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At least 163 records · Page 9

Vector send operation for message-based communication

Methods and systems for conducting vector send operations are provided. The processor of a sender node receives a request to perform a collective send operation (e.g., MPI_Broadcast) from a user application, requesting a copy of data in one or more send buffers by sent to each of a plurality of destinations in a destination vector. The processor invokes a vector send operation from a software communications library, placing a remote enqueue atomic send command for each destination node of the destination vector in an entry of a transmit data mover (XDM) command queue in a single call. The processor executes all of the commands in the XDM command queue and writes the data in the one or more send buffers into each receive queue of each destination identified in the destination vector.

Byrne, John L.↗

PERFORMANCE CHARACTERISTICS OF A VECTOR SENSOR ARRAY IN AN ENERGETIC TIDAL CHANNEL

A compact three-dimensional vector sensor array (termed the NoiseSpotter) was recently developed with the goal of characterizing and localizing sources of sound in energetic environments such as those where marine renewable energy devices are likely to be located. The three vector sensors on the NoiseSpotter are mounted on a bottom platform with each sensor suspended inside an optional flow noise removal shield. The multiple pressure and particle velocity channels on the NoiseSpotter are simultaneously sampled and stored on-board to enable coherent array processing of vector sensor array data. A series of field trials were conducted where the NoiseSpotter was deployed on a bottom platform in an 8 m deep tidal channel in Sequim Bay, Washington. Pure tones were transmitted from a drifting vessel whose distance from the bottom platform varied between 50 m and 500 m. The effect of flow noise on vector sensor array performance is quantified along with the detectability of low intensity sound in an energetic environment. Flow noise removal efficiency for each channel of every vector sensor is demonstrated using multiple metrics derived from the active and reactive intensities computed using the pressure-velocity cross-spectral density matrix. A flow noise removal shield is shown to improve the detectability of low intensity sound such as those that are expected to be emitted by marine renewable energy devices.

Raghukumar, Kaustubha↗

Model-Based Iterative Reconstruction of Magnetization Using Vector Field Electron Tomography

Vector field electron tomography (VFET) is extensively used for three-dimensional (3-D) imaging of magnetic materials at nanometer resolutions. The conventional approach is to reconstruct and visualize the magnetic vector potential or the magnetic field associated with the sample. There is a lack of algorithms capable of reconstructing the 3-D distribution of magnetization from VFET data. Unlike magnetic vector potential and magnetic field, magnetization is a fundamental physical property of the sample that does not extend beyond the dimensions of the sample. We present a model-based iterative reconstruction algorithm (MBIR) that reconstructs the magnetization by minimizing a cost function consisting of a forward model term and a prior model term. The forward model uses the physics of imaging to model the VFET data as a function of the magnetization, and the prior model enforces sparsity in the magnetization reconstruction. We then formulate an optimization algorithm based on the theory of alternate direction method of multipliers to minimize the resulting MBIR cost function. In conclusion, using simulated and real data, we show that our algorithm accurately reconstructs both the magnetization and the magnetic vector potential.

97 MATHEMATICS AND COMPUTING↗

On the use of finite difference matrix-vector products in Newton-Krylov solvers for implicit climate dynamics with spectral elements

Efficient solutions of global climate models require effectively handling disparate length and time scales. Implicit solution approaches allow time integration of the physical system with a step size governed by accuracy of the processes of interest rather than by stability of the fastest time scales present. Implicit approaches, however, require the solution of nonlinear systems within each time step. Usually, a Newton's method is applied to solve these systems. Each iteration of the Newton's method, in turn, requires the solution of a linear model of the nonlinear system. This model employs the Jacobian of the problem-defining nonlinear residual, but this Jacobian can be costly to form. If a Krylov linear solver is used for the solution of the linear system, the action of the Jacobian matrix on a given vector is required. In the case of spectral element methods, the Jacobian is not calculated but only implemented through matrix-vector products. The matrix-vector multiply can also be approximated by a finite difference approximation which may introduce inaccuracy in the overall nonlinear solver. In this paper, we review the advantages and disadvantages of finite difference approximations of these matrix-vector products for climate dynamics within the spectral element shallow water dynamical core of the Community Atmosphere Model.

54 ENVIRONMENTAL SCIENCES↗

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.

36 MATERIALS SCIENCE↗

A heterologous prime-boosting strategy with replicating Vaccinia virus vectors and plant-produced HIV-1 Gag/dgp41 virus-like particles

Showing modest efficacy, the RV144 HIV-1 vaccine clinical trial utilized a non-replicating canarypox viral vector and a soluble gp120 protein boost. Here we built upon the RV144 strategy by developing a novel combination of a replicating, but highly-attenuated Vaccinia virus vector, NYVAC-KC, and plant-produced HIV-1 virus-like particles (VLPs). Both components contained the full-length Gag and a membrane anchored truncated gp41 presenting the membrane proximal external region with its conserved broadly neutralizing epitopes in the pre-fusion conformation. We tested different prime/boost combinations of these components in mice and showed that the group primed with NYVAC-KC and boosted with both the viral vectors and plant-produced VLPs have the most robust Gag-specific CD8 T cell responses, at 12.7% of CD8 T cells expressing IFN-γ in response to stimulation with five Gag epitopes. The same immunization group elicited the best systemic and mucosal antibody responses to Gag and dgp41 with a bias towards IgG1. - Highlights: • We devised a prime/boost anti HIV-1 vaccination strategy modeled after RV144. • We used plant-derived virus-like particles (VLPs) consisting of Gag and dgp41. • We used attenuated, replicating vaccinia virus vectors expressing the same antigens. • The immunogens elicited strong cellular and humoral immune responses.

60 APPLIED LIFE SCIENCES↗

Electrical Detection of Single-Domain Néel Vector Reorientation across the Spin–Flop Transition in Cr 2 O 3 Crystals

Electrical transport measurements in heterostructures of antiferromagnetic Cr 2 O 3 bulk crystals and a thin Pt layer exhibit sharp responses as the Néel vector of Cr 2 O 3 undergoes the spin−flop transition. This abrupt change can arise from several distinct mechanisms including magnetostriction, proximity-induced anomalous Hall, spin Hall anomalous Hall, and spin Hall planar Hall effects. While large Pt devices sensing multiple up/ down domains can produce indistinguishable Hall signal jumps due to different initial Néel vector orientations, smaller Pt devices that sense single domains isolate the proximity-induced Hall signals. This allows direct electrical detection of Néel vector reorientation across the spin−flop transition in single-domain regions. Furthermore, the single-domain state can be prepared by magnetic field cooling or magnetoelectric cooling. We demonstrate a method to control and characterize the three-dimensional orientation of single-domain Néel vectors by exploiting Hall measurements and cooling techniques, crucial for future antiferromagnetic spintronic applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Vector spin modeling for magnetic tunnel junctions with voltage dependent effects

Integration and co-design of CMOS and spin transfer devices requires accurate vector spin conduction modeling of magnetic tunnel junction (MTJ) devices. A physically realistic model of the MTJ should comprehend the spin torque dynamics of nanomagnet interacting with an injected vector spin current and the voltage dependent spin torque. Vector spin modeling allows for calculation of 3 component spin currents and potentials along with the charge currents/potentials in non-collinear magnetic systems. Here, we show 4-component vector spin conduction modeling of magnetic tunnel junction devices coupled with spin transfer torque in the nanomagnet. Nanomagnet dynamics, voltage dependent spin transport, and thermal noise are comprehended in a self-consistent fashion. We show comparison of the model with experimental magnetoresistance (MR) of MTJs and voltage degradation of MR with voltage. Proposed model enables MTJ circuit design that comprehends voltage dependent spin torque effects, switching error rates, spin degradation, and back hopping effects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Is there supercurvature mode of massive vector field in open inflation?

We investigate the Euclidean vacuum mode functions of a massive vector field in a spatially open chart of de Sitter spacetime. In the one-bubble open inflationary scenario that naturally predicts a negative spatial curvature after a quantum tunneling, it is known that a light scalar field has the so-called supercurvature mode, i.e. an additional discrete mode which describes fluctuations over scales larger than the spatial curvature scale. If such supercurvature modes exist for a vector field with a sufficiently light mass, then they would decay slower and easily survive the inflationary era. However, the existence of supercurvature mode strongly depends on details of the system. To clarify whether a massive vector field has supercurvature modes, we consider a U(1) gauge field with gauge and conformal invariances spontaneously broken through the Higgs mechanism, and present explicit expressions for the Euclidean vacuum mode functions. We find that, for any values of the vector field mass, there is no supercurvature mode. In the massless limit, the absence of supercurvature modes in the scalar sector stems from the gauge symmetry.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Super-inflation and generation of first order vector perturbations in ELKO

In this work we construct a model where the first order vector perturbations can be generated during inflationary expansion. For the non-standard spinors, known as ELKO, we show that the components of the first order perturbed energy-momentum tensor of the ELKO is non-zero for pure vector part of the metric perturbation (B{sub i}). We show that vector perturbations do not decay in the super-Hubble scale and for a specific super-inflation background model we show that the vector perturbations are nearly scale invariant, while its amplitude is smaller than the primordial scalar perturbations. We also comment on the generation of vorticity.

79 ASTRONOMY AND ASTROPHYSICS↗

f(R) gravity on non-linear scales: the post-Friedmann expansion and the vector potential

Many modified gravity theories are under consideration in cosmology as the source of the accelerated expansion of the universe and linear perturbation theory, valid on the largest scales, has been examined in many of these models. However, smaller non-linear scales offer a richer phenomenology with which to constrain modified gravity theories. Here, we consider the Hu-Sawicki form of f(R) gravity and apply the post-Friedmann approach to derive the leading order equations for non-linear scales, i.e. the equations valid in the Newtonian-like regime. We reproduce the standard equations for the scalar field, gravitational slip and the modified Poisson equation in a coherent framework. In addition, we derive the equation for the leading order correction to the Newtonian regime, the vector potential. We measure this vector potential from f(R) N-body simulations at redshift zero and one, for two values of the f{sub R{sub 0}} parameter. We find that the vector potential at redshift zero in f(R) gravity can be close to 50% larger than in GR on small scales for |f{sub R{sub 0}}|=1.289 × 10{sup −5}, although this is less for larger scales, earlier times and smaller values of the f{sub R{sub 0}} parameter. Similarly to in GR, the small amplitude of this vector potential suggests that the Newtonian approximation is highly accurate for f(R) gravity, and also that the non-linear cosmological behaviour of f(R) gravity can be completely described by just the scalar potentials and the f(R) field.

79 ASTRONOMY AND ASTROPHYSICS↗

Stable solutions of inflation driven by vector fields

Many models of inflation driven by vector fields alone have been known to be plagued by pathological behaviors, namely ghost and/or gradient instabilities. In this work, we seek a new class of vector-driven inflationary models that evade all of the mentioned instabilities. We build our analysis on the Generalized Proca Theory with an extension to three vector fields to realize isotropic expansion. We obtain the conditions required for quasi de-Sitter solutions to be an attractor analogous to the standard slow-roll one and those for their stability at the level of linearized perturbations. Identifying the remedy to the existing unstable models, we provide a simple example and explicitly show its stability. This significantly broadens our knowledge on vector inflationary scenarios, reviving potential phenomenological interests for this class of models.

79 ASTRONOMY AND ASTROPHYSICS↗

A New Suite of Plasmid Vectors for Fluorescence-Based Imaging of Root Colonizing Pseudomonads

In the terrestrial ecosystem, plant-microbe symbiotic associations are ecologically and economically important processes. To better understand these associations at structural and functional levels, different molecular and biochemical tools are applied. In this study, we have constructed a suite of vectors that incorporates several new elements into the rhizosphere stable, broad-host vector pME6031. The new vectors are useful for studies requiring multi-color tagging and visualization of plant-associated, Gram negative bacterial strains such as Pseudomonas plant growth promotion and biocontrol strains. A number of genetic elements, including constitutive promoters and signal peptides that target secretion to the periplasm, have been evaluated. Several next generation fluorescent proteins, namely mTurquoise2, mNeonGreen, mRuby2, DsRed-Express2 and E2-Crimson have been incorporated into the vectors for whole cell labeling or protein tagging. Secretion of mTurquoise2 and mNeonGreen into the periplasm of Pseudomonas fluorescens SBW25 has also been demonstrated, providing a vehicle for tagging proteins in the periplasmic compartment. A higher copy number version of select plasmids has been produced by introduction of a previously described repA mutation, affording an increase in protein expression levels. The utility of these plasmids for fluorescence-based imaging is demonstrated by root colonization of Solanum lycopersicum seedlings by P. fluorescens SBW25 in a hydroponic growth system. As a result, the plasmids are stably maintained during root colonization in the absence of selective pressure for more than two weeks.

59 BASIC BIOLOGICAL SCIENCES↗

Forecasting Zoonotic Infectious Disease Response to Climate Change: Mosquito Vectors and a Changing Environment

Infectious diseases are changing due to the environment and altered interactions among hosts, reservoirs, vectors, and pathogens. This is particularly true for zoonotic diseases that infect humans, agricultural animals, and wildlife. Within the subset of zoonoses, vector-borne pathogens are changing more rapidly with climate change, and have a complex epidemiology, which may allow them to take advantage of a changing environment. Most mosquito-borne infectious diseases are transmitted by mosquitoes in three genera: Aedes, Anopheles, and Culex, and the expansion of these genera is well documented. There is an urgent need to study vector-borne diseases in response to climate change and to produce a generalizable approach capable of generating risk maps and forecasting outbreaks. Here, we provide a strategy for coupling climate and epidemiological models for zoonotic infectious diseases. We discuss the complexity and challenges of data and model fusion, baseline requirements for data, and animal and human population movement. Disease forecasting needs significant investment to build the infrastructure necessary to collect data about the environment, vectors, and hosts at all spatial and temporal resolutions. These investments can contribute to building a modeling community around the globe to support public health officials so as to reduce disease burden through forecasts with quantified uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗

DIRECT OBSERVATION OF SOLAR CORONAL MAGNETIC FIELDS BY VECTOR TOMOGRAPHY OF THE CORONAL EMISSION LINE POLARIZATIONS

We present the first direct “observation” of the global-scale, 3D coronal magnetic fields of Carrington Rotation (CR) Cycle 2112 using vector tomographic inversion techniques. The vector tomographic inversion uses measurements of the Fe xiii 10747 Å Hanle effect polarization signals by the Coronal Multichannel Polarimeter (CoMP) and 3D coronal density and temperature derived from scalar tomographic inversion of Solar Terrestrial Relations Observatory (STEREO)/Extreme Ultraviolet Imager (EUVI) coronal emission lines (CELs) intensity images as inputs to derive a coronal magnetic field model that best reproduces the observed polarization signals. While independent verifications of the vector tomography results cannot be performed, we compared the tomography inverted coronal magnetic fields with those constructed by magnetohydrodynamic (MHD) simulations based on observed photospheric magnetic fields of CR 2112 and 2113. We found that the MHD model for CR 2112 is qualitatively consistent with the tomography inverted result for most of the reconstruction domain except for several regions. Particularly, for one of the most noticeable regions, we found that the MHD simulation for CR 2113 predicted a model that more closely resembles the vector tomography inverted magnetic fields. In another case, our tomographic reconstruction predicted an open magnetic field at a region where a coronal hole can be seen directly from a STEREO-B/EUVI image. We discuss the utilities and limitations of the tomographic inversion technique, and present ideas for future developments.

79 ASTRONOMY AND ASTROPHYSICS↗

On the Use of Finite Difference Matrix-Vector Products in Newton-Krylov Solvers for Implicit Climate Dynamics with Spectral Elements

Efficient solution of global climate models requires effectively handling disparate length and time scales. Implicit solution approaches allow time integration of the physical system with a time step dictated by accuracy of the processes of interest rather than by stability governed by the fastest of the time scales present. Implicit approaches, however, require the solution of nonlinear systems within each time step. Usually, a Newton s method is applied for these systems. Each iteration of the Newton s method, in turn, requires the solution of a linear model of the nonlinear system. This model employs the Jacobian of the problem-defining nonlinear residual, but this Jacobian can be costly to form. If a Krylov linear solver is used for the solution of the linear system, the action of the Jacobian matrix on a given vector is required. In the case of spectral element methods, the Jacobian is not calculated but only implemented through matrix-vector products. The matrix-vector multiply can also be approximated by a finite-difference which may show a loss of accuracy in the overall nonlinear solver. In this paper, we review the advantages and disadvantages of finite-difference approximations of these matrix-vector products for climate dynamics within the spectral-element based shallow-water dynamical-core of the Community Atmosphere Model (CAM).

climate modeling↗

Electromagnetics Simulations with Vector-valued Finite Elements in MOOSE

Vector-valued finite elements have become an essential part of modern electromagnetic (EM) numerical simulation. This talk will describe the development and initial validation of a MOOSE-based EM solver application, ELK (Electromagnetics Library for Kinetics and fluids), that utilizes the recently added vector-valued finite element system. The primary motivation for the development of ELK was to study EM wave propagation in radio-frequency (rf) driven systems, such as those encountered in the study of antenna structures, waveguides, and plasma physics. In simulating these scenarios with traditional scalar-valued finite elements, boundary conditions on tangential field components can sometimes be difficult to define, and field discontinuities encountered with certain geometric or structural features (e.g., abrupt corners and inhomogeneous materials) can often lead to non-physical results. Vector-valued elements can largely mitigate and even eliminate these difficulties. ELK verification and validation efforts thus far have focused on standard wave propagation benchmarks for antennas and waveguides, and the impact of vector-valued elements on the implementation and results of these simulations will be described. Progress using ELK for plasma physics simulation, where inhomogeneous simulation domains are commonplace, will also be discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Linear matrix inequalities for analysis and control of linear vector second-order systems

Many dynamical systems are modeled as vector second-order differential equations. This paper presents analysis and synthesis conditions in terms of LMI with explicit dependence in the coefficient matrices of vector second-order systems. These conditions benefit from the separation between the Lyapunov matrix and the system matrices by introducing matrix multipliers, which potentially reduce conservativeness in hard control problems. Multipliers facilitate the usage of parameter-dependent Lyapunov functions as certificates of stability of uncertain and time-varying vector second-order systems. The conditions introduced in this work have the potential to increase the practice of analyzing and controlling systems directly in vector second-order form.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗