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

PubMed

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

2015-05-15

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

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field

PubMed Central

Shen, Hujun; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM). However, in implementing REM in molecular dynamics simulations, synchronization between processors on parallel computers is required, and communication between processors limits its ability to sample conformational space in a complex system efficiently. To minimize communication between processors during the simulation, a Serial Replica Exchange Method (SREM) has been proposed recently by Hagan et al. (J. Phys. Chem. B 2007, 111, 1416–1423). Here, we report the implementation of this new SREM algorithm with our physics-based united-residue (UNRES) force field. The method has been tested on the protein 1E0L with a temperature-independent UNRES force field and on terminally blocked deca-alanine (Ala10) and 1GAB with the recently introduced temperature-dependent UNRES force field. With the temperature-independent force field, SREM reproduces the results of REM but is more efficient in terms of wall-clock time and scales better on distributed-memory machines. However, exact application of SREM to the temperature-dependent UNRES algorithm requires the determination of a four-dimensional distribution of UNRES energy components instead of a one-dimensional energy distribution for each temperature, which is prohibitively expensive. Hence, we assumed that the temperature dependence of the force field can be ignored for neighboring temperatures. This version of SREM worked for Ala10 which is a simple system but failed to reproduce the thermodynamic results as well as regular REM on the more complex 1GAB protein. Hence, SREM can be applied to the temperature-independent but not to the temperature-dependent UNRES force field. PMID:20011673

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2015-09-01

The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Technique for forcing high Reynolds number isotropic turbulence in physical space

NASA Astrophysics Data System (ADS)

Palmore, John A.; Desjardins, Olivier

2018-03-01

Many common engineering problems involve the study of turbulence interaction with other physical processes. For many such physical processes, solutions are expressed most naturally in physical space, necessitating the use of physical space solutions. For simulating isotropic turbulence in physical space, linear forcing is a commonly used strategy because it produces realistic turbulence in an easy-to-implement formulation. However, the method resolves a smaller range of scales on the same mesh than spectral forcing. We propose an alternative approach for turbulence forcing in physical space that uses the low-pass filtered velocity field as the basis of the forcing term. This method is shown to double the range of scales captured by linear forcing while maintaining the flexibility and low computational cost of the original method. This translates to a 60% increase of the Taylor microscale Reynolds number on the same mesh. An extension is made to scalar mixing wherein a scalar field is forced to have an arbitrarily chosen, constant variance. Filtered linear forcing of the scalar field allows for control over the length scale of scalar injection, which could be important when simulating scalar mixing.

Fokker-Planck equation for the non-Markovian Brownian motion in the presence of a magnetic field

NASA Astrophysics Data System (ADS)

Das, Joydip; Mondal, Shrabani; Bag, Bidhan Chandra

2017-10-01

In the present study, we have proposed the Fokker-Planck equation in a simple way for a Langevin equation of motion having ordinary derivative (OD), the Gaussian random force and a generalized frictional memory kernel. The equation may be associated with or without conservative force field from harmonic potential. We extend this method for a charged Brownian particle in the presence of a magnetic field. Thus, the present method is applicable for a Langevin equation of motion with OD, the Gaussian colored thermal noise and any kind of linear force field that may be conservative or not. It is also simple to apply this method for the colored Gaussian noise that is not related to the damping strength.

Fokker-Planck equation for the non-Markovian Brownian motion in the presence of a magnetic field.

PubMed

Das, Joydip; Mondal, Shrabani; Bag, Bidhan Chandra

2017-10-28

In the present study, we have proposed the Fokker-Planck equation in a simple way for a Langevin equation of motion having ordinary derivative (OD), the Gaussian random force and a generalized frictional memory kernel. The equation may be associated with or without conservative force field from harmonic potential. We extend this method for a charged Brownian particle in the presence of a magnetic field. Thus, the present method is applicable for a Langevin equation of motion with OD, the Gaussian colored thermal noise and any kind of linear force field that may be conservative or not. It is also simple to apply this method for the colored Gaussian noise that is not related to the damping strength.

Magnetic Helicity Estimations in Models and Observations of the Solar Magnetic Field. III. Twist Number Method

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

Guo, Y.; Pariat, E.; Moraitis, K.

We study the writhe, twist, and magnetic helicity of different magnetic flux ropes, based on models of the solar coronal magnetic field structure. These include an analytical force-free Titov–Démoulin equilibrium solution, non-force-free magnetohydrodynamic simulations, and nonlinear force-free magnetic field models. The geometrical boundary of the magnetic flux rope is determined by the quasi-separatrix layer and the bottom surface, and the axis curve of the flux rope is determined by its overall orientation. The twist is computed by the Berger–Prior formula, which is suitable for arbitrary geometry and both force-free and non-force-free models. The magnetic helicity is estimated by the twistmore » multiplied by the square of the axial magnetic flux. We compare the obtained values with those derived by a finite volume helicity estimation method. We find that the magnetic helicity obtained with the twist method agrees with the helicity carried by the purely current-carrying part of the field within uncertainties for most test cases. It is also found that the current-carrying part of the model field is relatively significant at the very location of the magnetic flux rope. This qualitatively explains the agreement between the magnetic helicity computed by the twist method and the helicity contributed purely by the current-carrying magnetic field.« less

Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.

PubMed

Kamath, Ganesh; Kurnikov, Igor; Fain, Boris; Leontyev, Igor; Illarionov, Alexey; Butin, Oleg; Olevanov, Michael; Pereyaslavets, Leonid

2016-11-01

We present the performance of blind predictions of water-cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF's are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.

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

PubMed

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

2010-01-01

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

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

PubMed

Bell, David R; Qi, Rui; Jing, Zhifeng; Xiang, Jin Yu; Mejias, Christopher; Schnieders, Michael J; Ponder, Jay W; Ren, Pengyu

2016-11-09

Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

On the extraction of pressure fields from PIV velocity measurements in turbines

NASA Astrophysics Data System (ADS)

Villegas, Arturo; Diez, Fancisco J.

2012-11-01

In this study, the pressure field for a water turbine is derived from particle image velocimetry (PIV) measurements. Measurements are performed in a recirculating water channel facility. The PIV measurements include calculating the tangential and axial forces applied to the turbine by solving the integral momentum equation around the airfoil. The results are compared with the forces obtained from the Blade Element Momentum theory (BEMT). Forces are calculated by using three different methods. In the first method, the pressure fields are obtained from PIV velocity fields by solving the Poisson equation. The boundary conditions are obtained from the Navier-Stokes momentum equations. In the second method, the pressure at the boundaries is determined by spatial integration of the pressure gradients along the boundaries. In the third method, applicable only to incompressible, inviscid, irrotational, and steady flow, the pressure is calculated using the Bernoulli equation. This approximated pressure is known to be accurate far from the airfoil and outside of the wake for steady flows. Additionally, the pressure is used to solve for the force from the integral momentum equation on the blade. From the three methods proposed to solve for pressure and forces from PIV measurements, the first one, which is solved by using the Poisson equation, provides the best match to the BEM theory calculations.

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

PubMed Central

Vanommeslaeghe, K.

2014-01-01

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

Reconstruction and separation of vibratory field using structural holography

NASA Astrophysics Data System (ADS)

Chesnais, C.; Totaro, N.; Thomas, J.-H.; Guyader, J.-L.

2017-02-01

A method for reconstructing and separating vibratory field on a plate-like structure is presented. The method, called "Structural Holography" is derived from classical Near-field Acoustic Holography (NAH) but in the vibratory domain. In this case, the plate displacement is measured on one-dimensional lines (the holograms) and used to reconstruct the entire two-dimensional displacement field. As a consequence, remote measurements on non directly accessible zones are possible with Structural Holography. Moreover, as it is based on the decomposition of the field into forth and back waves, Structural Holography permits to separate forces in the case of multi-sources excitation. The theoretical background of the Structural Holography method is described first. Then, to illustrate the process and the possibilities of Structural Holography, the academic test case of an infinite plate excited by few point forces is presented. With the principle of vibratory field separation, the displacement fields produced by each point force separately is reconstructed. However, the displacement field is not always meaningful and some additional treatments are mandatory to localize the position of point forces for example. From the simple example of an infinite plate, a post-processing based on the reconstruction of the structural intensity field is thus proposed. Finally, Structural Holography is generalized to finite plates and applied to real experimental measurements

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

PubMed

Vanommeslaeghe, K; MacKerell, A D

2015-05-01

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

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.

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

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

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

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

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

2011-10-15

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

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

PubMed

Abella, Jayvee R; Cheng, Sara Y; Wang, Qiantao; Yang, Wei; Ren, Pengyu

2014-07-08

The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.

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

PubMed

Piquemal, Jean-Philip; Jordan, Kenneth D

2017-10-28

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

Preface: Special Topic: From Quantum Mechanics to Force Fields

NASA Astrophysics Data System (ADS)

Piquemal, Jean-Philip; Jordan, Kenneth D.

2017-10-01

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

Force-free magnetic fields - The magneto-frictional method

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

Molecular Mechanics

PubMed Central

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

2014-01-01

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

Enhancement of force patterns classification based on Gaussian distributions.

PubMed

Ertelt, Thomas; Solomonovs, Ilja; Gronwald, Thomas

2018-01-23

Description of the patterns of ground reaction force is a standard method in areas such as medicine, biomechanics and robotics. The fundamental parameter is the time course of the force, which is classified visually in particular in the field of clinical diagnostics. Here, the knowledge and experience of the diagnostician is relevant for its assessment. For an objective and valid discrimination of the ground reaction force pattern, a generic method, especially in the medical field, is absolutely necessary to describe the qualities of the time-course. The aim of the presented method was to combine the approaches of two existing procedures from the fields of machine learning and the Gauss approximation in order to take advantages of both methods for the classification of ground reaction force patterns. The current limitations of both methods could be eliminated by an overarching method. Twenty-nine male athletes from different sports were examined. Each participant was given the task of performing a one-legged stopping maneuver on a force plate from the maximum possible starting speed. The individual time course of the ground reaction force of each subject was registered and approximated on the basis of eight Gaussian distributions. The descriptive coefficients were then classified using Bayesian regulated neural networks. The different sports served as the distinguishing feature. Although the athletes were all given the same task, all sports referred to a different quality in the time course of ground reaction force. Meanwhile within each sport, the athletes were homogeneous. With an overall prediction (R = 0.938) all subjects/sports were classified correctly with 94.29% accuracy. The combination of the two methods: the mathematical description of the time course of ground reaction forces on the basis of Gaussian distributions and their classification by means of Bayesian regulated neural networks, seems an adequate and promising method to discriminate the ground reaction forces without any loss of information. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

La Delfa, Nicholas J; Potvin, Jim R

2017-03-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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

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

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

2015-08-06

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

Method and apparatus for shaping and enhancing acoustical levitation forces

NASA Technical Reports Server (NTRS)

Oran, W. A.; Berge, L. H.; Reiss, D. A.; Johnson, J. L. (Inventor)

1980-01-01

A method and apparatus for enhancing and shaping acoustical levitation forces in a single-axis acoustic resonance system wherein specially shaped drivers and reflectors are utilized to enhance to levitation force and better contain fluid substance by means of field shaping is described.

Magnetic domain structure imaging near sample surface with alternating magnetic force microscopy by using AC magnetic field modulated superparamagnetic tip.

PubMed

Cao, Yongze; Nakayama, Shota; Kumar, Pawan; Zhao, Yue; Kinoshita, Yukinori; Yoshimura, Satoru; Saito, Hitoshi

2018-05-03

For magnetic domain imaging with a very high spatial resolution by magnetic force microscopy the tip-sample distance should be as small as possible. However, magnetic imaging near sample surface is very difficult with conventional MFM because the interactive forces between tip and sample includes van der Waals and electrostatic forces along with magnetic force. In this study, we proposed an alternating magnetic force microscopy (A-MFM) which extract only magnetic force near sample surface without any topographic and electrical crosstalk. In the present method, the magnetization of a FeCo-GdOx superparamagnetic tip is modulated by an external AC magnetic field in order to measure the magnetic domain structure without any perturbation from the other forces near the sample surface. Moreover, it is demonstrated that the proposed method can also measure the strength and identify the polarities of the second derivative of the perpendicular stray field from a thin-film permanent magnet with DC demagnetized state and remanent state. © 2018 IOP Publishing Ltd.

Interactions and reversal-field memory in complex magnetic nanowire arrays

NASA Astrophysics Data System (ADS)

Rotaru, Aurelian; Lim, Jin-Hee; Lenormand, Denny; Diaconu, Andrei; Wiley, John. B.; Postolache, Petronel; Stancu, Alexandru; Spinu, Leonard

2011-10-01

Interactions and magnetization reversal of Ni nanowire arrays have been investigated by the first-order reversal curve (FORC) method. Several series of samples with controlled spatial distribution were considered including simple wires of different lengths and diameters (70 and 110 nm) and complex wires with a single modulated diameter along their length. Subtle features of magnetic interactions are revealed through a quantitative analysis of the local interaction field profile distributions obtained from the FORC method. In addition, the FORC analysis indicates that the nanowire systems with a mean diameter of 70 nm appear to be organized in symmetric clusters indicative of a reversal-field memory effect.

Tunnel effect measuring systems and particle detectors

NASA Technical Reports Server (NTRS)

Kaiser, William J. (Inventor); Waltman, Steven B. (Inventor); Kenny, Thomas W. (Inventor)

1994-01-01

Methods and apparatus for measuring gravitational and inertial forces, magnetic fields, or wave or radiant energy acting on an object or fluid in space provide an electric tunneling current through a gap between an electrode and that object or fluid in space and vary that gap with any selected one of such forces, magnetic fields, or wave or radiant energy acting on that object or fluid. These methods and apparatus sense a corresponding variation in an electric property of that gap and determine the latter force, magnetic fields, or wave or radiant energy in response to that corresponding variation, and thereby sense or measure such parameters as acceleration, position, particle mass, velocity, magnetic field strength, presence or direction, or wave or radiant energy intensity, presence or direction.

Tunnel effect measuring systems and particle detectors

NASA Technical Reports Server (NTRS)

Kaiser, William J. (Inventor); Waltman, Steven B. (Inventor); Kenny, Thomas W. (Inventor)

1993-01-01

Methods and apparatus for measuring gravitational and inertial forces, magnetic fields, or wave or radiant energy acting on an object or fluid in space provide an electric tunneling current through a gap between an electrode and that object or fluid in space and vary that gap with any selected one of such forces, magnetic fields, or wave or radiant energy acting on that object or fluid. These methods and apparatus sense a corresponding variation in an electric property of that gap and determine the latter force, magnetic fields, or wave or radiant energy in response to that corresponding variation, and thereby sense or measure such parameters as acceleration, position, particle mass, velocity, magnetic field strength, presence or direction, or wave or radiant energy intensity, presence or direction.

Tunnel effect wave energy detection

NASA Technical Reports Server (NTRS)

Kaiser, William J. (Inventor); Waltman, Steven B. (Inventor); Kenny, Thomas W. (Inventor)

1995-01-01

Methods and apparatus for measuring gravitational and inertial forces, magnetic fields, or wave or radiant energy acting on an object or fluid in space provide an electric tunneling current through a gap between an electrode and that object or fluid in space and vary that gap with any selected one of such forces, magnetic fields, or wave or radiant energy acting on that object or fluid. These methods and apparatus sense a corresponding variation in an electric property of that gap and determine the latter force, magnetic fields, or wave or radiant energy in response to that corresponding variation, and thereby sense or measure such parameters as acceleration, position, particle mass, velocity, magnetic field strength, presence or direction, or wave or radiant energy intensity, presence or direction.

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.

Apparatus and method for producing an artificial gravitational field

NASA Technical Reports Server (NTRS)

Mccanna, Jason (Inventor)

1993-01-01

An apparatus and method is disclosed for producing an artificial gravitational field in a spacecraft by rotating the same around a spin axis. The centrifugal force thereby created acts as an artificial gravitational force. The apparatus includes an engine which produces a drive force offset from the spin axis to drive the spacecraft towards a destination. The engine is also used as a counterbalance for a crew cabin for rotation of the spacecraft. Mass of the spacecraft, which may include either the engine or crew cabin, is shifted such that the centrifugal force acting on that mass is no longer directed through the center of mass of the craft. This off-center centrifugal force creates a moment that counterbalances the moment produced by the off-center drive force to eliminate unwanted rotation which would otherwise be precipitated by the offset drive force.

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

PubMed Central

2015-01-01

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

Casting the Coronal Magnetic Field Reconstructions with Magnetic Field Constraints above the Photosphere in 3D Using MHD Bifrost Model

NASA Astrophysics Data System (ADS)

Fleishman, G. D.; Anfinogentov, S.; Loukitcheva, M.; Mysh'yakov, I.; Stupishin, A.

2017-12-01

Measuring and modeling coronal magnetic field, especially above active regions (ARs), remains one of the central problems of solar physics given that the solar coronal magnetism is the key driver of all solar activity. Nowadays the coronal magnetic field is often modelled using methods of nonlinear force-free field reconstruction, whose accuracy has not yet been comprehensively assessed. Given that the coronal magnetic probing is routinely unavailable, only morphological tests have been applied to evaluate performance of the reconstruction methods and a few direct tests using available semi-analytical force-free field solution. Here we report a detailed casting of various tools used for the nonlinear force-free field reconstruction, such as disambiguation methods, photospheric field preprocessing methods, and volume reconstruction methods in a 3D domain using a 3D snapshot of the publicly available full-fledged radiative MHD model. We take advantage of the fact that from the realistic MHD model we know the magnetic field vector distribution in the entire 3D domain, which enables us to perform "voxel-by-voxel" comparison of the restored magnetic field and the true magnetic field in the 3D model volume. Our tests show that the available disambiguation methods often fail at the quiet sun areas, where the magnetic structure is dominated by small-scale magnetic elements, while they work really well at the AR photosphere and (even better) chromosphere. The preprocessing of the photospheric magnetic field, although does produce a more force-free boundary condition, also results in some effective `elevation' of the magnetic field components. The effective `elevation' height turns out to be different for the longitudinal and transverse components of the magnetic field, which results in a systematic error in absolute heights in the reconstructed magnetic data cube. The extrapolation performed starting from actual AR photospheric magnetogram (i.e., without preprocessing) are free from this systematic error, while have other metrics either comparable or only marginally worse than those estimated for extrapolations from the preprocessed magnetograms. This finding favors the use of extrapolations from the original photospheric magnetogram without preprocessing.

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

PubMed Central

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-01-01

Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases. PMID:19493356

Bespoke optical springs and passive force clamps from shaped dielectric particles

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids

PubMed Central

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

2003-01-01

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

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

PubMed

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

2015-02-10

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

Exact Green's function method of solar force-free magnetic-field computations with constant alpha. I - Theory and basic test cases

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Hilton, H. H.

1977-01-01

Exact closed-form solutions to the solar force-free magnetic-field boundary-value problem are obtained for constant alpha in Cartesian geometry by a Green's function approach. The uniqueness of the physical problem is discussed. Application of the exact results to practical solar magnetic-field calculations is free of series truncation errors and is at least as economical as the approximate methods currently in use. Results of some test cases are presented.

Origin and structures of solar eruptions II: Magnetic modeling

NASA Astrophysics Data System (ADS)

Guo, Yang; Cheng, Xin; Ding, MingDe

2017-07-01

The topology and dynamics of the three-dimensional magnetic field in the solar atmosphere govern various solar eruptive phenomena and activities, such as flares, coronal mass ejections, and filaments/prominences. We have to observe and model the vector magnetic field to understand the structures and physical mechanisms of these solar activities. Vector magnetic fields on the photosphere are routinely observed via the polarized light, and inferred with the inversion of Stokes profiles. To analyze these vector magnetic fields, we need first to remove the 180° ambiguity of the transverse components and correct the projection effect. Then, the vector magnetic field can be served as the boundary conditions for a force-free field modeling after a proper preprocessing. The photospheric velocity field can also be derived from a time sequence of vector magnetic fields. Three-dimensional magnetic field could be derived and studied with theoretical force-free field models, numerical nonlinear force-free field models, magnetohydrostatic models, and magnetohydrodynamic models. Magnetic energy can be computed with three-dimensional magnetic field models or a time series of vector magnetic field. The magnetic topology is analyzed by pinpointing the positions of magnetic null points, bald patches, and quasi-separatrix layers. As a well conserved physical quantity, magnetic helicity can be computed with various methods, such as the finite volume method, discrete flux tube method, and helicity flux integration method. This quantity serves as a promising parameter characterizing the activity level of solar active regions.

Faster modified protocol for first order reversal curve measurements

NASA Astrophysics Data System (ADS)

De Biasi, Emilio

2017-10-01

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

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

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Influence of Waiting Time on the Levitation Force Between a Permanent Magnet and a Superconductor

NASA Astrophysics Data System (ADS)

Zhang, Xing-Yi; Zhou, You-He; Zhou, Jun

This paper describes the experimental results of the levitation force of single-grained YBaCuO bulk superconductors preparing by the top-seeded melt-growth method with different waiting time tw below an NdFeB permanent magnet. It was found that waiting time has large effects on the zero-field-cooled (ZFC) and field-cooled (FC) levitation force, and the levitation force shows aging characteristics at the liquid nitrogen temperature.

Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

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

Lin, Bin; Pettitt, Bernard M.

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLSAA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirmsmore » that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.« less

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

PubMed

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

2017-11-01

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

Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.

PubMed

Sieradzan, Adam K; Jakubowski, Rafał

2017-03-30

In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

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

2018-05-28

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

The fast multipole method and point dipole moment polarizable force fields.

PubMed

Coles, Jonathan P; Masella, Michel

2015-01-14

We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

PubMed

Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Ocean Wave Simulation Based on Wind Field

PubMed Central

2016-01-01

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

Ocean Wave Simulation Based on Wind Field.

PubMed

Li, Zhongyi; Wang, Hao

2016-01-01

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

Free magnetic energy and relative magnetic helicity diagnostics for the quality of NLFF field extrapolations

NASA Astrophysics Data System (ADS)

Moraitis, Kostas; Archontis, Vasilis; Tziotziou, Konstantinos; Georgoulis, Manolis K.

We calculate the instantaneous free magnetic energy and relative magnetic helicity of solar active regions using two independent approaches: a) a non-linear force-free (NLFF) method that requires only a single photospheric vector magnetogram, and b) well known semi-analytical formulas that require the full three-dimensional (3D) magnetic field structure. The 3D field is obtained either from MHD simulations, or from observed magnetograms via respective NLFF field extrapolations. We find qualitative agreement between the two methods and, quantitatively, a discrepancy not exceeding a factor of 4. The comparison of the two methods reveals, as a byproduct, two independent tests for the quality of a given force-free field extrapolation. We find that not all extrapolations manage to achieve the force-free condition in a valid, divergence-free, magnetic configuration. This research has been co-financed by the European Union (European Social Fund - ESF) and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) - Research Funding Program: Thales. Investing in knowledge society through the European Social Fund.

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

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

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

Mass determination with the magnetic levitation method—proposal for a new design of electromechanical system

NASA Astrophysics Data System (ADS)

Kajastie, H.; Riski, K.; Satrapinski, A.

2009-06-01

The method for realization of the kilogram using 'superconducting magnetic levitation' was re-evaluated at MIKES. The realization of the kilogram based on the traditional levitation method is limited by the imperfections of the superconducting materials and the indefinable dependence between supplied electrical energy and the gravitational potential energy of the superconducting mass. This indefiniteness is proportional to the applied magnetic field and is caused by increasing losses and trapped magnetic fluxes. A new design of an electromechanical system for the levitation method is proposed. In the proposed system the required magnetic field and the corresponding force are reduced, as the mass of the body (hanging from a mass comparator) is compensated by the reference weight on the mass comparator. The direction of the magnetic force can be upward (levitation force, when the body is over the coil) or downward (repulsive force, when the body is under the coil). The initial force to move the body from the coil is not needed and magnetic field sensitivity is increased, providing linearization of displacement versus applied current. This new construction allows a lower magnetic induction, reduces energy losses compared with previous designs of electromechanical system and reduces the corresponding systematic error.

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

NASA Technical Reports Server (NTRS)

Lyell, Margaret J.

1992-01-01

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

Dynamic analysis of a hollow cylinder subject to a dual traveling force imposed on its inner surface

NASA Astrophysics Data System (ADS)

Lee, Sooyoung; Seok, Jongwon

2015-03-01

The dynamic behavior of a hollow cylinder under a dual traveling force applied to the inner surface is investigated in this study. The cylinder is constrained at both the top and bottom surfaces not to move in the length direction but free in other directions. And a dual force travels at a constant velocity along the length direction on the inner surface of the hollow cylinder. The resulting governing field equations and the associated boundary conditions are ruled by the general Hooke's law. Due to the nature of the field equations, proper adjoint system of equations and biorthogonality conditions were derived in a precise and detailed manner. To solve these field equations in this study, the method of separation of variable is used and the method of Fro¨benius is employed for the differential equations in the radial direction. Using the field equations, the eigenanalyses on both the original and its adjoint system were performed with great care, which results in the eigenfunction sets of both systems. The biorthogonality conditions were applied to the field equations to obtain the discretized equation for each mode. Using the solutions of the discretized equations that account for the boundary forcing terms, the critical speed for a dual traveling force for each mode could be computed.

Comparison of different force fields for the study of disaccharides

USDA-ARS?s Scientific Manuscript database

Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying ß-cellobiose, a-maltose, and a-galabiose [a-D-Galp-(1'4)-a-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl and glycosidic linkage orientatio...

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

PubMed Central

Latour, Robert A.

2014-01-01

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

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M Baris; Kravchenko, Ivan I; Kalinin, Sergei V; Tselev, Alexander

2017-01-04

Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm -1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

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.

Analysis of space charge fields using the Lienard-Wiechert potential and the method of images during the photoemission of the electron beam from the cathode

NASA Astrophysics Data System (ADS)

Salah, Wa'el

2017-01-01

We present a numerical analysis of the space charge effect and the effect of image charge force on the cathode surface for a laser-driven RF-photocathode gun. In this numerical analysis, in the vicinity of the cathode surface, we used an analytical method based on Lienard-Weichert retarded potentials. The analytical method allows us to calculate longitudinal and radial electric fields, and the azimuth magnetic field due to both space charge effect and the effect of the image charge force. We calculate the electro-magnetic fields in the following two conditions for the "ELSA" photoinjector. The first condition is in the progress of photoemission, which corresponds to the inside of the emitted beam, and the second condition is at the end of the photoemission. The electromagnetic fields due to the space charge effect and the effect of the image charge force, and the sum of them, which corresponds to the global electro-magnetic fields, are shown. Based on these numerical results, we discussed the effects of the space charge and the image charge in the immediate vicinity of the cathode.

Embedding Circular Force-Free Flux Ropes in Potential Magnetic Fields

NASA Astrophysics Data System (ADS)

Titov, V. S.; Torok, T.; Mikic, Z.; Linker, J.

2013-12-01

We propose a method for constructing approximate force-free equilibria in active regions that locally have a potential bipolar-type magnetic field with a thin force-free flux rope embedded inside it. The flux rope has a circular-arc axis and circular cross-section in which the interior magnetic field is predominantly toroidal (axial). Its magnetic pressure is balanced outside by that of the poloidal (azimuthal) field created at the boundary by the electric current sheathing the flux rope. To facilitate the implementation of the method in our numerical magnetohydrodynamic (MHD) code, the entire solution is described in terms of the vector potential of the magnetic field. The parameters of the flux rope can be chosen so that a subsequent MHD relaxation of the constructed configuration under line-tied conditions at the boundary provides a numerically exact equilibrium. Such equilibria are an approximation for the magnetic configuration preceding solar eruptions, which can be triggered in our model by imposing suitable photospheric flows beneath the flux rope. The proposed method is a useful tool for constructing pre-eruption magnetic fields in data-driven simulations of solar active events. Research supported by NASA's Heliophysics Theory and LWS Programs, and NSF/SHINE and NSF/FESD.

Simulation-Based Joint Estimation of Body Deformation and Elasticity Parameters for Medical Image Analysis

PubMed Central

Foskey, Mark; Niethammer, Marc; Krajcevski, Pavel; Lin, Ming C.

2014-01-01

Estimation of tissue stiffness is an important means of noninvasive cancer detection. Existing elasticity reconstruction methods usually depend on a dense displacement field (inferred from ultrasound or MR images) and known external forces. Many imaging modalities, however, cannot provide details within an organ and therefore cannot provide such a displacement field. Furthermore, force exertion and measurement can be difficult for some internal organs, making boundary forces another missing parameter. We propose a general method for estimating elasticity and boundary forces automatically using an iterative optimization framework, given the desired (target) output surface. During the optimization, the input model is deformed by the simulator, and an objective function based on the distance between the deformed surface and the target surface is minimized numerically. The optimization framework does not depend on a particular simulation method and is therefore suitable for different physical models. We show a positive correlation between clinical prostate cancer stage (a clinical measure of severity) and the recovered elasticity of the organ. Since the surface correspondence is established, our method also provides a non-rigid image registration, where the quality of the deformation fields is guaranteed, as they are computed using a physics-based simulation. PMID:22893381

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

Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

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

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field.

PubMed

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

2015-07-14

The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.

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

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

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

Observation of force-detected nuclear magnetic resonance in a homogeneous field

PubMed Central

Madsen, L. A.; Leskowitz, G. M.; Weitekamp, D. P.

2004-01-01

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to μm-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the μm and nm scales. PMID:15326302

Spectral simulations of an axisymmetric force-free pulsar magnetosphere

NASA Astrophysics Data System (ADS)

Cao, Gang; Zhang, Li; Sun, Sineng

2016-02-01

A pseudo-spectral method with an absorbing outer boundary is used to solve a set of time-dependent force-free equations. In this method, both electric and magnetic fields are expanded in terms of the vector spherical harmonic (VSH) functions in spherical geometry and the divergence-free state of the magnetic field is enforced analytically by a projection method. Our simulations show that the Deutsch vacuum solution and the Michel monopole solution can be reproduced well by our pseudo-spectral code. Further, the method is used to present a time-dependent simulation of the force-free pulsar magnetosphere for an aligned rotator. The simulations show that the current sheet in the equatorial plane can be resolved well and the spin-down luminosity obtained in the steady state is in good agreement with the value given by Spitkovsky.

Cutting Force Predication Based on Integration of Symmetric Fuzzy Number and Finite Element Method

PubMed Central

Wang, Zhanli; Hu, Yanjuan; Wang, Yao; Dong, Chao; Pang, Zaixiang

2014-01-01

In the process of turning, pointing at the uncertain phenomenon of cutting which is caused by the disturbance of random factors, for determining the uncertain scope of cutting force, the integrated symmetric fuzzy number and the finite element method (FEM) are used in the prediction of cutting force. The method used symmetric fuzzy number to establish fuzzy function between cutting force and three factors and obtained the uncertain interval of cutting force by linear programming. At the same time, the change curve of cutting force with time was directly simulated by using thermal-mechanical coupling FEM; also the nonuniform stress field and temperature distribution of workpiece, tool, and chip under the action of thermal-mechanical coupling were simulated. The experimental result shows that the method is effective for the uncertain prediction of cutting force. PMID:24790556

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

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

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Quantification of In-Contact Probe-Sample Electrostatic Forces with Dynamic Atomic Force Microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M; Kravchenko, Ivan; Kalinin, Sergei; Tselev, Alexander

2016-12-13

Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V/nm at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids. Copyright 2016 IOP Publishing Ltd.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

DOE PAGES

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.; ...

2017-01-04

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

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

PubMed

Kundu, Sangeeta

2018-02-01

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

Hierarchical Shared Control of Cane-Type Walking-Aid Robot

PubMed Central

Tao, Chunjing

2017-01-01

A hierarchical shared-control method of the walking-aid robot for both human motion intention recognition and the obstacle emergency-avoidance method based on artificial potential field (APF) is proposed in this paper. The human motion intention is obtained from the interaction force measurements of the sensory system composed of 4 force-sensing registers (FSR) and a torque sensor. Meanwhile, a laser-range finder (LRF) forward is applied to detect the obstacles and try to guide the operator based on the repulsion force calculated by artificial potential field. An obstacle emergency-avoidance method which comprises different control strategies is also assumed according to the different states of obstacles or emergency cases. To ensure the user's safety, the hierarchical shared-control method combines the intention recognition method with the obstacle emergency-avoidance method based on the distance between the walking-aid robot and the obstacles. At last, experiments validate the effectiveness of the proposed hierarchical shared-control method. PMID:29093805

Layering of inertial confinement fusion targets in microgravity environments

NASA Astrophysics Data System (ADS)

Parks, P. B.; Fagaly, R. L.

1995-02-01

A critical concern in the fabrication of targets for inertial confinement fusion is ensuring that the hydrogenic (D2 or DT) fuel layer maintains spherical symmetry. Because of gravitationally induced sagging of the liquid prior to freezing, only relatively thin (less than 10 micrometers) layers of solid fuel can be produced by fast refreeze methods. One method to reduce the effective gravitational field environment is free-fall insertion into the target chamber. Another method to counterbalance the gravitational force is to use an applied magnetic field combined with a gradient field to induce a magnetic dipole force (F(sub m)) on the liquid fuel layer. For liquid deuterium, the required B dot product del(vector differential operator) B product to counterbalance the gravitational force (F(sub g)) is approximately 10 T(exp 2)/cm. In this paper, we examine the time-dependent dynamics of the liquid fuel layer in a reduced gravitational field environment. We employ an energy method which takes into account the sum of the free energy associated with the surface tension forces, net vertical force (F = F(sub m) - F(sub g) (in the case of magnetic field-assisted microgravity) or F(sub D) (the drag force in the case of free fall)), London-van der Waals forces, the kinetic energy of motion and viscous dissipation. By assuming that the motions are incompressible and irrotational, the volume integrals of the free energies over the deformed liquid fuel layer may be converted to surface integrals. With the surface expressed as the sum of Legendre polynomials, r(sub surface) = a + Sigma a(sub l)(t)P(sub l)(mu), the perturbed amplitude of the individual modes, a(sub l)(t) can be obtained. We show that the l = 1 vertical shift mode takes the longest to damp out, and may be problematic for free-fall insertion even for thin approximately 1 micrometer overfilled foam targets. For a given liquid fuel layer thickness delta, the equilibrium value of a(sub 1)/a (the concentricity of the inner fuel layer) is shown to be dependent on the net vertical force F and layer thickness, i.e., a(sub 1) approximately F delta(exp 5), but independent of the surface tension.

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

PubMed Central

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

2011-01-01

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

On the numerical computation of nonlinear force-free magnetic fields. [from solar photosphere

NASA Technical Reports Server (NTRS)

Wu, S. T.; Sun, M. T.; Chang, H. M.; Hagyard, M. J.; Gary, G. A.

1990-01-01

An algorithm has been developed to extrapolate nonlinear force-free magnetic fields from the photosphere, given the proper boundary conditions. This paper presents the results of this work, describing the mathematical formalism that was developed, the numerical techniques employed, and comments on the stability criteria and accuracy developed for these numerical schemes. An analytical solution is used for a benchmark test; the results show that the computational accuracy for the case of a nonlinear force-free magnetic field was on the order of a few percent (less than 5 percent). This newly developed scheme was applied to analyze a solar vector magnetogram, and the results were compared with the results deduced from the classical potential field method. The comparison shows that additional physical features of the vector magnetogram were revealed in the nonlinear force-free case.

Quantum Chemical Topology: Knowledgeable atoms in peptides

NASA Astrophysics Data System (ADS)

Popelier, Paul L. A.

2012-06-01

The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

Acoustic levitation in the presence of gravity

NASA Technical Reports Server (NTRS)

Collas, P.; Barmatz, M.; Shipley, C.

1989-01-01

The method of Gor'kov (1961) has been applied to derive general expressions for the total potential and force on a small spherical object in a resonant chamber in the presence of both acoustic and gravitational force fields. The levitation position is also determined in rectangular resonators for the simultaneous excitation of up to three acoustic modes, and the results are applied to the triple-axis acoustic levitator. The analysis is applied to rectangular, spherical, and cylindrical single-mode levitators that are arbitrarily oriented relative to the gravitational force field. Criteria are determined for isotropic force fields in rectangular and cylindrical resonators. It is demonstrated that an object will be situated within a volume of possible levitation positions at a point determined by the relative strength of the acoustic and gravitational fields and the orientation of the chamber relative to gravity.

Unorthodox theoretical methods

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

Nedd, Sean

2012-01-01

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

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

PubMed

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

2003-12-01

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

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2017-05-01

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12-23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.

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.

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

NASA Technical Reports Server (NTRS)

Haw, Richard C.; Foss, John F.

1990-01-01

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

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

PubMed

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

2014-02-01

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

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.

Machine learning of accurate energy-conserving molecular force fields.

PubMed

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

2017-05-01

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

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-06-14

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

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

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

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

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

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.

1985-01-01

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

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

PubMed

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

2018-06-12

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

Parallel alignment of bacteria using near-field optical force array for cell sorting

NASA Astrophysics Data System (ADS)

Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

2017-08-01

This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Combining single-molecule manipulation and single-molecule detection.

PubMed

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

2014-10-01

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

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.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

The correlation of fractal structures in the photospheric and the coronal magnetic field

NASA Astrophysics Data System (ADS)

Dimitropoulou, M.; Georgoulis, M.; Isliker, H.; Vlahos, L.; Anastasiadis, A.; Strintzi, D.; Moussas, X.

2009-10-01

Context: This work examines the relation between the fractal properties of the photospheric magnetic patterns and those of the coronal magnetic fields in solar active regions. Aims: We investigate whether there is any correlation between the fractal dimensions of the photospheric structures and the magnetic discontinuities formed in the corona. Methods: To investigate the connection between the photospheric and coronal complexity, we used a nonlinear force-free extrapolation method that reconstructs the 3d magnetic fields using 2d observed vector magnetograms as boundary conditions. We then located the magnetic discontinuities, which are considered as spatial proxies of reconnection-related instabilities. These discontinuities form well-defined volumes, called here unstable volumes. We calculated the fractal dimensions of these unstable volumes and compared them to the fractal dimensions of the boundary vector magnetograms. Results: Our results show no correlation between the fractal dimensions of the observed 2d photospheric structures and the extrapolated unstable volumes in the corona, when nonlinear force-free extrapolation is used. This result is independent of efforts to (1) bring the photospheric magnetic fields closer to a nonlinear force-free equilibrium and (2) omit the lower part of the modeled magnetic field volume that is almost completely filled by unstable volumes. A significant correlation between the fractal dimensions of the photospheric and coronal magnetic features is only observed at the zero level (lower limit) of approximation of a current-free (potential) magnetic field extrapolation. Conclusions: We conclude that the complicated transition from photospheric non-force-free fields to coronal force-free ones hampers any direct correlation between the fractal dimensions of the 2d photospheric patterns and their 3d counterparts in the corona at the nonlinear force-free limit, which can be considered as a second level of approximation in this study. Correspondingly, in the zero and first levels of approximation, namely, the potential and linear force-free extrapolation, respectively, we reveal a significant correlation between the fractal dimensions of the photospheric and coronal structures, which can be attributed to the lack of electric currents or to their purely field-aligned orientation.

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

USGS Publications Warehouse

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

PubMed

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

2016-03-05

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

PubMed

Sanchez-Martinez, M; Crehuet, R

2014-12-21

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

Effect of Electrodynamic Forces on the Attitude Stabilization of a Satellite in Ecliptic orbits

NASA Astrophysics Data System (ADS)

Abdel-Aziz, Yehia

This work is based on the previous paper of the author [1]. The present paper is devoted to the investigation of the attitude dynamics of an ecliptic satellite moving in the magnetic field of the Earth. Eelectrodynamic forces result from the motion of a charged satelite relative to the magnetic field of the Earth. The torque due to electrodynamic effect of the Lorentz forces on the attitude stabilization of the satellite is studied with the detailed model of the Earth's magnetic field. A method for estimating the stable and unstable regions of the equilibrium positions based on Euler's equation is also discussed. The results show that Lorentz forces can affect the stablization of the satellite, in particular for highly eccentric orbits and also for large satellte. [1] Abdel-Aziz, Y. A. Attitude Stabilization of a Rigid Spacecraft in the Geomagnetic Field. AdSpR 40, 18-24, 2007.

Optoelectrofluidic field separation based on light-intensity gradients

PubMed Central

Lee, Sanghyun; Park, Hyun Jin; Yoon, Jin Sung; Kang, Kwan Hyoung

2010-01-01

Optoelectrofluidic field separation (OEFS) of particles under light -intensity gradient (LIG) is reported, where the LIG illumination on the photoconductive layer converts the short-ranged dielectrophoresis (DEP) force to the long-ranged one. The long-ranged DEP force can compete with the hydrodynamic force by alternating current electro-osmosis (ACEO) over the entire illumination area for realizing effective field separation of particles. In the OEFS system, the codirectional illumination and observation induce the levitation effect, compensating the attenuation of the DEP force under LIG illumination by slightly floating particles from the surface. Results of the field separation and concentration of diverse particle pairs (0.82–16 μm) are well demonstrated, and conditions determining the critical radius and effective particle manipulation are discussed. The OEFS with codirectional LIG strategy could be a promising particle manipulation method in many applications where a rapid manipulation of biological cells and particles over the entire working area are of interest. PMID:20697461

Optoelectrofluidic field separation based on light-intensity gradients.

PubMed

Lee, Sanghyun; Park, Hyun Jin; Yoon, Jin Sung; Kang, Kwan Hyoung

2010-07-14

Optoelectrofluidic field separation (OEFS) of particles under light -intensity gradient (LIG) is reported, where the LIG illumination on the photoconductive layer converts the short-ranged dielectrophoresis (DEP) force to the long-ranged one. The long-ranged DEP force can compete with the hydrodynamic force by alternating current electro-osmosis (ACEO) over the entire illumination area for realizing effective field separation of particles. In the OEFS system, the codirectional illumination and observation induce the levitation effect, compensating the attenuation of the DEP force under LIG illumination by slightly floating particles from the surface. Results of the field separation and concentration of diverse particle pairs (0.82-16 mum) are well demonstrated, and conditions determining the critical radius and effective particle manipulation are discussed. The OEFS with codirectional LIG strategy could be a promising particle manipulation method in many applications where a rapid manipulation of biological cells and particles over the entire working area are of interest.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

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

Validity of a Simple Method for Measuring Force-Velocity-Power Profile in Countermovement Jump.

PubMed

Jiménez-Reyes, Pedro; Samozino, Pierre; Pareja-Blanco, Fernando; Conceição, Filipe; Cuadrado-Peñafiel, Víctor; González-Badillo, Juan José; Morin, Jean-Benoît

2017-01-01

To analyze the reliability and validity of a simple computation method to evaluate force (F), velocity (v), and power (P) output during a countermovement jump (CMJ) suitable for use in field conditions and to verify the validity of this computation method to compute the CMJ force-velocity (F-v) profile (including unloaded and loaded jumps) in trained athletes. Sixteen high-level male sprinters and jumpers performed maximal CMJs under 6 different load conditions (0-87 kg). A force plate sampling at 1000 Hz was used to record vertical ground-reaction force and derive vertical-displacement data during CMJ trials. For each condition, mean F, v, and P of the push-off phase were determined from both force-plate data (reference method) and simple computation measures based on body mass, jump height (from flight time), and push-off distance and used to establish the linear F-v relationship for each individual. Mean absolute bias values were 0.9% (± 1.6%), 4.7% (± 6.2%), 3.7% (± 4.8%), and 5% (± 6.8%) for F, v, P, and slope of the F-v relationship (S Fv ), respectively. Both methods showed high correlations for F-v-profile-related variables (r = .985-.991). Finally, all variables computed from the simple method showed high reliability, with ICC >.980 and CV <1.0%. These results suggest that the simple method presented here is valid and reliable for computing CMJ force, velocity, power, and F-v profiles in athletes and could be used in practice under field conditions when body mass, push-off distance, and jump height are known.

Computation of Relative Magnetic Helicity in Spherical Coordinates

NASA Astrophysics Data System (ADS)

Moraitis, Kostas; Pariat, Étienne; Savcheva, Antonia; Valori, Gherardo

2018-06-01

Magnetic helicity is a quantity of great importance in solar studies because it is conserved in ideal magnetohydrodynamics. While many methods for computing magnetic helicity in Cartesian finite volumes exist, in spherical coordinates, the natural coordinate system for solar applications, helicity is only treated approximately. We present here a method for properly computing the relative magnetic helicity in spherical geometry. The volumes considered are finite, of shell or wedge shape, and the three-dimensional magnetic field is considered to be fully known throughout the studied domain. Testing of the method with well-known, semi-analytic, force-free magnetic-field models reveals that it has excellent accuracy. Further application to a set of nonlinear force-free reconstructions of the magnetic field of solar active regions and comparison with an approximate method used in the past indicates that the proposed method can be significantly more accurate, thus making our method a promising tool in helicity studies that employ spherical geometry. Additionally, we determine and discuss the applicability range of the approximate method.

Force fields and scoring functions for carbohydrate simulation.

PubMed

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

2015-01-12

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

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 rolling locomotion method for untethered magnetic microrobots

NASA Astrophysics Data System (ADS)

Hou, Max T.; Shen, Hui-Mei; Jiang, Guan-Lin; Lu, Chiang-Ni; Hsu, I.-Jen; Yeh, J. Andrew

2010-01-01

It is a challenge to achieve free and efficient motion of microrobots on arbitrary surfaces. We report a rolling locomotion method for a magnetic microrobot with a rectangular body (300×200×50 μm3); this method is based on an external rotating magnetic field. The magnetic force, accompanied by normal and friction forces, enables the successive rotations of the microrobot. A magnetic field with a rotational speed of 2 rps rolls the microrobot, giving it a translation speed of 1.4 mm/s. With this locomotion ability, microrobots can move along a line or curve and can climb slopes or stairs.

Quantitative modeling of forces in electromagnetic tweezers

NASA Astrophysics Data System (ADS)

Bijamov, Alex; Shubitidze, Fridon; Oliver, Piercen M.; Vezenov, Dmitri V.

2010-11-01

This paper discusses numerical simulations of the magnetic field produced by an electromagnet for generation of forces on superparamagnetic microspheres used in manipulation of single molecules or cells. Single molecule force spectroscopy based on magnetic tweezers can be used in applications that require parallel readout of biopolymer stretching or biomolecular binding. The magnetic tweezers exert forces on the surface-immobilized macromolecule by pulling a magnetic bead attached to the free end of the molecule in the direction of the field gradient. In a typical force spectroscopy experiment, the pulling forces can range between subpiconewton to tens of piconewtons. In order to effectively provide such forces, an understanding of the source of the magnetic field is required as the first step in the design of force spectroscopy systems. In this study, we use a numerical technique, the method of auxiliary sources, to investigate the influence of electromagnet geometry and material parameters of the magnetic core on the magnetic forces pulling the target beads in the area of interest. The close proximity of the area of interest to the magnet body results in deviations from intuitive relations between magnet size and pulling force, as well as in the force decay with distance. We discuss the benefits and drawbacks of various geometric modifications affecting the magnitude and spatial distribution of forces achievable with an electromagnet.

A potential method for lift evaluation from velocity field data

NASA Astrophysics Data System (ADS)

de Guyon-Crozier, Guillaume; Mulleners, Karen

2017-11-01

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

Precise measurement of surface plasmon forces at a metal-dielectric interface using a calibrated evanescent wave

NASA Astrophysics Data System (ADS)

Liu, Lulu; Woolf, Alex

2015-03-01

By observing the motion of an optically trapped microscopic colloid, sub-piconewton static and dynamical forces have been measured using a technique called photonic force microscopy. This technique, though potentially powerful, has in the past struggled to make precise measurements in the vicinity of a reflective or metallic interface, due to distortions of the optical field. We introduce a new in-situ, contact-free calibration method for particle tracking using an evanescent wave, and demonstrate its expanded capability by the precise measurement of forces of interaction between a single colloid and the optical field generated by a propagating surface plasmon polariton on gold.

The Meaning of Data Magnets and Magnetic Fields, 1st Experimental Edition.

ERIC Educational Resources Information Center

Hall, Gene E.

By using this instructional module the participants should be able to: (1) predict the behavior of two magnets prior to their being placed close to each other; (2) identify and describe the magnetic forces acting on a bar magnet that is free to rotate; (3) demonstrate a method for determining the lines of force in a magnetic field; (4) identify…

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.

Detecting the gravitational sensitivity of Paramecium caudatum using magnetic forces

NASA Astrophysics Data System (ADS)

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

2006-03-01

Under normal conditions, Paramecium cells regulate their swimming speed in response to the pN level mechanical force of gravity. This regulation, known as gravikinesis, is more pronounced when the external force is increased by methods such as centrifugation. Here we present a novel technique that simulates gravity fields using the interactions between strong inhomogeneous magnetic fields and cells. We are able to achieve variable gravities spanning from 10xg to -8xg; where g is earth's gravity. Our experiments show that the swimming speed regulation of Paramecium caudatum to magnetically simulated gravity is a true physiological response. In addition, they reveal a maximum propulsion force for paramecia. This advance establishes a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

Selective structural source identification

NASA Astrophysics Data System (ADS)

Totaro, Nicolas

2018-04-01

In the field of acoustic source reconstruction, the inverse Patch Transfer Function (iPTF) has been recently proposed and has shown satisfactory results whatever the shape of the vibrating surface and whatever the acoustic environment. These two interesting features are due to the virtual acoustic volume concept underlying the iPTF methods. The aim of the present article is to show how this concept of virtual subsystem can be used in structures to reconstruct the applied force distribution. Some virtual boundary conditions can be applied on a part of the structure, called virtual testing structure, to identify the force distribution applied in that zone regardless of the presence of other sources outside the zone under consideration. In the present article, the applicability of the method is only demonstrated on planar structures. However, the final example show how the method can be applied to a complex shape planar structure with point welded stiffeners even in the tested zone. In that case, if the virtual testing structure includes the stiffeners the identified force distribution only exhibits the positions of external applied forces. If the virtual testing structure does not include the stiffeners, the identified force distribution permits to localize the forces due to the coupling between the structure and the stiffeners through the welded points as well as the ones due to the external forces. This is why this approach is considered here as a selective structural source identification method. It is demonstrated that this approach clearly falls in the same framework as the Force Analysis Technique, the Virtual Fields Method or the 2D spatial Fourier transform. Even if this approach has a lot in common with these latters, it has some interesting particularities like its low sensitivity to measurement noise.

Electromagnetic panel deployment and retraction using the geomagnetic field in LEO satellite missions

NASA Astrophysics Data System (ADS)

Inamori, Takaya; Sugawara, Yoshiki; Satou, Yasutaka

2015-12-01

Increasingly, spacecraft are installed with large-area structures that are extended and deployed post-launch. These extensible structures have been applied in several missions for power generation, thermal radiation, and solar propulsion. Here, we propose a deployment and retraction method using the electromagnetic force generated when the geomagnetic field interacts with electric current flowing on extensible panels. The panels are installed on a satellite in low Earth orbit. Specifically, electrical wires placed on the extensible panels generate magnetic moments, which interfere with the geomagnetic field. The resulting repulsive and retraction forces enable panel deployment and retraction. In the proposed method, a satellite realizes structural deployment using simple electrical wires. Furthermore, the satellite can achieve not only deployment but also retraction for avoiding damage from space debris and for agile attitude maneuvers. Moreover, because the proposed method realizes quasi-static deployment and the retraction of panels by electromagnetic forces, low impulsive force is exerted on fragile panels. The electrical wires can also be used to detect the panel deployment and retraction and generate a large magnetic moment for attitude control. The proposed method was assessed in numerical simulations based on multibody dynamics. Simulation results shows that a small cubic satellite with a wire current of 25 AT deployed 4 panels (20 cm × 20 cm) in 500 s and retracted 4 panels in 100 s.

Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance.

PubMed

Noel, Martin; Fortin, Karine; Bouyer, Laurent J

2009-06-03

Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO) was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Eleven healthy subjects walked on a treadmill before (3 min), during (5 min) and after (5 min) exposure to 2 force fields applied by the EHO (mid-stance/push-off; approximately 10 Nm, towards dorsiflexion). To evaluate modifications in feedforward control, strides with no force field ('catch strides') were unexpectedly inserted during the force field walking period. When initially exposed to a mid-stance force field (FF 20%), subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF 20% were similar to baseline (P > 0.99). Subjects gradually adapted by returning ankle velocity to baseline over approximately 50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF 50%), plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm) were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF 50% catch strides were not simply due to a large ankle impedance. Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive control of the ankle during locomotion. Our data suggest that, for short duration exposure, a feedforward modification in torque output occurs during mid-stance but not during push-off. These findings are important for the design of novel rehabilitation methods, as they suggest that the ability to use resistive force fields for training may depend on targeted gait phases.

Hybrid immersed interface-immersed boundary methods for AC dielectrophoresis

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

Hossan, Mohammad Robiul; Department of Engineering and Physics, University of Central Oklahoma, Edmond, OK 73034-5209; Dillon, Robert

2014-08-01

Dielectrophoresis, a nonlinear electrokinetic transport mechanism, has become popular in many engineering applications including manipulation, characterization and actuation of biomaterials, particles and biological cells. In this paper, we present a hybrid immersed interface–immersed boundary method to study AC dielectrophoresis where an algorithm is developed to solve the complex Poisson equation using a real variable formulation. An immersed interface method is employed to obtain the AC electric field in a fluid media with suspended particles and an immersed boundary method is used for the fluid equations and particle transport. The convergence of the proposed algorithm as well as validation of themore » hybrid scheme with experimental results is presented. In this paper, the Maxwell stress tensor is used to calculate the dielectrophoretic force acting on particles by considering the physical effect of particles in the computational domain. Thus, this study eliminates the approximations used in point dipole methods for calculating dielectrophoretic force. A comparative study between Maxwell stress tensor and point dipole methods for computing dielectrophoretic forces are presented. The hybrid method is used to investigate the physics of dielectrophoresis in microfluidic devices using an AC electric field. The numerical results show that with proper design and appropriate selection of applied potential and frequency, global electric field minima can be obtained to facilitate multiple particle trapping by exploiting the mechanism of negative dielectrophoresis. Our numerical results also show that electrically neutral particles form a chain parallel to the applied electric field irrespective of their initial orientation when an AC electric field is applied. This proposed hybrid numerical scheme will help to better understand dielectrophoresis and to design and optimize microfluidic devices.« less

Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent.

PubMed

Rodriguez, Alex; Mokoema, Pol; Corcho, Francesc; Bisetty, Khrisna; Perez, Juan J

2011-02-17

The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.

ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

PubMed Central

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

2017-01-01

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

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Angular momentum and torque described with the complex octonion

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

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

2014-08-15

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

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

PubMed

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A

2009-03-10

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

PubMed Central

Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A.

2009-01-01

The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster. PMID:20161452

Demonstration of motion control of ZrO2 microparticles in uniform/non-uniform electric field

NASA Astrophysics Data System (ADS)

Onishi, Genki; Trung, Ngo Nguyen Chi; Matsutani, Naoto; Nakayama, Tadachika; Suzuki, Tsuneo; Suematsu, Hisayuki; Niihara, Koichi

2018-02-01

This study aims to elucidate the mechanism that drives dielectric microparticles under an electric field. The driving of microstructures is affected by various electrical phenomena occurring at the same time such as surface potential, polarization, and electrostatic force. It makes the clarification of the driving mechanism challenging. A simple experimental system was used to observe the behavior of spherical ZrO2 microparticles in a nonaqueous solution under an electric field. The results suggest that the mechanism that drives the ZrO2 microparticles under an electric field involved the combination of an electric image force, a gradient force, and the contact charging phenomenon. A method is proposed to control the motion of micro- and nanostructures in further study and applications.

Nonlinear Force-free Coronal Magnetic Stereoscopy

NASA Astrophysics Data System (ADS)

Chifu, Iulia; Wiegelmann, Thomas; Inhester, Bernd

2017-03-01

Insights into the 3D structure of the solar coronal magnetic field have been obtained in the past by two completely different approaches. The first approach are nonlinear force-free field (NLFFF) extrapolations, which use photospheric vector magnetograms as boundary condition. The second approach uses stereoscopy of coronal magnetic loops observed in EUV coronal images from different vantage points. Both approaches have their strengths and weaknesses. Extrapolation methods are sensitive to noise and inconsistencies in the boundary data, and the accuracy of stereoscopy is affected by the ability of identifying the same structure in different images and by the separation angle between the view directions. As a consequence, for the same observational data, the 3D coronal magnetic fields computed with the two methods do not necessarily coincide. In an earlier work (Paper I) we extended our NLFFF optimization code by including stereoscopic constrains. The method was successfully tested with synthetic data, and within this work, we apply the newly developed code to a combined data set from SDO/HMI, SDO/AIA, and the two STEREO spacecraft. The extended method (called S-NLFFF) contains an additional term that monitors and minimizes the angle between the local magnetic field direction and the orientation of the 3D coronal loops reconstructed by stereoscopy. We find that when we prescribe the shape of the 3D stereoscopically reconstructed loops, the S-NLFFF method leads to a much better agreement between the modeled field and the stereoscopically reconstructed loops. We also find an appreciable decrease by a factor of two in the angle between the current and the magnetic field. This indicates the improved quality of the force-free solution obtained by S-NLFFF.

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

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.

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.

Higher-order force moments of active particles

NASA Astrophysics Data System (ADS)

Nasouri, Babak; Elfring, Gwynn J.

2018-04-01

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

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

NASA Technical Reports Server (NTRS)

Ramachandran N.; Leslie, F.

1999-01-01

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

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

PubMed Central

2016-01-01

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

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

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

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

Rapid parameterization of small molecules using the Force Field Toolkit.

PubMed

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

2013-12-15

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

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Magnetic force microscopy method and apparatus to detect and image currents in integrated circuits

DOEpatents

Campbell, Ann. N.; Anderson, Richard E.; Cole, Jr., Edward I.

1995-01-01

A magnetic force microscopy method and improved magnetic tip for detecting and quantifying internal magnetic fields resulting from current of integrated circuits. Detection of the current is used for failure analysis, design verification, and model validation. The interaction of the current on the integrated chip with a magnetic field can be detected using a cantilevered magnetic tip. Enhanced sensitivity for both ac and dc current and voltage detection is achieved with voltage by an ac coupling or a heterodyne technique. The techniques can be used to extract information from analog circuits.

Magnetic force microscopy method and apparatus to detect and image currents in integrated circuits

DOEpatents

Campbell, A.N.; Anderson, R.E.; Cole, E.I. Jr.

1995-11-07

A magnetic force microscopy method and improved magnetic tip for detecting and quantifying internal magnetic fields resulting from current of integrated circuits are disclosed. Detection of the current is used for failure analysis, design verification, and model validation. The interaction of the current on the integrated chip with a magnetic field can be detected using a cantilevered magnetic tip. Enhanced sensitivity for both ac and dc current and voltage detection is achieved with voltage by an ac coupling or a heterodyne technique. The techniques can be used to extract information from analog circuits. 17 figs.

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

PubMed

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

Shaw, Gordon A.

2018-07-01

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

Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

PubMed Central

Baumketner, Andrij

2009-01-01

The performance of reaction-field methods to treat electrostatic interactions is tested in simulations of ions solvated in water. The potential of mean force between sodium chloride pair of ions and between side chains of lysine and aspartate are computed using umbrella sampling and molecular dynamics simulations. It is found that in comparison with lattice sum calculations, the charge-group-based approaches to reaction-field treatments produce a large error in the association energy of the ions that exhibits strong systematic dependence on the size of the simulation box. The atom-based implementation of the reaction field is seen to (i) improve the overall quality of the potential of mean force and (ii) remove the dependence on the size of the simulation box. It is suggested that the atom-based truncation be used in reaction-field simulations of mixed media. PMID:19292522

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

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.

The Relationship between Appendage Geometry and Propeller Blade Unsteady Forces.

DTIC Science & Technology

1987-11-01

unsteady thrust and torque for a given propeller geometry. The results indicate that unsteady force reduction can be obtained by modification of the flow ... unsteady force calculation methods available are: 1) quasi-steady using uniform flow ; 2) quasi-steady using lifting-line theory; 3) two-dimensional... experimental data and the calculated unsteady forces that both the flow field near the body surface and behind the appendage tip must be

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

NASA Technical Reports Server (NTRS)

Mendelson, A.; Ghosn, L. J.

1986-01-01

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

Uniform hydrogen fuel layers for inertial fusion targets by microgravity

NASA Technical Reports Server (NTRS)

Parks, P. B.; Fagaly, Robert L.

1994-01-01

A critical concern in the fabrication of targets for inertial confinement fusion (ICF) is ensuring that the hydrogenic (D(sub 2) or DT) fuel layer maintains spherical symmetry. Solid layered targets have structural integrity, but lack the needed surface smoothness. Liquid targets are inherently smooth, but suffer from gravitationally induced sagging. One method to reduce the effective gravitational field environment is freefall insertion into the target chamber. Another method to counterbalance field gravitational force is to use an applied magnetic field combined with a gradient field to induce a magnetic dipole force on the liquid fuel layer. Based on time dependent calculations of the dynamics of the liquid fuel layer in microgravity environments, we show that it may be possible to produce a liquid layered ICF target that satisfies both smoothness and symmetry requirements.

The force analysis for superparamagnetic nanoparticles-based gene delivery in an oscillating magnetic field

NASA Astrophysics Data System (ADS)

Sun, Jiajia; Shi, Zongqian; Jia, Shenli; Zhang, Pengbo

2017-04-01

Due to the peculiar magnetic properties and the ability to function in cell-level biological interaction, superparamagnetic nanoparticles (SMNP) have been being the attractive carrier for gene delivery. The superparamagnetic nanoparticles with surface-bound gene vector can be attracted to the surface of cells by the Kelvin force provided by external magnetic field. In this article, the influence of the oscillating magnetic field on the characteristics of magnetofection is studied in terms of the magnetophoretic velocity. The magnetic field of a cylindrical permanent magnet is calculated by equivalent current source (ECS) method, and the Kelvin force is derived by using the effective moment method. The results show that the static magnetic field accelerates the sedimentation of the particles, and drives the particles inward towards the axis of the magnet. Based on the investigation of the magnetophoretic velocity of the particle under horizontally oscillating magnetic field, an oscillating velocity within the amplitude of the magnet oscillation is observed. Furthermore, simulation results indicate that the oscillating amplitude plays an important role in regulating the active region, where the particles may present oscillating motion. The analysis of the magnetophoretic velocity gives us an insight into the physical mechanism of the magnetofection. It's also helpful to the optimal design of the magnetofection system.

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

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

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

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

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.

A comparison between progressive extension method (PEM) and iterative method (IM) for magnetic field extrapolations in the solar atmosphere

NASA Technical Reports Server (NTRS)

Wu, S. T.; Sun, M. T.; Sakurai, Takashi

1990-01-01

This paper presents a comparison between two numerical methods for the extrapolation of nonlinear force-free magnetic fields, viz the Iterative Method (IM) and the Progressive Extension Method (PEM). The advantages and disadvantages of these two methods are summarized, and the accuracy and numerical instability are discussed. On the basis of this investigation, it is claimed that the two methods do resemble each other qualitatively.

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.

Improved atomistic simulation of diffusion and sorption in metal oxides

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

2001-01-01

Gas diffusion and sorption on the surface of metal oxides are investigated using atomistic simulations, that make use of two different force fields for the description of the intramolecular and intermolecular interactions. MD and MC computations are presented and estimates of the mean residence time, Henry's constant, and the heat of adsorption are provided for various common gases (CO, CO2, O2, CH4, Xe), and semiconducting substrates that hold promise for gas sensor applications (SnO2, BaTiO3). Comparison is made between the performance of a simple, first generation force field (Universal) and a more detailed, second generation field (COMPASS) under the same conditions and the same assumptions regarding the generation of the working configurations. It is found that the two force fields yield qualitatively similar results in all cases examined here. However, direct comparison with experimental data reveals that the accuracy of the COMPASS-based computations is not only higher than that of the first generation force field but exceeds even that of published specialized methods, based on ab initio computations.

An Immersed Boundary method with divergence-free velocity interpolation and force spreading

NASA Astrophysics Data System (ADS)

Bao, Yuanxun; Donev, Aleksandar; Griffith, Boyce E.; McQueen, David M.; Peskin, Charles S.

2017-10-01

The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid-structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an Eulerian representation of the fluid and a Lagrangian representation of the structure. The Lagrangian and Eulerian frames are coupled by integral transforms with delta function kernels. The discretized IB equations use approximations to these transforms with regularized delta function kernels to interpolate the fluid velocity to the structure, and to spread structural forces to the fluid. It is well-known that the conventional IB method can suffer from poor volume conservation since the interpolated Lagrangian velocity field is not generally divergence-free, and so this can cause spurious volume changes. In practice, the lack of volume conservation is especially pronounced for cases where there are large pressure differences across thin structural boundaries. The aim of this paper is to greatly reduce the volume error of the IB method by introducing velocity-interpolation and force-spreading schemes with the properties that the interpolated velocity field in which the structure moves is at least C1 and satisfies a continuous divergence-free condition, and that the force-spreading operator is the adjoint of the velocity-interpolation operator. We confirm through numerical experiments in two and three spatial dimensions that this new IB method is able to achieve substantial improvement in volume conservation compared to other existing IB methods, at the expense of a modest increase in the computational cost. Further, the new method provides smoother Lagrangian forces (tractions) than traditional IB methods. The method presented here is restricted to periodic computational domains. Its generalization to non-periodic domains is important future work.

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

NASA Astrophysics Data System (ADS)

Canter, Martin; Barth, Alexander

2016-04-01

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

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.

Review of Railgun Modeling Techniques: The Computation of Railgun Force and Other Key Factors

NASA Astrophysics Data System (ADS)

Eckert, Nathan James

Currently, railgun force modeling either uses the simple "railgun force equation" or finite element methods. It is proposed here that a middle ground exists that does not require the solution of partial differential equations, is more readily implemented than finite element methods, and is more accurate than the traditional force equation. To develop this method, it is necessary to examine the core railgun factors: power supply mechanisms, the distribution of current in the rails and in the projectile which slides between them (called the armature), the magnetic field created by the current flowing through these rails, the inductance gradient (a key factor in simplifying railgun analysis, referred to as L'), the resultant Lorentz force, and the heating which accompanies this action. Common power supply technologies are investigated, and the shape of their current pulses are modeled. The main causes of current concentration are described, and a rudimentary method for computing current distribution in solid rails and a rectangular armature is shown to have promising accuracy with respect to outside finite element results. The magnetic field is modeled with two methods using the Biot-Savart law, and generally good agreement is obtained with respect to finite element methods (5.8% error on average). To get this agreement, a factor of 2 is added to the original formulation after seeing a reliable offset with FEM results. Three inductance gradient calculations are assessed, and though all agree with FEM results, the Kerrisk method and a regression analysis method developed by Murugan et al. (referred to as the LRM here) perform the best. Six railgun force computation methods are investigated, including the traditional railgun force equation, an equation produced by Waindok and Piekielny, and four methods inspired by the work of Xu et al. Overall, good agreement between the models and outside data is found, but each model's accuracy varies significantly between comparisons. Lastly, an approximation of the temperature profile in railgun rails originally presented by McCorkle and Bahder is replicated. In total, this work describes railgun technology and moderately complex railgun modeling methods, but is inconclusive about the presence of a middle-ground modeling method.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Interchain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: new insights from molecular dynamics.

PubMed

Meher, Biswa Ranjan; Kumar, Mattaparthi Venkata Satish; Bandyopadhyay, Pradipta

2014-01-01

The dynamics of HIV-1 protease (HIV-pr), a drug target for HIV infection, has been studied extensively by both computational and experimental methods. The flap dynamics of HIV-pr is considered to be more important for better ligand binding and enzymatic actions. Moreover, it has been demonstrated that the drug-induced mutations can change the flap dynamics of HIV-pr affecting the binding affinity of the ligands. Therefore, detailed understanding of flap dynamics is essential for designing better inhibitors. Previous computational investigations observed significant variation in the flap opening in nanosecond time scale indicating that the dynamics is highly sensitive to the simulation protocols. To understand the sensitivity of the flap dynamics on the force field and simulation protocol, molecular dynamics simulations of HIV-pr have been performed with two different AMBER force fields, ff99 and ff02. Two different trajectories (20 ns each) were obtained using the ff99 and ff02 force field. The results showed polarizable force field (ff02) make the flap tighter than the nonpolarizable force field (ff99). Some polar interactions and hydrogen bonds involving flap residues were found to be stronger with ff02 force field. The formation of interchain hydrophobic cluster (between flap tip of one chain and active site wall of another chain) was found to be dominant in the semi-open structures obtained from the simulations irrespective of the force field. It is proposed that an inhibitor, which will promote this interchain hydrophobic clustering, may make the flaps more rigid, and presumably the effect of mutation would be small on ligand binding.

Non-Maxwellian and magnetic field effects in complex plasma wakes★

NASA Astrophysics Data System (ADS)

Ludwig, Patrick; Jung, Hendrik; Kählert, Hanno; Joost, Jan-Philip; Greiner, Franko; Moldabekov, Zhandos; Carstensen, Jan; Sundar, Sita; Bonitz, Michael; Piel, Alexander

2018-05-01

In a streaming plasma, negatively charged dust particles create complex charge distributions on the downstream side of the particle, which are responsible for attractive forces between the like-charged particles. This wake phenomenon is studied by means of refined linear response theory and molecular dynamics simulations as well as in experiments. Particular attention is paid to non-Maxwellian velocity distributions that are found in the plasma sheath and to situations with strong magnetic fields, which are becoming increasingly important. Non-Maxwellian distributions and strong magnetic fields result in a substantial damping of the oscillatory wake potential. The interaction force in particle pairs is explored with the phase-resolved resonance method, which demonstrates the non-reciprocity of the interparticle forces in unmagnetized and magnetized systems.

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

PubMed

Emperador, Agustí; Sfriso, Pedro; Villarreal, Marcos Ariel; Gelpí, Josep Lluis; Orozco, Modesto

2015-12-08

Molecular dynamics simulations of proteins are usually performed on a single molecule, and coarse-grained protein models are calibrated using single-molecule simulations, therefore ignoring intermolecular interactions. We present here a new coarse-grained force field for the study of many protein systems. The force field, which is implemented in the context of the discrete molecular dynamics algorithm, is able to reproduce the properties of folded and unfolded proteins, in both isolation, complexed forming well-defined quaternary structures, or aggregated, thanks to its proper evaluation of protein-protein interactions. The accuracy and computational efficiency of the method makes it a universal tool for the study of the structure, dynamics, and association/dissociation of proteins.

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

PubMed

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

2011-02-01

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

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

General Anisotropy Identification of Paperboard with Virtual Fields Method

Treesearch

J.M. Considine; F. Pierron; K.T. Turner; D.W. Vahey

2014-01-01

This work extends previous efforts in plate bending of Virtual Fields Method (VFM) parameter identification to include a general 2-D anisotropicmaterial. Such an extension was needed for instances in which material principal directions are unknown or when specimen orientation is not aligned with material principal directions. A new fixture with a multiaxial force...

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

PubMed Central

2016-01-01

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

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.

Sparse deconvolution for the large-scale ill-posed inverse problem of impact force reconstruction

NASA Astrophysics Data System (ADS)

Qiao, Baijie; Zhang, Xingwu; Gao, Jiawei; Liu, Ruonan; Chen, Xuefeng

2017-01-01

Most previous regularization methods for solving the inverse problem of force reconstruction are to minimize the l2-norm of the desired force. However, these traditional regularization methods such as Tikhonov regularization and truncated singular value decomposition, commonly fail to solve the large-scale ill-posed inverse problem in moderate computational cost. In this paper, taking into account the sparse characteristic of impact force, the idea of sparse deconvolution is first introduced to the field of impact force reconstruction and a general sparse deconvolution model of impact force is constructed. Second, a novel impact force reconstruction method based on the primal-dual interior point method (PDIPM) is proposed to solve such a large-scale sparse deconvolution model, where minimizing the l2-norm is replaced by minimizing the l1-norm. Meanwhile, the preconditioned conjugate gradient algorithm is used to compute the search direction of PDIPM with high computational efficiency. Finally, two experiments including the small-scale or medium-scale single impact force reconstruction and the relatively large-scale consecutive impact force reconstruction are conducted on a composite wind turbine blade and a shell structure to illustrate the advantage of PDIPM. Compared with Tikhonov regularization, PDIPM is more efficient, accurate and robust whether in the single impact force reconstruction or in the consecutive impact force reconstruction.

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.

Comparison of forcing functions in magnetohydrodynamics

NASA Astrophysics Data System (ADS)

McKay, Mairi E.; Linkmann, Moritz; Clark, Daniel; Chalupa, Adam A.; Berera, Arjun

2017-11-01

Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different mechanical forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale velocity field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity, and cross helicity), the time-averaged energy spectra, the energy ratios, and the dissipation ratios are examined. All three forcing functions produce qualitatively similar steady states with regard to the time evolution of the energy and magnetic helicity. However, differences in the cross-helicity evolution are observed, particularly in the case of the static sinusoidal method of energy injection. Indeed, an ensemble of sinusoidally forced simulations with identical parameters shows significant variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems in which the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored.

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

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-03-01

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

PIV-based estimation of unsteady loads on a flat plate at high angle of attack using momentum equation approaches

NASA Astrophysics Data System (ADS)

Guissart, Amandine; Bernal, Luis; Dimitriadis, Gregorios; Terrapon, Vincent

2015-11-01

The direct measurement of loads with force balance can become challenging when the forces are small or when the body is moving. An alternative is the use of Particle Image Velocimetry (PIV) velocity fields to indirectly obtain the aerodynamic coefficients. This can be done by the use of control volume approaches which lead to the integration of velocities, and other fields deriving from them, on a contour surrounding the studied body and its supporting surface. This work exposes and discusses results obtained with two different methods: the direct use of the integral formulation of the Navier-Stokes equations and the so-called Noca's method. The latter is a reformulation of the integral Navier-Stokes equations in order to get rid of the pressure. Results obtained using the two methods are compared and the influence of different parameters is discussed. The methods are applied to PIV data obtained from water channel testing for the flow around a 16:1 plate. Two cases are considered: a static plate at high angle of attack and a large amplitude imposed pitching motion. Two-dimensional PIV velocity fields are used to compute the aerodynamic forces. Direct measurements of dynamic loads are also carried out in order to assess the quality of the indirectly calculated coefficients.

A Novel Method to Reconstruct the Force Curve by Higher Harmonics of the First Two Flexural Modes in Frequency Modulation Atomic Force Microscope (FM-AFM).

PubMed

Zhang, Suoxin; Qian, Jianqiang; Li, Yingzi; Zhang, Yingxu; Wang, Zhenyu

2018-06-04

Atomic force microscope (AFM) is an idealized tool to measure the physical and chemical properties of the sample surfaces by reconstructing the force curve, which is of great significance to materials science, biology, and medicine science. Frequency modulation atomic force microscope (FM-AFM) collects the frequency shift as feedback thus having high force sensitivity and it accomplishes a true noncontact mode, which means great potential in biological sample detection field. However, it is a challenge to establish the relationship between the cantilever properties observed in practice and the tip-sample interaction theoretically. Moreover, there is no existing method to reconstruct the force curve in FM-AFM combining the higher harmonics and the higher flexural modes. This paper proposes a novel method that a full force curve can be reconstructed by any order higher harmonics of the first two flexural modes under any vibration amplitude in FM-AFM. Moreover, in the small amplitude regime, short range forces are reconstructed more accurately by higher harmonics analysis compared with fundamental harmonics using the Sader-Jarvis formula.

Systems and methods for separating particles utilizing engineered acoustic contrast capture particles

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

Kaduchak, Gregory; Ward, Michael D.

An apparatus for separating particles from a medium includes a capillary defining a flow path therein that is in fluid communication with a medium source. The medium source includes engineered acoustic contrast capture particle having a predetermined acoustic contrast. The apparatus includes a vibration generator that is operable to produce at least one acoustic field within the flow path. The acoustic field produces a force potential minima for positive acoustic contrast particles and a force potential minima for negative acoustic contrast particles in the flow path and drives the engineered acoustic contrast capture particles to either the force potential minimamore » for positive acoustic contrast particles or the force potential minima for negative acoustic contrast particles.« less

A Lifting-Surface Program for Contrarotating Propellers

DTIC Science & Technology

1989-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Impact of Short-Range Forces on Defect Production from High-Energy Collisions

DOE PAGES

Stoller, R. E.; Tamm, A.; Béland, L. K.; ...

2016-04-25

Primary radiation damage formation in solid materials typically involves collisions between atoms that have up to a few hundred keV of kinetic energy. The distance between two colliding atoms can approach 0.05 nm during these collisions. At such small atomic separations, force fields fitted to equilibrium properties tend to significantly underestimate the potential energy of the colliding dimer. To enable molecular dynamics simulations of high-energy collisions, it is common practice to use a screened Coulomb force field to describe the interactions and to smoothly join this to the equilibrium force field at a suitable interatomic spacing. But, there is nomore » accepted standard method for choosing the parameters used in the joining process, and our results prove that defect production is sensitive to how the force fields are linked. A new procedure is presented that involves the use of ab initio calculations to determine the magnitude and spatial dependence of the pair interactions at intermediate distances, along with systematic criteria for choosing the joining parameters. Results are presented for the case of nickel, which demonstrate the use and validity of the procedure.« less

How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

PubMed

Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

2015-06-09

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the ligands. This improved the root-mean-square error (RMSE) for the predicted binding free energy from 1.9 kcal/mol with the original partial charges to 1.3 kcal/mol with the corrected partial charges.

How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

PubMed Central

2016-01-01

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the ligands. This improved the root-mean-square error (RMSE) for the predicted binding free energy from 1.9 kcal/mol with the original partial charges to 1.3 kcal/mol with the corrected partial charges. PMID:26085821

Variation in predicting pantograph-catenary interaction contact forces, numerical simulations and field measurements

NASA Astrophysics Data System (ADS)

Nåvik, Petter; Rønnquist, Anders; Stichel, Sebastian

2017-09-01

The contact force between the pantograph and the contact wire ensures energy transfer between the two. Too small of a force leads to arching and unstable energy transfer, while too large of a force leads to unnecessary wear on both parts. Thus, obtaining the correct contact force is important for both field measurements and estimates using numerical analysis. The field contact force time series is derived from measurements performed by a self-propelled diagnostic vehicle containing overhead line recording equipment. The measurements are not sampled at the actual contact surface of the interaction but by force transducers beneath the collector strips. Methods exist for obtaining more realistic measurements by adding inertia and aerodynamic effects to the measurements. The variation in predicting the pantograph-catenary interaction contact force is studied in this paper by evaluating the effect of the force sampling location and the effects of signal processing such as filtering. A numerical model validated by field measurements is used to study these effects. First, this paper shows that the numerical model can reproduce a train passage with high accuracy. Second, this study introduces three different options for contact force predictions from numerical simulations. Third, this paper demonstrates that the standard deviation and the maximum and minimum values of the contact force are sensitive to a low-pass filter. For a specific case, an 80 Hz cut-off frequency is compared to a 20 Hz cut-off frequency, as required by EN 50317:2012; the results show an 11% increase in standard deviation, a 36% increase in the maximum value and a 19% decrease in the minimum value.

A combined vector potential-scalar potential method for FE computation of 3D magnetic fields in electrical devices with iron cores

NASA Technical Reports Server (NTRS)

Wang, R.; Demerdash, N. A.

1991-01-01

A method of combined use of magnetic vector potential based finite-element (FE) formulations and magnetic scalar potential (MSP) based formulations for computation of three-dimensional magnetostatic fields is introduced. In this method, the curl-component of the magnetic field intensity is computed by a reduced magnetic vector potential. This field intensity forms the basic of a forcing function for a global magnetic scalar potential solution over the entire volume of the region. This method allows one to include iron portions sandwiched in between conductors within partitioned current-carrying subregions. The method is most suited for large-scale global-type 3-D magnetostatic field computations in electrical devices, and in particular rotating electric machinery.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

A Maximum-Likelihood Approach to Force-Field Calibration.

PubMed

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

2015-09-28

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

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.

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.

On the Adaptation of Pelvic Motion by Applying 3-dimensional Guidance Forces Using TPAD.

PubMed

Kang, Jiyeon; Vashista, Vineet; Agrawal, Sunil K

2017-09-01

Pelvic movement is important to human locomotion as the center of mass is located near the center of pelvis. Lateral pelvic motion plays a crucial role to shift the center of mass on the stance leg, while swinging the other leg and keeping the body balanced. In addition, vertical pelvic movement helps to reduce metabolic energy expenditure by exchanging potential and kinetic energy during the gait cycle. However, patient groups with cerebral palsy or stroke have excessive pelvic motion that leads to high energy expenditure. In addition, they have higher chances of falls as the center ofmass could deviate outside the base of support. In this paper, a novel control method is suggested using tethered pelvic assist device (TPAD) to teach subjects to walk with a specified target pelvic trajectory while walking on a treadmill. In this method, a force field is applied to the pelvis to guide it to move on a target trajectory and correctional forces are applied, if the pelvis motion has excessive deviations from the target trajectory. Three different experimentswith healthy subjects were conducted to teach them to walk on a new target pelvic trajectory with the presented control method. For all three experiments, the baseline trajectory of the pelvis was experimentally determined for each participating subject. To design a target pelvic trajectory which is different from the baseline, Experiment I scaled up the lateral component of the baseline pelvic trajectory, while Experiment II scaled down the lateral component of the baseline trajectory. For both Experiments I and II, the controller generated a 2-D force field in the transverse plane to provide the guidance force. In this paper, seven subjects were recruited for each experiment who walked on the treadmill with suggested control methods and visual feedback of their pelvic trajectory. The results show that the subjects were able to learn the target pelvic trajectory in each experiment and also retained the training effects after the completion of the experiment. In Experiment III, both lateral and vertical components of the pelvic trajectory were scaled down from the baseline trajectory. The force field was extended to three dimensions in order to correct the vertical pelvic movement as well. Three subgroups (force feedback alone, visual feedback alone, and both force and visual feedback) were recruited to understand the effects of force feedback and visual feedback alone to distinguish the results from Experiments I and II. The results showthat a trainingmethod that combines visual and force feedback is superior to the training methods with visual or force feedback alone. We believe that the present control strategy holds potential in training and correcting abnormal pelvic movements in different patient populations.

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

Trnka, Tomáš; Tvaroška, Igor; Koča, Jaroslav

2018-01-09

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

Exact Solution for Capillary Bridges Properties by Shooting Method

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

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

PubMed Central

Wickstrom, Lauren; Okur, Asim; Simmerling, Carlos

2009-01-01

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

Transient electrophoretic motion of a charged particle through a converging-diverging microchannel: effect of direct current-dielectrophoretic force.

PubMed

Ai, Ye; Joo, Sang W; Jiang, Yingtao; Xuan, Xiangchun; Qian, Shizhi

2009-07-01

Transient electrophoretic motion of a charged particle through a converging-diverging microchannel is studied by solving the coupled system of the Navier-Stokes equations for fluid flow and the Laplace equation for electrical field with an arbitrary Lagrangian-Eulerian finite-element method. A spatially non-uniform electric field is induced in the converging-diverging section, which gives rise to a direct current dielectrophoretic (DEP) force in addition to the electrostatic force acting on the charged particle. As a sequence, the symmetry of the particle velocity and trajectory with respect to the throat is broken. We demonstrate that the predicted particle trajectory shifts due to DEP show quantitative agreements with the existing experimental data. Although converging-diverging microchannels can be used for super fast electrophoresis due to the enhancement of the local electric field, it is shown that large particles may be blocked due to the induced DEP force, which thus must be taken into account in the study of electrophoresis in microfluidic devices where non-uniform electric fields are present.

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.

Manipulation of dielectric Rayleigh particles using highly focused elliptically polarized vector fields.

PubMed

Gu, Bing; Xu, Danfeng; Rui, Guanghao; Lian, Meng; Cui, Yiping; Zhan, Qiwen

2015-09-20

Generation of vectorial optical fields with arbitrary polarization distribution is of great interest in areas where exotic optical fields are desired. In this work, we experimentally demonstrate the versatile generation of linearly polarized vector fields, elliptically polarized vector fields, and circularly polarized vortex beams through introducing attenuators in a common-path interferometer. By means of Richards-Wolf vectorial diffraction method, the characteristics of the highly focused elliptically polarized vector fields are studied. The optical force and torque on a dielectric Rayleigh particle produced by these tightly focused vector fields are calculated and exploited for the stable trapping of dielectric Rayleigh particles. It is shown that the additional degree of freedom provided by the elliptically polarized vector field allows one to control the spatial structure of polarization, to engineer the focusing field, and to tailor the optical force and torque on a dielectric Rayleigh particle.

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

PubMed

Herges, T; Wenzel, W

2005-01-14

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

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

NASA Astrophysics Data System (ADS)

Herges, T.; Wenzel, W.

2005-01-01

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

Experimental study on inter-particle acoustic forces.

PubMed

Garcia-Sabaté, Anna; Castro, Angélica; Hoyos, Mauricio; González-Cinca, Ricard

2014-03-01

A method for the experimental measurement of inter-particle forces (secondary Bjerknes force) generated by the action of an acoustic field in a resonator micro-channel is presented. The acoustic radiation force created by an ultrasonic standing wave moves suspended particles towards the pressure nodes and the acoustic pressure induces particle volume oscillations. Once particles are in the levitation plane, transverse and secondary Bjerknes forces become important. Experiments were carried out in a resonator filled with a suspension composed of water and latex particles of different size (5-15 μm) at different concentrations. Ultrasound was generated by means of a 2.5 MHz nominal frequency transducer. For the first time the acoustic force generated by oscillating particles acting on other particles has been measured, and the critical interaction distance in various cases has been determined. Inter-particle forces on the order of 10(-14) N have been measured by using this method.

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

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

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

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

NASA Astrophysics Data System (ADS)

Aschwanden, M. J.

2013-12-01

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

Indirect boundary force measurements in beam-like structures using a derivative estimator

NASA Astrophysics Data System (ADS)

Chesne, Simon

2014-12-01

This paper proposes a new method for the identification of boundary forces (shear force or bending moment) in a beam, based on displacement measurements. The problem is considered in terms of the determination of the boundary spatial derivatives of transverse displacements. By assuming the displacement fields to be approximated by Taylor expansions in a domain close to the boundaries, the spatial derivatives can be estimated using specific point-wise derivative estimators. This approach makes it possible to extract the derivatives using a weighted spatial integration of the displacement field. Following the theoretical description, numerical simulations made with exact and noisy data are used to determine the relationship between the size of the integration domain and the wavelength of the vibrations. The simulations also highlight the self-regularization of the technique. Experimental measurements demonstrate the feasibility and accuracy of the proposed method.

Transferable Coarse-Grained Models for Ionic Liquids.

PubMed

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

2009-04-14

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

Radiation-reaction force on a small charged body to second order

NASA Astrophysics Data System (ADS)

Moxon, Jordan; Flanagan, Éanna

2018-05-01

In classical electrodynamics, an accelerating charged body emits radiation and experiences a corresponding radiation-reaction force, or self-force. We extend to higher order in the total charge a previous rigorous derivation of the electromagnetic self-force in flat spacetime by Gralla, Harte, and Wald. The method introduced by Gralla, Harte, and Wald computes the self-force from the Maxwell field equations and conservation of stress-energy in a limit where the charge, size, and mass of the body go to zero, and it does not require regularization of a singular self-field. For our higher-order computation, an adjustment of the definition of the mass of the body is necessary to avoid including self-energy from the electromagnetic field sourced by the body in the distant past. We derive the evolution equations for the mass, spin, and center-of-mass position of the body through second order. We derive, for the first time, the second-order acceleration dependence of the evolution of the spin (self-torque), as well as a mixing between the extended body effects and the acceleration-dependent effects on the overall body motion.

Visualization and analysis of vortex-turbine intersections in wind farms.

PubMed

Shafii, Sohail; Obermaier, Herald; Linn, Rodman; Koo, Eunmo; Hlawitschka, Mario; Garth, Christoph; Hamann, Bernd; Joy, Kenneth I

2013-09-01

Characterizing the interplay between the vortices and forces acting on a wind turbine's blades in a qualitative and quantitative way holds the potential for significantly improving large wind turbine design. This paper introduces an integrated pipeline for highly effective wind and force field analysis and visualization. We extract vortices induced by a turbine's rotation in a wind field, and characterize vortices in conjunction with numerically simulated forces on the blade surfaces as these vortices strike another turbine's blades downstream. The scientifically relevant issue to be studied is the relationship between the extracted, approximate locations on the blades where vortices strike the blades and the forces that exist in those locations. This integrated approach is used to detect and analyze turbulent flow that causes local impact on the wind turbine blade structure. The results that we present are based on analyzing the wind and force field data sets generated by numerical simulations, and allow domain scientists to relate vortex-blade interactions with power output loss in turbines and turbine life expectancy. Our methods have the potential to improve turbine design to save costs related to turbine operation and maintenance.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Moving force identification based on redundant concatenated dictionary and weighted l1-norm regularization

NASA Astrophysics Data System (ADS)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin; Chen, Ze-Peng; Luo, Wen-Feng

2018-01-01

Moving force identification (MFI) is an important inverse problem in the field of bridge structural health monitoring (SHM). Reasonable signal structures of moving forces are rarely considered in the existing MFI methods. Interaction forces are complex because they contain both slowly-varying harmonic and impact signals due to bridge vibration and bumps on a bridge deck, respectively. Therefore, the interaction forces are usually hard to be expressed completely and sparsely by using a single basis function set. Based on the redundant concatenated dictionary and weighted l1-norm regularization method, a hybrid method is proposed for MFI in this study. The redundant dictionary consists of both trigonometric functions and rectangular functions used for matching the harmonic and impact signal features of unknown moving forces. The weighted l1-norm regularization method is introduced for formulation of MFI equation, so that the signal features of moving forces can be accurately extracted. The fast iterative shrinkage-thresholding algorithm (FISTA) is used for solving the MFI problem. The optimal regularization parameter is appropriately chosen by the Bayesian information criterion (BIC) method. In order to assess the accuracy and the feasibility of the proposed method, a simply-supported beam bridge subjected to a moving force is taken as an example for numerical simulations. Finally, a series of experimental studies on MFI of a steel beam are performed in laboratory. Both numerical and experimental results show that the proposed method can accurately identify the moving forces with a strong robustness, and it has a better performance than the Tikhonov regularization method. Some related issues are discussed as well.

Potential theory of radiation

NASA Technical Reports Server (NTRS)

Chiu, Huei-Huang

1989-01-01

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

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

NASA Astrophysics Data System (ADS)

Xu, Jian-Jun; Ren, Weiqing

2014-04-01

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

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

NASA Astrophysics Data System (ADS)

Rädler, K.-H.

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

Surface‐wave Green’s tensors in the near field

USGS Publications Warehouse

Haney, Matt; Nakahara, Hisashi

2014-01-01

We demonstrate the connection between theoretical expressions for the correlation of ambient noise Rayleigh and Love waves and the exact surface‐wave Green’s tensors for a point force. The surface‐wave Green’s tensors are well known in the far‐field limit. On the other hand, the imaginary part of the exact Green’s tensors, including near‐field effects, arises in correlation techniques such as the spatial autocorrelation (SPAC) method. Using the imaginary part of the exact Green’s tensors from the SPAC method, we find the associated real part using the Kramers–Kronig relations. The application of the Kramers–Kronig relations is not straightforward, however, because the causality properties of the different tensor components vary. In addition to the Green’s tensors for a point force, we also derive expressions for a general point moment tensor source.

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.

Radiation force on absorbing targets and power measurements of a high intensity focused ultrasound (HIFU) source

NASA Astrophysics Data System (ADS)

Qian, Zuwen; Zhu, Zhemin; Ye, Shigong; Jiang, Wenhua; Zhu, Houqing; Yu, Jinshen

2010-10-01

Based on the analytic expressions for the radiated field of a circular concave piston given by Hasegawa et al., an integral for calculation of the radiation force on a plane absorbing target in a spherically focused field is derived. A general relation between acoustic power P and normal radiation force F n is obtained under the condition of kr ≫ 1. Numerical computation is carried out by using the symbolic computation program for practically focused sources and absorbing circular targets. The results show that, for a given source, there is a range of target positions where the radiation force is independent of the target’s position under the assumption that the contribution of the acoustic field behind the target to the radiation force can be neglected. The experiments are carried out and confirm that there is a range of target positions where the measured radiation force is basically independent of the target’s position even at high acoustic power (up to 700 W). It is believed that when the radiation force method is used to measure the acoustic power radiated from a focused source, the size of the target must be selected in such a way that no observable sound can be found in the region behind the target.

Combining configurational energies and forces for molecular force field optimization

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

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

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

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

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

2017-07-21

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

Force sensor

DOEpatents

Grahn, A.R.

1993-05-11

A force sensor and related method for determining force components is described. The force sensor includes a deformable medium having a contact surface against which a force can be applied, a signal generator for generating signals that travel through the deformable medium to the contact surface, a signal receptor for receiving the signal reflected from the contact surface, a generation controller, a reception controller, and a force determination apparatus. The signal generator has one or more signal generation regions for generating the signals. The generation controller selects and activates the signal generation regions. The signal receptor has one or more signal reception regions for receiving signals and for generating detections signals in response thereto. The reception controller selects signal reception regions and detects the detection signals. The force determination apparatus measures signal transit time by timing activation and detection and, optionally, determines force components for selected cross-field intersections. The timer which times by activation and detection can be any means for measuring signal transit time. A cross-field intersection is defined by the overlap of a signal generation region and a signal reception region.

Force sensor

DOEpatents

Grahn, Allen R.

1993-01-01

A force sensor and related method for determining force components. The force sensor includes a deformable medium having a contact surface against which a force can be applied, a signal generator for generating signals that travel through the deformable medium to the contact surface, a signal receptor for receiving the signal reflected from the contact surface, a generation controller, a reception controller, and a force determination apparatus. The signal generator has one or more signal generation regions for generating the signals. The generation controller selects and activates the signal generation regions. The signal receptor has one or more signal reception regions for receiving signals and for generating detections signals in response thereto. The reception controller selects signal reception regions and detects the detection signals. The force determination apparatus measures signal transit time by timing activation and detection and, optionally, determines force components for selected cross-field intersections. The timer which times by activation and detection can be any means for measuring signal transit time. A cross-field intersection is defined by the overlap of a signal generation region and a signal reception region.

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

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

An overview of a Lagrangian method for analysis of animal wake dynamics.

PubMed

Peng, Jifeng; Dabiri, John O

2008-01-01

The fluid dynamic analysis of animal wakes is becoming increasingly popular in studies of animal swimming and flying, due in part to the development of quantitative flow visualization techniques such as digital particle imaging velocimetry (DPIV). In most studies, quasi-steady flow is assumed and the flow analysis is based on velocity and/or vorticity fields measured at a single time instant during the stroke cycle. The assumption of quasi-steady flow leads to neglect of unsteady (time-dependent) wake vortex added-mass effects, which can contribute significantly to the instantaneous locomotive forces. In this paper we review a Lagrangian approach recently introduced to determine unsteady wake vortex structure by tracking the trajectories of individual fluid particles in the flow, rather than by analyzing the velocity/vorticity fields at fixed locations and single instants in time as in the Eulerian perspective. Once the momentum of the wake vortex and its added mass are determined, the corresponding unsteady locomotive forces can be quantified. Unlike previous studies that estimated the time-averaged forces over the stroke cycle, this approach enables study of how instantaneous locomotive forces evolve over time. The utility of this method for analyses of DPIV velocity measurements is explored, with the goal of demonstrating its applicability to data that are typically available to investigators studying animal swimming and flying. The methods are equally applicable to computational fluid dynamics studies where velocity field calculations are available.

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

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

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

The use of electromagnetic body forces to enhance the quality of laser welds

NASA Astrophysics Data System (ADS)

Ambrosy, Guenter; Berger, P.; Huegel, H.; Lindenau, D.

2003-11-01

The use of electromagnetic body forces in laser beam welding of aluminum alloys is a new method to shape the geometry and to enhance the quality of the weld seams. In this new approach, electromagnetic volume forces are utilized by applying magnetic fields and electric currents of various origins. Acting in the liquid metal, they directly affect the flow field and can lead to favourable conditions for the melt dynamics and energy coupling. Numerous welds with full and partial penetration using both CO2 and Nd:YAG lasers demonstrate that this method directly influences the seam geometry and top-bead topography as well as the penetration depth and the evolution of pores and cracks. In the case of full penetration, it is also possible to lift or to lower the weld pool. The method, therefore, can be used to shape the geometry and to enhance the quality of the weld seam. Depending on the orientation of an external magnetic field, significant impacts are achieved in CO2 welding, even without an external current: the shape of the cross-sectional area can be increased of up to 50% and also the seam width is changed. Whereas for such conditions with Nd:YAG lasers no significant effect could be observed, it turned out that, when an external electric current is applied, similar effects are present with both wavelengths. In further investigations, the effect of electromagnetic body forces resulting from the interaction of an external current and its self-induced magnetic field was studied. Hereby, the current was fed into the workpiece via a tungsten electrode or a filler wire. The resulting phenomena are the same independent from wavelength and means of current feed.

Dynamic force signal processing system of a robot manipulator

NASA Technical Reports Server (NTRS)

Uchiyama, M.; Kitagaki, K.; Hakomori, K.

1987-01-01

If dynamic noises such as those caused by the inertia forces of the hand can be eliminated from the signal of the force sensor installed on the wrist of the robot manipulator and if the necessary information of the external force can be detected with high sensitivity and high accuracy, a fine force feedback control for robots used in high speed and various fields will be possible. As the dynamic force sensing system, an external force estimate method with the extended Kalman filter is suggested and simulations and tests for a one axis force were performed. Later a dynamic signal processing system of six axes was composed and tested. The results are presented.

Experimental studies of protozoan response to intense magnetic fields and forces

NASA Astrophysics Data System (ADS)

Guevorkian, Karine

Intense static magnetic fields of up to 31 Tesla were used as a novel tool to manipulate the swimming mechanics of unicellular organisms. It is shown that homogenous magnetic fields alter the swimming trajectories of the single cell protozoan Paramecium caudatum, by aligning them parallel to the applied field. Immobile neutrally buoyant paramecia also oriented in magnetic fields with similar rates as the motile ones. It was established that the magneto-orientation is mostly due to the magnetic torques acting on rigid structures in the cell body and therefore the response is a non-biological, passive response. From the orientation rate of paramecia in various magnetic field strengths, the average anisotropy of the diamagnetic susceptibility of the cell was estimated. It has also been demonstrated that magnetic forces can be used to create increased, decreased and even inverted simulated gravity environments for the investigation of the gravi-responses of single cells. Since the mechanisms by which Earth's gravity affects cell functioning are still not fully understood, a number of methods to simulate different strength gravity environments, such as centrifugation, have been employed. Exploiting the ability to exert magnetic forces on weakly diamagnetic constituents of the cells, we were able to vary the gravity from -8 g to 10 g, where g is Earth's gravity. Investigations of the swimming response of paramecia in these simulated gravities revealed that they actively regulate their swimming speed to oppose the external force. This result is in agreement with centrifugation experiments, confirming the credibility of the technique. Moreover, the Paramecium's swimming ceased in simulated gravity of 10 g, indicating a maximum possible propulsion force of 0.7 nN. The magnetic force technique to simulate gravity is the only earthbound technique that can create increased and decreased simulated gravities in the same experimental setup. These findings establish a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

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

PubMed

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

2007-11-30

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

Dynamics of structures in active suspensions of paramagnetic particles and applications to artificial micro-swimmers

NASA Astrophysics Data System (ADS)

Keaveny, Eric Edward

Micron-size paramagnetic particles suspended in viscous fluid will aggregate to form linear chains when subject to a uniform magnetic field. This process provides a way of changing the rheological properties of a suspension or building structures for microfluidic devices. We present a method to efficiently and accurately quantify the magnetic interactions between these particles. With this model and the force-coupling method, we perform simulations of both small ensembles and suspensions of thousands of paramagnetic particles subject to shear flows or rotating applied magnetic fields and demonstrate that in these situations an accurate representation of the fluid forces is necessary to estimate chain length. The artificial micro-swimmer is a device constructed from a flagellum-like tail of chemically linked paramagnetic beads tethered to a human red blood cell. To simulate this device, we develop an elastic coupling model that treats each chemical link as an inextensible, flexible rod. We demonstrate that when this device is subject to a rotating applied magnetic field, the filament tail will deform into a helical shape rotating with the field and propel the swimmer through the viscous fluid. Using a continuous elastica/resistive force model, we explore further the dependence of the swimming speed on the magnetic forces and swimmer geometry in the low frequency limit. We then examine the interactions between two comoving swimmers and ascertain at what separation distance a far-field approximation of the hydrodynamics is sufficient to reproduce the swimmers' dynamics. We also provide simulations of a single swimmer near a rigid surface and demonstrate that under certain conditions the presence of a wall can enhance the swimming speed. We determine further the height dependence of the repulsion from the surface, and, in the case of the spiral swimmer, the lateral drift speed. Finally, we consider a "squirmer" model for a swimming microorganism, appropriate for ciliary propulsion on time-scales much larger than the period of ciliary beating. We show that the "squirmer" model within the force-coupling method framework provides an effective simulation tool for studying low volume fraction suspensions of microorganisms.

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

PubMed

Herges, Thomas; Wenzel, Wolfgang

2005-04-01

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

Bio-inspired magnetic swimming microrobots for biomedical applications.

PubMed

Peyer, Kathrin E; Zhang, Li; Nelson, Bradley J

2013-02-21

Microrobots have been proposed for future biomedical applications in which they are able to navigate in viscous fluidic environments. Nature has inspired numerous microrobotic locomotion designs, which are suitable for propulsion generation at low Reynolds numbers. This article reviews the various swimming methods with particular focus on helical propulsion inspired by E. coli bacteria. There are various magnetic actuation methods for biomimetic and non-biomimetic microrobots, such as rotating fields, oscillating fields, or field gradients. They can be categorized into force-driven or torque-driven actuation methods. Both approaches are reviewed and a previous publication has shown that torque-driven actuation scales better to the micro- and nano-scale than force-driven actuation. Finally, the implementation of swarm or multi-agent control is discussed. The use of multiple microrobots may be beneficial for in vivo as well as in vitro applications. Thus, the frequency-dependent behavior of helical microrobots is discussed and preliminary experimental results are presented showing the decoupling of an individual agent within a group of three microrobots.

Pushing, pulling and electromagnetic radiation force cloaking by a pair of conducting cylindrical particles

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2018-02-01

The present analysis shows that two conducting cylindrical particles illuminated by an axially-polarized electric field of plane progressive waves at arbitrary incidence will attract, repel or become totally cloaked (i.e., invisible to the transfer of linear momentum carried by the incident waves), depending on their sizes, the interparticle distance as well as the angle of incidence of the incident field. Based on the rigorous multipole expansion method and the translational addition theorem of cylindrical wave functions, the electromagnetic (EM) radiation forces arising from multiple scattering effects between a pair of perfectly conducting cylindrical particles of circular cross-sections are derived and computed. An effective incident field on a particular particle is determined first, and used subsequently with its corresponding scattered field to derive the closed-form analytical expressions for the radiation force vector components. The mathematical expressions for the EM radiation force components (i.e. longitudinal and transverse) are exact, and have been formulated in partial-wave series expansions in cylindrical coordinates involving the angle of incidence, the interparticle distance and the expansion coefficients. Numerical examples illustrate the analysis for two perfectly conducting circular cylinders in a homogeneous nonmagnetic medium of wave propagation. The computations for the dimensionless radiation force functions are performed with particular emphasis on varying the angle of incidence, the interparticle distance, and the sizes of the particles. Depending on the interparticle distance and angle of incidence, the cylinders yield total neutrality (or invisibility); they experience no force and become unresponsive to the transfer of the EM linear momentum due to multiple scattering cancellation effects. Moreover, pushing or pulling EM forces between the two cylinders arise depending on the interparticle distance, the angle of incidence and their size parameters. This study provides a complete analytical method and computations for the longitudinal and transverse radiation force components in the multiple scattering of EM plane progressive waves with potential applications in particle manipulation, optically-engineered metamaterials with reconfigurable periodicities and cloaking devices to name a few examples.

A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures

PubMed Central

Zeng, Jia; Mohammadreza, Aida; Gao, Weimin; Merza, Saeed; Smith, Dean; Kelbauskas, Laimonas; Meldrum, Deirdre R.

2014-01-01

The field of single-cell analysis has gained a significant momentum over the last decade. Separation and isolation of individual cells is an indispensable step in almost all currently available single-cell analysis technologies. However, stress levels introduced by such manipulations remain largely unstudied. We present a method for minimally invasive retrieval of selected individual adherent cells of different types from cell cultures. The method is based on a combination of mechanical (shear flow) force and biochemical (trypsin digestion) treatment. We quantified alterations in the transcription levels of stress response genes in individual cells exposed to varying levels of shear flow and trypsinization. We report optimal temperature, RNA preservation reagents, shear force and trypsinization conditions necessary to minimize changes in the stress-related gene expression levels. The method and experimental findings are broadly applicable and can be used by a broad research community working in the field of single cell analysis. PMID:24957932

Novel Control Scheme of Power Assisted Wheelchair for Preventing Overturn (Part I)-Adjustment of Assisted Torque and Performance Evaluation From Field Test-

NASA Astrophysics Data System (ADS)

Seki, Hirokazu; Hata, Naoki; Koyasu, Yuichi; Hori, Yoichi

Aged people and disabled people who have difficulty in walking are increasing. As one of mobility support, significance of power assisted wheelchair which assists driving force using electric motors and spreads their living areas has been enhanced. However, the increased driving force often causes a dangerous overturn of wheelchair. In this paper, control method to prevent power assisted wheelchair from overturning is proposed. It is found the front wheels rising is caused by magnitude and rapid increase of assisted torque. Therefore, feedforward control method to limit the assisted torque by tuning its magnitude or time constant is proposed. In order to emphasize safety and feeling of security, these methods make the front wheels no rise. The effectiveness of the proposed method is verified by the practical experiments and field test based performance evaluation using many trial subjects.

Acoustic attraction, repulsion and radiation force cancellation on a pair of rigid particles with arbitrary cross-sections in 2D: Circular cylinders example

NASA Astrophysics Data System (ADS)

Mitri, F. G.

2017-11-01

The acoustic radiation forces arising on a pair of sound impenetrable cylindrical particles of arbitrary cross-sections are derived. Plane progressive, standing or quasi-standing waves with an arbitrary incidence angle are considered. Multiple scattering effects are described using the multipole expansion formalism and the addition theorem of cylindrical wave functions. An effective incident acoustic field on a particular object is determined, and used with the scattered field to derive closed-form analytical expressions for the radiation force vector components. The mathematical expressions for the radiation force components are exact, and have been formulated in partial-wave series expansions in cylindrical coordinates involving the angle of incidence, the reflection coefficient forming the progressive or the (quasi)standing wave field, the addition theorem, and the expansion coefficients. Numerical examples illustrate the analysis for two rigid circular cross-sections immersed in a non-viscous fluid. Computations for the dimensionless radiation force functions are performed with emphasis on varying the angle of incidence, the interparticle distance, the sizes of the particles as well as the characteristics of the incident field. Depending on the interparticle distance and angle of incidence, one of the particles yields neutrality; it experiences no force and becomes unresponsive (i.e., ;invisible;) to the linear momentum transfer of the effective incident field due to multiple scattering cancellation effects. Moreover, attractive or repulsive forces between the two particles may arise depending on the interparticle distance, the angle of incidence and size parameters of the particles. This study provides a complete analytical method and computations for the axial and transverse radiation force components in multiple acoustic scattering encompassing the cases of plane progressive, standing or quasi-standing waves of arbitrary incidence by a pair of scatterers. Potential applications concern the prediction of the forces used in acoustically-engineered metamaterials with reconfigurable periodicities, cloaking devices, and liquid crystals to name a few examples.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

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

Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

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

PubMed

Zhong, Xiujuan; Liu, Zhiping; Cao, Dapeng

2011-08-25

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

Simulating the electrohydrodynamics of a viscous droplet

NASA Astrophysics Data System (ADS)

Theillard, Maxime; Saintillan, David

2016-11-01

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

Dynamical and fractal properties in periodically forced stretch-twist-fold (STF) flow

NASA Astrophysics Data System (ADS)

Aqeel, Muhammad; Ahmad, Salman; Azam, Anam; Ahmed, Faizan

2017-05-01

The periodically forced stretch-twist-fold (STF) flow is introduced in this article. The nonlinear behavior of the STF flow with periodic force along the y -axis is investigated analytically and numerically. The STF flow is a prototype of the dynamo theory that proposes a mechanism of magnetic field generation continuously. The stability analysis is done by Routh Huwritz criteria and Cardano method. Chasing chaos through numerical simulation is determined to demonstrate the chaotic behavior of the forced STF flow. With the help of fractal processes based on the forced STF flow, a multi-wing forced STF flow is obtained that gives a n -wing forced STF flow system.

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Active magnetic force microscopy of Sr-ferrite magnet by stimulating magnetization under an AC magnetic field: Direct observation of reversible and irreversible magnetization processes

NASA Astrophysics Data System (ADS)

Cao, Yongze; Kumar, Pawan; Zhao, Yue; Yoshimura, Satoru; Saito, Hitoshi

2018-05-01

Understanding the dynamic magnetization process of magnetic materials is crucial to improving their fundamental properties and technological applications. Here, we propose active magnetic force microscopy for observing reversible and irreversible magnetization processes by stimulating magnetization with an AC magnetic field based on alternating magnetic force microscopy with a sensitive superparamagnetic tip. This approach simultaneously measures sample's DC and AC magnetic fields. We used this microscopy approach to an anisotropic Sr-ferrite (SrF) sintered magnet. This is a single domain type magnet where magnetization mainly changes via magnetic rotation. The proposed method can directly observe the reversible and irreversible magnetization processes of SrF and clearly reveal magnetic domain evolution of SrF (without stimulating magnetization—stimulating reversible magnetization—stimulating irreversible magnetization switching) by slowly increasing the amplitude of the external AC magnetic field. This microscopy approach can evaluate magnetic inhomogeneity and explain the local magnetic process within the permanent magnet.

The Force-Free Magnetosphere of a Rotating Black Hole

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Magnetospheric Multiscale Mission Examination of Stress Balance in FTE-Type Flux Ropes at the Earth's Magnetopause

NASA Astrophysics Data System (ADS)

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

2016-12-01

Determining the magnetic field structure, electric currents, and plasma distribution within flux transfer event (FTE)-type flux ropes is critical to the understanding of their origin, evolution, and dynamics. We analyze FTEs observed by the Magnetospheric Multiscale (MMS) mission in the vicinity of the sub-solar magnetopause, i.e. 12 ± 22.5' Local Time and XGSM > 7 RE. High-resolution data from the Fluxgate Magnetometer (FGM) and Fast Plasma Investigation (FPI) are used to determine and compare the extent to which large (> 1 RE) and small (ion scale) diameter FTEs are force-free, i.e. J×B=0, or non-force-free, i.e. J×B= gradP. Three independent methods are used: i) current density parallel and perpendicular to the magnetic field derived from the plasma measurements or magnetic field using the curlometer technique; ii) direct measurement of the plasma pressure gradient by FPI; and iii) fitting magnetic field to force-free (J=αB) flux rope models. Our initial results indicate that the plasma content of the ion-scale FTEs often exceeds that of larger FTEs. This results in higher plasma pressure gradients inside smaller FTEs and a magnetic field that is less force-free than the larger flux ropes.

Numerical and experimental study on the steady cone-jet mode of electro-centrifugal spinning

NASA Astrophysics Data System (ADS)

Hashemi, Ali Reza; Pishevar, Ahmad Reza; Valipouri, Afsaneh; Pǎrǎu, Emilian I.

2018-01-01

This study focuses on a numerical investigation of an initial stable jet through the air-sealed electro-centrifugal spinning process, which is known as a viable method for the mass production of nanofibers. A liquid jet undergoing electric and centrifugal forces, as well as other forces, first travels in a stable trajectory and then goes through an unstable curled path to the collector. In numerical modeling, hydrodynamic equations have been solved using the perturbation method—and the boundary integral method has been implemented to efficiently solve the electric potential equation. Hydrodynamic equations have been coupled with the electric field using stress boundary conditions at the fluid-fluid interface. Perturbation equations were discretized by a second order finite difference method, and the Newton method was implemented to solve the discretized non-linear system. Also, the boundary element method was utilized to solve electrostatic equations. In the theoretical study, the fluid was described as a leaky dielectric with charges only on the surface of the jet traveling in dielectric air. The effect of the electric field induced around the nozzle tip on the jet instability and trajectory deviation was also experimentally studied through plate-plate geometry as well as point-plate geometry. It was numerically found that the centrifugal force prevails on electric force by increasing the rotational speed. Therefore, the alteration of the applied voltage does not significantly affect the jet thinning profile or the jet trajectory.

A new electromagnetic NDI-technique based on the measurement of source-sample reaction forces

NASA Astrophysics Data System (ADS)

Fitzpatrick, G. L.; Skaugset, R. L.; Shih, W. C. L.

2001-04-01

Faraday's law of induction, Lenz's law, the Lorentz force law and Newton's third law, taken together, insure that sources (e.g., coil sources) of time-dependent electromagnetic fields, and nearby "nonmagnetic" electrical conductors (e.g., aluminum), always experience mutually repulsive (source-conductor) forces. This fact forms the basis for a new method for detecting cracks and corrosion in (aging) multi-layer airframes. The presence of cracks or corrosion (e.g., material thinning) in these structures is observed to reduce (second-harmonic) source-conductor reaction forces.

Portable dual field gradient force multichannel flow cytometer device with a dual wavelength low noise detection scheme

DOEpatents

James, Conrad D; Galambos, Paul C; Derzon, Mark S; Graf, Darin C; Pohl, Kenneth R; Bourdon, Chris J

2012-10-23

Systems and methods for combining dielectrophoresis, magnetic forces, and hydrodynamic forces to manipulate particles in channels formed on top of an electrode substrate are discussed. A magnet placed in contact under the electrode substrate while particles are flowing within the channel above the electrode substrate allows these three forces to be balanced when the system is in operation. An optical detection scheme using near-confocal microscopy for simultaneously detecting two wavelengths of light emitted from the flowing particles is also discussed.

FDTD approach to optical forces of tightly focused vector beams on metal particles.

PubMed

Qin, Jian-Qi; Wang, Xi-Lin; Jia, Ding; Chen, Jing; Fan, Ya-Xian; Ding, Jianping; Wang, Hui-Tian

2009-05-11

We propose an improved FDTD method to calculate the optical forces of tightly focused beams on microscopic metal particles. Comparison study on different kinds of tightly focused beams indicates that trapping efficiency can be altered by adjusting the polarization of the incident field. The results also show the size-dependence of trapping forces exerted on metal particles. Transverse tapping forces produced by different illumination wavelengths are also evaluated. The numeric simulation demonstrates the possibility of trapping moderate-sized metal particles whose radii are comparable to wavelength.

Circular Conditional Autoregressive Modeling of Vector Fields.

PubMed

Modlin, Danny; Fuentes, Montse; Reich, Brian

2012-02-01

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

Circular Conditional Autoregressive Modeling of Vector Fields*

PubMed Central

Modlin, Danny; Fuentes, Montse; Reich, Brian

2013-01-01

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

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

PubMed

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

2014-10-07

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

LIPID11: A Modular Framework for Lipid Simulations using Amber

PubMed Central

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

2013-01-01

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

An Advanced Actuator Line Method for Wind Energy Applications and Beyond

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

Churchfield, Matthew J.; Schreck, Scott; Martinez-Tossas, Luis A.

The actuator line method to represent rotor aerodynamics within computational fluid dynamics has been in use for over a decade. This method applies a body force to the flow field along rotating lines corresponding to the individual rotor blades and employs tabular airfoil data to compute the force distribution. The actuator line method is attractive because compared to blade-resolved simulations, the required mesh is much simpler and the computational cost is lower. This work proposes a higher fidelity variant of the actuator line method meant to fill the space between current actuator line and blade-resolved simulations. It contains modifications inmore » two key areas. The first is that of freestream velocity vector estimation along the line, which is necessary to compute the lift and drag along the line using tabular airfoil data. Most current methods rely on point sampling in which the location of sampling is ambiguous. Here we test a velocity sampling method that uses a properly weighted integral over space, removing this ambiguity. The second area of improvement is the function used to project the one-dimensional actuator line force onto the three-dimensional fluid mesh as a body force. We propose and test a projection function that spreads the force over a region that looks something like a real blade with the hope that it will produce the blade local and near wake flow features with more accuracy and higher fidelity. Our goal is that between these two improvements, not only will the flow field predictions be enhanced, but also the spanwise loading will be made more accurate. We refer to this combination of improvements as the advanced actuator line method. We apply these improvements to two different wind turbine cases. Although there is a strong wind energy motivation in our work, there is no reason these advanced actuator line ideas cannot be used in other applications, such as helicopter rotors.« less

An Advanced Actuator Line Method for Wind Energy Applications and Beyond: Preprint

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

Churchfield, Matthew; Schreck, Scott; Martinez-Tossas, Luis A.

The actuator line method to represent rotor aerodynamics within computational fluid dynamics has been in use for over a decade. This method applies a body force to the flow field along rotating lines corresponding to the individual rotor blades and employs tabular airfoil data to compute the force distribution. The actuator line method is attractive because compared to blade-resolved simulations, the required mesh is much simpler and the computational cost is lower. This work proposes a higher fidelity variant of the actuator line method meant to fill the space between current actuator line and blade-resolved simulations. It contains modifications inmore » two key areas. The first is that of freestream velocity vector estimation along the line, which is necessary to compute the lift and drag along the line using tabular airfoil data. Most current methods rely on point sampling in which the location of sampling is ambiguous. Here we test a velocity sampling method that uses a properly weighted integral over space, removing this ambiguity. The second area of improvement is the function used to project the one-dimensional actuator line force onto the three-dimensional fluid mesh as a body force. We propose and test a projection function that spreads the force over a region that looks something like a real blade with the hope that it will produce the blade local and near wake flow features with more accuracy and higher fidelity. Our goal is that between these two improvements, not only will the flow field predictions be enhanced, but also the spanwise loading will be made more accurate. We refer to this combination of improvements as the advanced actuator line method. We apply these improvements to two different wind turbine cases. Although there is a strong wind energy motivation in our work, there is no reason these advanced actuator line ideas cannot be used in other applications, such as helicopter rotors.« less

Molybdenum disulfide and water interaction parameters

NASA Astrophysics Data System (ADS)

Heiranian, Mohammad; Wu, Yanbin; Aluru, Narayana R.

2017-09-01

Understanding the interaction between water and molybdenum disulfide (MoS2) is of crucial importance to investigate the physics of various applications involving MoS2 and water interfaces. An accurate force field is required to describe water and MoS2 interactions. In this work, water-MoS2 force field parameters are derived using the high-accuracy random phase approximation (RPA) method and validated by comparing to experiments. The parameters obtained from the RPA method result in water-MoS2 interface properties (solid-liquid work of adhesion) in good comparison to the experimental measurements. An accurate description of MoS2-water interaction will facilitate the study of MoS2 in applications such as DNA sequencing, sea water desalination, and power generation.

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

PubMed

Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

2013-10-08

We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

PubMed Central

Dodda, Leela S.

2017-01-01

Abstract The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements. PMID:28444340

Mechanism of travelling-wave transport of particles

NASA Astrophysics Data System (ADS)

Kawamoto, Hiroyuki; Seki, Kyogo; Kuromiya, Naoyuki

2006-03-01

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

Visualization and Analysis of Vortex-Turbine Intersections in Wind Farms.

PubMed

Shafii, Sohail; Obermaier, Harald; Linn, Rodman; Koo, Eunmo; Hlawitschka, Mario; Garth, Christoph; Hamann, Bernd; Joy, Kenneth

2013-02-13

Characterizing the interplay between the vortices and forces acting on a wind turbine's blades in a qualitative and quantitative way holds the potential for significantly improving large wind turbine design. The paper introduces an integrated pipeline for highly effective wind and force field analysis and visualization. We extract vortices induced by a turbine's rotation in a wind field, and characterize vortices in conjunction with numerically simulated forces on the blade surfaces as these vortices strike another turbine's blades downstream. The scientifically relevant issue to be studied is the relationship between the extracted, approximate locations on the blades where vortices strike the blades and the forces that exist in those locations. This integrated approach is used to detect and analyze turbulent flow that causes local impact on the wind turbine blade structure. The results that we present are based on analyzing the wind and force field data sets generated by numerical simulations, and allow domain scientists to relate vortex-blade interactions with power output loss in turbines and turbine life-expectancy. Our methods have the potential to improve turbine design in order to save costs related to turbine operation and maintenance.

Modelling bucket excavation by finite element

NASA Astrophysics Data System (ADS)

Pecingina, O. M.

2015-11-01

Changes in geological components of the layers from lignite pits have an impact on the sustainability of the cup path elements and under the action of excavation force appear efforts leading to deformation of the entire assembly. Application of finite element method in the optimization of components leads to economic growth, to increase the reliability and durability of the studied machine parts thus the machine. It is obvious usefulness of knowledge the state of mechanical tensions that the designed piece or the assembly not to break under the action of tensions that must cope during operation. In the course of excavation work on all bucket cutting force components, the first coming into contact with the material being excavated cutting edge. Therefore in the study with finite element analysis is retained only cutting edge. To study the field of stress and strain on the cutting edge will be created geometric patterns for each type of cup this will be subject to static analysis. The geometric design retains the cutting edge shape and on this on the tooth cassette location will apply an areal force on the abutment tooth. The cutting edge real pattern is subjected to finite element study for the worst case of rock cutting by symmetrical and asymmetrical cups whose profile is different. The purpose of this paper is to determine the displacement and tensions field for both profiles considering the maximum force applied on the cutting edge and the depth of the cutting is equal with the width of the cutting edge of the tooth. It will consider the worst case when on the structure will act both the tangential force and radial force on the bucket profile. For determination of stress and strain field on the form design of cutting edge profile will apply maximum force assuming uniform distribution and on the edge surface force will apply a radial force. After geometric patterns discretization on the cutting knives and determining stress field, can be seen that at the rectangular profile appears the "clogging" phenomenon of the cutting edge and at the polygonal profile the point of application remains constant without going inside. From the finite element method done in this paper it can be concluded that the polygonal profiles made of dihedral angles are much more durable and asymmetric cups tend to have uniform tension along the entire perimeter.

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

PubMed

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

2014-09-16

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

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

NASA Astrophysics Data System (ADS)

Ding, Kun; Chan, C. T.

2018-04-01

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

Quenching and anisotropy of hydromagnetic turbulent transport

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

Karak, Bidya Binay; Brandenburg, Axel; Rheinhardt, Matthias

2014-11-01

Hydromagnetic turbulence affects the evolution of large-scale magnetic fields through mean-field effects like turbulent diffusion and the α effect. For stronger fields, these effects are usually suppressed or quenched, and additional anisotropies are introduced. Using different variants of the test-field method, we determine the quenching of the turbulent transport coefficients for the forced Roberts flow, isotropically forced non-helical turbulence, and rotating thermal convection. We see significant quenching only when the mean magnetic field is larger than the equipartition value of the turbulence. Expressing the magnetic field in terms of the equipartition value of the quenched flows, we obtain for themore » quenching exponents of the turbulent magnetic diffusivity about 1.3, 1.1, and 1.3 for Roberts flow, forced turbulence, and convection, respectively. However, when the magnetic field is expressed in terms of the equipartition value of the unquenched flows, these quenching exponents become about 4, 1.5, and 2.3, respectively. For the α effect, the exponent is about 1.3 for the Roberts flow and 2 for convection in the first case, but 4 and 3, respectively, in the second. In convection, the quenching of turbulent pumping follows the same power law as turbulent diffusion, while for the coefficient describing the Ω×J effect nearly the same quenching exponent is obtained as for α. For forced turbulence, turbulent diffusion proportional to the second derivative along the mean magnetic field is quenched much less, especially for larger values of the magnetic Reynolds number. However, we find that in corresponding axisymmetric mean-field dynamos with dominant toroidal field the quenched diffusion coefficients are the same for the poloidal and toroidal field constituents.« less

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

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

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

Casting the Coronal Magnetic Field Reconstruction Tools in 3D Using the MHD Bifrost Model

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

Fleishman, Gregory D.; Loukitcheva, Maria; Anfinogentov, Sergey

Quantifying the coronal magnetic field remains a central problem in solar physics. Nowadays, the coronal magnetic field is often modeled using nonlinear force-free field (NLFFF) reconstructions, whose accuracy has not yet been comprehensively assessed. Here we perform a detailed casting of the NLFFF reconstruction tools, such as π -disambiguation, photospheric field preprocessing, and volume reconstruction methods, using a 3D snapshot of the publicly available full-fledged radiative MHD model. Specifically, from the MHD model, we know the magnetic field vector in the entire 3D domain, which enables us to perform a “voxel-by-voxel” comparison of the restored and the true magnetic fieldsmore » in the 3D model volume. Our tests show that the available π -disambiguation methods often fail in the quiet-Sun areas dominated by small-scale magnetic elements, while they work well in the active region (AR) photosphere and (even better) chromosphere. The preprocessing of the photospheric magnetic field, although it does produce a more force-free boundary condition, also results in some effective “elevation” of the magnetic field components. This “elevation” height is different for the longitudinal and transverse components, which results in a systematic error in absolute heights in the reconstructed magnetic data cube. The extrapolations performed starting from the actual AR photospheric magnetogram are free from this systematic error, while other metrics are comparable with those for extrapolations from the preprocessed magnetograms. This finding favors the use of extrapolations from the original photospheric magnetogram without preprocessing. Our tests further suggest that extrapolations from a force-free chromospheric boundary produce measurably better results than those from a photospheric boundary.« less

General methods for determining the linear stability of coronal magnetic fields

NASA Technical Reports Server (NTRS)

Craig, I. J. D.; Sneyd, A. D.; Mcclymont, A. N.

1988-01-01

A time integration of a linearized plasma equation of motion has been performed to calculate the ideal linear stability of arbitrary three-dimensional magnetic fields. The convergence rates of the explicit and implicit power methods employed are speeded up by using sequences of cyclic shifts. Growth rates are obtained for Gold-Hoyle force-free equilibria, and the corkscrew-kink instability is found to be very weak.

General methods for determining the linear stability of coronal magnetic fields

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

Craig, I.J.D.; Sneyd, A.D.; McClymont, A.N.

1988-12-01

A time integration of a linearized plasma equation of motion has been performed to calculate the ideal linear stability of arbitrary three-dimensional magnetic fields. The convergence rates of the explicit and implicit power methods employed are speeded up by using sequences of cyclic shifts. Growth rates are obtained for Gold-Hoyle force-free equilibria, and the corkscrew-kink instability is found to be very weak. 19 references.

Scientific study of data analysis

NASA Technical Reports Server (NTRS)

Wu, S. T.

1990-01-01

We present a comparison between two numerical methods for the extrapolation of nonlinear force-free magnetic fields, the Iterative Method (IM) and the Progressive Extension Method (PEM). The advantages and disadvantages of these two methods are summarized and the accuracy and numerical instability are discussed. On the basis of this investigation, we claim that the two methods do resemble each other qualitatively.

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

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

PubMed Central

Marzinek, Jan K.; Lakshminarayanan, Rajamani; Goh, Eunice; Huber, Roland G.; Panzade, Sadhana; Verma, Chandra; Bond, Peter J.

2016-01-01

Conformational changes in the envelope proteins of flaviviruses help to expose the highly conserved fusion peptide (FP), a region which is critical to membrane fusion and host cell infection, and which represents a significant target for antiviral drugs and antibodies. In principle, extended timescale atomic-resolution simulations may be used to characterize the dynamics of such peptides. However, the resultant accuracy is critically dependent upon both the underlying force field and sufficient conformational sampling. In the present study, we report a comprehensive comparison of three simulation methods and four force fields comprising a total of more than 40 μs of sampling. Additionally, we describe the conformational landscape of the FP fold across all flavivirus family members. All investigated methods sampled conformations close to available X-ray structures, but exhibited differently populated ensembles. The best force field / sampling combination was sufficiently accurate to predict that the solvated peptide fold is less ordered than in the crystallographic state, which was subsequently confirmed via circular dichroism and spectrofluorometric measurements. Finally, the conformational landscape of a mutant incapable of membrane fusion was significantly shallower than wild-type variants, suggesting that dynamics should be considered when therapeutically targeting FP epitopes. PMID:26785994

Characterization of an induced pressure pumping force for microfluidics

NASA Astrophysics Data System (ADS)

Jiang, Hai; Fan, Na; Peng, Bei; Weng, Xuan

2017-05-01

The electro-osmotic pumping and pressure-driven manipulation of fluids are considered as the most common strategies in microfluidic devices. However, both of them exhibit major disadvantages such as hard integration and high reagent consumption, and they are destructive methods for detection and photo bleaching. In this paper, an electric field-effect flow control approach, combining the electro-osmotic pumping force and the pressure-driven pumping force, was developed to generate the induced pressure-driven flow in a T-shaped microfluidic chip. Electro-osmotic flow between the T-intersection and two reservoirs was demonstrated, and it provided a stable, continuous, and electric field-free flow in the section of the microchannel without the electrodes. The velocity of the induced pressure-driven flow was linearly proportional to the applied voltages. Both numerical and experimental investigations were conducted to prove the concept, and the experimental results showed good agreement with the numerical simulations. In comparison to other induced pressure pumping methods, this approach can induce a high and controllable pressure drop in the electric field-free segment, subsequently causing an induced pressure-driven flow for transporting particles or biological cells. In addition, the generation of bubbles and the blocking of the microchannel are avoided.

Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration.

PubMed

Huang, Jinfeng; Zhu, Yali; Sun, Bin; Yao, Yuan; Liu, Junjun

2016-03-01

The protonation state of the Asp dyad is important as it can reveal enzymatic mechanisms, and the information this provides can be used in the development of drugs for proteins such as memapsin 2 (BACE-1), HIV-1 protease, and rennin. Conventional molecular dynamics (MD) simulations have been successfully used to determine the preferred protonation state of the Asp dyad. In the present work, we demonstrate that the results obtained from conventional MD simulations can be greatly influenced by the particular force field applied or the values used for control parameters. In principle, free-energy changes between possible protonation states can be used to determine the protonation state. We show that protonation state prediction by the thermodynamic integration (TI) method is insensitive to force field version or to the cutoff for calculating nonbonded interactions (a control parameter). In the present study, the protonation state of the Asp dyad predicted by TI calculations was the same regardless of the force field and cutoff value applied. Contrary to the intuition that conventional MD is more efficient, our results clearly show that the TI method is actually more efficient and more reliable for determining the protonation state of the Asp dyad.

Disaggregation and separation dynamics of magnetic particles in a microfluidic flow under an alternating gradient magnetic field

NASA Astrophysics Data System (ADS)

Cao, Quanliang; Li, Zhenhao; Wang, Zhen; Qi, Fan; Han, Xiaotao

2018-05-01

How to prevent particle aggregation in the magnetic separation process is of great importance for high-purity separation, while it is a challenging issue in practice. In this work, we report a novel method to solve this problem for improving the selectivity of size-based separation by use of a gradient alternating magnetic field. The specially designed magnetic field is capable of dynamically adjusting the magnetic field direction without changing the direction of magnetic gradient force acting on the particles. Using direct numerical simulations, we show that particles within a certain center-to-center distance are inseparable under a gradient static magnetic field since they are easy aggregated and then start moving together. By contrast, it has been demonstrated that alternating repulsive and attractive interaction forces between particles can be generated to avoid the formation of aggregations when the alternating gradient magnetic field with a given alternating frequency is applied, enabling these particles to be continuously separated based on size-dependent properties. The proposed magnetic separation method and simulation results have the significance for fundamental understanding of particle dynamic behavior and improving the separation efficiency.

Anti-gravity with present technology - Implementation and theoretical foundation

NASA Astrophysics Data System (ADS)

Alzofon, F. E.

1981-07-01

This paper proposes a semi-empirical model of the processes leading to the gravitational field based on accepted features of subatomic processes. Through an analogy with methods of cryogenics, a method of decreasing (or increasing) the gravitational force on a vehicle, using presently-known technology, is suggested. Various ways of ultilizing this effect in vehicle propulsion are described. A unified field theory is then detailed which provides a more formal foundation for the gravitational field model first introduced. In distinction to the general theory of relativity, it features physical processes which generate the gravitational field.

Conceptual design of a Bitter-magnet toroidal-field system for the ZEPHYR Ignition Test Reactor

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

Williams, J.E.C.; Becker, H.D.; Bobrov, E.S.

1981-05-01

The following problems are described and discussed: (1) parametric studies - these studies examine among other things the interdependence of throat stresses, plasma parameters (margins of ignition) and stored energy. The latter is a measure of cost and is minimized in the present design; (2) magnet configuration - the shape of the plates are considered in detail including standard turns, turns located at beam ports, diagnostic and closure flanges; (3) ripple computation - this section describes the codes by which ripple is computed; (4) field diffusion and nuclear heating - the effect of magnetic field diffusion on heating is consideredmore » along with neutron heating. Current, field and temperature profiles are computed; (5) finite element analysis - the two and three dimensional finite element codes are described and the results discussed in detail; (6) structures engineering - this considers the calculation of critical stresses due to toroidal and overturning forces and discusses the method of constraint of these forces. The Materials Testing Program is also discussed; (7) fabrication - the methods available for the manufacture of the constituent parts of the Bitter plates, the method of assembly and remote maintenance are summarized.« less

Acoustic radiation force optical coherence elastography using vibro-acoustography

NASA Astrophysics Data System (ADS)

Qu, Yueqiao (.; Ma, Teng; Li, Rui; Qi, Wenjuan; Zhu, Jiang; He, Youmin; Shung, K. K.; Zhou, Qifa; Chen, Zhongping

2015-03-01

High-resolution elasticity mapping of tissue biomechanical properties is crucial in early detection of many diseases. We report a method of acoustic radiation force optical coherence elastography (ARF-OCE) based on the methods of vibroacoustography, which uses a dual-ring ultrasonic transducer in order to excite a highly localized 3-D field. The single element transducer introduced previously in our ARF imaging has low depth resolution because the ARF is difficult to discriminate along the entire ultrasound propagation path. The novel dual-ring approach takes advantage of two overlapping acoustic fields and a few-hundred-Hertz difference in the signal frequencies of the two unmodulated confocal ring transducers in order to confine the acoustic stress field within a smaller volume. This frequency difference is the resulting "beating" frequency of the system. The frequency modulation of the transducers has been validated by comparing the dual ring ARF-OCE measurement to that of the single ring using a homogeneous silicone phantom. We have compared and analyzed the phantom resonance frequency to show the feasibility of our approach. We also show phantom images of the ARF-OCE based vibro-acoustography method and map out its acoustic stress region. We concluded that the dual-ring transducer is able to better localize the excitation to a smaller region to induce a focused force, which allows for highly selective excitation of small regions. The beat-frequency elastography method has great potential to achieve high-resolution elastography for ophthalmology and cardiovascular applications.

Simulation on Thermocapillary-Driven Drop Coalescence by Hybrid Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Xie, Haiqiong; Zeng, Zhong; Zhang, Liangqi; Yokota, Yuui; Kawazoe, Yoshiyuki; Yoshikawa, Akira

2016-04-01

A hybrid two-phase model, incorporating lattice Boltzmann method (LBM) and finite difference method (FDM), was developed to investigate the coalescence of two drops during their thermocapillary migration. The lattice Boltzmann method with a multi-relaxation-time (MRT) collision model was applied to solve the flow field for incompressible binary fluids, and the method was implemented in an axisymmetric form. The deformation of the drop interface was captured with the phase-field theory, and the continuum surface force model (CSF) was adopted to introduce the surface tension, which depends on the temperature. Both phase-field equation and the energy equation were solved with the finite difference method. The effects of Marangoni number and Capillary numbers on the drop's motion and coalescence were investigated.

Axial and transverse acoustic radiation forces on a fluid sphere placed arbitrarily in Bessel beam standing wave tweezers

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

Mitri, F.G., E-mail: mitri@chevron.com

The axial and transverse radiation forces on a fluid sphere placed arbitrarily in the acoustical field of Bessel beams of standing waves are evaluated. The three-dimensional components of the time-averaged force are expressed in terms of the beam-shape coefficients of the incident field and the scattering coefficients of the fluid sphere using a partial-wave expansion (PWE) method. Examples are chosen for which the standing wave field is composed of either a zero-order (non-vortex) Bessel beam, or a first-order Bessel vortex beam. It is shown here, that both transverse and axial forces can push or pull the fluid sphere to anmore » equilibrium position depending on the chosen size parameter ka (where k is the wave-number and a the sphere’s radius). The corresponding results are of particular importance in biophysical applications for the design of lab-on-chip devices operating with Bessel beams standing wave tweezers. Moreover, potential investigations in acoustic levitation and related applications in particle rotation in a vortex beam may benefit from the results of this study. -- Highlights: •The axial and transverse forces on a fluid sphere in acoustical Bessel beams tweezers are evaluated. •The attraction or repulsion to an equilibrium position in the standing wave field is examined. •Potential applications are in particle manipulation using standing waves.« less

Computation of the acoustic radiation force using the finite-difference time-domain method.

PubMed

Cai, Feiyan; Meng, Long; Jiang, Chunxiang; Pan, Yu; Zheng, Hairong

2010-10-01

The computational details related to calculating the acoustic radiation force on an object using a 2-D grid finite-difference time-domain method (FDTD) are presented. The method is based on propagating the stress and velocity fields through the grid and determining the energy flow with and without the object. The axial and radial acoustic radiation forces predicted by FDTD method are in excellent agreement with the results obtained by analytical evaluation of the scattering method. In particular, the results indicate that it is possible to trap the steel cylinder in the radial direction by optimizing the width of Gaussian source and the operation frequency. As the sizes of the relating objects are smaller than or comparable to wavelength, the algorithm presented here can be easily extended to 3-D and include torque computation algorithms, thus providing a highly flexible and universally usable computation engine.

Lorentz force particle analyzer

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Thess, André; Moreau, René; Tan, Yanqing; Dai, Shangjun; Tao, Zhen; Yang, Wenzhi; Wang, Bo

2016-07-01

A new contactless technique is presented for the detection of micron-sized insulating particles in the flow of an electrically conducting fluid. A transverse magnetic field brakes this flow and tends to become entrained in the flow direction by a Lorentz force, whose reaction force on the magnetic-field-generating system can be measured. The presence of insulating particles suspended in the fluid produce changes in this Lorentz force, generating pulses in it; these pulses enable the particles to be counted and sized. A two-dimensional numerical model that employs a moving mesh method demonstrates the measurement principle when such a particle is present. Two prototypes and a three-dimensional numerical model are used to demonstrate the feasibility of a Lorentz force particle analyzer (LFPA). The findings of this study conclude that such an LFPA, which offers contactless and on-line quantitative measurements, can be applied to an extensive range of applications. These applications include measurements of the cleanliness of high-temperature and aggressive molten metal, such as aluminum and steel alloys, and the clean manufacturing of semiconductors.

Small strain multiphase-field model accounting for configurational forces and mechanical jump conditions

NASA Astrophysics Data System (ADS)

Schneider, Daniel; Schoof, Ephraim; Tschukin, Oleg; Reiter, Andreas; Herrmann, Christoph; Schwab, Felix; Selzer, Michael; Nestler, Britta

2018-03-01

Computational models based on the phase-field method have become an essential tool in material science and physics in order to investigate materials with complex microstructures. The models typically operate on a mesoscopic length scale resolving structural changes of the material and provide valuable information about the evolution of microstructures and mechanical property relations. For many interesting and important phenomena, such as martensitic phase transformation, mechanical driving forces play an important role in the evolution of microstructures. In order to investigate such physical processes, an accurate calculation of the stresses and the strain energy in the transition region is indispensable. We recall a multiphase-field elasticity model based on the force balance and the Hadamard jump condition at the interface. We show the quantitative characteristics of the model by comparing the stresses, strains and configurational forces with theoretical predictions in two-phase cases and with results from sharp interface calculations in a multiphase case. As an application, we choose the martensitic phase transformation process in multigrain systems and demonstrate the influence of the local homogenization scheme within the transition regions on the resulting microstructures.

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

PubMed

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

2005-01-01

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

Decay characteristics of electroadhesive forces by periodic electrodes in dielectric layers

NASA Astrophysics Data System (ADS)

Lee, Junseok; Cha, Youngsu

2017-07-01

Electroadhesive force is the force generated by induced dipoles in the gradient of an electric field. Owing to its benefits of mechanical characteristics and versatility, it is widely used to hold and manipulate objects in robotic applications. So far, most studies in this field have been focused on the maximization of the magnitude of electroadhesive force. In this paper, we focus on the decay characteristics of electroadhesive force depending on the spatial distance from electrodes to employ the force to precisely separate a single layer from stacked dielectric layers. It turns out that all configurations with periodically repeating electrodes' arrangement, have the same decay characteristics which significantly depend on the geometrical period of the electrode patterns. Also, we find that the other parameters including the applied voltage and geometry of electrodes have little effect on the decay characteristics. The electric potential of an arbitrary electrode configuration is expanded in terms of the Fourier series, and we use it to analytically prove the high dependence of decay characteristics on the geometrical period. Numerical analysis is performed using the finite element method.

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

PubMed

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

2016-02-01

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

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

PubMed

Shen, Lin; Hu, Hao

2014-06-10

We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

Trapping of a micro-bubble by non-paraxial Gaussian beam: computation using the FDTD method.

PubMed

Sung, Seung-Yong; Lee, Yong-Gu

2008-03-03

Optical forces on a micro-bubble were computed using the Finite Difference Time Domain method. Non-paraxial Gaussian beam equation was used to represent the incident laser with high numerical aperture, common in optical tweezers. The electromagnetic field distribution around a micro-bubble was computed using FDTD method and the electromagnetic stress tensor on the surface of a micro-bubble was used to compute the optical forces. By the analysis of the computational results, interesting relations between the radius of the circular trapping ring and the corresponding stability of the trap were found.

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.

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.

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

DTIC Science & Technology

1991-08-01

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

Solvent electronic polarization effects on a charge transfer excitation studied by the mean-field QM/MM method

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

Nakano, Hiroshi; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8245

2015-12-31

Electronic polarization effects of a medium can have a significant impact on a chemical reaction in condensed phases. We discuss the effects on the charge transfer excitation of a chromophore, N,N-dimethyl-4-nitroaniline, in various solvents using the mean-field QM/MM method with a polarizable force field. The results show that the explicit consideration of the solvent electronic polarization effects is important especially for a solvent with a low dielectric constant when we study the solvatochromism of the chromophore.

Measurement of circulation around wing-tip vortices and estimation of lift forces using stereo PIV

NASA Astrophysics Data System (ADS)

Asano, Shinichiro; Sato, Haru; Sakakibara, Jun

2017-11-01

Applying the flapping flight to the development of an aircraft as Mars space probe and a small aircraft called MAV (Micro Air Vehicle) is considered. This is because Reynolds number assumed as the condition of these aircrafts is low and similar to of insects and small birds flapping on the earth. However, it is difficult to measure the flow around the airfoil in flapping flight directly because of its three-dimensional and unsteady characteristics. Hence, there is an attempt to estimate the flow field and aerodynamics by measuring the wake of the airfoil using PIV, for example the lift estimation method based on a wing-tip vortex. In this study, at the angle of attack including the angle after stall, we measured the wing-tip vortex of a NACA 0015 cross-sectional and rectangular planform airfoil using stereo PIV. The circulation of the wing-tip vortex was calculated from the obtained velocity field, and the lift force was estimated based on Kutta-Joukowski theorem. Then, the validity of this estimation method was examined by comparing the estimated lift force and the force balance data at various angles of attack. The experiment results are going to be presented in the conference.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

PubMed

Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

2013-12-01

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. Copyright © 2013 Wiley Periodicals, Inc.

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

PubMed

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

2015-04-13

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

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

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.

A triangular prism solid and shell interactive mapping element for electromagnetic sheet metal forming process

NASA Astrophysics Data System (ADS)

Cui, Xiangyang; Li, She; Feng, Hui; Li, Guangyao

2017-05-01

In this paper, a novel triangular prism solid and shell interactive mapping element is proposed to solve the coupled magnetic-mechanical formulation in electromagnetic sheet metal forming process. A linear six-node "Triprism" element is firstly proposed for transient eddy current analysis in electromagnetic field. In present "Triprism" element, shape functions are given explicitly, and a cell-wise gradient smoothing operation is used to obtain the gradient matrices without evaluating derivatives of shape functions. In mechanical field analysis, a shear locking free triangular shell element is employed in internal force computation, and a data mapping method is developed to transfer the Lorentz force on solid into the external forces suffered by shell structure for dynamic elasto-plasticity deformation analysis. Based on the deformed triangular shell structure, a "Triprism" element generation rule is established for updated electromagnetic analysis, which means inter-transformation of meshes between the coupled fields can be performed automatically. In addition, the dynamic moving mesh is adopted for air mesh updating based on the deformation of sheet metal. A benchmark problem is carried out for confirming the accuracy of the proposed "Triprism" element in predicting flux density in electromagnetic field. Solutions of several EMF problems obtained by present work are compared with experiment results and those of traditional method, which are showing excellent performances of present interactive mapping element.

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.

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

Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

PubMed

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO 2 , without fitting to experimental data.

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase.

PubMed

De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris

2011-07-30

4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.

Numerical simulation of forced convection in a duct subjected to microwave heating

NASA Astrophysics Data System (ADS)

Zhu, J.; Kuznetsov, A. V.; Sandeep, K. P.

2007-01-01

In this paper, forced convection in a rectangular duct subjected to microwave heating is investigated. Three types of non-Newtonian liquids flowing through the duct are considered, specifically, apple sauce, skim milk, and tomato sauce. A finite difference time domain method is used to solve Maxwell’s equations simulating the electromagnetic field. The three-dimensional temperature field is determined by solving the coupled momentum, energy, and Maxwell’s equations. Numerical results show that the heating pattern strongly depends on the dielectric properties of the fluid in the duct and the geometry of the microwave heating system.

Refined tip preparation by electrochemical etching and ultrahigh vacuum treatment to obtain atomically sharp tips for scanning tunneling microscope and atomic force microscope.

PubMed

Hagedorn, Till; El Ouali, Mehdi; Paul, William; Oliver, David; Miyahara, Yoichi; Grütter, Peter

2011-11-01

A modification of the common electrochemical etching setup is presented. The described method reproducibly yields sharp tungsten tips for usage in the scanning tunneling microscope and tuning fork atomic force microscope. In situ treatment under ultrahigh vacuum (p ≤10(-10) mbar) conditions for cleaning and fine sharpening with minimal blunting is described. The structure of the microscopic apex of these tips is atomically resolved with field ion microscopy and cross checked with field emission. © 2011 American Institute of Physics

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

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

1992-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1996-01-01

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

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

PubMed Central

Karniel, Amir; Nisky, Ilana

2015-01-01

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

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

PubMed

Leib, Raz; Karniel, Amir; Nisky, Ilana

2015-05-01

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

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

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

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

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

2014-01-01

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

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

DOE PAGES

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

2016-03-04

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

Induction of cell death by magnetic particles in response to a gradient magnetic field inside a uniform magnetic field

NASA Astrophysics Data System (ADS)

Amaya-Jaramillo, Carlos David; Pérez-Portilla, Adriana Patricia; Serrano-Olmedo, José Javier; Ramos-Gómez, Milagros

2017-10-01

A new instrument based on a magnetic force produced by an alternating magnetic field gradient, which is obtained through Maxwell coils, inside a constant field magnet has been designed and used to produce cell death. We have determined the interaction of microparticles and cells under different conditions such as incubation time with microparticles, particle size, magnetic field exposition time, and different current waveforms at different frequencies to produce a magnetic field gradient. We determined that the highest rate of cell death occurs at a frequency of 1 Hz with a square waveform and 1 h of irradiation. This method could be of great interest to remove cancer cells due mainly to the alterations in stiffness observed in the membranes of the tumor cells. Cancer cells can be eliminated in response to the forces caused by the movement of magnetic nanoparticles of the appropriate size under the application of a specific magnetic field. [Figure not available: see fulltext.

Robot Training With Vector Fields Based on Stroke Survivors' Individual Movement Statistics.

PubMed

Wright, Zachary A; Lazzaro, Emily; Thielbar, Kelly O; Patton, James L; Huang, Felix C

2018-02-01

The wide variation in upper extremity motor impairments among stroke survivors necessitates more intelligent methods of customized therapy. However, current strategies for characterizing individual motor impairments are limited by the use of traditional clinical assessments (e.g., Fugl-Meyer) and simple engineering metrics (e.g., goal-directed performance). Our overall approach is to statistically identify the range of volitional movement capabilities, and then apply a robot-applied force vector field intervention that encourages under-expressed movements. We investigated whether explorative training with such customized force fields would improve stroke survivors' (n = 11) movement patterns in comparison to a control group that trained without forces (n = 11). Force and control groups increased Fugl-Meyer UE scores (average of 1.0 and 1.1, respectively), which is not considered clinically meaningful. Interestingly, participants from both groups demonstrated dramatic increases in their range of velocity during exploration following only six days of training (average increase of 166.4% and 153.7% for the Force and Control group, respectively). While both groups showed evidence of improvement, we also found evidence that customized forces affected learning in a systematic way. When customized forces were active, we observed broader distributions of velocity that were not present in the controls. Second, we found that these changes led to specific changes in unassisted motion. In addition, while the shape of movement distributions changed significantly for both groups, detailed analysis of the velocity distributions revealed that customized forces promoted a greater proportion of favorable changes. Taken together, these results provide encouraging evidence that patient-specific force fields based on individuals' movement statistics can be used to create new movement patterns and shape them in a customized manner. To the best of our knowledge, this paper is the first to directly link engineering assessments of stroke survivors' exploration movement behaviors to the design of customized robot therapy.

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

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Accuracy of State-of-the-Art Actuator-Line Modeling for Wind Turbine Wakes

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

Jha, Pankaj; Churchfield, Matthew; Moriarty, Patrick

The current actuator line method (ALM) within an OpenFOAM computational fluid dynamics (CFD) solver was used to perform simulations of the NREL Phase VI rotor under rotating and parked conditions, two fixed-wing designs both with an elliptic spanwise loading, and the NREL 5-MW turbine. The objective of this work is to assess and improve the accuracy of the state-of-the-art ALM in predicting rotor blade loads, particularly by focusing on the method used to project the actuator forces onto the flow field as body forces. Results obtained for sectional normal and tangential force coefficients were compared to available experimental data andmore » to the in-house performance code XTurb-PSU. It was observed that the ALM results agree well with measured data and results obtained from XTurb-PSU except in the root and tip regions if a three-dimensional Gaussian of width, ε, constant along the blade span is used to project the actuator force onto the flow field. A new method is proposed where the Gaussian width, ε, varies along the blade span following an elliptic distribution. A general criterion is derived that applies to any planform shape. It is found that the new criterion for ε leads to improved prediction of blade tip loads for a variety of blade planforms and rotor conditions considered.« less

Dissolved organic carbon--contaminant interaction descriptors found by 3D force field calculations.

PubMed

Govers, H A J; Krop, H B; Parsons, J R; Tambach, T; Kubicki, J D

2002-03-01

Enthalpies of transfer at 300 K of various partitioning processes were calculated in order to study the suitability of 3D force fields for the calculation of partitioning constants. A 3D fulvic acid (FA) model of dissolved organic carbon (DOC) was built in a MM+ force field using AMI atomic charges and geometrical optimization (GO). 3,5-Dichlorobiphenyl (PCB14), 4,4'-dichlorobiphenyl (PCB15), 1,1,1-trichloro-2,2-bis-(4-chlorophenyl)-ethane (PPDDT) and 2-chloro-4-ethylamino-6-isopropylamino-s-triazine (Atrazine) were inserted into different sites and their interaction energies with FA were calculated. Energies of hydration were calculated and subtracted from FA-contaminant interactions of selected sites. The resulting values for the enthalpies of transfer from water to DOC were 2.8, -1.4, -6.4 and 0.0 kcal/mol for PCB 14, PCB15, PPDDT and Atrazine, respectively. The value of PPDDT compared favorably with the experimental value of -5.0 kcal/mol. Prior to this, the method was studied by the calculation of the enthalpies of vaporization and aqueous solution using various force fields. In the MM + force field GO predicted enthalpies of vaporization deviated by +0.7 (PCB14), +3.6 (PCB15) and -0.7 (PPDDT)kcal/mol from experimental data, whereas enthalpies of aqueous solution deviated by -3.6 (PCB14), +5.8 (PCB15) and +3.7 (PPDDT) kcal/mol. Only for PCB14 the wrong sign of this enthalpy value was predicted. Potential advantages and limitations of the approach were discussed.

Inverse tissue mechanics of cell monolayer expansion.

PubMed

Kondo, Yohei; Aoki, Kazuhiro; Ishii, Shin

2018-03-01

Living tissues undergo deformation during morphogenesis. In this process, cells generate mechanical forces that drive the coordinated cell motion and shape changes. Recent advances in experimental and theoretical techniques have enabled in situ measurement of the mechanical forces, but the characterization of mechanical properties that determine how these forces quantitatively affect tissue deformation remains challenging, and this represents a major obstacle for the complete understanding of morphogenesis. Here, we proposed a non-invasive reverse-engineering approach for the estimation of the mechanical properties, by combining tissue mechanics modeling and statistical machine learning. Our strategy is to model the tissue as a continuum mechanical system and to use passive observations of spontaneous tissue deformation and force fields to statistically estimate the model parameters. This method was applied to the analysis of the collective migration of Madin-Darby canine kidney cells, and the tissue flow and force were simultaneously observed by the phase contrast imaging and traction force microscopy. We found that our monolayer elastic model, whose elastic moduli were reverse-engineered, enabled a long-term forecast of the traction force fields when given the tissue flow fields, indicating that the elasticity contributes to the evolution of the tissue stress. Furthermore, we investigated the tissues in which myosin was inhibited by blebbistatin treatment, and observed a several-fold reduction in the elastic moduli. The obtained results validate our framework, which paves the way to the estimation of mechanical properties of living tissues during morphogenesis.

Continuous micro-feeding of fine cohesive powders actuated by pulse inertia force and acoustic radiation force in ultrasonic standing wave field.

PubMed

Wang, Hongcheng; Wu, Liqun; Zhang, Ting; Chen, Rangrang; Zhang, Linan

2018-07-10

Stable continuous micro-feeding of fine cohesive powders has recently gained importance in many fields. However, it remains a great challenge in practice because of the powder aggregate caused by interparticle cohesive forces in small capillaries. This paper describes a novel method of feeding fine cohesive powder actuated by a pulse inertia force and acoustic radiation force simultaneously in an ultrasonic standing wave field using a tapered glass nozzle. Nozzles with different outlet diameters are fabricated using glass via a heating process. A pulse inertia force is excited to drive powder movement to the outlet section of the nozzle in a consolidated columnar rod mode. An acoustic radiation force is generated to suspend the particles and make the rod break into large quantities of small agglomerates which impact each other randomly. So the aggregation phenomenon in the fluidization of cohesive powders can be eliminated. The suspended powder is discharged continuously from the nozzle orifice owing to the self-gravities and collisions between the inner particles. The micro-feeding rates can be controlled accurately and the minimum values for RespitoseSV003 and Granulac230 are 0.4 mg/s and 0.5 mg/s respectively. The relative standard deviations of all data points are below 0.12, which is considerably smaller than those of existing vibration feeders with small capillaries. Copyright © 2018 Elsevier B.V. All rights reserved.

Electro-hydrodynamic force field and flow patterns generated by a DC corona discharge in the air

NASA Astrophysics Data System (ADS)

Monrolin, Nicolas; Plouraboue, Franck; Praud, Olivier

2016-11-01

Ionic wind refers to the electro-convection of ionised air between high voltage electrodes. Microscopic ion-neutral collisions are responsible for momentum transfer from accelerated ions, subjected to the electric field, to the neutral gas molecules resulting in a macroscopic airflow acceleration. In the past decades it has been investigated for various purposes from food drying through aerodynamic flow control and eventually laptop cooling. One consequence of air acceleration between the electrodes is thrust generation, often referred to as the Biefeld-Brown effect or electro-hydrodynamic thrust. In this experimental study, the ionic wind velocity field is measured with the PIV method. From computing the acceleration of the air we work out the electrostatic force field for various electrodes configurations. This enables an original direct evaluation of the force distribution as well as the influence of electrodes shape and position. Thrust computation based on the flow acceleration are compared with digital scale measurements. Complex flow features are highlighted such as vortex shedding, indicating that aerodynamic effects may play a significant role. Furthermore, the aerodynamic drag force exerted on the electrodes is quantified by choosing an appropriate control volume. Authors thank Region Midi-Pyrenee and CNES Launcher Directorate for financial support.

Evaluating the far-field sound of a turbulent jet with one-way Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Pickering, Ethan; Rigas, Georgios; Towne, Aaron; Colonius, Tim

2017-11-01

The one-way Navier-Stokes (OWNS) method has shown promising ability to predict both near field coherent structures (i.e. wave packets) and far field acoustics of turbulent jets while remaining computationally efficient through implementation of a spatial marching scheme. Considering the speed and relative accuracy of OWNS, a predictive model for various jet configurations may be conceived and applied for noise control. However, there still remain discrepancies between OWNS and large eddy simulation (LES) databases which may be linked to the previous neglect of nonlinear forcing. Therefore, to better predict wave packets and far field acoustics, this study investigates the effect of nonlinear forcing terms derived from high-fidelity LES databases. The results of the nonlinear forcings are evaluated for several azimuthal modes and frequencies, as well as compared to LES derived acoustics using spectral proper orthogonal decomposition (SPOD). This research was supported by the Department of Defense (DoD) through the Office of Naval Research (Grant No. N00014-16-1-2445) and the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.

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

PubMed

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

2015-07-15

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

Convection Induced by Traveling Magnetic Fields in Semiconductor Melts

NASA Technical Reports Server (NTRS)

Konstantin, Mazuruk

2000-01-01

Axisymmetric traveling magnetic fields (TMF) can be beneficial for crystal growth applications. such as the vertical Bridgman, float zone or traveling heater methods. TMF induces a basic flow in the form of a single roll. This type of flow can enhance mass and heat transfer to the growing crystal. More importantly, the TMF Lorentz body force induced in the system can counterbalance the buoyancy forces, so the resulting convection can be much smaller and even the direction of it can be changed. In this presentation, we display basic features of this novel technique. In particular, numerical calculations of the Lorentz force for arbitrary frequencies will be presented along with induced steady-state fluid flow profiles. Also, numerical modeling of the TMF counter-balancing natural convection in vertical Bridgman systems will be demonstrated.

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

NASA Astrophysics Data System (ADS)

Ohnishi, Teruaki

2016-08-01

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

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Modelling landscape change in paddy fields using logistic regression and GIS

NASA Astrophysics Data System (ADS)

Franjaya, E. E.; Syartinilia; Setiawan, Y.

2018-05-01

Paddy field in karawang district, as an important agricultural land in west java, has been decreased since 1994. From previous study, paddy fields dominantly turned into built area. The changes were almost occured in the middle area of the district where roadways, industries, settlements, and commercial buildings were existed. These were estimated as driving forces. But, we still need to prove it. This study aimed to construct the paddy field probability change model, subsequently the driving forces will be obtained. GIS combined with logistic regression using environmental variables were used as main method in this study. Ten environmental variables were elevation 0–500 m, elevation>500 m, slope<8%, slope>8%, CBD, build up area, river, irrigation, toll and national roadway, and collector and local roadway. The result indicated that four variables were significantly played as driving forces (slope>8%, CBD area, build up area, and collector and local roadway). Paddy field has high, medium, and low probability to change which covered about 27.8%, 7.8%, and 64.4% area in Karawang respectively. Based on landscape ecology, the recommendation that suitable with landscape change is adaptive management.

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

Chifu, Iulia; Wiegelmann, Thomas; Inhester, Bernd, E-mail: chifu@mps.mpg.de

Insights into the 3D structure of the solar coronal magnetic field have been obtained in the past by two completely different approaches. The first approach are nonlinear force-free field (NLFFF) extrapolations, which use photospheric vector magnetograms as boundary condition. The second approach uses stereoscopy of coronal magnetic loops observed in EUV coronal images from different vantage points. Both approaches have their strengths and weaknesses. Extrapolation methods are sensitive to noise and inconsistencies in the boundary data, and the accuracy of stereoscopy is affected by the ability of identifying the same structure in different images and by the separation angle betweenmore » the view directions. As a consequence, for the same observational data, the 3D coronal magnetic fields computed with the two methods do not necessarily coincide. In an earlier work (Paper I) we extended our NLFFF optimization code by including stereoscopic constrains. The method was successfully tested with synthetic data, and within this work, we apply the newly developed code to a combined data set from SDO /HMI, SDO /AIA, and the two STEREO spacecraft. The extended method (called S-NLFFF) contains an additional term that monitors and minimizes the angle between the local magnetic field direction and the orientation of the 3D coronal loops reconstructed by stereoscopy. We find that when we prescribe the shape of the 3D stereoscopically reconstructed loops, the S-NLFFF method leads to a much better agreement between the modeled field and the stereoscopically reconstructed loops. We also find an appreciable decrease by a factor of two in the angle between the current and the magnetic field. This indicates the improved quality of the force-free solution obtained by S-NLFFF.« less

Minor loop dependence of the magnetic forces and stiffness in a PM-HTS levitation system

NASA Astrophysics Data System (ADS)

Yang, Yong; Li, Chengshan

2017-12-01

Based upon the method of current vector potential and the critical state model of Bean, the vertical and lateral forces with different sizes of minor loop are simulated in two typical cooling conditions when a rectangular permanent magnet (PM) above a cylindrical high temperature superconductor (HTS) moves vertically and horizontally. The different values of average magnetic stiffness are calculated by various sizes of minor loop changing from 0.1 to 2 mm. The magnetic stiffness with zero traverse is obtained by using the method of linear extrapolation. The simulation results show that the extreme values of forces decrease with increasing size of minor loop. The magnetic hysteresis of the force curves also becomes small as the size of minor loop increases. This means that the vertical and lateral forces are significantly influenced by the size of minor loop because the forces intensely depend on the moving history of the PM. The vertical stiffness at every vertical position when the PM vertically descends to 1 mm is larger than that as the PM vertically ascents to 30 mm. When the PM moves laterally, the lateral stiffness during the PM passing through any horizontal position in the first time almost equal to the value during the PM passing through the same position in the second time in zero-field cooling (ZFC), however, the lateral stiffness in field cooling (FC) and the cross stiffness in ZFC and FC are significantly affected by the moving history of the PM.

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.

On the stress calculation within phase-field approaches: a model for finite deformations

NASA Astrophysics Data System (ADS)

Schneider, Daniel; Schwab, Felix; Schoof, Ephraim; Reiter, Andreas; Herrmann, Christoph; Selzer, Michael; Böhlke, Thomas; Nestler, Britta

2017-08-01

Numerical simulations based on phase-field methods are indispensable in order to investigate interesting and important phenomena in the evolution of microstructures. Microscopic phase transitions are highly affected by mechanical driving forces and therefore the accurate calculation of the stresses in the transition region is essential. We present a method for stress calculations within the phase-field framework, which satisfies the mechanical jump conditions corresponding to sharp interfaces, although the sharp interface is represented as a volumetric region using the phase-field approach. This model is formulated for finite deformations, is independent of constitutive laws, and allows using any type of phase inherent inelastic strains.

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

PubMed

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

2010-05-11

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

Acoustophoretic separation of airborne millimeter-size particles by a Fresnel lens.

PubMed

Cicek, Ahmet; Korozlu, Nurettin; Adem Kaya, Olgun; Ulug, Bulent

2017-03-02

We numerically demonstrate acoustophoretic separation of spherical solid particles in air by means of an acoustic Fresnel lens. Beside gravitational and drag forces, freely-falling millimeter-size particles experience large acoustic radiation forces around the focus of the lens, where interplay of forces lead to differentiation of particle trajectories with respect to either size or material properties. Due to the strong acoustic field at the focus, radiation force can divert particles with source intensities significantly smaller than those required for acoustic levitation in a standing field. When the lens is designed to have a focal length of 100 mm at 25 kHz, finite-element method simulations reveal a sharp focus with a full-width at half-maximum of 0.5 wavelenghts and a field enhancement of 18 dB. Through numerical calculation of forces and simulation of particle trajectories, we demonstrate size-based separation of acrylic particles at a source sound pressure level of 153 dB such that particles with diameters larger than 0.5 mm are admitted into the central hole, whereas smaller particles are rejected. Besides, efficient separation of particles with similar acoustic properties such as polyethylene, polystyrene and acrylic particles of the same size is also demonstrated.

Acoustophoretic separation of airborne millimeter-size particles by a Fresnel lens

NASA Astrophysics Data System (ADS)

Cicek, Ahmet; Korozlu, Nurettin; Adem Kaya, Olgun; Ulug, Bulent

2017-03-01

We numerically demonstrate acoustophoretic separation of spherical solid particles in air by means of an acoustic Fresnel lens. Beside gravitational and drag forces, freely-falling millimeter-size particles experience large acoustic radiation forces around the focus of the lens, where interplay of forces lead to differentiation of particle trajectories with respect to either size or material properties. Due to the strong acoustic field at the focus, radiation force can divert particles with source intensities significantly smaller than those required for acoustic levitation in a standing field. When the lens is designed to have a focal length of 100 mm at 25 kHz, finite-element method simulations reveal a sharp focus with a full-width at half-maximum of 0.5 wavelenghts and a field enhancement of 18 dB. Through numerical calculation of forces and simulation of particle trajectories, we demonstrate size-based separation of acrylic particles at a source sound pressure level of 153 dB such that particles with diameters larger than 0.5 mm are admitted into the central hole, whereas smaller particles are rejected. Besides, efficient separation of particles with similar acoustic properties such as polyethylene, polystyrene and acrylic particles of the same size is also demonstrated.

Acoustophoretic separation of airborne millimeter-size particles by a Fresnel lens

PubMed Central

Cicek, Ahmet; Korozlu, Nurettin; Adem Kaya, Olgun; Ulug, Bulent

2017-01-01

We numerically demonstrate acoustophoretic separation of spherical solid particles in air by means of an acoustic Fresnel lens. Beside gravitational and drag forces, freely-falling millimeter-size particles experience large acoustic radiation forces around the focus of the lens, where interplay of forces lead to differentiation of particle trajectories with respect to either size or material properties. Due to the strong acoustic field at the focus, radiation force can divert particles with source intensities significantly smaller than those required for acoustic levitation in a standing field. When the lens is designed to have a focal length of 100 mm at 25 kHz, finite-element method simulations reveal a sharp focus with a full-width at half-maximum of 0.5 wavelenghts and a field enhancement of 18 dB. Through numerical calculation of forces and simulation of particle trajectories, we demonstrate size-based separation of acrylic particles at a source sound pressure level of 153 dB such that particles with diameters larger than 0.5 mm are admitted into the central hole, whereas smaller particles are rejected. Besides, efficient separation of particles with similar acoustic properties such as polyethylene, polystyrene and acrylic particles of the same size is also demonstrated. PMID:28252033

AN IN SILICO INVESTIGATION OF THE ENANTIOSELECTIVE METABOLISM RATES OF TRIAZOLE FUGICIDES

EPA Science Inventory

The objective of this work is to use in silico methods such as ab initio quantum and classical force-field methods to explore and develop an understanding for the enantioselective metabolism rates experimentally observed in the triazole fungicide bromuconazole. This directed stud...

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

NASA Astrophysics Data System (ADS)

Liwo, Adam; Czaplewski, Cezary; Pillardy, Jarosław; Scheraga, Harold A.

2001-08-01

A general method to derive site-site or united-residue potentials is presented. The basic principle of the method is the separation of the degrees of freedom of a system into the primary and secondary ones. The primary degrees of freedom describe the basic features of the system, while the secondary ones are averaged over when calculating the potential of mean force, which is hereafter referred to as the restricted free energy (RFE) function. The RFE can be factored into one-, two-, and multibody terms, using the cluster-cumulant expansion of Kubo. These factors can be assigned the functional forms of the corresponding lowest-order nonzero generalized cumulants, which can, in most cases, be evaluated analytically, after making some simplifying assumptions. This procedure to derive coarse-grain force fields is very valuable when applied to multibody terms, whose functional forms are hard to deduce in another way (e.g., from structural databases). After the functional forms have been derived, they can be parametrized based on the RFE surfaces of model systems obtained from all-atom models or on the statistics derived from structural databases. The approach has been applied to our united-residue force field for proteins. Analytical expressions were derived for the multibody terms pertaining to the correlation between local and electrostatic interactions within the polypeptide backbone; these expressions correspond to up to sixth-order terms in the cumulant expansion of the RFE. These expressions were subsequently parametrized by fitting to the RFEs of selected peptide fragments, calculated with the empirical conformational energy program for peptides force field. The new multibody terms enable not only the heretofore predictable α-helical segments, but also regular β-sheets, to form as the lowest-energy structures, as assessed by test calculations on a model helical protein A, as well as a model 20-residue polypeptide (betanova); the latter was not possible without introducing these new terms.

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

USDA-ARS?s Scientific Manuscript database

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

Path planning for mobile robot using the novel repulsive force algorithm

NASA Astrophysics Data System (ADS)

Sun, Siyue; Yin, Guoqiang; Li, Xueping

2018-01-01

A new type of repulsive force algorithm is proposed to solve the problem of local minimum and the target unreachable of the classic Artificial Potential Field (APF) method in this paper. The Gaussian function that is related to the distance between the robot and the target is added to the traditional repulsive force, solving the problem of the goal unreachable with the obstacle nearby; variable coefficient is added to the repulsive force component to resize the repulsive force, which can solve the local minimum problem when the robot, the obstacle and the target point are in the same line. The effectiveness of the algorithm is verified by simulation based on MATLAB and actual mobile robot platform.

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

PubMed

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

2016-03-15

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

An assessment of mean-field mixed semiclassical approaches: Equilibrium populations and algorithm stability

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

Bellonzi, Nicole; Jain, Amber; Subotnik, Joseph E.

2016-04-21

We study several recent mean-field semiclassical dynamics methods, focusing on the ability to recover detailed balance for long time (equilibrium) populations. We focus especially on Miller and Cotton’s [J. Phys. Chem. A 117, 7190 (2013)] suggestion to include both zero point electronic energy and windowing on top of Ehrenfest dynamics. We investigate three regimes: harmonic surfaces with weak electronic coupling, harmonic surfaces with strong electronic coupling, and anharmonic surfaces with weak electronic coupling. In most cases, recent additions to Ehrenfest dynamics are a strong improvement upon mean-field theory. However, for methods that include zero point electronic energy, we show thatmore » anharmonic potential energy surfaces often lead to numerical instabilities, as caused by negative populations and forces. We also show that, though the effect of negative forces can appear hidden in harmonic systems, the resulting equilibrium limits do remain dependent on any windowing and zero point energy parameters.« less

UAV formation control design with obstacle avoidance in dynamic three-dimensional environment.

PubMed

Chang, Kai; Xia, Yuanqing; Huang, Kaoli

2016-01-01

This paper considers the artificial potential field method combined with rotational vectors for a general problem of multi-unmanned aerial vehicle (UAV) systems tracking a moving target in dynamic three-dimensional environment. An attractive potential field is generated between the leader and the target. It drives the leader to track the target based on the relative position of them. The other UAVs in the formation are controlled to follow the leader by the attractive control force. The repulsive force affects among the UAVs to avoid collisions and distribute the UAVs evenly on the spherical surface whose center is the leader-UAV. Specific orders or positions of the UAVs are not required. The trajectories of avoidance obstacle can be obtained through two kinds of potential field with rotation vectors. Every UAV can choose the optimal trajectory to avoid the obstacle and reconfigure the formation after passing the obstacle. Simulations study on UAV are presented to demonstrate the effectiveness of proposed method.

Vertical electrostatic force in MEMS cantilever IR sensor

NASA Astrophysics Data System (ADS)

Rezadad, Imen; Boroumand Azad, Javaneh; Smith, Evan M.; Alhasan, Ammar; Peale, Robert E.

2014-06-01

A MEMS cantilever IR detector that repetitively lifts from the surface under the influence of a saw-tooth electrostatic force, where the contact duty cycle is a measure of the absorbed IR radiation, is analyzed. The design is comprised of three parallel conducting plates. Fixed buried and surface plates are held at opposite potential. A moveable cantilever is biased the same as the surface plate. Calculations based on energy methods with position-dependent capacity and electrostatic induction coefficients demonstrate the upward sign of the force on the cantilever and determine the force magnitude. 2D finite element method calculations of the local fields confirm the sign of the force and determine its distribution across the cantilever. The upward force is maximized when the surface plate is slightly larger than the other two. The electrostatic repulsion is compared with Casimir sticking force to determine the maximum useful contact area. MEMS devices were fabricated and the vertical displacement of the cantilever was observed in a number of experiments. The approach may be applied also to MEMS actuators and micromirrors.

Thickness dependence of the levitation performance of double-layer high-temperature superconductor bulks above a magnetic rail

NASA Astrophysics Data System (ADS)

Sun, R. X.; Zheng, J.; Liao, X. L.; Che, T.; Gou, Y. F.; He, D. B.; Deng, Z. G.

2014-10-01

A double-layer high-temperature superconductor (HTSC) arrangement was proposed and proved to be able to bring improvements to both levitation force and guidance force compared with present single-layer HTSC arrangement. To fully exploit the applied magnetic field by a magnetic rail, the thickness dependence of a double-layer HTSC arrangement on the levitation performance was further investigated in the paper. In this study, the lower-layer bulk was polished step by step to different thicknesses, and the upper-layer bulk with constant thickness was directly superimposed on the lower-layer one. The levitation force and the force relaxation of the double-layer HTSC arrangement were measured above a Halbach magnetic rail. Experimental result shows that a bigger levitation force and a less levitation force decay could be achieved by optimizing the thickness of the lower-layer bulk HTSC. This thickness optimization method could be applied together with former reported double-layer HTSC arrangement method with aligned growth sector boundaries pattern. This series of study on the optimized combination method do bring a significant improvement on the levitation performance of present HTS maglev systems.

Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm.

PubMed

Wu, Guosheng; Robertson, Daniel H; Brooks, Charles L; Vieth, Michal

2003-10-01

The influence of various factors on the accuracy of protein-ligand docking is examined. The factors investigated include the role of a grid representation of protein-ligand interactions, the initial ligand conformation and orientation, the sampling rate of the energy hyper-surface, and the final minimization. A representative docking method is used to study these factors, namely, CDOCKER, a molecular dynamics (MD) simulated-annealing-based algorithm. A major emphasis in these studies is to compare the relative performance and accuracy of various grid-based approximations to explicit all-atom force field calculations. In these docking studies, the protein is kept rigid while the ligands are treated as fully flexible and a final minimization step is used to refine the docked poses. A docking success rate of 74% is observed when an explicit all-atom representation of the protein (full force field) is used, while a lower accuracy of 66-76% is observed for grid-based methods. All docking experiments considered a 41-member protein-ligand validation set. A significant improvement in accuracy (76 vs. 66%) for the grid-based docking is achieved if the explicit all-atom force field is used in a final minimization step to refine the docking poses. Statistical analysis shows that even lower-accuracy grid-based energy representations can be effectively used when followed with full force field minimization. The results of these grid-based protocols are statistically indistinguishable from the detailed atomic dockings and provide up to a sixfold reduction in computation time. For the test case examined here, improving the docking accuracy did not necessarily enhance the ability to estimate binding affinities using the docked structures. Copyright 2003 Wiley Periodicals, Inc.

A theoretical method for the analysis and design of axisymmetric bodies. [flow distribution and incompressible fluids

NASA Technical Reports Server (NTRS)

Beatty, T. D.

1975-01-01

A theoretical method is presented for the computation of the flow field about an axisymmetric body operating in a viscous, incompressible fluid. A potential flow method was used to determine the inviscid flow field and to yield the boundary conditions for the boundary layer solutions. Boundary layer effects in the forces of displacement thickness and empirically modeled separation streamlines are accounted for in subsequent potential flow solutions. This procedure is repeated until the solutions converge. An empirical method was used to determine base drag allowing configuration drag to be computed.

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

PubMed

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

2011-02-01

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

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

Acquisition and deconvolution of seismic signals by different methods to perform direct ground-force measurements

NASA Astrophysics Data System (ADS)

Poletto, Flavio; Schleifer, Andrea; Zgauc, Franco; Meneghini, Fabio; Petronio, Lorenzo

2016-12-01

We present the results of a novel borehole-seismic experiment in which we used different types of onshore-transient-impulsive and non-impulsive-surface sources together with direct ground-force recordings. The ground-force signals were obtained by baseplate load cells located beneath the sources, and by buried soil-stress sensors installed in the very shallow-subsurface together with accelerometers. The aim was to characterize the source's emission by its complex impedance, function of the near-field vibrations and soil stress components, and above all to obtain appropriate deconvolution operators to remove the signature of the sources in the far-field seismic signals. The data analysis shows the differences in the reference measurements utilized to deconvolve the source signature. As downgoing waves, we process the signals of vertical seismic profiles (VSP) recorded in the far-field approximation by an array of permanent geophones cemented at shallow-medium depth outside the casing of an instrumented well. We obtain a significant improvement in the waveform of the radiated seismic-vibrator signals deconvolved by ground force, similar to that of the seismograms generated by the impulsive sources, and demonstrates that the results obtained by different sources present low values in their repeatability norm. The comparison evidences the potentiality of the direct ground-force measurement approach to effectively remove the far-field source signature in VSP onshore data, and to increase the performance of permanent acquisition installations for time-lapse application purposes.

Efficient solution of the Wigner-Liouville equation using a spectral decomposition of the force field

NASA Astrophysics Data System (ADS)

Van de Put, Maarten L.; Sorée, Bart; Magnus, Wim

2017-12-01

The Wigner-Liouville equation is reformulated using a spectral decomposition of the classical force field instead of the potential energy. The latter is shown to simplify the Wigner-Liouville kernel both conceptually and numerically as the spectral force Wigner-Liouville equation avoids the numerical evaluation of the highly oscillatory Wigner kernel which is nonlocal in both position and momentum. The quantum mechanical evolution is instead governed by a term local in space and non-local in momentum, where the non-locality in momentum has only a limited range. An interpretation of the time evolution in terms of two processes is presented; a classical evolution under the influence of the averaged driving field, and a probability-preserving quantum-mechanical generation and annihilation term. Using the inherent stability and reduced complexity, a direct deterministic numerical implementation using Chebyshev and Fourier pseudo-spectral methods is detailed. For the purpose of illustration, we present results for the time-evolution of a one-dimensional resonant tunneling diode driven out of equilibrium.

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.

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

PubMed

Riniker, Sereina

2018-03-26

In molecular dynamics or Monte Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focuses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS, and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of (bio)molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

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

PubMed

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

2013-06-05

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

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

PubMed

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

2013-01-08

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

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.

PubMed

Zuo, Zhili; Gandhi, Neha S; Mancera, Ricardo L

2010-12-27

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

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

PubMed

Zhu, Jiang; Alexov, Emil; Honig, Barry

2005-02-24

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

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.

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

PubMed Central

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

2010-01-01

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

Molecular Mechanics: The Method and Its Underlying Philosophy.

ERIC Educational Resources Information Center

Boyd, Donald B.; Lipkowitz, Kenny B.

1982-01-01

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

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS

NASA Astrophysics Data System (ADS)

Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru

2015-05-01

An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-source molecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a spherical symmetry such as micelles and vesicles. These methods yield precise pressure fields based on the Irving-Kirkwood contour integration and are particularly useful for biomolecular force fields. The present methods are applied to several systems including a buckled membrane and a vesicle.

Numerical analysis on the action of centrifuge force in magnetic fluid rotating shaft seals

NASA Astrophysics Data System (ADS)

Zou, Jibin; Li, Xuehui; Lu, Yongping; Hu, Jianhui

2002-11-01

The magnetic fluid seal is suitable for high-speed rotating shaft seal applications. Centrifuge force will have evident influence on magnetic fluid rotating shaft seals. The seal capacity of the rotating shaft seal can be improved or increased by some measures. Through hydrodynamic analysis the moving status of the magnetic fluid is worked out. By numerical method, the magnetic field and the isobars in the magnetic fluid of a seal device are computed. Then the influence of the centrifuge force on the magnetic fluid seal is calculated quantitatively.

Variable Acceleration Force Calibration System (VACS)

NASA Technical Reports Server (NTRS)

Rhew, Ray D.; Parker, Peter A.; Johnson, Thomas H.; Landman, Drew

2014-01-01

Conventionally, force balances have been calibrated manually, using a complex system of free hanging precision weights, bell cranks, and/or other mechanical components. Conventional methods may provide sufficient accuracy in some instances, but are often quite complex and labor-intensive, requiring three to four man-weeks to complete each full calibration. To ensure accuracy, gravity-based loading is typically utilized. However, this often causes difficulty when applying loads in three simultaneous, orthogonal axes. A complex system of levers, cranks, and cables must be used, introducing increased sources of systematic error, and significantly increasing the time and labor intensity required to complete the calibration. One aspect of the VACS is a method wherein the mass utilized for calibration is held constant, and the acceleration is changed to thereby generate relatively large forces with relatively small test masses. Multiple forces can be applied to a force balance without changing the test mass, and dynamic forces can be applied by rotation or oscillating acceleration. If rotational motion is utilized, a mass is rigidly attached to a force balance, and the mass is exposed to a rotational field. A large force can be applied by utilizing a large rotational velocity. A centrifuge or rotating table can be used to create the rotational field, and fixtures can be utilized to position the force balance. The acceleration may also be linear. For example, a table that moves linearly and accelerates in a sinusoidal manner may also be utilized. The test mass does not have to move in a path that is parallel to the ground, and no re-leveling is therefore required. Balance deflection corrections may be applied passively by monitoring the orientation of the force balance with a three-axis accelerometer package. Deflections are measured during each test run, and adjustments with respect to the true applied load can be made during the post-processing stage. This paper will present the development and testing of the VASC concept.

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

NASA Astrophysics Data System (ADS)

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

1983-12-01

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

Prediction of Mechanical Properties of Polymers With Various Force Fields

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

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.

First Use of Synoptic Vector Magnetograms for Global Nonlinear, Force-Free Coronal Magnetic Field Models

NASA Technical Reports Server (NTRS)

Tadesse, T.; Wiegelmann, T.; Gosain, S.; MacNeice, P.; Pevtsov, A. A.

2014-01-01

Context. The magnetic field permeating the solar atmosphere is generally thought to provide the energy for much of the activity seen in the solar corona, such as flares, coronal mass ejections (CMEs), etc. To overcome the unavailability of coronal magnetic field measurements, photospheric magnetic field vector data can be used to reconstruct the coronal field. Currently, there are several modelling techniques being used to calculate three-dimensional field lines into the solar atmosphere. Aims. For the first time, synoptic maps of a photospheric-vector magnetic field synthesized from the vector spectromagnetograph (VSM) on Synoptic Optical Long-term Investigations of the Sun (SOLIS) are used to model the coronal magnetic field and estimate free magnetic energy in the global scale. The free energy (i.e., the energy in excess of the potential field energy) is one of the main indicators used in space weather forecasts to predict the eruptivity of active regions. Methods. We solve the nonlinear force-free field equations using an optimization principle in spherical geometry. The resulting threedimensional magnetic fields are used to estimate the magnetic free energy content E(sub free) = E(sub nlfff) - E(sub pot), which is the difference of the magnetic energies between the nonpotential field and the potential field in the global solar corona. For comparison, we overlay the extrapolated magnetic field lines with the extreme ultraviolet (EUV) observations by the atmospheric imaging assembly (AIA) on board the Solar Dynamics Observatory (SDO). Results. For a single Carrington rotation 2121, we find that the global nonlinear force-free field (NLFFF) magnetic energy density is 10.3% higher than the potential one. Most of this free energy is located in active regions.

Numerical analyses of trapped field magnet and stable levitation region of HTSC

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

Tsuchimoto, M.; Kojima, T.; Waki, H.

Stable levitation with a permanent magnet and a bulk high {Tc} superconductor (HTSC) is examined numerically by using the critical state model and the frozen field model. Differences between a permanent magnet and a trapped field magnet are first discussed from property of levitation force. Stable levitation region of the HTSC on a ring magnet and on a solenoid coil are calculated with the numerical methods. Obtained results are discussed from difference of the magnetic field configuration.

A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies

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

Nangia, Nishant; Johansen, Hans; Patankar, Neelesh A.

Here, we present a moving control volume (CV) approach to computing hydrodynamic forces and torques on complex geometries. The method requires surface and volumetric integrals over a simple and regular Cartesian box that moves with an arbitrary velocity to enclose the body at all times. The moving box is aligned with Cartesian grid faces, which makes the integral evaluation straightforward in an immersed boundary (IB) framework. Discontinuous and noisy derivatives of velocity and pressure at the fluid–structure interface are avoided and far-field (smooth) velo city and pressure information is used. We re-visit the approach to compute hydrodynamic forces and torquesmore » through force/torque balance equations in a Lagrangian frame that some of us took in a prior work (Bhalla et al., 2013 [13]). We prove the equivalence of the two approaches for IB methods, thanks to the use of Peskin's delta functions. Both approaches are able to suppress spurious force oscillations and are in excellent agreement, as expected theoretically. Test cases ranging from Stokes to high Reynolds number regimes are considered. We discuss regridding issues for the moving CV method in an adaptive mesh refinement (AMR) context. The proposed moving CV method is not limited to a specific IB method and can also be used, for example, with embedded boundary methods.« less

A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies

DOE PAGES

Nangia, Nishant; Johansen, Hans; Patankar, Neelesh A.; ...

2017-10-01

Here, we present a moving control volume (CV) approach to computing hydrodynamic forces and torques on complex geometries. The method requires surface and volumetric integrals over a simple and regular Cartesian box that moves with an arbitrary velocity to enclose the body at all times. The moving box is aligned with Cartesian grid faces, which makes the integral evaluation straightforward in an immersed boundary (IB) framework. Discontinuous and noisy derivatives of velocity and pressure at the fluid–structure interface are avoided and far-field (smooth) velo city and pressure information is used. We re-visit the approach to compute hydrodynamic forces and torquesmore » through force/torque balance equations in a Lagrangian frame that some of us took in a prior work (Bhalla et al., 2013 [13]). We prove the equivalence of the two approaches for IB methods, thanks to the use of Peskin's delta functions. Both approaches are able to suppress spurious force oscillations and are in excellent agreement, as expected theoretically. Test cases ranging from Stokes to high Reynolds number regimes are considered. We discuss regridding issues for the moving CV method in an adaptive mesh refinement (AMR) context. The proposed moving CV method is not limited to a specific IB method and can also be used, for example, with embedded boundary methods.« less

Magnetic Signals of High-Temperature Superconductor Bulk During the Levitation Force Measurement Process

NASA Astrophysics Data System (ADS)

Huang, Huan; Zheng, Jun; Qian, Nan; Che, Tong; Zheng, Botian; Jin, Liwei; Deng, Zigang

2017-05-01

In order to study the commonly neglected magnetic field information in the course of levitation force measurement process in a superconducting maglev system, a multipoint magnetic field measurement platform was employed to acquire magnetic signals of a bulk high-Tc superconductor on both the top and the bottom surface. Working conditions including field cooling (FC) and zero field cooling were investigated for these vertical down and up motions above a permanent magnet guideway performed on a HTS maglev measurement system. We have discussed the magnetic flux variation process based on the Bean model. A magnetic hysteresis effect similar to the levitation force hysteresis loop of the bulk superconductor was displayed and analyzed in this paper. What is more valuable, there exists some available magnetic flux on the top surface of the bulk superconductor, and the proportion is as high as 62.42% in the FC condition, which provides an experimental hint to design the superconductor bulk and the applied field for practical use in a more efficient way. In particular, this work reveals real-time magnetic flux variation of the bulk superconductor in the levitation application, which is the other important information in contrast to the macroscopic levitation and guidance force investigations in previous studies, and it enriches the existing research methods. The results are significant for understanding the magnetic characteristic of superconductors, and they can contribute to optimize the present HTS maglev system design.

Numerical calculation and analysis of radial force on the single-action vane pump

NASA Astrophysics Data System (ADS)

Y He, Y.; Y Kong, F.

2013-12-01

Unbalanced radial force is a serious adversity that restricts the working pressure and reduces service life of the single-action vane pump. For revealing and predicting the distribution of radial force on the rotor, a numerical simulation about its transient flow field was performed by using dynamic mesh method with RNG κ ε-turbulent model. The details of transient flow characteristic and pressure fluctuation were obtained, and the radial force and periodic variation can be calculated based on the details. The results show: the radial force has a close relationship with the pressure pulsation; the radial force can be reduced drastically by optimizing the angle of port plate and installing the V-shaped cavity; if the odd number vanes are chosen, it will help reduce the radial force of rotor and optimize the pressure fluctuation effectively.

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

NASA Astrophysics Data System (ADS)

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

2008-09-01

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

Design, analysis and test verification of advanced encapsulation systems

NASA Technical Reports Server (NTRS)

Garcia, A., III

1984-01-01

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

Vertical Alignment of Single-Walled Carbon Nanotubes on Nanostructure Fabricated by Atomic Force Microscope

DTIC Science & Technology

2007-02-16

SWNT films by Langmuir - Blodgett methods,8 and chemical assembly of SWNTs on a large substrate.9 Al- though these methods provide a good way to control... Langmuir - Blodgett to Self-Assembly. Academic: New York, (1991). [10] Moon, J.H., Shin, J.W., Kim, S.Y., Park, J.W. Langmuir , 12, 4621, (1996...aligning CNTs in solu- tion by applying an electric field5 or a magnetic field,6 align- ing SWNTs by blending them with liquid crystal,7 assem- bling

A Pilot Study of Individual Muscle Force Prediction during Elbow Flexion and Extension in the Neurorehabilitation Field

PubMed Central

Hou, Jiateng; Sun, Yingfei; Sun, Lixin; Pan, Bingyu; Huang, Zhipei; Wu, Jiankang; Zhang, Zhiqiang

2016-01-01

This paper proposes a neuromusculoskeletal (NMS) model to predict individual muscle force during elbow flexion and extension. Four male subjects were asked to do voluntary elbow flexion and extension. An inertial sensor and surface electromyography (sEMG) sensors were attached to subject's forearm. Joint angle calculated by fusion of acceleration and angular rate using an extended Kalman filter (EKF) and muscle activations obtained from the sEMG signals were taken as the inputs of the proposed NMS model to determine individual muscle force. The result shows that our NMS model can predict individual muscle force accurately, with the ability to reflect subject-specific joint dynamics and neural control solutions. Our method incorporates sEMG and motion data, making it possible to get a deeper understanding of neurological, physiological, and anatomical characteristics of human dynamic movement. We demonstrate the potential of the proposed NMS model for evaluating the function of upper limb movements in the field of neurorehabilitation. PMID:27916853

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

PubMed Central

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

2008-01-01

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

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

PubMed

Plocková, J; Chmelík, J

2001-05-25

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

Overcoming ocular drug delivery barriers through the use of physical forces.

PubMed

Huang, Di; Chen, Ying-Shan; Rupenthal, Ilva D

2018-02-15

Overcoming the physiological barriers in the eye remains a key obstacle in the field of ocular drug delivery. While ocular barriers naturally have a protective function, they also limit drug entry into the eye. Various pharmaceutical strategies, such as novel formulations and physical force-based techniques, have been investigated to weaken these barriers and transport therapeutic agents effectively to both the anterior and the posterior segments of the eye. This review summarizes and discusses the recent research progress in the field of ocular drug delivery with a focus on the application of physical methods, including electrical fields, sonophoresis, and microneedles, which can enhance penetration efficiency by transiently disrupting the ocular barriers in a minimally or non-invasive manner. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

PubMed Central

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

2015-01-01

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

Probing local work function of electron emitting Si-nanofacets

NASA Astrophysics Data System (ADS)

Basu, Tanmoy; Som, Tapobrata

2017-10-01

Large area, Si-nanofacets are synthesized by obliquely incident low energy Ar+-ion-beam bombardment at room temperature (RT). The field emission properties of such nanofacets are studied based on current-voltage measurements and the Fowler-Nordheim equation. Low turn-on field with relatively high current density is obtained due to the shape and an overall rough morphology. We demonstrate a tunable field emission property from the silicon nanofacets by varying the ion exposure time. Atomic force microscopy (AFM) in conjunction with Kelvin probe force microscopy (KPFM) measurements provide the information on the aspect ratio and confirms the presence of native oxide layer near the apexes of the facets, respectively. The inhomogeneous oxidation leads to an increase in the local work function at the apexes of the facets, restricting the electron emission from the same. Due to its room temperature fabrication, the present method is of great significance to the low-cost vacuum field emission devices fabrication.

Eliminating crystals in non-oxide optical fiber preforms and optical fibers

NASA Technical Reports Server (NTRS)

LaPointe, Michael R. (Inventor); Tucker, Dennis S. (Inventor)

2010-01-01

A method is provided for eliminating crystals in non-oxide optical fiber preforms as well as optical fibers drawn therefrom. The optical-fiber-drawing axis of the preform is aligned with the force of gravity. A magnetic field is applied to the preform as it is heated to at least a melting temperature thereof. The magnetic field is applied in a direction that is parallel to the preform's optical-fiber-drawing axis. The preform is then cooled to a temperature that is less than a glass transition temperature of the preform while the preform is maintained in the magnetic field. When the processed preform is to have an optical fiber drawn therefrom, the preform's optical-fiber-drawing axis is again aligned with the force of gravity and a magnetic field is again applied along the axis as the optical fiber is drawn from the preform.

2016 Consequence Management Advisory Division's (CMAD) Annual Report

EPA Pesticide Factsheets

CMAD annual report for 2016 which covers activities such as radiation task force leaders annual training, national criminal enforcement response team annual training, field technology demonstrations, and a new method to detect perfluorinated compounds.

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

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

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

Dynamic behaviors of historical wrought iron truss bridges: a field testing case study

NASA Astrophysics Data System (ADS)

Dai, Kaoshan; Wang, Ying; Hedric, Andrew; Huang, Zhenhua

2016-04-01

The U.S. transportation infrastructure has many wrought iron truss bridges that are more than a century old and still remain in use. Understanding the structural properties and identifying the health conditions of these historical bridges are essential to deciding the maintenance or rebuild plan of the bridges. This research involved an on-site full-scale system identification test case study on the historical Old Alton Bridge (a wrought iron truss bridge built in 1884 in Denton, Texas) using a wireless sensor network. The study results demonstrate a practical and convenient experimental system identification method for historical bridge structures. The method includes the basic steps of the in-situ experiment and in-house data analysis. Various excitation methods are studied for field testing, including ambient vibration by wind load, forced vibration by human jumping load, and forced vibration by human pulling load. Structural responses of the bridge under these different excitation approaches were analyzed and compared with numerical analysis results.

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.

Sensing mode atomic force microscope

DOEpatents

Hough, Paul V. C.; Wang, Chengpu

2006-08-22

An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

Sensing mode atomic force microscope

DOEpatents

Hough, Paul V.; Wang, Chengpu

2004-11-16

An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

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

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

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

Identification of moving vehicle forces on bridge structures via moving average Tikhonov regularization

NASA Astrophysics Data System (ADS)

Pan, Chu-Dong; Yu, Ling; Liu, Huan-Lin

2017-08-01

Traffic-induced moving force identification (MFI) is a typical inverse problem in the field of bridge structural health monitoring. Lots of regularization-based methods have been proposed for MFI. However, the MFI accuracy obtained from the existing methods is low when the moving forces enter into and exit a bridge deck due to low sensitivity of structural responses to the forces at these zones. To overcome this shortcoming, a novel moving average Tikhonov regularization method is proposed for MFI by combining with the moving average concepts. Firstly, the bridge-vehicle interaction moving force is assumed as a discrete finite signal with stable average value (DFS-SAV). Secondly, the reasonable signal feature of DFS-SAV is quantified and introduced for improving the penalty function (∣∣x∣∣2 2) defined in the classical Tikhonov regularization. Then, a feasible two-step strategy is proposed for selecting regularization parameter and balance coefficient defined in the improved penalty function. Finally, both numerical simulations on a simply-supported beam and laboratory experiments on a hollow tube beam are performed for assessing the accuracy and the feasibility of the proposed method. The illustrated results show that the moving forces can be accurately identified with a strong robustness. Some related issues, such as selection of moving window length, effect of different penalty functions, and effect of different car speeds, are discussed as well.

High sensitive space electric field sensing based on micro fiber interferometer with field force driven gold nanofilm.

PubMed

Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei

2015-10-28

The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection.

High sensitive space electric field sensing based on micro fiber interferometer with field force driven gold nanofilm

PubMed Central

Zhu, Tao; Zhou, Liming; Liu, Min; Zhang, Jingdong; Shi, Leilei

2015-01-01

The traditional electrical field sensing can be realized by utilizing electro-optic materials or liquid crystals, and has limitations of easy breakdown, free assembly and difficult measurement of low-frequency. Here, we propose a new method to realize safe measurement of spatial dynamic electric field by using a micro fiber interferometer integrated with gold nanofilm. The energy of the electric charge received through antenna forms the intrinsic electric field with two micro electrodes, one of which is the 120 nm gold film vibration beam micromachined by femtosecond lasers and integrated with the micro fiber. The change of the intrinsic electric field force due to the spatial electric field will cause the vibration of the film beam. By demodulating the output signal of the micro fiber interferometer, the electric field can be measured. We demonstrate the detectable frequency ranges from tens of Hz to tens of KHz, and the minimum electric field intensity is ~200 V/m at 1 KHz. Our electric field measurement technology combining optical fiber interference with gold nanostructures shows the advantages of security, high sensitivity, compact size, and multiplexed multi-point and remote detection. PMID:26507680

A Microcontroller-Based Device for Monitoring Blood Pressure in the Field

DTIC Science & Technology

1993-12-01

Service de sant6 des Forces armies canadiennes. On a mis au point un appareil de mesure des signes vitaux, qui peut mesurer la fr~quence cardiaque et...methods for taking systolic and diastolic pressure readings include the auscultation method, the oscillometric method, and the ultrasonic method...pressures are determined from its output, are the best ways of distinguishing between the three main methods previously listed. The auscultation method

First order reversal curves (FORC) analysis of individual magnetic nanostructures using micro-Hall magnetometry.

PubMed

Pohlit, Merlin; Eibisch, Paul; Akbari, Maryam; Porrati, Fabrizio; Huth, Michael; Müller, Jens

2016-11-01

Alongside the development of artificially created magnetic nanostructures, micro-Hall magnetometry has proven to be a versatile tool to obtain high-resolution hysteresis loop data and access dynamical properties. Here we explore the application of First Order Reversal Curves (FORC)-a technique well-established in the field of paleomagnetism for studying grain-size and interaction effects in magnetic rocks-to individual and dipolar-coupled arrays of magnetic nanostructures using micro-Hall sensors. A proof-of-principle experiment performed on a macroscopic piece of a floppy disk as a reference sample well known in the literature demonstrates that the FORC diagrams obtained by magnetic stray field measurements using home-built magnetometers are in good agreement with magnetization data obtained by a commercial vibrating sample magnetometer. We discuss in detail the FORC diagrams and their interpretation of three different representative magnetic systems, prepared by the direct-write Focused Electron Beam Induced Deposition (FEBID) technique: (1) an isolated Co-nanoisland showing a simple square-shaped hysteresis loop, (2) a more complex CoFe-alloy nanoisland exhibiting a wasp-waist-type hysteresis, and (3) a cluster of interacting Co-nanoislands. Our findings reveal that the combination of FORC and micro-Hall magnetometry is a promising tool to investigate complex magnetization reversal processes within individual or small ensembles of nanomagnets grown by FEBID or other fabrication methods. The method provides sub-μm spatial resolution and bridges the gap of FORC analysis, commonly used for studying macroscopic samples and rather large arrays, to studies of small ensembles of interacting nanoparticles with the high moment sensitivity inherent to micro-Hall magnetometry.

Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.

PubMed

Itoh, Satoru G; Okumura, Hisashi

2013-03-30

We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free-energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica-exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local-minimum free-energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid-β peptide (Aβ) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aβ fragment more efficiently than the other methods. We obtained β-helix, α-helix, 3(10)-helix, β-hairpin, and β-sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free-energy landscape. Copyright © 2012 Wiley Periodicals, Inc.

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.

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

Maiolo, M., E-mail: massimo.maiolo@zhaw.ch; ZHAW, Institut für Angewandte Simulation, Grüental, CH-8820 Wädenswil; Vancheri, A., E-mail: alberto.vancheri@supsi.ch

In this paper, we apply Multiresolution Analysis (MRA) to develop sparse but accurate representations for the Multiscale Coarse-Graining (MSCG) approximation to the many-body potential of mean force. We rigorously framed the MSCG method into MRA so that all the instruments of this theory become available together with a multitude of new basis functions, namely the wavelets. The coarse-grained (CG) force field is hierarchically decomposed at different resolution levels enabling to choose the most appropriate wavelet family for each physical interaction without requiring an a priori knowledge of the details localization. The representation of the CG potential in this new efficientmore » orthonormal basis leads to a compression of the signal information in few large expansion coefficients. The multiresolution property of the wavelet transform allows to isolate and remove the noise from the CG force-field reconstruction by thresholding the basis function coefficients from each frequency band independently. We discuss the implementation of our wavelet-based MSCG approach and demonstrate its accuracy using two different condensed-phase systems, i.e. liquid water and methanol. Simulations of liquid argon have also been performed using a one-to-one mapping between atomistic and CG sites. The latter model allows to verify the accuracy of the method and to test different choices of wavelet families. Furthermore, the results of the computer simulations show that the efficiency and sparsity of the representation of the CG force field can be traced back to the mathematical properties of the chosen family of wavelets. This result is in agreement with what is known from the theory of multiresolution analysis of signals.« less

Field emission microplasma actuation for microchannel flows

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Method for the unique identification of hyperelastic material properties using full-field measures. Application to the passive myocardium material response.

PubMed

Perotti, Luigi E; Ponnaluri, Aditya V S; Krishnamoorthi, Shankarjee; Balzani, Daniel; Ennis, Daniel B; Klug, William S

2017-11-01

Quantitative measurement of the material properties (eg, stiffness) of biological tissues is poised to become a powerful diagnostic tool. There are currently several methods in the literature to estimating material stiffness, and we extend this work by formulating a framework that leads to uniquely identified material properties. We design an approach to work with full-field displacement data-ie, we assume the displacement field due to the applied forces is known both on the boundaries and also within the interior of the body of interest-and seek stiffness parameters that lead to balanced internal and external forces in a model. For in vivo applications, the displacement data can be acquired clinically using magnetic resonance imaging while the forces may be computed from pressure measurements, eg, through catheterization. We outline a set of conditions under which the least-square force error objective function is convex, yielding uniquely identified material properties. An important component of our framework is a new numerical strategy to formulate polyconvex material energy laws that are linear in the material properties and provide one optimal description of the available experimental data. An outcome of our approach is the analysis of the reliability of the identified material properties, even for material laws that do not admit unique property identification. Lastly, we evaluate our approach using passive myocardium experimental data at the material point and show its application to identifying myocardial stiffness with an in silico experiment modeling the passive filling of the left ventricle. Copyright © 2017 John Wiley & Sons, Ltd.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

PubMed

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

2012-02-14

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

Mechanical properties investigation on single-wall ZrO2 nanotubes: A finite element method with equivalent Poisson's ratio for chemical bonds

NASA Astrophysics Data System (ADS)

Yang, Xiao; Li, Huijian; Hu, Minzheng; Liu, Zeliang; Wärnå, John; Cao, Yuying; Ahuja, Rajeev; Luo, Wei

2018-04-01

A method to obtain the equivalent Poisson's ratio in chemical bonds as classical beams with finite element method was proposed from experimental data. The UFF (Universal Force Field) method was employed to calculate the elastic force constants of Zrsbnd O bonds. By applying the equivalent Poisson's ratio, the mechanical properties of single-wall ZrNTs (ZrO2 nanotubes) were investigated by finite element analysis. The nanotubes' Young's modulus (Y), Poisson's ratio (ν) of ZrNTs as function of diameters, length and chirality have been discussed, respectively. We found that the Young's modulus of single-wall ZrNTs is calculated to be between 350 and 420 GPa.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Field sampling of loose erodible material: A new method to consider the full particle-size range

NASA Astrophysics Data System (ADS)

Klose, Martina; Gill, Thomas E.

2017-04-01

The aerodynamic entrainment of sand and dust is determined by the atmospheric forces exerted onto the soil surface and by the soil-surface condition. If aerodynamic forces are strong enough to generate sand and dust lifting, the entrained sediment amount still critically depends on the supply of loose particles readily available for lifting. This loose erodible material (LEM) is sometimes defined as the thin layer of loose particles on top of a crusted surface. Here, we more generally define LEM as loose particles or particle aggregates available for entrainment, which may or may not overlay a soil crust. Field sampling of LEM is difficult and only few attempts have been made. Motivated by saltation as the most efficient process to generate dust emission, methods have focused on capturing LEM in the sand-size range or on determining the potential of a soil surface to be eroded by aerodynamic forces and particle impacts. Here, our focus is to capture the full particle-size distribution of LEM in situ, including the dust and sand-size range, to investigate the potential and likelihood of dust emission mechanisms (aerodynamic entrainment, saltation bombardment, aggregate disintegration) to occur. A new vacuum method is introduced and its capability to sample LEM without significant alteration of the LEM particle-size distribution is investigated.

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.

Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II)

NASA Astrophysics Data System (ADS)

David, Laurent; Amara, Patricia; Field, Martin J.; Major, François

2002-08-01

Although techniques for the simulation of biomolecules, such as proteins and RNAs, have greatly advanced in the last decade, modeling complexes of biomolecules with metal ions remains problematic. Precise calculations can be done with quantum mechanical methods but these are prohibitive for systems the size of macromolecules. More qualitative modeling can be done with molecular mechanical potentials but the parametrization of force fields for metals is often difficult, particularly if the bonding between the metal and the groups in its coordination shell has significant covalent character. In this paper we present a method for deriving bond and bond-angle parameters for metal complexes from experimental bond and bond-angle distributions obtained from the Cambridge Structural Database. In conjunction with this method, we also introduce a non-standard energy term of gaussian form that allows us to obtain a stable description of the coordination about a metal center during a simulation. The method was evaluated on Fe(II)-porphyrin complexes, on simple Cu(II) ion complexes and a number of complexes of the Pb(II) ion.

Fabricating Atom-Sized Gaps by Field-Aided Atom Migration in Nanoscale Junctions

NASA Astrophysics Data System (ADS)

Liu, Ran; Bi, Jun-Jie; Xie, Zhen; Yin, Kaikai; Wang, Dunyou; Zhang, Guang-Ping; Xiang, Dong; Wang, Chuan-Kui; Li, Zong-Liang

2018-05-01

The gap sizes between electrodes generated by typical methods are generally much larger than the dimension of a common molecule when fabricating a single-molecule junction, which dramatically suppresses the yield of single-molecule junctions. Based on the ab initio calculations, we develop a strategy named the field-aided method to accurately fabricate an atomic-sized gap between gold nanoelectrodes. To understand the mechanism of this strategy, configuration evolutions of gold nanojunction in stretching and compressing processes are calculated. The numerical results show that, in the stretching process, the gold atoms bridged between two electrodes are likely to form atomic chains. More significantly, lattice vacant positions can be easily generated in stretching and compressing processes, which make field-aided gap generation possible. In field-aided atom migration (FAAM), the external field can exert driving force, enhance the initial energy of the system, and decrease the barrier in the migration path, which makes the atom migration feasible. Conductance and stretching and compressing forces, as measurable variables in stretching and compressing processes, present very useful signals for determining the time to perform FAAM. Following this desirable strategy, we successfully fabricate gold nanogaps with a dimension of 0.38 ±0.05 nm in the experiment, as our calculation simulates.

Extrusion Process by Finite Volume Method Using OpenFoam Software

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

Matos Martins, Marcelo; Tonini Button, Sergio; Divo Bressan, Jose

The computational codes are very important tools to solve engineering problems. In the analysis of metal forming process, such as extrusion, this is not different because the computational codes allow analyzing the process with reduced cost. Traditionally, the Finite Element Method is used to solve solid mechanic problems, however, the Finite Volume Method (FVM) have been gaining force in this field of applications. This paper presents the velocity field and friction coefficient variation results, obtained by numerical simulation using the OpenFoam Software and the FVM to solve an aluminum direct cold extrusion process.

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

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

Kelley, Anne Myers

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

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

PubMed

Best, Robert B; Hummer, Gerhard

2009-07-02

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

Measurement of time-varying displacement fields in cell culture for traction force optical coherence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Mulligan, Jeffrey A.; Adie, Steven G.

2017-02-01

Mechanobiology is an emerging field which seeks to link mechanical forces and properties to the behaviors of cells and tissues in cancer, stem cell growth, and other processes. Traction force microscopy (TFM) is an imaging technique that enables the study of traction forces exerted by cells on their environment to migrate as well as sense and manipulate their surroundings. To date, TFM research has been performed using incoherent imaging modalities and, until recently, has been largely confined to the study of cell-induced tractions within two-dimensions using highly artificial and controlled environments. As the field of mechanobiology advances, and demand grows for research in physiologically relevant 3D culture and in vivo models, TFM will require imaging modalities that support such settings. Optical coherence microscopy (OCM) is an interferometric imaging modality which enables 3D cellular resolution imaging in highly scattering environments. Moreover, optical coherence elastography (OCE) enables the measurement of tissue mechanical properties. OCE relies on the principle of measuring material deformations in response to artificially applied stress. By extension, similar techniques can enable the measurement of cell-induced deformations, imaged with OCM. We propose traction force optical coherence microscopy (TF-OCM) as a natural extension and partner to existing OCM and OCE methods. We report the first use of OCM data and digital image correlation to track temporally varying displacement fields exhibited within a 3D culture setting. These results mark the first steps toward the realization of TF-OCM in 2D and 3D settings, bolstering OCM as a platform for advancing research in mechanobiology.

Systematic parameter inference in stochastic mesoscopic modeling

NASA Astrophysics Data System (ADS)

Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

Computational study of the effect of gradient magnetic field in navigation of spherical particles

NASA Astrophysics Data System (ADS)

Karvelas, E. G.; Lampropoulos, N. K.; Papadimitriou, D. I.; Karakasidis, T. E.; Sarris, I. E.

2017-11-01

The use of spherical magnetic nanoparticles that are coated with drugs and can be navigated in arteries to attack tumors is proposed as an alternative to chemotherapy. Navigation of particles is due to magnetic field gradients that may be produced in an MRI device. In the present work, a computational study for the evaluation of the magnitude of the gradient magnetic field for particles navigation in Y bifurcations is presented. For this purpose, the presented method solves for the fluid flow and includes all the important forces that act on the particles in their discrete motion. The method is based on an iteration algorithm that adjusts the gradient magnetic field to minimize the particles’ deviation from a desired trajectory. Using the above mentioned method, the appropriate range of the gradient magnetic field for optimum navigation of nanoparticles’s aggregation is found.

Mathematical modeling of the flow field and particle motion in a rotating bioreactor at unit gravity and microgravity

NASA Technical Reports Server (NTRS)

Boyd, Ernest J.

1990-01-01

The biotechnology group at NASA Johnson Space Center is developing systems for culturing mammalian cells that stimulate some aspect of microgravity and provide a low shear environment for microgravity-based studies on suspension and anchorage dependent cells. The design of these vessels for culturing cells is based on the need to suspend cells and aggregates of cells and microcarrier beads continually in the culturing medium. The design must also provide sufficient circulation for adequate mass transfer of nutrients to the cells and minimize the total force on the cells. Forces, resulting from sources such as hydrodynamic fluid shear and collisions of cells and walls of the vessels, may damage delicate cells and degrade the formation of three dimensional structures. This study examines one particular design in both unit gravity and microgravity based on two concentric cylinders rotating in the same direction at different speeds to create a Couette flow between them. A numerical simulation for the flow field and the trajectories of particles in the vessel. The flow field for the circulation of the culturing medium is modeled by the Navier-Stokes equations. The forces on a particle are assumed to be drag from the fluid's circulation, buoyancy from the gravitational force and centrifugal force from the rotation of the vessel. The problem requires first solving the system of partial differential equations for the fluid flow by a finite difference method and then solving the system of ordinary differential equations for the trajectories by Gear's stiff method. Results of the study indicate that the trajectories in unit gravity and microgravity are very similar except for small spatial deviations on the fast time scale in unit gravity. The total force per unit cross sectional area on a particle in microgravity, however, is significantly smaller than the corresponding value in unit gravity, which is also smaller than anticipated. Hence, this study indicates that this design for a bioreactor with optimal rates of rotation can provide a good environment for culturing cells in microgravity with adequate circulation and minimal force on the cells.

pmx: Automated protein structure and topology generation for alchemical perturbations

PubMed Central

Gapsys, Vytautas; Michielssens, Servaas; Seeliger, Daniel; de Groot, Bert L

2015-01-01

Computational protein design requires methods to accurately estimate free energy changes in protein stability or binding upon an amino acid mutation. From the different approaches available, molecular dynamics-based alchemical free energy calculations are unique in their accuracy and solid theoretical basis. The challenge in using these methods lies in the need to generate hybrid structures and topologies representing two physical states of a system. A custom made hybrid topology may prove useful for a particular mutation of interest, however, a high throughput mutation analysis calls for a more general approach. In this work, we present an automated procedure to generate hybrid structures and topologies for the amino acid mutations in all commonly used force fields. The described software is compatible with the Gromacs simulation package. The mutation libraries are readily supported for five force fields, namely Amber99SB, Amber99SB*-ILDN, OPLS-AA/L, Charmm22*, and Charmm36. PMID:25487359

Assimilating concentration observations for transport and dispersion modeling in a meandering wind field

NASA Astrophysics Data System (ADS)

Haupt, Sue Ellen; Beyer-Lout, Anke; Long, Kerrie J.; Young, George S.

Assimilating concentration data into an atmospheric transport and dispersion model can provide information to improve downwind concentration forecasts. The forecast model is typically a one-way coupled set of equations: the meteorological equations impact the concentration, but the concentration does not generally affect the meteorological field. Thus, indirect methods of using concentration data to influence the meteorological variables are required. The problem studied here involves a simple wind field forcing Gaussian dispersion. Two methods of assimilating concentration data to infer the wind direction are demonstrated. The first method is Lagrangian in nature and treats the puff as an entity using feature extraction coupled with nudging. The second method is an Eulerian field approach akin to traditional variational approaches, but minimizes the error by using a genetic algorithm (GA) to directly optimize the match between observations and predictions. Both methods show success at inferring the wind field. The GA-variational method, however, is more accurate but requires more computational time. Dynamic assimilation of a continuous release modeled by a Gaussian plume is also demonstrated using the genetic algorithm approach.

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

Field Balancing of Magnetically Levitated Rotors without Trial Weights

PubMed Central

Fang, Jiancheng; Wang, Yingguang; Han, Bangcheng; Zheng, Shiqiang

2013-01-01

Unbalance in magnetically levitated rotor (MLR) can cause undesirable synchronous vibrations and lead to the saturation of the magnetic actuator. Dynamic balancing is an important way to solve these problems. However, the traditional balancing methods, using rotor displacement to estimate a rotor's unbalance, requiring several trial-runs, are neither precise nor efficient. This paper presents a new balancing method for an MLR without trial weights. In this method, the rotor is forced to rotate around its geometric axis. The coil currents of magnetic bearing, rather than rotor displacement, are employed to calculate the correction masses. This method provides two benefits when the MLR's rotation axis coincides with the geometric axis: one is that unbalanced centrifugal force/torque equals the synchronous magnetic force/torque, and the other is that the magnetic force is proportional to the control current. These make calculation of the correction masses by measuring coil current with only a single start-up precise. An unbalance compensation control (UCC) method, using a general band-pass filter (GPF) to make the MLR spin around its geometric axis is also discussed. Experimental results show that the novel balancing method can remove more than 92.7% of the rotor unbalance and a balancing accuracy of 0.024 g mm kg−1 is achieved.

A moving control volume method for smooth computation of hydrodynamic forces and torques on immersed bodies

NASA Astrophysics Data System (ADS)

Nangia, Nishant; Patankar, Neelesh A.; Bhalla, Amneet P. S.

2017-11-01

Fictitious domain methods for simulating fluid-structure interaction (FSI) have been gaining popularity in the past few decades because of their robustness in handling arbitrarily moving bodies. Often the transient net hydrodynamic forces and torques on the body are desired quantities for these types of simulations. In past studies using immersed boundary (IB) methods, force measurements are contaminated with spurious oscillations due to evaluation of possibly discontinuous spatial velocity of pressure gradients within or on the surface of the body. Based on an application of the Reynolds transport theorem, we present a moving control volume (CV) approach to computing the net forces and torques on a moving body immersed in a fluid. The approach is shown to be accurate for a wide array of FSI problems, including flow past stationary and moving objects, Stokes flow, and high Reynolds number free-swimming. The approach only requires far-field (smooth) velocity and pressure information, thereby suppressing spurious force oscillations and eliminating the need for any filtering. The proposed moving CV method is not limited to a specific IB method and is straightforward to implement within an existing parallel FSI simulation software. This work is supported by NSF (Award Numbers SI2-SSI-1450374, SI2-SSI-1450327, and DGE-1324585), the US Department of Energy, Office of Science, ASCR (Award Number DE-AC02-05CH11231), and NIH (Award Number HL117163).

Determination of Coronal Magnetic Fields from Vector Magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1997-01-01

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

Steps towards Improving GNSS Systematic Errors and Biases

NASA Astrophysics Data System (ADS)

Herring, T.; Moore, M.

2017-12-01

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

Methods And Apparatus For Acoustic Fiber Fractionation

DOEpatents

Brodeur, Pierre

1999-11-09

Methods and apparatus for acoustic fiber fractionation using a plane ultrasonic wave field interacting with water suspended fibers circulating in a channel flow using acoustic radiation forces to separate fibers into two or more fractions based on fiber radius, with applications of the separation concept in the pulp and paper industry. The continuous process relies on the use of a wall-mounted, rectangular cross-section piezoelectric ceramic transducer to selectively deflect flowing fibers as they penetrate the ultrasonic field. The described embodiment uses a transducer frequency of approximately 150 kHz. Depending upon the amount of dissolved gas in water, separation is obtained using a standing or a traveling wave field.

An operational search and rescue model for the Norwegian Sea and the North Sea

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Allen, Arthur A.

A new operational, ensemble-based search and rescue model for the Norwegian Sea and the North Sea is presented. The stochastic trajectory model computes the net motion of a range of search and rescue objects. A new, robust formulation for the relation between the wind and the motion of the drifting object (termed the leeway of the object) is employed. Empirically derived coefficients for 63 categories of search objects compiled by the US Coast Guard are ingested to estimate the leeway of the drifting objects. A Monte Carlo technique is employed to generate an ensemble that accounts for the uncertainties in forcing fields (wind and current), leeway drift properties, and the initial position of the search object. The ensemble yields an estimate of the time-evolving probability density function of the location of the search object, and its envelope defines the search area. Forcing fields from the operational oceanic and atmospheric forecast system of The Norwegian Meteorological Institute are used as input to the trajectory model. This allows for the first time high-resolution wind and current fields to be used to forecast search areas up to 60 h into the future. A limited set of field exercises show good agreement between model trajectories, search areas, and observed trajectories for life rafts and other search objects. Comparison with older methods shows that search areas expand much more slowly using the new ensemble method with high resolution forcing fields and the new leeway formulation. It is found that going to higher-order stochastic trajectory models will not significantly improve the forecast skill and the rate of expansion of search areas.

Biological Experiments in Microgravity Conditions Using Magnetic Micro- and Nano-Particles

NASA Astrophysics Data System (ADS)

Nechitailo, Galina S.; Kuznetsov, Anatoli; Kuznetsov, Oleg

2016-07-01

Gravity affects all living organisms on Earth, and plays a role in multiple processes in them. In microgravity conditions (e.g., on board of a spacecraft) many of these processes are disturbed, e.g., spatial orientation is lost, mass and heat exchange is distorted, many adaptive mechanisms no longer function, etc. Negation of these adverse effects by creation of pseudo-gravity to by centrifugation is complicated, expensive and unpractical. We propose to use naturally occurring magnetic heterogeneity of all living cells and high gradient magnetic fields as an alternative approach to negating the adverse effects of microgravity on living systems. In non-uniform magnetic field, magnetically heterogeneous objects experience a system of ponderomotive forces. For a weak magnetic particle, the net ponderomotive magnetic force: Fm = Δχ•V•grad(H2/2), where Δχ is the difference of susceptibilities of the particle and the surrounding media, V is the volume of the particle, grad(H2/2) is the dynamic factor of the magnetic field. We studied magnetic heterogeneity of plant gravity receptor cells, prepared and conducted experiments on board of the space station "Mir" on providing a gravity-like stimulus for flax seedlings using high gradient magnetic field ("Magnetogravistat" experiment). Later, a more sophisticated version of this experiment was flown on STS-107. These experiments provided new data on the mechanisms of plant gravity reception and created a method for substituting gravity for a living organism by a force of a different physical nature, to negate the adverse effects of microgravity. Since the ponderomotive force is proportional to the dynamic factor of the field grad(H2/2), the stronger the field, and the faster it changes over distance, the higher is the dynamic factor and the stronger the ponderomotive force. Therefore, in the small vicinity of a small ferromagnetic particle (preferably metallic micro or nano-particles), the forces are very significant even for weak magnetic objects, and can have significant effects on multiple processes in living cells/organisms. It was reported, that such high gradient magnetic fields can affect cell differentiation and cell proliferation processes in ground-based experiments. To prevent oxidation of ultradisperse ferromagnetic particles in aqueous media, it is beneficial to coat their surface with carbon. Suitable protected metallic micro- and nano-particles can be produced by a variety of techniques (CVD, plasmachemistry, joint grinding, etc.). Ferro-carbon particles produced by plasmachemical technique have high sorption capacities for various organic and inorganic compounds (as well as for various cell metabolites), can be formed in rather stable aqueous suspensions, and be controlled (e.g., sedimented) by a magnetic field. This makes these particles a very interesting research tool. In our opinion, biological experiments with ferro-carbon nano-structured particles in microgravity will generate important scientific data and will allow creating new methods of negating the adverse effects of microgravity on living systems.

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.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

SPIREs: A Finite-Difference Frequency-Domain electromagnetic solver for inhomogeneous magnetized plasma cylinders

NASA Astrophysics Data System (ADS)

Melazzi, D.; Curreli, D.; Manente, M.; Carlsson, J.; Pavarin, D.

2012-06-01

We present SPIREs (plaSma Padova Inhomogeneous Radial Electromagnetic solver), a Finite-Difference Frequency-Domain (FDFD) electromagnetic solver in one dimension for the rapid calculation of the electromagnetic fields and the deposited power of a large variety of cylindrical plasma problems. The two Maxwell wave equations have been discretized using a staggered Yee mesh along the radial direction of the cylinder, and Fourier transformed along the other two dimensions and in time. By means of this kind of discretization, we have found that mode-coupling of fast and slow branches can be fully resolved without singularity issues that flawed other well-established methods in the past. Fields are forced by an antenna placed at a given distance from the plasma. The plasma can be inhomogeneous, finite-temperature, collisional, magnetized and multi-species. Finite-temperature Maxwellian effects, comprising Landau and cyclotron damping, have been included by means of the plasma Z dispersion function. Finite Larmor radius effects have been neglected. Radial variations of the plasma parameters are taken into account, thus extending the range of applications to a large variety of inhomogeneous plasma systems. The method proved to be fast and reliable, with accuracy depending on the spatial grid size. Two physical examples are reported: fields in a forced vacuum waveguide with the antenna inside, and forced plasma oscillations in the helicon radiofrequency range.

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

PubMed Central

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

2007-01-01

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

Three-dimensional morphologies of inclined equiaxed dendrites growing under forced convection by phase-field-lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi; Shimokawabe, Takashi; Aoki, Takayuki

2018-02-01

Three-dimensional growth morphologies of equiaxed dendrites growing under forced convection, with their preferred growth direction inclined from the flow direction, were investigated by performing large-scale phase-field lattice Boltzmann simulations on a graphical-processing-unit supercomputer. The tip velocities of the dendrite arms with their preferred growth directions inclined toward the upstream and downstream directions increased and decreased, respectively, as a result of forced convection. In addition, the tip velocities decreased monotonically as the angle between the preferred growth direction and the upstream direction increased. Here, the degree of acceleration of the upstream tips was larger than the degree of deceleration of the downstream tips. The angles between the actual tip growth directions and the preferred growth direction of the dendrite arms exhibited a characteristic change with two local maxima and two local minima.

Rigorous force field optimization principles based on statistical distance minimization

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2015-10-12

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

First-order reversal curve of the magnetostructural phase transition in FeTe

DOE PAGES

Frampton, M. K.; Crocker, J.; Gilbert, D. A.; ...

2017-06-05

We apply the first-order reversal curve (FORC) method, adapted from studies of ferromagnetic materials, to the magnetostructural phase transition of Fe 1+yTe. FORC measurements reveal two features in the hysteretic phase transition, even in samples where traditional temperature measurements display only a single transition. For Fe 1.13Te, the influence of magnetic field suggests that the main feature is primarily structural while a smaller, slightly higher-temperature transition is magnetic in origin. By contrast, Fe 1.03Te has a single transition which shows a uniform response to magnetic field, indicating a stronger coupling of the magnetic and structural phase transitions. We also introducemore » uniaxial stress, which spreads the distribution width without changing the underlying energy barrier of the transformation. Finally, the work shows how FORC can help disentangle the roles of the magnetic and structural phase transitions in FeTe.« less

Electrorotation and levitation of cells and colloidal particles

PubMed Central

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

1992-01-01

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

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

PubMed

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

2018-03-01

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

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

PubMed Central

Stockinger, Christian; Focke, Anne; Stein, Thorsten

2014-01-01

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

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

PubMed

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

2016-11-09

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

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

NASA Astrophysics Data System (ADS)

Hu, Yuda; Wang, Tong

2015-11-01

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

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

NASA Technical Reports Server (NTRS)

El-Kaddah, N.; Szekely, J.

1982-01-01

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

Influence of various force fields in estimating the binding affinity of acetylcholinesterase inhibitors using fast pulling of ligand scheme

NASA Astrophysics Data System (ADS)

Tam, Nguyen Minh; Vu, Khanh B.; Vu, Van V.; Ngo, Son Tung

2018-06-01

Acetylcholinesterase (AChE) is considered as one of the most favored drug targets for Alzheimer's disease. The effects of different force fields (FFs) on ranking affinity of acetylcholinesterase inhibitors were obtained using the fast pulling of ligand (FPL) method in steered-molecular dynamics (SMD) simulations. GROMOS, AMBER, CHARMM, and OPLS-AA FFs were investigated in this work. The pulling work derived with GROMOS FF has the strongest correlation and smallest error compared with experimental binding affinity. Moreover, the CPU consumption in the calculations using GROMOS FF is the lowest, which could allow us to rank affinity of a large number of AChE ligands.

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

PubMed Central

2015-01-01

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

Controlling Two-dimensional Tethered Vesicle Motion Using an Electric Field

PubMed Central

Yoshina-Ishii, Chiaki; Boxer, Steven G.

2008-01-01

We recently introduced methods to tether phospholipid vesicles or proteoliposomes onto a fluid supported lipid bilayer using DNA hybridization. These intact tethered vesicles diffuse in two dimensions parallel to the supporting membrane surface. In this paper, we report the dynamic response of individual tethered vesicles to an electric field applied parallel to the bilayer surface. Vesicles respond to the field by moving in the direction of electro-osmotic flow, and this can be used to reversibly concentrate tethered vesicles against a barrier. By adding increasing amounts of negatively charged phosphatidylserine to the supporting bilayer to increase electro-osmosis, the electrophoretic mobility of the tethered vesicles can be increased. The electro-osmotic contribution can be modeled well by a sphere connected to a cylindrical anchor in a viscous membrane with charged head groups. The electrophoretic force on the negatively charged tethered vesicles opposes the electro-osmotic force. By increasing the amount of negative charge on the tethered vesicle, drift in the direction of electro-osmotic flow can be slowed; at high negative charge on the tethered vesicle, motion can be forced in the direction of electrophoresis. The balance between these forces can be visualized on a patterned supporting bilayer containing negatively charged lipids which themselves reorganize in an externally applied electric field to create a gradient of charge within a corralled region. The charge gradient at the surface creates a gradient of electro-osmotic flow, and vesicles carrying similar amounts of negative charge can be focused to a region perpendicular to the applied field where electrophoresis is balanced by electro-osmosis, away from the corral boundary. Electric fields are effective tools to direct tethered vesicles, concentrate them and to measure the tethered vesicle’s electrostatic properties. PMID:16489833

In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level

PubMed Central

Yang, Changwon; Kulkarni, Mandar; Lim, Manho

2017-01-01

Abstract The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers. PMID:29112755

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.

2013-01-01

Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand’s electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered. PMID:24015114

Modeling the mechanism of CLN025 beta-hairpin formation

NASA Astrophysics Data System (ADS)

McKiernan, Keri A.; Husic, Brooke E.; Pande, Vijay S.

2017-09-01

Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

The current and future status of the concealed information test for field use.

PubMed

Matsuda, Izumi; Nittono, Hiroshi; Allen, John J B

2012-01-01

The Concealed Information Test (CIT) is a psychophysiological technique for examining whether a person has knowledge of crime-relevant information. Many laboratory studies have shown that the CIT has good scientific validity. However, the CIT has seldom been used for actual criminal investigations. One successful exception is its use by the Japanese police. In Japan, the CIT has been widely used for criminal investigations, although its probative force in court is not strong. In this paper, we first review the current use of the field CIT in Japan. Then, we discuss two possible approaches to increase its probative force: sophisticated statistical judgment methods and combining new psychophysiological measures with classic autonomic measures. On the basis of these considerations, we propose several suggestions for future practice and research involving the field CIT.

The Current and Future Status of the Concealed Information Test for Field Use

PubMed Central

Matsuda, Izumi; Nittono, Hiroshi; Allen, John J. B.

2012-01-01

The Concealed Information Test (CIT) is a psychophysiological technique for examining whether a person has knowledge of crime-relevant information. Many laboratory studies have shown that the CIT has good scientific validity. However, the CIT has seldom been used for actual criminal investigations. One successful exception is its use by the Japanese police. In Japan, the CIT has been widely used for criminal investigations, although its probative force in court is not strong. In this paper, we first review the current use of the field CIT in Japan. Then, we discuss two possible approaches to increase its probative force: sophisticated statistical judgment methods and combining new psychophysiological measures with classic autonomic measures. On the basis of these considerations, we propose several suggestions for future practice and research involving the field CIT. PMID:23205018

A Numerical and Theoretical Study of Seismic Wave Diffraction in Complex Geologic Structure

DTIC Science & Technology

1989-04-14

element methods for analyzing linear and nonlinear seismic effects in the surficial geologies relevant to several Air Force missions. The second...exact solution evaluated here indicates that edge-diffracted seismic wave fields calculated by discrete numerical methods probably exhibits significant...study is to demonstrate and validate some discrete numerical methods essential for analyzing linear and nonlinear seismic effects in the surficial

An accurate and efficient method for piezoelectric coated functional devices based on the two-dimensional Green’s function for a normal line force and line charge

NASA Astrophysics Data System (ADS)

Hou, Peng-Fei; Zhang, Yang

2017-09-01

Because most piezoelectric functional devices, including sensors, actuators and energy harvesters, are in the form of a piezoelectric coated structure, it is valuable to present an accurate and efficient method for obtaining the electro-mechanical coupling fields of this coated structure under mechanical and electrical loads. With this aim, the two-dimensional Green’s function for a normal line force and line charge on the surface of coated structure, which is a combination of an orthotropic piezoelectric coating and orthotropic elastic substrate, is presented in the form of elementary functions based on the general solution method. The corresponding electro-mechanical coupling fields of this coated structure under arbitrary mechanical and electrical loads can then be obtained by the superposition principle and Gauss integration. Numerical results show that the presented method has high computational precision, efficiency and stability. It can be used to design the best coating thickness in functional devices, improve the sensitivity of sensors, and improve the efficiency of actuators and energy harvesters. This method could be an efficient tool for engineers in engineering applications.

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

PubMed

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

Effects of Deformation on Drag and Lift Forces Acting on a Droplet in a Shear Flow

NASA Astrophysics Data System (ADS)

Suh, Youngho; Lee, Changhoon

2010-11-01

The droplet behavior in a linear shear flow is studied numerically to investigate the effect of deformation on the drag and lift acting on droplet. The droplet shape is calculated by a level set method which is improved by incorporating a sharp-interface modeling technique for accurately enforcing the matching conditions at the liquid- gas interface. By adopting the feedback forces which can maintain the droplet at a fixed position, we determine the acting force on a droplet in shear flow field with efficient handling of deformation. Based on the numerical results, drag and lift forces acting on a droplet are observed to depend strongly on the deformation. Droplet shapes are observed to be spherical, deformed, and oscillating depending on the Reynolds number. Also, the present method is proven to be applicable to a three- dimensional deformation of droplet in the shear flow, which cannot be properly analyzed by the previous studies. Comparisons of the calculated results by the current method with those obtained from body-fitted methods [Dandy and Leal, J. Fluid Mech. 208, 161 (1989)] and empirical models [Feng and Beard, J. Atmos. Sci. 48, 1856 (1991)] show good agreement.

The connection characteristics of flux pinned docking interface

NASA Astrophysics Data System (ADS)

Zhang, Mingliang; Han, Yanjun; Guo, Xing; Zhao, Cunbao; Deng, Feiyue

2017-03-01

This paper presents the mechanism and potential advantages of flux pinned docking interface mainly composed of a high temperature superconductor and an electromagnet. In order to readily assess the connection characteristics of flux pinned docking interface, the force between a high temperature superconductor and an electromagnet needs to be investigated. Based on the magnetic dipole method and the Ampere law method, the force between two current coils can be compared, which shows that the Ampere law method has the higher calculated accuracy. Based on the improved frozen image model and the Ampere law method, the force between high temperature superconductor bulk and permanent magnet can be calculated, which is validated experimentally. Moreover, the force between high temperature superconductor and electromagnet applied to flux pinned docking interface is able to be predicted and analyzed. The connection stiffness between high temperature superconductor and permanent magnet can be calculated based on the improved frozen image model and Hooke's law. The relationship between the connection stiffness and field cooling height is analyzed. Furthermore, the connection stiffness of the flux pinned docking interface is predicted and optimized, and its effective working range is defined and analyzed in case of some different parameters.

Force-moment line element method for flexible slender bodies in Stokes flow.

PubMed

Jiang, H; Yang, B

2013-09-01

The hydrodynamics of flexible slender bodies in Stokes flow is studied by taking into account the fluid-structure interaction through both forces and coupled moments. The fluid subjected to line sources of forces and moments is described by using integral equations. Meanwhile, the flexible slender body is modeled using finite beam elements. The two sides are linked through interfacial continuity conditions. Upon discretization, it results in a higher-order line element method for efficient and accurate solution of slender-body hydrodynamics. Four examples are presented to demonstrate the validity and efficiency of the present method: (a) hydrodynamics of a flexible slender rod subjected to a torque at one end, (b) hydrodynamics of a flexible slender rod subjected to a bending moment at one end, (c) hydrodynamics of a flexible slender rod subjected to a cyclic force, and (d) hydrodynamics of a flexible slender rod with a magnetized head within a rotating magnetic field. Examples (a) and (b) may serve as benchmark solutions and examples (c) and (d) show how planar and spiral waves can be excited in a slender body.

Gravitational self-force on generic bound geodesics in Kerr spacetime

NASA Astrophysics Data System (ADS)

van de Meent, Maarten

2018-05-01

In this work we present the first calculation of the gravitational self-force on generic bound geodesics in Kerr spacetime to first order in the mass ratio. That is, the local correction to equations of motion for a compact object orbiting a larger rotating black hole due to its own impact on the gravitational field. This includes both dissipative and conservative effects. Our method builds on and extends earlier methods for calculating the gravitational self-force on equatorial orbits. In particular we reconstruct the local metric perturbation in the outgoing radiation gauge from the Weyl scalar ψ4 , which in turn is obtained by solving the Teukolsky equation using semianalytical frequency domain methods. The gravitational self-force is subsequently obtained using (spherical) l -mode regularization. We test our implementation by comparing the large l -behavior against the analytically known regularization parameters. In addition we validate our results by comparing the long-term average changes to the energy, angular momentum, and Carter constant to changes to these constants of motion inferred from the gravitational wave flux to infinity and down the horizon.

Molecular Mechanics: Illustrations of Its Application.

ERIC Educational Resources Information Center

Cox, Philip J.

1982-01-01

The application of molecular mechanics (a nonquantum mechanical method for solving problems concerning molecular geometries) to calculate force fields for n-butane and cyclohexane is discussed. Implications regarding the stable conformations of the example molecules are also discussed. (Author/SK)

Nanomaterials for in vivo imaging of mechanical forces and electrical fields

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

Xie, S.; Zhang, Y.

2011-12-01

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

Mapping alternating current electroosmotic flow at the dielectrophoresis crossover frequency of a colloidal probe.

PubMed

Wang, Jingyu; Wei, Ming-Tzo; Cohen, Joel A; Ou-Yang, H Daniel

2013-07-01

AC electroosmotic (ACEO) flow above the gap between coplanar electrodes is mapped by the measurement of Stokes forces on an optically trapped polystyrene colloidal particle. E²-dependent forces on the probe particle are selected by amplitude modulation (AM) of the ACEO electric field (E) and lock-in detection at twice the AM frequency. E²-dependent DEP of the probe is eliminated by driving the ACEO at the probe's DEP crossover frequency. The location-independent DEP crossover frequency is determined, in a separate experiment, as the limiting frequency of zero horizontal force as the probe is moved toward the midpoint between the electrodes. The ACEO velocity field, uncoupled from probe DEP effects, was mapped in the region 1-9 μm above a 28 μm gap between the electrodes. By use of variously sized probes, each at its DEP crossover frequency, the frequency dependence of the ACEO flow was determined at a point 3 μm above the electrode gap and 4 μm from an electrode tip. At this location the ACEO flow was maximal at ∼117 kHz for a low salt solution. This optical trapping method, by eliminating DEP forces on the probe, provides unambiguous mapping of the ACEO velocity field. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

Startsev, Edward A.; Davidson, Ronald C.

2011-05-01

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

Enhanced Dielectrophoretic Enrichment of Nanoparticles Using a Nanostructured Tip for Nanoengineered Medicine and Biology

NASA Astrophysics Data System (ADS)

Yeo, Woonhong

2011-12-01

Enrichment of low-concentration nanoparticles (NPs) is of great interest in the fields of medicine, biology, and environment. In particular, the enrichment of bioparticles such as virus, quantum dots, DNA, or protein can have broad impacts on disease diagnosis, drug discovery, and environmental monitoring. Currently available NP enrichment methods employ centrifugation, microfiltration, or magnetic field. However, these methods are limited in cumbersome preparation steps, low yield, and low throughput. Electric field-based methods have demonstrated potential for NP enrichment, but two-dimensional planar electrodes are limited in sensitivity, molecular transfer, and imaging capability. In addition, the detection of low abundance, non-amplifiable particles such as proteins and metals is very challenging due to the low efficiency of current methods. In this dissertation, the challenges are addressed by nanotip-based NP enrichment. Fundamentals of NP enrichment are studied with a nanostructured tip. The nanotip-based NP enrichment is investigated by correlating a dielectrophoretic (DEP) force with Brownian motion force. In experiment, the predicted NP enrichment is validated by using gold (Au) NPs. The DEP effective distance for NP enrichment with a nanotip is suggested. Sequence-specific enrichment of oligonucleotides is studied by considering DEP force, Brownian motion, and affinity binding. In experiment, the optimal parameters for ultimate enrichment performance are studied using a hybridization assay. In the assay, a nanotip is functionalized with probe-oligonucleotides for sequence-specific binding. Size-specific NP enrichment is explored by studying DEP, capillary action, and viscosity. The capillary action force with a nanotip is calculated analytically, which is then compared with the DEP force. The viscosity effect is considered for NP capturing on a nanotip. The studied size-specific enrichment mechanism is validated in experiment by using various polystyrene nanospheres. The studied enrichment mechanism of NPs with a nanotip is applied to the detection of viral particles. In the characterization study, T7 viral particles having 50 nm in diameter are observed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). In experiment, the viral particles in a buffer are enriched to a nanotip by DEP, and captured onto the nanotip by DEP and viscosity. The captured viral particles on the nanotip are detected by fluorescence microscopy for whole nanotip observation, and validated by SEM. The enhanced DEP enrichment of NPs using a nanotip shows great potential for highly sensitive NP detection and analysis in nanoengineered medicine and biology.

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.

Strong coupling in electromechanical computation

NASA Astrophysics Data System (ADS)

Füzi, János

2000-06-01

A method is presented to carry out simultaneously electromagnetic field and force computation, electrical circuit analysis and mechanical computation to simulate the dynamic operation of electromagnetic actuators. The equation system is solved by a predictor-corrector scheme containing a Powell error minimization algorithm which ensures that every differential equation (coil current, field strength rate, flux rate, speed of the keeper) is fulfilled within the same time step.

Effects of Traveling Magnetic Field on Dynamics of Solidification

NASA Technical Reports Server (NTRS)

2003-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

DTIC Science & Technology

1968-03-01

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

Nondestructive assessment of timber bridges using a vibration-based method

Treesearch

Xiping Wang; James P. Wacker; Robert J. Ross; Brian K. Brashaw

2005-01-01

This paper describes an effort to develop a global dynamic testing technique for evaluating the overall stiffness of timber bridge superstructures. A forced vibration method was used to measure the natural frequency of single-span timber bridges in the laboratory and field. An analytical model based on simple beam theory was proposed to represent the relationship...

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

NASA Astrophysics Data System (ADS)

Shibasaki, Kiyoto

2017-04-01

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

Dynamo action in dissipative, forced, rotating MHD turbulence

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

Shebalin, John V.

2016-06-15

Magnetohydrodynamic (MHD) turbulence is an inherent feature of large-scale, energetic astrophysical and geophysical magnetofluids. In general, these are rotating and are energized through buoyancy and shear, while viscosity and resistivity provide a means of dissipation of kinetic and magnetic energy. Studies of unforced, rotating, ideal (i.e., non-dissipative) MHD turbulence have produced interesting results, but it is important to determine how these results are affected by dissipation and forcing. Here, we extend our previous work and examine dissipative, forced, and rotating MHD turbulence. Incompressibility is assumed, and finite Fourier series represent turbulent velocity and magnetic field on a 64{sup 3} grid.more » Forcing occurs at an intermediate wave number by a method that keeps total energy relatively constant and allows for injection of kinetic and magnetic helicity. We find that 3-D energy spectra are asymmetric when forcing is present. We also find that dynamo action occurs when forcing has either kinetic or magnetic helicity, with magnetic helicity injection being more important. In forced, dissipative MHD turbulence, the dynamo manifests itself as a large-scale coherent structure that is similar to that seen in the ideal case. These results imply that MHD turbulence, per se, may play a fundamental role in the creation and maintenance of large-scale (i.e., dipolar) stellar and planetary magnetic fields.« less

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

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

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

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

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

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

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

PubMed

Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J Andrew

2017-07-13

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM ( M VISM) compares with atomistic VISM ( A VISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate M VISM's suitability to study the solvation properties of an interesting encounter complex, barnase-barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM's and MARTINI's applications in the near future.

A Multiscale Atomistic Method for Long-Range Electrical Interactions with Application to Multiphysics Calculations in Functional Materials

DTIC Science & Technology

2016-02-28

centered at a point, x, where the field is to be evaluated , and the far field region Ωfar. A single unit cell located at x′ in the far field region is...successive shell adds less total error as expected because of the increased distance from evaluation point. . . . . . . . . . . . . . . . . . 108...of freedom in the system to more manageable levels. Energies or forces in the system are then evaluated through numerical quadrature rules and allow

Bite Forces and Their Measurement in Dogs and Cats.

PubMed

Kim, Se Eun; Arzi, Boaz; Garcia, Tanya C; Verstraete, Frank J M

2018-01-01

Bite force is generated by the interaction of the masticatory muscles, the mandibles and maxillae, the temporomandibular joints (TMJs), and the teeth. Several methods to measure bite forces in dogs and cats have been described. Direct in vivo measurement of a bite in dogs has been done; however, bite forces were highly variable due to animal volition, situation, or specific measurement technique. Bite force has been measured in vivo from anesthetized dogs by electrical stimulation of jaw adductor muscles, but this may not be reflective of volitional bite force during natural activity. In vitro bite forces have been estimated by calculation of the force produced using mechanical equations representing the jaw adductor muscles and of the mandible and skull structure Bite force can be estimated in silico using finite element analysis (FEA) of the computed model of the anatomical structures. FEA can estimate bite force in extinct species; however, estimates may be lower than the measurements in live animals and would have to be validated specifically in domestic dogs and cats to be reliable. The main factors affecting the bite forces in dogs and cats are body weight and the skull's morphology and size. Other factors such as oral pain, TMJ disorders, masticatory muscle atrophy, and malocclusion may also affect bite force. Knowledge of bite forces in dogs and cats is essential for various clinical and research fields such as the development of implants, materials, and surgical techniques as well as for forensic medicine. This paper is a summary of current knowledge of bite forces in dogs and cats, including the effect of measurement methods and of other factors.

First order reversal curves (FORC) analysis of individual magnetic nanostructures using micro-Hall magnetometry

NASA Astrophysics Data System (ADS)

Pohlit, Merlin; Eibisch, Paul; Akbari, Maryam; Porrati, Fabrizio; Huth, Michael; Müller, Jens

2016-11-01

Alongside the development of artificially created magnetic nanostructures, micro-Hall magnetometry has proven to be a versatile tool to obtain high-resolution hysteresis loop data and access dynamical properties. Here we explore the application of First Order Reversal Curves (FORC)—a technique well-established in the field of paleomagnetism for studying grain-size and interaction effects in magnetic rocks—to individual and dipolar-coupled arrays of magnetic nanostructures using micro-Hall sensors. A proof-of-principle experiment performed on a macroscopic piece of a floppy disk as a reference sample well known in the literature demonstrates that the FORC diagrams obtained by magnetic stray field measurements using home-built magnetometers are in good agreement with magnetization data obtained by a commercial vibrating sample magnetometer. We discuss in detail the FORC diagrams and their interpretation of three different representative magnetic systems, prepared by the direct-write Focused Electron Beam Induced Deposition (FEBID) technique: (1) an isolated Co-nanoisland showing a simple square-shaped hysteresis loop, (2) a more complex CoFe-alloy nanoisland exhibiting a wasp-waist-type hysteresis, and (3) a cluster of interacting Co-nanoislands. Our findings reveal that the combination of FORC and micro-Hall magnetometry is a promising tool to investigate complex magnetization reversal processes within individual or small ensembles of nanomagnets grown by FEBID or other fabrication methods. The method provides sub-μm spatial resolution and bridges the gap of FORC analysis, commonly used for studying macroscopic samples and rather large arrays, to studies of small ensembles of interacting nanoparticles with the high moment sensitivity inherent to micro-Hall magnetometry.

MAGNETO-FRICTIONAL MODELING OF CORONAL NONLINEAR FORCE-FREE FIELDS. I. TESTING WITH ANALYTIC SOLUTIONS

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

Guo, Y.; Keppens, R.; Xia, C.

2016-09-10

We report our implementation of the magneto-frictional method in the Message Passing Interface Adaptive Mesh Refinement Versatile Advection Code (MPI-AMRVAC). The method aims at applications where local adaptive mesh refinement (AMR) is essential to make follow-up dynamical modeling affordable. We quantify its performance in both domain-decomposed uniform grids and block-adaptive AMR computations, using all frequently employed force-free, divergence-free, and other vector comparison metrics. As test cases, we revisit the semi-analytic solution of Low and Lou in both Cartesian and spherical geometries, along with the topologically challenging Titov–Démoulin model. We compare different combinations of spatial and temporal discretizations, and find thatmore » the fourth-order central difference with a local Lax–Friedrichs dissipation term in a single-step marching scheme is an optimal combination. The initial condition is provided by the potential field, which is the potential field source surface model in spherical geometry. Various boundary conditions are adopted, ranging from fully prescribed cases where all boundaries are assigned with the semi-analytic models, to solar-like cases where only the magnetic field at the bottom is known. Our results demonstrate that all the metrics compare favorably to previous works in both Cartesian and spherical coordinates. Cases with several AMR levels perform in accordance with their effective resolutions. The magneto-frictional method in MPI-AMRVAC allows us to model a region of interest with high spatial resolution and large field of view simultaneously, as required by observation-constrained extrapolations using vector data provided with modern instruments. The applications of the magneto-frictional method to observations are shown in an accompanying paper.« less