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At least 469 records · Page 26

Shape Servoing of Deformable Objects Using Model Estimation and Barrier Lyapunov Function

An adaptive shape servoing control method is presented in this article to manipulate a deformable object into a desired shape in 3-D. A finite-point-based representation of the deformable object is used and the deformation Jacobian matrix is approximated using Fourier series basis functions. The unknown parameters of the deformation Jacobian are learned by using the velocity applied to a control point on the object and corresponding change of positions of the points describing the entire object. An integral concurrent learning (ICL)-based parameter update law is designed along with a constrained controller to satisfy the state constraints on the motion of the control point using Barrier Lyapunov function analysis. ICL-based parameter update law uses data history of velocity and corresponding positions of the points along with their current values. An efficient algorithm to update the history stack using singular value maximization is proposed based on the structure of the regressor matrix. Simulations using a physical simulator and experiments using a robot platform are performed to validate the performance of the proposed controller on two different deformable objects.

Vrithik Raj Guthikonda↗

Immunotherapy-induced neutralizing antibodies disrupt allergen binding and sustain allergen tolerance in peanut allergy

In IgE-mediated food allergies, exposure to the allergen activates systemic allergic responses. Oral immunotherapy (OIT) treats food allergies through incremental increases in oral allergen exposure. However, OIT only induces sustained clinical tolerance and decreased basophil sensitivity in a subset of individuals despite increases in circulating allergen-specific IgG in all treated individuals. Therefore, we examined the allergen-specific antibodies from 2 OIT cohorts of patients with sustained and transient responses. Here, we compared antibodies from individuals with sustained or transient responses and discovered specific tolerance-associated conformational epitopes of the immunodominant allergen Ara h 2 recognized by neutralizing antibodies. First, we identified what we believe to be previously unknown conformational, intrahelical epitopes using x-ray crystallography with recombinant antibodies. We then identified epitopes only recognized in sustained tolerance. Finally, antibodies recognizing tolerance-associated epitopes effectively neutralized allergen to suppress IgE-mediated effector cell activation. Our results demonstrate the molecular basis of antibody-mediated protection in IgE-mediated food allergy, by defining how these antibodies disrupt IgE-allergen interactions to prevent allergic reactions. Our approach to studying the structural and functional basis for neutralizing antibodies demonstrates the clinical relevance of specific antibody clones in antibody-mediated tolerance. We anticipate that our findings will form the foundation for treatments of peanut allergy using neutralizing antibodies and hypoallergens.

60 APPLIED LIFE SCIENCES↗

FEOTS v0.0.0: a new offline code for the fast equilibration of tracers in the ocean

Abstract. In this paper we introduce a new software framework for the offline calculation of tracer transport in the ocean. The Fast Equilibration of Ocean Tracers Software (FEOTS) is an end-to-end set of tools to efficiently calculate tracer distributions on a global or regional sub-domain using transport operators diagnosed from a comprehensive ocean model. To the best of our knowledge, this is the first application of a transport matrix model to an eddying ocean state. While a Newton–Krylov-based equilibration capability is still under development and not presented here, we demonstrate in this paper the transient modeling capabilities of FEOTS in an application focused on the Argentine Basin, where intense eddy activity and the Zapiola Anticyclone lead to strong mixing of water masses. The demonstration illustrates progress in developing offline passive tracer simulation capabilities, while highlighting the challenges of the impulse response functions approach in capturing tracer transports by a non-linear advection scheme. Our future work will focus on improving the computational efficiency of the code to reduce time-to-solution, using different basis functions to better represent non-linear advection operators, applying FEOTS to a parent model with unstructured grids (Ocean Model for Prediction Across Scales, MPAS-Ocean), and fully implementing a Newton–Krylov steady-state solver.

54 ENVIRONMENTAL SCIENCES↗

Stochastic evaluation of four-component relativistic second-order many-body perturbation energies: A potentially quadratic-scaling correlation method

A second-order many-body perturbation correction to the relativistic Dirac-Hartree-Fock energy is evaluated stochastically by integrating 13-dimensional products of four-component spinors and Coulomb potentials. The integration in the real space of electron coordinates is carried out by the Monte Carlo (MC) method with the Metropolis sampling, whereas the MC integration in the imaginary-time domain is performed by the inverse-CDF (cumulative distribution function) method. The computational cost to reach a given relative statistical error for spatially compact but heavy molecules is observed to be no worse than cubic and possibly quadratic with the number of electrons or basis functions. This is a vast improvement over the quintic scaling of the conventional, deterministic second-order many-body perturbation method. The algorithm is also easily and efficiently parallelized with demonstrated 92% strong scalability going from 64 to 4096 processors for a fixed job size.

74 ATOMIC AND MOLECULAR PHYSICS↗

Application of a new hybrid particle swarm optimization-mixed kernels function-based support vector machine model for reservoir porosity prediction: A case study in Jacksonburg-Stringtown oil field, West Virginia, USA

Porosity is a fundamental property that characterizes the storage capability of fluid and gas-bearing formations in a reservoir. An accurate porosity value can be measured from core samples in the laboratory; however, core analysis is expensive and time consuming. Well-log data can be used to calculate porosity, but the availability of log suites is often limited in mature fields. Therefore, robust porosity prediction requires integration of core-measured porosity with available well-log suites to control for changes in lithology and fluid content. A support vector machine (SVM) model with mixed kernel function (MKF) is used to construct the relationship between limited conventional well-log suites and sparse core data. Porosity is the desired output, and two conventional well-log responses (gamma ray [GR] and bulk density) and three well-log-derived parameters (the slope of GR, the slope of density, and [Formula: see text]) are input parameters. A global stochastic searching algorithm, particle swarm optimization (PSO), is applied to improve the efficiency of locating the appropriate values of five control parameters in MKF-SVM model. The results of SVM with different traditional kernel functions were compared, and the MKF-SVM model provided an improvement over the traditional SVM model. To confirm the advantage of the hybrid PSO-MKF-SVM model, the results from three models: (1) radial basis function (RBF)-based least-squares SVM, (2) multilayer perceptron artificial neural network (ANN), and (3) RBF ANN, are compared with the result of the hybrid PSO-MKF-SVM model. The results indicate that the hybrid PSO-MKF-SVM model improves porosity prediction with the highest correlation coefficient ([Formula: see text] of 0.9560), the highest coefficient of determination ([Formula: see text] of 0.9140), the lowest root-mean-square error (1.6505), average absolute error value (1.4050), and maximum absolute error (2.717).

Geochemistry & Geophysics↗

Perceptually Lossless Wavelet Compression

The Discrete Wavelet Transform (DWT) decomposes an image into bands that vary in spatial frequency and orientation. It is widely used for image compression. Measures of the visibility of DWT quantization errors are required to achieve optimal compression. Uniform quantization of a single band of coefficients results in an artifact that is the sum of a lattice of random amplitude basis functions of the corresponding DWT synthesis filter, which we call DWT uniform quantization noise. We measured visual detection thresholds for samples of DWT uniform quantization noise in Y, Cb, and Cr color channels. The spatial frequency of a wavelet is r 2(exp -1), where r is display visual resolution in pixels/degree, and L is the wavelet level. Amplitude thresholds increase rapidly with spatial frequency. Thresholds also increase from Y to Cr to Cb, and with orientation from low-pass to horizontal/vertical to diagonal. We propose a mathematical model for DWT noise detection thresholds that is a function of level, orientation, and display visual resolution. This allows calculation of a 'perceptually lossless' quantization matrix for which all errors are in theory below the visual threshold. The model may also be used as the basis for adaptive quantization schemes.

Watson, Andrew B.↗

Visibility of Wavelet Quantization Noise

The Discrete Wavelet Transform (DWT) decomposes an image into bands that vary in spatial frequency and orientation. It is widely used for image compression. Measures of the visibility of DWT quantization errors are required to achieve optimal compression. Uniform quantization of a single band of coefficients results in an artifact that is the sum of a lattice of random amplitude basis functions of the corresponding DWT synthesis filter, which we call DWT uniform quantization noise. We measured visual detection thresholds for samples of DWT uniform quantization noise in Y, Cb, and Cr color channels. The spatial frequency of a wavelet is r 2(exp)-L , where r is display visual resolution in pixels/degree, and L is the wavelet level. Amplitude thresholds increase rapidly with spatial frequency. Thresholds also increase from Y to Cr to Cb, and with orientation from low-pass to horizontal/vertical to diagonal. We describe a mathematical model to predict DWT noise detection thresholds as a function of level, orientation, and display visual resolution. This allows calculation of a "perceptually lossless" quantization matrix for which all errors are in theory below the visual threshold. The model may also be used as the basis for adaptive quantization schemes.

Watson, Andrew B.↗

Visibility of wavelet quantization noise

The discrete wavelet transform (DWT) decomposes an image into bands that vary in spatial frequency and orientation. It is widely used for image compression. Measures of the visibility of DWT quantization errors are required to achieve optimal compression. Uniform quantization of a single band of coefficients results in an artifact that we call DWT uniform quantization noise; it is the sum of a lattice of random amplitude basis functions of the corresponding DWT synthesis filter. We measured visual detection thresholds for samples of DWT uniform quantization noise in Y, Cb, and Cr color channels. The spatial frequency of a wavelet is r 2-lambda, where r is display visual resolution in pixels/degree, and lambda is the wavelet level. Thresholds increase rapidly with wavelet spatial frequency. Thresholds also increase from Y to Cr to Cb, and with orientation from lowpass to horizontal/vertical to diagonal. We construct a mathematical model for DWT noise detection thresholds that is a function of level, orientation, and display visual resolution. This allows calculation of a "perceptually lossless" quantization matrix for which all errors are in theory below the visual threshold. The model may also be used as the basis for adaptive quantization schemes.

NASA Center ARC↗

Pn-FEM Method for Solving the First-Order Neutron Transport Equation

A deterministic method was investigated and developed for the photon-neutron transport calculation for fusion reactor blanket. Firstly, considering the fact that the second order transport equation cannot describe void region accurately due to the appearance of zero total cross section in the denominator, the first order equation was selected as the starting point of the solution. The angular discretization uses the spherical harmonics (Pn) method. Although discrete ordinates (Sn) method has been most commonly applied due to its efficiency, it suffers from the ray effect. To describe unstructured geometry, the finite element method was used to discrete spatial variable. It is well known that Bubnov-Galerkin discretization of the first-order equation is inappropriate which will create oscillations. To obtain robust solutions, Petrov- Galerkin methods have been developed such as the Streamline-Upwind Petrov-Galerkin (SUPG) method and the Generalized Least-Squares (GLS) method. These methods require a stabilization term added to its test functions, which will incur additional computational cost. Another finite element formulation that usually used for first order equation is the Discontinuous-Galerkin (DG) method. In this method, each element has a unique and separate set of basis function. Then the adjacent elements can be connected by using the in-coming flux. Its main drawback is the number of unknowns, much larger than Continuous-Galerkin (CG) method. The Sub-Grid Scale (SGS) finite element method combines the advantages of CG and DG methods together. It inserts the DG method in each element to correct the CG solution, and provides numerically stable solution of first-order equation without increasing the number of unknowns. The boundary conditions and interface conditions for Pn method is a hard nut to crack. We use Riemann method to deal with this problem. It decomposes the neutron angular flux into in-coming and out-going information through an interface, and applies boundary condition to the in-coming one. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

J-matrix method for calculations of three-body Coulomb wave functions and cross sections of physical processes

The review is devoted to a widely known method of numerical solution to the three-body Coulomb problem, namely, the J-matrix method. Special attention is paid to ways of solving the Lippmann-Schwinger integral equation without attraction of pseudostates. Difficulties related to the formulation of the integral equation in spherical coordinates, leading to the divergence of its integral part if the wave function is calculated with two asymptotically free electrons, are demonstrated. In addition, the relation between exact and approximate solutions turns out to be unclear if the matrix of a residual potential is restricted to a finite number of basis functions, with the latter being increased. It is shown that, in principle, these problems can be avoided by reformulating a problem in parabolic coordinates.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗

Hybrid grid/basis set discretizations of the Schrödinger equation

We present a new kind of basis function for discretizing the Schrödinger equation in electronic structure calculations, called a gausslet, which has wavelet-like features but is composed of a sum of Gaussians. Gausslets are placed on a grid and combine advantages of both grid and basis set approaches. They are orthogonal, infinitely smooth, symmetric, polynomially complete, and with a high degree of locality. Because they are formed from Gaussians, they are easily combined with traditional atom-centered Gaussian bases. As a result, we also introduce diagonal approximations that dramatically reduce the computational scaling of two-electron Coulomb terms in the Hamiltonian.

97 MATHEMATICS AND COMPUTING↗

Hamiltonians and order parameters for crystals of orientable molecules

Many modern functional materials exhibit microscopic degrees of freedom that are difficult to describe mathematically or do not conform to conventional models in solid state physics. In this paper, we consider crystals containing orientable molecular species, which encompass the class of promising photovoltaic materials CH 3 NH 3 PbX 3 . Abstracting these materials as crystals of orientable rigid rotors, we develop an effective Hamiltonian that expresses the crystal potential energy in terms of collective orientations of interacting rigid rotors. The approach is motivated by the cluster expansion framework from alloy theory and is appropriate for describing both chiral and achiral molecules. This framework utilizes a quaternion parametrization of molecular orientation and makes full use of the symmetry both of the rotors and of the crystal in order to constrain the functional form of the final Hamiltonian expression. The resulting Hamiltonian is compact, systematically improvable, and is suitable for Monte Carlo or molecular dynamics simulation. We apply this formalism to CH 3 NH 3 PbI 3 and report symmetry-adapted basis functions that can be used to construct order parameters or Hamiltonians that describe orientational correlation of methylammonium ions in hybrid organic-inorganic halide perovskite materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

MolSym : A Python package for handling symmetry in molecular quantum chemistry

A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program’s environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree–Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. Furthermore, this package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A spectral scheme for Kohn–Sham density functional theory of clusters

Starting from the observation that one of the most successful methods for solving the Kohn–Sham equations for periodic systems – the plane-wave method – is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn–Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn–Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix—required to propagate the electron dynamics—, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A spectral reflectance estimation technique using multispectral data from the Viking lander camera

A technique is formulated for constructing spectral reflectance curve estimates from multispectral data obtained with the Viking lander camera. The multispectral data are limited to six spectral channels in the wavelength range from 0.4 to 1.1 micrometers and most of these channels exhibit appreciable out-of-band response. The output of each channel is expressed as a linear (integral) function of the (known) solar irradiance, atmospheric transmittance, and camera spectral responsivity and the (unknown) spectral responsivity and the (unknown) spectral reflectance. This produces six equations which are used to determine the coefficients in a representation of the spectral reflectance as a linear combination of known basis functions. Natural cubic spline reflectance estimates are produced for a variety of materials that can be reasonably expected to occur on Mars. In each case the dominant reflectance features are accurately reproduced, but small period features are lost due to the limited number of channels. This technique may be a valuable aid in selecting the number of spectral channels and their responsivity shapes when designing a multispectral imaging system.

Park, S. K.↗

Solving many-body Schrödinger equations with kinetic energy partition method

We present a general formulation of our previously developed kinetic energy partition (KEP) method for solving many-bodySchrödinger equations. In atomic physics, as well as in general molecular and solid state physics, solving many-electronSchrödinger equations is a very challenging task, often called Dirac’s challenge. The central problem is how to properly handle the electron–electron Coulomb repulsion interactions. Using the KEP solution scheme, in addition to dividing the kinetic energy into partial terms, the electron–electron Coulomb interaction is also separated into parts to be associated with a “negative mass” kinetic energy term. Therefore, the full Hamiltonian can be expressed as a simple sum of subsystem Hamiltonians, each representing an effective one-body problem. Using a Hartree-like product in constructing the wave-function, we achieve fast convergence in the calculations of the ground state energies. First, the model Moshinsky atoms are used to illustrate the solution procedure. We then apply this new KEP method to harmonium atoms and obtain precise energies with an error less than 5% using only two basis functions from each subsystem. It is thus very promising that this methodology, when further extended, can be useful for general many-body systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗