MP2/6-31G*+ calculations (abbreviated as FF-2 and FF-3). Non-electrostatic parameters for both ions were taken from the literature and Lennard-Jones parameters for the [B(CN)4]- anion were fitted in two different ways to reproduce the experimental liquid density. Molecular dynamics (MD) simulations were performed over a wide temperature range to identify the effect of the electrostatic and non-electrostatic potential on the liquid density and on transport properties such as self-diffusion coefficient and viscosity. Predicted liquid densities for the three parameter sets deviate less than 0.5% from experimental data. The molecular mobility with FF-2 and FF-3 using reduced charge sets is appreciably faster than that obtained with FF-1. FF-3 presents a refined non-electrostatic potential that leads to a notable improvement in both transport properties when compared to experimental data.

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

Pratapa, Phanisri P.; Suryanarayana, Phanish; Pask, John E.

We present the Clenshaw–Curtis Spectral Quadrature (SQ) method for real-space O(N) Density Functional Theory (DFT) calculations. In this approach, all quantities of interest are expressed as bilinear forms or sums over bilinear forms, which are then approximated by spatially localized Clenshaw–Curtis quadrature rules. This technique is identically applicable to both insulating and metallic systems, and in conjunction with local reformulation of the electrostatics, enables the O(N) evaluation of the electronic density, energy, and atomic forces. The SQ approach also permits infinite-cell calculations without recourse to Brillouin zone integration or large supercells. We employ a finite difference representation in order tomore » exploit the locality of electronic interactions in real space, enable systematic convergence, and facilitate large-scale parallel implementation. In particular, we derive expressions for the electronic density, total energy, and atomic forces that can be evaluated in O(N) operations. We demonstrate the systematic convergence of energies and forces with respect to quadrature order as well as truncation radius to the exact diagonalization result. In addition, we show convergence with respect to mesh size to established O(N 3) planewave results. In conclusion, we establish the efficiency of the proposed approach for high temperature calculations and discuss its particular suitability for large-scale parallel computation.« less

A three-dimensional finite element evaluation of magnetic attachment attractive force and the influence of the magnetic circuit.

PubMed

Kumano, Hirokazu; Nakamura, Yoshinori; Kanbara, Ryo; Takada, Yukyo; Ochiai, Kent T; Tanaka, Yoshinobu

2014-01-01

The finite element method has been considered to be excellent evaluative technique to study magnetic circuit optimization. The present study analyzed and quantitatively evaluated the different effects of magnetic circuit on attractive force and magnetic flux density using a three-dimensional finite element method for comparative evaluation. The diameter of a non-magnetic material in the shield disk of a magnetic assembly was variably increased by 0.1 mm to a maximum 2.0 mm in this study design. The analysis results demonstrate that attractive force increases until the diameter of the non-magnetic spacing material reaches a diameter of 0.5 mm where it peaks and then decreases as the overall diameter increases over 0.5 mm. The present analysis suggested that the attractive force for a magnetic attachment is optimized with an appropriate magnetic assembly shield disk diameter using a non-magnetic material to effectively change the magnetic circuit efficiency and resulting retention.

Novel permanent magnet linear motor with isolated movers: analytical, numerical and experimental study.

PubMed

Yan, Liang; Peng, Juanjuan; Jiao, Zongxia; Chen, Chin-Yin; Chen, I-Ming

2014-10-01

This paper proposes a novel permanent magnet linear motor possessing two movers and one stator. The two movers are isolated and can interact with the stator poles to generate independent forces and motions. Compared with conventional multiple motor driving system, it helps to increase the system compactness, and thus improve the power density and working efficiency. The magnetic field distribution is obtained by using equivalent magnetic circuit method. Following that, the formulation of force output considering armature reaction is carried out. Then inductances are analyzed with finite element method to investigate the relationships of the two movers. It is found that the mutual-inductances are nearly equal to zero, and thus the interaction between the two movers is negligible. A research prototype of the linear motor and a measurement apparatus on thrust force have been developed. Both numerical computation and experiment measurement are conducted to validate the analytical model of thrust force. Comparison shows that the analytical model matches the numerical and experimental results well.

Maltodextrin-powered enzymatic fuel cell through a non-natural enzymatic pathway

NASA Astrophysics Data System (ADS)

Zhu, Zhiguang; Wang, Yiran; Minteer, Shelley D.; Percival Zhang, Y.-H.

Enzymatic fuel cells (EFCs) use a variety of fuels to generate electricity through oxidoreductase enzymes, such as oxidases or dehydrogenases, as catalysts on electrodes. We have developed a novel synthetic enzymatic pathway containing two free enzymes (maltodextrin phosphorylase and phosphoglucomutase) and one immobilized glucose-6-phosphate dehydrogenase that can utilize an oligomeric substrate maltodextrin for producing electrons mediated via a diaphorase and vitamin K 3 electron shuttle system. Three different enzyme immobilization approaches were compared based on electrostatic force entrapment, chemical cross-linking, and cross-linking with the aid of carbon nanotubes. At 10 mM glucose-6-phosphate (G6P) as a substrate concentration, the maximum power density of 0.06 mW cm -2 and retaining 42% of power output after 11 days were obtained through the method of chemical cross-linking with carbon nanotubes, approximately 6-fold and 3.5-fold better than those of the electrostatic force-based method, respectively. When changed to maltodextrin (degree of polymerization = 19) as the substrate, the EFC achieved a maximum power density of 0.085 mW cm -2. With the advantages of stable, low cost, high energy density, non-inhibitor to enzymes, and environmental friendly, maltodextrin is suggested to be an ideal fuel to power enzymatic fuel cells.

Density measurements of the lithium fluoride/lithium sulfide eutectic at high temperature

NASA Astrophysics Data System (ADS)

Lloyd, Charles L.; Gilbert, James B.

1994-10-01

A straightforward and reliable method to determine densities of molten salts at high temperatures was de-veloped by Janz and Lorenz several years ago.[1] This method was followed in order to determine the density of the LiF/Li2S eutectic[2] over the temperature range of 1176 to 1355 K in which the eutectic is liquid. The rel-ative lack of data for this eutectic is surprising given its potential usefulness in the study of advanced batteries'31 and electrowinning of metals from molten sulfides.[41] The method is based on the fact that a solid piece of metal of known volume suspended from a pan balance into a molten salt will weigh less than if it were sus-pended in air at the same temperature. This difference in weight measured in grams will be equal to the buoyant force of the liquid at that temperature. The density of the salt bath can then readily be determined by dividing this difference by the volume of the solid piece of metal that is immersed in the bath. The procedure can be re-peated to give density values over a range of temperatures.

High-resolution gamma ray attenuation density measurements on mining exploration drill cores, including cut cores

NASA Astrophysics Data System (ADS)

Ross, P.-S.; Bourke, A.

2017-01-01

Physical property measurements are increasingly important in mining exploration. For density determinations on rocks, one method applicable on exploration drill cores relies on gamma ray attenuation. This non-destructive method is ideal because each measurement takes only 10 s, making it suitable for high-resolution logging. However calibration has been problematic. In this paper we present new empirical, site-specific correction equations for whole NQ and BQ cores. The corrections force back the gamma densities to the "true" values established by the immersion method. For the NQ core caliber, the density range extends to high values (massive pyrite, 5 g/cm3) and the correction is thought to be very robust. We also present additional empirical correction factors for cut cores which take into account the missing material. These "cut core correction factors", which are not site-specific, were established by making gamma density measurements on truncated aluminum cylinders of various residual thicknesses. Finally we show two examples of application for the Abitibi Greenstone Belt in Canada. The gamma ray attenuation measurement system is part of a multi-sensor core logger which also determines magnetic susceptibility, geochemistry and mineralogy on rock cores, and performs line-scan imaging.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Pondermotive versus mirror force in creation of the filamentary cavities in auroral plasma

NASA Technical Reports Server (NTRS)

Singh, Nagendra

1994-01-01

Recently rocket observations on spikelets of lower-hybrid waves along with strong density cavities and transversely heated ions were reported. The observed thin filamentary cavities oriented along the magnetic field in the auroral plasma have density depletions up to several tens of percent. These observations have been interpreted in terms of a theory for lower-hybrid wave condensation and collapse. The modulational instability leading to the wave consensation of the lower-hybrid waves yields only weak density perturbations, which cannot explain the above strong density depletions. The wave collapse theory is based on the nonlinear pondermotive force in a homogeneous ambient plasma and the density depletion is determined by the balance between the wave pressure (pondermotive force) and the plasma pressure. In the auroral plasma, the balance is achieved in a time tau(sub wc) equal to or less than 1 ms. It is shown here that the mirror force, acting on the transversely heated ions at a relatively long time scale, is an effective mechanism for creating the strong plasma cavities. We suggest that the process of wave condensation, through the pondermotive force causing generation of short wavelength waves from relatively long wavelength waves, is a dominant process until the former waves evolve and become effective in the transverse heating of ions. As soon as this happens, mirror force on ions becomes an important factor in the creation of the density cavities, which may further trap and enhance the waves. Results from a model of cavity formation by transverse ion heating show that the observed depletions in the density cavities can be produced by the heating rates determined by the observed wave amplitudes near the lower-hybrid frequency. It is found that the creation of a strong density cavity takes a few minutes.

Thermospheric density estimation from SLR observations of LEO satellites - A case study with the ANDE-Pollux satellite

NASA Astrophysics Data System (ADS)

Blossfeld, M.; Schmidt, M.; Erdogan, E.

2016-12-01

The thermospheric neutral density plays a crucial role within the equation of motion of Earth orbiting objects since drag, lift or side forces are one of the largest non-gravitational perturbations acting on the satellite. Precise Orbit Determination (POD) methods can be used to estimate thermospheric density variations from measured orbit determinations. One method which provides highly accurate measurements of the satellite position is Satellite Laser Ranging (SLR). Within the POD process, scaling factors are estimated frequently. These scaling factors can be either used for the scaling of the so called satellite-specific drag (ballistic) coefficients or the integrated thermospheric neutral density. We present a method for analytically model the drag coefficient based on a couple of physical assumptions and key parameters. In this paper, we investigate the possibility to use SLR observations to the very low Earth orbiting satellite ANDE-Pollux (approximately at 350km altitude) to determine scaling factors for different a priori thermospheric density models. We perform a POD for ANDE-Pollux covering 49 days between August 2009 and September 2009 which means the time span containing the largest number of observations during the short lifetime of the satellite. Finally, we compare the obtained scaled thermospheric densities w.r.t. each other

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

Magneto-motive detection of tissue-based macrophages by differential phase optical coherence tomography.

PubMed

Oh, Junghwan; Feldman, Marc D; Kim, Jihoon; Kang, Hyun Wook; Sanghi, Pramod; Milner, Thomas E

2007-03-01

A novel method to detect tissue-based macrophages using a combination of superparamagnetic iron oxide (SPIO) nanoparticles and differential phase optical coherence tomography (DP-OCT) with an external oscillating magnetic field is reported. Magnetic force acting on iron-laden tissue-based macrophages was varied by applying a sinusoidal current to a solenoid containing a conical iron core that substantially focused and increased magnetic flux density. Nanoparticle motion was detected with DP-OCT, which can detect tissue movement with nanometer resolution. Frequency response of iron-laden tissue movement was twice the modulation frequency since the magnetic force is proportional to the product of magnetic flux density and gradient. Results of our experiments indicate that DP-OCT can be used to identify tissue-based macrophage when excited by an external focused oscillating magnetic field. (c) 2007 Wiley-Liss, Inc

Simulation of IR and Raman spectra of p-hydroxyanisole and p-nitroanisole based on scaled DFT force fields and their vibrational assignments.

PubMed

Krishnakumar, V; Prabavathi, N

2009-09-15

This work deals with the vibrational spectroscopy of p-hydroxyanisole (PHA) and p-nitroanisole (PNA) by means of quantum chemical calculations. The mid and far FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* method and basis set combination and were scaled using various scale factors which yield a good agreement between observed and calculated frequencies. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The results of the calculations were applied to simulate infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra.

Weighing the galactic disc using the Jeans equation: lessons from simulations

NASA Astrophysics Data System (ADS)

Candlish, G. N.; Smith, R.; Moni Bidin, C.; Gibson, B. K.

2016-03-01

Using three-dimensional stellar kinematic data from simulated galaxies, we examine the efficacy of a Jeans equation analysis in reconstructing the total disk surface density, including the dark matter, at the `Solar' radius. Our simulation data set includes galaxies formed in a cosmological context using state-of-the-art high-resolution cosmological zoom simulations, and other idealized models. The cosmologically formed galaxies have been demonstrated to lie on many of the observed scaling relations for late-type spirals, and thus offer an interesting surrogate for real galaxies with the obvious advantage that all the kinematical data are known perfectly. We show that the vertical velocity dispersion is typically the dominant kinematic quantity in the analysis, and that the traditional method of using only the vertical force is reasonably effective at low heights above the disk plane. At higher heights the inclusion of the radial force becomes increasingly important. We also show that the method is sensitive to uncertainties in the measured disk parameters, particularly the scalelengths of the assumed double exponential density distribution, and the scalelength of the radial velocity dispersion. In addition, we show that disk structure and low number statistics can lead to significant errors in the calculated surface densities. Finally, we examine the implications of our results for previous studies of this sort, suggesting that more accurate measurements of the scalelengths may help reconcile conflicting estimates of the local dark matter density in the literature.

Pleural pressure theory revisited: a role for capillary equilibrium

PubMed Central

Caruana-Gauci, Roberto; Manche, Alexander; Gauci, Marilyn; Chetcuti, Stanley; Bertolaccini, Luca

2017-01-01

Background Theories elucidating pleural pressures should explain all observations including the equal and opposite recoil of the chest wall and lungs, the less than expected pleural hydrostatic gradient and its variation at lobar margins, why pleural pressures are negative and how pleural fluid circulation functions. Methods A theoretical model describing equilibrium between buoyancy, hydrostatic forces, and capillary forces is proposed. The capillary equilibrium model described depends on control of pleural fluid volume and protein content, powered by an active pleural pump. Results The interaction between buoyancy forces, hydrostatic pressure and capillary pressure was calculated, and values for pleural thickness and pressure were determined using values for surface tension, contact angle, pleural fluid and lung densities found in the literature. Modelling can explain the issue of the differing hydrostatic vertical pleural pressure gradient at the lobar margins for buoyancy forces between the pleural fluid and the lung floating in the pleural fluid according to Archimedes’ hydrostatic paradox. The capillary equilibrium model satisfies all salient requirements for a pleural pressure model, with negative pressures maximal at the apex, equal and opposite forces in the lung and chest wall, and circulatory pump action. Conclusions This model predicts that pleural effusions cannot occur in emphysema unless concomitant heart failure increases lung density. This model also explains how the non-confluence of the lung with the chest wall (e.g., lobar margins) makes the pleural pressure more negative, and why pleural pressures would be higher after an upper lobectomy compared to a lower lobectomy. Pathological changes in pleural fluid composition and lung density alter the equilibrium between capillarity and buoyancy hydrostatic pressure to promote pleural effusion formation. PMID:28523153

Method using a density field for locating related items for data mining

DOEpatents

Wylie, Brian N.

2002-01-01

A method for locating related items in a geometric space transforms relationships among items to geometric locations. The method locates items in the geometric space so that the distance between items corresponds to the degree of relatedness. The method facilitates communication of the structure of the relationships among the items. The method makes use of numeric values as a measure of similarity between each pairing of items. The items are given initial coordinates in the space. An energy is then determined for each item from the item's distance and similarity to other items, and from the density of items assigned coordinates near the item. The distance and similarity component can act to draw items with high similarities close together, while the density component can act to force all items apart. If a terminal condition is not yet reached, then new coordinates can be determined for one or more items, and the energy determination repeated. The iteration can terminate, for example, when the total energy reaches a threshold, when each item's energy is below a threshold, after a certain amount of time or iterations.

The topology of the Coulomb potential density. A comparison with the electron density, the virial energy density, and the Ehrenfest force density.

PubMed

Ferreira, Lizé-Mari; Eaby, Alan; Dillen, Jan

2017-12-15

The topology of the Coulomb potential density has been studied within the context of the theory of Atoms in Molecules and has been compared with the topologies of the electron density, the virial energy density and the Ehrenfest force density. The Coulomb potential density is found to be mainly structurally homeomorphic with the electron density. The Coulomb potential density reproduces the non-nuclear attractor which is observed experimentally in the molecular graph of the electron density of a Mg dimer, thus, for the first time ever providing an alternative and energetic foundation for the existence of this critical point. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-01

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

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

PubMed

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-14

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

Energy Dissipation of Rayleigh Waves due to Absorption Along the Path by the Use of Finite Element Method

DTIC Science & Technology

1979-07-31

3 x 3 t Strain vector a ij,j Space derivative of the stress tensor Fi Force vector per unit volume o Density x CHAPTER III F Total force K Stiffness...matrix 6Vector displacements M Mass matrix B Space operating matrix DO Matrix moduli 2 x 3 DZ Operating matrix in Z direction N Matrix of shape...dissipating medium the deformation of a solid is a function of time, temperature and space . Creep phenomenon is a deformation process in which there is

Higher-Order Spectral Analysis of F-18 Flight Flutter Data

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Dunn, Shane

2005-01-01

Royal Australian Air Force (RAAF) F/A-18 flight flutter test data is presented and analyzed using various techniques. The data includes high-quality measurements of forced responses and limit cycle oscillation (LCO) phenomena. Standard correlation and power spectral density (PSD) techniques are applied to the data and presented. Novel applications of experimentally-identified impulse responses and higher-order spectral techniques are also applied to the data and presented. The goal of this research is to develop methods that can identify the onset of nonlinear aeroelastic phenomena, such as LCO, during flutter testing.

Contact inhibition of locomotion determines cell-cell and cell-substrate forces in tissues.

PubMed

Zimmermann, Juliane; Camley, Brian A; Rappel, Wouter-Jan; Levine, Herbert

2016-03-08

Cells organized in tissues exert forces on their neighbors and their environment. Those cellular forces determine tissue homeostasis as well as reorganization during embryonic development and wound healing. To understand how cellular forces are generated and how they can influence the tissue state, we develop a particle-based simulation model for adhesive cell clusters and monolayers. Cells are contractile, exert forces on their substrate and on each other, and interact through contact inhibition of locomotion (CIL), meaning that cell-cell contacts suppress force transduction to the substrate and propulsion forces align away from neighbors. Our model captures the traction force patterns of small clusters of nonmotile cells and larger sheets of motile Madin-Darby canine kidney (MDCK) cells. In agreement with observations in a spreading MDCK colony, the cell density in the center increases as cells divide and the tissue grows. A feedback between cell density, CIL, and cell-cell adhesion gives rise to a linear relationship between cell density and intercellular tensile stress and forces the tissue into a nonmotile state characterized by a broad distribution of traction forces. Our model also captures the experimentally observed tissue flow around circular obstacles, and CIL accounts for traction forces at the edge.

Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon

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

Desgranges, Caroline; Delhommelle, Jerome

We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term thatmore » favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%–15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.« less

ALARIC: An algorithm for constructing arbitrarily complex initial density distributions with low particle noise for SPH/SPMHD applications

NASA Astrophysics Data System (ADS)

Vela Vela, Luis; Sanchez, Raul; Geiger, Joachim

2018-03-01

A method is presented to obtain initial conditions for Smoothed Particle Hydrodynamic (SPH) scenarios where arbitrarily complex density distributions and low particle noise are needed. Our method, named ALARIC, tampers with the evolution of the internal variables to obtain a fast and efficient profile evolution towards the desired goal. The result has very low levels of particle noise and constitutes a perfect candidate to study the equilibrium and stability properties of SPH/SPMHD systems. The method uses the iso-thermal SPH equations to calculate hydrodynamical forces under the presence of an external fictitious potential and evolves them in time with a 2nd-order symplectic integrator. The proposed method generates tailored initial conditions that perform better in many cases than those based on purely crystalline lattices, since it prevents the appearance of anisotropies.

Advances in three-dimensional field analysis and evaluation of performance parameters of electrical machines

NASA Astrophysics Data System (ADS)

Sivasubramaniam, Kiruba

This thesis makes advances in three dimensional finite element analysis of electrical machines and the quantification of their parameters and performance. The principal objectives of the thesis are: (1)the development of a stable and accurate method of nonlinear three-dimensional field computation and application to electrical machinery and devices; and (2)improvement in the accuracy of determination of performance parameters, particularly forces and torque computed from finite elements. Contributions are made in two general areas: a more efficient formulation for three dimensional finite element analysis which saves time and improves accuracy, and new post-processing techniques to calculate flux density values from a given finite element solution. A novel three-dimensional magnetostatic solution based on a modified scalar potential method is implemented. This method has significant advantages over the traditional total scalar, reduced scalar or vector potential methods. The new method is applied to a 3D geometry of an iron core inductor and a permanent magnet motor. The results obtained are compared with those obtained from traditional methods, in terms of accuracy and speed of computation. A technique which has been observed to improve force computation in two dimensional analysis using a local solution of Laplace's equation in the airgap of machines is investigated and a similar method is implemented in the three dimensional analysis of electromagnetic devices. A new integral formulation to improve force calculation from a smoother flux-density profile is also explored and implemented. Comparisons are made and conclusions drawn as to how much improvement is obtained and at what cost. This thesis also demonstrates the use of finite element analysis to analyze torque ripples due to rotor eccentricity in permanent magnet BLDC motors. A new method for analyzing torque harmonics based on data obtained from a time stepping finite element analysis of the machine is explored and implemented.

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

Measurement of Cohesion in Asteroid Regolith Materials

NASA Technical Reports Server (NTRS)

Kleinhenz, Julie E.; Gaier, James R.; Waters, Deborah L.; Harvey, Ralph; Zeszut, Zoe; Carreno, Brandon; Shober, Patrick

2017-01-01

A study has been initiated to examine cohesive forces in asteroid materials to contribute to a better understanding of low density bodies such as asteroids and Phobos, and assist in exploration missions involving interaction with their surface material. The test specimen used in this study was a lightly weathered CM2 meteorite which is spectroscopically similar to Type C (carbonaceous) asteroids, and thought to have representative surface chemistry. To account for sample heterogeneity, adhesion forces were measured between the CM2 sample and its five primary mineral phase components. These adhesive forces bound the range of cohesive force that can be expected for the bulk material. All materials were characterized using a variety of optical and spectroscopic methods. Adhesive forces on the order of 50 to 400 µN were measured using a torsion balance in an ultrahigh vacuum chamber. The mineral samples exhibited clearly different adhesive strengths in the following hierarchy: Serpentine > Siderite > Bronzite > Olivine ˜ Fe-Ni.

Electrostatically frequency tunable micro-beam-based piezoelectric fluid flow energy harvester

NASA Astrophysics Data System (ADS)

Rezaee, Mousa; Sharafkhani, Naser

2017-07-01

This research investigates the dynamic behavior of a sandwich micro-beam based piezoelectric energy harvester with electrostatically adjustable resonance frequency. The system consists of a cantilever micro-beam immersed in a fluid domain and is subjected to the simultaneous action of cross fluid flow and nonlinear electrostatic force. Two parallel piezoelectric laminates are extended along the length of the micro-beam and connected to an external electric circuit which generates an output power as a result of the micro-beam oscillations. The fluid-coupled structure is modeled using Euler-Bernoulli beam theory and the equivalent force terms for the fluid flow. Fluid induced forces comprise the added inertia force which is evaluated using equivalent added mass and the drag and lift forces which are evaluated using relative velocity and Van der Pol equation. In addition to flow velocity and fluid density, the influence of several design parameters such as external electrical resistance, piezo layer position, and dc voltage on the generated power are investigated by using Galerkin and step by step linearization method. It is shown that for given flowing fluid parameters, i.e., density and velocity, one can adjust the applied dc voltage to tune resonance frequency so that the lock-in phenomenon with steady large amplitude oscillations happens, also by adjusting the harvester parameters including the mechanical and electrical ones, the maximal output power of the harvester becomes possible.

First-principles simulations of heat transport

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

2017-11-01

Advances in understanding heat transport in solids were recently reported by both experiment and theory. However an efficient and predictive quantum simulation framework to investigate thermal properties of solids, with the same complexity as classical simulations, has not yet been developed. Here we present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at close to equilibrium conditions, which only requires calculations of first-principles trajectories and atomic forces, thus avoiding direct computation of heat currents and energy densities. In addition the method requires much shorter sequential simulation times than ordinary molecular dynamics techniques, making it applicable within density functional theory. We discuss results for a representative oxide, MgO, at different temperatures and for ordered and nanostructured morphologies, showing the performance of the method in different conditions.

An effective purification method using large bottles for human pancreatic islet isolation

PubMed Central

Shimoda, Masayuki; Itoh, Takeshi; Iwahashi, Shuichi; Takita, Morihito; Sugimoto, Koji; Kanak, Mazhar A.; Chujo, Daisuke; Naziruddin, Bashoo; Levy, Marlon F.; Grayburn, Paul A.; Matsumoto, Shinichi

2012-01-01

The purification process is one of the most difficult procedures in pancreatic islet isolation. It was demonstrated that the standard purification method using a COBE 2991 cell processor with Ficoll density gradient solution harmed islets mechanically by high shear force. We reported that purification using large bottles with a lower viscosity gradient solution could improve the efficacy of porcine islet purification. In this study, we examined whether the new bottle purification method could improve the purification of human islets. Nine human pancreata from brain-dead donors were used. After pancreas digestion, the digested tissue was divided into three groups. Each group was purified by continuous density gradient using ET-Kyoto and iodixanol gradient solution with either the standard COBE method (COBE group) or the top loading (top group) or bottom loading (bottom group) bottle purification methods. Islet yield, purity, recovery rate after purification, and in vitro and in vivo viability were compared. Islet yield per pancreas weight (IE/g) and the recovery rate in the top group were significantly higher than in the COBE and bottom groups. Furthermore, the average size of purified islets in the top group was significantly larger than in the COBE group, which indicated that the bottle method could reduce the shear force to the islets. In vivo viability was also significantly higher in the top group compared with the COBE group. In conclusion, the top-loading bottle method could improve the quality and quantity of human islets after purification. PMID:23221740

Effects of visual cues of object density on perception and anticipatory control of dexterous manipulation.

PubMed

Crajé, Céline; Santello, Marco; Gordon, Andrew M

2013-01-01

Anticipatory force planning during grasping is based on visual cues about the object's physical properties and sensorimotor memories of previous actions with grasped objects. Vision can be used to estimate object mass based on the object size to identify and recall sensorimotor memories of previously manipulated objects. It is not known whether subjects can use density cues to identify the object's center of mass (CM) and create compensatory moments in an anticipatory fashion during initial object lifts to prevent tilt. We asked subjects (n = 8) to estimate CM location of visually symmetric objects of uniform densities (plastic or brass, symmetric CM) and non-uniform densities (mixture of plastic and brass, asymmetric CM). We then asked whether subjects can use density cues to scale fingertip forces when lifting the visually symmetric objects of uniform and non-uniform densities. Subjects were able to accurately estimate an object's center of mass based on visual density cues. When the mass distribution was uniform, subjects could scale their fingertip forces in an anticipatory fashion based on the estimation. However, despite their ability to explicitly estimate CM location when object density was non-uniform, subjects were unable to scale their fingertip forces to create a compensatory moment and prevent tilt on initial lifts. Hefting object parts in the hand before the experiment did not affect this ability. This suggests a dichotomy between the ability to accurately identify the object's CM location for objects with non-uniform density cues and the ability to utilize this information to correctly scale their fingertip forces. These results are discussed in the context of possible neural mechanisms underlying sensorimotor integration linking visual cues and anticipatory control of grasping.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

2017-06-01

Atomistic modeling of chemistry at extreme conditions remains a challenge, despite continuing advances in computing resources and simulation tools. While first principles methods provide a powerful predictive tool, the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

Understanding chemistry at extreme conditions is crucial in fields including geochemistry, astrobiology, and alternative energy. First principles methods can provide valuable microscopic insights into such systems while circumventing the risks of physical experiments, however the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Semiphenomenological model for gas-liquid phase transitions.

PubMed

Benilov, E S; Benilov, M S

2016-03-01

We examine a rarefied gas with inter-molecular attraction. It is argued that the attraction force amplifies random density fluctuations by pulling molecules from lower-density regions into high-density regions and thus may give rise to an instability. To describe this effect, we use a kinetic equation where the attraction force is taken into account in a way similar to how electromagnetic forces in plasma are treated in the Vlasov model. It is demonstrated that the instability occurs when the temperature T is lower than a certain threshold value T(s) depending on the gas density. It is further shown that, even if T is only marginally lower than T(s), the instability generates clusters with density much higher than that of the gas. These results suggest that the instability should be interpreted as a gas-liquid phase transition, with T(s) being the temperature of saturated vapor and the high-density clusters representing liquid droplets.

Quantitative nanoscale electrostatics of viruses

NASA Astrophysics Data System (ADS)

Hernando-Pérez, M.; Cartagena-Rivera, A. X.; Lošdorfer Božič, A.; Carrillo, P. J. P.; San Martín, C.; Mateu, M. G.; Raman, A.; Podgornik, R.; de Pablo, P. J.

2015-10-01

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04274g

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

PubMed Central

Andrews, Casey T.

2013-01-01

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

Recent Applications of Higher-Order Spectral Analysis to Nonlinear Aeroelastic Phenomena

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Hajj, Muhammad R.; Dunn, Shane; Strganac, Thomas W.; Powers, Edward J.; Stearman, Ronald

2005-01-01

Recent applications of higher-order spectral (HOS) methods to nonlinear aeroelastic phenomena are presented. Applications include the analysis of data from a simulated nonlinear pitch and plunge apparatus and from F-18 flight flutter tests. A MATLAB model of the Texas A&MUniversity s Nonlinear Aeroelastic Testbed Apparatus (NATA) is used to generate aeroelastic transients at various conditions including limit cycle oscillations (LCO). The Gaussian or non-Gaussian nature of the transients is investigated, related to HOS methods, and used to identify levels of increasing nonlinear aeroelastic response. Royal Australian Air Force (RAAF) F/A-18 flight flutter test data is presented and analyzed. The data includes high-quality measurements of forced responses and LCO phenomena. Standard power spectral density (PSD) techniques and HOS methods are applied to the data and presented. The goal of this research is to develop methods that can identify the onset of nonlinear aeroelastic phenomena, such as LCO, during flutter testing.

High Density Methane Storage in Nanoporous Carbon

NASA Astrophysics Data System (ADS)

Rash, Tyler; Dohnke, Elmar; Soo, Yuchoong; Maland, Brett; Doynov, Plamen; Lin, Yuyi; Pfeifer, Peter; Mriglobal Collaboration; All-Craft Team

2014-03-01

Development of low-pressure, high-capacity adsorbent based storage technology for natural gas (NG) as fuel for advanced transportation (flat-panel tank for NG vehicles) is necessary in order to address the temperature, pressure, weight, and volume constraints present in conventional storage methods (CNG & LNG.) Subcritical nitrogen adsorption experiments show that our nanoporous carbon hosts extended narrow channels which generate a high surface area and strong Van der Waals forces capable of increasing the density of NG into a high-density fluid. This improvement in storage density over compressed natural gas without an adsorbent occurs at ambient temperature and pressures ranging from 0-260 bar (3600 psi.) The temperature, pressure, and storage capacity of a 40 L flat-panel adsorbed NG tank filled with 20 kg of nanoporous carbon will be featured.

Critical current densities of Jelly-Roll and powder metallurgy Nb{sub 3}Al wires as a function of temperature and magnetic field

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

Thieme, C.L.H.; Kim, J.B.; Takayasu, M.

Critical current densities of multi-filamentary Nb{sub 3}Al wire made with the Jelly-Roll process (JR) and mono-core powder metallurgy process (PM) wire were measured as a function of temperature and magnetic field. The temperature dependence of the resistive critical field B{sub c2} was measured in PM wires. There is a significant difference between these resistive B{sub c2} values and the ones determined by Kramer plots. The field dependence of the critical current depends on the manufacturing method. In general, it follows a relationship that falls between pure Kramer and one where the pinning force is inversely proportional with B{sup 2}. Inmore » contrast with Nb{sub 3}Sn no maximum in the bulk pinning force is observed down to 3 T (0.15MxB{sub c2}).« less

Contact inhibition of locomotion determines cell–cell and cell–substrate forces in tissues

PubMed Central

Zimmermann, Juliane; Camley, Brian A.; Rappel, Wouter-Jan; Levine, Herbert

2016-01-01

Cells organized in tissues exert forces on their neighbors and their environment. Those cellular forces determine tissue homeostasis as well as reorganization during embryonic development and wound healing. To understand how cellular forces are generated and how they can influence the tissue state, we develop a particle-based simulation model for adhesive cell clusters and monolayers. Cells are contractile, exert forces on their substrate and on each other, and interact through contact inhibition of locomotion (CIL), meaning that cell–cell contacts suppress force transduction to the substrate and propulsion forces align away from neighbors. Our model captures the traction force patterns of small clusters of nonmotile cells and larger sheets of motile Madin–Darby canine kidney (MDCK) cells. In agreement with observations in a spreading MDCK colony, the cell density in the center increases as cells divide and the tissue grows. A feedback between cell density, CIL, and cell–cell adhesion gives rise to a linear relationship between cell density and intercellular tensile stress and forces the tissue into a nonmotile state characterized by a broad distribution of traction forces. Our model also captures the experimentally observed tissue flow around circular obstacles, and CIL accounts for traction forces at the edge. PMID:26903658

Processing of Swarm Accelerometer Data into Thermospheric Neutral Densities

NASA Astrophysics Data System (ADS)

Doornbos, E.; Siemes, C.; Encarnacao, J.; Peřestý, R.; Grunwaldt, L.; Kraus, J.; Holmdahl Olsen, P. E.; van den IJssel, J.; Flury, J.; Apelbaum, G.

2015-12-01

The Swarm satellites were launched on 22 November 2013 and carry accelerometers and GPS receivers as part of their scientific payload. The GPS receivers are not only used for locating the position and time of the magnetic measurements, but also for determining non-gravitational forces like drag and radiation pressure acting on the spacecraft. The accelerometers measure these forces directly, at much finer resolution than the GPS receivers, from which thermospheric neutral densities and potentially winds can be derived. Unfortunately, the acceleration measurements suffer from a variety of disturbances, the most prominent being slow temperature-induced bias variations and sudden bias changes. These disturbances have caused a significant delay of the accelerometer data release. In this presentation, we describe the new three-stage processing that is required for transforming the disturbed acceleration measurements into scientifically valuable thermospheric neutral densities. In the first stage, the sudden bias changes in the acceleration measurements are removed using a dedicated software tool. The second stage is the calibration of the accelerometer measurements against the non-gravitational accelerations derived from the GPS receiver, which includes the correction for the slow temperature-induced bias variations. The third stage consists of transforming the corrected and calibrated accelerations into thermospheric neutral densities. We describe the methods used in each stage, highlight the difficulties encountered, and comment on the quality of the thermospheric neutral density data set, which covers the geomagnetic storm on 17 March 2015.

Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

2017-06-01

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (<10 ps), but the effects on slow reactions and the free energy surface are not well-known. We present a force matching approach to improve the chemical accuracy of DFTB. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

NASA Astrophysics Data System (ADS)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (<10 ps), but the effects on slow chemistry and the free energy surface are not well-known. We present a force matching approach to increase the accuracy of DFTB predictions for free energy surfaces. Accelerated sampling techniques are combined with path collective variables to generate the reference DFT data set and validate fitted DFTB potentials without a priori knowledge of transition states. Accuracy of force-matched DFTB free energy surfaces is assessed for slow peptide-forming reactions by direct comparison to DFT results for particular paths. Extensions to model prebiotic chemistry under shock conditions are discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Experimental transonic steady state and unsteady pressure measurements on a supercritical wing during flutter and forced discrete frequency oscillations

NASA Technical Reports Server (NTRS)

Piette, Douglas S.; Cazier, Frank W., Jr.

1989-01-01

Present flutter analysis methods do not accurately predict the flutter speeds in the transonic flow region for wings with supercritical airfoils. Aerodynamic programs using computational fluid dynamic (CFD) methods are being developed, but these programs need to be verified before they can be used with confidence. A wind tunnel test was performed to obtain all types of data necessary for correlating with CFD programs to validate them for use on high aspect ratio wings. The data include steady state and unsteady aerodynamic measurements on a nominal stiffness wing and a wing four times that stiffness. There is data during forced oscillations and during flutter at several angles of attack, Mach numbers, and tunnel densities.

MgB2 wire diameter reduction by hot isostatic pressing—a route for enhanced critical current density

NASA Astrophysics Data System (ADS)

Morawski, A.; Cetner, T.; Gajda, D.; Zaleski, A. J.; Häßler, W.; Nenkov, K.; Rindfleisch, M. A.; Tomsic, M.; Przysłupski, P.

2018-07-01

The effect of wire diameter reduction on the critical current density of pristine MgB2 wire was studied. Wires were treated by a hot isostatic pressing method at 570 °C and at pressures of up to 1.1 GPa. It was found that the wire diameter reduction induces an increase of up to 70% in the mass density of the superconducting cores. This feature leads to increases in critical current, critical current density, and pinning force density. The magnitude and field dependence of the critical current density are related to both grain connectivity and structural defects, which act as effective pinning centers. High field transport properties were obtained without doping of the MgB2 phase. A critical current density jc of 3500 A mm‑2 was reached at 4 K, 6 T for the best sample, which was a five-fold increase compared to MgB2 samples synthesized at ambient pressure.

Depositing nanoparticles on a silicon substrate using a freeze drying technique.

PubMed

Sigehuzi, Tomoo

2017-08-28

For the microscopic observation of nanoparticles, an adequate sample preparation is an essential part of this task. Much research has been performed for usable preparation methods that will yield aggregate-free samples. A freeze drying technique, which only requires a -80  ° C freezer and a freeze dryer, is shown to provide an on-substrate dispersion of mostly isolated nanoparticles. The particle density could be made sufficiently high for efficient observations using atomic force microscopy. Since this sandwich method is purely physical, it could be applied to deposit various nanoparticles independent of their surface chemical properties. Suspension film thickness, or the dimensionality of the suspension film, was shown to be crucial for the isolation of the particles. Silica nanoparticles were dispersed on a silicon substrate using this method and the sample properties were examined using atomic force microscopy.

Characterization of perovskite film prepared by pulsed laser deposition on ferritic stainless steel using microscopic and optical methods

NASA Astrophysics Data System (ADS)

Durda, E.; Jaglarz, J.; Kąc, S.; Przybylski, K.; El Kouari, Y.

2016-06-01

The perovskite La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF48) film was deposited on Crofer 22 APU ferritic stainless steel by pulsed laser deposition (PLD). Morphological studies of the sample were performed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Information about film thickness and surface topography of the film and the steel substrate were obtained using following optical methods: spectroscopic ellipsometry (SE), bidirectional reflection distribution function (BRDF) and total integrated reflectometry (TIS). In particular, the BRDF study, being complementary to atomic force microscopy, yielded information about surface topography. Using the previously mentioned methods, the following statistic surface parameters were determined: root-mean square (rms) roughness and autocorrelation length by determining the power spectral density (PSD) function of surface irregularities.

Directivity analysis of meander-line-coil EMATs with a wholly analytical method.

PubMed

Xie, Yuedong; Liu, Zenghua; Yin, Liyuan; Wu, Jiande; Deng, Peng; Yin, Wuliang

2017-01-01

This paper presents the simulation and experimental study of the radiation pattern of a meander-line-coil EMAT. A wholly analytical method, which involves the coupling of two models: an analytical EM model and an analytical UT model, has been developed to build EMAT models and analyse the Rayleigh waves' beam directivity. For a specific sensor configuration, Lorentz forces are calculated using the EM analytical method, which is adapted from the classic Deeds and Dodd solution. The calculated Lorentz force density are imported to an analytical ultrasonic model as driven point sources, which produce the Rayleigh waves within a layered medium. The effect of the length of the meander-line-coil on the Rayleigh waves' beam directivity is analysed quantitatively and verified experimentally. Copyright © 2016 Elsevier B.V. All rights reserved.

Forces Generated by High Velocity Impact of Ice on a Rigid Structure

NASA Technical Reports Server (NTRS)

Pereira, J. Michael; Padula, Santo A., II; Revilock, Duane M.; Melis, Matthew E.

2006-01-01

Tests were conducted to measure the impact forces generated by cylindrical ice projectiles striking a relatively rigid target. Two types of ice projectiles were used, solid clear ice and lower density fabricated ice. Three forms of solid clear ice were tested: single crystal, poly-crystal, and "rejected" poly-crystal (poly-crystal ice in which defects were detected during inspection.) The solid ice had a density of approximately 56 lb/cu ft (0.9 gm/cu cm). A second set of test specimens, termed "low density ice" was manufactured by molding shaved ice into a cylindrical die to produce ice with a density of approximately 40 lb/cu ft (0.65 gm/cu cm). Both the static mechanical characteristics and the crystalline structure of the ice were found to have little effect on the observed transient response. The impact forces generated by low density ice projectiles, which had very low mechanical strength, were comparable to those of full density solid ice. This supports the hypothesis that at a velocity significantly greater than that required to produce fracture in the ice, the mechanical properties become relatively insignificant, and the impact forces are governed by the shape and mass of the projectile.

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

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

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

DFT-based method for more accurate adsorption energies: An adaptive sum of energies from RPBE and vdW density functionals

DOE PAGES

Hensley, Alyssa J. R.; Ghale, Kushal; Rieg, Carolin; ...

2017-01-26

In recent years, the popularity of density functional theory with periodic boundary conditions (DFT) has surged for the design and optimization of functional materials. However, no single DFT exchange–correlation functional currently available gives accurate adsorption energies on transition metals both when bonding to the surface is dominated by strong covalent or ionic bonding and when it has strong contributions from van der Waals interactions (i.e., dispersion forces). Here we present a new, simple method for accurately predicting adsorption energies on transition-metal surfaces based on DFT calculations, using an adaptively weighted sum of energies from RPBE and optB86b-vdW (or optB88-vdW) densitymore » functionals. This method has been benchmarked against a set of 39 reliable experimental energies for adsorption reactions. Our results show that this method has a mean absolute error and root mean squared error relative to experiments of 13.4 and 19.3 kJ/mol, respectively, compared to 20.4 and 26.4 kJ/mol for the BEEF-vdW functional. For systems with large van der Waals contributions, this method decreases these errors to 11.6 and 17.5 kJ/mol. Furthermore, this method provides predictions of adsorption energies both for processes dominated by strong covalent or ionic bonding and for those dominated by dispersion forces that are more accurate than those of any current standard DFT functional alone.« less

Derivation of Poisson and Nernst-Planck equations in a bath and channel from a molecular model.

PubMed

Schuss, Z; Nadler, B; Eisenberg, R S

2001-09-01

Permeation of ions from one electrolytic solution to another, through a protein channel, is a biological process of considerable importance. Permeation occurs on a time scale of micro- to milliseconds, far longer than the femtosecond time scales of atomic motion. Direct simulations of atomic dynamics are not yet possible for such long-time scales; thus, averaging is unavoidable. The question is what and how to average. In this paper, we average a Langevin model of ionic motion in a bulk solution and protein channel. The main result is a coupled system of averaged Poisson and Nernst-Planck equations (CPNP) involving conditional and unconditional charge densities and conditional potentials. The resulting NP equations contain the averaged force on a single ion, which is the sum of two components. The first component is the gradient of a conditional electric potential that is the solution of Poisson's equation with conditional and permanent charge densities and boundary conditions of the applied voltage. The second component is the self-induced force on an ion due to surface charges induced only by that ion at dielectric interfaces. The ion induces surface polarization charge that exerts a significant force on the ion itself, not present in earlier PNP equations. The proposed CPNP system is not complete, however, because the electric potential satisfies Poisson's equation with conditional charge densities, conditioned on the location of an ion, while the NP equations contain unconditional densities. The conditional densities are closely related to the well-studied pair-correlation functions of equilibrium statistical mechanics. We examine a specific closure relation, which on the one hand replaces the conditional charge densities by the unconditional ones in the Poisson equation, and on the other hand replaces the self-induced force in the NP equation by an effective self-induced force. This effective self-induced force is nearly zero in the baths but is approximately equal to the self-induced force in and near the channel. The charge densities in the NP equations are interpreted as time averages over long times of the motion of a quasiparticle that diffuses with the same diffusion coefficient as that of a real ion, but is driven by the averaged force. In this way, continuum equations with averaged charge densities and mean-fields can be used to describe permeation through a protein channel.

Mechanics of Carbon Nanotubes and their Polymer Composites

NASA Technical Reports Server (NTRS)

Wei, Chenyu; Cho, K. J.; Srivastava, Deepak; Tang, Harry (Technical Monitor)

2002-01-01

Contents include the folloving: carbon nanotube (CNT): structures, application of carbon nanotubes, simulation method, Elastic properties of carbon nanotubes, yield strain of CNT, yielding under tensile stress, yielding: strain-rate and temperature dependence, yield strain under tension, yielding at realistic conditions, nano fibers, polymer CNT composite, force field, density dependency on temperature, diffusion coefficients, young modulus, and conclusions.

Probing lipid membrane electrostatics

NASA Astrophysics Data System (ADS)

Yang, Yi

The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by <2%. One important application of this technique is to estimate the dipole density of lipid membrane. Electrostatic analysis of DOPC lipid bilayers with the AFM reveals a repulsive force between the negatively charged probe tips and the zwitterionic lipid bilayers. This unexpected interaction has been analyzed quantitatively to reveal that the repulsion is due to a weak external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful probe of membrane electrostatics.

A material-sparing method for simultaneous determination of true density and powder compaction properties--aspartame as an example.

PubMed

Sun, Changquan Calvin

2006-12-01

True density results for a batch of commercial aspartame are highly variable when helium pycnometry is used. Alternatively, the true density of the problematic aspartame lot was obtained by fitting tablet density versus pressure data. The fitted true density was in excellent agreement with that predicted from single crystal structure. Tablet porosity was calculated from the true density and tablet apparent density. After making the necessary measurements for calculating tablet apparent density, the breaking force of each intact tablet was measured and tensile strength was calculated. With the knowledge of compaction pressure, tablet porosity and tensile strength, powder compaction properties were characterized using tabletability (tensile strength versus pressure), compactibility (tensile strength versus porosity), compressibility (porosity versus pressure) and Heckel analysis. Thus, a wealth of additional information on the compaction properties of the powder was obtained through little added work. A total of approximately 4 g of powder was used in this study. Depending on the size of tablet tooling, tablet thickness and true density, 2-10 g of powder would be sufficient for characterizing most pharmaceutical powders.

Quantification of Daily Physical Activity

NASA Technical Reports Server (NTRS)

Whalen, Robert; Breit, Greg; Quintana, Jason

1994-01-01

The influence of physical activity on the maintenance and adaptation of musculoskeletal tissue is difficult to assess. Cumulative musculoskeletal loading is hard to quantify and the attributes of the daily tissue loading history affecting bone metabolism have not been completely identified. By monitoring the vertical component of the daily ground reaction force (GRFz), we have an indirect measure of cumulative daily lower limb musculoskeletal loading to correlate with bone density and structure. The objective of this research is to develop instrumentation and methods of analysis to quantify activity level in terms of the daily history of ground reaction forces.

Effect of dispersion forces on the capillary-wave fluctuations of liquid surfaces.

PubMed

Chacón, Enrique; Fernández, Eva M; Tarazona, Pedro

2014-04-01

We present molecular dynamics evidence for the nonanalytic effects of the long-range dispersion forces on the capillary waves fluctuations of a Lennard-Jones liquid surface. The results of the intrinsic sampling method, for the analysis of the instantaneous interfacial shape, are obtained in large systems for several cut-off distances of the potential tail, and they show good agreement with the theoretical prediction by Napiórkowski and Dietrich, based on a density functional analysis. The enhancement of the capillary waves is quantified to be within 1% for a simple liquid near its triple point.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

PubMed

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

The effect of adsorbed liquid and material density on saltation threshold: Insight from laboratory and wind tunnel experiments

NASA Astrophysics Data System (ADS)

Yu, Xinting; Hörst, Sarah M.; He, Chao; Bridges, Nathan T.; Burr, Devon M.; Sebree, Joshua A.; Smith, James K.

2017-11-01

Saltation threshold, the minimum wind speed for sediment transport, is a fundamental parameter in aeolian processes. Measuring this threshold using boundary layer wind tunnels, in which particles are mobilized by flowing air, for a subset of different planetary conditions can inform our understanding of physical processes of sediment transport. The presence of liquid, such as water on Earth or methane on Titan, may affect the threshold values to a great extent. Sediment density is also crucial for determining threshold values. Here we provide quantitative data on density and water content of common wind tunnel materials (including chromite, basalt, quartz sand, beach sand, glass beads, gas chromatograph packing materials, walnut shells, iced tea powder, activated charcoal, instant coffee, and glass bubbles) that have been used to study conditions on Earth, Titan, Mars, and Venus. The measured density values for low density materials are higher compared to literature values (e.g., ∼30% for walnut shells), whereas for the high density materials, there is no such discrepancy. We also find that low density materials have much higher water content and longer atmospheric equilibration timescales compared to high density sediments. We used thermogravimetric analysis (TGA) to quantify surface and internal water and found that over 80% of the total water content is surface water for low density materials. In the Titan Wind Tunnel (TWT), where Reynolds number conditions similar to those on Titan can be achieved, we performed threshold experiments with the standard walnut shells (125-150 μm, 7.2% water by mass) and dried walnut shells, in which the water content was reduced to 1.7%. The threshold results for the two scenarios are almost the same, which indicates that humidity had a negligible effect on threshold for walnut shells in this experimental regime. When the water content is lower than 11.0%, the interparticle forces are dominated by adsorption forces, whereas at higher values the interparticle forces are dominated by much larger capillary forces. For materials with low equilibrium water content, like quartz sand, capillary forces dominate. When the interparticle forces are dominated by adsorption forces, the threshold does not increase with increasing relative humidity (RH) or water content. Only when the interparticle forces are dominated by capillary forces does the threshold start to increase with increasing RH/water content. Since tholins have a low methane content (0.3% at saturation, [Curtis, D. B., Hatch, C. D., Hasenkopf, C. A., et al., 2008. Laboratory studies of methane and ethane adsorption and nucleation onto organic particles: Application to Titan's clouds. Icarus, 195, 792. http://dx.doi.org/10.1016/j.icarus.2008.02.003]), we believe tholins would behave similarly to quartz sand when subjected to methane moisture.

A Non-Destructive and Direction-Insensitive Method Using a Strain Sensor and Two Single Axis Angle Sensors for Evaluating Corn Stalk Lodging Resistance.

PubMed

Guo, Qingqian; Chen, Ruipeng; Sun, Xiaoquan; Jiang, Min; Sun, Haifeng; Wang, Shun; Ma, Liuzheng; Yang, Yatao; Hu, Jiandong

2018-06-06

Corn stalk lodging is caused by different factors, including severe wind storms, stalk cannibalization, and stalk rots, and it leads to yield loss. Determining how to rapidly evaluate corn lodging resistance will assist scientists in the field of crop breeding to understand the contributing factors in managing the moisture, chemical fertilizer, and weather conditions for corn growing. This study proposes a non-destructive and direction-insensitive method, using a strain sensor and two single axis angle sensors to measure the corn stalk lodging resistance in the field. An equivalent force whose direction is perpendicular to the stalk is utilized to evaluate the corn lodging properties when a pull force is applied on the corn stalk. A novel measurement device is designed to obtain the equivalent force with the coefficient of variation (CV) of 4.85%. Five corn varieties with two different planting densities are arranged to conduct the experiment using the novel measurement device. The experimental results show that the maximum equivalent force could reach up to 44 N. A strong relationship with the square of the correlation coefficient of 0.88 was obtained between the maximum equivalent forces and the corn field’s stalk lodging rates. Moreover, the stalk lodging angles corresponding to the different pull forces over a measurement time of 20 s shift monotonically along the equivalent forces. Thus, the non-destructive and direction-insensitive method is an excellent tool for rapid analysis of stalk lodging resistance in corn, providing critical information on in-situ lodging dynamics.

Force feedback controls motor activity and mechanical properties of self-assembling branched actin networks

PubMed Central

Bieling, Peter; Li, Tai-De; Weichsel, Julian; McGorty, Ryan; Jreij, Pamela; Huang, Bo; Fletcher, Daniel A.; Mullins, R. Dyche

2016-01-01

Branched actin networks–created by the Arp2/3 complex, capping protein, and a nucleation promoting factor– generate and transmit forces required for many cellular processes, but their response to force is poorly understood. To address this, we assembled branched actin networks in vitro from purified components and used simultaneous fluorescence and atomic force microscopy to quantify their molecular composition and material properties under various forces. Remarkably, mechanical loading of these self-assembling materials increases their density, power, and efficiency. Microscopically, increased density reflects increased filament number and altered geometry, but no change in average length. Macroscopically, increased density enhances network stiffness and resistance to mechanical failure beyond those of isotropic actin networks. These effects endow branched actin networks with memory of their mechanical history that shapes their material properties and motor activity. This work reveals intrinsic force feedback mechanisms by which mechanical resistance makes self-assembling actin networks stiffer, stronger, and more powerful. PMID:26771487

Quantum molecular dynamics simulations of dense matter

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

Collins, L.; Kress, J.; Troullier, N.

1997-12-31

The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB,more » which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.« less

Growth and characterization of magnetite-maghemite thin films by the dip coating method

NASA Astrophysics Data System (ADS)

Velásquez, A. A.; Arnedo, A.

2017-11-01

We present the process of growth and characterization of magnetite-maghemite thin films obtained by the dip coating method. The thin films were deposited on glass substrates, using a ferrofluid of nanostructured magnetite-maghemite particles as precursor solution. During the growth of the films the following parameters were controlled: number of dips of the substrates, dip velocity of the substrates and drying times. The films were characterized by Atomic Force Microscopy, Scanning Elelectron Microscopy, four-point method for resistance measurement, Room Temperature Mössbauer Spectroscopy and Hall effect. Mössbauer measurements showed the presence of a sextet attributed to maghemite ( γ-Fe2O3) and two doublets attributed to superparamagnetic magnetite (Fe3O4), indicating a distribution of oxidation states of the iron as well as a particle size distribution of the magnetic phases in the films. Atomic force microscopy measurements showed that the films cover quasi uniformly the substrates, existing in them some pores with sub-micron size. Scanning Electron Microscopy measurements showed a uniform structure in the films, with spherical particles with size around 10 nm. Voltage versus current measurements showed an ohmic response of the films for currents between 0 and 100 nA. On the other hand, Hall effect measurements showed a nonlinear response of the Hall voltage with the magnetic flux density applied perpendicular to the plane of the films, however the response is fairly linear for magnetic flux densities between 0.15 and 0.35 T approximately. The results suggest that the films are promising for application as magnetic flux density sensors.

Analytical excited state forces for the time-dependent density-functional tight-binding method.

PubMed

Heringer, D; Niehaus, T A; Wanko, M; Frauenheim, Th

2007-12-01

An analytical formulation for the geometrical derivatives of excitation energies within the time-dependent density-functional tight-binding (TD-DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD-DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time-dependent density-functional theory. As a consequence of the special form of the approximations made in TD-DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD-DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms. (c) 2007 Wiley Periodicals, Inc.

Bench-top Comparison of Physical Properties of 4 Commercially-Available Self-Expanding Intracranial Stents

PubMed Central

Cho, Su-hee; Jo, Won-il; Jo, Ye-eun; Yang, Ku Hyun; Park, Jung Cheol

2017-01-01

Purpose To better understand the performance of four commercially available neurovascular stents in intracranial aneurysm embolization, the stents were compared in terms of their basic morphological and mechanical properties. Materials and Methods Four different types of stents that are currently being used for cerebral aneurysm embolization were prepared (two stents per type). Two were laser-cut stents (Neuroform and Enterprise) and two were braided from a single nitinol wire (LEO and LVIS stents). All were subjected to quantitative measurements of stent size, pore density, metal coverage, the force needed to load, push, and deploy the stent, radial force on deployment, surface roughness, and corrosion resistance. Results Compared to their nominal diameters, all stents had greater diameters after deployment. The length generally decreased after deployment. This was particularly marked in the braided stents. The braided stents also had higher pore densities than the laser-cut stents. Metal coverage was highest in the LEO stent (14%) and lowest in the Enterprise stent (5%). The LIVS stent had the highest microcatheter loading force (81.5 gf). The LEO stent had the highest passage force (55.0 gf) and deployment force (78.9 gf). The LVIS and LEO stents had the highest perpendicular (37.1 gf) and circumferential (178.4 gf) radial forces, respectively. The Enterprise stent had the roughest stent wire, followed by the LVIS, LEO, and Neuroform stents. Conclusion The four neurovascular stent types differed in terms of morphological and physical characteristics. An understanding of this diversity may help to decide which stent is most suitable for specific clinical situations. PMID:28316867

Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide

NASA Astrophysics Data System (ADS)

Pellegrini, Matteo; Grønbech-Jensen, Niels; Doniach, Sebastian

1996-06-01

We describe a technique for generating potentials of mean force (PMF) between solutes in an aqueous solution. We first generate solute-solvent correlation functions (CF) using Monte Carlo (MC) simulations in which we place a single atom solute in a periodic boundary box containing a few hundred water molecules. We then make use of the Kirkwood superposition approximation, where the 3-body correlation function is approximated as the product of 2-body CFs, to describe the mean water density around two solutes. Computing the force generated on the solutes by this average water density allows us to compute potentials of mean force between the two solutes. For charged solutes an additional approximation involving dielectric screening is made, by setting the dielectric constant of water to ɛ=80. These potentials account, in an approximate manner, for the average effect of water on the atoms. Following the work of Pettitt and Karplus [Chem. Phys. Lett. 121, 194 (1985)], we approximate the n-body potential of mean force as a sum of the pairwise potentials of mean force. This allows us to run simulations of biomolecules without introducing explicit water, hence gaining several orders of magnitude in efficiency with respect to standard molecular dynamics techniques. We demonstrate the validity of this technique by first comparing the PMFs for methane-methane and sodium-chloride generated with this procedure, with those calculated with a standard Monte Carlo simulation with explicit water. We then compare the results of the free energy profiles between the equilibria of alanine dipeptide generated by the two methods.

Foot-ankle complex injury risk curves using calcaneus bone mineral density data.

PubMed

Yoganandan, Narayan; Chirvi, Sajal; Voo, Liming; DeVogel, Nicholas; Pintar, Frank A; Banerjee, Anjishnu

2017-08-01

Biomechanical data from post mortem human subject (PMHS) experiments are used to derive human injury probability curves and develop injury criteria. This process has been used in previous and current automotive crashworthiness studies, Federal safety standards, and dummy design and development. Human bone strength decreases as the individuals reach their elderly age. Injury risk curves using the primary predictor variable (e.g., force) should therefore account for such strength reduction when the test data are collected from PMHS specimens of different ages (age at the time of death). This demographic variable is meant to be a surrogate for fracture, often representing bone strength as other parameters have not been routinely gathered in previous experiments. However, bone mineral densities (BMD) can be gathered from tested specimens (presented in this manuscript). The objective of this study is to investigate different approaches of accounting for BMD in the development of human injury risk curves. Using simulated underbody blast (UBB) loading experiments conducted with the PMHS lower leg-foot-ankle complexes, a comparison is made between the two methods: treating BMD as a covariate and pre-scaling test data based on BMD. Twelve PMHS lower leg-foot-ankle specimens were subjected to UBB loads. Calcaneus BMD was obtained from quantitative computed tomography (QCT) images. Fracture forces were recorded using a load cell. They were treated as uncensored data in the survival analysis model which used the Weibull distribution in both methods. The width of the normalized confidence interval (NCIS) was obtained using the mean and ± 95% confidence limit curves. The mean peak forces of 3.9kN and 8.6kN were associated with the 5% and 50% probability of injury for the covariate method of deriving the risk curve for the reference age of 45 years. The mean forces of 5.4 kN and 9.2kN were associated with the 5% and 50% probability of injury for the pre-scaled method. The NCIS magnitudes were greater in the covariate-based risk curves (0.52-1.00) than in the risk curves based on the pre-scaled method (0.24-0.66). The pre-scaling method resulted in a generally greater injury force and a tighter injury risk curve confidence interval. Although not directly applicable to the foot-ankle fractures, when compared with the use of spine BMD from QCT scans to pre-scale the force, the calcaneus BMD scaled data produced greater force at the same risk level in general. Pre-scaling the force data using BMD is an alternate, and likely a more accurate, method instead of using covariate to account for the age-related bone strength change in deriving risk curves from biomechanical experiments using PMHS. Because of the proximity of the calcaneus bone to the impacting load, it is suggested to use and determine the BMD of the foot-ankle bone in future UBB and other loading conditions to derive human injury probability curves for the foot-ankle complex. Copyright © 2017. Published by Elsevier Ltd.

Electrostatic forces in planetary rings

NASA Technical Reports Server (NTRS)

Goertz, C. K.; Shan, Linhua; Havnes, O.

1988-01-01

The average charge on a particle in a particle-plasma cloud, the plasma potential inside the cloud, and the Coulomb force acting on the particle are calculated. The net repulsive electrostatic force on a particle depends on the plasma density, temperature, density of particles, particle size, and the gradient of the particle density. In a uniformly dense ring the electrostatic repulsion is zero. It is also shown that the electrostatic force acts like a pressure force, that even a collisionless ring can be stable against gravitational collapse, and that a finite ring thickness does not necessarily imply a finite velocity dispersion. A simple criterion for the importance of electrostatic forces in planetary rings is derived which involves the calculation of the vertical ring thickness which would result if only electrostatic repulsion were responsible for the finite ring thickness. Electrostatic forces are entirely negligible in the main rings of Saturn and the E and G rings. They may also be negligible in the F ring. However, the Uranian rings and Jupiter's ring seem to be very much influenced by electrostatic repulsion. In fact, electrostatic forces could support a Jovian ring which is an order of magnitude more dense than observed.

Accurate fluid force measurement based on control surface integration

NASA Astrophysics Data System (ADS)

Lentink, David

2018-01-01

Nonintrusive 3D fluid force measurements are still challenging to conduct accurately for freely moving animals, vehicles, and deforming objects. Two techniques, 3D particle image velocimetry (PIV) and a new technique, the aerodynamic force platform (AFP), address this. Both rely on the control volume integral for momentum; whereas PIV requires numerical integration of flow fields, the AFP performs the integration mechanically based on rigid walls that form the control surface. The accuracy of both PIV and AFP measurements based on the control surface integration is thought to hinge on determining the unsteady body force associated with the acceleration of the volume of displaced fluid. Here, I introduce a set of non-dimensional error ratios to show which fluid and body parameters make the error negligible. The unsteady body force is insignificant in all conditions where the average density of the body is much greater than the density of the fluid, e.g., in gas. Whenever a strongly deforming body experiences significant buoyancy and acceleration, the error is significant. Remarkably, this error can be entirely corrected for with an exact factor provided that the body has a sufficiently homogenous density or acceleration distribution, which is common in liquids. The correction factor for omitting the unsteady body force, {{{ {ρ f}} {1 - {ρ f} ( {{ρ b}+{ρ f}} )}.{( {{{{ρ }}b}+{ρ f}} )}}} , depends only on the fluid, {ρ f}, and body, {{ρ }}b, density. Whereas these straightforward solutions work even at the liquid-gas interface in a significant number of cases, they do not work for generalized bodies undergoing buoyancy in combination with appreciable body density inhomogeneity, volume change (PIV), or volume rate-of-change (PIV and AFP). In these less common cases, the 3D body shape needs to be measured and resolved in time and space to estimate the unsteady body force. The analysis shows that accounting for the unsteady body force is straightforward to non-intrusively and accurately determine fluid force in most applications.

Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients.

PubMed

Li, Hui

2009-11-14

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Coalescence induced dislocation reduction in selectively grown lattice-mismatched heteroepitaxy: Theoretical prediction and experimental verification

NASA Astrophysics Data System (ADS)

Yako, Motoki; Ishikawa, Yasuhiko; Wada, Kazumi

2018-05-01

A method for reduction of threading dislocation density (TDD) in lattice-mismatched heteroepitaxy is proposed, and the reduction is experimentally verified for Ge on Si. Flat-top epitaxial layers are formed through coalescences of non-planar selectively grown epitaxial layers, and enable the TDD reduction in terms of image force. Numerical calculations and experiments for Ge on Si verify the TDD reduction by this method. The method should be applicable to not only Ge on Si but also other lattice-mismatched heteroepitaxy such as III-V on Si.

On the way to a microscopic derivation of covariant density functionals in nuclei

NASA Astrophysics Data System (ADS)

Ring, Peter

2018-02-01

Several methods are discussed to derive covariant density functionals from the microscopic input of bare nuclear forces. In a first step there are semi-microscopic functionals, which are fitted to ab-initio calculations of nuclear matter and depend in addition on very few phenomenological parameters. They are able to describe nuclear properties with the same precision as fully phenomenological functionals. In a second step we present first relativistic Brueckner-Hartree-Fock calculations in finite nuclei in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

The Elegance of Disordered Granular Packings: A Validation of Edwards' Hypothesis

NASA Technical Reports Server (NTRS)

Metzger, Philip T.; Donahue, Carly M.

2004-01-01

We have found a way to analyze Edwards' density of states for static granular packings in the special case of round, rigid, frictionless grains assuming constant coordination number. It obtains the most entropic density of single grain states, which predicts several observables including the distribution of contact forces. We compare these results against empirical data obtained in dynamic simulations of granular packings. The agreement between theory and the empirics is quite good, helping validate the use of statistical mechanics methods in granular physics. The differences between theory and empirics are mainly due to the variable coordination number, and when the empirical data are sorted by that number we obtain several insights that suggest an underlying elegance in the density of states

A predictive bone drilling force model for haptic rendering with experimental validation using fresh cadaveric bone.

PubMed

Lin, Yanping; Chen, Huajiang; Yu, Dedong; Zhang, Ying; Yuan, Wen

2017-01-01

Bone drilling simulators with virtual and haptic feedback provide a safe, cost-effective and repeatable alternative to traditional surgical training methods. To develop such a simulator, accurate haptic rendering based on a force model is required to feedback bone drilling forces based on user input. Current predictive bone drilling force models based on bovine bones with various drilling conditions and parameters are not representative of the bone drilling process in bone surgery. The objective of this study was to provide a bone drilling force model for haptic rendering based on calibration and validation experiments in fresh cadaveric bones with different bone densities. Using a commonly used drill bit geometry (2 mm diameter), feed rates (20-60 mm/min) and spindle speeds (4000-6000 rpm) in orthognathic surgeries, the bone drilling forces of specimens from two groups were measured and the calibration coefficients of the specific normal and frictional pressures were determined. The comparison of the predicted forces and the measured forces from validation experiments with a large range of feed rates and spindle speeds demonstrates that the proposed bone drilling forces can predict the trends and average forces well. The presented bone drilling force model can be used for haptic rendering in surgical simulators.

Test surfaces useful for calibration of surface profilometers

DOEpatents

Yashchuk, Valeriy V; McKinney, Wayne R; Takacs, Peter Z

2013-12-31

The present invention provides for test surfaces and methods for calibration of surface profilometers, including interferometric and atomic force microscopes. Calibration is performed using a specially designed test surface, or the Binary Pseudo-random (BPR) grating (array). Utilizing the BPR grating (array) to measure the power spectral density (PSD) spectrum, the profilometer is calibrated by determining the instrumental modulation transfer.

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

NASA Astrophysics Data System (ADS)

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

2006-11-01

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

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

PubMed Central

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

2007-01-01

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

Investigating gravity waves evidences in the Venus upper atmosphere

NASA Astrophysics Data System (ADS)

Migliorini, Alessandra; Altieri, Francesca; Shakun, Alexey; Zasova, Ludmila; Piccioni, Giuseppe; Bellucci, Giancarlo; Grassi, Davide

2014-05-01

We present a method to investigate gravity waves properties in the upper mesosphere of Venus, through the O2 nightglow observations acquired with the imaging spectrometer VIRTIS on board Venus Express. Gravity waves are important dynamical features that transport energy and momentum. They are related to the buoyancy force, which lifts air particles. Then, the vertical displacement of air particles produces density changes that cause gravity to act as restoring force. Gravity waves can manifest through fluctuations on temperature and density fields, and hence on airglow intensities. We use the O2 nightglow profiles showing double peaked structures to study the influence of gravity waves in shaping the O2 vertical profiles and infer the waves properties. In analogy to the Earth's and Mars cases, we use a well-known theory to model the O2 nightglow emissions affected by gravity waves propagation. Here we propose a statistical discussion of the gravity waves characteristics, namely vertical wavelength and wave amplitude, with respect to local time and latitude. The method is applied to about 30 profiles showing double peaked structures, and acquired with the VIRTIS/Venus Express spectrometer, during the mission period from 2006-07-05 to 2008-08-15.

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

PubMed Central

Neumann, Marcus A.

2017-01-01

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

Urologist Density and County-Level Urologic Cancer Mortality

PubMed Central

Odisho, Anobel Y.; Cooperberg, Matthew R.; Fradet, Vincent; Ahmad, Ardalan E.; Carroll, Peter R.

2010-01-01

Purpose The surgical work force distribution at the county level varies widely across the United States, and the impact of differential access on cancer outcomes is unclear. We used urologists as a test case because they are the first care providers for urologic cancers, can easily be identified from available data sources, and are unevenly distributed throughout the country. The goal of this study was to determine the effect of increasing urologist density on local prostate, bladder, and kidney cancer mortality. Patients and Methods Using county-level data from the Area Resource File, US Census, National Cancer Institute, and Centers for Disease Control, regression models were built for prostate, bladder, and kidney cancer mortality, controlling for categorized urologist density, county demographics, socioeconomic factors, and preexisting health care infrastructure. Results For each of the three cancers, there was a statistically significant cancer-specific mortality reduction associated with counties that had more than zero urologists (16% to 22% reduction for prostate cancer, 17% to 20% reduction for bladder cancer, and 8% to 14% reduction for kidney cancer with increasing urologist density) relative to zero urologists. However, increasing density greater than two urologists per 100,000 people had no statistically significant impact on mortality for any of the tumors studied. Conclusion The presence of a urologist is associated with lower mortality for urologic cancers in that county, but increasing urologist density does not yield further improvements. Therefore, a nuanced and geographically aware policy toward the size and distribution of the future work force is most likely to provide the greatest population-level improvement in cancer mortality outcomes. PMID:20406931

Quantitative computed tomography of lung parenchyma in patients with emphysema: analysis of higher-density lung regions

NASA Astrophysics Data System (ADS)

Lederman, Dror; Leader, Joseph K.; Zheng, Bin; Sciurba, Frank C.; Tan, Jun; Gur, David

2011-03-01

Quantitative computed tomography (CT) has been widely used to detect and evaluate the presence (or absence) of emphysema applying the density masks at specific thresholds, e.g., -910 or -950 Hounsfield Unit (HU). However, it has also been observed that subjects with similar density-mask based emphysema scores could have varying lung function, possibly indicating differences of disease severity. To assess this possible discrepancy, we investigated whether density distribution of "viable" lung parenchyma regions with pixel values > -910 HU correlates with lung function. A dataset of 38 subjects, who underwent both pulmonary function testing and CT examinations in a COPD SCCOR study, was assembled. After the lung regions depicted on CT images were automatically segmented by a computerized scheme, we systematically divided the lung parenchyma into different density groups (bins) and computed a number of statistical features (i.e., mean, standard deviation (STD), skewness of the pixel value distributions) in these density bins. We then analyzed the correlations between each feature and lung function. The correlation between diffusion lung capacity (DLCO) and STD of pixel values in the bin of -910HU <= PV < -750HU was -0.43, as compared with a correlation of -0.49 obtained between the post-bronchodilator ratio (FEV1/FVC) measured by the forced expiratory volume in 1 second (FEV1) dividing the forced vital capacity (FVC) and the STD of pixel values in the bin of -1024HU <= PV < -910HU. The results showed an association between the distribution of pixel values in "viable" lung parenchyma and lung function, which indicates that similar to the conventional density mask method, the pixel value distribution features in "viable" lung parenchyma areas may also provide clinically useful information to improve assessments of lung disease severity as measured by lung functional tests.

Driving forces of heavy metal changes in agricultural soils in a typical manufacturing center.

PubMed

Qiu, Menglong; Li, Fangbai; Wang, Qi; Chen, Junjian; Yang, Guoyi; Liu, Liming

2015-05-01

Heavy metal concentrations in 2002 and 2012 in agricultural soils in Dongguan, a manufacturing center in southern China, were analyzed to determine the impact of rapid economic development on soil pollution. The level of pollution was assessed using the Nemerow synthetic pollution index (NPI), and its changing characteristics and driving forces were analyzed using multivariate statistical and geostatistical methods. The results indicate that the mean NPI was 0.79 in 2002 and 0.84 in 2012, which indicates aggravated heavy metal contamination in the agricultural soils. The concentrations of Cd and Zn increased 54.7 and 20.8 %, respectively, whereas Hg and Pb decreased 35.3 and 24.5 %, respectively. Cr, As, Cu, and Ni remained relatively stable. The Hg and Cd concentrations were highly correlated with soil types (P < 0.01), the secondary industrial output per unit of land (P < 0.01), proportion of cereal fields (P < 0.01), proportion of vegetable fields (P < 0.01), population density (P < 0.05), and road density (P < 0.05). The Pb and As concentrations were greatly influenced by soil types (P < 0.01), river density (P < 0.01), fertilizer rate (P < 0.01), and road density (P < 0.05). Cr, Zn, Cu, and Ni concentrations were primarily driven by soil types (P < 0.01), river density (P < 0.01), and fertilizer rate (P < 0.05).

Optimization and Analysis of a U-Shaped Linear Piezoelectric Ultrasonic Motor Using Longitudinal Transducers

PubMed Central

Yu, Hongpeng; Quan, Qiquan; Tian, Xinqi; Li, He

2018-01-01

A novel U-shaped piezoelectric ultrasonic motor that mainly focused on miniaturization and high power density was proposed, fabricated, and tested in this work. The longitudinal vibrations of the transducers were excited to form the elliptical movements on the driving feet. Finite element method (FEM) was used for design and analysis. The resonance frequencies of the selected vibration modes were tuned to be very close to each other with modal analysis and the movement trajectories of the driving feet were gained with transient simulation. The vibration modes and the mechanical output abilities were tested to evaluate the proposed motor further by a prototype. The maximum output speed was tested to be 416 mm/s, the maximum thrust force was 21 N, and the maximum output power was 5.453 W under frequency of 29.52 kHz and voltage of 100 Vrms. The maximum output power density of the prototype reached 7.59 W/kg, which was even greater than a previous similar motor under the exciting voltage of 200 Vrms. The proposed motor showed great potential for linear driving of large thrust force and high power density. PMID:29518963

Optimization and Analysis of a U-Shaped Linear Piezoelectric Ultrasonic Motor Using Longitudinal Transducers.

PubMed

Yu, Hongpeng; Quan, Qiquan; Tian, Xinqi; Li, He

2018-03-07

A novel U-shaped piezoelectric ultrasonic motor that mainly focused on miniaturization and high power density was proposed, fabricated, and tested in this work. The longitudinal vibrations of the transducers were excited to form the elliptical movements on the driving feet. Finite element method (FEM) was used for design and analysis. The resonance frequencies of the selected vibration modes were tuned to be very close to each other with modal analysis and the movement trajectories of the driving feet were gained with transient simulation. The vibration modes and the mechanical output abilities were tested to evaluate the proposed motor further by a prototype. The maximum output speed was tested to be 416 mm/s, the maximum thrust force was 21 N, and the maximum output power was 5.453 W under frequency of 29.52 kHz and voltage of 100 V rms . The maximum output power density of the prototype reached 7.59 W/kg, which was even greater than a previous similar motor under the exciting voltage of 200 V rms . The proposed motor showed great potential for linear driving of large thrust force and high power density.

Analysis of laboratory compaction methods of roller compacted concrete

NASA Astrophysics Data System (ADS)

Trtík, Tomáš; Chylík, Roman; Bílý, Petr; Fládr, Josef

2017-09-01

Roller-Compacted Concrete (RCC) is an ordinary concrete poured and compacted with machines typically used for laying of asphalt road layers. One of the problems connected with this technology is preparation of representative samples in the laboratory. The aim of this work was to analyse two methods of preparation of RCC laboratory samples with bulk density as the comparative parameter. The first method used dynamic compaction by pneumatic hammer. The second method of compaction had a static character. The specimens were loaded by precisely defined force in laboratory loading machine to create the same conditions as during static rolling (in the Czech Republic, only static rolling is commonly used). Bulk densities obtained by the two compaction methods were compared with core drills extracted from real RCC structure. The results have shown that the samples produced by pneumatic hammer tend to overestimate the bulk density of the material. For both compaction methods, immediate bearing index test was performed to verify the quality of compaction. A fundamental difference between static and dynamic compaction was identified. In static compaction, initial resistance to penetration of the mandrel was higher, after exceeding certain limit the resistance was constant. This means that the samples were well compacted just on the surface. Specimens made by pneumatic hammer actively resisted throughout the test, the whole volume was uniformly compacted.

Mapping forest structure and composition from low-density LiDAR for informed forest, fuel, and fire management at Eglin Air Force Base, Florida, USA

Treesearch

Andrew T. Hudak; Benjamin C. Bright; Scott M. Pokswinski; E. Louise Loudermilk; Joseph J. O' Brien; Benjamin S. Hornsby; Carine Klauberg; Carlos A. Silva

2016-01-01

Eglin Air Force Base (AFB) in Florida, in the United States, conserves a large reservoir of native longleaf pine (Pinus palustris Mill.) stands that land managers maintain by using frequent fires. We predicted tree density, basal area, and dominant tree species from 195 forest inventory plots, low-density airborne LiDAR, and Landsat data available across the entirety...

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.

Fluid flow through a high cell density fluidized-bed during centrifugal bioreactor culture.

PubMed

Detzel, Christopher J; Van Wie, Bernard J; Ivory, Cornelius F

2010-01-01

An increasing demand for products such as tissues, proteins, and antibodies from mammalian cell suspension cultures is driving interest in increasing production through high-cell density bioreactors. The centrifugal bioreactor (CCBR) retains cells by balancing settling forces with surface drag forces due to medium throughput and is capable of maintaining cell densities above 10(8) cells/mL. This article builds on a previous study where the fluid mechanics of an empty CCBR were investigated showing fluid flow is nonuniform and dominated by Coriolis forces, raising concerns about nutrient and cell distribution. In this article, we demonstrate that the previously reported Coriolis forces are still present in the CCBR, but masked by the presence of cells. Experimental dye injection observations during culture of 15 microm hybridoma cells show a continual uniform darkening of the cell bed, indicating the region of the reactor containing cells is well mixed. Simulation results also indicate the cell bed is well mixed during culture of mammalian cells ranging in size from 10 to 20 microm. However, simulations also allow for a slight concentration gradient to be identified and attributed to Coriolis forces. Experimental results show cell density increases from 0.16 to 0.26 when centrifugal force is doubled by increasing RPM from 650 to 920 at a constant inlet velocity of 6.5 cm/s; an effect also observed in the simulation. Results presented in this article indicate cells maintained in the CCBR behave as a high-density fluidized bed of cells providing a homogeneous environment to ensure optimal growth conditions. (c) 2010 American Institute of Chemical Engineers

Fluid Flow through a High Cell Density Fluidized-Bed during Centrifugal Bioreactor Culture

PubMed Central

Detzel, Christopher J.; Van Wie, Bernard J.; Ivory, Cornelius F.

2010-01-01

An increasing demand for products such as tissues, proteins, and antibodies from mammalian cell suspension cultures is driving interest in increasing production through high-cell density bioreactors. The centrifugal bioreactor (CCBR) retains cells by balancing settling forces with surface drag forces due to medium throughput and is capable of maintaining cell densities above 108 cells/mL. This article builds on a previous study where the fluid mechanics of an empty CCBR were investigated showing fluid flow is nonuniform and dominated by Coriolis forces, raising concerns about nutrient and cell distribution. In this article, we demonstrate that the previously reported Coriolis forces are still present in the CCBR, but masked by the presence of cells. Experimental dye injection observations during culture of 15 μm hybridoma cells show a continual uniform darkening of the cell bed, indicating the region of the reactor containing cells is well mixed. Simulation results also indicate the cell bed is well mixed during culture of mammalian cells ranging in size from 10 to 20 μm. However, simulations also allow for a slight concentration gradient to be identified and attributed to Coriolis forces. Experimental results show cell density increases from 0.16 to 0.26 when centrifugal force is doubled by increasing RPM from 650 to 920 at a constant inlet velocity of 6.5 cm/s; an effect also observed in the simulation. Results presented in this article indicate cells maintained in the CCBR behave as a high-density fluidized bed of cells providing a homogeneous environment to ensure optimal growth conditions. PMID:20205172

Muscle Velocity and Inertial Force from Phase Contrast Magnetic Resonance Imaging

PubMed Central

Wentland, Andrew L.; McWalter, Emily J.; Pal, Saikat; Delp, Scott L.; Gold, Garry E.

2014-01-01

Purpose To evaluate velocity waveforms in muscle and to create a tool and algorithm for computing and analyzing muscle inertial forces derived from 2D phase contrast (PC) MRI. Materials and Methods PC MRI was performed in the forearm of four healthy volunteers during 1 Hz cycles of wrist flexion-extension as well as in the lower leg of six healthy volunteers during 1 Hz cycles of plantarflexion-dorsiflexion. Inertial forces (F) were derived via the equation F = ma. The mass, m, was derived by multiplying voxel volume by voxel-by-voxel estimates of density via fat-water separation techniques. Acceleration, a, was obtained via the derivative of the PC MRI velocity waveform. Results Mean velocities in the flexors of the forearm and lower leg were 1.94 ± 0.97 cm/s and 5.57 ± 2.72 cm/s, respectively, as averaged across all subjects; the inertial forces in the flexors of the forearm and lower leg were 1.9 × 10-3 ± 1.3 × 10-3 N and 1.1 × 10-2 ± 6.1 × 10-3 N, respectively, as averaged across all subjects. Conclusion PC MRI provided a promising means of computing muscle velocities and inertial forces—providing the first method for quantifying inertial forces. PMID:25425185

Interplanetary Coronal Mass Ejection effects on thermospheric density as inferred from International Space Station orbital data

NASA Astrophysics Data System (ADS)

Mendaza, T.; Blanco-Ávalos, J. J.; Martín-Torres, J.

2017-11-01

The solar activity induces long term and short term periodical variations in the dynamics and composition of Earth's atmosphere. The Sun also shows non periodical (i.e., impulsive) activity that reaches the planets orbiting around it. In particular, Interplanetary Coronal Mass Ejections (ICMEs) reach Earth and interact with its magnetosphere and upper neutral atmosphere. Nevertheless, the interaction with the upper atmosphere is not well characterized because of the absence of regular and dedicated in situ measurements at high altitudes; thus, current descriptions of the thermosphere are based on semi empirical models. In this paper, we present the total neutral mass densities of the thermosphere retrieved from the orbital data of the International Space Station (ISS) using the General Perturbation Method, and we applied these densities to routinely compiled trajectories of the ISS in low Earth orbit (LEO). These data are explicitly independent of any atmospheric model. Our density values are consistent with atmospheric models, which demonstrates that our method is reliable for the inference of thermospheric density. We have inferred the thermospheric total neutral density response to impulsive solar activity forcing from 2001 to the end of 2006 and determined how solar events affect this response. Our results reveal that the ISS orbital parameters can be used to infer the thermospheric density and analyze solar effects on the thermosphere.

Cell-populated collagen lattice contraction model for the investigation of fibroblast collagen interactions.

PubMed

Ehrlich, H Paul; Moyer, Kurtis E

2013-01-01

The fibroblast-populated collagen lattice (FPCL) was intended to act as the dermal component for "skin-equivalent" or artificial skin developed for skin grafting burn patients. The "skin-equivalent" was clinically unsuccessful as a skin graft, but today it is successfully used as a dressing for the management of chronic wounds. The FPCL has, however, become an instrument for investigating cell-connective tissue interactions within a three-dimensional matrix. Through the capacity of cell compaction of collagen fibrils, the FPCL undergoes a reduction in volume referred to as lattice contraction. Lattice contraction proceeds by cell-generated forces that reduce the water mass between collagen fibers, generating a closer relationship between collagen fibers. The compaction of collagen fibers is responsible for the reduction in the FPCL volume. Cell-generated forces through the linkage of collagen fibers with fibroblast's cytoskeletal actin-rich microfilament structures are responsible for the completion of the collagen matrix compaction. The type of culture dish used to cast FPCL as well as the cell number will dictate the mechanism for compacting collagen matrices. Fibroblasts, at moderate density, cast as an FPCL within a petri dish and released from the surface of the dish soon after casting compact collagen fibers through cell tractional forces. Fibroblasts at moderate density cast as an FPCL within a tissue culture dish and not released for 4 days upon release show rapid lattice contraction through a mechanism of cell contraction forces. Fibroblasts at high density cast in an FPCL within a petri dish, released from the surface of the dish soon after casting, compact a collagen lattice very rapidly through forces related to cell elongation. The advantage of the FPCL contraction model is the study of cells in the three-dimensional environment, which is similar to the environment from which these cells were isolated. In this chapter methods are described for manufacturing collagen lattices, which assess the three forces involved in compacting and/or organizing collagen fibrils into thicker collagen fibers. The clinical relevance of the FPCL contraction model is related to advancing our understanding of wound contraction and scar contracture.

Quantitative nanoscale electrostatics of viruses.

PubMed

Hernando-Pérez, M; Cartagena-Rivera, A X; Lošdorfer Božič, A; Carrillo, P J P; San Martín, C; Mateu, M G; Raman, A; Podgornik, R; de Pablo, P J

2015-11-07

Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed ϕ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.

Drag force in a D-instanton background

NASA Astrophysics Data System (ADS)

Zhang, Zi-qiang; Luo, Zhong-jie; Hou, De-fu

2018-06-01

We study the drag force and diffusion coefficient with respect to a moving heavy quark in a D-instanton background, which corresponds to the Yang-Mills theory in the deconfining, high-temperature phase. It is shown that the presence of the D-instanton density tends to increase the drag force and decrease the diffusion coefficient, reverse to the effects of the velocity and the temperature. Moreover, the inclusion of the D-instanton density makes the medium less viscous.

A Weakly Nonlinear Model for the Damping of Resonantly Forced Density Waves in Dense Planetary Rings

NASA Astrophysics Data System (ADS)

Lehmann, Marius; Schmidt, Jürgen; Salo, Heikki

2016-10-01

In this paper, we address the stability of resonantly forced density waves in dense planetary rings. Goldreich & Tremaine have already argued that density waves might be unstable, depending on the relationship between the ring’s viscosity and the surface mass density. In the recent paper Schmidt et al., we have pointed out that when—within a fluid description of the ring dynamics—the criterion for viscous overstability is satisfied, forced spiral density waves become unstable as well. In this case, linear theory fails to describe the damping, but nonlinearity of the underlying equations guarantees a finite amplitude and eventually a damping of the wave. We apply the multiple scale formalism to derive a weakly nonlinear damping relation from a hydrodynamical model. This relation describes the resonant excitation and nonlinear viscous damping of spiral density waves in a vertically integrated fluid disk with density dependent transport coefficients. The model consistently predicts density waves to be (linearly) unstable in a ring region where the conditions for viscous overstability are met. Sufficiently far away from the Lindblad resonance, the surface mass density perturbation is predicted to saturate to a constant value due to nonlinear viscous damping. The wave’s damping lengths of the model depend on certain input parameters, such as the distance to the threshold for viscous overstability in parameter space and the ground state surface mass density.

Estradiol or fluoxetine alters depressive behavior and tryptophan hydroxylase in rat raphe.

PubMed

Yang, Fu-Zhong; Wu, Yan; Zhang, Wei-Guo; Cai, Yi-Yun; Shi, Shen-Xun

2010-03-10

The effects of 17beta-estradiol and fluoxetine on behavior of ovariectomized rats subjected to the forced swimming test and the expression of tryptophan hydroxylase (TPH) in dorsal and median raphe were investigated, respectively through time sampling technique of behavior scoring and immunohistochemistry. Both estradiol and fluoxetine increased swimming and decreased immobility in the forced swimming test. The forced swimming stress decreased integrated optical density of TPH-positive regions in dorsal and median raphe. Both estradiol and fluoxetine administration prevented integrated optical density of TPH-positive regions from being decreased by forced swimming stress. These observations suggest that both estradiol and fluoxetine have protective bearing on ovariectomized rats enduring forced swimming stress.

Marginal rigidity and history dependence in packings of attractive athermal emulsions

NASA Astrophysics Data System (ADS)

Bargteil, Dylan; Pontani, Lea-Laetitia; Brujic, Jasna

2014-03-01

The geometry and stress through particulate packings depends on the method of preparation and the interaction potential between the particles. Previously, we discovered that creaming frictionless, athermal emulsions with a short-range depletion attraction leads to an initial increase in the packing density above random close packing, followed by a monotonic decrease in density (Jorjadze et al, PNAS, 2011). This decrease is because the attractive force stabilizes loose voids, thus reducing the average coordination number, , of the packing. In order to understand the mechanism of packing creation, we investigate whether the final density is influenced by the polydispersity or the initial volume fraction of droplets, as it is in frictional packings. Finally, we compress the attractive packings by centrifugation to probe the scaling laws of pressure versus density and and compare them with those found in repulsive packings (Jorjadze et al, PRL, 2013).

Acoustic Sensing Based on Density Shift of Microspheres by Surface Binding of Gold Nanoparticles.

PubMed

Miyagawa, Akihisa; Inoue, Yoshinori; Harada, Makoto; Okada, Tetsuo

2017-01-01

Herein, we propose a concept for sensing based on density changes of microparticles (MPs) caused by a biochemical reaction. The MPs are levitated by a combined acoustic-gravitational force at a position determined by the density and compressibility. Importantly, the levitation is independent of the MPs sizes. When gold nanoparticles (AuNPs) are bound on the surface of polymer MPs through a reaction, the density of the MPs dramatically increases, and their levitation position in the acoustic-gravitational field is lowered. Because the shift of the levitation position is proportional to the number of AuNPs bound on one MP, we can determine the number of molecules involved in the reaction. The avidin-biotin reaction is used to demonstrate the effectiveness of this concept. The number of molecules involved in the reaction is very small because the reaction space is small for an MP; thus, the method has potential for highly sensitive detection.

Mass variation effect of teki grass (cyperus rotundus) composite against tensile strength and density

NASA Astrophysics Data System (ADS)

Rafiq Yanhar, Muhammad; Haris Nasution, A.

2018-05-01

The primary purpose of this study is to determine the tensile strength using ASTM D638 - 02a type IVB and density of teki grass (Cyperus rotundus) composite. The production process is carried out by mass variation of 2 gr, 3 gr, and 4 gr. Hand lay-up method with three repetitions is applied. Teki grass is chosen because it is easy to find and has some advantages biodegradable, harmless to health, available in large quantities, and cost-efficient. The test result showed the largest tensile strength is 21,61 MPa at 2-gram mass fiber. Fiber addition to 3 gram and 4-gram cause tensile strength decreases to 18,51 MPa and 11,65 MPa. It happens because the fibers are random and spread in all directions, so many fibers are undirectional with the tensile force. Beside that fibers addition made matrix volume reduced and a bond between fiber and matrix decreases, finally make fiber unable to hold the tensile force properly. It is recommended to use another type of ASTM D638 - 02a which has a larger narrow section like type I (13 mm) and type III (19mm) so specimens are not broken when removed from the mold, and there isn’t any decrease in tensile strength.Density test showed that fiber mass does not significantly affect the density.

Good Biocompatibility and Sintering Properties of Zirconia Nanoparticles Synthesized via Vapor-phase Hydrolysis

PubMed Central

Wang, Jigang; Yin, Wenyan; He, Xiao; Wang, Qiang; Guo, Ming; Chen, Shaowei

2016-01-01

ZrO2 nanoparticles were synthesized by a vapor-phase hydrolysis process, and characterized in terms of crystalline structures, hardness and microstructures by X-ray diffraction, Vickers hardness test method, and atomic force microscopy (AFM) measurements. Moreover, in vitro cytotoxicity evaluation and hemolysis assay showed that the nanoparticles possessed good biocompatibility. Hardness investigations and AFM measurements indicated that both the sintering temperature and compression force played an important role in determining the physical behaviors (hardness, roughness and density) of flakes of the ZrO2 nanoparticles. When ZrO2 nanoparticles synthesized at 500 °C were pressed into flakes under 6 MPa and sintered at 1400 °C, the resulting flakes exhibited an optimal combination of hardness (534.58 gf·mm−2), roughness (0.07 μm) and density (4.41 g·cm−3). As the Vickers hardness value of human bones is of 315~535 gf·mm−2 and the density of adult femuris about 1.3~1.7 g·cm−3, the experimental results showed that the ZrO2 flakes were comparable to human bones with a higher density. As a result, the synthesized ZrO2 NPs may be useful for biomedical applications, especially for bone repair and replacement in future. PMID:27725744

Operational Data Reduction Procedure for Determining Density and Vertical Structure of the Martian Upper Atmosphere from Mars Global Surveyor Accelerometer Measurements

NASA Technical Reports Server (NTRS)

Cancro, George J.; Tolson, Robert H.; Keating, Gerald M.

1998-01-01

The success of aerobraking by the Mars Global Surveyor (MGS) spacecraft was partly due to the analysis of MGS accelerometer data. Accelerometer data was used to determine the effect of the atmosphere on each orbit, to characterize the nature of the atmosphere, and to predict the atmosphere for future orbits. To interpret the accelerometer data, a data reduction procedure was developed to produce density estimations utilizing inputs from the spacecraft, the Navigation Team, and pre-mission aerothermodynamic studies. This data reduction procedure was based on the calculation of aerodynamic forces from the accelerometer data by considering acceleration due to gravity gradient, solar pressure, angular motion of the MGS, instrument bias, thruster activity, and a vibration component due to the motion of the damaged solar array. Methods were developed to calculate all of the acceleration components including a 4 degree of freedom dynamics model used to gain a greater understanding of the damaged solar array. The total error inherent to the data reduction procedure was calculated as a function of altitude and density considering contributions from ephemeris errors, errors in force coefficient, and instrument errors due to bias and digitization. Comparing the results from this procedure to the data of other MGS Teams has demonstrated that this procedure can quickly and accurately describe the density and vertical structure of the Martian upper atmosphere.

1,3,5-trinitro-1,3,5-triazine decomposition and chemisorption on Al(111) surface: first-principles molecular dynamics study.

PubMed

Umezawa, Naoto; Kalia, Rajiv K; Nakano, Aiichiro; Vashista, Priya; Shimojo, Fuyuki

2007-06-21

We have investigated the decomposition and chemisorption of a 1,3,5-trinitro-1,3,5-triazine (RDX) molecule on Al(111) surface using molecular dynamics simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). The real-space DFT calculations are based on higher-order finite difference and norm-conserving pseudopotential methods. Strong attractive forces between oxygen and aluminum atoms break N-O and N-N bonds in the RDX and, subsequently, the dissociated oxygen atoms and NO molecules oxidize the Al surface. In addition to these Al surface-assisted decompositions, ring cleavage of the RDX molecule is also observed. These reactions occur spontaneously without potential barriers and result in the attachment of the rest of the RDX molecule to the surface. This opens up the possibility of coating Al nanoparticles with RDX molecules to avoid the detrimental effect of oxidation in high energy density material applications.

Amplification due to two-stream instability of self-electric and magnetic fields of an ion beam propagating in background plasma

NASA Astrophysics Data System (ADS)

Tokluoglu, Erinc K.; Kaganovich, Igor D.; Carlsson, Johan A.; Hara, Kentaro; Startsev, Edward A.

2018-05-01

Propagation of charged particle beams in background plasma as a method of space charge neutralization has been shown to achieve a high degree of charge and current neutralization and therefore enables nearly ballistic propagation and focusing of charged particle beams. Correspondingly, the use of plasmas for propagation of charged particle beams has important applications for transport and focusing of intense particle beams in inertial fusion and high energy density laboratory plasma physics. However, the streaming of beam ions through a background plasma can lead to the development of two-stream instability between the beam ions and the plasma electrons. The beam electric and magnetic fields enhanced by the two-stream instability can lead to defocusing of the ion beam. Using particle-in-cell simulations, we study the scaling of the instability-driven self-electromagnetic fields and consequent defocusing forces with the background plasma density and beam ion mass. We identify plasma parameters where the defocusing forces can be reduced.

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

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

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

An updated Lagrangian discontinuous Galerkin hydrodynamic method for gas dynamics

DOE PAGES

Wu, Tong; Shashkov, Mikhail Jurievich; Morgan, Nathaniel Ray; ...

2018-04-09

Here, we present a new Lagrangian discontinuous Galerkin (DG) hydrodynamic method for gas dynamics. The new method evolves conserved unknowns in the current configuration, which obviates the Jacobi matrix that maps the element in a reference coordinate system or the initial coordinate system to the current configuration. The density, momentum, and total energy (ρ, ρu, E) are approximated with conservative higher-order Taylor expansions over the element and are limited toward a piecewise constant field near discontinuities using a limiter. Two new limiting methods are presented for enforcing the bounds on the primitive variables of density, velocity, and specific internal energymore » (ρ, u, e). The nodal velocity, and the corresponding forces, are calculated by solving an approximate Riemann problem at the element nodes. An explicit second-order method is used to temporally advance the solution. This new Lagrangian DG hydrodynamic method conserves mass, momentum, and total energy. 1D Cartesian coordinates test problem results are presented to demonstrate the accuracy and convergence order of the new DG method with the new limiters.« less

Motor unit number estimation based on high-density surface electromyography decomposition.

PubMed

Peng, Yun; He, Jinbao; Yao, Bo; Li, Sheng; Zhou, Ping; Zhang, Yingchun

2016-09-01

To advance the motor unit number estimation (MUNE) technique using high density surface electromyography (EMG) decomposition. The K-means clustering convolution kernel compensation algorithm was employed to detect the single motor unit potentials (SMUPs) from high-density surface EMG recordings of the biceps brachii muscles in eight healthy subjects. Contraction forces were controlled at 10%, 20% and 30% of the maximal voluntary contraction (MVC). Achieved MUNE results and the representativeness of the SMUP pools were evaluated using a high-density weighted-average method. Mean numbers of motor units were estimated as 288±132, 155±87, 107±99 and 132±61 by using the developed new MUNE at 10%, 20%, 30% and 10-30% MVCs, respectively. Over 20 SMUPs were obtained at each contraction level, and the mean residual variances were lower than 10%. The new MUNE method allows a convenient and non-invasive collection of a large size of SMUP pool with great representativeness. It provides a useful tool for estimating the motor unit number of proximal muscles. The present new MUNE method successfully avoids the use of intramuscular electrodes or multiple electrical stimuli which is required in currently available MUNE techniques; as such the new MUNE method can minimize patient discomfort for MUNE tests. Copyright © 2016 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

EFFECTS OF LASER RADIATION ON MATTER. LASER PLASMA: Steepening of the density profile under the action of a ponderomotive force during isothermal planar plasma expansion

NASA Astrophysics Data System (ADS)

Garanin, Sergey G.; Kir'yanov, Yu F.; Kochemasov, G. G.

1990-06-01

A theoretical investigation is reported of the deformation of the density profile of a plasma by a ponderomotive force under transient conditions. Initially, the structure of the density profile near the critical point coincides exactly with the solution of the steady-state problem. Plasma expansion is accompanied by growth of a spiky instability in the form of stimulated Brillouin scattering.

Nowcasting Cloud Fields for U.S. Air Force Special Operations

DTIC Science & Technology

2017-03-01

application of Bayes’ Rule offers many advantages over Kernel Density Estimation (KDE) and other commonly used statistical post-processing methods...reflectance and probability of cloud. A statistical post-processing technique is applied using Bayesian estimation to train the system from a set of past...nowcasting, low cloud forecasting, cloud reflectance, ISR, Bayesian estimation, statistical post-processing, machine learning 15. NUMBER OF PAGES

Damping of Resonantly Forced Density Waves in Dense Planetary Rings

NASA Astrophysics Data System (ADS)

Lehmann, Marius; Schmidt, Jürgen; Salo, Heikki

2016-10-01

We address the stability of resonantly forced density waves in dense planetary rings.Already by Goldreich and Tremaine (1978) it has been argued that density waves might be unstable, depending on the relationship between the ring's viscosity and the surface mass density. In the recent paper (Schmidt et al. 2016) we have pointed out that when - within a fluid description of the ring dynamics - the criterion for viscous overstability is satisfied, forced spiral density waves become unstable as well. In this case, linear theory fails to describe the damping.We apply the multiple scale formalism to derive a weakly nonlinear damping relation from a hydrodynamical model.This relation describes the resonant excitation and nonlinear viscous damping of spiral density waves in a vertically integrated fluid disk with density dependent transport coefficients. The model consistently predicts linear instability of density waves in a ring region where the conditions for viscous overstability are met. In this case, sufficiently far away from the Lindblad resonance, the surface mass density perturbation is predicted to saturate to a constant value due to nonlinear viscous damping. In general the model wave damping lengths depend on a set of input parameters, such as the distance to the threshold for viscous overstability and the ground state surface mass density.Our new model compares reasonably well with the streamline model for nonlinear density waves of Borderies et al. 1986.Deviations become substantial in the highly nonlinear regime, corresponding to strong satellite forcing.Nevertheless, we generally observe good or at least qualitative agreement between the wave amplitude profiles of both models. The streamline approach is superior at matching the total wave profile of waves observed in Saturn's rings, while our new damping relation is a comparably handy tool to gain insight in the evolution of the wave amplitude with distance from resonance, and the different regimes of wave formation and the dependence on the parameters of the model.

Influence of particle size distribution on nanopowder cold compaction processes

NASA Astrophysics Data System (ADS)

Boltachev, G.; Volkov, N.; Lukyashin, K.; Markov, V.; Chingina, E.

2017-06-01

Nanopowder uniform and uniaxial cold compaction processes are simulated by 2D granular dynamics method. The interaction of particles in addition to wide-known contact laws involves the dispersion forces of attraction and possibility of interparticle solid bridges formation, which have a large importance for nanopowders. Different model systems are investigated: monosized systems with particle diameter of 10, 20 and 30 nm; bidisperse systems with different content of small (diameter is 10 nm) and large (30 nm) particles; polydisperse systems corresponding to the log-normal size distribution law with different width. Non-monotone dependence of compact density on powder content is revealed in bidisperse systems. The deviations of compact density in polydisperse systems from the density of corresponding monosized system are found to be minor, less than 1 per cent.

FTIR of binary lead borate glass: Structural investigation

NASA Astrophysics Data System (ADS)

Othman, H. A.; Elkholy, H. S.; Hager, I. Z.

2016-02-01

The glass samples were prepared according to the following formula: (100-x) B2O3 - x PbO, where x = 20-80 mol% by melt quenching method. The density of the prepared samples was measured and molar volume was calculated. IR spectra were measured for the prepared samples to investigate the glass structure. The IR spectra were deconvoluted using curves of Gaussian shape at approximately the same frequencies. The deconvoluted data were used to study the effect of PbO content on all the structural borate groups. Some structural parameters such as density, packing density, bond length and bond force constant were theoretically calculated and were compared to the obtained experimental results. Deviation between the experimental and theoretically calculated parameters reflects the dual role of PbO content on the network of borate glass.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Disproportionate loss of thin filaments in human soleus muscle after 17-day bed rest

NASA Technical Reports Server (NTRS)

Riley, D. A.; Bain, J. L.; Thompson, J. L.; Fitts, R. H.; Widrick, J. J.; Trappe, S. W.; Trappe, T. A.; Costill, D. L.

1998-01-01

Previously we reported that, after 17-day bed rest unloading of 8 humans, soleus slow fibers atrophied and exhibited increased velocity of shortening without fast myosin expression. The present ultrastructural study examined fibers from the same muscle biopsies to determine whether decreased myofilament packing density accounted for the observed speeding. Quantitation was by computer-assisted morphometry of electron micrographs. Filament densities were normalized for sarcomere length, because density depends directly on length. Thick filament density was unchanged by bed rest. Thin filaments/microm2 decreased 16-23%. Glycogen filled the I band sites vacated by filaments. The percentage decrease in thin filaments (Y) correlated significantly (P < 0.05) with the percentage increase in velocity (X), (Y = 0.1X + 20%, R2 = 0.62). An interpretation is that fewer filaments increases thick to thin filament spacing and causes earlier cross-bridge detachment and faster cycling. Increased velocity helps maintain power (force x velocity) as atrophy lowers force. Atrophic muscles may be prone to sarcomere reloading damage because force/microm2 was near normal, and force per thin filament increased an estimated 30%.

Energy-free machine learning force field for aluminum.

PubMed

Kruglov, Ivan; Sergeev, Oleg; Yanilkin, Alexey; Oganov, Artem R

2017-08-17

We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential. The results are in excellent agreement with experimental data and results of full ab initio calculations.

Estimation of lattice strain in nanocrystalline RuO2 by Williamson-Hall and size-strain plot methods

NASA Astrophysics Data System (ADS)

Sivakami, R.; Dhanuskodi, S.; Karvembu, R.

2016-01-01

RuO2 nanoparticles (RuO2 NPs) have been successfully synthesized by the hydrothermal method. Structure and the particle size have been determined by X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and transmission electron microscopy (TEM). UV-Vis spectra reveal that the optical band gap of RuO2 nanoparticles is red shifted from 3.95 to 3.55 eV. BET measurements show a high specific surface area (SSA) of 118-133 m2/g and pore diameter (10-25 nm) has been estimated by Barret-Joyner-Halenda (BJH) method. The crystallite size and lattice strain in the samples have been investigated by Williamson-Hall (W-H) analysis assuming uniform deformation, deformation stress and deformation energy density, and the size-strain plot method. All other relevant physical parameters including stress, strain and energy density have been calculated. The average crystallite size and the lattice strain evaluated from XRD measurements are in good agreement with the results of TEM.

Numerical simulation and prediction of coastal ocean circulation

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

Chen, P.

1992-01-01

Numerical simulation and prediction of coastal ocean circulation have been conducted in three cases. 1. A process-oriented modeling study is conducted to study the interaction of a western boundary current (WBC) with coastal water, and its responses to upstream topographic irregularities. It is hypothesized that the interaction of propagating WBC frontal waves and topographic Rossby waves are responsible for upstream variability. 2. A simulation of meanders and eddies in the Norwegian Coastal Current (NCC) for February and March of 1988 is conducted with a newly developed nested dynamic interactive model. The model employs a coarse-grid, large domain to account formore » non-local forcing and a fine-grid nested domain to resolve meanders and eddies. The model is forced by wind stresses, heat fluxes and atmospheric pressure corresponding Feb/March of 1988, and accounts for river/fjord discharges, open ocean inflow and outflow, and M[sub 2] tides. The simulation reproduced fairly well the observed circulation, tides, and salinity features in the North Sea, Norwegian Trench and NCC region in the large domain and fairly realistic meanders and eddies in the NCC in the nested region. 3. A methodology for practical coastal ocean hindcast/forecast is developed, taking advantage of the disparate time scales of various forcing and considering wind to be the dominant factor in affecting density fluctuation in the time scale of 1 to 10 days. The density field obtained from a prognostic simulation is analyzed by the empirical orthogonal function method (EOF), and correlated with the wind; these information are then used to drive a circulation model which excludes the density calculation. The method is applied to hindcast the circulation in the New York Bight for spring and summer season of 1988. The hindcast fields compare favorably with the results obtained from the prognostic circulation model.« less

Development of a shape memory alloy actuator for a robotic eye prosthesis

NASA Astrophysics Data System (ADS)

Bunton, T. B. Wolfe; Faulkner, M. G.; Wolfaardt, J.

2005-08-01

The quality of life of patients who wear an orbital prosthesis would be vastly improved if their prostheses were also able to execute vertical and horizontal motion. This requires appropriate actuation and control systems to create an intelligent prosthesis. A method of actuation that meets the demanding design criteria is currently not available. The present work considers an activation system that follows a design philosophy of biomimicry, simplicity and space optimization. While several methods of actuation were considered, shape memory alloys were chosen for their high power density, high actuation forces and high displacements. The behaviour of specific shape memory alloys as an actuator was investigated to determine the force obtained, the transformation temperatures and details of the material processing. In addition, a large-scale prototype was constructed to validate the response of the proposed system.

How well can an amoeba climb?

PubMed Central

Fukui, Yoshio; Uyeda, Taro Q. P.; Kitayama, Chikako; Inoué, Shinya

2000-01-01

We report here our efforts to measure the crawling force generated by cells undergoing amoeboid locomotion. In a centrifuge microscope, acceleration was increased until amoebae of Dictyostelium discoideum were “stalled” or no longer able to “climb up.” The “apparent weight” of the amoebae at stalling rpm in myosin mutants depended on the presence of myosin II (but not myosins IA and IB) and paralleled the cortical strength of the cells. Surprisingly, however, the cell stalled not only in low-density media as expected but also in media with densities greater than the cell density where the buoyant force should push the amoeba upward. We find that the leading pseudopod is bent under centrifugal force in all stalled amoebae, suggesting that this pseudopod is very dense indeed. This finding also suggests that directional cell locomotion against resistive forces requires a turgid forward-pointing pseudopod, most likely sustained by cortical actomyosin II. PMID:10963666

Effect of attractive interactions between polymers on the effective force acting between colloids immersed in a polymer system: Analytic liquid-state theory.

PubMed

Chervanyov, A I

2016-12-28

By making use of the polymer reference interaction site model, we analytically study the effect of attractive interactions between polymers on the effective forces acting between colloids immersed in a polymer system. The performed theoretical analysis has no restrictions with respect to the polymer density and relative sizes of the colloids and polymers. The polymer mediated (PM) potential acting between colloids is shown to significantly depend on the strength and range of the polymer-polymer interactions. In the nano-particle limit, where the colloid radius is much smaller than the polymer gyration radius, the presence of attractive polymer-polymer interactions causes only quantitative changes to the PM potential. In the opposite limit of relatively large colloids, the polymer-polymer interactions revert the sign of the total effective force acting between colloids so that this force becomes attractive at sufficiently large polymer densities. With the objective to study an intricate interplay between the attractive PM forces and steric repulsion in different polymer density regimes, we calculate the second virial coefficient B of the total effective potential acting between colloids. The dependence of B on the polymer density is discussed in detail, revealing several novel features of the PM interactions caused by the presence of attractive polymer-polymer interactions.

Trouble with the Lorentz law of force: incompatibility with special relativity and momentum conservation.

PubMed

Mansuripur, Masud

2012-05-11

The Lorentz law of force is the fifth pillar of classical electrodynamics, the other four being Maxwell's macroscopic equations. The Lorentz law is the universal expression of the force exerted by electromagnetic fields on a volume containing a distribution of electrical charges and currents. If electric and magnetic dipoles also happen to be present in a material medium, they are traditionally treated by expressing the corresponding polarization and magnetization distributions in terms of bound-charge and bound-current densities, which are subsequently added to free-charge and free-current densities, respectively. In this way, Maxwell's macroscopic equations are reduced to his microscopic equations, and the Lorentz law is expected to provide a precise expression of the electromagnetic force density on material bodies at all points in space and time. This Letter presents incontrovertible theoretical evidence of the incompatibility of the Lorentz law with the fundamental tenets of special relativity. We argue that the Lorentz law must be abandoned in favor of a more general expression of the electromagnetic force density, such as the one discovered by Einstein and Laub in 1908. Not only is the Einstein-Laub formula consistent with special relativity, it also solves the long-standing problem of "hidden momentum" in classical electrodynamics.

Study of adhesion and friction properties on a nanoparticle gradient surface: transition from JKR to DMT contact mechanics.

PubMed

Ramakrishna, Shivaprakash N; Nalam, Prathima C; Clasohm, Lucy Y; Spencer, Nicholas D

2013-01-08

We have previously investigated the dependence of adhesion on nanometer-scale surface roughness by employing a roughness gradient. In this study, we correlate the obtained adhesion forces on nanometer-scale rough surfaces to their frictional properties. A roughness gradient with varying silica particle (diameter ≈ 12 nm) density was prepared, and adhesion and frictional forces were measured across the gradient surface in perfluorodecalin by means of atomic force microscopy with a polyethylene colloidal probe. Similarly to the pull-off measurements, the frictional forces initially showed a reduction with decreasing particle density and later an abrupt increase as the colloidal sphere began to touch the flat substrate beneath, at very low particle densities. The friction-load relation is found to depend on the real contact area (A(real)) between the colloid probe and the underlying particles. At high particle density, the colloidal sphere undergoes large deformations over several nanoparticles, and the contact adhesion (JKR type) dominates the frictional response. However, at low particle density (before the colloidal probe is in contact with the underlying surface), the colloidal sphere is suspended by a few particles only, resulting in local deformations of the colloid sphere, with the frictional response to the applied load being dominated by long-range, noncontact (DMT-type) interactions with the substrate beneath.

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

PubMed

Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

2014-09-04

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization.

Free-energy-based lattice Boltzmann model for the simulation of multiphase flows with density contrast.

PubMed

Shao, J Y; Shu, C; Huang, H B; Chew, Y T

2014-03-01

A free-energy-based phase-field lattice Boltzmann method is proposed in this work to simulate multiphase flows with density contrast. The present method is to improve the Zheng-Shu-Chew (ZSC) model [Zheng, Shu, and Chew, J. Comput. Phys. 218, 353 (2006)] for correct consideration of density contrast in the momentum equation. The original ZSC model uses the particle distribution function in the lattice Boltzmann equation (LBE) for the mean density and momentum, which cannot properly consider the effect of local density variation in the momentum equation. To correctly consider it, the particle distribution function in the LBE must be for the local density and momentum. However, when the LBE of such distribution function is solved, it will encounter a severe numerical instability. To overcome this difficulty, a transformation, which is similar to the one used in the Lee-Lin (LL) model [Lee and Lin, J. Comput. Phys. 206, 16 (2005)] is introduced in this work to change the particle distribution function for the local density and momentum into that for the mean density and momentum. As a result, the present model still uses the particle distribution function for the mean density and momentum, and in the meantime, considers the effect of local density variation in the LBE as a forcing term. Numerical examples demonstrate that both the present model and the LL model can correctly simulate multiphase flows with density contrast, and the present model has an obvious improvement over the ZSC model in terms of solution accuracy. In terms of computational time, the present model is less efficient than the ZSC model, but is much more efficient than the LL model.

Differential force balances during levitation

NASA Astrophysics Data System (ADS)

Todd, Paul

The simplest arithmetic of inertial, buoyant, magnetic and electrokinetic levitation is explored in the context of a model living system with “acceleration-sensitive structures” in which motion, if allowed, produces a biological effect. The simple model is a finite-sized object enclosed within another finite-sized object suspended in an outer fluid (liquid or vapor) medium. The inner object has density and electrical and magnetic properties quantitatively different from those of the outer object and the medium. In inertial levitation (“weightlessness”) inertial accelerations are balanced, and the forces due to them are canceled in accordance with Newton’s third law. In the presence of inertial acceleration (gravity, centrifugal) motionlessness depends on a balance between the levitating force and the inertial force. If the inner and outer objects differ in density one or the other will be subjected to an unbalanced force when one object is levitated by any other force (buoyant, magnetic, electrokinetic). The requirements for motionlessness of the internal object in the presence of a levitating force are equality of density in the case of buoyant levitation, equality of magnetic susceptibility in the case of magnetic levitation, and equality of zeta potential and dielectric constant in the case of electrokinetic levitation. Examples of internal “acceleration-sensitive structures” are cellular organelles and the organs of advanced plants and animals. For these structures fundamental physical data are important in the interpretation of the effects of forces used for levitation.

Modelling and characteristic analysis of tri-axle trucks with hydraulically interconnected suspensions

NASA Astrophysics Data System (ADS)

Ding, Fei; Han, Xu; Luo, Zhen; Zhang, Nong

2012-12-01

In this paper, a new hydraulically interconnected suspension (HIS) system is proposed for the implementation of a resistance control for the pitch and bounce modes of tri-axle heavy trucks. A lumped-mass half-truck model is established using the free-body diagram method. The equations of motion of a mechanical and hydraulic coupled system are developed by incorporating the hydraulic strut forces into the mechanical subsystem as externally applied forces. The transfer matrix method (TMM) is used to evaluate the impedance matrix of the hydraulic subsystem consisting of models of fluid pipes, damper valves, accumulators, and three-way junctions. The TMM is further applied to find the quantitative relationships between the hydraulic strut forces and boundary flow of the mechanical-fluid interactive subsystem. The modal analysis method is employed to perform the vibration analysis between the trucks with the conventional suspension and the proposed HIS. Comparison analysis focuses on free vibration with identified eigenvalues and eigenvectors, isolation vibration capacity, and force vibration in terms of the power spectrum density responses. The obtained results show the effectiveness of the proposed HIS system in reducing the pitch motion of sprung mass and simultaneously maintaining the ride comfort. The pitch stiffness is increased while the bounce stiffness is slightly softened. The peak values of sprung mass and wheel hop motions are greatly reduced, and the vibration decay rate of sprung mass is also significantly increased.

Drag force scaling for penetration into granular media.

PubMed

Katsuragi, Hiroaki; Durian, Douglas J

2013-05-01

Impact dynamics is measured for spherical and cylindrical projectiles of many different densities dropped onto a variety non-cohesive granular media. The results are analyzed in terms of the material-dependent scaling of the inertial and frictional drag contributions to the total stopping force. The inertial drag force scales similar to that in fluids, except that it depends on the internal friction coefficient. The frictional drag force scales as the square-root of the density of granular medium and projectile, and hence cannot be explained by the combination of granular hydrostatic pressure and Coulomb friction law. The combined results provide an explanation for the previously observed penetration depth scaling.

Microscopic Theory for the Role of Attractive Forces in the Dynamics of Supercooled Liquids.

PubMed

Dell, Zachary E; Schweizer, Kenneth S

2015-11-13

We formulate a microscopic, no adjustable parameter, theory of activated relaxation in supercooled liquids directly in terms of the repulsive and attractive forces within the framework of pair correlations. Under isochoric conditions, attractive forces can nonperturbatively modify slow dynamics, but at high enough density their influence vanishes. Under isobaric conditions, attractive forces play a minor role. High temperature apparent Arrhenius behavior and density-temperature scaling are predicted. Our results are consistent with recent isochoric simulations and isobaric experiments on a deeply supercooled molecular liquid. The approach can be generalized to treat colloidal gelation and glass melting, and other soft matter slow dynamics problems.

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

Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas

The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom’s test-particle insertion method, and other methods and modelsmore » are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.« less

Data Series Subtraction with Unknown and Unmodeled Background Noise

NASA Technical Reports Server (NTRS)

Vitale, Stefano; Congedo, Giuseppe; Dolesi, Rita; Ferroni, Valerio; Hueller, Mauro; Vetrugno, Daniele; Weber, William Joseph; Audley, Heather; Danzmann, Karsten; Diepholz, Ingo;

Propulsive force of Paramecium as revealed by the video centrifuge microscope.

PubMed

Kuroda, K; Kamiya, N

1989-09-01

Using the video centrifuge microscope we constructed, we observed the behavior of Paramecium cells in a solution of graded densities under centrifugal acceleration. Beyond 300g, they not only gather in the zone where the density is closest to theirs, but also orient themselves with their longitudinal axis parallel to the direction of centrifugation turning their anterior ends toward either centripetal or centrifugal direction. Since all of them retain still active swimming capacity, it is possible to calculate their propulsive force from the difference in density between theirs (1.04 g cm-3) and that of the upper or lower layer which they can reach. The propulsive force of single Paramecium cells thus obtained was calculated to be about 7 x 10(-4) dyn.

Charged anisotropic matter with linear or nonlinear equation of state

NASA Astrophysics Data System (ADS)

Varela, Victor; Rahaman, Farook; Ray, Saibal; Chakraborty, Koushik; Kalam, Mehedi

2010-08-01

Ivanov pointed out substantial analytical difficulties associated with self-gravitating, static, isotropic fluid spheres when pressure explicitly depends on matter density. Simplifications achieved with the introduction of electric charge were noticed as well. We deal with self-gravitating, charged, anisotropic fluids and get even more flexibility in solving the Einstein-Maxwell equations. In order to discuss analytical solutions we extend Krori and Barua’s method to include pressure anisotropy and linear or nonlinear equations of state. The field equations are reduced to a system of three algebraic equations for the anisotropic pressures as well as matter and electrostatic energy densities. Attention is paid to compact sources characterized by positive matter density and positive radial pressure. Arising solutions satisfy the energy conditions of general relativity. Spheres with vanishing net charge contain fluid elements with unbounded proper charge density located at the fluid-vacuum interface. Notably the electric force acting on these fluid elements is finite, although the acting electric field is zero. Net charges can be huge (1019C) and maximum electric field intensities are very large (1023-1024statvolt/cm) even in the case of zero net charge. Inward-directed fluid forces caused by pressure anisotropy may allow equilibrium configurations with larger net charges and electric field intensities than those found in studies of charged isotropic fluids. Links of these results with charged strange quark stars as well as models of dark matter including massive charged particles are highlighted. The van der Waals equation of state leading to matter densities constrained by cubic polynomial equations is briefly considered. The fundamental question of stability is left open.

Molecular conformational analysis, vibrational spectra and normal coordinate analysis of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene based on density functional theory calculations.

PubMed

Joseph, Lynnette; Sajan, D; Chaitanya, K; Isac, Jayakumary

2014-03-25

The conformational behavior and structural stability of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene (TDBE) were investigated by using density functional theory (DFT) method with the B3LYP/6-311++G(d,p) basis set combination. The vibrational wavenumbers of TDBE were computed at DFT level and complete vibrational assignments were made on the basis of normal coordinate analysis calculations (NCA). The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The infrared and Raman spectra were also predicted from the calculated intensities. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Copyright © 2013 Elsevier B.V. All rights reserved.

Multiscale Macromolecular Simulation: Role of Evolving Ensembles

PubMed Central

Singharoy, A.; Joshi, H.; Ortoleva, P.J.

2013-01-01

Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin timestep is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers. PMID:22978601

Force characteristic analysis of a magnetic gravity compensator with annular magnet array for magnetic levitation positioning system

NASA Astrophysics Data System (ADS)

Zhou, Yiheng; Kou, Baoquan; Liu, Peng; Zhang, He; Xing, Feng; Yang, Xiaobao

2018-05-01

Magnetic levitation positioning system (MLPS) is considered to be the state of the art in inspection and manufacturing systems in vacuum. In this paper, a magnetic gravity compensator with annular magnet array (AMA-MGC) for MLPS is proposed. Benefiting from the double-layer annular Halbach magnet array on the stator, the proposed AMA-MGC possesses the advantages of symmetrical force, high force density and small force fluctuation. Firstly, the basic structure and operation principle of the AMA-MGC are introduced. Secondly, the basic characteristics of the AMA-MGC such as magnetic field distribution, levitation force, parasitic force and parasitic torque are analyzed by the three-dimensional finite element analysis (3-D FEA). Thirdly, the influence of structural parameters on force density and force fluctuation is investigated, which is conductive to the design and optimization of the AMA-MGC. Finally, a prototype of the AMA-MGC is constructed, and the experiment shows good agreement with the 3-D FEA results.

Organic Crystal Engineering of Thermosetting Cyanate Ester Monomers: Influence of Structure on Melting Point

DTIC Science & Technology

2016-05-27

often discussed in the field of thermosetting materials, crystal engineering1-4 plays a key role in facilitating the successful utilization of these...not to alter the desirable properties of the polymerized networks. Fortunately, the field of crystal engineering provides examples where even very...Chickos and Acree.26 For molecular modeling, methods ranging from atomistic simulations with semi-empirical force fields to density functional

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

NASA Astrophysics Data System (ADS)

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.; Alam, Aftab

2017-09-01

Gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au1 -xFex alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: (1) an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic the homogeneously disordered alloy and (2) a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x =0.19 , which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x =0.19 , suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

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

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

DOE PAGES

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.; ...

2017-09-20

Here, gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au 1–xFe x alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic themore » homogeneously disordered alloy and a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x=0.19, which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x=0.19, suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.« less

Anomalous random correlations of force constants on the lattice dynamical properties of disordered Au-Fe alloys

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

Kangsabanik, Jiban; Chouhan, Rajiv K.; Johnson, D. D.

Here, gold iron (Au-Fe) alloys are of immense interest due to their biocompatibility, anomalous Hall conductivity, and applications in various medical treatments. However, irrespective of the method of preparation, they often exhibit a high level of disorder with properties sensitive to the thermal or magnetic annealing temperatures. We calculate the lattice dynamical properties of Au 1–xFe x alloys using density functional theory methods where, being multisite properties, reliable interatomic force constant (IFC) calculations in disordered alloys remain a challenge. We follow a twofold approach: an accurate IFC calculation in an environment with nominally zero chemical pair correlations to mimic themore » homogeneously disordered alloy and a configurational averaging for the desired phonon properties (e.g., dispersion, density of states, and entropy). We find an anomalous change in the IFC's and phonon dispersion (split bands) near x=0.19, which is attributed to the local stiffening of the Au-Au bonds when Au is in the vicinity of Fe. Other results based on mechanical and thermophysical properties reflect a similar anomaly: Phonon entropy, e.g., becomes negative below x=0.19, suggesting a tendency for chemical unmixing, reflecting the onset of a miscibility gap in the phase diagram. Our results match fairly well with reported data wherever available.« less

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

DOE PAGES

Gao, Zhiwen; Gao, Yanfei

2016-05-14

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

Why do receptor–ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

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

Gao, Zhiwen; Gao, Yanfei

We report that cell adhesion often exhibits the clustering of the receptor–ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation formore » the clustering/assembling of the receptor–ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor–ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Finally, cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.« less

Performance of tablet disintegrants: impact of storage conditions and relative tablet density.

PubMed

Quodbach, Julian; Kleinebudde, Peter

2015-01-01

Tablet disintegration can be influenced by several parameters, such as storage conditions, type and amount of disintegrant, and relative tablet density. Even though these parameters have been mentioned in the literature, the understanding of the disintegration process is limited. In this study, water uptake and force development of disintegrating tablets are analyzed, as they reveal underlying processes and interactions. Measurements were performed on dibasic calcium phosphate tablets containing seven different disintegrants stored at different relative humidities (5-97%), and on tablets containing disintegrants with different mechanisms of action (swelling and shape recovery), compressed to different relative densities. Disintegration times of tablets containing sodium starch glycolate are affected most by storage conditions, which is displayed in decreased water uptake and force development kinetics. Disintegration times of tablets with a swelling disintegrant are only marginally affected by relative tablet density, whereas the shape recovery disintegrant requires high relative densities for quick disintegration. The influence of relative tablet density on the kinetics of water uptake and force development greatly depends on the mechanism of action. Acquired data allows a detailed analysis of the influence of storage conditions and mechanisms of action on disintegration behavior.

An adaptive reconstruction for Lagrangian, direct-forcing, immersed-boundary methods

NASA Astrophysics Data System (ADS)

Posa, Antonio; Vanella, Marcos; Balaras, Elias

2017-12-01

Lagrangian, direct-forcing, immersed boundary (IB) methods have been receiving increased attention due to their robustness in complex fluid-structure interaction problems. They are very sensitive, however, on the selection of the Lagrangian grid, which is typically used to define a solid or flexible body immersed in a fluid flow. In the present work we propose a cost-efficient solution to this problem without compromising accuracy. Central to our approach is the use of isoparametric mapping to bridge the relative resolution requirements of Lagrangian IB, and Eulerian grids. With this approach, the density of surface Lagrangian markers, which is essential to properly enforce boundary conditions, is adapted dynamically based on the characteristics of the underlying Eulerian grid. The markers are not stored and the Lagrangian data-structure is not modified. The proposed scheme is implemented in the framework of a moving least squares reconstruction formulation, but it can be adapted to any Lagrangian, direct-forcing formulation. The accuracy and robustness of the approach is demonstrated in a variety of test cases of increasing complexity.

Weld defect identification in friction stir welding using power spectral density

NASA Astrophysics Data System (ADS)

Das, Bipul; Pal, Sukhomay; Bag, Swarup

2018-04-01

Power spectral density estimates are powerful in extraction of useful information retained in signal. In the current research work classical periodogram and Welch periodogram algorithms are used for the estimation of power spectral density for vertical force signal and transverse force signal acquired during friction stir welding process. The estimated spectral densities reveal notable insight in identification of defects in friction stir welded samples. It was observed that higher spectral density against each process signals is a key indication in identifying the presence of possible internal defects in the welded samples. The developed methodology can offer preliminary information regarding presence of internal defects in friction stir welded samples can be best accepted as first level of safeguard in monitoring the friction stir welding process.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Airspace Dimension Assessment with nanoparticles reflects lung density as quantified by MRI

PubMed Central

Jakobsson, Jonas K; Löndahl, Jakob; Olsson, Lars E; Diaz, Sandra; Zackrisson, Sophia; Wollmer, Per

2018-01-01

Background Airspace Dimension Assessment with inhaled nanoparticles is a novel method to determine distal airway morphology. This is the first empirical study using Airspace Dimension Assessment with nanoparticles (AiDA) to estimate distal airspace radius. The technology is relatively simple and potentially accessible in clinical outpatient settings. Method Nineteen never-smoking volunteers performed nanoparticle inhalation tests at multiple breath-hold times, and the difference in nanoparticle concentration of inhaled and exhaled gas was measured. An exponential decay curve was fitted to the concentration of recovered nanoparticles, and airspace dimensions were assessed from the half-life of the decay. Pulmonary tissue density was measured using magnetic resonance imaging (MRI). Results The distal airspace radius measured by AiDA correlated with lung tissue density as measured by MRI (ρ = −0.584; p = 0.0086). The linear intercept of the logarithm of the exponential decay curve correlated with forced expiratory volume in one second (FEV1) (ρ = 0.549; p = 0.0149). Conclusion The AiDA method shows potential to be developed into a tool to assess conditions involving changes in distal airways, eg, emphysema. The intercept may reflect airway properties; this finding should be further investigated.

A Study of Oil Viscosity Mental Model

NASA Astrophysics Data System (ADS)

Albaiti; Liliasari; Sumarna, Omay; Abdulkadir Martoprawiro, Muhamad

2017-02-01

There is no study regarding on how to learn viscosity of the liquid (e.g. oil) by interconnecting macroscopic, sub-microscopic and symbolic levels. Therefore, the purpose of this research was to study the mental model of the oil viscosity. Intermolecular attractive force of oil constituent on the sub-microscopic level is depicted in the form of mental models. In this research, the viscosity data for some types of oil was measured by using Hoppler method. Viscosity of mineral oil SAE 20W-50, mineral oil SAE 15W-40 and synthetic oil SAE 10W-40 were 1.75, 1.31, and 1.03 Pa s, and the densities of these oils were 908.64, 885.04, and 877.02 kg/m3, respectively. The results showed that the greater density of the mineral oil that is assumed to be composed of linear chains of hydrocarbons, the longer the chain of hydrocarbon linear. Consequently, there are stronger the London force and greater the oil viscosity. The density and viscosity of synthetic oil are lower than that of both mineral oils. Synthetic oil structurally forms polymers with large branching. This structure affects a lower synthetic oil viscosity. This study contributes to construct a mental model of pre-service chemistry teachers.

High-density force myography: A possible alternative for upper-limb prosthetic control.

PubMed

Radmand, Ashkan; Scheme, Erik; Englehart, Kevin

2016-01-01

Several multiple degree-of-freedom upper-limb prostheses that have the promise of highly dexterous control have recently been developed. Inadequate controllability, however, has limited adoption of these devices. Introducing more robust control methods will likely result in higher acceptance rates. This work investigates the suitability of using high-density force myography (HD-FMG) for prosthetic control. HD-FMG uses a high-density array of pressure sensors to detect changes in the pressure patterns between the residual limb and socket caused by the contraction of the forearm muscles. In this work, HD-FMG outperforms the standard electromyography (EMG)-based system in detecting different wrist and hand gestures. With the arm in a fixed, static position, eight hand and wrist motions were classified with 0.33% error using the HD-FMG technique. Comparatively, classification errors in the range of 2.2%-11.3% have been reported in the literature for multichannel EMG-based approaches. As with EMG, position variation in HD-FMG can introduce classification error, but incorporating position variation into the training protocol reduces this effect. Channel reduction was also applied to the HD-FMG technique to decrease the dimensionality of the problem as well as the size of the sensorized area. We found that with informed, symmetric channel reduction, classification error could be decreased to 0.02%.

Microcrack healing in non-ferrous metal tubes through eddy current pulse treatment.

PubMed

Xu, Wenchen; Yang, Chuan; Yu, Haiping; Jin, Xueze; Guo, Bin; Shan, Debin

2018-04-16

This study proposed a novel method to heal microcrack within Mg alloy tubes using high density eddy current pulse treatment (ECPT). Through electromagnetic induction inside a copper coil connected with a high density pulse power source supply, the high density (greater than 5 × 10 9  A/m 2 ) and short duration eddy current was generated in tube specimens of Mg alloy. The results show that the microcracks in tube specimens was healed evidently and the mechanical properties of the tubes subjected to ECPT were improved simultaneously. The crack healing during ECPT was ascribed to not only the thermal stress around the microcrack tips and the softening or melting of metals in the vicinity of microcrack tips, but also the squeezing action acted by the Lorentz force. In the inward-discharging scheme, both the compressive radial stress and tangential stress induced by the Lorentz force contributed to more sufficient crack healing and thus better mechanical properties of tube specimens after the ECPT experiment, compared to the outward-discharging scheme. The ECPT can heal microcracks automatically without directly contacting tubular specimens and is not limited by the length of tubular workpieces, exhibiting great potential for crack healing in non-ferrous alloy tubes.

Optimization of digital image processing to determine quantum dots' height and density from atomic force microscopy.

PubMed

Ruiz, J E; Paciornik, S; Pinto, L D; Ptak, F; Pires, M P; Souza, P L

2018-01-01

An optimized method of digital image processing to interpret quantum dots' height measurements obtained by atomic force microscopy is presented. The method was developed by combining well-known digital image processing techniques and particle recognition algorithms. The properties of quantum dot structures strongly depend on dots' height, among other features. Determination of their height is sensitive to small variations in their digital image processing parameters, which can generate misleading results. Comparing the results obtained with two image processing techniques - a conventional method and the new method proposed herein - with the data obtained by determining the height of quantum dots one by one within a fixed area, showed that the optimized method leads to more accurate results. Moreover, the log-normal distribution, which is often used to represent natural processes, shows a better fit to the quantum dots' height histogram obtained with the proposed method. Finally, the quantum dots' height obtained were used to calculate the predicted photoluminescence peak energies which were compared with the experimental data. Again, a better match was observed when using the proposed method to evaluate the quantum dots' height. Copyright © 2017 Elsevier B.V. All rights reserved.

Proceedings of Workshop on Atmospheric Density and Aerodynamic Drag Models for Air Force Operations Held at Air Force Geophysics Laboratory on 20-22 October 1987. Volume 1

DTIC Science & Technology

1990-02-13

considered with these production processes in a simple photochemical equilibrium calculation , we are able to determine the contribution each makes to the...Hessian matrix of second derivatives (which is required in the Newton-Raphson procedure) by the vector product of the gradient (VJ) and its transpose...was focused on the altitude region 80-250 Km. Papers were presented in the folowing areas: Air Force requirements , physics of density and drag

Design Considerations and Experimental Verification of a Rail Brake Armature Based on Linear Induction Motor Technology

NASA Astrophysics Data System (ADS)

Sakamoto, Yasuaki; Kashiwagi, Takayuki; Hasegawa, Hitoshi; Sasakawa, Takashi; Fujii, Nobuo

This paper describes the design considerations and experimental verification of an LIM rail brake armature. In order to generate power and maximize the braking force density despite the limited area between the armature and the rail and the limited space available for installation, we studied a design method that is suitable for designing an LIM rail brake armature; we considered adoption of a ring winding structure. To examine the validity of the proposed design method, we developed a prototype ring winding armature for the rail brakes and examined its electromagnetic characteristics in a dynamic test system with roller rigs. By repeating various tests, we confirmed that unnecessary magnetic field components, which were expected to be present under high speed running condition or when a ring winding armature was used, were not present. Further, the necessary magnetic field component and braking force attained the desired values. These studies have helped us to develop a basic design method that is suitable for designing the LIM rail brake armatures.

Improvement in thrust force estimation of solenoid valve considering minor hysteresis loop

NASA Astrophysics Data System (ADS)

Yoon, Myung-Hwan; Choi, Yun-Yong; Hong, Jung-Pyo

2017-05-01

Solenoid valve is a very important hydraulic actuator for an automatic transmission in terms of shift quality. The same form of pressure for the clutch and the input current are required for an ideal control. However, the gap between a pressure and a current can occur which brings a delay in a transmission and a decrease in quality. This problem is caused by hysteresis phenomenon. As the ascending or descending magnetic field is applied to the solenoid, different thrust forces are generated. This paper suggests the calculation method of the thrust force considering the hysteresis phenomenon and consequently the accurate force can be obtained. Such hysteresis occurs in ferromagnetic materials, however the hysteresis phenomenon includes a minor hysteresis loop which begins with an initial magnetization curve and is generated by DC biased field density. As the core of the solenoid is ferromagnetic material, an accurate thrust force is obtained by applying the minor hysteresis loop compared to the force calculated by considering only the initial magnetization curve. An analytical background and the detailed explanation of measuring the minor hysteresis loop are presented. Furthermore experimental results and finite element analysis results are compared for the verification.

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

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

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

Electrodeless RF Plasma Thruster Using m = 0 Coil

NASA Astrophysics Data System (ADS)

Nishimura, Shuichi; Arai, Daisuke; Kuwahara, Daisuke; Shinohara, Shunjiro

2016-10-01

In order to realize a deep space exploration in the future, we have been developing a next generation electrodeless electric propulsion system by electromagnetic acceleration of high-density helicon plasma. A new proposed method by m = 0 coil plasma acceleration (m is an azimuthal mode number) is based on the Lorentz force: a product of the induced azimuthal current by supplying an AC current to the m = 0 coil and the radial component of the externally applied magnetic field (divergent field configuration). Here, we have investigated the dependences of an ion velocity and an electron density on the external parameters, leading to optimized conditions, using the SHD device. By increasing AC current on the order of 100 A, we could see the increase of ion velocity and electron density by a factor of 2.5 and 3, respectively.

Effect of a new physiotherapy concept on bone mineral density, muscle force and gross motor function in children with bilateral cerebral palsy.

PubMed

Stark, C; Nikopoulou-Smyrni, P; Stabrey, A; Semler, O; Schoenau, E

2010-06-01

The purpose of this study was to determine the effect of a new physiotherapy concept on bone density, muscle force and motor function in bilateral spastic cerebral palsy children. In a retrospective data analysis 78 children were analysed. The concept included whole body vibration, physiotherapy, resistance training and treadmill training. The concept is structured in two in-patient stays and two periods of three months home-based vibration training. Outcome measures were dual-energy x-ray absorption (DXA), Leonardo Tilt Table and a modified Gross Motor Function Measure before and after six months of training. Percent changes were highly significant for bone mineral density, -content, muscle mass and significant for angle of verticalisation, muscle force and modified Gross Motor Function Measure after six months training. The new physiotherapy concept had a significant effect on bone mineral density, muscle force and gross motor function in bilateral spastic cerebral palsy children. This implicates an amelioration in all International Classification of Functioning, Disability and Health levels. The study serves as a basis for future research on evidence based paediatric physiotherapy taking into account developmental implications.

Correlations between U.S. county annual cancer incidence and population density.

PubMed

Vares, David Ae; St-Pierre, Linda S; Persinger, Michael A

2015-01-01

Population density implicitly involves specific distances between living individuals who exhibit biophysical forces and energies. Objective was to investigate major data bases of cancer incidence and population data to help understand the emergent properties of diseases that become apparent only when large populations and areas are considered. Correlation analyses of the annual incidence (years 2007 to 2011) of cancer in counties (2,885) of the U.S. and population densities were convergent with these quantitative predictions and suggested an inflection threshold around 50 people per square mile. The potential role of subtle or even "non-local" factors coupled to averaged population density in the viability and mortality of the human species may serve as alternative explanations to the attribution of malignancy to "chance" factors. Calculations indicated average distances between the electric force dipole of the brains or bodies of human beings generate forces known to affect DNA extension and when distributed over the Compton wavelength of the electron could produce energies sufficient to affect the binding of base nucleotides. An inclusive science of human ecology might benefit from considering subtle forces and energies associated with the individual members within the habitat that could determine the probability of cellular anomalies.

Plasmonically enhanced electromotive force of narrow bandgap PbS QD-based photovoltaics.

PubMed

Li, Xiaowei; McNaughter, Paul D; O'Brien, Paul; Minamimoto, Hiro; Murakoshi, Kei

2018-05-30

Electromotive force of photovoltaics is a key to define the output power density of photovoltaics. Multiple exciton generation (MEG) exhibited by semiconductor quantum dots (QDs) has great potential to enhance photovoltaic performance owing to the ability to generate more than one electron-hole pairs when absorbing a single photon. However, even in MEG-based photovoltaics, limitation of modifying the electromotive force exists due to the intrinsic electrochemical potential of the conduction band-edges of QDs. Here we report a pronouncedly improved photovoltaic performance by constructing a PbS QD-sensitized electrode that comprises plasmon-active Au nanoparticles embedded in a titanium dioxide thin film. Significant enhancement on electromotive force is characterized by the onset potential of photocurrent generation using MEG-effective PbS QDs with a narrow bandgap energy (Eg = 0.9 eV). By coupling with localized surface plasmon resonance (LSPR), such QDs exhibit improved photoresponses and the highest output power density over the other QDs with larger bandgap energies (Eg = 1.1 and 1.7 eV) under visible light irradiation. The wavelength-dependent onset potential and the output power density suggest effective electron injection owing to the enhanced density of electrons excited by energy overlapping between MEG and LSPR.

Computing mammographic density from a multiple regression model constructed with image-acquisition parameters from a full-field digital mammographic unit

PubMed Central

Lu, Lee-Jane W.; Nishino, Thomas K.; Khamapirad, Tuenchit; Grady, James J; Leonard, Morton H.; Brunder, Donald G.

2009-01-01

Breast density (the percentage of fibroglandular tissue in the breast) has been suggested to be a useful surrogate marker for breast cancer risk. It is conventionally measured using screen-film mammographic images by a labor intensive histogram segmentation method (HSM). We have adapted and modified the HSM for measuring breast density from raw digital mammograms acquired by full-field digital mammography. Multiple regression model analyses showed that many of the instrument parameters for acquiring the screening mammograms (e.g. breast compression thickness, radiological thickness, radiation dose, compression force, etc) and image pixel intensity statistics of the imaged breasts were strong predictors of the observed threshold values (model R2=0.93) and %density (R2=0.84). The intra-class correlation coefficient of the %-density for duplicate images was estimated to be 0.80, using the regression model-derived threshold values, and 0.94 if estimated directly from the parameter estimates of the %-density prediction regression model. Therefore, with additional research, these mathematical models could be used to compute breast density objectively, automatically bypassing the HSM step, and could greatly facilitate breast cancer research studies. PMID:17671343

Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

NASA Astrophysics Data System (ADS)

Asiaee, Alireza; Benjamin, Kenneth M.

2016-08-01

For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (no SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0-1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.

Pumping Liquid Oxygen by Use of Pulsed Magnetic Fields

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Modeling of Thermospheric Neutral Density Variations in Response to Geomagnetic Forcing using GRACE Accelerometer Data

NASA Astrophysics Data System (ADS)

Calabia, A.; Matsuo, T.; Jin, S.

2017-12-01

The upper atmospheric expansion refers to an increase in the temperature and density of Earth's thermosphere due to increased geomagnetic and space weather activities, producing anomalous atmospheric drag on LEO spacecraft. Increased drag decelerates satellites, moving their orbit closer to Earth, decreasing the lifespan of satellites, and making satellite orbit determination difficult. In this study, thermospheric neutral density variations due to geomagnetic forcing are investigated from 10 years (2003-2013) of GRACE's accelerometer-based estimates. In order to isolate the variations produced by geomagnetic forcing, 99.8% of the total variability has been modeled and removed through the parameterization of annual, LST, and solar-flux variations included in the primary Empirical Orthogonal Functions. The residual disturbances of neutral density variations have been investigated further in order to unravel their relationship to several geomagnetic indices and space weather activity indicators. Stronger fluctuations have been found in the southern polar cap, following the dipole-tilt angle variations. While the parameterization of the residual disturbances in terms of Dst index results in the best fit to training data, the use of merging electric field as a predictor leads to the best forecasting performance. An important finding is that modeling of neutral density variations in response geomagnetic forcing can be improved by accounting for the latitude-dependent delay. Our data-driven modeling results are further compared to modeling with TIEGCM.

A NEW DENSITY VARIANCE-MACH NUMBER RELATION FOR SUBSONIC AND SUPERSONIC ISOTHERMAL TURBULENCE

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

Konstandin, L.; Girichidis, P.; Federrath, C.

The probability density function of the gas density in subsonic and supersonic, isothermal, driven turbulence is analyzed using a systematic set of hydrodynamical grid simulations with resolutions of up to 1024{sup 3} cells. We perform a series of numerical experiments with root-mean-square (rms) Mach number M ranging from the nearly incompressible, subsonic (M=0.1) to the highly compressible, supersonic (M=15) regime. We study the influence of two extreme cases for the driving mechanism by applying a purely solenoidal (divergence-free) and a purely compressive (curl-free) forcing field to drive the turbulence. We find that our measurements fit the linear relation between themore » rms Mach number and the standard deviation (std. dev.) of the density distribution in a wide range of Mach numbers, where the proportionality constant depends on the type of forcing. In addition, we propose a new linear relation between the std. dev. of the density distribution {sigma}{sub {rho}} and that of the velocity in compressible modes, i.e., the compressible component of the rms Mach number, M{sub comp}. In this relation the influence of the forcing is significantly reduced, suggesting a linear relation between {sigma}{sub {rho}} and M{sub comp}, independent of the forcing, and ranging from the subsonic to the supersonic regime.« less

A general description of detachment for multidimensional modelling of biofilms.

PubMed

Xavier, Joao de Bivar; Picioreanu, Cristian; van Loosdrecht, Mark C M

2005-09-20

A general method for describing biomass detachment in multidimensional biofilm modelling is introduced. Biomass losses from processes acting on the entire surface of the biofilm, such as erosion, are modelled using a continuous detachment speed function F(det). Discrete detachment events, i.e. sloughing, are implicitly derived from simulations. The method is flexible to allow F(det) to take several forms, including expressions dependent on any state variables such as the local biofilm density. This methodology for biomass detachment was integrated with multidimensional (2D and 3D) particle-based multispecies biofilm models by using a novel application of the level set method. Application of the method is illustrated by trends in the dynamics of biofilms structure and activity derived from simulations performed on a simple model considering uniform biomass (case study I) and a model discriminating biomass composition in heterotrophic active mass, extracellular polymeric substances (EPS) and inert mass (case study II). Results from case study I demonstrate the effect of applied detachment forces as a fundamental factor influencing steady-state biofilm activity and structure. Trends from experimental observations reported in literature were correctly described. For example, simulation results indicated that biomass sloughing is reduced when erosion forces are increased. Case study II illustrates the application of the detachment methodology to systems with non-uniform biomass composition. Simulations carried out at different bulk concentrations of substrate show changes in biofilm structure (in terms of shape, density and spatial distribution of biomass components) and activity (in terms of oxygen and substrate consumption) as a consequence of either oxygen-limited or substrate-limited growth. (c) 2005 Wiley Periodicals, Inc.

Brush in the bath of active particles: Anomalous stretching of chains and distribution of particles

NASA Astrophysics Data System (ADS)

Li, Hui-shu; Zhang, Bo-kai; Li, Jian; Tian, Wen-de; Chen, Kang

2015-12-01

The interaction between polymer brush and colloidal particles has been intensively studied in the last two decades. Here, we consider a flat chain-grafted substrate immersed in a bath of active particles. Simulations show that an increase in the self-propelling force causes an increase in the number of particles that penetrate into the brush. Anomalously, the particle density inside the main body of the brush eventually becomes higher than that outside the brush at very large self-propelling force. The grafted chains are further stretched due to the steric repulsion from the intruded particles. Upon the increase of the self-propelling force, distinct stretching behaviors of the chains were observed for low and high grafting densities. Surprisingly, we find a weak descent of the average end-to-end distance of chains at high grafting density and very large force which is reminiscent of the compression effect of a chain in the active bath.

Design Difficulties in Stand Density Studies

Treesearch

Frank A. Bennett

1969-01-01

Designing unbiased stand density studies is difficult. An acceptable sample requires stratification of the plots of age, site, and density. When basal area, percent stocking, or Reineke's stand density index is used as the density measure, this stratification forces a high negative correlation between site and number of trees per acre. Mortality in trees per acre...

A parameter identification method for the rotordynamic coefficients of a high Reynolds number hydrostatic bearing

NASA Technical Reports Server (NTRS)

Rouvas, C.; Childs, D. W.

1993-01-01

In identifying the rotordynamic coefficients of a high-Reynolds-number hydrostatic bearing, fluid-flow induced forces present a unique problem, in that they provide an unmeasureable and uncontrollable excitation to the bearing. An analysis method is developed that effectively eliminates the effects of fluid-flow induced excitation on the estimation of the bearing rotordynamic coefficients, by using power spectral densities. In addition to the theoretical development, the method is verified experimentally by single-frequency testing, and repeatability tests. Results obtained for a bearing are the twelve rotordynamic coefficients (stiffness, damping, and inertia coefficients) as functions of eccentricity ratio, speed, and supply pressure.

Dependence of the Radiation Pressure on the Background Refractive Index

NASA Astrophysics Data System (ADS)

Webb, Kevin J.

2013-07-01

The 1978 experiments by Jones and Leslie showing that the radiation pressure on a mirror depends on the background medium refractive index have yet to be adequately explained using a force model and have provided a leading challenge to the Abraham form of the electromagnetic momentum. Those experimental results are predicted for the first time using a force representation that incorporates the Abraham momentum by utilizing the power calibration method employed in the Jones and Leslie experiments. With an extension of the same procedure, the polarization and angle independence of the experimental data are also explained by this model. Prospects are good for this general form of the electromagnetic force density to be effective in predicting other experiments with macroscopic materials. Furthermore, the rigorous representation of material dispersion makes the representation important for metamaterials that operate in the vicinity of homogenized material resonances.

Experimental rig to estimate the coefficient of friction between tire and surface in airplane touchdown simulations.

PubMed

Li, Chengwei; Zhan, Liwei

2015-08-01

To estimate the coefficient of friction between tire and runway surface during airplane touchdowns, we designed an experimental rig to simulate such events and to record the impact and friction forces being executed. Because of noise in the measured signals, we developed a filtering method that is based on the ensemble empirical mode decomposition and the bandwidth of probability density function of each intrinsic mode function to extract friction and impact force signals. We can quantify the coefficient of friction by calculating the maximum values of the filtered force signals. Signal measurements are recorded for different drop heights and tire rotational speeds, and the corresponding coefficient of friction is calculated. The result shows that the values of the coefficient of friction change only slightly. The random noise and experimental artifact are the major reason of the change.

Numerical simulations of unsteady transonic flow in diffusers

NASA Technical Reports Server (NTRS)

Liou, M.-S.; Coakley, T. J.

1982-01-01

Forced and naturally occurring, self-sustaining oscillations of transonic flows in two-dimensional diffusers were computed using MacCormack's hybrid method. Depending upon the shock strengths and the area ratios, the flow was fully attached or separated by either the shock or the adverse pressure gradient associated with the enlarging diffuser area. In the case of forced oscillations, a sinusoidal plane pressure wave at frequency 300 Hz was prescribed at the exit. A sufficiently large amount of data were acquired and Fourier analyzed. The distrbutions of time-mean pressures, the power spectral density, and the amplitude with phase angle along the top wall and in the core region were determined. Comparison with experimental results for the forced oscillation generally gave very good agreement; some success was achieved for the case of self-sustaining oscillation despite substantial three-dimensionality in the test. An observation of the sequence of self-sustaining oscillations was given.

A parametric study of hard tissue injury prediction using finite elements: consideration of geometric complexity, subfailure material properties, CT-thresholding, and element characteristics.

PubMed

Arregui-Dalmases, Carlos; Del Pozo, Eduardo; Duprey, Sonia; Lopez-Valdes, Francisco J; Lau, Anthony; Subit, Damien; Kent, Richard

2010-06-01

The objectives of this study were to examine the axial response of the clavicle under quasistatic compressions replicating the body boundary conditions and to quantify the sensitivity of finite element-predicted fracture in the clavicle to several parameters. Clavicles were harvested from 14 donors (age range 14-56 years). Quasistatic axial compression tests were performed using a custom rig designed to replicate in situ boundary conditions. Prior to testing, high-resolution computed tomography (CT) scans were taken of each clavicle. From those images, finite element models were constructed. Factors varied parametrically included the density used to threshold cortical bone in the CT scans, the presence of trabecular bone, the mesh density, Young's modulus, the maximum stress, and the element type (shell vs. solid, triangular vs. quadrilateral surface elements). The experiments revealed significant variability in the peak force (2.41 +/- 0.72 kN) and displacement to peak force (4.9 +/- 1.1 mm), with age (p < .05) and with some geometrical traits of the specimens. In the finite element models, the failure force and location were moderately dependent upon the Young's modulus. The fracture force was highly sensitive to the yield stress (80-110 MPa). Neither fracture location nor force was strongly dependent on mesh density as long as the element size was less than 5 x 5 mm(2). Both the fracture location and force were strongly dependent upon the threshold density used to define the thickness of the cortical shell.

Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation.

PubMed

Boitard, Simon; Loisel, Patrice

2007-05-01

The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift ...is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright-Fisher model is almost impossible to compute because of numerical reasons. However the Wright-Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models including selection or mutations. We show by several tests that this method is accurate for computing the conditional joint density of haplotype frequencies given that no haplotype has been lost. We also prove that it is far less time consuming than other methods such as Monte Carlo simulations.

Measuring the local mobility of graphene on semiconductors

NASA Astrophysics Data System (ADS)

Zhong, Haijian; Liu, Zhenghui; Wang, Jianfeng; Pan, Anlian; Xu, Gengzhao; Xu, Ke

2018-04-01

Mobility is an important parameter to gauge the performance of graphene devices, which is usually measured by FET or Hall methods relying on the use of insulating substrates. However, these methods are not applicable for the case of graphene on semiconductors, because some current will inevitably cross their junctions and flow through the semiconductors except directly traversing the graphene surface. Here we demonstrate a method for measuring the local mobility of graphene on gallium nitrides combining Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy (C-AFM). The carrier density related to Fermi level shifts in graphene can be acquired from KPFM. The local mobility of graphene is calculated from the carrier mean free path available from the effective contact area, which can be fitted from the local I-V curves in graphene/GaN junctions by C-AFM. Our method can be used to investigate an arbitrary region in graphene and also be applied to other semiconductor substrates and do not introduce damages. These results will benefit recent topical application researches for graphene integration in various semiconductor devices.

On the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures.

PubMed

Santra, Biswajit; Klimes, Jirí; Tkatchenko, Alexandre; Alfè, Dario; Slater, Ben; Michaelides, Angelos; Car, Roberto; Scheffler, Matthias

2013-10-21

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimeš, D. Alfè, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water.

Processing parameter optimization for the laser dressing of bronze-bonded diamond wheels

NASA Astrophysics Data System (ADS)

Deng, H.; Chen, G. Y.; Zhou, C.; Li, S. C.; Zhang, M. J.

2014-01-01

In this paper, a pulsed fiber-laser dressing method for bronze-bonded diamond wheels was studied systematically and comprehensively. The mechanisms for the laser dressing of bronze-bonded diamond wheels were theoretically analyzed, and the key processing parameters that determine the results of laser dressing, including the laser power density, pulse overlap ratio, ablation track line overlap ratio, and number of scanning cycles, were proposed for the first time. Further, the effects of these four key parameters on the oxidation-damaged layer of the material surface, the material removal efficiency, the material surface roughness, and the average protrusion height of the diamond grains were explored and summarized through pulsed laser ablation experiments. Under the current experimental conditions, the ideal values of the laser power density, pulse overlap ratio, ablation track line overlap ratio, and number of scanning cycles were determined to be 4.2 × 107 W/cm2, 30%, 30%, and 16, respectively. Pulsed laser dressing experiments were conducted on bronze-bonded diamond wheels using the optimized processing parameters; next, both the normal and tangential grinding forces produced by the dressed grinding wheel were measured while grinding alumina ceramic materials. The results revealed that the normal and tangential grinding forces produced by the laser-dressed grinding wheel during grinding were smaller than those of grinding wheels dressed using the conventional mechanical method, indicating that the pulsed laser dressing technology provides irreplaceable advantages relative to the conventional mechanical dressing method.

Synthesis and First Principles Investigation of HMX/NMP Cocrystal Explosive

NASA Astrophysics Data System (ADS)

Lin, He; Zhu, Shun-Guan; Zhang, Lin; Peng, Xin-Hua; LI, Hong-Zhen

2013-10-01

1,3,5,7-Tetranitro-l,3,5,7-tetrazocine (HMX)/N-methyl-2-pyrrolidone (NMP) cocrystal explosive was prepared by a solution evaporation method. This cocrystal explosive crystallized in the trigonal system (space group ? ), with cell parameters a = 16.605(8) Å and c = 31.496(4) Å. Theoretical investigations of the formation mechanism of HMX/NMP cocrystal were carried out in Cambridge serial total energy package (CASTEP) based on dispersion-corrected density functional theory (DFT-D) with a plane wave scheme. The exchange-correlation potential was treated with the Perdew-Burke-Ernzerhof function of generalized gradient approximation, and dispersion force was correlated using Grimme's method. The band structure, density of states, projected density of states, and Mulliken populations were calculated at the generalized gradient approximation level. The results showed that the main host-guest interactions in HMX/NMP cocrystal were hydrogen bonds and stacking interactions, which were the same as those analyzed using X-ray diffraction. Theoretical investigations of HMX/NMP cocrystal explosive may provide the basis for the preparation of cocrystal explosive composed of HMX and energetic materials.

On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: The anisole-ammonia 1:1 complex

NASA Astrophysics Data System (ADS)

Biczysko, Malgorzata; Piani, Giovanni; Pasquini, Massimiliano; Schiccheri, Nicola; Pietraperzia, Giangaetano; Becucci, Maurizio; Pavone, Michele; Barone, Vincenzo

2007-10-01

State-of-the-art spectroscopic and theoretical methods have been exploited in a joint effort to elucidate the subtle features of the structure and the energetics of the anisole-ammonia 1:1 complex, a prototype of microsolvation processes. Resonance enhanced multiphoton ionization and laser-induced fluorescence spectra are discussed and compared to high-level first-principles theoretical models, based on density functional, many body second order perturbation, and coupled cluster theories. In the most stable nonplanar structure of the complex, the ammonia interacts with the delocalized π electron density of the anisole ring: hydrogen bonding and dispersive forces provide a comparable stabilization energy in the ground state, whereas in the excited state the dispersion term is negligible because of electron density transfer from the oxygen to the aromatic ring. Ground and excited state geometrical parameters deduced from experimental data and computed by quantum mechanical methods are in very good agreement and allow us to unambiguously determine the molecular structure of the anisole-ammonia complex.

Ionic liquids-mediated interactions between nanorods

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

Yu, Zhou; Zhang, Fei; Huang, Jingsong

Surface forces mediated by room-temperature ionic liquids (RTILs) play an essential role in diverse applications including self-assembly, lubrication, and electrochemical energy storage. In this work, using molecular simulations we study the interactions between two nanorods immersed in model RTILs at rod-rod separations where both structural and double layer forces are important. The interaction force between neutral rods oscillates as the two rods approach each other, similar to the classical structural forces. Such oscillatory force originates from the density oscillation of RTILs near each rod and is affected by the packing constraints imposed by the neighboring rods. The oscillation period andmore » decay length of the oscillatory force are mainly dictated by the ion density distribution near isolated nanorods. When charges are introduced on the rods, the interaction force remains short-range and oscillatory, similar to the interactions between planar walls mediated by some protic RTILs reported earlier. Nevertheless, introducing net charges to the rods greatly changes the rod-rod interactions, e.g., by delaying the appearance of the first force trough and increasing the oscillation period and decay length of the interaction force. The oscillation period and decay length of the oscillatory force and free energy are commensurate with those of the space charge density near an isolated, charged rod. The free energy of rod-rod interactions reaches local minima (maxima) at rod-rod separations when the space charges near the two rods interfere constructively (destructively). Here, the insight on the short-range interactions between nanorods in RTILs helps guide the design of novel materials, e.g., crystalline ion gels based on rigid-rod polyanions and RTILs.« less

Configurational forces in electronic structure calculations using Kohn-Sham density functional theory

NASA Astrophysics Data System (ADS)

Motamarri, Phani; Gavini, Vikram

2018-04-01

We derive the expressions for configurational forces in Kohn-Sham density functional theory, which correspond to the generalized variational force computed as the derivative of the Kohn-Sham energy functional with respect to the position of a material point x . These configurational forces that result from the inner variations of the Kohn-Sham energy functional provide a unified framework to compute atomic forces as well as stress tensor for geometry optimization. Importantly, owing to the variational nature of the formulation, these configurational forces inherently account for the Pulay corrections. The formulation presented in this work treats both pseudopotential and all-electron calculations in a single framework, and employs a local variational real-space formulation of Kohn-Sham density functional theory (DFT) expressed in terms of the nonorthogonal wave functions that is amenable to reduced-order scaling techniques. We demonstrate the accuracy and performance of the proposed configurational force approach on benchmark all-electron and pseudopotential calculations conducted using higher-order finite-element discretization. To this end, we examine the rates of convergence of the finite-element discretization in the computed forces and stresses for various materials systems, and, further, verify the accuracy from finite differencing the energy. Wherever applicable, we also compare the forces and stresses with those obtained from Kohn-Sham DFT calculations employing plane-wave basis (pseudopotential calculations) and Gaussian basis (all-electron calculations). Finally, we verify the accuracy of the forces on large materials systems involving a metallic aluminum nanocluster containing 666 atoms and an alkane chain containing 902 atoms, where the Kohn-Sham electronic ground state is computed using a reduced-order scaling subspace projection technique [P. Motamarri and V. Gavini, Phys. Rev. B 90, 115127 (2014), 10.1103/PhysRevB.90.115127].

Ionic liquids-mediated interactions between nanorods

DOE PAGES

Yu, Zhou; Zhang, Fei; Huang, Jingsong; ...

2017-10-06

Surface forces mediated by room-temperature ionic liquids (RTILs) play an essential role in diverse applications including self-assembly, lubrication, and electrochemical energy storage. In this work, using molecular simulations we study the interactions between two nanorods immersed in model RTILs at rod-rod separations where both structural and double layer forces are important. The interaction force between neutral rods oscillates as the two rods approach each other, similar to the classical structural forces. Such oscillatory force originates from the density oscillation of RTILs near each rod and is affected by the packing constraints imposed by the neighboring rods. The oscillation period andmore » decay length of the oscillatory force are mainly dictated by the ion density distribution near isolated nanorods. When charges are introduced on the rods, the interaction force remains short-range and oscillatory, similar to the interactions between planar walls mediated by some protic RTILs reported earlier. Nevertheless, introducing net charges to the rods greatly changes the rod-rod interactions, e.g., by delaying the appearance of the first force trough and increasing the oscillation period and decay length of the interaction force. The oscillation period and decay length of the oscillatory force and free energy are commensurate with those of the space charge density near an isolated, charged rod. The free energy of rod-rod interactions reaches local minima (maxima) at rod-rod separations when the space charges near the two rods interfere constructively (destructively). Here, the insight on the short-range interactions between nanorods in RTILs helps guide the design of novel materials, e.g., crystalline ion gels based on rigid-rod polyanions and RTILs.« less

On Rolling Resonance and Slightly Asymmetrical Aerodynamic Force of the Reentry Body,

DTIC Science & Technology

1986-12-15

center of gravity -center of pressure. Migotsky [2 6 1 , under the condition of linear trajectory theand density changing with index, included resistance...and greater. Therefore, it is significant to study rolling speed control, and adopting active controls such as a mobile motor or a center of gravity ...through selection of nosetip configuration and ablative meterial , and adjusting wrapping method and spacing of the heat resistance layer for

[Measurements of the flux densities of static magnetic fields generated by two types of dental magnetic attachments and their retentive forces].

PubMed

Xu, Chun; Chao, Yong-lie; Du, Li; Yang, Ling

2004-05-01

To measure and analyze the flux densities of static magnetic fields generated by two types of commonly used dental magnetic attachments and their retentive forces, and to provide guidance for the clinical application of magnetic attachments. A digital Gaussmeter was used to measure the flux densities of static magnetic fields generated by two types of magnetic attachments, under four circumstances: open-field circuit; closed-field circuit; keeper and magnet slid laterally for a certain distance; and existence of air gap between keeper and magnet. The retentive forces of the magnetic attachments in standard closed-field circuit, with the keeper and magnet sliding laterally for a certain distance or with a certain air gap between keeper and magnet were measured by a tensile testing machine. There were flux leakages under both the open-field circuit and closed-field circuit of the two types of magnetic attachments. The flux densities on the surfaces of MAGNEDISC 800 (MD800) and MAGFIT EX600W (EX600) magnetic attachments under open-field circuit were 275.0 mT and 147.0 mT respectively. The flux leakages under closed-field circuit were smaller than those under open-field circuit. The respective flux densities on the surfaces of MD800 and EX600 magnetic attachments decreased to 11.4 mT and 4.5 mT under closed-field circuit. The flux density around the magnetic attachment decreased as the distance from the surface of the attachment increased. When keeper and magnet slid laterally for a certain distance or when air gap existed between keeper and magnet, the flux leakage increased in comparison with that under closed-field circuit. Under the standard closed-field circuit, the two types of magnetic attachments achieved the largest retentive forces. The retentive forces of MD800 and EX600 magnetic attachments under the standard closed-field circuit were 6.20 N and 4.80 N respectively. The retentive forces decreased with the sliding distance or with the increase of air gap between keeper and magnet. The magnetic attachments have flux leakages. When they are used in patients' oral cavities, if keeper and magnet are not attached accurately, the flux leakage will increase, and at the same time the retentive force will decrease. Therefore the keeper and magnet should be attached accurately in clinical application.

Quantum theory of multiscale coarse-graining.

PubMed

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

2018-03-14

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

Governing equations for electro-conjugate fluid flow

NASA Astrophysics Data System (ADS)

Hosoda, K.; Takemura, K.; Fukagata, K.; Yokota, S.; Edamura, K.

2013-12-01

An electro-conjugation fluid (ECF) is a kind of dielectric liquid, which generates a powerful flow when high DC voltage is applied with tiny electrodes. This study deals with the derivation of the governing equations for electro-conjugate fluid flow based on the Korteweg-Helmholtz (KH) equation which represents the force in dielectric liquid subjected to high DC voltage. The governing equations consist of the Gauss's law, charge conservation with charge recombination, the KH equation, the continuity equation and the incompressible Navier-Stokes equations. The KH equation consists of coulomb force, dielectric constant gradient force and electrostriction force. The governing equation gives the distribution of electric field, charge density and flow velocity. In this study, direct numerical simulation (DNS) is used in order to get these distribution at arbitrary time. Successive over-relaxation (SOR) method is used in analyzing Gauss's law and constrained interpolation pseudo-particle (CIP) method is used in analyzing charge conservation with charge recombination. The third order Runge-Kutta method and conservative second-order-accurate finite difference method is used in analyzing the Navier-Stokes equations with the KH equation. This study also deals with the measurement of ECF ow generated with a symmetrical pole electrodes pair which are made of 0.3 mm diameter piano wire. Working fluid is FF-1EHA2 which is an ECF family. The flow is observed from the both electrodes, i.e., the flow collides in between the electrodes. The governing equation successfully calculates mean flow velocity in between the collector pole electrode and the colliding region by the numerical simulation.

Free energy calculations: an efficient adaptive biasing potential method.

PubMed

Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul

2010-05-06

We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.

A novel consistent and well-balanced algorithm for simulations of multiphase flows on unstructured grids

NASA Astrophysics Data System (ADS)

Patel, Jitendra Kumar; Natarajan, Ganesh

2017-12-01

We discuss the development and assessment of a robust numerical algorithm for simulating multiphase flows with complex interfaces and high density ratios on arbitrary polygonal meshes. The algorithm combines the volume-of-fluid method with an incremental projection approach for incompressible multiphase flows in a novel hybrid staggered/non-staggered framework. The key principles that characterise the algorithm are the consistent treatment of discrete mass and momentum transport and the similar discretisation of force terms appearing in the momentum equation. The former is achieved by invoking identical schemes for convective transport of volume fraction and momentum in the respective discrete equations while the latter is realised by representing the gravity and surface tension terms as gradients of suitable scalars which are then discretised in identical fashion resulting in a balanced formulation. The hybrid staggered/non-staggered framework employed herein solves for the scalar normal momentum at the cell faces, while the volume fraction is computed at the cell centroids. This is shown to naturally lead to similar terms for pressure and its correction in the momentum and pressure correction equations respectively, which are again treated discretely in a similar manner. We show that spurious currents that corrupt the solution may arise both from an unbalanced formulation where forces (gravity and surface tension) are discretised in dissimilar manner and from an inconsistent approach where different schemes are used to convect the mass and momentum, with the latter prominent in flows which are convection-dominant with high density ratios. Interestingly, the inconsistent approach is shown to perform as well as the consistent approach even for high density ratio flows in some cases while it exhibits anomalous behaviour for other scenarios, even at low density ratios. Using a plethora of test problems of increasing complexity, we conclusively demonstrate that the consistent transport and balanced force treatment results in a numerically stable solution procedure and physically consistent results. The algorithm proposed in this study qualifies as a robust approach to simulate multiphase flows with high density ratios on unstructured meshes and may be realised in existing flow solvers with relative ease.

Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization

PubMed Central

Wang, Junmei; Tingjun, Hou

2011-01-01

Molecular mechanical force field (FF) methods are useful in studying condensed phase properties. They are complementary to experiment and can often go beyond experiment in atomic details. Even a FF is specific for studying structures, dynamics and functions of biomolecules, it is still important for the FF to accurately reproduce the experimental liquid properties of small molecules that represent the chemical moieties of biomolecules. Otherwise, the force field may not describe the structures and energies of macromolecules in aqueous solutions properly. In this work, we have carried out a systematic study to evaluate the General AMBER Force Field (GAFF) in studying densities and heats of vaporization for a large set of organic molecules that covers the most common chemical functional groups. The latest techniques, such as the particle mesh Ewald (PME) for calculating electrostatic energies, and Langevin dynamics for scaling temperatures, have been applied in the molecular dynamics (MD) simulations. For density, the average percent error (APE) of 71 organic compounds is 4.43% when compared to the experimental values. More encouragingly, the APE drops to 3.43% after the exclusion of two outliers and four other compounds for which the experimental densities have been measured with pressures higher than 1.0 atm. For heat of vaporization, several protocols have been investigated and the best one, P4/ntt0, achieves an average unsigned error (AUE) and a root-mean-square error (RMSE) of 0.93 and 1.20 kcal/mol, respectively. How to reduce the prediction errors through proper van der Waals (vdW) parameterization has been discussed. An encouraging finding in vdW parameterization is that both densities and heats of vaporization approach their “ideal” values in a synchronous fashion when vdW parameters are tuned. The following hydration free energy calculation using thermodynamic integration further justifies the vdW refinement. We conclude that simple vdW parameterization can significantly reduce the prediction errors. We believe that GAFF can greatly improve its performance in predicting liquid properties of organic molecules after a systematic vdW parameterization, which will be reported in a separate paper. PMID:21857814

Synthesis, Characterization, Detonation Performance, and DFT Calculation of HMX/PNO Cocrystal Explosive

NASA Astrophysics Data System (ADS)

Lin, He; Chen, Jian-Fu; Zhu, Shun-Guan; Li, Hong-Zhen; Huang, Yong

2017-01-01

A novel 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX)/pyridine-N-oxide (PNO) cocrystal at 1:1 molar ratio was synthesized by a solvent evaporation method, and its crystal structure was determined using X-ray diffraction (XRD). It crystallizes in the orthorhombic system with the Pbcn space group and cell parameters a = 12.712(3)Å, b = 9.315(3)Å, c = 12.909(3)Å. In addition, detonation performance of this cocrystal was estimated. The predicted detonation velocity and detonation pressure of this cocrystal are 7.47 km/s and 23.20 GPa, respectively, suggesting that it is less powerful than β-HMX. Finally, density functional theory, involving binding energy, atoms in molecule (AIM) theory, natural bond orbital (NBO) analysis, band structure, and density of states, was adopted to characterize the driving forces for the formation of this cocrystal. The results show that driving forces are dominated by the interactions between O atoms of PNO and methylene groups of HMX. It is expected that this research provides some bases for further HMX cocrystal design and preparation.

Development of liquid-environment frequency modulation atomic force microscope with low noise deflection sensor for cantilevers of various dimensions

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Jarvis, Suzanne P.

2006-04-01

We have developed a liquid-environment frequency modulation atomic force microscope (FM-AFM) with a low noise deflection sensor for a wide range of cantilevers with different dimensions. A simple yet accurate equation describing the theoretical limit of the optical beam deflection method in air and liquid is presented. Based on the equation, we have designed a low noise deflection sensor. Replaceable microscope objective lenses are utilized for providing a high magnification optical view (resolution: <3μm) as well as for focusing a laser beam (laser spot size: ˜10μm). Even for a broad range of cantilevers with lengths from 35to125μm, the sensor provides deflection noise densities of less than 11fm/√Hz in air and 16fm/√Hz in water. In particular, a cantilever with a length of 50μm gives the minimum deflection noise density of 5.7fm/√Hz in air and 7.3fm/√Hz in water. True atomic resolution of the developed FM-AFM is demonstrated by imaging mica in water.

Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

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

Thomas, Robert E.; Overy, Catherine; Opalka, Daniel

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, themore » present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.« less

A Experimental Investigation of Hydrodynamic Forces on Circular Cylinders in Sinusoidal and Random Oscillating Flow

NASA Astrophysics Data System (ADS)

Longoria, Raul Gilberto

An experimental apparatus has been developed which can be used to generate a general time-dependent planar flow across a cylinder. A mass of water enclosed with no free surface within a square cross-section tank and two spring pre-loaded pistons is oscillated using a hydraulic actuator. A circular cylinder is suspended horizontally in the tank by two X-Y force transducers used to simultaneously measure the total in-line and transverse forces. Fluid motion is measured using a differential pressure transducer for instantaneous acceleration and an LVDT for displacement. This investigation provides measurement of forces on cylinders subjected to planar fluid flow velocity with a time (and frequency) dependence which more accurately represent the random conditions encountered in a natural ocean environment. The use of the same apparatus for both sinusoidal and random experiments provides a quantified assessment of the applicability of sinusoidal planar oscillatory flow data in offshore structure design methods. The drag and inertia coefficients for a Morison equation representation of the inline force are presented for both sinusoidal and random flow. Comparison of the sinusoidal results is favorable with those of previous investigations. The results from random experiments illustrates the difference in the force mechanism by contrasting the force transfer coefficients for the inline and transverse forces. It is found that application of sinusoidal results to random hydrodynamic inline force prediction using the Morison equation wrongly weighs the drag and inertia components, and the transverse force is overpredicted. The use of random planar oscillatory flow in the laboratory, contrasted with sinusoidal planar oscillatory flow, quantifies the accepted belief that the force transfer coefficients from sinusoidal flow experiments are conservative for prediction of forces on cylindrical structures subjected to random sea waves and the ensuing forces. Further analysis of data is conducted in the frequency domain to illustrate models used for predicting the power spectral density of the inline force including a nonlinear describing function method. It is postulated that the large-scale vortex activity prominent in sinusoidal oscillatory flow is subdued in random flow conditions.

A weak-coupling immersed boundary method for fluid-structure interaction with low density ratio of solid to fluid

NASA Astrophysics Data System (ADS)

Kim, Woojin; Lee, Injae; Choi, Haecheon

2018-04-01

We present a weak-coupling approach for fluid-structure interaction with low density ratio (ρ) of solid to fluid. For accurate and stable solutions, we introduce predictors, an explicit two-step method and the implicit Euler method, to obtain provisional velocity and position of fluid-structure interface at each time step, respectively. The incompressible Navier-Stokes equations, together with these provisional velocity and position at the fluid-structure interface, are solved in an Eulerian coordinate using an immersed-boundary finite-volume method on a staggered mesh. The dynamic equation of an elastic solid-body motion, together with the hydrodynamic force at the provisional position of the interface, is solved in a Lagrangian coordinate using a finite element method. Each governing equation for fluid and structure is implicitly solved using second-order time integrators. The overall second-order temporal accuracy is preserved even with the use of lower-order predictors. A linear stability analysis is also conducted for an ideal case to find the optimal explicit two-step method that provides stable solutions down to the lowest density ratio. With the present weak coupling, three different fluid-structure interaction problems were simulated: flows around an elastically mounted rigid circular cylinder, an elastic beam attached to the base of a stationary circular cylinder, and a flexible plate, respectively. The lowest density ratios providing stable solutions are searched for the first two problems and they are much lower than 1 (ρmin = 0.21 and 0.31, respectively). The simulation results agree well with those from strong coupling suggested here and also from previous numerical and experimental studies, indicating the efficiency and accuracy of the present weak coupling.

Dynamics of shearing force and its correlations with chemical compositions and in vitro dry matter digestibility of stylo (Stylosanthes guianensis) stem.

PubMed

Zi, Xuejuan; Li, Mao; Zhou, Hanlin; Tang, Jun; Cai, Yimin

2017-12-01

The study explored the dynamics of shearing force and its correlation with chemical compositions and in vitro dry matter digestibility (IVDMD) of stylo. The shearing force, diameter, linear density, chemical composition, and IVDMD of different height stylo stem were investigated. Linear regression analysis was done to determine the relationships between the shearing force and cut height, diameter, chemical composition, or IVDMD. The results showed that shearing force of stylo stem increased with plant height increasing and the crude protein (CP) content and IVDMD decreased but fiber content increased over time, resulting in decreased forage value. In addition, tall stem had greater shearing force than short stem. Moreover, shearing force is positively correlated with stem diameter, linear density and fiber fraction, but negatively correlated with CP content and IVDMD. Overall, shearing force is an indicator more direct, easier and faster to measure than chemical composition and digestibility for evaluation of forage nutritive value related to animal performance. Therefore, it can be used to evaluate the nutritive value of stylo.

Ground reaction forces and bone parameters in females with tibial stress fracture.

PubMed

Bennell, Kim; Crossley, Kay; Jayarajan, Jyotsna; Walton, Elizabeth; Warden, Stuart; Kiss, Z Stephen; Wrigley, Tim

2004-03-01

Tibial stress fracture is a common overuse running injury that results from the interplay of repetitive mechanical loading and bone strength. This research project aimed to determine whether female runners with a history of tibial stress fracture (TSF) differ in ground reaction force (GRF) parameters during running, regional bone density, and tibial bone geometry from those who have never sustained a stress fracture (NSF). Thirty-six female running athletes (13 TSF; 23 NSF) ranging in age from 18 to 44 yr were recruited for this cross-sectional study. The groups were well matched for demographic, training, and menstrual parameters. A force platform measured selected GRF parameters (peak and time to peak for vertical impact and active forces, and horizontal braking and propulsive forces) during overground running at 4.0 m.s.(-1). Lumbar spine, proximal femur, and distal tibial bone mineral density were assessed by dual energy x-ray absorptiometry. Tibial bone geometry (cross-sectional dimensions and areas, and second moments of area) was calculated from a computerized tomography scan at the junction of the middle and distal thirds. There were no significant differences between the groups for any of the GRF, bone density, or tibial bone geometric parameters (P > 0.05). Both TSF and NSF subjects had bone density levels that were average or above average compared with a young adult reference range. Factor analysis followed by discriminant function analysis did not find any combinations of variables that differentiated between TSF and NSF groups. These findings do not support a role for GRF, bone density, or tibial bone geometry in the development of tibial stress fractures, suggesting that other risk factors were more important in this cohort of female runners.

The Cassie-Wenzel transition of fluids on nanostructured substrates: Macroscopic force balance versus microscopic density-functional theory.

PubMed

Tretyakov, Nikita; Papadopoulos, Periklis; Vollmer, Doris; Butt, Hans-Jürgen; Dünweg, Burkhard; Daoulas, Kostas Ch

2016-10-07

Classical density functional theory is applied to investigate the validity of a phenomenological force-balance description of the stability of the Cassie state of liquids on substrates with nanoscale corrugation. A bulk free-energy functional of third order in local density is combined with a square-gradient term, describing the liquid-vapor interface. The bulk free energy is parameterized to reproduce the liquid density and the compressibility of water. The square-gradient term is adjusted to model the width of the water-vapor interface. The substrate is modeled by an external potential, based upon the Lennard-Jones interactions. The three-dimensional calculation focuses on substrates patterned with nanostripes and square-shaped nanopillars. Using both the force-balance relation and density-functional theory, we locate the Cassie-to-Wenzel transition as a function of the corrugation parameters. We demonstrate that the force-balance relation gives a qualitatively reasonable description of the transition even on the nanoscale. The force balance utilizes an effective contact angle between the fluid and the vertical wall of the corrugation to parameterize the impalement pressure. This effective angle is found to have values smaller than the Young contact angle. This observation corresponds to an impalement pressure that is smaller than the value predicted by macroscopic theory. Therefore, this effective angle embodies effects specific to nanoscopically corrugated surfaces, including the finite range of the liquid-solid potential (which has both repulsive and attractive parts), line tension, and the finite interface thickness. Consistently with this picture, both patterns (stripes and pillars) yield the same effective contact angles for large periods of corrugation.

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

A New Approach in Generating Meteorological Forecasts for Ensemble Streamflow Forecasting using Multivariate Functions

NASA Astrophysics Data System (ADS)

Khajehei, S.; Madadgar, S.; Moradkhani, H.

2014-12-01

The reliability and accuracy of hydrological predictions are subject to various sources of uncertainty, including meteorological forcing, initial conditions, model parameters and model structure. To reduce the total uncertainty in hydrological applications, one approach is to reduce the uncertainty in meteorological forcing by using the statistical methods based on the conditional probability density functions (pdf). However, one of the requirements for current methods is to assume the Gaussian distribution for the marginal distribution of the observed and modeled meteorology. Here we propose a Bayesian approach based on Copula functions to develop the conditional distribution of precipitation forecast needed in deriving a hydrologic model for a sub-basin in the Columbia River Basin. Copula functions are introduced as an alternative approach in capturing the uncertainties related to meteorological forcing. Copulas are multivariate joint distribution of univariate marginal distributions, which are capable to model the joint behavior of variables with any level of correlation and dependency. The method is applied to the monthly forecast of CPC with 0.25x0.25 degree resolution to reproduce the PRISM dataset over 1970-2000. Results are compared with Ensemble Pre-Processor approach as a common procedure used by National Weather Service River forecast centers in reproducing observed climatology during a ten-year verification period (2000-2010).

On deriving the Maxwell stress tensor method for calculating the optical force and torque on an object in harmonic electromagnetic fields

NASA Astrophysics Data System (ADS)

Ye, Qian; Lin, Haoze

2017-07-01

Though extensively used in calculating optical force and torque acting on a material object illuminated by laser, the Maxwell stress tensor (MST) method follows the electromagnetic linear and angular momentum balance that is usually derived in most textbooks for a continuous volume charge distribution in free space, if not resorting to the application of Noether’s theorem in electrodynamics. To cast the conservation laws into a physically appealing form involving the current densities of linear and angular momentum, on which the MST method is based, the divergence theorem is employed to transform a volume integral into a surface integral. When a material object of finite volume is put into the field, it brings about a discontinuity of field across its surface, due to the presence of induced surface charge and surface current. Ambiguity arises among students in whether the divergence theorem can still be directly used without any justification. By taking into account the effect of the induced surface charge and current, we present a simple pedagogical derivation for the MST method for calculating the optical force and torque on an object immersed in monochromatic optical field, without resorting to Noether’s theorem. Although the results turn out to be identical to those given in the standard textbooks, our derivation avoids the direct use of the divergence theorem on a discontinuous function.

Capture-recapture of white-tailed deer using DNA from fecal pellet-groups

USGS Publications Warehouse

Goode, Matthew J; Beaver, Jared T; Muller, Lisa I; Clark, Joseph D.; van Manen, Frank T.; Harper, Craig T; Basinger, P Seth

2014-01-01

Traditional methods for estimating white-tailed deer population size and density are affected by behavioral biases, poor detection in densely forested areas, and invalid techniques for estimating effective trapping area. We evaluated a noninvasive method of capture—recapture for white-tailed deer (Odocoileus virginianus) density estimation using DNA extracted from fecal pellets as an individual marker and for gender determination, coupled with a spatial detection function to estimate density (spatially explicit capture—recapture, SECR). We collected pellet groups from 11 to 22 January 2010 at randomly selected sites within a 1-km2 area located on Arnold Air Force Base in Coffee and Franklin counties, Tennessee. We searched 703 10-m radius plots and collected 352 pellet-group samples from 197 plots over five two-day sampling intervals. Using only the freshest pellets we recorded 140 captures of 33 different animals (15M:18F). Male and female densities were 1.9 (SE = 0.8) and 3.8 (SE = 1.3) deer km-2, or a total density of 5.8 deer km-2 (14.9 deer mile-2). Population size was 20.8 (SE = 7.6) over a 360-ha area, and sex ratio was 1.0 M: 2.0 F (SE = 0.71). We found DNA sampling from pellet groups improved deer abundance, density and sex ratio estimates in contiguous landscapes which could be used to track responses to harvest or other management actions.

Estimation of Local Bone Loads for the Volume of Interest.

PubMed

Kim, Jung Jin; Kim, Youkyung; Jang, In Gwun

2016-07-01

Computational bone remodeling simulations have recently received significant attention with the aid of state-of-the-art high-resolution imaging modalities. They have been performed using localized finite element (FE) models rather than full FE models due to the excessive computational costs of full FE models. However, these localized bone remodeling simulations remain to be investigated in more depth. In particular, applying simplified loading conditions (e.g., uniform and unidirectional loads) to localized FE models have a severe limitation in a reliable subject-specific assessment. In order to effectively determine the physiological local bone loads for the volume of interest (VOI), this paper proposes a novel method of estimating the local loads when the global musculoskeletal loads are given. The proposed method is verified for the three VOI in a proximal femur in terms of force equilibrium, displacement field, and strain energy density (SED) distribution. The effect of the global load deviation on the local load estimation is also investigated by perturbing a hip joint contact force (HCF) in the femoral head. Deviation in force magnitude exhibits the greatest absolute changes in a SED distribution due to its own greatest deviation, whereas angular deviation perpendicular to a HCF provides the greatest relative change. With further in vivo force measurements and high-resolution clinical imaging modalities, the proposed method will contribute to the development of reliable patient-specific localized FE models, which can provide enhanced computational efficiency for iterative computing processes such as bone remodeling simulations.

Correlation between border traps and exposed surface properties in gate recessed normally-off Al2O3/GaN MOSFET

NASA Astrophysics Data System (ADS)

Yin, Ruiyuan; Li, Yue; Sun, Yu; Wen, Cheng P.; Hao, Yilong; Wang, Maojun

2018-06-01

We report the effect of the gate recess process and the surface of as-etched GaN on the gate oxide quality and first reveal the correlation between border traps and exposed surface properties in normally-off Al2O3/GaN MOSFET. The inductively coupled plasma (ICP) dry etching gate recess with large damage presents a rough and active surface that is prone to form detrimental GaxO validated by atomic force microscopy and X-ray photoelectron spectroscopy. Lower drain current noise spectral density of the 1/f form and less dispersive ac transconductance are observed in GaN MOSFETs fabricated with oxygen assisted wet etching compared with devices based on ICP dry etching. One decade lower density of border traps is extracted in devices with wet etching according to the carrier number fluctuation model, which is consistent with the result from the ac transconductance method. Both methods show that the density of border traps is skewed towards the interface, indicating that GaxO is of higher trap density than the bulk gate oxide. GaxO located close to the interface is the major location of border traps. The damage-free oxidation assisted wet etching gate recess technique presents a relatively smooth and stable surface, resulting in lower border trap density, which would lead to better MOS channel quality and improved device reliability.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Estimation of lattice strain in nanocrystalline RuO2 by Williamson-Hall and size-strain plot methods.

PubMed

Sivakami, R; Dhanuskodi, S; Karvembu, R

2016-01-05

RuO2 nanoparticles (RuO2 NPs) have been successfully synthesized by the hydrothermal method. Structure and the particle size have been determined by X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and transmission electron microscopy (TEM). UV-Vis spectra reveal that the optical band gap of RuO2 nanoparticles is red shifted from 3.95 to 3.55eV. BET measurements show a high specific surface area (SSA) of 118-133m(2)/g and pore diameter (10-25nm) has been estimated by Barret-Joyner-Halenda (BJH) method. The crystallite size and lattice strain in the samples have been investigated by Williamson-Hall (W-H) analysis assuming uniform deformation, deformation stress and deformation energy density, and the size-strain plot method. All other relevant physical parameters including stress, strain and energy density have been calculated. The average crystallite size and the lattice strain evaluated from XRD measurements are in good agreement with the results of TEM. Copyright © 2015 Elsevier B.V. All rights reserved.

Electromagnetic Properties Analysis on Hybrid-driven System of Electromagnetic Motor

NASA Astrophysics Data System (ADS)

Zhao, Jingbo; Han, Bingyuan; Bei, Shaoyi

2018-01-01

The hybrid-driven system made of permanent-and electromagnets applied in the electromagnetic motor was analyzed, equivalent magnetic circuit was used to establish the mathematical models of hybrid-driven system, based on the models of hybrid-driven system, the air gap flux, air-gap magnetic flux density, electromagnetic force was proposed. Taking the air-gap magnetic flux density and electromagnetic force as main research object, the hybrid-driven system was researched. Electromagnetic properties of hybrid-driven system with different working current modes is studied preliminary. The results shown that analysis based on hybrid-driven system can improve the air-gap magnetic flux density and electromagnetic force more effectively and can also guarantee the output stability, the effectiveness and feasibility of the hybrid-driven system are verified, which proved theoretical basis for the design of hybrid-driven system.

Higher-order symmetry energy and neutron star core-crust transition with Gogny forces

NASA Astrophysics Data System (ADS)

Gonzalez-Boquera, C.; Centelles, M.; Viñas, X.; Rios, A.

2017-12-01

Background: An accurate determination of the core-crust transition is necessary in the modeling of neutron stars for astrophysical purposes. The transition is intimately related to the isospin dependence of the nuclear force at low baryon densities. Purpose: To study the symmetry energy and the core-crust transition in neutron stars using the finite-range Gogny nuclear interaction and to examine the deduced crustal thickness and crustal moment of inertia. Methods: The second-, fourth-, and sixth-order coefficients of the Taylor expansion of the energy per particle in powers of the isospin asymmetry are analyzed for Gogny forces. These coefficients provide information about the departure of the symmetry energy from the widely used parabolic law. The neutron star core-crust transition is evaluated by looking at the onset of thermodynamical instability of the liquid core. The calculation is performed with the exact Gogny equation of state (EoS) (i.e., the Gogny EoS with the full isospin dependence) for the β -equilibrated matter of the core, and also with the Taylor expansion of the Gogny EoS in order to assess the influence of isospin expansions on locating the inner edge of neutron star crusts. Results: The properties of the core-crust transition derived from the exact EoS differ from the predictions of the Taylor expansion even when the expansion is carried through sixth order in the isospin asymmetry. Gogny forces, using the exact EoS, predict the ranges 0.094 fm-3≲ρt≲0.118 fm-3 for the transition density and 0.339 MeVfm-3≲Pt≲0.665 MeVfm-3 for the transition pressure. The transition densities show an anticorrelation with the slope parameter L of the symmetry energy. The transition pressures are not found to correlate with L . Neutron stars obtained with Gogny forces have maximum masses below 1.74 M⊙ and relatively small moments of inertia. The crustal mass and moment of inertia are evaluated and comparisons are made with the constraints from observed glitches in pulsars. Conclusions: The finite-range exchange contribution of the nuclear force, and its associated nontrivial isospin dependence, is key in determining the core-crust transition properties. Finite-order isospin expansions do not reproduce the core-crust transition results of the exact EoS. The predictions of the Gogny D1M force for the stellar crust are overall in broad agreement with those obtained using the Skyrme-Lyon EoS.

An N-body Integrator for Planetary Rings

NASA Astrophysics Data System (ADS)

Hahn, Joseph M.

2011-04-01

A planetary ring that is disturbed by a satellite's resonant perturbation can respond in an organized way. When the resonance lies in the ring's interior, the ring responds via an m-armed spiral wave, while a ring whose edge is confined by the resonance exhibits an m-lobed scalloping along the ring-edge. The amplitude of these disturbances are sensitive to ring surface density and viscosity, so modelling these phenomena can provide estimates of the ring's properties. However a brute force attempt to simulate a ring's full azimuthal extent with an N-body code will likely fail because of the large number of particles needed to resolve the ring's behavior. Another impediment is the gravitational stirring that occurs among the simulated particles, which can wash out the ring's organized response. However it is possible to adapt an N-body integrator so that it can simulate a ring's collective response to resonant perturbations. The code developed here uses a few thousand massless particles to trace streamlines within the ring. Particles are close in a radial sense to these streamlines, which allows streamlines to be treated as straight wires of constant linear density. Consequently, gravity due to these streamline is a simple function of the particle's radial distance to all streamlines. And because particles are responding to smooth gravitating streamlines, rather than discrete particles, this method eliminates the stirring that ordinarily occurs in brute force N-body calculations. Note also that ring surface density is now a simple function of streamline separations, so effects due to ring pressure and viscosity are easily accounted for, too. A poster will describe this N-body method in greater detail. Simulations of spiral density waves and scalloped ring-edges are executed in typically ten minutes on a desktop PC, and results for Saturn's A and B rings will be presented at conference time.

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.

Magneto-optical cooling of atoms.

PubMed

Raizen, Mark G; Budker, Dmitry; Rochester, Simon M; Narevicius, Julia; Narevicius, Edvardas

2014-08-01

We propose an alternative method to laser cooling. Our approach utilizes the extreme brightness of a supersonic atomic beam, and the adiabatic atomic coilgun to slow atoms in the beam or to bring them to rest. We show how internal-state optical pumping and stimulated optical transitions, combined with magnetic forces, can be used to cool the translational motion of atoms. This approach does not rely on momentum transfer from photons to atoms, as in laser cooling. We predict that our method can surpass laser cooling in terms of flux of ultracold atoms and phase-space density, with lower required laser power.

DFT calculations for anharmonic force field and spectroscopic constants of YC2 and its 13C isotopologues

NASA Astrophysics Data System (ADS)

Zhao, Yanliang; Wang, Meishan; Yang, Chuanlu; Ma, Xiaoguang; Li, Jing

2018-02-01

The construction of the complete third and the semi-diagonal quartic force fields including the anharmonicity of the ground state (X˜2A1) for yttrium dicarbide (YC2) is carried out employing the vibrational second-order perturbation theory (VPT2) in combination with the density functional theory (DFT). The equilibrium geometries optimization, anharmonic force field and vibrational spectroscopic constants of YC2 are calculated by B3LYP, B3PW91 and B3P86 methods. Aug-cc-pVnZ (n = D, T, Q) and cc-pVnZ-PP (n = D, T, Q) basis sets are chosen for C and Y atoms, respectively. The calculated geometry parameters of YC2 agree well with the corresponding experimental and previous theoretical results. The bonding characters of Ysbnd C2 or Csbnd C are discussed. Based on the optimized equilibrium geometries, the spectroscopic constants and anharmonic force field of YC2 are calculated. Comparing with the spectroscopic constants of YC2 derived from the experiment, the calculated results show that the B3PW91 and B3P86 methods are superior to B3LYP for YC2. The Coriolis coupling constants, cubic and quartic force constants of YC2 are reasonably predicted. Besides, the spectroscopic constants and anharmonic force field of Y13C2 (X˜2A1) and Y13CC (X˜2A‧) are calculated for the first time, which are expected to guide the high resolution experimental work for YC2 and its 13C isotopologues.

Accelerating molecular property calculations with nonorthonormal Krylov space methods

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

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

Accelerating molecular property calculations with nonorthonormal Krylov space methods

DOE PAGES

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.; ...

2016-05-03

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

BRIEF COMMUNICATION: A note on the Coulomb collision operator in curvilinear coordinates

NASA Astrophysics Data System (ADS)

Goncharov, P. R.

2010-10-01

The dynamic friction force, diffusion tensor, flux density in velocity space and Coulomb collision term are expressed in curvilinear coordinates via Trubnikov potential functions corresponding to each species of a background plasma. For comparison, explicit formulae are given for the dynamic friction force, diffusion tensor and collisional flux density in velocity space in curvilinear coordinates via Rosenbluth potential functions summed over all species of the background plasma.

Repulsive tip tilting as the dominant mechanism for hydrogen bond-like features in atomic force microscopy imaging

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

Lee, Alex J.; Sakai, Yuki; Kim, Minjung

2016-05-09

Experimental atomic force microscopy (AFM) studies have reported distinct features in regions with little electron density for various organic systems. These unexpected features have been proposed to be a direct visualization of intermolecular hydrogen bonding. Here, we apply a computational method using ab initio real-space pseudopotentials along with a scheme to account for tip tilting to simulate AFM images of the 8-hydroxyquinoline dimer and related systems to develop an understanding of the imaging mechanism for hydrogen bonds. We find that contrast for the observed “hydrogen bond” feature comes not from the electrostatic character of the bonds themselves but rather frommore » repulsive tip tilting induced by neighboring electron-rich atoms.« less

Determination of the surface charge density and temperature dependence of purple membrane by electric force microscopy.

PubMed

Du, Huiwen; Li, Denghua; Wang, Yibing; Wang, Chenxuan; Zhang, Dongdong; Yang, Yan-lian; Wang, Chen

2013-08-29

We report here the measurement of the temperature-dependent surface charge density of purple membrane (PM) by using electrostatic force microscopy (EFM). The surface charge density was measured to be 3.4 × 10(5) e/cm(2) at room temperature and reaches the minimum at around 52 °C. The initial decrease of the surface charge density could be attributed to the reduced dipole alignment because of the thermally induced protein mobility in PM. The increase of charge density at higher temperature could be ascribed to the weakened interaction between proteins and the lipids, which leads to the exposure of the charged amino acids. This work could be a benefit to the direct assessment of the structural stability and electric properties of biological membranes at the nanoscale.

Enhanced settling of nonheavy inertial particles in homogeneous isotropic turbulence: The role of the pressure gradient and the Basset history force.

PubMed

van Hinsberg, M A T; Clercx, H J H; Toschi, F

2017-02-01

The Stokes drag force and the gravity force are usually sufficient to describe the behavior of sub-Kolmogorov-size (or pointlike) heavy particles in turbulence, in particular when the particle-to-fluid density ratio ρ_{p}/ρ_{f}≳10^{3} (with ρ_{p} and ρ_{f} the particle and fluid density, respectively). This is, in general, not the case for smaller particle-to-fluid density ratios, in particular not for ρ_{p}/ρ_{f}≲10^{2}. In that case the pressure gradient force, added mass effects, and the Basset history force also play important roles. In this study we focus on the understanding of the role of these additional forces, all of hydrodynamic origin, in the settling of particles in turbulence. In order to qualitatively elucidate the complex dynamics of such particles in homogeneous isotropic turbulence, we first focus on the case of settling of such particles in the flow field of a single vortex. After having explored this simplified case we extend our analysis to homogeneous isotropic turbulence. In general, we found that the pressure gradient force leads to a decrease in the settling velocity. This can be qualitatively understood by the fact that this force prevents the particles from sweeping out of vortices, a mechanism known as preferential sweeping which causes enhanced settling. Additionally, we found that the Basset history force can both increase and decrease the enhanced settling, depending on the particle Stokes number. Finally, the role of the nonlinear Stokes drag has been explored, confirming that it affects settling of inertial particles in turbulence, but only in a limited way for the parameter settings used in this investigation.

An arbitrary boundary with ghost particles incorporated in coupled FEM-SPH model for FSI problems

NASA Astrophysics Data System (ADS)

Long, Ting; Hu, Dean; Wan, Detao; Zhuang, Chen; Yang, Gang

2017-12-01

It is important to treat the arbitrary boundary of Fluid-Structure Interaction (FSI) problems in computational mechanics. In order to ensure complete support condition and restore the first-order consistency near the boundary of Smoothed Particle Hydrodynamics (SPH) method for coupling Finite Element Method (FEM) with SPH model, a new ghost particle method is proposed by dividing the interceptive area of kernel support domain into subareas corresponding to boundary segments of structure. The ghost particles are produced automatically for every fluid particle at each time step, and the properties of ghost particles, such as density, mass and velocity, are defined by using the subareas to satisfy the boundary condition. In the coupled FEM-SPH model, the normal and shear forces from a boundary segment of structure to a fluid particle are calculated through the corresponding ghost particles, and its opposite forces are exerted on the corresponding boundary segment, then the momentum of the present method is conservation and there is no matching requirements between the size of elements and the size of particles. The performance of the present method is discussed and validated by several FSI problems with complex geometry boundary and moving boundary.

Compression of high-density EMG signals for trapezius and gastrocnemius muscles

PubMed Central

2014-01-01

Background New technologies for data transmission and multi-electrode arrays increased the demand for compressing high-density electromyography (HD EMG) signals. This article aims the compression of HD EMG signals recorded by two-dimensional electrode matrices at different muscle-contraction forces. It also shows methodological aspects of compressing HD EMG signals for non-pinnate (upper trapezius) and pinnate (medial gastrocnemius) muscles, using image compression techniques. Methods HD EMG signals were placed in image rows, according to two distinct electrode orders: parallel and perpendicular to the muscle longitudinal axis. For the lossless case, the images obtained from single-differential signals as well as their differences in time were compressed. For the lossy algorithm, the images associated to the recorded monopolar or single-differential signals were compressed for different compression levels. Results Lossless compression provided up to 59.3% file-size reduction (FSR), with lower contraction forces associated to higher FSR. For lossy compression, a 90.8% reduction on the file size was attained, while keeping the signal-to-noise ratio (SNR) at 21.19 dB. For a similar FSR, higher contraction forces corresponded to higher SNR Conclusions The computation of signal differences in time improves the performance of lossless compression while the selection of signals in the transversal order improves the lossy compression of HD EMG, for both pinnate and non-pinnate muscles. PMID:24612604

Measurement of the densities of Cu and Ag vapours in a low-voltage switch using the hook method

NASA Astrophysics Data System (ADS)

Lins, Günter

2012-05-01

In a research model of a low-voltage circuit breaker with fixed contacts and windows for optical access, arcs powered by either a high-current transformer or a capacitor bank were initiated by the explosion of tungsten wires. Air at atmospheric pressure was the switching medium. The number densities of neutral silver and copper vapours from contacts and arc runners were measured simultaneously by the hook method using a Mach-Zehnder interferometer combined with a 1 m spectrograph and a gated intensified CCD camera. When an arc current was flowing, a substantial fraction of the metal vapour was ionized, and thus not amenable to a density measurement with the technique chosen. To nevertheless obtain approximate density values, the arc current was forced to zero within 8 to 10 µs at a preset time and measurements were carried out 100 µs after extinction of the arc. At that time the metal vapour was expected to have recombined to a large extent but not yet diffused to the walls in significant amounts. Depending on the current amplitude reached within the arc duration the arc remained anchored to the silver contacts or commutated to the copper arc runners. At a maximum current amplitude of 650 A Ag vapour densities of the order of 1022 m-3 were observed near the anode outweighing the Cu vapour density by a factor of 20. When at 1600 A the arc commutated to the arc runners a Cu vapour density of 8 × 1021 m-3 was reached while the Ag density remained limited to 2 × 1021 m-3.

Scalar Dispersion from Point Sources in a Realistic Urban Environment

NASA Astrophysics Data System (ADS)

Salesky, S.; Giometto, M. G.; Christen, A.; Parlange, M. B.

2016-12-01

Accurate modeling of scalar dispersion within and above urban canopies is critical to properly predict air quality and dispersion (e.g. accidental contaminant release) in urban environments. We perform large eddy simulations (LES) of scalar dispersion from point sources in a typical North American neighborhood using topography and foliage density derived from airborne LIDAR scans with 1 m resolution in Vancouver, BC, Canada. The added drag force due to trees is parameterized in the LES as a function of the leaf area density (LAD) profile. Conversely, drag from buildings is accounted for using a direct forcing approach immersed-boundary method. The scalar advection-diffusion equation is discretized in a finite-volume framework, and accurate mass conservation is enforced through a recently developed Cartesian cut cell method. Simulations are performed with trees for different values of LAD, representative of summer and winter conditions, as well as a case without trees. The effects of varying mean wind direction (derived from observed wind climatologies) on dispersion patterns are also considered. Scalar release locations in the LES are informed by spatially distributed measurements of carbon dioxide concentration; CO2 is used as a tracer for fossil fuel emissions, since source strengths are well-known and the contribution from biological processes in this setting is small (<10%). The effects of leaf area density, source height, and wind direction on scalar statistics including the growth of the mean concentration plume and the fraction that escapes the urban canopy layer will be considered. In a companion study, the presence of trees was found to strongly modify sweep and ejection patterns for the momentum flux; here we consider the related issue of how vegetation influences coherent structures responsible for scalar transport.

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

DOE PAGES

Sándor, Csand; Libál, Andras; Reichhardt, Charles; ...

2017-01-17

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

Collective transport for active matter run-and-tumble disk systems on a traveling-wave substrate

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

Sándor, Csand; Libál, Andras; Reichhardt, Charles

Here, we examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure and net flux of disks. We find that there is a sharp transition into a state in which the disks are only partially coupled to the substrate and form a phase-separated cluster state. This transition is associated with a drop in the net disk flux, and it can occur as a function of themore » substrate speed, maximum substrate force, disk run time, and disk density. Since variation of the disk activity parameters produces different disk drift rates for a fixed traveling-wave speed on the substrate, the system we consider could be used as an efficient method for active matter species separation. Within the cluster phase, we find that in some regimes the motion of the cluster center of mass is in the opposite direction to that of the traveling wave, while when the maximum substrate force is increased, the cluster drifts in the direction of the traveling wave. This suggests that swarming or clustering motion can serve as a method by which an active system can collectively move against an external drift.« less

Effects of high power ultrasonic vibration on the cold compaction of titanium.

PubMed

Fartashvand, Vahid; Abdullah, Amir; Ali Sadough Vanini, Seyed

2017-05-01

Titanium has widely been used in chemical and aerospace industries. In order to overcome the drawbacks of cold compaction of titanium, the process was assisted by an ultrasonic vibration system. For this purpose, a uniaxial ultrasonic assisted cold powder compaction system was designed and fabricated. The process variables were powder size, compaction pressure and initial powder compact thickness. Density, friction force, ejection force and spring back of the fabricated samples were measured and studied. The density was observed to improve under the action of ultrasonic vibration. Fine size powders showed better results of consolidation while using ultrasonic vibration. Under the ultrasonic action, it is thought that the friction forces between the die walls and the particles and those friction forces among the powder particles are reduced. Spring back and ejection force didn't considerably change when using ultrasonic vibration. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Design of a self-aligned, wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with 10 nm magnetic force microscope resolution

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

Karcı, Özgür; Department of Nanotechnology and Nanomedicine, Hacettepe University, Beytepe, 06800 Ankara; Dede, Münir

We describe the design of a wide temperature range (300 mK-300 K) atomic force microscope/magnetic force microscope with a self-aligned fibre-cantilever mechanism. An alignment chip with alignment groves and a special mechanical design are used to eliminate tedious and time consuming fibre-cantilever alignment procedure for the entire temperature range. A low noise, Michelson fibre interferometer was integrated into the system for measuring deflection of the cantilever. The spectral noise density of the system was measured to be ~12 fm/√Hz at 4.2 K at 3 mW incident optical power. Abrikosov vortices in BSCCO(2212) single crystal sample and a high density hardmore » disk sample were imaged at 10 nm resolution to demonstrate the performance of the system.« less

A Double-Sided Linear Primary Permanent Magnet Vernier Machine

PubMed Central

2015-01-01

The purpose of this paper is to present a new double-sided linear primary permanent magnet (PM) vernier (DSLPPMV) machine, which can offer high thrust force, low detent force, and improved power factor. Both PMs and windings of the proposed machine are on the short translator, while the long stator is designed as a double-sided simple iron core with salient teeth so that it is very robust to transmit high thrust force. The key of this new machine is the introduction of double stator and the elimination of translator yoke, so that the inductance and the volume of the machine can be reduced. Hence, the proposed machine offers improved power factor and thrust force density. The electromagnetic performances of the proposed machine are analyzed including flux, no-load EMF, thrust force density, and inductance. Based on using the finite element analysis, the characteristics and performances of the proposed machine are assessed. PMID:25874250

A double-sided linear primary permanent magnet vernier machine.

PubMed

Du, Yi; Zou, Chunhua; Liu, Xianxing

2015-01-01

The purpose of this paper is to present a new double-sided linear primary permanent magnet (PM) vernier (DSLPPMV) machine, which can offer high thrust force, low detent force, and improved power factor. Both PMs and windings of the proposed machine are on the short translator, while the long stator is designed as a double-sided simple iron core with salient teeth so that it is very robust to transmit high thrust force. The key of this new machine is the introduction of double stator and the elimination of translator yoke, so that the inductance and the volume of the machine can be reduced. Hence, the proposed machine offers improved power factor and thrust force density. The electromagnetic performances of the proposed machine are analyzed including flux, no-load EMF, thrust force density, and inductance. Based on using the finite element analysis, the characteristics and performances of the proposed machine are assessed.

Support for the existence of invertible maps between electronic densities and non-analytic 1-body external potentials in non-relativistic time-dependent quantum mechanics

NASA Astrophysics Data System (ADS)

Mosquera, Martín A.

2017-10-01

Provided the initial state, the Runge-Gross theorem establishes that the time-dependent (TD) external potential of a system of non-relativistic electrons determines uniquely their TD electronic density, and vice versa (up to a constant in the potential). This theorem requires the TD external potential and density to be Taylor-expandable around the initial time of the propagation. This paper presents an extension without this restriction. Given the initial state of the system and evolution of the density due to some TD scalar potential, we show that a perturbative (not necessarily weak) TD potential that induces a non-zero divergence of the external force-density, inside a small spatial subset and immediately after the initial propagation time, will cause a change in the density within that subset, implying that the TD potential uniquely determines the TD density. In this proof, we assume unitary evolution of wavefunctions and first-order differentiability (which does not imply analyticity) in time of the internal and external force-densities, electronic density, current density, and their spatial derivatives over the small spatial subset and short time interval.

Benchmarking density functionals for hydrogen-helium mixtures with quantum Monte Carlo: Energetics, pressures, and forces

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

Clay, Raymond C.; Holzmann, Markus; Ceperley, David M.

An accurate understanding of the phase diagram of dense hydrogen and helium mixtures is a crucial component in the construction of accurate models of Jupiter, Saturn, and Jovian extrasolar planets. Though DFT based rst principles methods have the potential to provide the accuracy and computational e ciency required for this task, recent benchmarking in hydrogen has shown that achieving this accuracy requires a judicious choice of functional, and a quanti cation of the errors introduced. In this work, we present a quantum Monte Carlo based benchmarking study of a wide range of density functionals for use in hydrogen-helium mixtures atmore » thermodynamic conditions relevant for Jovian planets. Not only do we continue our program of benchmarking energetics and pressures, but we deploy QMC based force estimators and use them to gain insights into how well the local liquid structure is captured by di erent density functionals. We nd that TPSS, BLYP and vdW-DF are the most accurate functionals by most metrics, and that the enthalpy, energy, and pressure errors are very well behaved as a function of helium concentration. Beyond this, we highlight and analyze the major error trends and relative di erences exhibited by the major classes of functionals, and estimate the magnitudes of these e ects when possible.« less

Benchmarking density functionals for hydrogen-helium mixtures with quantum Monte Carlo: Energetics, pressures, and forces

DOE PAGES

Clay, Raymond C.; Holzmann, Markus; Ceperley, David M.; ...

2016-01-19

An accurate understanding of the phase diagram of dense hydrogen and helium mixtures is a crucial component in the construction of accurate models of Jupiter, Saturn, and Jovian extrasolar planets. Though DFT based rst principles methods have the potential to provide the accuracy and computational e ciency required for this task, recent benchmarking in hydrogen has shown that achieving this accuracy requires a judicious choice of functional, and a quanti cation of the errors introduced. In this work, we present a quantum Monte Carlo based benchmarking study of a wide range of density functionals for use in hydrogen-helium mixtures atmore » thermodynamic conditions relevant for Jovian planets. Not only do we continue our program of benchmarking energetics and pressures, but we deploy QMC based force estimators and use them to gain insights into how well the local liquid structure is captured by di erent density functionals. We nd that TPSS, BLYP and vdW-DF are the most accurate functionals by most metrics, and that the enthalpy, energy, and pressure errors are very well behaved as a function of helium concentration. Beyond this, we highlight and analyze the major error trends and relative di erences exhibited by the major classes of functionals, and estimate the magnitudes of these e ects when possible.« less

Accurate identification of motor unit discharge patterns from high-density surface EMG and validation with a novel signal-based performance metric

NASA Astrophysics Data System (ADS)

Holobar, A.; Minetto, M. A.; Farina, D.

2014-02-01

Objective. A signal-based metric for assessment of accuracy of motor unit (MU) identification from high-density surface electromyograms (EMG) is introduced. This metric, so-called pulse-to-noise-ratio (PNR), is computationally efficient, does not require any additional experimental costs and can be applied to every MU that is identified by the previously developed convolution kernel compensation technique. Approach. The analytical derivation of the newly introduced metric is provided, along with its extensive experimental validation on both synthetic and experimental surface EMG signals with signal-to-noise ratios ranging from 0 to 20 dB and muscle contraction forces from 5% to 70% of the maximum voluntary contraction. Main results. In all the experimental and simulated signals, the newly introduced metric correlated significantly with both sensitivity and false alarm rate in identification of MU discharges. Practically all the MUs with PNR > 30 dB exhibited sensitivity >90% and false alarm rates <2%. Therefore, a threshold of 30 dB in PNR can be used as a simple method for selecting only reliably decomposed units. Significance. The newly introduced metric is considered a robust and reliable indicator of accuracy of MU identification. The study also shows that high-density surface EMG can be reliably decomposed at contraction forces as high as 70% of the maximum.

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

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

Lisal, Martin; Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab.; Izak, Pavel

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and itsmore » value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.« less

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

PubMed

Lísal, Martin; Izák, Pavel

2013-07-07

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

Elliptical instability in stably stratified fluid interiors

NASA Astrophysics Data System (ADS)

Vidal, J.; Hollerbach, R.; Schaeffer, N.; Cebron, D.

2016-12-01

Self-sustained magnetic fields in celestial bodies (planets, moons, stars) are due to flows in internal electrically conducting fluids. These fluid motions are often attributed to convection, as it is the case for the Earth's liquid core and the Sun. However some past or present liquid cores may be stably stratified. Alternative mechanisms may thus be needed to understand the dynamo process in these celestial objects. Turbulent flows driven by mechanical forcings, such as tides or precession, seem very promising since they are dynamo capable. However the effect of density stratification is not clear, because it can stabilize or destabilize mechanically-driven flows.To mimic an elliptical distortion due to tidal forcing in spherical geometry (full sphere and shell), we consider a theoretical base flow with elliptical streamlines and an associated density profile. It allows to keep the numerical efficiency of spectral methods in this geometry. The flow satisfies the stress-free boundary condition. We perform the stability analysis of the base state using three-dimensional simulations to study both the linear and nonlinear regimes. Stable and unstable density profiles are considered. A complementary local stability analysis (WKB) is also performed. We show that elliptical instability can still grow upon a stable stratification. We also study the mixing of the stratification by the elliptical instability. Finally we look at the dynamo capability of these flows.

Quantum mechanical study and spectroscopic (FT-IR, FT-Raman, 13C, 1H) study, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis of 2-acetoxybenzoic acid by density functional methods

NASA Astrophysics Data System (ADS)

Bhavani, K.; Renuga, S.; Muthu, S.; Sankara narayanan, K.

2015-02-01

In this work, colorless crystals of 2-acetoxybenzoic acid were grown by slow evaporation method and the FT-IR and FT-Raman spectra of the sample were recorded in the region 4000-500 cm-1 and 4000-100 cm-1 respectively. Molecular structure is optimized with the help of density functional theory method (B3LYP) with 6-31+G(d,p), 6-311++G(d,p) basis sets. Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ∗ antibonding orbitals and E(2) energies confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis following the scaled quantum mechanical force field (SQMFF) methodology. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. Mulliken population analysis on atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule.

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

A Novel Approach to Visualizing Dark Matter Simulations.

PubMed

Kaehler, R; Hahn, O; Abel, T

2012-12-01

In the last decades cosmological N-body dark matter simulations have enabled ab initio studies of the formation of structure in the Universe. Gravity amplified small density fluctuations generated shortly after the Big Bang, leading to the formation of galaxies in the cosmic web. These calculations have led to a growing demand for methods to analyze time-dependent particle based simulations. Rendering methods for such N-body simulation data usually employ some kind of splatting approach via point based rendering primitives and approximate the spatial distributions of physical quantities using kernel interpolation techniques, common in SPH (Smoothed Particle Hydrodynamics)-codes. This paper proposes three GPU-assisted rendering approaches, based on a new, more accurate method to compute the physical densities of dark matter simulation data. It uses full phase-space information to generate a tetrahedral tessellation of the computational domain, with mesh vertices defined by the simulation's dark matter particle positions. Over time the mesh is deformed by gravitational forces, causing the tetrahedral cells to warp and overlap. The new methods are well suited to visualize the cosmic web. In particular they preserve caustics, regions of high density that emerge, when several streams of dark matter particles share the same location in space, indicating the formation of structures like sheets, filaments and halos. We demonstrate the superior image quality of the new approaches in a comparison with three standard rendering techniques for N-body simulation data.

Emergent interparticle interactions in thermal amorphous solids

NASA Astrophysics Data System (ADS)

Gendelman, Oleg; Lerner, Edan; Pollack, Yoav G.; Procaccia, Itamar; Rainone, Corrado; Riechers, Birte

2016-11-01

Amorphous media at finite temperatures, be them liquids, colloids, or glasses, are made of interacting particles that move chaotically due to thermal energy, continuously colliding and scattering off each other. When the average configuration in these systems relaxes only at long times, one can introduce effective interactions that keep the mean positions in mechanical equilibrium. We introduce a framework to determine the effective force laws that define an effective Hessian that can be employed to discuss stability properties and the density of states of the amorphous system. We exemplify the approach with a thermal glass of hard spheres; these experience zero forces when not in contact and infinite forces when they touch. Close to jamming we recapture the effective interactions that at temperature T depend on the gap h between spheres as T /h [C. Brito and M. Wyart, Europhys. Lett. 76, 149 (2006), 10.1209/epl/i2006-10238-x]. For hard spheres at lower densities or for systems whose binary bare interactions are longer ranged (at any density), the emergent force laws include ternary, quaternary, and generally higher-order many-body terms, leading to a temperature-dependent effective Hessian.

Chameleon gravity, electrostatics, and kinematics in the outer galaxy

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

Pourhasan, R.; Mann, R.B.; Afshordi, N.

2011-12-01

Light scalar fields are expected to arise in theories of high energy physics (such as string theory), and find phenomenological motivations in dark energy, dark matter, or neutrino physics. However, the coupling of light scalar fields to ordinary (or dark) matter is strongly constrained from laboratory, solar system, and astrophysical tests of the fifth force. One way to evade these constraints in dense environments is through the chameleon mechanism, where the field's mass steeply increases with ambient density. Consequently, the chameleonic force is only sourced by a thin shell near the surface of dense objects, which significantly reduces its magnitude.more » In this paper, we argue that thin-shell conditions are equivalent to ''conducting'' boundary conditions in electrostatics. As an application, we use the analogue of the method of images to calculate the back-reaction (or self-force) of an object around a spherical gravitational source. Using this method, we can explicitly compute the violation of the equivalence principle in the outskirts of galactic haloes (assuming an NFW dark matter profile): Intermediate mass satellites can be slower than their larger/smaller counterparts by as much as 10% close to a thin shell.« less

First principles calculation of current-induced forces in atomic gold contacts

NASA Astrophysics Data System (ADS)

Brandbyge, Mads; Stokbro, Kurt; Taylor, Jeremy; Mozos, Jose-Luis; Ordejon, Pablo

2002-03-01

We have recently developed an first principles method [1] for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested SIESTA program [2]. We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. In this talk we show results for the forces acting on the contact atoms due to the nonequilibrium situation in the electronic subsystem, i.e. in the presence of an electronic current. We concentrate on one atom wide gold contacts/wires connected to bulk gold electrodes. References [1] Our implementation is called TranSIESTA and is described in M. Brandbyge, J. Taylor, K. Stokbro, J-L. Mozos, and P. Ordejon, cond-mat/0110650 [2] D. Sanchez-Portal, P. Ordejon, E. Artacho and J. Soler, Int. J. Quantum Chem. 65, 453 (1997).

Understanding the effects of decompaction maintenance on the infill state and play performance of third-generation artificial grass pitches

PubMed Central

Forrester, Stephanie E; McLaren, Nicholas J

2015-01-01

Third generation artificial grass pitches have been observed to get harder over time. The maintenance technique of rubber infill decompaction is intended to help slow, or reverse, this process. At present, little is understood about either the science of the infill compaction process or the efficacy of decompaction maintenance. The objective of this study was to measure the changes in rubber infill net bulk density, force reduction (impact absorption) and vertical ball rebound under various levels of compactive effort in controlled laboratory-based testing. The assessments were repeated after the systems had been raked to simulate the decompaction maintenance techniques. These tests defined the limits of compaction (loose to maximally compacted) in terms of the change in rubber infill net bulk density, force reduction and vertical ball rebound. Site testing was also undertaken at four third generation pitches immediately pre and post decompaction, to determine the measurable effects in the less well controlled field environment. Rubber infill net bulk density was found to increase as compactive effort increased, resulting in increased hardness. Decompacting the surface was found to approximately fully reverse these effects. In comparison, the site measurements demonstrated similar but notably smaller magnitudes of change following the decompaction process suggesting that the field state pre and post decompaction did not reach the extremes obtained in the laboratory. The findings suggest that rubber infill net bulk density is an important parameter influencing the hardness of artificial grass and that decompactions can be an effective method to reverse compaction related hardness changes. PMID:29708108

Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

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

Asiaee, Alireza; Benjamin, Kenneth M., E-mail: kenneth.benjamin@sdsmt.edu

2016-08-28

For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (nomore » SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0–1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.« less

Uncertainty quantification and propagation in nuclear density functional theory

DOE PAGES

Schunck, N.; McDonnell, J. D.; Higdon, D.; ...

2015-12-23

Nuclear density functional theory (DFT) is one of the main theoretical tools used to study the properties of heavy and superheavy elements, or to describe the structure of nuclei far from stability. While on-going eff orts seek to better root nuclear DFT in the theory of nuclear forces, energy functionals remain semi-phenomenological constructions that depend on a set of parameters adjusted to experimental data in fi nite nuclei. In this study, we review recent eff orts to quantify the related uncertainties, and propagate them to model predictions. In particular, we cover the topics of parameter estimation for inverse problems, statisticalmore » analysis of model uncertainties and Bayesian inference methods. Illustrative examples are taken from the literature.« less

Multiple steady solutions in a driven cavity

NASA Astrophysics Data System (ADS)

Osman, Kahar; McHugh, John

2004-11-01

The symmetric driven cavity (Farias and McHugh, Phys. Fluids, 2002) in two and three dimensions is considered. Results are obtained via numerical computations of the Navier-Stokes equations, assuming constant density. The numerical algorithm is a splitting method, using finite differences. The forcing at the top is sinusoidal, and the forcing wavelength is allowed to vary in subsequent trials. The two dimensional results with 2, 4, and 6 oscillations in the forcing show a subcritical bifurcation to an asymmetric solution, with the Reynolds number as the important parameter. The symmetric solution is found to have vortex flow with streamlines that conform to the boundary shape. The asymmetric solution has vortex flow with streamlines that are approximately circular near the vortex center. Two dimensional results with 8 or more oscillations in the forcing show a supercritical bifurcation to an asymmetric solution. Three dimensional simulations show that the length ratios play a critical role, and the depth of the cavity must be large compared to the height in order to acheive the same subcritical bifurcation as with two dimensions.

Analysis of a new PM motor design for a rotary dynamic blood Pump.

PubMed

Xu, L; Wang, F; Fu, M; Medvedev, A; Smith, W A; Golding, L A

1997-01-01

The permanent magnet (PM) motor for a rotary dynamic blood pump requires high power density to coordinate the motor size with the limited pump space and high efficiency to reduce the size and weight of the associated batteries. The motor also serves as a passive axial magnetic thrust bearing, a reacting hydraulic force, and provides a stabilizing force for the radial journal bearing. This article presents analysis of a new PM motor for the blood pump application. High power density is achieved by using the Halbach magnetic array, and high efficiency is accomplished by optimizing the rotor magnet assembly and the stator slots/windings. While both radial and axial forces are greatly enhanced, pulsating components of the torque and force are also significantly reduced.

Quantification of surface charge density and its effect on boundary slip.

PubMed

Jing, Dalei; Bhushan, Bharat

2013-06-11

Reduction of fluid drag is important in the micro-/nanofluidic systems. Surface charge and boundary slip can affect the fluid drag, and surface charge is also believed to affect boundary slip. The quantification of surface charge and boundary slip at a solid-liquid interface has been widely studied, but there is a lack of understanding of the effect of surface charge on boundary slip. In this paper, the surface charge density of borosilicate glass and octadecyltrichlorosilane (OTS) surfaces immersed in saline solutions with two ionic concentrations and deionized (DI) water with different pH values and electric field values is quantified by fitting experimental atomic force microscopy (AFM) electrostatic force data using a theoretical model relating the surface charge density and electrostatic force. Results show that pH and electric field can affect the surface charge density of glass and OTS surfaces immersed in saline solutions and DI water. The mechanisms of the effect of pH and electric field on the surface charge density are discussed. The slip length of the OTS surface immersed in saline solutions with two ionic concentrations and DI water with different pH values and electric field values is measured, and their effects on the slip length are analyzed from the point of surface charge. Results show that a larger absolute value of surface charge density leads to a smaller slip length for the OTS surface.

Current Flow and Pair Creation at Low Altitude in Rotation-Powered Pulsars' Force-Free Magnetospheres: Space Charge Limited Flow

NASA Technical Reports Server (NTRS)

Timokhin, A. N.; Arons, J.

2013-01-01

We report the results of an investigation of particle acceleration and electron-positron plasma generation at low altitude in the polar magnetic flux tubes of rotation-powered pulsars, when the stellar surface is free to emit whatever charges and currents are demanded by the force-free magnetosphere. We apply a new 1D hybrid plasma simulation code to the dynamical problem, using Particle-in-Cell methods for the dynamics of the charged particles, including a determination of the collective electrostatic fluctuations in the plasma, combined with a Monte Carlo treatment of the high-energy gamma-rays that mediate the formation of the electron-positron pairs.We assume the electric current flowing through the pair creation zone is fixed by the much higher inductance magnetosphere, and adopt the results of force-free magnetosphere models to provide the currents which must be carried by the accelerator. The models are spatially one dimensional, and designed to explore the physics, although of practical relevance to young, high-voltage pulsars. We observe novel behaviour (a) When the current density j is less than the Goldreich-Julian value (0 < j/j(sub GJ) < 1), space charge limited acceleration of the current carrying beam is mild, with the full Goldreich-Julian charge density comprising the charge densities of the beam and a cloud of electrically trapped particles with the same sign of charge as the beam. The voltage drops are of the order of mc(sup 2)/e, and pair creation is absent. (b) When the current density exceeds the Goldreich-Julian value (j/j(sub GJ) > 1), the system develops high voltage drops (TV or greater), causing emission of curvature gamma-rays and intense bursts of pair creation. The bursts exhibit limit cycle behaviour, with characteristic time-scales somewhat longer than the relativistic fly-by time over distances comparable to the polar cap diameter (microseconds). (c) In return current regions, where j/j(sub GJ) < 0, the system develops similar bursts of pair creation. These discharges are similar to those encountered in previous calculations by Timokhin of pair creation when the surface has a high work function and cannot freely emit charge. In cases (b) and (c), the intermittently generated pairs allow the system to simultaneously carry the magnetospherically prescribed currents and adjust the charge density and average electric field to force-free conditions. We also elucidate the conditions for pair creating beam flow to be steady (stationary with small fluctuations in the rotating frame), finding that such steady flows can occupy only a small fraction of the current density parameter space exhibited by the force-free magnetospheric model. The generic polar flow dynamics and pair creation are strongly time dependent. The model has an essential difference from almost all previous quantitative studies, in that we sought the accelerating voltage (with pair creation, when the voltage drops are sufficiently large; without, when they are small) as a function of the applied current.

Atomic force microscopy evaluation of aqueous interfaces of immobilized hyaluronan.

PubMed

Morra, Marco; Cassinelli, Clara; Pavesio, Alessandra; Renier, Davide

2003-03-15

Hyaluronan (HA) was immobilized on aminated glass surfaces in three different ways: by simple ionic interaction and by covalent linking at low density and at full density. In agreement with previous reports, in vitro experiments show that the outcome of fibroblast adhesion tests is markedly affected by the details of the coupling procedure, suggesting that different interfacial forces are operating at the aqueous/HA interface in the three cases investigated. The interfacial properties of the HA-coated surfaces were probed by force-distance curves obtained with the atomic force microscope (AFM). This approach readily shows significant differences among the tested samples, which are directly related to the coupling strategy and to results of cell adhesion tests. In particular, the range of interaction between the tip and the surface is much lower when HA is covalently linked than when it is ionically coupled, suggesting a more compact surface structure in the former case. Increasing HA surface density minimizes the interaction force between the surface and the AFM tip, likely reflecting more complete shielding by the HA chains of the underlying substrate. In summary, these measurements clearly show the different nature of the aqueous interfaces tested, and underline the role of this analytical approach in the development and control of finely tuned biomaterial surfaces.

Generation of a wakefield undulator in plasma with transverse density gradient

DOE PAGES

Stupakov, Gennady V.

2017-11-30

Here, we show that a short relativistic electron beam propagating in a plasma with a density gradient perpendicular to the direction of motion generates a wakefield in which a witness bunch experiences a transverse force. A density gradient oscillating along the beam path would create a periodically varying force$-$an undulator, with an estimated strength of the equivalent magnetic field more than ten Tesla. This opens an avenue for creation of a high-strength, short-period undulators, which eventually may lead to all-plasma, free electron lasers where a plasma wakefield acceleration is naturally combined with a plasma undulator in a unifying, compact setup.

Generation of a wakefield undulator in plasma with transverse density gradient

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

Stupakov, Gennady V.

Here, we show that a short relativistic electron beam propagating in a plasma with a density gradient perpendicular to the direction of motion generates a wakefield in which a witness bunch experiences a transverse force. A density gradient oscillating along the beam path would create a periodically varying force$-$an undulator, with an estimated strength of the equivalent magnetic field more than ten Tesla. This opens an avenue for creation of a high-strength, short-period undulators, which eventually may lead to all-plasma, free electron lasers where a plasma wakefield acceleration is naturally combined with a plasma undulator in a unifying, compact setup.

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

PubMed

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

2015-07-14

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

KIDS Nuclear Energy Density Functional: 1st Application in Nuclei

NASA Astrophysics Data System (ADS)

Gil, Hana; Papakonstantinou, Panagiota; Hyun, Chang Ho; Oh, Yongseok

We apply the KIDS (Korea: IBS-Daegu-Sungkyunkwan) nuclear energy density functional model, which is based on the Fermi momentum expansion, to the study of properties of lj-closed nuclei. The parameters of the model are determined by the nuclear properties at the saturation density and theoretical calculations on pure neutron matter. For applying the model to the study of nuclei, we rely on the Skyrme force model, where the Skyrme force parameters are determined through the KIDS energy density functional. Solving Hartree-Fock equations, we obtain the energies per particle and charge radii of closed magic nuclei, namely, 16O, 28O, 40Ca, 48Ca, 60Ca, 90Zr, 132Sn, and 208Pb. The results are compared with the observed data and further improvement of the model is shortly mentioned.

Mechanical coupling limits the density and quality of self-organized carbon nanotube growth

NASA Astrophysics Data System (ADS)

Bedewy, Mostafa; Hart, A. John

2013-03-01

Aligned carbon nanotube (CNT) structures are promising for many applications; however, as-grown CNT "forests" synthesized by chemical vapor deposition (CVD) are typically low-density and mostly comprise tortuous defective CNTs. Here, we present evidence that the density and alignment of self-organized CNT growth is limited by mechanical coupling among CNTs in contact, in combination with their diameter-dependent growth rates. This study is enabled by comprehensive X-ray characterization of the spatially and temporally-varying internal morphology of CNT forests. Based on this data, we model the time evolution and diameter-dependent scaling of the ensuing mechanical forces on catalyst nanoparticles during CNT growth, which arise from the mismatch between the collective lengthening rate of the forest and the diameter-dependent growth rates of individual CNTs. In addition to enabling self-organization of CNTs into forests, time-varying forces between CNTs in contact dictate the hierarchical tortuous morphology of CNT forests, and may be sufficient to influence the structural quality of CNTs. These forces reach a maximum that is coincident with the maximum density observed in our growth process, and are proportional to CNT diameter. Therefore, we propose that improved manufacturing strategies for self-organized CNTs should consider both chemical and mechanical effects. This may be especially necessary to achieve high density CNT forests with low defect density, such as for improved thermal interfaces and high-permeability membranes.Aligned carbon nanotube (CNT) structures are promising for many applications; however, as-grown CNT "forests" synthesized by chemical vapor deposition (CVD) are typically low-density and mostly comprise tortuous defective CNTs. Here, we present evidence that the density and alignment of self-organized CNT growth is limited by mechanical coupling among CNTs in contact, in combination with their diameter-dependent growth rates. This study is enabled by comprehensive X-ray characterization of the spatially and temporally-varying internal morphology of CNT forests. Based on this data, we model the time evolution and diameter-dependent scaling of the ensuing mechanical forces on catalyst nanoparticles during CNT growth, which arise from the mismatch between the collective lengthening rate of the forest and the diameter-dependent growth rates of individual CNTs. In addition to enabling self-organization of CNTs into forests, time-varying forces between CNTs in contact dictate the hierarchical tortuous morphology of CNT forests, and may be sufficient to influence the structural quality of CNTs. These forces reach a maximum that is coincident with the maximum density observed in our growth process, and are proportional to CNT diameter. Therefore, we propose that improved manufacturing strategies for self-organized CNTs should consider both chemical and mechanical effects. This may be especially necessary to achieve high density CNT forests with low defect density, such as for improved thermal interfaces and high-permeability membranes. Electronic supplementary information (ESI) available: Detailed description of the cold-wall CVD reactor used for growing CNTs; fitting the diameter-dependent model-predicted CNT growth kinetics; time evolution of compressive stresses as a function of CNT diameter; time evolution of the diameter dependent variations in CNT number density; cumulative forest mass kinetics normalized to the number of CNTs. See DOI: 10.1039/c3nr34067h

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.

Confinement of plasma along shaped open magnetic fields from the centrifugal force of supersonic plasma rotation.

PubMed

Teodorescu, C; Young, W C; Swan, G W S; Ellis, R F; Hassam, A B; Romero-Talamas, C A

2010-08-20

Interferometric density measurements in plasmas rotating in shaped, open magnetic fields demonstrate strong confinement of plasma parallel to the magnetic field, with density drops of more than a factor of 10. Taken together with spectroscopic measurements of supersonic E × B rotation of sonic Mach 2, these measurements are in agreement with ideal MHD theory which predicts large parallel pressure drops balanced by centrifugal forces in supersonically rotating plasmas.

A new solution-adaptive grid generation method for transonic airfoil flow calculations

NASA Technical Reports Server (NTRS)

Nakamura, S.; Holst, T. L.

1981-01-01

The clustering algorithm is controlled by a second-order, ordinary differential equation which uses the airfoil surface density gradient as a forcing function. The solution to this differential equation produces a surface grid distribution which is automatically clustered in regions with large gradients. The interior grid points are established from this surface distribution by using an interpolation scheme which is fast and retains the desirable properties of the original grid generated from the standard elliptic equation approach.

Microgravity processing of particulate reinforced metal matrix composites

NASA Technical Reports Server (NTRS)

Morel, Donald E.; Stefanescu, Doru M.; Curreri, Peter A.

1989-01-01

The elimination of such gravity-related effects as buoyancy-driven sedimentation can yield more homogeneous microstructures in composite materials whose individual constituents have widely differing densities. A comparison of composite samples consisting of particulate ceramics in a nickel aluminide matrix solidified under gravity levels ranging from 0.01 to 1.8 G indicates that the G force normal to the growth direction plays a fundamental role in determining the distribution of the reinforcement in the matrix. Composites with extremely uniform microstructures can be produced by these methods.

III-Nitride, SiC and Diamond Materials for Electronic Devices. Symposium Held April 8-12 1996, San Francisco, California, U.S.A. Volume 423.

DTIC Science & Technology

1996-12-01

gallium, nitrogen and gallium nitride structures. Thus it can be shown to be transferable and efficient for predictive molecular -dynamic simulations on...potentials and forces for the molecular dynamics simulations are derived by means of a density-functional based nonorthogonal tight-binding (DF-TB) scheme...LDA). Molecular -dynamics simulations for determining the different reconstructions of the SiC surface use the slab method (two-dimensional periodic

Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

PubMed Central

Abramyan, Tigran M.; Hyde-Volpe, David L.; Stuart, Steven J.; Latour, Robert A.

2017-01-01

The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation. As a means to circumvent these problems, the authors demonstrate the application of an efficient advanced sampling method (TIGER2A) for the simulation of the adsorption of hen egg-white lysozyme on a crystalline (110) high-density polyethylene surface plane. Simulations are conducted to generate a Boltzmann-weighted ensemble of sampled states using force field parameters that were validated to represent interfacial behavior for this system. The resulting ensembles of sampled states were then analyzed using an in-house-developed cluster analysis method to predict the most probable orientations and conformations of the protein on the surface based on the amount of sampling performed, from which free energy differences between the adsorbed states were able to be calculated. In addition, by conducting two independent sets of TIGER2A simulations combined with cluster analyses, the authors demonstrate a method to estimate the degree of convergence achieved for a given amount of sampling. The results from these simulations demonstrate that these methods enable the most probable orientations and conformations of an adsorbed protein to be predicted and that the use of our validated interfacial force field parameter set provides closer agreement to available experimental results compared to using standard CHARMM force field parameterization to represent molecular behavior at the interface. PMID:28514864

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

NASA Astrophysics Data System (ADS)

Gilbert, Kathleen M.; Skawinski, William J.; Misra, Milind; Paris, Kristina A.; Naik, Neelam H.; Buono, Ronald A.; Deutsch, Howard M.; Venanzi, Carol A.

2004-11-01

Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.

Left atrial ejection force predicts the outcome after catheter ablation for paroxysmal atrial fibrillation.

PubMed

Kishima, Hideyuki; Mine, Takanao; Takahashi, Satoshi; Ashida, Kenki; Ishihara, Masaharu; Masuyama, Tohru

2018-02-01

Left atrium (LA) systolic dysfunction is observed in the early stages of atrial fibrillation (AF) prior to LA anatomical change. We investigated whether LA systolic dysfunction predicts recurrent AF after catheter ablation (CA) in patients with paroxysmal AF. We studied 106 patients who underwent CA for paroxysmal AF. LA systolic function was assessed with the LA emptying volume = Maximum LA volume (LAV max ) - Minimum LA volume (LAV min ), LA emptying fraction = [(LAV max - LAV min )/LAV max ] × 100, and LA ejection force calculated with Manning's method [LA ejection force = (0.5 × ρ × mitral valve area × A 2 )], where ρ is the blood density and A is the late-diastolic mitral inflow velocity. Recurrent AF was detected in 35/106 (33%) during 14.6 ± 9.1 months. Univariate analysis revealed reduced LA ejection force, decreased LA emptying fraction, larger LA diameter, and elevated brain natriuretic peptide as significant variables. On multivariate analysis, reduced LA ejection force and larger LA diameter were independently associated with recurrent AF. Moreover, patients with reduced LA ejection force and larger LA diameter had a higher risk of recurrent AF than preserved LA ejection force (log-rank P = 0.0004). Reduced LA ejection force and larger LA diameter were associated with poor outcome after CA for paroxysmal AF, and could be a new index to predict recurrent AF. © 2017 Wiley Periodicals, Inc.

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

PubMed

Hassan, Sergio A

2012-08-21

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

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

NASA Astrophysics Data System (ADS)

Hassan, Sergio A.

2012-08-01

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

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

PubMed Central

Hassan, Sergio A.

2012-01-01

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

Competition between drag and Coulomb interactions in turbulent particle-laden flows using a coupled-fluid-Ewald-summation based approach

NASA Astrophysics Data System (ADS)

Yao, Yuan; Capecelatro, Jesse

2018-03-01

We present a numerical study on inertial electrically charged particles suspended in a turbulent carrier phase. Fluid-particle interactions are accounted for in an Eulerian-Lagrangian (EL) framework and coupled to a Fourier-based Ewald summation method, referred to as the particle-particle-particle-mesh (P3M ) method, to accurately capture short- and long-range electrostatic forces in a tractable manner. The EL P3M method is used to assess the competition between drag and Coulomb forces for a range of Stokes numbers and charge densities. Simulations of like- and oppositely charged particles suspended in a two-dimensional Taylor-Green vortex and three-dimensional homogeneous isotropic turbulence are reported. It is found that even in dilute suspensions, the short-range electric potential plays an important role in flows that admit preferential concentration. Suspensions of oppositely charged particles are observed to agglomerate in the form of chains and rings. Comparisons between the particle-mesh method typically employed in fluid-particle calculations and P3M are reported, in addition to one-point and two-point statistics to quantify the level of clustering as a function of Reynolds number, Stokes number, and nondimensional electric settling velocity.

Electromotive force in strongly compressible magnetohydrodynamic turbulence

NASA Astrophysics Data System (ADS)

Yokoi, N.

2017-12-01

Variable density fluid turbulence is ubiquitous in geo-fluids, not to mention in astrophysics. Depending on the source of density variation, variable density fluid turbulence may be divided into two categories: the weak compressible (entropy mode) turbulence for slow flow and the strong compressible (acoustic mode) turbulence for fast flow. In the strong compressible turbulence, the pressure fluctuation induces a strong density fluctuation ρ ', which is represented by the density variance <ρ'2> (<·> denotes the ensemble average). The turbulent effect on the large-scale magnetic-field B induction is represented by the turbulent electromotive force (EMF) (u': velocity fluctuation, b': magnetic-field fluctuation). In the usual treatment in the dynamo theory, the expression for the EMF has been obtained in the framework of incompressible or weak compressible turbulence, where only the variation of the mean density <ρ>, if any, is taken into account. We see from the equation of the density fluctuation ρ', the density variance <ρ'2> is generated by the large mean density variation ∂<ρ> coupled with the turbulent mass flux <ρ'u'>. This means that in the region where the mean density steeply changes, the density variance effect becomes relevant for the magnetic field evolution. This situation is typically the case for phenomena associated with shocks and compositional discontinuities. With the aid of the analytical theory of inhomogeneous compressible magnetohydrodynamic (MHD) turbulence, the expression for the turbulent electromotive force is investigated. It is shown that, among others, an obliqueness (misalignment) between the mean density gradient ∂<ρ> and the mean magnetic field B may contribute to the EMF as ≈χ B×∂<ρ> with the turbulent transport coefficient χ proportional to the density variance (χ <ρ'2>). This density variance effect is expected to strongly affect the EMF near the interface, and changes the transport properties of turbulence. In the case of an interface under the MHD slow shock, the magnetic reconnection rate may be enhanced by this effect. Physical origin of this effect is discussed in some possible geophysical applications.

An accurate real-time model of maglev planar motor based on compound Simpson numerical integration

NASA Astrophysics Data System (ADS)

Kou, Baoquan; Xing, Feng; Zhang, Lu; Zhou, Yiheng; Liu, Jiaqi

2017-05-01

To realize the high-speed and precise control of the maglev planar motor, a more accurate real-time electromagnetic model, which considers the influence of the coil corners, is proposed in this paper. Three coordinate systems for the stator, mover and corner coil are established. The coil is divided into two segments, the straight coil segment and the corner coil segment, in order to obtain a complete electromagnetic model. When only take the first harmonic of the flux density distribution of a Halbach magnet array into account, the integration method can be carried out towards the two segments according to Lorenz force law. The force and torque analysis formula of the straight coil segment can be derived directly from Newton-Leibniz formula, however, this is not applicable to the corner coil segment. Therefore, Compound Simpson numerical integration method is proposed in this paper to solve the corner segment. With the validation of simulation and experiment, the proposed model has high accuracy and can realize practical application easily.

Evaluation of van der Waals density functionals for layered materials

NASA Astrophysics Data System (ADS)

Tawfik, Sherif Abdulkader; Gould, Tim; Stampfl, Catherine; Ford, Michael J.

2018-03-01

In 2012, Björkman et al. posed the question "Are we van der Waals ready?" [T. Björkman et al., J. Phys.: Condens. Matter 24, 424218 (2012), 10.1088/0953-8984/24/42/424218] about the ability of ab initio modeling to reproduce van der Waals (vdW) dispersion forces in layered materials. The answer at that time was no, however. Here we report on a new generation of vdW dispersion models and show that one, i.e., the fractionally ionic atom theory with many-body dispersions, offers close to quantitative predictions for layered structures. Furthermore, it does so from a qualitatively correct picture of dispersion forces. Other methods, such as D3 and optB88vdW, also work well, albeit with some exceptions. We thus argue that we are nearly vdW ready and that some modern dispersion methods are accurate enough to be used for nanomaterial prediction, albeit with some caution required.

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Spectroscopic studies (FT-IR, FT-Raman, UV-Visible), normal co-ordinate analysis, first-order hyperpolarizability and HOMO, LUMO studies of 3,4-dichlorobenzophenone by using Density Functional Methods.

PubMed

Venkata Prasad, K; Samatha, K; Jagadeeswara Rao, D; Santhamma, C; Muthu, S; Mark Heron, B

2015-01-01

The vibrational frequencies of 3,4-dichlorobenzophenone (DCLBP) were obtained from the FT-IR and Raman spectral data, and evaluated based on the Density Functional Theory using the standard method B3LYP with 6-311+G(d,p) as the basis set. On the basis of potential energy distribution together with the normal-co-ordinate analysis and following the scaled quantum mechanical force methodology, the assignments for the various frequencies were described. The values of the electric dipole moment (μ) and the first-order hyperpolarizability (β) of the molecule were computed. The UV-absorption spectrum was also recorded to study the electronic transitions. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The NBO analysis, to study the intramolecular hyperconjugative interactions, was carried out. Mulliken's net charges were evaluated. The MEP and thermodynamic properties were also calculated. The electron density-based local reactivity descriptor, such as Fukui functions, was calculated to explain the chemical selectivity or reactivity site in 3,4-dichlorobenzophenone. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of Lithospheric Stresses Using Satellite Gravimetry: Hypotheses and Applications to North Atlantic

NASA Astrophysics Data System (ADS)

Minakov, A.; Medvedev, S.

2017-12-01

Analysis of lithospheric stresses is necessary to gain understanding of the forces that drive plate tectonics and intraplate deformations and the structure and strength of the lithosphere. A major source of lithospheric stresses is believed to be in variations of surface topography and lithospheric density. The traditional approach to stress estimation is based on direct calculations of the Gravitational Potential Energy (GPE), the depth integrated density moment of the lithosphere column. GPE is highly sensitive to density structure which, however, is often poorly constrained. Density structure of the lithosphere may be refined using methods of gravity modeling. However, the resulted density models suffer from non-uniqueness of the inverse problem. An alternative approach is to directly estimate lithospheric stresses (depth integrated) from satellite gravimetry data. Satellite gravity gradient measurements by the ESA GOCE mission ensures a wealth of data for mapping lithospheric stresses if a link between data and stresses or GPE can be established theoretically. The non-uniqueness of interpretation of sources of the gravity signal holds in this case as well. Therefore, the data analysis was tested for the North Atlantic region where reliable additional constraints are supplied by both controlled-source and earthquake seismology. The study involves comparison of three methods of stress modeling: (1) the traditional modeling approach using a thin sheet approximation; (2) the filtered geoid approach; and (3) the direct utilization of the gravity gradient tensor. Whereas the first two approaches (1)-(2) calculate GPE and utilize a computationally expensive finite element mechanical modeling to calculate stresses, the approach (3) uses a much simpler numerical treatment but requires simplifying assumptions that yet to be tested. The modeled orientation of principal stresses and stress magnitudes by each of the three methods are compared with the World Stress Map.

The Tarsometatarsus of the Ostrich Struthio camelus: Anatomy, Bone Densities, and Structural Mechanics

PubMed Central

Gilbert, Meagan M.; Snively, Eric; Cotton, John

2016-01-01

Background The ostrich Struthio camelus reaches the highest speeds of any extant biped, and has been an extraordinary subject for studies of soft-tissue anatomy and dynamics of locomotion. An elongate tarsometatarsus in adult ostriches contributes to their speed. The internal osteology of the tarsometatarsus, and its mechanical response to forces of running, are potentially revealing about ostrich foot function. Methods/Principal Findings Computed tomography (CT) reveals anatomy and bone densities in tarsometatarsi of an adult and a young juvenile ostrich. A finite element (FE) model for the adult was constructed with properties of compact and cancellous bone where these respective tissues predominate in the original specimen. The model was subjected to a quasi-static analysis under the midstance ground reaction and muscular forces of a fast run. Anatomy–Metatarsals are divided proximally and distally and unify around a single internal cavity in most adult tarsometatarsus shafts, but the juvenile retains an internal three-part division of metatarsals throughout the element. The juvenile has a sparsely ossified hypotarsus for insertion of the m. fibularis longus, as part of a proximally separate third metatarsal. Bone is denser in all regions of the adult tarsometatarsus, with cancellous bone concentrated at proximal and distal articulations, and highly dense compact bone throughout the shaft. Biomechanics–FE simulations show stress and strain are much greater at midshaft than at force applications, suggesting that shaft bending is the most important stressor of the tarsometatarsus. Contraction of digital flexors, inducing a posterior force at the TMT distal condyles, likely reduces buildup of tensile stresses in the bone by inducing compression at these locations, and counteracts bending loads. Safety factors are high for von Mises stress, consistent with faster running speeds known for ostriches. Conclusions/Significance High safety factors suggest that bone densities and anatomy of the ostrich tarsometatarsus confer strength for selectively critical activities, such as fleeing and kicking predators. Anatomical results and FE modeling of the ostrich tarsometatarsus are a useful baseline for testing the structure’s capabilities and constraints for locomotion, through ontogeny and the full step cycle. With this foundation, future analyses can incorporate behaviorally realistic strain rates and distal joint forces, experimental validation, and proximal elements of the ostrich hind limb. PMID:27015416

Investigating the settling dynamics of cohesive silt particles with particle-resolving simulations

NASA Astrophysics Data System (ADS)

Sun, Rui; Xiao, Heng; Sun, Honglei

2018-01-01

The settling of cohesive sediment is ubiquitous in aquatic environments, and the study of the settling process is important for both engineering and environmental reasons. In the settling process, the silt particles show behaviors that are different from non-cohesive particles due to the influence of inter-particle cohesive force. For instance, the flocs formed in the settling process of cohesive silt can loosen the packing, and thus the structural densities of cohesive silt beds are much smaller than that of non-cohesive sand beds. While there is a consensus that cohesive behaviors depend on the characteristics of sediment particles (e.g., Bond number, particle size distribution), little is known about the exact influence of these characteristics on the cohesive behaviors. In addition, since the cohesive behaviors of the silt are caused by the inter-particle cohesive forces, the motions of and the contacts among silt particles should be resolved to study these cohesive behaviors in the settling process. However, studies of the cohesive behaviors of silt particles in the settling process based on particle-resolving approach are still lacking. In the present work, three-dimensional settling process is investigated numerically by using CFD-DEM (Computational Fluid Dynamics-Discrete Element Method). The inter-particle collision force, the van der Waals force, and the fluid-particle interaction forces are considered. The numerical model is used to simulate the hindered settling process of silt based on the experimental setup in the literature. The results obtained in the simulations, including the structural densities of the beds, the characteristic lines, and the particle terminal velocity, are in good agreement with the experimental observations in the literature. To the authors' knowledge, this is the first time that the influences of non-dimensional Bond number and particle polydispersity on the structural densities of silt beds have been investigated separately. The results demonstrate that the cohesive behavior of silt in the settling process is attributed to both the cohesion among silt particles themselves and the particle polydispersity. To guide to the macro-scale modeling of cohesive silt sedimentation, the collision frequency functions obtained in the numerical simulations are also presented based on the micromechanics of particles. The results obtained by using CFD-DEM indicate that the binary collision theory over-estimated the particle collision frequency in the flocculation process at high solid volume fraction.

Parameterizing deep convection using the assumed probability density function method

DOE PAGES

Storer, R. L.; Griffin, B. M.; Höft, J.; ...

2014-06-11

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method. The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing ismore » weak. The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Realistic inversion of diffraction data for an amorphous solid: The case of amorphous silicon

NASA Astrophysics Data System (ADS)

Pandey, Anup; Biswas, Parthapratim; Bhattarai, Bishal; Drabold, D. A.

2016-12-01

We apply a method called "force-enhanced atomic refinement" (FEAR) to create a computer model of amorphous silicon (a -Si) based upon the highly precise x-ray diffraction experiments of Laaziri et al. [Phys. Rev. Lett. 82, 3460 (1999), 10.1103/PhysRevLett.82.3460]. The logic underlying our calculation is to estimate the structure of a real sample a -Si using experimental data and chemical information included in a nonbiased way, starting from random coordinates. The model is in close agreement with experiment and also sits at a suitable energy minimum according to density-functional calculations. In agreement with experiments, we find a small concentration of coordination defects that we discuss, including their electronic consequences. The gap states in the FEAR model are delocalized compared to a continuous random network model. The method is more efficient and accurate, in the sense of fitting the diffraction data, than conventional melt-quench methods. We compute the vibrational density of states and the specific heat, and we find that both compare favorably to experiments.

Parameterizing deep convection using the assumed probability density function method

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

Storer, R. L.; Griffin, B. M.; Höft, J.

2015-01-06

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method.The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and midlatitude deep convection. These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing is weak.more » The same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Parameterizing deep convection using the assumed probability density function method

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

Storer, R. L.; Griffin, B. M.; Hoft, Jan

2015-01-06

Due to their coarse horizontal resolution, present-day climate models must parameterize deep convection. This paper presents single-column simulations of deep convection using a probability density function (PDF) parameterization. The PDF parameterization predicts the PDF of subgrid variability of turbulence, clouds, and hydrometeors. That variability is interfaced to a prognostic microphysics scheme using a Monte Carlo sampling method.The PDF parameterization is used to simulate tropical deep convection, the transition from shallow to deep convection over land, and mid-latitude deep convection.These parameterized single-column simulations are compared with 3-D reference simulations. The agreement is satisfactory except when the convective forcing is weak. Themore » same PDF parameterization is also used to simulate shallow cumulus and stratocumulus layers. The PDF method is sufficiently general to adequately simulate these five deep, shallow, and stratiform cloud cases with a single equation set. This raises hopes that it may be possible in the future, with further refinements at coarse time step and grid spacing, to parameterize all cloud types in a large-scale model in a unified way.« less

Benchmarking Density Functional Theory Based Methods To Model NiOOH Material Properties: Hubbard and van der Waals Corrections vs Hybrid Functionals.

PubMed

Zaffran, Jeremie; Caspary Toroker, Maytal

2016-08-09

NiOOH has recently been used to catalyze water oxidation by way of electrochemical water splitting. Few experimental data are available to rationalize the successful catalytic capability of NiOOH. Thus, theory has a distinctive role for studying its properties. However, the unique layered structure of NiOOH is associated with the presence of essential dispersion forces within the lattice. Hence, the choice of an appropriate exchange-correlation functional within Density Functional Theory (DFT) is not straightforward. In this work, we will show that standard DFT is sufficient to evaluate the geometry, but DFT+U and hybrid functionals are required to calculate the oxidation states. Notably, the benefit of DFT with van der Waals correction is marginal. Furthermore, only hybrid functionals succeed in opening a bandgap, and such methods are necessary to study NiOOH electronic structure. In this work, we expect to give guidelines to theoreticians dealing with this material and to present a rational approach in the choice of the DFT method of calculation.

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.

The Tai Chi in Star Formation

NASA Astrophysics Data System (ADS)

Li, Hua-bai

2017-10-01

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

Semiclassical theory of sub-Doppler forces in an asymmetric magneto-optical trap with unequal laser detunings

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

Noh, Heung-Ryoul; Jhe, Wonho

We present a semiclassical theory of the sub-Doppler forces in an asymmetric magneto-optical trap where the trap-laser frequencies are unequal to one another. To solve the optical Bloch equations, which contain explicit time dependence, unlike in the symmetric case of equal laser detunings, we have developed a convenient and efficient method to calculate the atomic forces at various oscillating frequencies for each atomic density matrix element. In particular, the theory provides a qualitative understanding of the array of sub-Doppler traps (SDTs) recently observed in such an asymmetric trap. We find that the distances between SDTs are proportional to the relativemore » detuning differences, in good agreement with experimental results. The theory presented here can be applied to a dynamic system with multiple laser frequencies involved; the number of coupled equations to solve is much reduced and the resulting numerical calculation can be performed rather simply and efficiently.« less

Solvent effects and potential of mean force study of the SN2 reaction of CH3+CN‑ in water

NASA Astrophysics Data System (ADS)

Li, Chen; Liu, Peng; Li, Yongfang; Wang, Dunyou

2018-03-01

We used a combined quantum mechanics and molecular mechanics (QM/MM) method to investigate the solvent effects and potential of mean force of the CH3F+CN‑ reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects’ contributions to the reaction: 1.7 kcal/mol to the activation barrier and ‑26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at ‑43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at ‑39.7 kcal/mol. Project supported by the National Natural Science Foundation of China (Grant No. 11774206) and Taishan Scholarship Fund from Shandong Province, China.

Path-programmable water droplet manipulations on an adhesion controlled superhydrophobic surface

PubMed Central

Seo, Jungmok; Lee, Seoung-Ki; Lee, Jaehong; Seung Lee, Jung; Kwon, Hyukho; Cho, Seung-Woo; Ahn, Jong-Hyun; Lee, Taeyoon

2015-01-01

Here, we developed a novel and facile method to control the local water adhesion force of a thin and stretchable superhydrophobic polydimethylsiloxane (PDMS) substrate with micro-pillar arrays that allows the individual manipulation of droplet motions including moving, merging and mixing. When a vacuum pressure was applied below the PDMS substrate, a local dimple structure was formed and the water adhesion force of structure was significantly changed owing to the dynamically varied pillar density. With the help of the lowered water adhesion force and the slope angle of the formed dimple structure, the motion of individual water droplets could be precisely controlled, which facilitated the creation of a droplet-based microfluidic platform capable of a programmable manipulation of droplets. We showed that the platform could be used in newer and emerging microfluidic operations such as surface-enhanced Raman spectroscopy with extremely high sensing capability (10−15 M) and in vitro small interfering RNA transfection with enhanced transfection efficiency of ~80%. PMID:26202206

AFM-porosimetry: density and pore volume measurements of particulate materials.

PubMed

Sörensen, Malin H; Valle-Delgado, Juan J; Corkery, Robert W; Rutland, Mark W; Alberius, Peter C

2008-06-01

We introduced the novel technique of AFM-porosimetry and applied it to measure the total pore volume of porous particles with a spherical geometry. The methodology is based on using an atomic force microscope as a balance to measure masses of individual particles. Several particles within the same batch were measured, and by plotting particle mass versus particle volume, the bulk density of the sample can be extracted from the slope of the linear fit. The pore volume is then calculated from the densities of the bulk and matrix materials, respectively. In contrast to nitrogen sorption and mercury porosimetry, this method is capable of measuring the total pore volume regardless of pore size distribution and pore connectivity. In this study, three porous samples were investigated by AFM-porosimetry: one ordered mesoporous sample and two disordered foam structures. All samples were based on a matrix of amorphous silica templated by a block copolymer, Pluronic F127, swollen to various degrees with poly(propylene glycol). In addition, the density of silica spheres without a template was measured by two independent techniques: AFM and the Archimedes principle.

A density-functional study on the electronic and vibrational properties of layered antimony telluride.

PubMed

Stoffel, Ralf P; Deringer, Volker L; Simon, Ronnie E; Hermann, Raphaël P; Dronskowski, Richard

2015-03-04

We present a comprehensive survey of electronic and lattice-dynamical properties of crystalline antimony telluride (Sb2Te3). In a first step, the electronic structure and chemical bonding have been investigated, followed by calculations of the atomic force constants, phonon dispersion relationships and densities of states. Then, (macroscopic) physical properties of Sb2Te3 have been computed, namely, the atomic thermal displacement parameters, the Grüneisen parameter γ, the volume expansion of the lattice, and finally the bulk modulus B. We compare theoretical results from three popular and economic density-functional theory (DFT) approaches: the local density approximation (LDA), the generalized gradient approximation (GGA), and a posteriori dispersion corrections to the latter. Despite its simplicity, the LDA shows excellent performance for all properties investigated-including the Grüneisen parameter, which only the LDA is able to recover with confidence. In the absence of computationally more demanding hybrid DFT methods, the LDA seems to be a good choice for further lattice dynamical studies of Sb2Te3 and related layered telluride materials.

Sound Transmission through Cylindrical Shell Structures Excited by Boundary Layer Pressure Fluctuations

NASA Technical Reports Server (NTRS)

Tang, Yvette Y.; Silcox, Richard J.; Robinson, Jay H.

1996-01-01

This paper examines sound transmission into two concentric cylindrical sandwich shells subject to turbulent flow on the exterior surface of the outer shell. The interior of the shells is filled with fluid medium and there is an airgap between the shells in the annular space. The description of the pressure field is based on the cross-spectral density formulation of Corcos, Maestrello, and Efimtsov models of the turbulent boundary layer. The classical thin shell theory and the first-order shear deformation theory are applied for the inner and outer shells, respectively. Modal expansion and the Galerkin approach are used to obtain closed-form solutions for the shell displacements and the radiation and transmission pressures in the cavities including both the annular space and the interior. The average spectral density of the structural responses and the transmitted interior pressures are expressed explicitly in terms of the summation of the cross-spectral density of generalized force induced by the boundary layer turbulence. The effects of acoustic and hydrodynamic coincidences on the spectral density are observed. Numerical examples are presented to illustrate the method for both subsonic and supersonic flows.

In Vitro Evaluation and Mechanism Analysis of the Fiber Shedding Property of Textile Pile Debridement Materials

PubMed Central

Fu, Yijun; Xie, Qixue; Lao, Jihong; Wang, Lu

2016-01-01

Fiber shedding is a critical problem in biomedical textile debridement materials, which leads to infection and impairs wound healing. In this work, single fiber pull-out test was proposed as an in vitro evaluation for the fiber shedding property of a textile pile debridement material. Samples with different structural design (pile densities, numbers of ground yarns and coating times) were prepared and estimated under this testing method. Results show that single fiber pull-out test offers an appropriate in vitro evaluation for the fiber shedding property of textile pile debridement materials. Pull-out force for samples without back-coating exhibited a slight escalating trend with the supplement in pile density and number of ground yarn plies, while back-coating process significantly raised the single fiber pull-out force. For fiber shedding mechanism analysis, typical pull-out behavior and failure modes of the single fiber pull-out test were analyzed in detail. Three failure modes were found in this study, i.e., fiber slippage, coating point rupture and fiber breakage. In summary, to obtain samples with desirable fiber shedding property, fabric structural design, preparation process and raw materials selection should be taken into full consideration. PMID:28773428

Vitamin K2 improves femoral bone strength without altering bone mineral density in gastrectomized rats.

PubMed

Iwamoto, Jun; Sato, Yoshihiro; Matsumoto, Hideo

2014-01-01

Gastrectomy (GX) induces osteopenia in rats. The present study examined the skeletal effects of vitamin K2 in GX rats. Thirty male Sprague-Dawley rats (12 wk old) were randomized by the stratified weight method into the following three groups of 10 animals each: sham operation (control) group; GX group; and GX+oral vitamin K2 (menatetrenone, 30 mg/kg, 5 d/wk) group. Treatment was initiated at 1 wk after surgery. After 6 wk of treatment, the bone mineral content (BMC), bone mineral density (BMD), and mechanical strength of the femoral diaphysis and distal metaphysis were determined by peripheral quantitative computed tomography and mechanical strength tests, respectively. GX induced decreases in the BMC, BMD, and ultimate force of the femoral diaphysis and distal metaphysis. Vitamin K2 did not significantly influence the BMC or BMD of the femoral diaphysis or distal metaphysis in GX rats, but attenuated the decrease in the ultimate force and increased the stiffness of the femoral diaphysis. The present study showed that administration of vitamin K2 to GX rats improved the bone strength of the femoral diaphysis without altering the BMC or BMD, suggesting effects of vitamin K2 on the cortical bone quality.

Bone histological correlates of soaring and high-frequency flapping flight in the furculae of birds.

PubMed

Mitchell, Jessica; Legendre, Lucas J; Lefèvre, Christine; Cubo, Jorge

2017-06-01

The furcula is a specialized bone in birds involved in flight function. Its morphology has been shown to reflect different flight styles from soaring/gliding birds, subaqueous flight to high-frequency flapping flyers. The strain experienced by furculae can vary depending on flight type. Bone remodeling is a response to damage incurred from different strain magnitudes and types. In this study, we tested whether a bone microstructural feature, namely Haversian bone density, differs in birds with different flight styles, and reassessed previous work using phylogenetic comparative methods that assume an evolutionary model with additional taxa. We show that soaring birds have higher Haversian bone densities than birds with a flapping style of flight. This result is probably linked to the fact that the furculae of soaring birds provide less protraction force and more depression force than furculae of birds showing other kinds of flight. The whole bone area is another explanatory factor, which confirms the fact that size is an important consideration in Haversian bone development. All birds, however, display Haversian bone development in their furculae, and other factors like age could be affecting the response of Haversian bone development. Copyright © 2017 Elsevier GmbH. All rights reserved.

A Status Report from the Task Force on Marketing Research.

ERIC Educational Resources Information Center

Keim, William A.; And Others

Concerned with changes in enrollment and credit hour patterns, the chancellor of the Kansas City Metropolitan Community Colleges (MCC) created a special Task Force to consider recommendations for marketing strategies for the 1978-79 academic year. The Task Force reviewed regional and district demography, area population trends and density, age and…

Use of a Force Sensor in Archimedes' Principle Experiment, Determination of Buoyant Force and Acceleration Due To Gravity

NASA Astrophysics Data System (ADS)

Aurora, Tarlok

2013-04-01

In introductory physics, students verify Archimedes' principle by immersing an object in water in a container, with a side-spout to collect the displaced water, resulting in a large uncertainty, due to surface tension. A modified procedure was introduced, in which a plastic bucket is suspended from a force sensor, and an object hangs underneath the bucket. The object is immersed in water in a glass beaker (without any side spout), and the weight loss is measured with a computer-controlled force sensor. Instead of collecting the water displaced by the object, tap water was added to the bucket to compensate for the weight loss, and the Archimedes' principle was verified within less than a percent. With this apparatus, buoyant force was easily studied as a function of volume of displaced water; as well as a function of density of saline solution. By graphing buoyant force as a function of volume (or density of liquid), value of g was obtained from slope. Apparatus and sources of error will be discussed.

EDITORIAL: Van der Waals interactions in advanced materials, in memory of David C Langreth Van der Waals interactions in advanced materials, in memory of David C Langreth

NASA Astrophysics Data System (ADS)

Hyldgaard, Per; Rahman, Talat S.

2012-10-01

The past decade has seen a dramatic rise in interest in exploring the role that van der Waals (vdW) or dispersion forces play in materials and in material behavior. Part of this stems from the obvious fact that vdW interactions (and other weak forces, such as Casimir) underpin molecular recognition, i.e., nature's approach to search for a match between genes and anti-genes and hence enable biological function. Less obvious is the recognition that vdW interactions affect a multitude of properties of a vast variety of materials in general, some of which also have strong technological applications. While for two atom- or orbital-sized material fragments the dispersive contributions to binding are small compared to those from the better known forms (ionic, covalent, metallic), those between sparse materials (spread over extended areas) can be of paramount importance. For example, an understanding of binding in graphite cannot arise solely from a study of the graphene layers individually, but also requires insight from inter-sheet graphene vdW bonding. It is the extended-area vdW bonding that provides sufficient cohesion to make graphite a robust, naturally occurring material. In fact, it is the vdW-bonded graphite, and not the all-covalently bonded diamond, that is the preferred form of pure carbon under ambient conditions. Also important is the understanding that vdW attraction can attain a dramatic relevance even if the material fragments, the building blocks, are not necessarily parallel from the outset or smooth when viewed in isolation (such as a graphene sheet or a carbon nanotube). This can happen if the building blocks have some softness and flexibility and allow an internal relative alignment to emerge. The vdW forces can then cause increasingly larger parts of the interacting fragments to line up at sub-nanometer separations and thus beget more areas with a sizable vdW bonding contribution. The gecko can scale a wall because it can bring its flexible hairs sufficiently close to any corrugated—and/or any smooth—surface and thus enforce a strong vdW-type adhesion; it exploits what is then essentially a contact force (dominated by the attraction exerted in the near-surface regions) to defy the pull of gravity on its own bulk. This Journal of Physics: Condensed Matter special issue is dedicated to the memory of David C Langreth. David is a dearly missed friend and mentor who inspired many of us. He was an outstanding condensed matter theorist and a scholar who greatly influenced us through his many-particle-physics based insights into density functional theory (DFT), surface science and related areas. His seminal works range from conserving formulations of interacting nonequilibrium transport [1] and formal-scattering theory [2] to an explicit formulation [3] of the exact DFT exchange-correlation energy in the adiabatic connection formula (ACF), the latter also being derived independently by Gunnarsson and Lundqvist [4]. David's portfolio also includes an analysis [5] that helped catalyze and guide the development of DFT from the local-density approximation (LDA) to the formulations of generalized gradient approximations (GGAs). Another salient contribution of David's is in the area of vdW interactions in materials. He was a key architect of the vdW density functional (vdW-DF) method [6, 7]. This method was developed in a long-standing Rutgers-Chalmers collaboration between David's group and that of Bengt I Lundqvist, later extending to a wider group of researchers on both sides of the Atlantic. Plasmons are collective excitations that depend on electron-density variation. The plasmon response can be seen as defining the nature of the LDA [4] and their description can thus also be seen as contributing to the success of GGA. The vdW-DF method is a regular constraint-based density functional (for ground-state DFT) which is derived within the ACF framework and which emphasizes the electrodynamical nature of the coupling between these collective plasmon excitations. The vdW-DF method thus seeks to utilise the implicit plasmon nature of the LDA/GGA success to also provide a nonempirical account of the fully nonlocal correlations that underpin the vdW bond [8]. The method retains a seamless integration [6] with the semilocal density functional components. We know that David was pleased to see how this quantitative, material-specific theory helped address problems in a broad class of materials that are sparse, i.e., that contain low electron density regions which are of significant consequence in determining material characteristics [9]. In a DFT framework, the vdW-DF method supplements other nonlocal functional descriptions [10] and the DFT-dispersion class of methods, extending GGA-DFT with an atom-based asymptotic description which relies on the vdW interaction coefficients [11]. The recent quest to understand the role of vdW forces in materials has certainly been facilitated and intensified by the set of recent developments in DFT itself. This is because these vdW-aware methods provide an opportunity to deliver a computationally effective account of the quantum-physical behavior even when the materials are sparse. It is the expectation that with such new-found theoretical capability, one may further extend the immense progress already attained by traditional (GGA) DFT calculations in reliably predicting the characteristics of materials and phenomena in materials, nanoscience, chemistry and other related fields [12]. This special issue contains a wealth of exciting contributions, mostly on vdW forces in materials. The special issue was suggested following the well-attended first focused vdW and materials session arranged by the Division of Materials Physics (DMP) of the American Physical Society (APS) at the March Meeting in 2011. The sad and unexpected passing of David in the spring of 2011 caused some rethinking and at the memorial symposium, held by David's colleagues at Rutgers in November 2011, we proposed to dedicate this special issue to David's contributions to the field. We are delighted with the overwhelmingly positive reaction that we received in response to our call for papers. We are also delighted to now be able to bring so many exciting contributions to you. The papers included in this special issue focus, in general, either through experiments or through theoretical characterization, on material properties in which vdW forces represent a central component. These articles contain arguments for and against a broader usage of DFT with vdW to account for material description, as well as establishing benchmarks which measure progress in the field. This special issue also includes fundamental theoretical analysis and suggestions for sensitive experiments that can resolve outstanding issues underlying the nature and role of the interaction. We believe that these papers will help stimulate further material-theory developments and, even more importantly, more discussions and feedback between theory and experiment. Physisorption is important to enable lubrication. This is because physisorption keeps the lubricating molecules at the interface at which a pair of internal surfaces must be free to move relative to each other. In turn, physisorbed (or perhaps weakly chemisorbed) lubricants prevent, for example, the formation of stronger bonding that will impede mechanical operation. However, it is also important to further characterize the nature and dynamics of the vdW bonding of lubricants: while physisorption means a weak binding further from the surface, there are still important friction effects. Walker et al present an experimental study, along with theoretical analysis, that directly determines the frictional heating of a Kr overlayer on graphene through quartz crystal microbalance measurements. The properties of materials reflect their atomic structure and hence indirectly their bonding nature and character. We can explore the role of dispersion forces by examining the impact their inclusion has on predictions of material properties. On the other hand, the experimental and theoretical study of Casimir forces also plays a vital role in the exploration of material behavior. vdW forces are related to the Casimir force but lack retardation effects. While the vdW bonding depends on additional effects (for example, the multipole contributions that reflect image-plane effects), the study of Casimir forces provides direct (and not indirect) measurements of the nature of interactions. Klimchitskaya et al note that to reconcile explicit measurements of the Casmir forces between semiconductor fragments within the Lifshitz description, it is relevant to question the Drude-like description of the contributions from free carriers and instead proceed with a formulation based only on optical observations of the permittivity. This optical response can be seen as a reflection of a more plasmon-like behavior. The authors suggest an experiment involving the study of the impact on the Casimir forces by a Mott transition in doped semiconductors. Such an experiment would permit explicit testing of the validity of the present model for Casimir forces and hence provide additional perspectives on the nature of dispersive interactions. There is an effort to store energy, e.g. H2 or CO2, inside a range of open cage-like structures, such as metal organics frameworks (MOF) or clathrates. The fact that the internal molecular adhesion is dominated by vdW forces suggests that the storage and retrieval costs could perhaps be lowered as compared to an approach that involves more traditional chemical compounds. Nijem et al have provided spectroscopic characterization of vdW interactions of both hydrogen molecules and CO in a specific MOF. The study includes a vdW-DF calculation of structure and a theoretical prediction of expected infrared activity. The potential applications to energy materials have motivated more theoretical characterizations. Li and Thonhauser use the vdW-DF method to investigate the limitations and hydrogen storage potential of hydrogen-methane compounds in a MOF. Similarly, Ihm et al combine vdW-DF studies with a thermodynamics argument to characterize the potential for molecular hydrogen uptake in expanded graphite, for example, through intercalation. The relevance of vdW-aware DFT calculations and the usefulness of such methods reaches beyond the study of molecules, surfaces and adsorption/absorption problems. Moellmann et al present a dispersion-DFT study of TiO2 bulk and surfaces, which illustrates that vdW forces can also play a prominent role when comparing the energies of different oxide structures. Perdew et al present a spherical-shell model and a simplified classical electrodynamical determination of the vdW interaction coefficients that describes the asymptotic interaction between fullerenes or other nearly spherical nanoclusters. The overall modeling framework also permits a formal expression of multipole contributions. Dappe et al used a combination of DFT and second-order perturbation theory to analyze the interactions between graphene layers, thus also exploring the role of dynamical screening in the vdW binding. The work of Sabatini et al extends the vdW-DF description with accounts of the stress tensor, providing the method with the same versatility as one has grown to expect in traditional LDA/GGA-DFT calculations. The method is illustrated with investigations of amino acid crystals under various pressures. The vdW-DF method was originally perceived as computationally more expensive than other approaches. It has now benefited from the development of efficient algorithms so the computational cost is comparable to that of traditional GGA-DFT calculations. As is also the case for some of the dispersion-DFT methods, there is an overhead when these are implemented self-consistently. Noting that sparse-matter structure determination and relaxations may well employ a sequence of methods, Le et al have suggested a simplified (cost-free relative to GGA) formulation of self-consistent dispersion-DFT calculations that is cost-free in the evaluation of forces and yet adapts the atom-centered pair-wise interaction coefficients through the change in local electron distributions. There is a need for continued testing of accuracy in the description of material properties and of the robustness and transferability of predictions across systems and length scales. This need is widely appreciated and is also reflected in the fact that many of the contributions touch on, suggest, or pursue a systematic benchmarking. There is an interest in careful analysis of detailed experiments on the physisorption of inert atoms, light molecules and organic molecules on smooth surfaces. Chen et al investigated the role of vdW forces in noble gas adsorption on various metal surfaces. Londero et al analyzed a set of experimental results for the desorption of n-alkanes from graphene in a program that had undergraduate participation. Lee et al benchmarked the performance of the vdW-DF2 functional and other methods against the physisorption potential curve that can be established from a rich data set of resonant backscattering of hydrogen molecules on various facets of Cu crystals. A few of the investigations included here noted that the vdW-DF method permits a more detailed analysis of the nature of strong physisorption and/or weak chemisorption cases than do DFT-dispersion methods and discussed the ramifications of the fact that GGA-DFT often, and vdW-aware DFT sometimes, pose difficulties for systems with a partial vdW component in the binding. Caciuc et al thus present a combined ab initio and semi-empirical vdW study comparing benzene/triazine/broazine adsorption on graphene and on boron-nitride sheets. On a more strategic note, Lazic et al broadened the discussion of a graphene/Ir(111) system and used the documented limitation of a GGA description to discuss a rationale for considering a more general switch to nonlocal functionals. Graziano et al note that the accuracy in the description of some soft layered systems like graphene and boron-nitride can be increased by changing the exchange description away from what was suggested in the original vdW-DF method. Hanke et al focused on the weak chemisorption of ethene on the various Cu facets that have an increasing degree of openness and provide a method for benchmarking through comparison with experimental observations. Finally, Björkman et al raise the question 'Are we van der Waals ready?' and proceed to test our readiness by benchmarking the performance of a range of vdW-aware methods for the group of 96 known layered structures. We have also included in this special issue one study of nonequilibrium transport which is linked to David's work in formal scattering theory [1, 2] and which observes that vdW forces (and possible generalizations to nonequilibrium transport conditions) will be of central importance in a richer computational characterization of molecular electronics under operational conditions. David was always keen to spearhead the development of tools that improved descriptions of nature and addressed actual experiments. We know that he was happy that DMP started the focused session on vdW and materials in 2011. We know that he would have thoroughly appreciated the articles in this special issue. He would have hoped, as we do, that materials theory may continue to learn how to tackle even more exciting experimental problems and that we may continue to deepen our understanding of materials and their functionality. Bibliography [1]Langreth D C 1976 1975 Nato Advanced Study Institute on Linear and Nonlinear Transport in Solids, Antwerben vol B17 (New York: Plenum) pp 3-32 [2]Langreth D C 1966 Friedel sum rule for Anderson's model of localized impurity states Phys. Rev. 150 516 [3]Langreth D C and Perdew J P 1975 The exchange-correlation energy of a metallic surface Solid State Commun. 17 1425 [4]Gunnarsson O and Lundqvist B I 1976 Exchange and correlation in atoms, molecules, and solids by the spin-density-functional formalism Phys. Rev. B 13 4274 [5]Langreth D C and Mehl M J 1981 Beyond the local-density approximation in calculations of ground-state electronic properties Phys. Rev. B 47 446 [6]Dion M, Rydberg H, Schröder E, Langreth D C and Lundqvist B I 2004 Van der Waals density functional for general geometries Phys. Rev. Lett. 92 246401 Thonhauser T, Cooper V R, Li S, Puzder A, Hyldgaard P and Langreth D C 2007 Van der Waals density functional: self-consistent potential and the nature of the van der Waals bond Phys. Rev. B 76 125112 [7]Lee K, Murray E D, Kong L, Lundqvist B I and Langreth D C 2010 A higher-accuracy van der Waals density functional Phys. Rev. B 82 081101 [8]Rapcewicz K and Ashcroft N W 1991 Fluctuation attraction in condensed matter: a nonlocal functional approach Phys. Rev. B 44 4032 Lundqvist B I, Andersson Y, Shao H, Chan S and Langreth D C 1995 Density functional theory including van der Waals forces Int. J. Quant. Chem. 56 247 [9]Langreth D C et al 2009 A density functional for sparse matter J. Phys.: Condens. Matter 21 084203 [10]For example, Kohn W, Meir Y and Makarov D E 1998 The exchange-correlation energy of a metallic surface Phys. Rev. Lett. 80 4153 Kurth S and Perdew J P 1999 Phys. Rev. B 59 10461 Dobson J F and Wang J 1999 Phys. Rev. Lett. 82 2123 Pitarke J M and Perdew J P 2003 Phys. Rev. B 67 045101 Vydrov O A and van Voorhi T 2009 Phys. Rev. Lett. 103 063004 [11]For example, Grimme S 2004 J. Comput. Phys. 25 1463 Tkatchenko A and Scheffler M 2009 Phys. Rev. Lett. 102 073005 Grimme S, Antony J, Ehrlich S and Krieg H 2010 J. Chem. Phys. 132 154004 [12]Burke K 2012 Perspectives on density functional theory J. Chem. Phys. 136 150901 Van der Waals interactions in advanced materials contents Van der Waals interactions in advanced materials, in memory of David C LangrethPer Hyldgaard and Talat S Rahman Frictional temperature rise in a sliding physisorbed monolayer of Kr/grapheneM Walker, C Jaye, J Krim and Milton W Cole How to modify the van der Waals and Casimir forces without change of the dielectric permittivityG L Klimchitskaya, U Mohideen and V M Mostepanenko Spectroscopic characterization of van der Waals interactions in a metal organic framework with unsaturated metal centers: MOF-74-MgNour Nijem, Pieremanuele Canepa, Lingzhu Kong, Haohan Wu, Jing Li, Timo Thonhauser and Yves J Chabal A theoretical study of the hydrogen-storage potential of (H2)4CH4 in metal organic framework materials and carbon nanotubesQ Li and T Thonhauser The influence of dispersion interactions on the hydrogen adsorption properties of expanded graphiteYungok Ihm, Valentino R Cooper, Lujian Peng and James R Morris A DFT-D study of structural and energetic properties of TiO2 modificationsJonas Moellmann, Stephan Ehrlich, Ralf Tonner and Stefan Grimme Spherical-shell model for the van der Waals coefficients between fullerenes and/or nearly spherical nanoclustersJohn P Perdew, Jianmin Tao, Pan Hao, Adrienn Ruzsinszky, Gábor I Csonka and J M Pitarke Dynamical screening of the van der Waals interaction between graphene layersY J Dappe, P G Bolcatto, J Ortega and F Flores Structural evolution of amino acid crystals under stress from a non-empirical density functionalRiccardo Sabatini, Emine Küçükbenli, Brian Kolb, T Thonhauser and Stefano de Gironcoli Physisorption of nucleobases on graphene: a comparative van der Waals studyDuy Le, Abdelkader Kara, Elsebeth Schröder, Per Hyldgaard and Talat S Rahman The role of van der Waals interactions in the adsorption of noble gases on metal surfacesDe-Li Chen, W A Al-Saidi and J Karl Johnson Desorption of n-alkanes from graphene: a van der Waals density functional studyElisa Londero, Emma K Karlson, Marcus Landahl, Dimitri Ostrovskii, Jonatan D Rydberg and Elsebeth Schröder Benchmarking van der Waals density functionals with experimental data: potential-energy curves for H2 molecules on Cu(111), (100) and (110) surfacesKyuho Lee, Kristian Berland, Mina Yoon, Stig Andersson, Elsebeth Schröder, Per Hyldgaard and Bengt I Lundqvist Ab initio and semi-empirical van der Waals study of graphene-boron nitride interaction from a molecular point of viewVasile Caciuc, Nicolae Atodiresei, Martin Callsen, Predrag Lazić and Stefan Blügel Rationale for switching to nonlocal functionals in density functional theoryP Lazić, N Atodiresei, V Caciuc, R Brako, B Gumhalter and S Blügel Improved description of soft layered materials with van der Waals density functional theoryGabriella Graziano, Jiří Klimeš, Felix Fernandez-Alonso and Angelos Michaelides Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactionsFelix Hanke, Matthew S Dyer, Jonas Björk and Mats Persson Are we van der Waals ready?T Björkman, A Gulans, A V Krasheninnikov and R M Nieminen Nonequilibrium thermodynamics of interacting tunneling transport: variational grand potential, density functional formulation and nature of steady-state forcesP Hyldgaard

The influence of environmental forcing on biodiversity and extinction in a resource competition model

NASA Astrophysics Data System (ADS)

Vakulenko, Sergey A.; Sudakov, Ivan; Mander, Luke

2018-03-01

In this paper, we study a model of many species that compete, directly or indirectly, for a pool of common resources under the influence of periodic, stochastic, and/or chaotic environmental forcing. Using numerical simulations, we find the number and sequence of species going extinct when the community is initially packed with a large number of species of random initial densities. Thereby, any species with a density below a given threshold is regarded to be extinct.

The influence of environmental forcing on biodiversity and extinction in a resource competition model.

PubMed

Vakulenko, Sergey A; Sudakov, Ivan; Mander, Luke

2018-03-01

In this paper, we study a model of many species that compete, directly or indirectly, for a pool of common resources under the influence of periodic, stochastic, and/or chaotic environmental forcing. Using numerical simulations, we find the number and sequence of species going extinct when the community is initially packed with a large number of species of random initial densities. Thereby, any species with a density below a given threshold is regarded to be extinct.

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Selective particle trapping using an oscillating microbubble.

PubMed

Rogers, Priscilla; Neild, Adrian

2011-11-07

The ability to isolate and sort analytes within complex microfluidic volumes is essential to the success of lab-on-a-chip (LOC) devices. In this study, acoustically-excited oscillating bubbles are used to selectively trap particles, with the selectivity being a function of both particle size and density. The operating principle is based on the interplay between the strong microstreaming-induced drag force and the attractive secondary Bjerknes force. Depending upon the size of the bubble, and thus its resonant frequency, it is possible to cause one force to dominate over the other, resulting in either particle attraction or repulsion. A theoretical analysis reveals the extent of the contribution of each force for a given particle size; in close agreement with experimental findings. Density-based trapping is also demonstrated, highlighting that denser particles experience a larger secondary Bjerknes force resulting in their attraction. This study showcases the excellent applicability and versatility of using oscillating bubbles as a trapping and sorting mechanism within LOC devices. This journal is © The Royal Society of Chemistry 2011

A new equation of state for core-collapse supernovae based on realistic nuclear forces and including a full nuclear ensemble

NASA Astrophysics Data System (ADS)

Furusawa, S.; Togashi, H.; Nagakura, H.; Sumiyoshi, K.; Yamada, S.; Suzuki, H.; Takano, M.

2017-09-01

We have constructed a nuclear equation of state (EOS) that includes a full nuclear ensemble for use in core-collapse supernova simulations. It is based on the EOS for uniform nuclear matter that two of the authors derived recently, applying a variational method to realistic two- and three-body nuclear forces. We have extended the liquid drop model of heavy nuclei, utilizing the mass formula that accounts for the dependences of bulk, surface, Coulomb and shell energies on density and/or temperature. As for light nuclei, we employ a quantum-theoretical mass evaluation, which incorporates the Pauli- and self-energy shifts. In addition to realistic nuclear forces, the inclusion of in-medium effects on the full ensemble of nuclei makes the new EOS one of the most realistic EOSs, which covers a wide range of density, temperature and proton fraction that supernova simulations normally encounter. We make comparisons with the FYSS EOS, which is based on the same formulation for the nuclear ensemble but adopts the relativistic mean field theory with the TM1 parameter set for uniform nuclear matter. The new EOS is softer than the FYSS EOS around and above nuclear saturation densities. We find that neutron-rich nuclei with small mass numbers are more abundant in the new EOS than in the FYSS EOS because of the larger saturation densities and smaller symmetry energy of nuclei in the former. We apply the two EOSs to 1D supernova simulations and find that the new EOS gives lower electron fractions and higher temperatures in the collapse phase owing to the smaller symmetry energy. As a result, the inner core has smaller masses for the new EOS. It is more compact, on the other hand, due to the softness of the new EOS and bounces at higher densities. It turns out that the shock wave generated by core bounce is a bit stronger initially in the simulation with the new EOS. The ensuing outward propagations of the shock wave in the outer core are very similar in the two simulations, which may be an artifact, though, caused by the use of the same tabulated electron capture rates for heavy nuclei ignoring differences in the nuclear composition between the two EOSs in these computations.

A study of solid wall models for weakly compressible SPH

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

Valizadeh, Alireza, E-mail: alireza.valizadeh@monash.edu; Monaghan, Joseph J., E-mail: joe.monaghan@monash.edu

2015-11-01

This paper is concerned with a comparison of two methods of treating solid wall boundaries in the weakly compressible (SPH) method. They have been chosen because of their wide use in simulations. These methods are the boundary force particles of Monaghan and Kajtar [24] and the use of layers of fixed boundary particles. The latter was first introduced by Morris et al. [26] but has since been improved by Adami et al. [1] whose algorithm involves interpolating the pressure and velocity from the actual fluid to the boundary particles. For each method, we study the effect of the density diffusivemore » terms proposed by Molteni and Colagrossi [19] and modified by Antuono et al. [3]. We test the methods by a series of simulations commencing with the time-dependent spin-down of fluid within a cylinder and the behaviour of fluid in a box subjected to constant acceleration at an angle to the walls of the box, and concluding with a dam break over a triangular obstacle. In the first two cases the results from the two methods can be compared to analytical solutions while, in the latter case, they can be compared with experiments and other methods. These results show that the method of Adami et al. together with density diffusion is in very satisfactory agreement with the experimental results and is, overall, the best of the methods discussed here.« less

Density Functional O(N) Calculations

NASA Astrophysics Data System (ADS)

Ordejón, Pablo

1998-03-01

We have developed a scheme for performing Density Functional Theory calculations with O(N) scaling.(P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B, 53), 10441 (1996) The method uses arbitrarily flexible and complete Atomic Orbitals (AO) basis sets. This gives a wide range of choice, from extremely fast calculations with minimal basis sets, to greatly accurate calculations with complete sets. The size-efficiency of AO bases, together with the O(N) scaling of the algorithm, allow the application of the method to systems with many hundreds of atoms, in single processor workstations. I will present the SIESTA code,(D. Sanchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65), 453 (1997) in which the method is implemented, with several LDA, LSD and GGA functionals available, and using norm-conserving, non-local pseudopotentials (in the Kleinman-Bylander form) to eliminate the core electrons. The calculation of static properties such as energies, forces, pressure, stress and magnetic moments, as well as molecular dynamics (MD) simulations capabilities (including variable cell shape, constant temperature and constant pressure MD) are fully implemented. I will also show examples of the accuracy of the method, and applications to large-scale materials and biomolecular systems.

Orientational order as the origin of the long-range hydrophobic effect.

PubMed

Banerjee, Saikat; Singh, Rakesh S; Bagchi, Biman

2015-04-07

The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation-this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL.

Orientational order as the origin of the long-range hydrophobic effect

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Singh, Rakesh S.; Bagchi, Biman

2015-04-01

The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation—this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL.

How do roll compaction/dry granulation affect the tableting behaviour of inorganic materials? Comparison of four magnesium carbonates.

PubMed

Freitag, Franziska; Kleinebudde, Peter

2003-07-01

The effect of roll compaction/dry granulation on the particle and bulk material characteristics of different magnesium carbonates was evaluated. The flowability of all materials could be improved, even by the application of low specific compaction forces. The tablet properties made of powder and dry granulated magnesium carbonate were compared. Roll compaction/dry granulation resulted in a modified compactibility of the material and, consequently, tablets with reduced tensile strength. The higher relative tap density of the compacted material does not allow a densification to the same extent as the uncompacted powder. The degree of densification during tableting can be expressed as the ratio of the relative tablet density to the relative tap density of the feed material. Increasing the specific compaction forces resulted in higher apparent mean yield pressure, gained from Heckel plots, of all materials analysed. The partial loss of compactibility leads to the demand of low loads during roll compaction. Comparing the tablet properties of different magnesium carbonates reveals an obvious capping disposition. However, it depends on the type of magnesium carbonate, the specific compaction force and also on the tableting force applied.

From intermolecular interactions to structures and properties of a novel cocrystal explosive: a first-principles study.

PubMed

Zhang, Lei; Wu, Ji-Zhou; Jiang, Sheng-Li; Yu, Yi; Chen, Jun

2016-09-29

By employing a first-principles method, we conducted a thorough study on a novel cocrystal explosive 1 : 1 NTO : TZTN and gained insight into the interaction-structure-property interrelationship. Mulliken bond orders, Hirshfeld surfaces, intermolecular binding energies, packing coefficients, and oxygen balance were calculated to analyze the intermolecular interactions and structures of the cocrystal explosive. The cocrystallization of NTO and TZTN molecules enhances the intermolecular binding force, which drives the synthesis of the cocrystal. However, the cocrystallization decreases the molecular packing density along the closest packed directions, which reduces the density by 10.5% and deteriorates the oxygen balance. All of these lead to a reduction in the detonation performance compared to NTO explosives. We have also proposed a new method to evaluate the impact sensitivity according to the lattice dynamics calculation. The cocrystal explosive has a lower impact sensitivity than TZTN but higher than NTO, which agrees well with experiments.

Coordinated Control of Cross-Flow Turbines

NASA Astrophysics Data System (ADS)

Strom, Benjamin; Brunton, Steven; Polagye, Brian

2016-11-01

Cross-flow turbines, also known as vertical-axis turbines, have several advantages over axial-flow turbines for a number of applications including urban wind power, high-density arrays, and marine or fluvial currents. By controlling the angular velocity applied to the turbine as a function of angular blade position, we have demonstrated a 79 percent increase in cross-flow turbine efficiency over constant-velocity control. This strategy uses the downhill simplex method to optimize control parameter profiles during operation of a model turbine in a recirculating water flume. This optimization method is extended to a set of two turbines, where the blade motions and position of the downstream turbine are optimized to beneficially interact with the coherent structures in the wake of the upstream turbine. This control scheme has the potential to enable high-density arrays of cross-flow turbines to operate at cost-effective efficiency. Turbine wake and force measurements are analyzed for insight into the effect of a coordinated control strategy.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

PubMed

Meng, Yilin; Roux, Benoît

2015-08-11

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression

PubMed Central

2015-01-01

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. PMID:26574437

Squeeze strengthening of magnetorheological fluids using mixed mode operation

NASA Astrophysics Data System (ADS)

Becnel, A. C.; Sherman, S. G.; Hu, W.; Wereley, N. M.

2015-05-01

This research details a novel method of increasing the shear yield stress of magnetorheological fluids by combining shear and squeeze modes of operation to manipulate particle chain structures, so-called squeeze strengthening. Using a custom built Searle cell magnetorheometer, which is a model device emulating a rotary magnetorheological energy absorber (MREA), the contribution of squeeze strengthening to the total controllable yield force is experimentally investigated. Using an eccentric rotating inner cylinder, characterization data from large (1 mm) and small (0.25 mm) nominal gap geometries are compared to investigate the squeeze strengthening effect. Details of the experimental setup and method are presented, and a hybrid model is used to explain experimental trends. This study demonstrates that it is feasible, utilizing squeeze strengthening to increase yield stress, to either (1) design a rotary MREA of a given volume to achieve higher energy absorption density (energy absorbed normalized by active fluid volume), or (2) reduce the volume of a given rotary MREA to achieve the same energy absorption density.

Vibrational spectroscopic investigation and normal coordinate analysis of the fibrate hypolipidemic agent 5-(2,5-dimethylphenoxy)-2,2-dimethyl pentanoic acid (Gemfibrozil)

NASA Astrophysics Data System (ADS)

Priya, M. Siva; Benitta, T. Asenath; James, C.

2011-03-01

Colorless crystals of 5-(2,5-dimethylphenoxy)-2,2-dimethyl pentanoic acid were grown by slow evaporation method and the FT-IR and FT-Raman spectra of the sample were recorded in the region 4000-450 cm -1 and 4000-50 cm -1 respectively. Molecular structure is optimized with the help of B3LYP/6-31G (d) density functional theory method. Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ ∗ antibonding orbitals and E (2) energies confirms the occurrence of intra-molecular charge transfer (ICT) within the molecule. The assignments of the vibrational spectra have been carried out with the help of Normal coordinate analysis following the scaled quantum mechanical force field (SQMFF) methodology. Mulliken population analysis on atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule.

The effect of glycerin solution density and viscosity on vibration amplitude of oblique different piezoelectric MC near the surface in 3D modeling

NASA Astrophysics Data System (ADS)

Korayem, A. H.; Abdi, M.; Korayem, M. H.

2018-06-01

The surface topography in nanoscale is one of the most important applications of AFM. The analysis of piezoelectric microcantilevers vibration behavior is essential to improve the AFM performance. To this end, one of the appropriate methods to simulate the dynamic behavior of microcantilever (MC) is a numerical solution with FEM in the 3D modeling using COMSOL software. The present study aims to simulate different geometries of the four-layered AFM piezoelectric MCs in 2D and 3D modeling in a liquid medium using COMSOL software. The 3D simulation was done in a spherical container using FSI domain in COMSOL. In 2D modeling by applying Hamilton's Principle based on Euler-Bernoulli Beam theory, the governing motion equation was derived and discretized with FEM. In this mode, the hydrodynamic force was assumed with a string of spheres. The effect of this force along with the squeezed-film force was considered on MC equations. The effect of fluid density and viscosity on the MC vibrations that immersed in different glycerin solutions was investigated in 2D and 3D modes and the results were compared with the experimental results. The frequencies and time responses of MC close to the surface were obtained considering tip-sample forces. The surface topography of MCs different geometries were compared in the liquid medium and the comparison was done in both tapping and non-contact mode. Various types of surface roughness were considered in the topography for MC different geometries. Also, the effect of geometric dimensions on the surface topography was investigated. In liquid medium, MC is installed at an oblique position to avoid damaging the MC due to the squeezed-film force in the vicinity of MC surface. Finally, the effect of MC's angle on surface topography and time response of the system was investigated.

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

NASA Astrophysics Data System (ADS)

Bérces, Attila; Ziegler, Tom

1993-03-01

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

Primary stability, insertion torque, and bone density of conical implants with internal hexagon: is there a relationship?

PubMed

Trisi, Paolo; Berardi, Davide; Paolantonio, Michele; Spoto, Giuseppe; D'Addona, Antonio; Perfetti, Giorgio

2013-05-01

Between implants and peri-implant bone, there should be a minimum gap, without micromotions over a threshold, which could cause resorption and fibrosis. The higher the implant insertion torque, the higher will be the initial stability. The aim was to evaluate in vitro the correlation between micromotions and insertion torque of implants in bone of different densities. The test was performed on bovine bone of hard, medium, and soft density: 150 implants were used, 10 for each torque (20, 35, 45, 70, and 100 N/cm). Samples were fixed on a loading device. On each sample, we applied a 25-N horizontal force. Insertion torque and micromotions are statistically correlated. In soft bone with an insertion force of 20 and 35 N/cm, the micromotion resulted significantly over the risk threshold, which was not found with an insertion force of 45 and 70 N/cm and in hard and medium bones with any insertion torque. The increase in insertion torque reduces the amount of micromotions between implant and bone. Therefore, the immediate loading may be considered a valid therapeutic choice, even in low-density bone, as long as at least 45 N/cm of insertion torque is reached.

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

PubMed

Tack, Jeremy L; Ford, David M

2008-06-01

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

Surface force and vibrational spectroscopic analyses of interfacial water molecules in the vicinity of methoxy-tri(ethylene glycol)-terminated monolayers: mechanisms underlying the effect of lateral packing density on bioinertness.

PubMed

Sekine, Taito; Asatyas, Syifa; Sato, Chikako; Morita, Shigeaki; Tanaka, Masaru; Hayashi, Tomohiro

Unequivocal dependence of bioinertness of self-assembled monolayers of methoxy-tri(ethylene glycol)-terminated alkanethiol (EG3-OMe SAMs) on their packing density has been a mystery for more than two decades. We tackled this long-standing question by performing surface force and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements. Our surface force measurements revealed a physical barrier of interfacial water in the vicinity of the Au-supported EG3-OMe SAM (low packing density), whereas the Ag-supported one (high packing density) did not possess such interfacial water. In addition, the results of SEIRA measurements clearly exhibited that hydrogen bonding states of the interfacial water differ depending on the substrates. We also characterized the bioinertness of these SAMs by protein adsorption tests and adhesion assays of platelet and human umbilical vein endothelial cells. The hydrogen bonding states of the interfacial water and water-induced interaction clearly correlated with the bioinertness of the SAMs, suggesting that the interfacial water plays an important role determining the interaction of the SAMs with biomolecules and cells.

Particle-in-cell simulations of electron beam control using an inductive current divider

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

Swanekamp, S. B.; Angus, J. R.; Cooperstein, G.

2015-11-15

Kinetic, time-dependent, electromagnetic, particle-in-cell simulations of the inductive current divider are presented. The inductive current divider is a passive method for controlling the trajectory of an intense, hollow electron beam using a vacuum structure that inductively splits the beam's return current. The current divider concept was proposed and studied theoretically in a previous publication [Swanekamp et al., Phys. Plasmas 22, 023107 (2015)]. A central post carries a portion of the return current (I{sub 1}), while the outer conductor carries the remainder (I{sub 2}) with the injected beam current given by I{sub b} = I{sub 1} + I{sub 2}. The simulations are in agreement withmore » the theory which predicts that the total force on the beam trajectory is proportional to (I{sub 2}−I{sub 1}) and the force on the beam envelope is proportional to I{sub b}. Independent control over both the current density and the beam angle at the target is possible by choosing the appropriate current-divider geometry. The root-mean-square (RMS) beam emittance (ε{sub RMS}) varies as the beam propagates through the current divider to the target. For applications where control of the beam trajectory is desired and the current density at the target is similar to the current density at the entrance foil, there is a modest 20% increase in ε{sub RMS} at the target. For other applications where the beam is pinched to a current density ∼5 times larger at the target, ε{sub RMS} is 2–3 times larger at the target.« less

Levitation properties of maglev systems using soft ferromagnets

NASA Astrophysics Data System (ADS)

Huang, Chen-Guang; Zhou, You-He

2015-03-01

Soft ferromagnets are widely used as flux-concentration materials in the design of guideways for superconducting magnetic levitation transport systems. In order to fully understand the influence of soft ferromagnets on the levitation performance, in this work we apply a numerical model based on the functional minimization method and the Bean’s critical state model to study the levitation properties of an infinitely long superconductor immersed in the magnetic field created by a guideway of different sets of infinitely long parallel permanent magnets with soft ferromagnets between them. The levitation force, guidance force, magnetic stiffness and magnetic pole density are calculated considering the coupling between the superconductor and soft ferromagnets. The results show that the levitation performance is closely associated with the permanent magnet configuration and with the location and dimension of the soft ferromagnets. Introducing the soft ferromagnet with a certain width in a few configurations always decreases the levitation force. However, for most configurations, the soft ferromagnets contribute to improve the levitation performance only when they have particular locations and dimensions in which the optimized location and thickness exist to increase the levitation force the most. Moreover, if the superconductor is laterally disturbed, the presence of soft ferromagnets can effectively improve the lateral stability for small lateral displacement and reduce the degradation of levitation force.

Migration And Entrapment Of Mercury In The Subsurface

NASA Astrophysics Data System (ADS)

M, D.; Nambi, I. M.

2009-12-01

Elemental mercury is an immiscible liquid with high density and high surface tension. The movement of mercury in the saturated subsurface region is therefore considered a case of two phase flow involving mercury and water and is expected to be governed by gravity, viscous and capillary forces. Fundamental investigation into the migration and capillary entrapment of mercury in the subsurface was done by controlled laboratory capillary pressure saturation experiments using mercury and water as non wetting and wetting fluid respectively. Residual mercury saturation and van Genuchten’s capillary entrapment parameters were determined independently for different sizes of porous media. Based on the experimental data, theoretical investigations were done on the role of the three predominant forces and their influence on mercury migration and entrapment. The effects of fluid density and interfacial tension and the influence of Capillary and Bond number on mercury entrapment were analyzed with the help of similar capillary pressure - saturation experiments using Tetrachloroethylene (PCE)-water fluid pair. Mercury-water systems exhibited a low residual saturation of 0.02 and 0.07 as compared to 0.16 and 0.27 for PCE-water systems. Less residual mercury saturation, lack of apparent hysteresis in capillary pressure saturation curves and large variation in van Genuchten’s parameters 'α'(inverse of displacement pressure) and ‘n’ (pore size distribution index) for mercury-water systems compared to PCE-water systems were observed. These anomalies between the two systems elucidate that the capillary trapping is equally dependent on the fluid characteristics especially for high density immiscible fluids. Gravity force nevertheless a predominant controlling factor in the migration of highly dense mercury, is counteracted by not less trivial capillary force which was 1.22x104 times higher than gravity force. The capillary forces thus surmount the gravity forces and cause entrapment of mercury in the soil pores even in homogeneous porous medium system. Bond number (Bond number relates gravity and capillary forces) for mercury-water system was found to 2.5 times higher than PCE-water systems. Large density differences between mercury and water lead to high Bond number and thus less residual saturation. Capillary number (Capillary number relates viscous and capillary forces) was found to be less for mercury-water systems. Literature review unveils that low Capillary number does not influence non wetting residual saturation. But for high density mercury with natural infiltration, even low Capillary number influences residual saturation. With the alarming increase in number of mercury spill sites, results of this study showed a better understanding of the capillary entrapment phenomena and the extent of influence of each predominant force during displacement of highly dense mercury. The fundamental inputs to NAPL entrapment models were generated in this study for mercury for the first time. This data will be used to assess the distribution of mercury in contaminated sites and design suitable remedial alternatives.

Revealing energy level structure of individual quantum dots by tunneling rate measured by single-electron sensitive electrostatic force spectroscopy.

PubMed

Roy-Gobeil, Antoine; Miyahara, Yoichi; Grutter, Peter

2015-04-08

We present theoretical and experimental studies of the effect of the density of states of a quantum dot (QD) on the rate of single-electron tunneling that can be directly measured by electrostatic force microscopy (e-EFM) experiments. In e-EFM, the motion of a biased atomic force microscope cantilever tip modulates the charge state of a QD in the Coulomb blockade regime. The charge dynamics of the dot, which is detected through its back-action on the capacitavely coupled cantilever, depends on the tunneling rate of the QD to a back-electrode. The density of states of the QD can therefore be measured through its effect on the energy dependence of tunneling rate. We present experimental data on individual 5 nm colloidal gold nanoparticles that exhibit a near continuous density of state at 77 K. In contrast, our analysis of already published data on self-assembled InAs QDs at 4 K clearly reveals discrete degenerate energy levels.

Modeling the subfilter scalar variance for large eddy simulation in forced isotropic turbulence

NASA Astrophysics Data System (ADS)

Cheminet, Adam; Blanquart, Guillaume

2011-11-01

Static and dynamic model for the subfilter scalar variance in homogeneous isotropic turbulence are investigated using direct numerical simulations (DNS) of a lineary forced passive scalar field. First, we introduce a new scalar forcing technique conditioned only on the scalar field which allows the fluctuating scalar field to reach a statistically stationary state. Statistical properties, including 2nd and 3rd statistical moments, spectra, and probability density functions of the scalar field have been analyzed. Using this technique, we performed constant density and variable density DNS of scalar mixing in isotropic turbulence. The results are used in an a-priori study of scalar variance models. Emphasis is placed on further studying the dynamic model introduced by G. Balarac, H. Pitsch and V. Raman [Phys. Fluids 20, (2008)]. Scalar variance models based on Bedford and Yeo's expansion are accurate for small filter width but errors arise in the inertial subrange. Results suggest that a constant coefficient computed from an assumed Kolmogorov spectrum is often sufficient to predict the subfilter scalar variance.

Near-resonant excitation and propagation of eccentric density waves by external forcing. [in accretion disks

NASA Technical Reports Server (NTRS)

Ostriker, Eve C.; Shu, Frank H.; Adams, Fred C.

1992-01-01

An overview is presented of the astronomical evidence that relatively massive, distended, gaseous disks form as a natural by-product of the process of star formation, and also the numerical evidence that SLING-amplified eccentric modes in the outer parts of such disks can drive one-armed spiral density waves in the inner parts by near-resonant excitation and propagation. An ordinary differential equation (ODE) of the second order that approximately governs the nonlocalized forcing of waves in a disk satisfying Lindblad resonance almost everywhere is derived. When transformed and appended with an extra model term, this ODE implies, for free waves, the usual asymptotic results of the WKBJ dispersion relationship and the propagation Goldreich-Tremaine (1978) formula for the resonant torque exerted on a localized Lindblad resonance. An analytical solution is given for the rate of energy and angular momentum transfer by nonlocalized near-resonant forcing in the case when the disk has power-law dependences on the radius of the surface density and temperature.

How does implant distribution affect 3D correction and bone-screw forces in thoracic adolescent idiopathic scoliosis spinal instrumentation?

PubMed

Le Navéaux, Franck; Larson, A Noelle; Labelle, Hubert; Wang, Xiaoyu; Aubin, Carl-Éric

2016-11-01

Optimal implant densities and configurations for thoracic spine instrumentation to treat adolescent idiopathic scoliosis remain unknown. The objective was to computationally assess the biomechanical effects of implant distribution on 3D curve correction and bone-implant forces. 3D patient-specific biomechanical spine models based on a multibody dynamic approach were created for 9 Lenke 1 patients who underwent posterior instrumentation (main thoracic Cobb: 43°-70°). For each case, a factorial design of experiments was used to generate 128 virtual implant configurations representative of existing implant patterns used in clinical practice. All instances except implant configuration were the same for each surgical scenario simulation. Simulation of the 128 implant configurations scenarios (mean implant density=1.32, range: 0.73-2) revealed differences of 2° to 10° in Cobb angle correction, 2° to 7° in thoracic kyphosis and 2° to 7° in apical vertebral rotation. The use of more implants, at the concave side only, was associated with higher Cobb angle correction (r=-0.41 to -0.90). Increased implant density was associated with higher apical vertebral rotation correction for seven cases (r=-0.20 to -0.48). It was also associated with higher bone-screw forces (r=0.22 to 0.64), with an average difference between the least and most constrained instrumentation constructs of 107N per implant at the end of simulated instrumentation. Low-density constructs, with implants mainly placed on the concave side, resulted in similar simulated curve correction as the higher-density patterns. Increasing the number of implants allows for only limited improvement of 3D correction and overconstrains the instrumentation construct, resulting in increased forces on the implants. Copyright © 2016 Elsevier Ltd. All rights reserved.